Biodiversity: Insects get tropical
The biodiversity of plant-eating insects across the lowland tropical rainforests of Papua New Guinea may be high, but species tend to be widely distributed. The finding
Vojtech Novotny and colleagues studied around 500 species of butterfly caterpillars, beetles and fruitflies over 75,000 square kilometres of contiguous rainforest. Although species richness was high, as would be expected for the tropics, the species found did not alter much even over hundreds of kilometres, despite a range of different geological terrains.
Host plant specificity of caterpillars, on the other hand, decreases as distance from the equator increases, according to a second paper by Lee A. Dyer and colleagues. So the number of specialist species decreases with increasing latitude. The finding is timely, as biologists have discussed the latitudinal gradient in ecological specialization since the time of Darwin and Wallace, yet quantitative evidence for its existence has been hard to find.
CONTACT
Vojtech Novotny (New Guinea Binatang Research Center, Madang, Papua New Guinea)
Author paper [3]
Tel: +675 853 3258; Email: binatangi@datec.net.pg or novotny@entu.cas.cz
Scott E. Miller (Smithsonian Institution, Washington, DC, USA) Co-author paper [3]
Tel: +1 202 633 5135; E- mail: millers@si.edu
Lee A. Dyer (Tulane University, New Orleans, LA, USA) Author paper [4]
Tel: +1 504 862 8288; E-mail: ldyer@tulane.edu
Nigel E. Stork (University of Melbourne, Australia) N&V author
Tel: +61 3 9250 6806; E-mail: nstork@unimelb.edu.au
Thursday, August 09, 2007
Neurology: Ubiquitin is ubiquitous in Huntington’s disease
The link between Huntington’s disease and a protein known as ubiquitin may be greater than previously thought
Huntington’s disease is an inherited neurodegenerative disorder, characterized by the accumulation of protein fragments in affected neurons. These so-called inclusion bodies are often abnormally enriched with ubiquitin, suggesting that alterations in the metabolism of this protein might contribute to the disease. Using mass spectrometry, Ron R. Kopito and colleagues systematically analysed the brains of patients with Huntington’s disease as well as two different mouse models of the disease. All of the brain samples contained an abundance of chains of polyubiquitin, establishing changes in the ubiquitin system as a consistent feature of Huntington’s disease pathology.
Protein modification with polyubiquitin chains regulates many essential cellular processes — such as the cell cycle and DNA repair — so altered ubiquitin signalling is likely to have broad consequences for the function and survival of neurons. The authors propose that their technique might be used to achieve a deeper insight into the molecular basis of a variety of neurodegenerative diseases.
CONTACT
Ron R. Kopito (Stanford University, CA, USA)
Tel: +1 650 723 7581; E-mail: kopito@stanford.edu
The link between Huntington’s disease and a protein known as ubiquitin may be greater than previously thought
Huntington’s disease is an inherited neurodegenerative disorder, characterized by the accumulation of protein fragments in affected neurons. These so-called inclusion bodies are often abnormally enriched with ubiquitin, suggesting that alterations in the metabolism of this protein might contribute to the disease. Using mass spectrometry, Ron R. Kopito and colleagues systematically analysed the brains of patients with Huntington’s disease as well as two different mouse models of the disease. All of the brain samples contained an abundance of chains of polyubiquitin, establishing changes in the ubiquitin system as a consistent feature of Huntington’s disease pathology.
Protein modification with polyubiquitin chains regulates many essential cellular processes — such as the cell cycle and DNA repair — so altered ubiquitin signalling is likely to have broad consequences for the function and survival of neurons. The authors propose that their technique might be used to achieve a deeper insight into the molecular basis of a variety of neurodegenerative diseases.
CONTACT
Ron R. Kopito (Stanford University, CA, USA)
Tel: +1 650 723 7581; E-mail: kopito@stanford.edu
Ultrafast X-rays: ‘Dusty mirror’ gets a makeover
Inspired by an old optics experiment carried out by Isaac Newton, researchers have devised a scheme to study microscopic particles with intense ultrafast X-ray pulses. It’s thought this type of X-ray ‘flash’ imaging may be used to explore the three-dimensional dynamics of materials at the timescale of atomic motion.
Newton was puzzled by the circular patterns that appeared when he illuminated a silver-plated mirror. As it turned out, this was caused by interference between two paths of light scattering from dust particles on the front of the mirror — one path of light on its way towards the mirror, and one reflecting from the silvered surface. In this week’s Nature, Henry N. Chapman and colleagues describe a modern, more dynamic version of this ‘dusty mirror’ experiment that uses X-rays.
The team fired their ultrafast light source at a thin membrane containing polystyrene particles placed in front of a mirrored backplate. The incident X-rays cause the polystyrene particles to explode, and they then hit the polystyrene particles a second time as they are reflected back from the mirrored plate. The resulting interference pattern can be used to retrieve information about the polystyrene particles with high time and space resolution.
CONTACT
Henry N. Chapman (Lawrence Livermore National Laboratory, Livermore, CA, USA)
Tel: +1 925 423 1580; E-mail: henry.chapman@llnl.gov
Andrea Cavalleri (University of Oxford, UK) N&V author
Tel: +44 1865 272 365; E-mail: a.cavalleri1@physics.ox.ac.uk
Inspired by an old optics experiment carried out by Isaac Newton, researchers have devised a scheme to study microscopic particles with intense ultrafast X-ray pulses. It’s thought this type of X-ray ‘flash’ imaging may be used to explore the three-dimensional dynamics of materials at the timescale of atomic motion.
Newton was puzzled by the circular patterns that appeared when he illuminated a silver-plated mirror. As it turned out, this was caused by interference between two paths of light scattering from dust particles on the front of the mirror — one path of light on its way towards the mirror, and one reflecting from the silvered surface. In this week’s Nature, Henry N. Chapman and colleagues describe a modern, more dynamic version of this ‘dusty mirror’ experiment that uses X-rays.
The team fired their ultrafast light source at a thin membrane containing polystyrene particles placed in front of a mirrored backplate. The incident X-rays cause the polystyrene particles to explode, and they then hit the polystyrene particles a second time as they are reflected back from the mirrored plate. The resulting interference pattern can be used to retrieve information about the polystyrene particles with high time and space resolution.
CONTACT
Henry N. Chapman (Lawrence Livermore National Laboratory, Livermore, CA, USA)
Tel: +1 925 423 1580; E-mail: henry.chapman@llnl.gov
Andrea Cavalleri (University of Oxford, UK) N&V author
Tel: +44 1865 272 365; E-mail: a.cavalleri1@physics.ox.ac.uk
Human evolution: Same place, same time
Two fossils discovered in Kenya cast doubt on theories of the early evolution of the genus Homo. They show that the species H. habilis and H. erectus — previously thought to have evolved one after the other — actually lived side-by-side in eastern Africa for almost half a million years. The H. erectus fossil is the smallest ever found, suggesting that this species was not as human-like as once thought.
The east-African hominins H. habilis and the generally larger and later H. erectus are often regarded as part of the same pre-human lineage. The new fossils, uncovered east of Lake Turkana in Kenya, now challenge the relationship between these two species. The researchers attribute the first specimen, fragments of an upper jaw bone, to H. habilis. These bones provide the last known occurrence date for this species — 1.44 million years ago — which is significantly younger than previous estimates. The second fossil, a beautifully preserved H. erectus skull from 1.55 million years ago, is remarkable because it is close to the average size of H. habilis. This indicates that the species displayed substantial sexual dimorphism with the male being much larger than the female, like modern day gorillas.
The new dates show that H. habilis and H. erectus did in fact live at the same time in the Turkana basin for nearly half a million years. Their co-existence makes it unlikely that H. erectus evolved from H. habilis — both species must have originated between 2 and 3 million years ago, a time from which few Homo fossils are known. The authors conclude that, because they stayed as separate individual species for such a long time, they probably each had their own ecological niche and avoided direct competition with each other.
CONTACT:
Fred Spoor (University College London, UK)
Please note the author is currently based in Kenya:
Tel: +254 727 497 787 or +254 20 375 2337
Satellite phone: +88 216 5115 6558
E-mail: f.spoor@ucl.ac.uk
Additional author contacts:
Meave Leakey (Koobi Fora Research Project, Kenya)
Satellite phone: +88 216 5115 6558
E-mail: meaveleakey@gmail.com
Louise Leakey (Koobi Fora Research Project, Kenya)
Tel: +254 722 528 586
E-mail: louiseleakey@gmail.com
Two fossils discovered in Kenya cast doubt on theories of the early evolution of the genus Homo. They show that the species H. habilis and H. erectus — previously thought to have evolved one after the other — actually lived side-by-side in eastern Africa for almost half a million years. The H. erectus fossil is the smallest ever found, suggesting that this species was not as human-like as once thought.
The east-African hominins H. habilis and the generally larger and later H. erectus are often regarded as part of the same pre-human lineage. The new fossils, uncovered east of Lake Turkana in Kenya, now challenge the relationship between these two species. The researchers attribute the first specimen, fragments of an upper jaw bone, to H. habilis. These bones provide the last known occurrence date for this species — 1.44 million years ago — which is significantly younger than previous estimates. The second fossil, a beautifully preserved H. erectus skull from 1.55 million years ago, is remarkable because it is close to the average size of H. habilis. This indicates that the species displayed substantial sexual dimorphism with the male being much larger than the female, like modern day gorillas.
The new dates show that H. habilis and H. erectus did in fact live at the same time in the Turkana basin for nearly half a million years. Their co-existence makes it unlikely that H. erectus evolved from H. habilis — both species must have originated between 2 and 3 million years ago, a time from which few Homo fossils are known. The authors conclude that, because they stayed as separate individual species for such a long time, they probably each had their own ecological niche and avoided direct competition with each other.
CONTACT:
Fred Spoor (University College London, UK)
Please note the author is currently based in Kenya:
Tel: +254 727 497 787 or +254 20 375 2337
Satellite phone: +88 216 5115 6558
E-mail: f.spoor@ucl.ac.uk
Additional author contacts:
Meave Leakey (Koobi Fora Research Project, Kenya)
Satellite phone: +88 216 5115 6558
E-mail: meaveleakey@gmail.com
Louise Leakey (Koobi Fora Research Project, Kenya)
Tel: +254 722 528 586
E-mail: louiseleakey@gmail.com
Wednesday, August 08, 2007
Embryos back to front
An important stage in the early development of an embryo is the formation of the dorsal–ventral axis, which distinguishes the front (ventral) side of the animal from the back (dorsal). RIKEN researchers are identifying the genes and proteins that contribute to this process in Xenopus laevis, the African clawed frog.
Several protein interactions help to establish the front and back sides of an embryo
An important stage in the early development of an embryo is the formation of the dorsal–ventral axis, which distinguishes the front (ventral) side of the animal from the back (dorsal). RIKEN researchers at the Center for Developmental Biology in Kobe are identifying the genes and proteins that contribute to this process in Xenopus laevis, the African clawed frog.
Before the dorsal–ventral axis becomes established, the embryo is essentially a symmetrical sphere. The first signs that the symmetry is broken are uneven distributions in a complex network of proteins called the Wnt signaling pathway. However the differences in Wnt activity are too small to induce such a dramatic polarization, implying that other factors may amplify the effect.
The researchers found that XTsh3, a protein produced by the so-called Teashirt (Tsh) gene family, was strongly expressed in dorsal areas of the embryo1. “In Xenopus, it is easy to see gene functions by RNA injection into embryos,” says team leader Yoshiki Sasai. “XTsh3 injection induced dorsalization of the embryos.” Furthermore, when XTsh3 activity was deliberately inhibited, the dorsal axis didn’t form at all.
The activity of XTsh3 was found to be strongly related to levels of a protein called β-catenin, which has a crucial role in Wnt signaling. β-catenin accumulates in the cell nucleus and activates target genes that contribute further to the dorsal development.
“XTsh3 is an essential amplifier of Wnt signaling, which is activated on the dorsal side soon after insemination,” says Sasai. However the formation of the dorsal axis doesn’t occur until several hours later. In future Sasai would like to investigate the specific timings of each event. “One of our favorite hypotheses is that XTsh3 may be involved in the persisting memory of Wnt activation on the dorsal side.”
XTsh3 may have even more functions that the team has not yet discovered, because the molecule has the potential to bind with DNA. For example, the high levels of XTsh3 in the nervous system may contribute to development of the spinal cord once the dorsal–ventral axis is established.
Abnormal Wnt activation is also known to cause certain types of colon cancer in mammals. Four Tsh family genes are known in humans, but the roles of the genes are still to be investigated. It is also not known how far Tsh’s functions are conserved across species. Studies on the Drosophila fruit fly have shown a possible role of Tsh in Wnt signaling, but so far no link between Tsh activity and axis formation.
Reference
1. Onai, T., Matsuo-Takasaki, M., Inomata, H., Aramaki, T., Matsumura, M., Yakura, R., Sasai, N. & Sasai, Y. XTsh3 is an essential enhancing factor of canonical Wnt signaling in Xenopus axial determination. The EMBO Journal 26, 2350–2360 (2007).
An important stage in the early development of an embryo is the formation of the dorsal–ventral axis, which distinguishes the front (ventral) side of the animal from the back (dorsal). RIKEN researchers are identifying the genes and proteins that contribute to this process in Xenopus laevis, the African clawed frog.
Several protein interactions help to establish the front and back sides of an embryo
An important stage in the early development of an embryo is the formation of the dorsal–ventral axis, which distinguishes the front (ventral) side of the animal from the back (dorsal). RIKEN researchers at the Center for Developmental Biology in Kobe are identifying the genes and proteins that contribute to this process in Xenopus laevis, the African clawed frog.
Before the dorsal–ventral axis becomes established, the embryo is essentially a symmetrical sphere. The first signs that the symmetry is broken are uneven distributions in a complex network of proteins called the Wnt signaling pathway. However the differences in Wnt activity are too small to induce such a dramatic polarization, implying that other factors may amplify the effect.
The researchers found that XTsh3, a protein produced by the so-called Teashirt (Tsh) gene family, was strongly expressed in dorsal areas of the embryo1. “In Xenopus, it is easy to see gene functions by RNA injection into embryos,” says team leader Yoshiki Sasai. “XTsh3 injection induced dorsalization of the embryos.” Furthermore, when XTsh3 activity was deliberately inhibited, the dorsal axis didn’t form at all.
The activity of XTsh3 was found to be strongly related to levels of a protein called β-catenin, which has a crucial role in Wnt signaling. β-catenin accumulates in the cell nucleus and activates target genes that contribute further to the dorsal development.
“XTsh3 is an essential amplifier of Wnt signaling, which is activated on the dorsal side soon after insemination,” says Sasai. However the formation of the dorsal axis doesn’t occur until several hours later. In future Sasai would like to investigate the specific timings of each event. “One of our favorite hypotheses is that XTsh3 may be involved in the persisting memory of Wnt activation on the dorsal side.”
XTsh3 may have even more functions that the team has not yet discovered, because the molecule has the potential to bind with DNA. For example, the high levels of XTsh3 in the nervous system may contribute to development of the spinal cord once the dorsal–ventral axis is established.
Abnormal Wnt activation is also known to cause certain types of colon cancer in mammals. Four Tsh family genes are known in humans, but the roles of the genes are still to be investigated. It is also not known how far Tsh’s functions are conserved across species. Studies on the Drosophila fruit fly have shown a possible role of Tsh in Wnt signaling, but so far no link between Tsh activity and axis formation.
Reference
1. Onai, T., Matsuo-Takasaki, M., Inomata, H., Aramaki, T., Matsumura, M., Yakura, R., Sasai, N. & Sasai, Y. XTsh3 is an essential enhancing factor of canonical Wnt signaling in Xenopus axial determination. The EMBO Journal 26, 2350–2360 (2007).
Neuroscience : Stimulating retinal repair
Repairing damaged retinas is now a possibility. Japanese researchers from RIKEN and Kyoto University have demonstrated retinal regeneration in a mammalian model. It is a discovery that may ultimately lead to new therapies for retinal diseases including the degenerative disease called retinitis pigmentosa.
Japanese researchers from RIKEN and Kyoto University have demonstrated retinal regeneration in a
mammalian model of retinal degeneration after stimulation of the Wnt signaling pathway, which functions
as a regulator of some adult stem cell populations—in addition to its better known roles in embryogenesis and development.
It is a discovery that may ultimately lead to new therapies for retinal diseases including the degenerative disease called retinitis pigmentosa.
Previous research by the team led by Masayo Takahashi at the RIKEN Center for Developmental Biology, Kobe, demonstrated that retinal support cells called Müller glia could de-differentiate to assume a neuronal fate, but the level of regeneration via this mechanism was very low, occurring in just a few cells.
But the new study, published recently in the Journal of Neuroscience (1), indicates that retinal cell regeneration in an in vitro model of retinal damage can be increased by as much as twenty-fold in the presence of the protein Wnt3a.
The researchers initially performed experiments in cultured retinas isolated from rats. When they administered Wnt3a, they found a significant increase in proliferation of neuronal progenitors from the de-differentiated cells.
“Newly generated cells constituted almost a layer of cells in the outer nuclear layer in the retinal degeneration model mice,” says Takahashi. “We only observed several cells per field without Wnt treatment. Furthermore, the retinal neurons were regenerated all over the retina.”
The regenerated cells migrated to the outer nuclear layer of the retina, where, in the presence of retinoic acid (a form of vitamin A) or valproic acid, the team observed differentiation into rod photoreceptor cells.
The phenomenon appears to involve the canonical Wnt signaling pathway, in which Wnt activation protects the β-catenin protein from degradation, allowing it to accumulate in the nucleus where it regulates gene transcription. The process could also be stimulated with small molecule inhibitors of glycogen synthase kinase-3β, which normally blocks activation of the pathway.
Treatment of retinas isolated from a murine model of retinitis pigmentosa with Wnt3a similarly resulted in the regeneration of retinal cells, suggesting that the Wnt/β-catenin signaling pathway contributes to central nervous system regeneration. Takahashi believes Wnt signaling may be a part of the natural
restoration mechanism in the retina.
Reference
1. Osakada, F., Ooto, S., Akagi, T., Mandai, M., Akaike, A. & Takahashi, M. Wnt signaling promotes regeneration in the retina of adult mammals. Journal of Neuroscience 27, 4210–4219 (2007).
Repairing damaged retinas is now a possibility. Japanese researchers from RIKEN and Kyoto University have demonstrated retinal regeneration in a mammalian model. It is a discovery that may ultimately lead to new therapies for retinal diseases including the degenerative disease called retinitis pigmentosa.
Japanese researchers from RIKEN and Kyoto University have demonstrated retinal regeneration in a
mammalian model of retinal degeneration after stimulation of the Wnt signaling pathway, which functions
as a regulator of some adult stem cell populations—in addition to its better known roles in embryogenesis and development.
It is a discovery that may ultimately lead to new therapies for retinal diseases including the degenerative disease called retinitis pigmentosa.
Previous research by the team led by Masayo Takahashi at the RIKEN Center for Developmental Biology, Kobe, demonstrated that retinal support cells called Müller glia could de-differentiate to assume a neuronal fate, but the level of regeneration via this mechanism was very low, occurring in just a few cells.
But the new study, published recently in the Journal of Neuroscience (1), indicates that retinal cell regeneration in an in vitro model of retinal damage can be increased by as much as twenty-fold in the presence of the protein Wnt3a.
The researchers initially performed experiments in cultured retinas isolated from rats. When they administered Wnt3a, they found a significant increase in proliferation of neuronal progenitors from the de-differentiated cells.
“Newly generated cells constituted almost a layer of cells in the outer nuclear layer in the retinal degeneration model mice,” says Takahashi. “We only observed several cells per field without Wnt treatment. Furthermore, the retinal neurons were regenerated all over the retina.”
The regenerated cells migrated to the outer nuclear layer of the retina, where, in the presence of retinoic acid (a form of vitamin A) or valproic acid, the team observed differentiation into rod photoreceptor cells.
The phenomenon appears to involve the canonical Wnt signaling pathway, in which Wnt activation protects the β-catenin protein from degradation, allowing it to accumulate in the nucleus where it regulates gene transcription. The process could also be stimulated with small molecule inhibitors of glycogen synthase kinase-3β, which normally blocks activation of the pathway.
Treatment of retinas isolated from a murine model of retinitis pigmentosa with Wnt3a similarly resulted in the regeneration of retinal cells, suggesting that the Wnt/β-catenin signaling pathway contributes to central nervous system regeneration. Takahashi believes Wnt signaling may be a part of the natural
restoration mechanism in the retina.
Reference
1. Osakada, F., Ooto, S., Akagi, T., Mandai, M., Akaike, A. & Takahashi, M. Wnt signaling promotes regeneration in the retina of adult mammals. Journal of Neuroscience 27, 4210–4219 (2007).
Vegetable matters
Japanese researchers identify genes controlling health-giving compounds in common food crops. Vegetables like cabbage, broccoli and cauliflower are anti-carcinogenic with antioxidant properties and offer a natural defense against crop pests, potentially reducing the need for synthetic pesticides.
Japanese scientists have identified genes controlling the production of important compounds, known as glucosinolates, produced in food crops. Vegetable plants from the family Brassicaceae, such as cabbage, broccoli and cauliflower, produce glucosinolates, which are useful in human health and to the environment. They are anti-carcinogenic with antioxidant properties and offer a natural defense against
crop pests, potentially reducing the need for synthetic pesticides.
The biosynthesis of glucosinolates was poorly understood until the research team, led by Masami Yokota Hirai and Kazuki Saito from RIKEN’s Plant Science Center in Yokohama, used an ‘omics-based approach’, combining transcriptome and metabolome data to describe this process1. The transcriptome includes all transcribed genes in certain conditions, and the metabolome comprises all the end products of gene
expression. Integrating these sets of information gives a more complete picture of the biosynthetic pathway under study.
According to Hirai and Saito, the omics-based approach can be used to comprehensively identify a set of genes involved in a particular metabolic pathway—it can be a powerful tool used to distinguish the most important gene of many that may encode a particular transcription factor. A transcription factor is a
protein that controls when and where those genes are expressed.
The researchers revealed that long-chain, or aliphatic, glucosinolate biosynthesis is associated with two uncharacterized transcription factor genes, Myb28 and Myb29, by comparing the condition-independent transcriptome data with condition-specific information—a procedure called transcriptome coexpression analysis. Myb28 is a master transcription factor controlling many genes and Myb29 is an accessory. In
the model plant Arabidopsis, the team then overexpressed Myb28 and found a huge increase in the production of glucosinolates; and in a mutant lacking Myb28, they found a decrease in production. The team later renamed these genes Production of Methionine-Derived Glucosinolate (PMG) 1 and 2.
This is the first report of genes regulating the aliphatic glucosinolate biosynthetic pathway. It shows that transcriptome coexpression analysis is highly versatile and suitable for comprehensively identifying genes involved in plant metabolism. A greater understanding of metabolic systems will lead to
subsequent biotechnological applications.
“We eat Brassicaceae vegetables daily,” says Hirai. “By over-expressing PMG1 or controlling the expression of its orthologs in these vegetables, we can develop physiologically functional vegetables with higher amount of glucosinolates.” This could be useful in human nutrition. These genes are promising targets for the genetic engineering of glucosinolate production, possibly on an industrial scale.
Reference
1. Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K. et al.
Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate
biosynthesis. Proceedings of the National Academy of Sciences USA 104, 6478–6483 (2007).
Japanese researchers identify genes controlling health-giving compounds in common food crops. Vegetables like cabbage, broccoli and cauliflower are anti-carcinogenic with antioxidant properties and offer a natural defense against crop pests, potentially reducing the need for synthetic pesticides.
Japanese scientists have identified genes controlling the production of important compounds, known as glucosinolates, produced in food crops. Vegetable plants from the family Brassicaceae, such as cabbage, broccoli and cauliflower, produce glucosinolates, which are useful in human health and to the environment. They are anti-carcinogenic with antioxidant properties and offer a natural defense against
crop pests, potentially reducing the need for synthetic pesticides.
The biosynthesis of glucosinolates was poorly understood until the research team, led by Masami Yokota Hirai and Kazuki Saito from RIKEN’s Plant Science Center in Yokohama, used an ‘omics-based approach’, combining transcriptome and metabolome data to describe this process1. The transcriptome includes all transcribed genes in certain conditions, and the metabolome comprises all the end products of gene
expression. Integrating these sets of information gives a more complete picture of the biosynthetic pathway under study.
According to Hirai and Saito, the omics-based approach can be used to comprehensively identify a set of genes involved in a particular metabolic pathway—it can be a powerful tool used to distinguish the most important gene of many that may encode a particular transcription factor. A transcription factor is a
protein that controls when and where those genes are expressed.
The researchers revealed that long-chain, or aliphatic, glucosinolate biosynthesis is associated with two uncharacterized transcription factor genes, Myb28 and Myb29, by comparing the condition-independent transcriptome data with condition-specific information—a procedure called transcriptome coexpression analysis. Myb28 is a master transcription factor controlling many genes and Myb29 is an accessory. In
the model plant Arabidopsis, the team then overexpressed Myb28 and found a huge increase in the production of glucosinolates; and in a mutant lacking Myb28, they found a decrease in production. The team later renamed these genes Production of Methionine-Derived Glucosinolate (PMG) 1 and 2.
This is the first report of genes regulating the aliphatic glucosinolate biosynthetic pathway. It shows that transcriptome coexpression analysis is highly versatile and suitable for comprehensively identifying genes involved in plant metabolism. A greater understanding of metabolic systems will lead to
subsequent biotechnological applications.
“We eat Brassicaceae vegetables daily,” says Hirai. “By over-expressing PMG1 or controlling the expression of its orthologs in these vegetables, we can develop physiologically functional vegetables with higher amount of glucosinolates.” This could be useful in human nutrition. These genes are promising targets for the genetic engineering of glucosinolate production, possibly on an industrial scale.
Reference
1. Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K. et al.
Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate
biosynthesis. Proceedings of the National Academy of Sciences USA 104, 6478–6483 (2007).
The Soul Boat and the Boat-Soul: An Inquiry into the Indigenous “Soul”
-Maria Bernadette L. Abrera, Ph.D.
This paper explores the indigenous world view in the Philippines and in particular, the concept of the soul in the animist context, as revealed in the pre-colonial rituals involving the use of the boats. These boats are commonly called by the general term bangka. The boat rituals as well as the boat terms are utilized to understand the belief system particularly in relation to beliefs about the soul and the afterlife.
The Boat Terms
The Philippine “bangka” comes from the Austronesian ba?ka[h] which means “boat,” a term also found in Indonesia and the Melanesian islands such as Fiji and Samoa (Dempwolff 15). In the Philippines, bangka was first recorded to refer to all kinds of small boats usually used in rivers or in shallow coastal waters (San Antonio 33). By the 18th century however, the term had expanded to include all kinds of water vessels of varying sizes (Noceda y Sanlucar). For example, in the Ilocos region, the bangka was originally a small boat that was comparable to the paraw, a slow-moving small water craft (Carro 46). However, the contemporary description of the bangka in the Ilocos likens it to a large bilog, which is a plank-built boat with no outriggers according to Vanoverbergh, thus indicating its capacity to sail in deep open waters (48). Similarly, the Ilocano boat bilog was a “small bangka” that was hollowed out from a single log in the 19th century that eventually became a large boat made of planks (Carro 57). At present, “bangka” is also found in almost all the Philippine languages including Kapampangan, Hiligaynon, Sebuano, Samar-Leyte, Batad Ifugao, Badjaw, and Sinama languages. Among the Badjaw or Sama Laut, “bangka” is the general term for all kinds of boats not used as houseboats, which are specifically called lipa (Nimmo 60, 61).
In Mindanao during the 17th century, the bangka was not a small boat since it could carry anywhere from twenty to 100 cavans of rice (Combes 786). The Jesuit priest Francisco Combes described it as carved from a single piece of log, which also indicated the length and size of the trees from which such large boats could be made. There were two kinds of bangka in Maguindanao based on the manner it was constructed: the binaluy, made from a single log, and the plank-built kumpit (Juanmarti 9). Today, the kumpit of the Sama and the Tausug is a huge boat made of planks that can measure between 50 to 120 feet in length (Lorenzo-Abrera). We may conclude then, that the bangka was originally a small boat. We may infer then, that the term bangka originally referred to a small boat. As the community and its trade grew, so did the boats, while generally retaining the original names. The term bangka was expanded to accommodate the larger boats that were built later. It is notable too that it was in Mindanao that the bangka is first described as a large trading boat although like the smaller versions it was still carved out of a single piece of log.
During the 18th century, the term “bangka” was found in several Philippine languages, among them Ilokano and Tagalog, but not in the Bikol and Visayan languages. In fact, neither term bangka nor bilog were found in the early Bicol and Visayan vocabularies. Instead, the Bicol term for boat was sacayan and if it were constructed from a single log, it was called a baloto (Lisboa 53). The term bangka is also absent in the 1637 vocabulary for the Visayan, Hiligaynon and Haraya of Panay island (de Mentrida). Likewise the 1668 dictionary for the Visayans of Leyte and Samar indicated that they called as baloto what the Tagalogs referred to as bangka (Alcina 134). In early 16th century Cebu, Pigafetta recorded that the small boat was called a baloto (Pigafetta 197). The baloto according to the Jesuit Alcina, was the smallest, simplest, and most common sea craft. It was hollowed out from a solid piece of log and could be carried ashore by a single person due to its diminuitive size. However, Alcina who was an accomplished navigator himself found it remarkable that this tiny baloto could be used to ride the huge waves off Samar island which was one of the most dangerous waters in the islands. He likened the sight of it to a ball floating on the waves.
However, the bangka was more than just a boat. The technology and its entire process of construction embodied the beliefs of the indigenous culture. Alcina, who was among the most detailed recorders of its native construction, noted that there were a “million superstitions” involved in cutting tree and shaping the log (Alcina 162). Nothing in its construction happened by chance. For example, the nodes of the tree were counted and determined in which part of the boat it would fall, because this would affect the fate of the boat. Such painstaking chore shows us the immense value attributed to the boats beyond the simple function of transporting people and trade.
The Boat Rituals
The rituals where the boats figured are most instructive in revealing the beliefs that lay beneath the surface. One such religious procedure was called the kibang. In Tagalog, this term meant the rocking motion of a boat on the waves. As a ceremony however, kibang was the old tradition of asking the anito (the spirit of the departed) what luck would befall the riders before sailing or docking, and the movement was attributed as the spirit’s response (de San Antonio 67). Visayans also had this ritual, similarly called guibang (Fernandez and Koback 442). It was usually done before a raiding or a fishing expedition, intoning before the small baloto, “Guibang, guibang cun magtoto cami” (Sway, sway, if we should proceed).” If the baloto did sway, it meant good fortune; the greater the rocking movement, the better one’s fortune. As the baloto swayed, they would ask who was causing the boat to sway, a deity or an ancestor’s spirit. Where the boat swayed at the mention of the name, deity or spirit, there was their answer. This ritual is practiced until the present time (Funtecha 13). Likewise, when the children or relatives of a person who had drowned got sick they would be placed in a boat called barangay together with a baylan (a female diviner) and at the place she indicated, they would throw down a wooden chest full of clothes and other belongings of the dead person (de Loarca 85-86). Simultaneously, they would ask their ancestors to help and heal the sick relatives.
The bacalag was an important Visayan boat launching ritual recorded in the 17th century. When a mangaiao (raiding boat) was to be launched, it would be rolled over several pieces of logs and at the end of these was an enslaved captive (Alcina 162-163). This was reportedly done so that through the blood of the human sacrifice, the boat would be feared by their enemies and would succeed in obtaining numerous captives. During the ritual, the appeal was uttered, “Daoharlucsin iginbabacalagna,” a request that people would fear the boat in the same manner that the sacrificed captive did. In Calagan (Caraga), the bacalag ritual was performed for the healing a of datu (chief) who was seriously ill.
Calag in Bicol and Visayan means “soul,” the root word in both bacalag and Calagan. We can conclude that Fr. Combes was referring to the bacalag ritual as a “revolting” ancient tradition in Caraga when he said, “for the boats to obtain good fortune, they promise it at the first instance a name, usually that of one of their slaves” (41). It would have been the name of the sacrificed slave, which made it so repulsive to the Jesuit observer. Remnants of this ritual remain although in less severe form. In Masbate island, the prow of a boat to be launched is brushed with chicken blood, while prayers are intoned. This is usually performed by an elderly person. A boatbuilder in Cavite also reported doing this practice on the boat of a businessman from Iloilo City, who had requested the ritual. In the movie “Muro-Ami” which was set in Bohol island and records its fishing practices, the captain’s father brushed chicken blood on the prow of the boat that would be used for fishing. The practice has even been transmitted to a modern form of transport: the wheels of a new car are also brushed with chicken blood. The sacrifice is believed to bring the boat good fortune. Fishermen in the northernmost Philippine island of Batanes offer up a pig to transfer to the animal whatever ill fortune may befall them or their boats (Mangahas 67, 77). When they do not find any catch, they perform the cleansing ritual not only on themselves but also on their boat, as they believe envy or witchcraft has made them dirty, along with the boats and the port (Mangahas 87).
These examples of rituals indicate a way of thinking about boats which go beyond its function of transportation. To understand this, we need to go to the basic tenets of the animist belief system, the most essential being the concept of the soul.
The Indigenous “Soul”
Bagobos, an indigenous Philippine ethnic group in Mindanao, believe that all things possess a gimokud or soul, including man-made objects (Benedict 54, 65). Similarly, the Sama of Cagayan de Tawi-Tawi believe that the sumangat or soul is found in all nature, even inanimate things (Casiño 113). This is believed to be the intrinsic spirit of an object that may be revealed at a particular time, according to Bottignolo and which gives the object its desirable characteristics as such (41). This is the reason why warriors, for example, show a reverential attitude toward their weapons; it is not simply the physical object of a metal weapon but a blade that possesses the soul of a blade. The soul of that object is what makes it hard and strong, whose strength would be revealed during battle. Thus, warriors give names to their personal weapons not as ownership of the object but in recognition of its animism. Forging the weapon then becomes not an ordinary, but a sacred, activity in order that the soul of the blade may not depart from it. As another example, there is also a ritual involving the “rice-soul”. The Mandaya pray to the “soul of the rice” before planting so that it would cause the plant to bear many grains.
This basic animist principle of plants and objects possessing “souls” enable us to understand oral literature better, beginning with the epics. The epic “Kudaman” of Palawan island’s Tagbanua people, for example, reveals that when Kudaman went down the house, the handrail shed tears of sorrow for the hero’s departure. This would show that they believe that the house possesses a life and therefore a soul, and can thus display its own emotions. In the epic of “Labaw Donggon” the hero’s boat is believed to be magical and charmed, as it possesses powers of its own and the hero can talk to it to do his bidding.
Bagobos believe that both men and animals possess two souls, the bad soul on the left and the good on the right. Man-made objects have only one soul, such as the soul of a betel nut box, or the soul of a lime container. Among the Ifugao, this has been rendered in English as “soulstuff” (alimaduan) which is different from the soul (linawa). The alimaduan is that which gives the object its distinctive characteristic. For example, the alimaduan of the rice is to yield grain; of the pigs and chickens, to grow and multiply; of the person, to have desirable traits (Barton 141-142). However, a knife that bends lacks soulstuff, so does a tree that does not bear fruit.
The term for soulstuff, alimaduan, is based on dua (two) which is also the root for kaluluwa (soul). This would indicate the belief in another, or a second, presence within the material object. The concept of an alimaduan is the reason why there are rituals to render proper homage to important objects: a ritual in forging a metal weapon, in weaving clothing, in making a boat. A very clear example of this is in the belief in the amulet or charm. Amulets are considered animate objects, going by the terms used to refer to these: amulets are “given food” to mean that they are prayed on, for if they lack “food” (prayers), they will “sulk” (magtatampo) and “leave” (maglalayas). What this boils down to is that if an amulet owner does not offer up sufficient prayers, he will lose the amulet. Through these terms, the concept is clarified that the amulet is not only animate, but possesses a “soul” from whence its power emanates. Based on the concept of the alimaduan, one may infer the presence of the soul in an object for so long as that object possesses the qualities that are proper to it. The Malays believe that human, animals, birds, plants, fishes, crocodiles, rocks, weapons, food, clothing, ornaments, and other objects have each their own autochthonous soul (Skeat 53).
Inferring from this, the boat then possesses its own soul, which is fundamentally related to the tree that had been used for its construction. The entire boat building process and construction rituals are rooted in the belief in the soul: offerings are made to the soul inhabiting the tree so that it would remain in the tree when the log is transformed into a boat. It is this soul of the boat that gives it its good qualities as a boat. We can get a glimpse of what these qualities are from a rowing song among the Ivatans of Batanes. Upon the start of a sea voyage, the boatmen address the boat, asking it to be steady of purpose, to be forceful, and to be alert in finding land with a beautiful bay (Scheerer 315-316). Similarly, Malays pray to the soul of a boat prior to a voyage and appeal that it keeps the planks together (Skeat 279).
In the epic “Sandayo” of the Subanon of Zamboanga, the hero’s boat Gadyong reveals that it has its own mind because when informed that they were going on a raid, it refused to budge. When Sandayo the hero finally relented and said that he was going to court a maiden, only then did the boat sail. The functions of thought, will, and movement are attributes of the soul, thus the need for the hero to entreat his boat as though it were a person.
This animist belief is seen in another aspect, the boat parts. Boats have a “face”, particularly eyes. The boat atop the burial jar found in the Manunggul cave in Palawan has a face at the prow, and one can see the eyes, nose, mouth and ears. Likewise, the prow of the lipa or houseboats in Sulu and Tawi-Tawi are called sampong (face) with a discernible eye, brow, nose, and mouth. Even the terms used in boat construction also refer to the face: sealing the planks is napirnga (to have a speck in the eye) and the sealant itself, pamota (speck, mote). According to Lorenzo-Abrera, the stern is called sampong buli (the face behind) by the Sama (Paghihinang Kumpit 183).
The belief in a soul in inanimate objects, plants and animals also explains the presence of grave goods. Since these objects have souls, then they can accompany the dead on his journey and be brought over to the afterlife, along with the souls of the slaves buried with him. When these grave goods are completely decomposed materially, then they can be useful to the soul of the dead (Benedict 54). The souls of these objects will be used by the soul of the dead person. This is why, among the Kankanay, not a single iron nail is used in the coffin because the dead person desires that everything should disintegrate together with his corpse (Canol 58). This could help explain why up to the 17th century, the Spaniards would note that not a single piece of iron was used in building the boats.
Mourning
Boats figured prominently in the death rituals as they were part and parcel of the entire animistic belief. There were several forms of mourning: maglahe, morotal, larao, and marabay. Maglahe (magarahe among the Tagalogs) was the mourning indicated by fasting, upon the death of a parent or close relative (Loarca 88-89). The mourner ate no rice, only bananas and sweet potatoes, and drank only tuba (coconut wine). He wound rattan vine around his entire arm and neck. The mourning ended when the mourner had taken a captive or killed someone.
Morotal was a woman’s mourning, where she would get on a barangay boat together with other women and three chosen warriors: one to steer the boat, another to bail, and the third to stay in the bow. The men sang about their bravery in war all the while rowing the boat filled with jars of wine. A great feast would be held upon reaching their destination, and the mourning came to an end with the woman eating rice again and wearing gold ornaments (Loarca 89).
Larao was the mourning for a datu (chief). Everyone observed this ritual, where no one could have any quarrel, the weapons were carried with the points down, daggers carried with reversed hilts, and no one could wear colorful clothing. All was silence. Along the shore signs were placed indicating a larao so that no one could transgress the silence on pain of death (Chirino 135). This practice is recorded in the Maranao epic “Darangen”, where white flags were placed at the river mouth and around the community. Singing was forbidden and silence was enforced. Whoever broke the rule would suffer death. Similarly, the Bilaans cease all activity and merriment when their datu dies, and all help out in preparation for the burial (Cabrera 191).
In the 16th century, a datu was buried in a boat with many rowers who would serve him in the other world (Chirino 135). Slaves, food and drink were placed in the vessel that would carry the dead chief to the next life (Chirino 134). Sometimes as many as 60 slaves would be made to accompany the datu in the afterlife. To accommodate this many passengers, the burial boat would have been a barangay.
According to Loarca, when a datu descended from Dumaguet dies, a slave is made to die in the same manner as the chief (88). He added that the slave chosen for this was the most wretched they could find, a foreigner and not one of them, for he remarked that they were “not at all cruel”. The dead were buried in wooden coffins, piled with gold, clothing, and other expensive objects as they believed that if a person left this world well off, he would be received well in the next life.
Tagalogs buried the dead beside his house; if it was a datu, he would be placed under a small house or porch constructed for this purpose (de Plasencia 122). There was a mourning period of four days, after which the corpse was placed in a boat and buried. Animals could be placed in the boat instead of rowers: a male and female species of the animal would be placed in the seat of the rowers, usually two goats, deers, or hens. If the dead person was a warrior, a living slave would be tied underneath the corpse to die in this manner. Songs about the warrior’s prowess and good qualities were sung by relatives during the wake.
Boat coffins
The archeological evidence of boat-shaped coffins abound from north to south of the Philippine islands as well as in the entire Southeast Asian region (Tenazas). While bangka is the general term for boats, in other minor Philippine languages it is transposed as kabang. The Tagalog term for coffin is kabaong. Briefly, we note that boats are used as houses up to the present by some Philippine ethnolingguistic groups, and that the shape and function of houses have been studied to closely resemble boats. The Bikol term for house is harong, which sounds similar to the Malay term for coffin, larong. This paper infers that the term kabaong meant a boathouse for the dead, intended to transport him to the afterlife.
If the dead had been a member of a raiding team, the coffin would be in the shape of the boat called barangay. Animals would be placed as rowers, with a slave to oversee everything (de San Antonio 152). If he were a renowned sailor, he would be buried in his boat, with slaves to row him to the afterlife. In Bohol, a datu was reported to have been buried with 70 armed slaves and food supplies, just as he had sailed when still living (Colin 174). This supposedly ensured that he could maintain his raiding prowess beyond this world.
It is notable that the kabaong, coffin, is very similarly made as the bangka/kabang, boat. Often, boats are simply mentioned as made of hardwood. In Butuan City, where the oldest balangays (boat) in the Philippines were discovered, there were also excavated coffins made from the hardwood dungon (Heretiera litorales) (Roxas-Lim 56). This hardwood is especially used to construct the boat keel. It had also been noted that coffin planks and its cover were very tightly sewn that not even air could pass through (Chirino 134). It meant that the coffin was likewise constructed watertight in anticipation of its passage in the river or sea.
Significantly, burial jars were almost always found near the shore or in coastal areas (Fox 159-160). In Samar and Leyte, the sea was within view from the site of the jars, and in Sorsogon and Tayabas, these were near the sea. The burial caves, including the elevated sites in Batanes, were facing the sea. In 1857, it was noted of the Ifugao that they buried their dead under their houses, which was attributed to have been an influence from the Chinese “as they had not previously done this” (Alarcon 89). The river and the sea served as passageways to the afterlife, thus the coffin was a boat.
Journey to the Afterlife
One important concept of this spiritual boat journey concerns abay, from where the mourning ritual called marabay takes its root. The marabay mourner stays beside the corpse, taking no solid food for three days. After this time, the mourner may then consume food but nothing that had been passed over fire, until he had taken a head.
Abay refers to boats traveling together. In Bikol it meant several boats sailing in tandem, but a second meaning was for the dead to travel with companions. Among the Sama Laut, the present-day burial ceremony actually consists of several boats sailing together to an island where the burial will take place (Nimmo 194). The stature of the dead person can be seen from the number of boats that accompany the burial boat procession.
In the Visayas, abay also referred to boats sailing together, but likewise contained a second meaning which signified being in another’s company until death (de Mentrida 4). It also meant a certain supernatural power manifested through words, an ability which a person possessed until death. This meaning is given more clarity with the Tagalog meaning of abay. First, it meant accompanying a person to another place; second, it signified a friend or a respected person whom one brought along to a gathering; and lastly, it referred to the person’s soul, in the sense of being a companion. When Spanish colonization began to spread the Christian faith, this indigenous concept was utilized to explain religious tenets, as when abay, referring to the soul, was used in a sample sentence as:
Abay. (…) y aplicado al alma, dicen: Paabay camo sa manga calagyo ninyong Santos
at sa manga catutubo. (Applying to the soul, they say: Ask to be guided by your
namesake saints and by the catutubo.)
Abay as a concept can thus be reduced to the idea of a companion, either as boats sailing in company or as persons traveling together. The nature of such travel could be temporary and brief, such as going to a gathering, or over the period of one’s entire lifetime, such as in indicated by having the soul as companion.
The concept of the abay (companion) explains why there are to be companions for the dead. They will help and serve him in the afterlife. Thus the mourning called mangabay, where one stays beside the corpse, shows that it is first and foremost the mourning relative who must accompany the dead while there are yet slaves to be found for the journey. Once their souls have been obtained for the journey – meaning that they were either killed or left to die, both through a ritual - then the mourner is freed from the task of acting as the abay. The avoidance of abay would also explain certain ethnic beliefs regarding death. For example, among the Bagobo, the sound of a cricket is deemed as the dead person’s invitation for one to become his abay. Thus the relative, upon hearing the insect, addresses it: “You can come here no more because you are now going to the Great City (the afterlife). You have still a little love for me; do not bring me sickness.” We see in this the idea that just as a person needs company while he is on earth, so does the soul as it travels and goes to the afterlife. Hence, there is both a physical and a spiritual abay.
The soul, since it is also a companion, is also considered an abay while the person is alive. However, in the sample sentence explaining the meaning of abay, we encounter another term, calagyo, to wit: calagyo ninyong santos, your namesake saints. A calagyo in pre-colonial culture was a person who was one’s namesake and it would be worthwhile investigating in another study whether this term for a namesake was indeed related to the concept of calag or soul. What can be established now is that these indigenous concepts were used to introduce and explain colonial concepts, in this case pertaining to religion. Thus, the native idea of the calagyo became the vehicle to introduce the idea of a patron saint and naming people after them in the process of Christianization. They would thus become the namesake’s guide in life.
The second term we encounter is catutubo, defined as a person who was the same age as oneself. This term reflected another belief about the soul as a companion, or abay, but in particular as one who grew up with the person from birth. From this, the Spanish missionaries were able to find a parallel concept by which to introduce the guardian angel as the spirit who was from the very beginning with the person it was watching over. Mixing the terms, this guardian spirit was called angel na ating catutubo, which would mean the angel who was the same age as the person. This would mean the indigenization of the Christian concept of the guardian angel who was not “born” at the same time as the person and therefore could have no age, as it was a spirit. The concept that would be the same as catutubo is in the Maranao belief in the tonong. This is believed to be one’s twin who is a spirit and who guards the person and defends him from harm. The tonong is given to a person upon birth. This spirit-twin keeps the person company at all times, warns him of impending danger, and helps him during battle. The tonong has the power to guard the person it accompanies through life, and can be the source of the person’s amazing abilities. There are three kinds of tonong based on its location: in the clouds, on top of trees, and in the water. The tonong who lives in the water is called a diwata.
Abay thus refers to the following: boats sailing together; a person who accompanies another in a journey; the soul of another that would accompany the dead to the afterlife. Marabay, the mourning ritual, thus meant seeking a soul to act as companion for the dead relative, which was why it ended only upon the taking of the life of another. These journeys, both on earth and to the next life, all involved the use of boats.
These boat rituals and terms show us that the boats themselves may be read as a repository of the animist belief system. The uses in the various rituals reveal the worldview and explain the interrelations among the different segments of the entire cosmic set-up in the indigenous mind. The boat served as a transport vehicle during one’s life and in the afterlife. The bangka was a boat that transported souls to the afterlife and a boat that had a soul of its own.
-Maria Bernadette L. Abrera, Ph.D.
This paper explores the indigenous world view in the Philippines and in particular, the concept of the soul in the animist context, as revealed in the pre-colonial rituals involving the use of the boats. These boats are commonly called by the general term bangka. The boat rituals as well as the boat terms are utilized to understand the belief system particularly in relation to beliefs about the soul and the afterlife.
The Boat Terms
The Philippine “bangka” comes from the Austronesian ba?ka[h] which means “boat,” a term also found in Indonesia and the Melanesian islands such as Fiji and Samoa (Dempwolff 15). In the Philippines, bangka was first recorded to refer to all kinds of small boats usually used in rivers or in shallow coastal waters (San Antonio 33). By the 18th century however, the term had expanded to include all kinds of water vessels of varying sizes (Noceda y Sanlucar). For example, in the Ilocos region, the bangka was originally a small boat that was comparable to the paraw, a slow-moving small water craft (Carro 46). However, the contemporary description of the bangka in the Ilocos likens it to a large bilog, which is a plank-built boat with no outriggers according to Vanoverbergh, thus indicating its capacity to sail in deep open waters (48). Similarly, the Ilocano boat bilog was a “small bangka” that was hollowed out from a single log in the 19th century that eventually became a large boat made of planks (Carro 57). At present, “bangka” is also found in almost all the Philippine languages including Kapampangan, Hiligaynon, Sebuano, Samar-Leyte, Batad Ifugao, Badjaw, and Sinama languages. Among the Badjaw or Sama Laut, “bangka” is the general term for all kinds of boats not used as houseboats, which are specifically called lipa (Nimmo 60, 61).
In Mindanao during the 17th century, the bangka was not a small boat since it could carry anywhere from twenty to 100 cavans of rice (Combes 786). The Jesuit priest Francisco Combes described it as carved from a single piece of log, which also indicated the length and size of the trees from which such large boats could be made. There were two kinds of bangka in Maguindanao based on the manner it was constructed: the binaluy, made from a single log, and the plank-built kumpit (Juanmarti 9). Today, the kumpit of the Sama and the Tausug is a huge boat made of planks that can measure between 50 to 120 feet in length (Lorenzo-Abrera). We may conclude then, that the bangka was originally a small boat. We may infer then, that the term bangka originally referred to a small boat. As the community and its trade grew, so did the boats, while generally retaining the original names. The term bangka was expanded to accommodate the larger boats that were built later. It is notable too that it was in Mindanao that the bangka is first described as a large trading boat although like the smaller versions it was still carved out of a single piece of log.
During the 18th century, the term “bangka” was found in several Philippine languages, among them Ilokano and Tagalog, but not in the Bikol and Visayan languages. In fact, neither term bangka nor bilog were found in the early Bicol and Visayan vocabularies. Instead, the Bicol term for boat was sacayan and if it were constructed from a single log, it was called a baloto (Lisboa 53). The term bangka is also absent in the 1637 vocabulary for the Visayan, Hiligaynon and Haraya of Panay island (de Mentrida). Likewise the 1668 dictionary for the Visayans of Leyte and Samar indicated that they called as baloto what the Tagalogs referred to as bangka (Alcina 134). In early 16th century Cebu, Pigafetta recorded that the small boat was called a baloto (Pigafetta 197). The baloto according to the Jesuit Alcina, was the smallest, simplest, and most common sea craft. It was hollowed out from a solid piece of log and could be carried ashore by a single person due to its diminuitive size. However, Alcina who was an accomplished navigator himself found it remarkable that this tiny baloto could be used to ride the huge waves off Samar island which was one of the most dangerous waters in the islands. He likened the sight of it to a ball floating on the waves.
However, the bangka was more than just a boat. The technology and its entire process of construction embodied the beliefs of the indigenous culture. Alcina, who was among the most detailed recorders of its native construction, noted that there were a “million superstitions” involved in cutting tree and shaping the log (Alcina 162). Nothing in its construction happened by chance. For example, the nodes of the tree were counted and determined in which part of the boat it would fall, because this would affect the fate of the boat. Such painstaking chore shows us the immense value attributed to the boats beyond the simple function of transporting people and trade.
The Boat Rituals
The rituals where the boats figured are most instructive in revealing the beliefs that lay beneath the surface. One such religious procedure was called the kibang. In Tagalog, this term meant the rocking motion of a boat on the waves. As a ceremony however, kibang was the old tradition of asking the anito (the spirit of the departed) what luck would befall the riders before sailing or docking, and the movement was attributed as the spirit’s response (de San Antonio 67). Visayans also had this ritual, similarly called guibang (Fernandez and Koback 442). It was usually done before a raiding or a fishing expedition, intoning before the small baloto, “Guibang, guibang cun magtoto cami” (Sway, sway, if we should proceed).” If the baloto did sway, it meant good fortune; the greater the rocking movement, the better one’s fortune. As the baloto swayed, they would ask who was causing the boat to sway, a deity or an ancestor’s spirit. Where the boat swayed at the mention of the name, deity or spirit, there was their answer. This ritual is practiced until the present time (Funtecha 13). Likewise, when the children or relatives of a person who had drowned got sick they would be placed in a boat called barangay together with a baylan (a female diviner) and at the place she indicated, they would throw down a wooden chest full of clothes and other belongings of the dead person (de Loarca 85-86). Simultaneously, they would ask their ancestors to help and heal the sick relatives.
The bacalag was an important Visayan boat launching ritual recorded in the 17th century. When a mangaiao (raiding boat) was to be launched, it would be rolled over several pieces of logs and at the end of these was an enslaved captive (Alcina 162-163). This was reportedly done so that through the blood of the human sacrifice, the boat would be feared by their enemies and would succeed in obtaining numerous captives. During the ritual, the appeal was uttered, “Daoharlucsin iginbabacalagna,” a request that people would fear the boat in the same manner that the sacrificed captive did. In Calagan (Caraga), the bacalag ritual was performed for the healing a of datu (chief) who was seriously ill.
Calag in Bicol and Visayan means “soul,” the root word in both bacalag and Calagan. We can conclude that Fr. Combes was referring to the bacalag ritual as a “revolting” ancient tradition in Caraga when he said, “for the boats to obtain good fortune, they promise it at the first instance a name, usually that of one of their slaves” (41). It would have been the name of the sacrificed slave, which made it so repulsive to the Jesuit observer. Remnants of this ritual remain although in less severe form. In Masbate island, the prow of a boat to be launched is brushed with chicken blood, while prayers are intoned. This is usually performed by an elderly person. A boatbuilder in Cavite also reported doing this practice on the boat of a businessman from Iloilo City, who had requested the ritual. In the movie “Muro-Ami” which was set in Bohol island and records its fishing practices, the captain’s father brushed chicken blood on the prow of the boat that would be used for fishing. The practice has even been transmitted to a modern form of transport: the wheels of a new car are also brushed with chicken blood. The sacrifice is believed to bring the boat good fortune. Fishermen in the northernmost Philippine island of Batanes offer up a pig to transfer to the animal whatever ill fortune may befall them or their boats (Mangahas 67, 77). When they do not find any catch, they perform the cleansing ritual not only on themselves but also on their boat, as they believe envy or witchcraft has made them dirty, along with the boats and the port (Mangahas 87).
These examples of rituals indicate a way of thinking about boats which go beyond its function of transportation. To understand this, we need to go to the basic tenets of the animist belief system, the most essential being the concept of the soul.
The Indigenous “Soul”
Bagobos, an indigenous Philippine ethnic group in Mindanao, believe that all things possess a gimokud or soul, including man-made objects (Benedict 54, 65). Similarly, the Sama of Cagayan de Tawi-Tawi believe that the sumangat or soul is found in all nature, even inanimate things (Casiño 113). This is believed to be the intrinsic spirit of an object that may be revealed at a particular time, according to Bottignolo and which gives the object its desirable characteristics as such (41). This is the reason why warriors, for example, show a reverential attitude toward their weapons; it is not simply the physical object of a metal weapon but a blade that possesses the soul of a blade. The soul of that object is what makes it hard and strong, whose strength would be revealed during battle. Thus, warriors give names to their personal weapons not as ownership of the object but in recognition of its animism. Forging the weapon then becomes not an ordinary, but a sacred, activity in order that the soul of the blade may not depart from it. As another example, there is also a ritual involving the “rice-soul”. The Mandaya pray to the “soul of the rice” before planting so that it would cause the plant to bear many grains.
This basic animist principle of plants and objects possessing “souls” enable us to understand oral literature better, beginning with the epics. The epic “Kudaman” of Palawan island’s Tagbanua people, for example, reveals that when Kudaman went down the house, the handrail shed tears of sorrow for the hero’s departure. This would show that they believe that the house possesses a life and therefore a soul, and can thus display its own emotions. In the epic of “Labaw Donggon” the hero’s boat is believed to be magical and charmed, as it possesses powers of its own and the hero can talk to it to do his bidding.
Bagobos believe that both men and animals possess two souls, the bad soul on the left and the good on the right. Man-made objects have only one soul, such as the soul of a betel nut box, or the soul of a lime container. Among the Ifugao, this has been rendered in English as “soulstuff” (alimaduan) which is different from the soul (linawa). The alimaduan is that which gives the object its distinctive characteristic. For example, the alimaduan of the rice is to yield grain; of the pigs and chickens, to grow and multiply; of the person, to have desirable traits (Barton 141-142). However, a knife that bends lacks soulstuff, so does a tree that does not bear fruit.
The term for soulstuff, alimaduan, is based on dua (two) which is also the root for kaluluwa (soul). This would indicate the belief in another, or a second, presence within the material object. The concept of an alimaduan is the reason why there are rituals to render proper homage to important objects: a ritual in forging a metal weapon, in weaving clothing, in making a boat. A very clear example of this is in the belief in the amulet or charm. Amulets are considered animate objects, going by the terms used to refer to these: amulets are “given food” to mean that they are prayed on, for if they lack “food” (prayers), they will “sulk” (magtatampo) and “leave” (maglalayas). What this boils down to is that if an amulet owner does not offer up sufficient prayers, he will lose the amulet. Through these terms, the concept is clarified that the amulet is not only animate, but possesses a “soul” from whence its power emanates. Based on the concept of the alimaduan, one may infer the presence of the soul in an object for so long as that object possesses the qualities that are proper to it. The Malays believe that human, animals, birds, plants, fishes, crocodiles, rocks, weapons, food, clothing, ornaments, and other objects have each their own autochthonous soul (Skeat 53).
Inferring from this, the boat then possesses its own soul, which is fundamentally related to the tree that had been used for its construction. The entire boat building process and construction rituals are rooted in the belief in the soul: offerings are made to the soul inhabiting the tree so that it would remain in the tree when the log is transformed into a boat. It is this soul of the boat that gives it its good qualities as a boat. We can get a glimpse of what these qualities are from a rowing song among the Ivatans of Batanes. Upon the start of a sea voyage, the boatmen address the boat, asking it to be steady of purpose, to be forceful, and to be alert in finding land with a beautiful bay (Scheerer 315-316). Similarly, Malays pray to the soul of a boat prior to a voyage and appeal that it keeps the planks together (Skeat 279).
In the epic “Sandayo” of the Subanon of Zamboanga, the hero’s boat Gadyong reveals that it has its own mind because when informed that they were going on a raid, it refused to budge. When Sandayo the hero finally relented and said that he was going to court a maiden, only then did the boat sail. The functions of thought, will, and movement are attributes of the soul, thus the need for the hero to entreat his boat as though it were a person.
This animist belief is seen in another aspect, the boat parts. Boats have a “face”, particularly eyes. The boat atop the burial jar found in the Manunggul cave in Palawan has a face at the prow, and one can see the eyes, nose, mouth and ears. Likewise, the prow of the lipa or houseboats in Sulu and Tawi-Tawi are called sampong (face) with a discernible eye, brow, nose, and mouth. Even the terms used in boat construction also refer to the face: sealing the planks is napirnga (to have a speck in the eye) and the sealant itself, pamota (speck, mote). According to Lorenzo-Abrera, the stern is called sampong buli (the face behind) by the Sama (Paghihinang Kumpit 183).
The belief in a soul in inanimate objects, plants and animals also explains the presence of grave goods. Since these objects have souls, then they can accompany the dead on his journey and be brought over to the afterlife, along with the souls of the slaves buried with him. When these grave goods are completely decomposed materially, then they can be useful to the soul of the dead (Benedict 54). The souls of these objects will be used by the soul of the dead person. This is why, among the Kankanay, not a single iron nail is used in the coffin because the dead person desires that everything should disintegrate together with his corpse (Canol 58). This could help explain why up to the 17th century, the Spaniards would note that not a single piece of iron was used in building the boats.
Mourning
Boats figured prominently in the death rituals as they were part and parcel of the entire animistic belief. There were several forms of mourning: maglahe, morotal, larao, and marabay. Maglahe (magarahe among the Tagalogs) was the mourning indicated by fasting, upon the death of a parent or close relative (Loarca 88-89). The mourner ate no rice, only bananas and sweet potatoes, and drank only tuba (coconut wine). He wound rattan vine around his entire arm and neck. The mourning ended when the mourner had taken a captive or killed someone.
Morotal was a woman’s mourning, where she would get on a barangay boat together with other women and three chosen warriors: one to steer the boat, another to bail, and the third to stay in the bow. The men sang about their bravery in war all the while rowing the boat filled with jars of wine. A great feast would be held upon reaching their destination, and the mourning came to an end with the woman eating rice again and wearing gold ornaments (Loarca 89).
Larao was the mourning for a datu (chief). Everyone observed this ritual, where no one could have any quarrel, the weapons were carried with the points down, daggers carried with reversed hilts, and no one could wear colorful clothing. All was silence. Along the shore signs were placed indicating a larao so that no one could transgress the silence on pain of death (Chirino 135). This practice is recorded in the Maranao epic “Darangen”, where white flags were placed at the river mouth and around the community. Singing was forbidden and silence was enforced. Whoever broke the rule would suffer death. Similarly, the Bilaans cease all activity and merriment when their datu dies, and all help out in preparation for the burial (Cabrera 191).
In the 16th century, a datu was buried in a boat with many rowers who would serve him in the other world (Chirino 135). Slaves, food and drink were placed in the vessel that would carry the dead chief to the next life (Chirino 134). Sometimes as many as 60 slaves would be made to accompany the datu in the afterlife. To accommodate this many passengers, the burial boat would have been a barangay.
According to Loarca, when a datu descended from Dumaguet dies, a slave is made to die in the same manner as the chief (88). He added that the slave chosen for this was the most wretched they could find, a foreigner and not one of them, for he remarked that they were “not at all cruel”. The dead were buried in wooden coffins, piled with gold, clothing, and other expensive objects as they believed that if a person left this world well off, he would be received well in the next life.
Tagalogs buried the dead beside his house; if it was a datu, he would be placed under a small house or porch constructed for this purpose (de Plasencia 122). There was a mourning period of four days, after which the corpse was placed in a boat and buried. Animals could be placed in the boat instead of rowers: a male and female species of the animal would be placed in the seat of the rowers, usually two goats, deers, or hens. If the dead person was a warrior, a living slave would be tied underneath the corpse to die in this manner. Songs about the warrior’s prowess and good qualities were sung by relatives during the wake.
Boat coffins
The archeological evidence of boat-shaped coffins abound from north to south of the Philippine islands as well as in the entire Southeast Asian region (Tenazas). While bangka is the general term for boats, in other minor Philippine languages it is transposed as kabang. The Tagalog term for coffin is kabaong. Briefly, we note that boats are used as houses up to the present by some Philippine ethnolingguistic groups, and that the shape and function of houses have been studied to closely resemble boats. The Bikol term for house is harong, which sounds similar to the Malay term for coffin, larong. This paper infers that the term kabaong meant a boathouse for the dead, intended to transport him to the afterlife.
If the dead had been a member of a raiding team, the coffin would be in the shape of the boat called barangay. Animals would be placed as rowers, with a slave to oversee everything (de San Antonio 152). If he were a renowned sailor, he would be buried in his boat, with slaves to row him to the afterlife. In Bohol, a datu was reported to have been buried with 70 armed slaves and food supplies, just as he had sailed when still living (Colin 174). This supposedly ensured that he could maintain his raiding prowess beyond this world.
It is notable that the kabaong, coffin, is very similarly made as the bangka/kabang, boat. Often, boats are simply mentioned as made of hardwood. In Butuan City, where the oldest balangays (boat) in the Philippines were discovered, there were also excavated coffins made from the hardwood dungon (Heretiera litorales) (Roxas-Lim 56). This hardwood is especially used to construct the boat keel. It had also been noted that coffin planks and its cover were very tightly sewn that not even air could pass through (Chirino 134). It meant that the coffin was likewise constructed watertight in anticipation of its passage in the river or sea.
Significantly, burial jars were almost always found near the shore or in coastal areas (Fox 159-160). In Samar and Leyte, the sea was within view from the site of the jars, and in Sorsogon and Tayabas, these were near the sea. The burial caves, including the elevated sites in Batanes, were facing the sea. In 1857, it was noted of the Ifugao that they buried their dead under their houses, which was attributed to have been an influence from the Chinese “as they had not previously done this” (Alarcon 89). The river and the sea served as passageways to the afterlife, thus the coffin was a boat.
Journey to the Afterlife
One important concept of this spiritual boat journey concerns abay, from where the mourning ritual called marabay takes its root. The marabay mourner stays beside the corpse, taking no solid food for three days. After this time, the mourner may then consume food but nothing that had been passed over fire, until he had taken a head.
Abay refers to boats traveling together. In Bikol it meant several boats sailing in tandem, but a second meaning was for the dead to travel with companions. Among the Sama Laut, the present-day burial ceremony actually consists of several boats sailing together to an island where the burial will take place (Nimmo 194). The stature of the dead person can be seen from the number of boats that accompany the burial boat procession.
In the Visayas, abay also referred to boats sailing together, but likewise contained a second meaning which signified being in another’s company until death (de Mentrida 4). It also meant a certain supernatural power manifested through words, an ability which a person possessed until death. This meaning is given more clarity with the Tagalog meaning of abay. First, it meant accompanying a person to another place; second, it signified a friend or a respected person whom one brought along to a gathering; and lastly, it referred to the person’s soul, in the sense of being a companion. When Spanish colonization began to spread the Christian faith, this indigenous concept was utilized to explain religious tenets, as when abay, referring to the soul, was used in a sample sentence as:
Abay. (…) y aplicado al alma, dicen: Paabay camo sa manga calagyo ninyong Santos
at sa manga catutubo. (Applying to the soul, they say: Ask to be guided by your
namesake saints and by the catutubo.)
Abay as a concept can thus be reduced to the idea of a companion, either as boats sailing in company or as persons traveling together. The nature of such travel could be temporary and brief, such as going to a gathering, or over the period of one’s entire lifetime, such as in indicated by having the soul as companion.
The concept of the abay (companion) explains why there are to be companions for the dead. They will help and serve him in the afterlife. Thus the mourning called mangabay, where one stays beside the corpse, shows that it is first and foremost the mourning relative who must accompany the dead while there are yet slaves to be found for the journey. Once their souls have been obtained for the journey – meaning that they were either killed or left to die, both through a ritual - then the mourner is freed from the task of acting as the abay. The avoidance of abay would also explain certain ethnic beliefs regarding death. For example, among the Bagobo, the sound of a cricket is deemed as the dead person’s invitation for one to become his abay. Thus the relative, upon hearing the insect, addresses it: “You can come here no more because you are now going to the Great City (the afterlife). You have still a little love for me; do not bring me sickness.” We see in this the idea that just as a person needs company while he is on earth, so does the soul as it travels and goes to the afterlife. Hence, there is both a physical and a spiritual abay.
The soul, since it is also a companion, is also considered an abay while the person is alive. However, in the sample sentence explaining the meaning of abay, we encounter another term, calagyo, to wit: calagyo ninyong santos, your namesake saints. A calagyo in pre-colonial culture was a person who was one’s namesake and it would be worthwhile investigating in another study whether this term for a namesake was indeed related to the concept of calag or soul. What can be established now is that these indigenous concepts were used to introduce and explain colonial concepts, in this case pertaining to religion. Thus, the native idea of the calagyo became the vehicle to introduce the idea of a patron saint and naming people after them in the process of Christianization. They would thus become the namesake’s guide in life.
The second term we encounter is catutubo, defined as a person who was the same age as oneself. This term reflected another belief about the soul as a companion, or abay, but in particular as one who grew up with the person from birth. From this, the Spanish missionaries were able to find a parallel concept by which to introduce the guardian angel as the spirit who was from the very beginning with the person it was watching over. Mixing the terms, this guardian spirit was called angel na ating catutubo, which would mean the angel who was the same age as the person. This would mean the indigenization of the Christian concept of the guardian angel who was not “born” at the same time as the person and therefore could have no age, as it was a spirit. The concept that would be the same as catutubo is in the Maranao belief in the tonong. This is believed to be one’s twin who is a spirit and who guards the person and defends him from harm. The tonong is given to a person upon birth. This spirit-twin keeps the person company at all times, warns him of impending danger, and helps him during battle. The tonong has the power to guard the person it accompanies through life, and can be the source of the person’s amazing abilities. There are three kinds of tonong based on its location: in the clouds, on top of trees, and in the water. The tonong who lives in the water is called a diwata.
Abay thus refers to the following: boats sailing together; a person who accompanies another in a journey; the soul of another that would accompany the dead to the afterlife. Marabay, the mourning ritual, thus meant seeking a soul to act as companion for the dead relative, which was why it ended only upon the taking of the life of another. These journeys, both on earth and to the next life, all involved the use of boats.
These boat rituals and terms show us that the boats themselves may be read as a repository of the animist belief system. The uses in the various rituals reveal the worldview and explain the interrelations among the different segments of the entire cosmic set-up in the indigenous mind. The boat served as a transport vehicle during one’s life and in the afterlife. The bangka was a boat that transported souls to the afterlife and a boat that had a soul of its own.
Monday, August 06, 2007
Behaviour: Of mice and man-eaters
The sexual behaviour of female mice can be altered dramatically by almost literally flicking a switch at the periphery of their brain. Disrupting the function of a sensory organ called the vomeronasal organ (VNO) causes female mice to display strikingly masculine sexual behaviours – such as mounting, pelvic thrust and solicitation.
It is thought that sex differences in mammalian behaviour arise as a result of exposure to hormones in the womb, which shape the development of either male- or female-specific neural circuits. The evidence Catherine Dulac and colleagues present in a study. They observed the behaviour of female mice after genetic or physical lesion of the VNO, and report that the mice display sexual and courtship behaviours that are uniquely male. The authors report that the lesioned female mice also show a reduction in female-specific behaviours such as nesting.
These results suggest that, in mice at least, the neural circuitry underlying masculine behaviour surprisingly still exists in adult females. This implies a new model of sex differences in behaviour, in which male and female circuits co-exist in the brains of both sexes and are switched on or off by sensory input such as the pheromones detected by the VNO.
Author contact:
Catherine Dulac (Harvard University, Cambridge, MA, USA)
Tel: +1 617 495 7893; E-mail: dulac@fas.harvard.edu
Marc Breedlove (Michigan State University, East Lansing, MI, USA) N&V author
Tel: +1 517 355 1749; E-mail: breedsm@msu.edu
The sexual behaviour of female mice can be altered dramatically by almost literally flicking a switch at the periphery of their brain. Disrupting the function of a sensory organ called the vomeronasal organ (VNO) causes female mice to display strikingly masculine sexual behaviours – such as mounting, pelvic thrust and solicitation.
It is thought that sex differences in mammalian behaviour arise as a result of exposure to hormones in the womb, which shape the development of either male- or female-specific neural circuits. The evidence Catherine Dulac and colleagues present in a study. They observed the behaviour of female mice after genetic or physical lesion of the VNO, and report that the mice display sexual and courtship behaviours that are uniquely male. The authors report that the lesioned female mice also show a reduction in female-specific behaviours such as nesting.
These results suggest that, in mice at least, the neural circuitry underlying masculine behaviour surprisingly still exists in adult females. This implies a new model of sex differences in behaviour, in which male and female circuits co-exist in the brains of both sexes and are switched on or off by sensory input such as the pheromones detected by the VNO.
Author contact:
Catherine Dulac (Harvard University, Cambridge, MA, USA)
Tel: +1 617 495 7893; E-mail: dulac@fas.harvard.edu
Marc Breedlove (Michigan State University, East Lansing, MI, USA) N&V author
Tel: +1 517 355 1749; E-mail: breedsm@msu.edu
Cancer: Gene reduces severity of lung cancer
A gene known to aid suppression of some tumours is shown to reduce the aggression of lung cancers along with the risk of metastasis. This demonstrates that Lkb1 loss, combined with the mutation of another factor, Kras, in a mouse model, causes more aggressive tumours to arise.
LKB1 is a tumour suppressor gene and is often found to be mutated in patients with Peutz–Jeghers syndrome, who have an increased incidence of cancer. Kras mutation and p53 loss lead to lung cancer in a mouse model, but Kwok-Kin Wong and colleagues found that, when combined with Lkb1 mutation, not only were tumours more aggressive but they were more likely to develop into squamous and large-cell carcinomas of the lung. This report also identifies LKB1 mutations in human lung cancers classified as squamous carcinomas.
Thus, LKB1 loss may be a marker for predicting disease development and spread, and the pathways regulated by LKB1 represent possible therapeutic targets.
Author contact:
Kwok-Kin Wong (Dana Farber Cancer Institute, Boston, MA, USA)
Tel: +1 617 632 6084; E-mail: kwong1@partners.org
A gene known to aid suppression of some tumours is shown to reduce the aggression of lung cancers along with the risk of metastasis. This demonstrates that Lkb1 loss, combined with the mutation of another factor, Kras, in a mouse model, causes more aggressive tumours to arise.
LKB1 is a tumour suppressor gene and is often found to be mutated in patients with Peutz–Jeghers syndrome, who have an increased incidence of cancer. Kras mutation and p53 loss lead to lung cancer in a mouse model, but Kwok-Kin Wong and colleagues found that, when combined with Lkb1 mutation, not only were tumours more aggressive but they were more likely to develop into squamous and large-cell carcinomas of the lung. This report also identifies LKB1 mutations in human lung cancers classified as squamous carcinomas.
Thus, LKB1 loss may be a marker for predicting disease development and spread, and the pathways regulated by LKB1 represent possible therapeutic targets.
Author contact:
Kwok-Kin Wong (Dana Farber Cancer Institute, Boston, MA, USA)
Tel: +1 617 632 6084; E-mail: kwong1@partners.org
CHEMICAL BIOLOGY : An unfolding antibiotics story
Scientists have identified the way an unusual antibiotic works. Lactivicin and similar molecules are a class of antibiotics that are unique because they do not contain a beta-lactam ring. This is significant because antibiotic resistance is frequently tied to the beta-lactam rings of the more common antibiotics, like penicillin.
Now a team led by Christopher Schofield and colleagues specifically demonstrate that lactivicin is an effective antibiotic against penicillin-resistant bacteria isolated from human patients. In addition, the authors explain lactivicin’s unique behaviour by providing a crystal structure of the compound bound to its protein target, in which the two rings of the compound have been opened. This discovery will undoubtedly lead to the design of new effective antibiotics that can be applied to resistant bacteria.
Author contact:
Christopher Schofield (Chemistry Research Laboratory, Oxford, UK)
Tel: +44 1865 275 625, Email: christopher.schofield@chem.ox.ac.uk
Scientists have identified the way an unusual antibiotic works. Lactivicin and similar molecules are a class of antibiotics that are unique because they do not contain a beta-lactam ring. This is significant because antibiotic resistance is frequently tied to the beta-lactam rings of the more common antibiotics, like penicillin.
Now a team led by Christopher Schofield and colleagues specifically demonstrate that lactivicin is an effective antibiotic against penicillin-resistant bacteria isolated from human patients. In addition, the authors explain lactivicin’s unique behaviour by providing a crystal structure of the compound bound to its protein target, in which the two rings of the compound have been opened. This discovery will undoubtedly lead to the design of new effective antibiotics that can be applied to resistant bacteria.
Author contact:
Christopher Schofield (Chemistry Research Laboratory, Oxford, UK)
Tel: +44 1865 275 625, Email: christopher.schofield@chem.ox.ac.uk
IMMUNOLOGY : How inflammatory lymphocytes develop
Researchers describe the development of a unique type of white blood cell and how this development is different in humans and mice. These cells are required for healthy gut biology but also, in other areas of the body such as the brain, are associated with dangerous inflammation.
Two groups, one led by Rene Waal de Malefyt and the other by Federica Sallusto, evaluated how human T cells develop into TH-17 cells, which make several inflammatory immune proteins associated with inflammation and with fighting certain microbial infections. Both groups found that the requirements for TH-17 cell development in humans and mice are different, a surprising finding that has great significance because mice are commonly used to study human disease. A third study led by Michael Lohoff evaluated TH-17 cells in mice only, and found that a specific cellular protein called interferon regulatory factor 4 is absolutely required for their development.
These three studies provide considerable insight into how TH-17 inflammatory cells are produced in both mice and humans. Understanding the unique developmental requirements for these inflammatory T cells may help to explain the cause of inflammatory diseases of the brain and gut in humans.
Author contacts:
Rene Waal de Malefyt (Schering-Plough Biopharma, Palo Alto, CA, USA)
Tel: +1 650 496 1164; E-mail: rene.de.waal.malefyt@spcorp.com Author paper [5]
Federica Sallusto (Institute for Research in Biomedicine, Bellinzona, Switzerland)
Tel: +41 91 820 0315; E-mail: federica.sallusto@irb.unisi.ch Author paper [6]
Michael Lohoff (Marburg University, Germany) Author paper [7]
Tel: +49 6421 286 6455; E-mail: lohoff@med.uni-marburg.de
Researchers describe the development of a unique type of white blood cell and how this development is different in humans and mice. These cells are required for healthy gut biology but also, in other areas of the body such as the brain, are associated with dangerous inflammation.
Two groups, one led by Rene Waal de Malefyt and the other by Federica Sallusto, evaluated how human T cells develop into TH-17 cells, which make several inflammatory immune proteins associated with inflammation and with fighting certain microbial infections. Both groups found that the requirements for TH-17 cell development in humans and mice are different, a surprising finding that has great significance because mice are commonly used to study human disease. A third study led by Michael Lohoff evaluated TH-17 cells in mice only, and found that a specific cellular protein called interferon regulatory factor 4 is absolutely required for their development.
These three studies provide considerable insight into how TH-17 inflammatory cells are produced in both mice and humans. Understanding the unique developmental requirements for these inflammatory T cells may help to explain the cause of inflammatory diseases of the brain and gut in humans.
Author contacts:
Rene Waal de Malefyt (Schering-Plough Biopharma, Palo Alto, CA, USA)
Tel: +1 650 496 1164; E-mail: rene.de.waal.malefyt@spcorp.com Author paper [5]
Federica Sallusto (Institute for Research in Biomedicine, Bellinzona, Switzerland)
Tel: +41 91 820 0315; E-mail: federica.sallusto@irb.unisi.ch Author paper [6]
Michael Lohoff (Marburg University, Germany) Author paper [7]
Tel: +49 6421 286 6455; E-mail: lohoff@med.uni-marburg.de
Structural & Molecular Biology - Seeing transcription in living colour
A closer look is taken at gene transcription in living organisms. Transcription by RNA polymerase II, the enzyme that transcribes DNA into messenger RNAs, is at the core of gene expression and is a major focus of biological regulatory mechanisms. Much of what is known about transcription comes from test tube experiments (in vitro) with purified components but little is known about how RNA polymerase works in vivo.
Robert Singer and co-workers have now taken the analysis of the mechanism of gene transcription in higher organisms to a new level by using advanced fluorescence imaging techniques to measure quantitatively the kinetics of gene transcription by RNA polymerase II in living mammalian cells. The ultimate goal of this work is a quantitative model of gene transcription in vivo. They find several novel and unexpected features concerning the nature of the in vivo transcription.
First, they conclude that only a surprisingly small fraction of RNA polymerases that bind to the start of a gene, amounting to about 1%, actually go on to transcribe the gene and produce a messenger RNA. Second, they find that RNA polymerases transcribe more rapidly than previously thought, often pausing for prolonged periods. This study represents a critical milestone on the way to building a quantitative understanding of the mechanism of transcription in single live cells.
Author contact:
Robert Singer (Albert Einstein College of Medicine, New York, NY, USA)
Tel: + 1 718 430 8646; E-mail: rhsinger@aecom.yu.edu
A closer look is taken at gene transcription in living organisms. Transcription by RNA polymerase II, the enzyme that transcribes DNA into messenger RNAs, is at the core of gene expression and is a major focus of biological regulatory mechanisms. Much of what is known about transcription comes from test tube experiments (in vitro) with purified components but little is known about how RNA polymerase works in vivo.
Robert Singer and co-workers have now taken the analysis of the mechanism of gene transcription in higher organisms to a new level by using advanced fluorescence imaging techniques to measure quantitatively the kinetics of gene transcription by RNA polymerase II in living mammalian cells. The ultimate goal of this work is a quantitative model of gene transcription in vivo. They find several novel and unexpected features concerning the nature of the in vivo transcription.
First, they conclude that only a surprisingly small fraction of RNA polymerases that bind to the start of a gene, amounting to about 1%, actually go on to transcribe the gene and produce a messenger RNA. Second, they find that RNA polymerases transcribe more rapidly than previously thought, often pausing for prolonged periods. This study represents a critical milestone on the way to building a quantitative understanding of the mechanism of transcription in single live cells.
Author contact:
Robert Singer (Albert Einstein College of Medicine, New York, NY, USA)
Tel: + 1 718 430 8646; E-mail: rhsinger@aecom.yu.edu
Virus-based screen for ion channel modulators
A virus-based method that screens for chemical or genetically-encoded inhibitors of ion channels. Ion channels are cell membrane-spanning proteins that, when activated, allow the influx of ions. They encompass a large family of over 400 proteins and play key roles in maintaining cellular function. While blocking their activity has proven useful for certain medical applications, these drugs usually elicit severe side effects due to their wide range action and lack of selectivity for the intended cell alone.
Joseph Glorioso and colleagues wanted to find more specific channel modulators and set up a virus-based screen in which the virus level is an indicator for inhibitor efficacy. They reasoned that overexpression of an ion channel in cells via a virus would be detrimental to the cell and consequently impede viral replication; while the presence of an inhibitor of channel function would keep the cells healthy and allow replication. The advance over other screens for channel inhibitors is that the technique can easily be adapted to screen for genetically-encoded inhibitors by coinfection of a second virus that encodes the inhibitor. The inhibitor’s DNA can then be easily retrieved from the viral genome.
This method can easily be scaled up to screen whole DNA libraries that express a wide range of potential channel modulators. These genetically encoded inhibitors will help reveal the biology behind channel regulation and are likely to lead to more specific inhibitors.
Author contact:
Joseph Glorioso (University of Pittsburgh School of Medicine, PA, USA)
Tel: +1 412 648 8105; E-mail: glorioso@pitt.edu
A virus-based method that screens for chemical or genetically-encoded inhibitors of ion channels. Ion channels are cell membrane-spanning proteins that, when activated, allow the influx of ions. They encompass a large family of over 400 proteins and play key roles in maintaining cellular function. While blocking their activity has proven useful for certain medical applications, these drugs usually elicit severe side effects due to their wide range action and lack of selectivity for the intended cell alone.
Joseph Glorioso and colleagues wanted to find more specific channel modulators and set up a virus-based screen in which the virus level is an indicator for inhibitor efficacy. They reasoned that overexpression of an ion channel in cells via a virus would be detrimental to the cell and consequently impede viral replication; while the presence of an inhibitor of channel function would keep the cells healthy and allow replication. The advance over other screens for channel inhibitors is that the technique can easily be adapted to screen for genetically-encoded inhibitors by coinfection of a second virus that encodes the inhibitor. The inhibitor’s DNA can then be easily retrieved from the viral genome.
This method can easily be scaled up to screen whole DNA libraries that express a wide range of potential channel modulators. These genetically encoded inhibitors will help reveal the biology behind channel regulation and are likely to lead to more specific inhibitors.
Author contact:
Joseph Glorioso (University of Pittsburgh School of Medicine, PA, USA)
Tel: +1 412 648 8105; E-mail: glorioso@pitt.edu
Friday, August 03, 2007
Fast and low cost Photographic Method
Researchers in the Philippines have revealed that a fast and low cost photographic method is just as effective as the more expensive videographic method in assessing the condition of coral reef benthic communities. Comparison Between Videographic and Photographic Methods in Assessing Coral Reef Benthic Communities by Patrick C. Cabaitan, Wilfredo Y. Licuanan, and Edgardo D. Gomez
Continuous degradation of coral reefs creates a need for techniques that can assess reef conditions rapidly and efficiently. The Video transect survey is commonly used to monitor benthic communities because it is rapid, provides a permanent historical record of the data, and can help minimize observer bias. But this technology is not readily available to most research institutions because of its high cost.
In this study, a low cost photographic method was used to survey benthic communities in the subtidal flat inside Caniogan Marine Sanctuary, Tondol, Anda, Pangasinan. Results from this method were then compared with those from videographic methods.
For the low cost photographic method, ten regularly spaced shots were directly taken from each 5m transect, totaling to 100 frames. Ten 5m x ~0.25m video transects were also run over each of the twenty selected patch reefs, covering the whole demarcated area. Ten regularly spaced frames were then taken from the videotape in each transect, totaling to 100 frames in each patch reef. In the laboratory, all frames were analyzed using the systematic 5-point method.
Both methods yielded comparable time in field data collection. However, videographic method demanded more time in post-collection computer analysis and it is more costly due to the required additional computer software and hardware. Pairwise T-tests and Analysis of similarities (ANOSIM) revealed that both methods gathered similar results in terms of the diversity (P>0.05) and in terms of percentage composition (P>0.05) of life forms recorded, suggesting that both can be used interchangeably in benthic community surveys.
(Science Diliman)E-mail: rduo.ovcrd@up.edu.ph
Telephone:+63 2 - 927-2309
Fax:+63 2 - 927-2568
Researchers in the Philippines have revealed that a fast and low cost photographic method is just as effective as the more expensive videographic method in assessing the condition of coral reef benthic communities. Comparison Between Videographic and Photographic Methods in Assessing Coral Reef Benthic Communities by Patrick C. Cabaitan, Wilfredo Y. Licuanan, and Edgardo D. Gomez
Continuous degradation of coral reefs creates a need for techniques that can assess reef conditions rapidly and efficiently. The Video transect survey is commonly used to monitor benthic communities because it is rapid, provides a permanent historical record of the data, and can help minimize observer bias. But this technology is not readily available to most research institutions because of its high cost.
In this study, a low cost photographic method was used to survey benthic communities in the subtidal flat inside Caniogan Marine Sanctuary, Tondol, Anda, Pangasinan. Results from this method were then compared with those from videographic methods.
For the low cost photographic method, ten regularly spaced shots were directly taken from each 5m transect, totaling to 100 frames. Ten 5m x ~0.25m video transects were also run over each of the twenty selected patch reefs, covering the whole demarcated area. Ten regularly spaced frames were then taken from the videotape in each transect, totaling to 100 frames in each patch reef. In the laboratory, all frames were analyzed using the systematic 5-point method.
Both methods yielded comparable time in field data collection. However, videographic method demanded more time in post-collection computer analysis and it is more costly due to the required additional computer software and hardware. Pairwise T-tests and Analysis of similarities (ANOSIM) revealed that both methods gathered similar results in terms of the diversity (P>0.05) and in terms of percentage composition (P>0.05) of life forms recorded, suggesting that both can be used interchangeably in benthic community surveys.
(Science Diliman)E-mail: rduo.ovcrd@up.edu.ph
Telephone:+63 2 - 927-2309
Fax:+63 2 - 927-2568
Commencement of Second Life Joint Research
Keio University and Dentsu Announce the Commencement of Second Life Joint Research -- Keio University Second Life Campus to Hold Japan’s First Metaverse-Based University Course --
Keio University (President: Yuichiro Anzai; Head Office: Tokyo) and Dentsu Inc. (President & COO: Tatsuyoshi Takashima; Head Office: Tokyo; Capital: 58,967.1 million yen) announced today that they will conduct joint research covering a number of issues relating to metaverses, and particularly Second Life® (See Note 1), a 3-D virtual community that has gained worldwide popularity. Planned research topics include issues on social systems, distance learning and continuing education, the potential for marketing activities within a metaverse, and the potential for technological development.
As a facility to carry out their joint research, Keio University and Dentsu plan to establish the Keio University Second Life® Campus within Virtual Tokyo (See Note 2), which Dentsu will open in August this year as a virtual city within the Second Life® metaverse. Through demonstration tests conducted in the Keio University Second Life® Campus, the joint research group aims to contribute to finding solutions to a range of issues relating to virtual societies. In addition, the joint research group plans to study the potential for educational content within 3-D virtual communities and consider various aspects about the future of education.
Outline of the Joint Research
Keio University Dentsu and will establish a joint research facility, Keio University Second Life® Campus, within Virtual Tokyo. Virtual land for the campus as well as authority to manage the campus will be provided by Dentsu to Keio University Research Institute at SFC. The research group will utilize this land to conduct their research. The land area allocated for the campus will be 1 SIM, which is the standard land unit in the Second Life® metaverse and is equal to 256 x 256 meters (16 acres).
Within this virtual space, the research group will conduct the following research
(1) Within the Keio University Second Life® Campus, the research group plans to explore new education possibilities by utilizing the experience Keio University has built up in distance teaching methods, for instance, through operating the Keio University SFC Global Campus (See Note 3). Utilizing the educational video content Keio University has accumulated until now, the research group plans to examine the
potential for Second Life® in the education field. This will be the first time for a university in Japan to offer lectures from regular university courses within Second Life®.
(2) The research group will conduct research within the Keio University Second Life® Campus and Virtual Tokyo on the behavior of Second Life® consumers and economic activities such as virtual currencies. Utilizing the Linden Dollar, the virtual currency circulating within Second Life®, the research group will study such areas as the virtual economic mechanism, analysis of consumer behavior, and legal or ethical issues within the metaverse. The research group also plans to collaborate with the makers of Second Life®, Linden Labs, in research on technical aspects of Second Life®.
Research Group Participants
A number of researchers from the Keio Research Institute at SFC, based at the Keio University Shonan Fujisawa Campus, will participate in the research. These researchers include such specialists in Internet, digital media, and other social applications for new technologies as Professor Jun Murai and Professor Masahiko Inakage from the Faculty of Environment and Information Studies; Professor Ikuyo Kaneko from the Graduate School of Media and Governance; and Professor Jiro Kokuryo from the Faculty of Policy Management.
From Dentsu, specialists in marketing and media content will participate in the joint research. Dentsu Group companies will also provide cooperation and support for the construction and operation of the virtual campus.
Note 1: Second Life® 3-D virtual community
Second Life® is a 3-D virtual community, created and operated by U.S.-based company Linden Lab, with a rapidly growing population from 100 countries around the globe. Residents of the Second Life®
metaverse themselves create and build the world that includes homes, vehicles, nightclubs, stores, landscapes, clothing, and games. The Second Life® Grid is a sophisticated development platform created by Linden Lab, a company founded in 1999 by Philip Rosedale, to create a revolutionary new form of shared 3-D experience. The former CTO of RealNetworks, Rosedale pioneered the development of many of today’s streaming media technologies, including RealVideo. In April 2003, noted software pioneer Mitch Kapor, founder of Lotus Development Corporation, was named Chairman. In 2006, Philip Rosedale and Linden Lab received WIRED’s Rave Award for Innovation in Business. Based in San Francisco, Linden Lab employs a senior team bringing together deep expertise in physics, 3-D graphics and networking.
Note 2: Virtual Tokyo
Virtual Tokyo is a comprehensive virtual city being created based on the concept of
"Vitality–Future–Tokyo.” It is a collaboration between Dentsu and Tetsuya Mizuguchi, CCO of Q Entertainment Inc. Virtual Tokyo will condense the images and energy of Tokyo and disseminate to the rest of the world the pop culture created within it. Virtual Tokyo will not be a one-way content source but provide a place for creators (users) to actively participate. By doing so, Dentsu wishes to recreate the
dynamism of Tokyo—an ever-changing city—within Second Life®. Virtual Tokyo will cover 85 hectares, making it one of the largest cities within Second Life®. It will comprise various zones, including a public zone with stadiums and museums, and other zones such as those focusing on education, experiential activities and commerce.
Note 3: Keio University SFC Global Campus (http://gc.sfc.keio.ac.jp/)
The Keio University Shonan Fujisawa Campus (SFC-GC) provides lectures that are shared globally and accessed by learners outside the university. It was opened in 2002 and from the 2002 autumn semester to the 2007 spring semester, 297 courses (each comprising 13 lectures) have been made available for access as approximately 4,000 video material content items. At present, Keio University runs the distance learning program, which allows people who are not Keio University students to utilize SFC-GC to enroll in courses. Furthermore, the content, which is provided free of charge, may be accessed without the need for user registration.
Contact: Rina Tanaka and Aiko Nakajima
Office of Communications and Public Relations
Keio University
Telephone: (813) 5427-1541
E-mail: m-koho@adst.keio.ac.jp
Keio University and Dentsu Announce the Commencement of Second Life Joint Research -- Keio University Second Life Campus to Hold Japan’s First Metaverse-Based University Course --
Keio University (President: Yuichiro Anzai; Head Office: Tokyo) and Dentsu Inc. (President & COO: Tatsuyoshi Takashima; Head Office: Tokyo; Capital: 58,967.1 million yen) announced today that they will conduct joint research covering a number of issues relating to metaverses, and particularly Second Life® (See Note 1), a 3-D virtual community that has gained worldwide popularity. Planned research topics include issues on social systems, distance learning and continuing education, the potential for marketing activities within a metaverse, and the potential for technological development.
As a facility to carry out their joint research, Keio University and Dentsu plan to establish the Keio University Second Life® Campus within Virtual Tokyo (See Note 2), which Dentsu will open in August this year as a virtual city within the Second Life® metaverse. Through demonstration tests conducted in the Keio University Second Life® Campus, the joint research group aims to contribute to finding solutions to a range of issues relating to virtual societies. In addition, the joint research group plans to study the potential for educational content within 3-D virtual communities and consider various aspects about the future of education.
Outline of the Joint Research
Keio University Dentsu and will establish a joint research facility, Keio University Second Life® Campus, within Virtual Tokyo. Virtual land for the campus as well as authority to manage the campus will be provided by Dentsu to Keio University Research Institute at SFC. The research group will utilize this land to conduct their research. The land area allocated for the campus will be 1 SIM, which is the standard land unit in the Second Life® metaverse and is equal to 256 x 256 meters (16 acres).
Within this virtual space, the research group will conduct the following research
(1) Within the Keio University Second Life® Campus, the research group plans to explore new education possibilities by utilizing the experience Keio University has built up in distance teaching methods, for instance, through operating the Keio University SFC Global Campus (See Note 3). Utilizing the educational video content Keio University has accumulated until now, the research group plans to examine the
potential for Second Life® in the education field. This will be the first time for a university in Japan to offer lectures from regular university courses within Second Life®.
(2) The research group will conduct research within the Keio University Second Life® Campus and Virtual Tokyo on the behavior of Second Life® consumers and economic activities such as virtual currencies. Utilizing the Linden Dollar, the virtual currency circulating within Second Life®, the research group will study such areas as the virtual economic mechanism, analysis of consumer behavior, and legal or ethical issues within the metaverse. The research group also plans to collaborate with the makers of Second Life®, Linden Labs, in research on technical aspects of Second Life®.
Research Group Participants
A number of researchers from the Keio Research Institute at SFC, based at the Keio University Shonan Fujisawa Campus, will participate in the research. These researchers include such specialists in Internet, digital media, and other social applications for new technologies as Professor Jun Murai and Professor Masahiko Inakage from the Faculty of Environment and Information Studies; Professor Ikuyo Kaneko from the Graduate School of Media and Governance; and Professor Jiro Kokuryo from the Faculty of Policy Management.
From Dentsu, specialists in marketing and media content will participate in the joint research. Dentsu Group companies will also provide cooperation and support for the construction and operation of the virtual campus.
Note 1: Second Life® 3-D virtual community
Second Life® is a 3-D virtual community, created and operated by U.S.-based company Linden Lab, with a rapidly growing population from 100 countries around the globe. Residents of the Second Life®
metaverse themselves create and build the world that includes homes, vehicles, nightclubs, stores, landscapes, clothing, and games. The Second Life® Grid is a sophisticated development platform created by Linden Lab, a company founded in 1999 by Philip Rosedale, to create a revolutionary new form of shared 3-D experience. The former CTO of RealNetworks, Rosedale pioneered the development of many of today’s streaming media technologies, including RealVideo. In April 2003, noted software pioneer Mitch Kapor, founder of Lotus Development Corporation, was named Chairman. In 2006, Philip Rosedale and Linden Lab received WIRED’s Rave Award for Innovation in Business. Based in San Francisco, Linden Lab employs a senior team bringing together deep expertise in physics, 3-D graphics and networking.
Note 2: Virtual Tokyo
Virtual Tokyo is a comprehensive virtual city being created based on the concept of
"Vitality–Future–Tokyo.” It is a collaboration between Dentsu and Tetsuya Mizuguchi, CCO of Q Entertainment Inc. Virtual Tokyo will condense the images and energy of Tokyo and disseminate to the rest of the world the pop culture created within it. Virtual Tokyo will not be a one-way content source but provide a place for creators (users) to actively participate. By doing so, Dentsu wishes to recreate the
dynamism of Tokyo—an ever-changing city—within Second Life®. Virtual Tokyo will cover 85 hectares, making it one of the largest cities within Second Life®. It will comprise various zones, including a public zone with stadiums and museums, and other zones such as those focusing on education, experiential activities and commerce.
Note 3: Keio University SFC Global Campus (http://gc.sfc.keio.ac.jp/)
The Keio University Shonan Fujisawa Campus (SFC-GC) provides lectures that are shared globally and accessed by learners outside the university. It was opened in 2002 and from the 2002 autumn semester to the 2007 spring semester, 297 courses (each comprising 13 lectures) have been made available for access as approximately 4,000 video material content items. At present, Keio University runs the distance learning program, which allows people who are not Keio University students to utilize SFC-GC to enroll in courses. Furthermore, the content, which is provided free of charge, may be accessed without the need for user registration.
Contact: Rina Tanaka and Aiko Nakajima
Office of Communications and Public Relations
Keio University
Telephone: (813) 5427-1541
E-mail: m-koho@adst.keio.ac.jp
Climate change: Brown haze spells bad news
The haze of air pollution over the Indian Ocean may be causing as much lower atmospheric warming as the recent increase in anthropogenic greenhouse gases.
During 18 missions, Veerabhadran Ramanathan and colleagues simultaneously flew three lightweight unmanned aerial vehicles below, into and above the polluted ‘Brown Clouds’ over the Indian Ocean. Tiny instruments were deployed to measure aerosol concentrations, soot amount and solar fluxes, allowing the team to calculate atmospheric solar heating rates. Using model simulations, they conclude that atmospheric Brown Clouds enhance lower atmospheric solar heating by around 50 per cent.
Atmospheric Brown Clouds consist of a mixture of light-absorbing and light-scattering aerosols and so contribute both to atmospheric solar heating and to surface cooling. The combined effects are thought to have masked up to 50 per cent of the global warming attributed to the recent, rapid rise in greenhouse gases. This study helps to tease out the effects of atmospheric solar heating.
CONTACT
Veerabhadran Ramanathan (University of California San Diego, La Jolla, CA, USA)
Tel: +1 858 337 3114; E-mail: vram@fiji.ucsd.edu or vraman000@hotmail.com
Peter Pilewskie (University of Colorado Boulder, CO, USA) N&V author
Tel: +1 303 492 5724; E-mail: peter.pilewskie@lasp.colorado.edu
The haze of air pollution over the Indian Ocean may be causing as much lower atmospheric warming as the recent increase in anthropogenic greenhouse gases.
During 18 missions, Veerabhadran Ramanathan and colleagues simultaneously flew three lightweight unmanned aerial vehicles below, into and above the polluted ‘Brown Clouds’ over the Indian Ocean. Tiny instruments were deployed to measure aerosol concentrations, soot amount and solar fluxes, allowing the team to calculate atmospheric solar heating rates. Using model simulations, they conclude that atmospheric Brown Clouds enhance lower atmospheric solar heating by around 50 per cent.
Atmospheric Brown Clouds consist of a mixture of light-absorbing and light-scattering aerosols and so contribute both to atmospheric solar heating and to surface cooling. The combined effects are thought to have masked up to 50 per cent of the global warming attributed to the recent, rapid rise in greenhouse gases. This study helps to tease out the effects of atmospheric solar heating.
CONTACT
Veerabhadran Ramanathan (University of California San Diego, La Jolla, CA, USA)
Tel: +1 858 337 3114; E-mail: vram@fiji.ucsd.edu or vraman000@hotmail.com
Peter Pilewskie (University of Colorado Boulder, CO, USA) N&V author
Tel: +1 303 492 5724; E-mail: peter.pilewskie@lasp.colorado.edu
Earthquakes: Love and stress
Non-volcanic tremor and slip along a plate boundary can be triggered by shear stress, rather than fluid movement.The analysis of seismic data has revealed long-duration, low-amplitude tremor, similar to that seen below active volcanoes, but associated with plate tectonic boundaries, rather than volcanoes. Episodes of tremors and slow slip have been observed to last up to months, and can be associated with as much deformation as a magnitude-7 earthquake. Although observations of this type of tremor are increasing, the mechanism behind it remains unclear, with some researchers pointing towards slip along the plate interface, and others the movement of fluids.
Justin Rubinstein and colleagues examined seismic recordings associated with the 2002 Denali earthquake and found clear evidence of bursts of tremor having been triggered within the Cascadia subduction zone near Vancouver Island, Canada. These episodes seem to be triggered when the Love wave (surface seismic wave) displacements were to the southwest — parallel to the direction of plate convergence. They conclude that the tremor and possibly slow-slip events can be induced by shear stress increases along the subduction interface.
CONTACT
Justin Rubinstein (University of Washington, Seattle, WA, USA)
Tel: +1 206 685 7563; E-mail: justin@ess.washington.edu
Non-volcanic tremor and slip along a plate boundary can be triggered by shear stress, rather than fluid movement.The analysis of seismic data has revealed long-duration, low-amplitude tremor, similar to that seen below active volcanoes, but associated with plate tectonic boundaries, rather than volcanoes. Episodes of tremors and slow slip have been observed to last up to months, and can be associated with as much deformation as a magnitude-7 earthquake. Although observations of this type of tremor are increasing, the mechanism behind it remains unclear, with some researchers pointing towards slip along the plate interface, and others the movement of fluids.
Justin Rubinstein and colleagues examined seismic recordings associated with the 2002 Denali earthquake and found clear evidence of bursts of tremor having been triggered within the Cascadia subduction zone near Vancouver Island, Canada. These episodes seem to be triggered when the Love wave (surface seismic wave) displacements were to the southwest — parallel to the direction of plate convergence. They conclude that the tremor and possibly slow-slip events can be induced by shear stress increases along the subduction interface.
CONTACT
Justin Rubinstein (University of Washington, Seattle, WA, USA)
Tel: +1 206 685 7563; E-mail: justin@ess.washington.edu
Neuroscience: Deep brain stimulation in a minimally conscious state
The responses of a single patient in a minimally conscious state have improved with deep brain stimulation.During this intervention, the patient’s arousal level and motor control increased to the point that he was able to chew and swallow food.
‘Minimally conscious state’ refers to a level of consciousness characterized by intermittent evidence of awareness of oneself or the environment, and is distinct from persistent vegetative state or coma. At present there are no reliable means for improving recovery from this extended loss of consciousness, which can occur following traumatic brain injury, although recent evidence suggests some brain activity may be preserved in minimally conscious patients. In the current study, Nicholas Schiff and colleagues implanted electrodes into the brain of a 38-year-old male, six years after he suffered a severe brain injury that resulted in a minimally conscious state. The electrodes were used to stimulate an area known as the thalamus, on both sides of the brain, which has been suggested to have a role in arousal. The authors report that during periods of stimulation, the frequency of communicative behaviours, functional limb control and oral feeding increased.
The authors caution that the extent to which their results might apply to other patients is unknown, and that expectations raised by their findings should be tempered — the specific injury suffered and its effects on responsiveness will not be shared by all patients in a minimally conscious state. The present findings should, however, motivate further research into the mechanisms of recovery, as their replication could have important implications for clinical practice.
CONTACT
Nicholas Schiff (Weill Cornell Medical College, New York, NY, USA)
Joseph Fins (Weill Cornell Medical College, New York, NY, USA)
Ali Rezai (Cleveland Clinic Foundation, OH, USA)
Joseph Giacino (JFK Johnson Rehabilitation Institute / New Jersey Neuroscience Institute, Edison, NJ, USA)
The responses of a single patient in a minimally conscious state have improved with deep brain stimulation.During this intervention, the patient’s arousal level and motor control increased to the point that he was able to chew and swallow food.
‘Minimally conscious state’ refers to a level of consciousness characterized by intermittent evidence of awareness of oneself or the environment, and is distinct from persistent vegetative state or coma. At present there are no reliable means for improving recovery from this extended loss of consciousness, which can occur following traumatic brain injury, although recent evidence suggests some brain activity may be preserved in minimally conscious patients. In the current study, Nicholas Schiff and colleagues implanted electrodes into the brain of a 38-year-old male, six years after he suffered a severe brain injury that resulted in a minimally conscious state. The electrodes were used to stimulate an area known as the thalamus, on both sides of the brain, which has been suggested to have a role in arousal. The authors report that during periods of stimulation, the frequency of communicative behaviours, functional limb control and oral feeding increased.
The authors caution that the extent to which their results might apply to other patients is unknown, and that expectations raised by their findings should be tempered — the specific injury suffered and its effects on responsiveness will not be shared by all patients in a minimally conscious state. The present findings should, however, motivate further research into the mechanisms of recovery, as their replication could have important implications for clinical practice.
CONTACT
Nicholas Schiff (Weill Cornell Medical College, New York, NY, USA)
Joseph Fins (Weill Cornell Medical College, New York, NY, USA)
Ali Rezai (Cleveland Clinic Foundation, OH, USA)
Joseph Giacino (JFK Johnson Rehabilitation Institute / New Jersey Neuroscience Institute, Edison, NJ, USA)
Tunable light sources lose their mirrors
A tunable infrared source that is ‘mirror-free’ and easy to align has been experimentally demonstrated for the first time and could result in a new source of light that is small, inexpensive and convenient to use.
Optical parametric oscillators (OPOs) are useful in the fields of spectroscopy, chemistry and other disciplines because they offer tunable coherent light – narrow-bandwidth light that has radiation with all the waves vibrating in phase – with wavelengths ranging from 2 to 10 micrometres, filling gaps that can’t be served by other sources. Unfortunately, conventional designs are hard to align and miniaturize as, apart from a nonlinear crystal, they also contain a pair of mirrors that need to be very precisely located. Although ‘mirrorless’ designs have been theoretically proposed in the past, an experimental prototype has not been demonstrated to date.
Carlota Canalias and Valdas Pasiskevicius have built a device that is highly compact, easy to align and has the ability to tune wavelengths with high precision in the near- and mid-infrared wavelengths. Their OPO relies solely on subtle modifications to the nonlinear crystal itself, rather than mirrors. The result is a new breed of OPO that consists of just the nonlinear crystal and a pump laser.
Author contact:
Carlota Canalias (Royal Institute of Technology, Stockholm, Sweden)
Tel: +46 855 378 159; E-mail: cc@laserphysics.kth.se
A tunable infrared source that is ‘mirror-free’ and easy to align has been experimentally demonstrated for the first time and could result in a new source of light that is small, inexpensive and convenient to use.
Optical parametric oscillators (OPOs) are useful in the fields of spectroscopy, chemistry and other disciplines because they offer tunable coherent light – narrow-bandwidth light that has radiation with all the waves vibrating in phase – with wavelengths ranging from 2 to 10 micrometres, filling gaps that can’t be served by other sources. Unfortunately, conventional designs are hard to align and miniaturize as, apart from a nonlinear crystal, they also contain a pair of mirrors that need to be very precisely located. Although ‘mirrorless’ designs have been theoretically proposed in the past, an experimental prototype has not been demonstrated to date.
Carlota Canalias and Valdas Pasiskevicius have built a device that is highly compact, easy to align and has the ability to tune wavelengths with high precision in the near- and mid-infrared wavelengths. Their OPO relies solely on subtle modifications to the nonlinear crystal itself, rather than mirrors. The result is a new breed of OPO that consists of just the nonlinear crystal and a pump laser.
Author contact:
Carlota Canalias (Royal Institute of Technology, Stockholm, Sweden)
Tel: +46 855 378 159; E-mail: cc@laserphysics.kth.se
Saturday, July 28, 2007
Filipino Physicists Awarded a US Patent for a New Semiconductor Circuit Imaging Technique
A microscope imaging technique for visualizing and analyzing semiconductor integrated circuits developed by a team of scientists from the University of the Philippines’ National Institute of Physics was awarded a patent by the United States Patent and Trademark Office.
Imagine if our computers, cellular phones and other electronic gadgets cease to work due to failures in the circuits that run them. These failures in the minuscule wires that make up the semiconductor integrated circuits embedded in our electronic products must be detected in order to make sure that our prized gadgets function. To detect such failures, an effective technique for visualizing and analyzing circuits has been developed by a team of scientists from the University of the Philippines’ National Institute of Physics (UP NIP), namely: Dr. Ceasar Saloma, Dr. Vincent Ricardo M. Daria and Ms. Jelda Jane C. Miranda. This microscope imaging technique entitled “Method for Generating High Contrast Images of Semiconductor Sites via One-Photon Optical Beam-induced Current (IP OBIC) Imaging and Confocal Reflectance Microscopy” was awarded a patent by the United States Patent and Trademark Office last June 26, 2007.
Saloma, currently Dean of the College of Science of the University of the Philippines, is recipient of prestigious international awards for outstanding scientific work, among them the Galileo Galilei Award from the International Commission on Optics. Daria, Associate Professor at the UP-NIP is one of its most active researchers, and Miranda, who was part of its Experimental Optics Group now works for Intel Corporation. The US patent gives Saloma and his team an exclusive right to commercialize their invention in the United States without fear of infringement. The patent is effective for 20 years after the filing of application in December 09, 2006. For more details on the invention, you may check out the United States Patents and Trademarks Office website at http://patft.uspto.gov/.
The invention combines two existing imaging techniques called confocal reflectance microscopy and 1P-OBIC. It uses computer software to produce a high-contrast image mapping of the semiconductor and metal sites in an integrated circuit. The technique is a major breakthrough in the semiconductor industry. It is particularly useful in the manufacturing of microprocessors, integrated circuits and memories for computers, cellular phones and other electronic devices. Creating sharp visual images of semiconductor integrated circuits is important for failure analysis since one can track which part of the device would produce electrical current when hit by laser beam. The method facilitates accurate identification of semiconductor and metal sites in an integrated circuit. With this technique, defects in the circuit can be detected, thus ensuring quality control of such devices.
The main claims of the patent include a description of a technique that facilitates discrimination of these two types of materials in an integrated circuit. The claims also include a description of the optical layout for a generic confocal microscope that allows for simultaneous acquisition of reflectance confocal image and single-photon optical beam induced current (OBIC) image. Moreover, the patent includes an algorithm and software control for microscopic image acquisition for both confocal and OBIC image.
Applications of the patent extend to a fully integrated microscope system for failure analysis of integrated circuits by improved visualization and mapping of materials in a semiconductor device. The microscope extends to a system for measuring optical beam induced current of semiconductor materials. Further applications of the patent may include the construction of a general purpose Confocal Reflectance microscope system for viewing microscopic objects.
Just last March 16, 2007, another scientist from the National Institute of Physics in the University of the Philippines, Dr. Henry J. Ramos, was awarded a Taiwan patent for his invention entitled “Titanium Nitride Thin Formation on Metal Substrate by Chemical Vapor Deposition in a Magnetized Sheet Plasma Source.” The invention has a wide range of applications: cutting tools manufacturing, and the production of aerospace components, marine hardware, medical devices, and pharmaceutical equipment among others.
-By Jennalyn S. Baraquio and Agnes A. Paculdar
A microscope imaging technique for visualizing and analyzing semiconductor integrated circuits developed by a team of scientists from the University of the Philippines’ National Institute of Physics was awarded a patent by the United States Patent and Trademark Office.
Imagine if our computers, cellular phones and other electronic gadgets cease to work due to failures in the circuits that run them. These failures in the minuscule wires that make up the semiconductor integrated circuits embedded in our electronic products must be detected in order to make sure that our prized gadgets function. To detect such failures, an effective technique for visualizing and analyzing circuits has been developed by a team of scientists from the University of the Philippines’ National Institute of Physics (UP NIP), namely: Dr. Ceasar Saloma, Dr. Vincent Ricardo M. Daria and Ms. Jelda Jane C. Miranda. This microscope imaging technique entitled “Method for Generating High Contrast Images of Semiconductor Sites via One-Photon Optical Beam-induced Current (IP OBIC) Imaging and Confocal Reflectance Microscopy” was awarded a patent by the United States Patent and Trademark Office last June 26, 2007.
Saloma, currently Dean of the College of Science of the University of the Philippines, is recipient of prestigious international awards for outstanding scientific work, among them the Galileo Galilei Award from the International Commission on Optics. Daria, Associate Professor at the UP-NIP is one of its most active researchers, and Miranda, who was part of its Experimental Optics Group now works for Intel Corporation. The US patent gives Saloma and his team an exclusive right to commercialize their invention in the United States without fear of infringement. The patent is effective for 20 years after the filing of application in December 09, 2006. For more details on the invention, you may check out the United States Patents and Trademarks Office website at http://patft.uspto.gov/.
The invention combines two existing imaging techniques called confocal reflectance microscopy and 1P-OBIC. It uses computer software to produce a high-contrast image mapping of the semiconductor and metal sites in an integrated circuit. The technique is a major breakthrough in the semiconductor industry. It is particularly useful in the manufacturing of microprocessors, integrated circuits and memories for computers, cellular phones and other electronic devices. Creating sharp visual images of semiconductor integrated circuits is important for failure analysis since one can track which part of the device would produce electrical current when hit by laser beam. The method facilitates accurate identification of semiconductor and metal sites in an integrated circuit. With this technique, defects in the circuit can be detected, thus ensuring quality control of such devices.
The main claims of the patent include a description of a technique that facilitates discrimination of these two types of materials in an integrated circuit. The claims also include a description of the optical layout for a generic confocal microscope that allows for simultaneous acquisition of reflectance confocal image and single-photon optical beam induced current (OBIC) image. Moreover, the patent includes an algorithm and software control for microscopic image acquisition for both confocal and OBIC image.
Applications of the patent extend to a fully integrated microscope system for failure analysis of integrated circuits by improved visualization and mapping of materials in a semiconductor device. The microscope extends to a system for measuring optical beam induced current of semiconductor materials. Further applications of the patent may include the construction of a general purpose Confocal Reflectance microscope system for viewing microscopic objects.
Just last March 16, 2007, another scientist from the National Institute of Physics in the University of the Philippines, Dr. Henry J. Ramos, was awarded a Taiwan patent for his invention entitled “Titanium Nitride Thin Formation on Metal Substrate by Chemical Vapor Deposition in a Magnetized Sheet Plasma Source.” The invention has a wide range of applications: cutting tools manufacturing, and the production of aerospace components, marine hardware, medical devices, and pharmaceutical equipment among others.
-By Jennalyn S. Baraquio and Agnes A. Paculdar
Breaking the frustration
The crystal structure of an oxide material is directly coupled to its ‘frustrated’ magnetic structure
Researchers from the RIKEN SPring-8 Center in Harima, the Japan Atomic Energy Agency and the universities of Tokyo and Virginia have discovered how changes to the crystal structure of the oxide material HgCr2O4 correlate to its magnetic state.
HgCr2O4 has an intriguing crystal structure where all relevant atoms are arranged in tetrahedra (Fig. 1 - Click on link below). When the interaction between the magnetic atoms at the corners of these tetrahedra is antiferromagnetic, a magnetic state with a zero net ‘moment’ is expected to occur—that is, there should be as many magnetic arrows pointing upwards as downwards. However, the geometry of the tetrahedra means that no perfectly homogeneous distribution of the moments is possible. This is known as ‘geometrically frustrated magnetism’.
To break the frustration, the system compensates for the uneven distribution of magnetic moments by distorting the crystal lattice (Fig. 1a). However, in response to an increasing external magnetic field, the magnetic moments realign and there is a stepwise reduction in crystal distortion (Fig. 1b). Once all magnetic moments are forced to point in the same direction, a perfectly symmetric crystal structure is assumed (Fig. 1c).
As reported in the journal Nature Physics (1), the research team studied the behavior of this material as they applied a slowly increasing magnetic field. They confirmed that the external magnetic field eventually breaks the zero magnetization of the sample and causes the magnetic spins to align along the external field—evidenced by sudden jumps in the sample magnetization followed by plateaus with constant magnetization.
Unlike other materials, HgCr2O4 is uniquely suited for this type of study, as these changes occur in magnetic fields small enough to be generated in experiments. Therefore, “the observation of magnetization plateaus in this compound over a wide range of magnetic fields is novel and a manifestation of the geometrical frustration,” explains Koichi Katsumata from the RIKEN team.
Importantly, the researchers studied for the first time the simultaneous evolution of the material’s crystal structure and found that as the magnetization jumps between the different plateaus, the crystal structure becomes less distorted (Fig. 1). Katsumata is therefore confident that this study “has unveiled the origin of some of the intriguing properties of geometrically frustrated magnets.” In particular, the results allow the validation and refinement of theoretical models describing the interaction between magnetism and crystal structure not only in this compound, but also in related systems.
Reference
1. Matsuda, M., Ueda, H., Kikkawa, A., Tanaka, Y., Katsumata, K., Narumi, Y., Inami, T., Ueda, Y. & Lee, S.-H. Spin-lattice instability to a fractional magnetization state in the spinel HgCr2O4. Nature Physics 3, 397–400 (2007).
The crystal structure of an oxide material is directly coupled to its ‘frustrated’ magnetic structure
Researchers from the RIKEN SPring-8 Center in Harima, the Japan Atomic Energy Agency and the universities of Tokyo and Virginia have discovered how changes to the crystal structure of the oxide material HgCr2O4 correlate to its magnetic state.
HgCr2O4 has an intriguing crystal structure where all relevant atoms are arranged in tetrahedra (Fig. 1 - Click on link below). When the interaction between the magnetic atoms at the corners of these tetrahedra is antiferromagnetic, a magnetic state with a zero net ‘moment’ is expected to occur—that is, there should be as many magnetic arrows pointing upwards as downwards. However, the geometry of the tetrahedra means that no perfectly homogeneous distribution of the moments is possible. This is known as ‘geometrically frustrated magnetism’.
To break the frustration, the system compensates for the uneven distribution of magnetic moments by distorting the crystal lattice (Fig. 1a). However, in response to an increasing external magnetic field, the magnetic moments realign and there is a stepwise reduction in crystal distortion (Fig. 1b). Once all magnetic moments are forced to point in the same direction, a perfectly symmetric crystal structure is assumed (Fig. 1c).
As reported in the journal Nature Physics (1), the research team studied the behavior of this material as they applied a slowly increasing magnetic field. They confirmed that the external magnetic field eventually breaks the zero magnetization of the sample and causes the magnetic spins to align along the external field—evidenced by sudden jumps in the sample magnetization followed by plateaus with constant magnetization.
Unlike other materials, HgCr2O4 is uniquely suited for this type of study, as these changes occur in magnetic fields small enough to be generated in experiments. Therefore, “the observation of magnetization plateaus in this compound over a wide range of magnetic fields is novel and a manifestation of the geometrical frustration,” explains Koichi Katsumata from the RIKEN team.
Importantly, the researchers studied for the first time the simultaneous evolution of the material’s crystal structure and found that as the magnetization jumps between the different plateaus, the crystal structure becomes less distorted (Fig. 1). Katsumata is therefore confident that this study “has unveiled the origin of some of the intriguing properties of geometrically frustrated magnets.” In particular, the results allow the validation and refinement of theoretical models describing the interaction between magnetism and crystal structure not only in this compound, but also in related systems.
Reference
1. Matsuda, M., Ueda, H., Kikkawa, A., Tanaka, Y., Katsumata, K., Narumi, Y., Inami, T., Ueda, Y. & Lee, S.-H. Spin-lattice instability to a fractional magnetization state in the spinel HgCr2O4. Nature Physics 3, 397–400 (2007).
Take your computer for a spin
RIKEN Large spin Hall effect measured at room temperature
RIKEN scientists have accurately measured a tiny voltage produced by segregating electrons according to their spin (1), a result which could help to usher in a new era of spin-based computing.
Conventional computers process and communicate information by shunting electrons around, but store data in the magnetic properties of tiny segments of a spinning disk drive. Yet that magnetism is also due to electrons—as each charged particle spins, it creates a magnetic moment. Electrons can spin ‘up’ or ‘down’, creating opposing poles like a bar magnet, and the burgeoning technology of spintronics uses these two states to represent bits of binary data. As well as storing information, these states can potentially be used to perform calculations.
The spin Hall effect (SHE) provides an important way to control these spinning electrons. The Hall effect itself (identified in 1879 by Edwin Hall) occurs when a magnetic field forces a current of electrons flowing through a flat plate to veer to one side. This causes charge to accumulate on that side of the plate, setting up a voltage across it. In a similar way, the SHE sends spin-up electrons to one side of the plate and spin-down to the other, setting up a ‘spin current’ (Fig. 1 - Click on link below).
Spin current is an important factor in operating future spintronic devices. Ferromagnets are normally used to differentiate spins, but interference between neighboring magnets makes it tricky to build working spintronic devices that way.
“However, if we use SHE, we can generate the spin current without using a ferromagnet,” says Takashi Kimura of RIKEN’s Frontier Research System, Wako. This could allow much easier integration of semiconductor and spintronic devices in the future.
Kimura and the team leader YoshiChika Otani have now found that the spin Hall conductivity—the potential for electrons to migrate due to the SHE—in a platinum wire is a thousand times greater than in previous experiments with semiconductor materials, making it easier to study and exploit the effect. Their electrical measurement technique is also more precise than the optical detection method usually employed.
It’s significant that the team has detected this effect at room temperature. It means that SHE is not only a physically interesting phenomenon, but also a useful way of manipulating spins in future spintronic devices, says Kimura.
The team is now trying to identify materials that produce even greater SHE conductivities. “We hope that new devices using SHE are proposed in near future,” says Kimura.
Reference
1. Kimura, T., Otani, Y., Sato, T., Takahashi, S. & Maekawa, S. Room-temperature reversible spin Hall effect. Physical Review Letters 98, 156601 (2007).
RIKEN Large spin Hall effect measured at room temperature
RIKEN scientists have accurately measured a tiny voltage produced by segregating electrons according to their spin (1), a result which could help to usher in a new era of spin-based computing.
Conventional computers process and communicate information by shunting electrons around, but store data in the magnetic properties of tiny segments of a spinning disk drive. Yet that magnetism is also due to electrons—as each charged particle spins, it creates a magnetic moment. Electrons can spin ‘up’ or ‘down’, creating opposing poles like a bar magnet, and the burgeoning technology of spintronics uses these two states to represent bits of binary data. As well as storing information, these states can potentially be used to perform calculations.
The spin Hall effect (SHE) provides an important way to control these spinning electrons. The Hall effect itself (identified in 1879 by Edwin Hall) occurs when a magnetic field forces a current of electrons flowing through a flat plate to veer to one side. This causes charge to accumulate on that side of the plate, setting up a voltage across it. In a similar way, the SHE sends spin-up electrons to one side of the plate and spin-down to the other, setting up a ‘spin current’ (Fig. 1 - Click on link below).
Spin current is an important factor in operating future spintronic devices. Ferromagnets are normally used to differentiate spins, but interference between neighboring magnets makes it tricky to build working spintronic devices that way.
“However, if we use SHE, we can generate the spin current without using a ferromagnet,” says Takashi Kimura of RIKEN’s Frontier Research System, Wako. This could allow much easier integration of semiconductor and spintronic devices in the future.
Kimura and the team leader YoshiChika Otani have now found that the spin Hall conductivity—the potential for electrons to migrate due to the SHE—in a platinum wire is a thousand times greater than in previous experiments with semiconductor materials, making it easier to study and exploit the effect. Their electrical measurement technique is also more precise than the optical detection method usually employed.
It’s significant that the team has detected this effect at room temperature. It means that SHE is not only a physically interesting phenomenon, but also a useful way of manipulating spins in future spintronic devices, says Kimura.
The team is now trying to identify materials that produce even greater SHE conductivities. “We hope that new devices using SHE are proposed in near future,” says Kimura.
Reference
1. Kimura, T., Otani, Y., Sato, T., Takahashi, S. & Maekawa, S. Room-temperature reversible spin Hall effect. Physical Review Letters 98, 156601 (2007).
Saturday, July 14, 2007
A concerted effort : proton transfer in a chemical reaction
Chemical reactions are processes in which one substance is transformed into another and involve the motion of atoms and electrons. Because these processes occur on short time-scales that are measured in femtoseconds (millionths of a billionth of a second), it is difficult to study what actually happens during a chemical reaction.
Of particular interest are reactions that involve the transfer of a hydrogen nucleus (a proton) between two molecules—an important process in biological systems. Tahei Tahara from RIKEN’s Discovery Research Institute in Wako has been studying proton transfer reactions for many years and views them as a challenge at the limits of science. “Because hydrogen is the lightest atomic species, it usually moves very quickly and is difficult to catch,” comments Tahara.
A model system in which proton transfer has been extensively studied is 7-azaindole. In solution, this compound exists in two different forms; discrete individual molecules (monomers), and pairs known as dimers. The dimers can be pushed into a higher energy ‘excited’ state by shining ultraviolet light on them, and subsequently undergo a double proton transfer reaction to form a structure known as a tautomer.
When Tahara published his first results on this system ten years ago, he says that, “the work triggered very intense world-wide debate.” The controversy stemmed from whether the two proton-transfer steps occurred sequentially in a step-wise reaction, or simultaneously in a ‘concerted’ process. Tahara has always argued that the concerted process is the correct one, a hypothesis that is further supported by his recent findings published in the Proceedings of the National Academy of Sciences of the USA (1).
By exciting the 7-azaindole dimer with different wavelengths of ultraviolet light and monitoring the fluorescence, Tahara and colleague, Satoshi Takeuchi, show conclusively that no intermediate structure is formed, thereby ruling out the possibility of a step-wise process. Significantly, their experiments demonstrate that a feature of the fluorescence decay that was attributed to a separate proton transfer actually corresponds to the conversion of the dimer from one excited state to another.
Because the 7-azaindole dimer is very similar in structure to the base pairs found in DNA, Tahara expects that this work may help to understand the chemical mechanism of how ultraviolet light affects DNA. In addition, Tahara and co-workers are now intending to observe nuclear motion in real-time using sub-10-femtosecond pulses of light, which he suggests, “may offer new opportunities for using light to control chemical reactions.”
Chemical reactions are processes in which one substance is transformed into another and involve the motion of atoms and electrons. Because these processes occur on short time-scales that are measured in femtoseconds (millionths of a billionth of a second), it is difficult to study what actually happens during a chemical reaction.
Of particular interest are reactions that involve the transfer of a hydrogen nucleus (a proton) between two molecules—an important process in biological systems. Tahei Tahara from RIKEN’s Discovery Research Institute in Wako has been studying proton transfer reactions for many years and views them as a challenge at the limits of science. “Because hydrogen is the lightest atomic species, it usually moves very quickly and is difficult to catch,” comments Tahara.
A model system in which proton transfer has been extensively studied is 7-azaindole. In solution, this compound exists in two different forms; discrete individual molecules (monomers), and pairs known as dimers. The dimers can be pushed into a higher energy ‘excited’ state by shining ultraviolet light on them, and subsequently undergo a double proton transfer reaction to form a structure known as a tautomer.
When Tahara published his first results on this system ten years ago, he says that, “the work triggered very intense world-wide debate.” The controversy stemmed from whether the two proton-transfer steps occurred sequentially in a step-wise reaction, or simultaneously in a ‘concerted’ process. Tahara has always argued that the concerted process is the correct one, a hypothesis that is further supported by his recent findings published in the Proceedings of the National Academy of Sciences of the USA (1).
By exciting the 7-azaindole dimer with different wavelengths of ultraviolet light and monitoring the fluorescence, Tahara and colleague, Satoshi Takeuchi, show conclusively that no intermediate structure is formed, thereby ruling out the possibility of a step-wise process. Significantly, their experiments demonstrate that a feature of the fluorescence decay that was attributed to a separate proton transfer actually corresponds to the conversion of the dimer from one excited state to another.
Because the 7-azaindole dimer is very similar in structure to the base pairs found in DNA, Tahara expects that this work may help to understand the chemical mechanism of how ultraviolet light affects DNA. In addition, Tahara and co-workers are now intending to observe nuclear motion in real-time using sub-10-femtosecond pulses of light, which he suggests, “may offer new opportunities for using light to control chemical reactions.”
Researchers find a gene controlling embryo orientation
Developmental biologists from RIKEN working with Japanese and Canadian colleagues have located an important gene that regulates the establishment of the head-to-tail or anterior-to-posterior (A–P) axis in mice. The future development of the whole embryo is orientated to this point of reference.
The A–P axis appears before the emergence of the three primary germ layers of body tissue during the process known as gastrulation, when the primitive ball of cells called the blastula folds in on itself to form the more complex, layered structure of the gastrula. Before gastrulation, there are only two types of tissue—epiblast from which the animal proper develops and visceral endoderm (VE) that forms all of the support structures such as blood vessels and nutrient cells.
The establishment of the A–P axis involves interplay between the VE cells and the underlying epiblast. In particular, a group of VE cells furthest from where embryonic structure attaches to the uterus migrates to close to where the head will develop in the epiblast. At the same time VE cells near the posterior end of the axis switch on a gene, Wnt, that produces a compound necessary to initiate gastrulation. In contrast, the VE cells at the head end or anterior visceral endoderm (AVE) produce compounds which block Wnt.
Earlier work has shown that the developmental gene known as Otx2 is critical in the generation and function of the AVE. In mutants lacking Otx2 there is no migration of VE cells to form the AVE and a key antagonist to Wnt is not produced. But the factors that regulated Otx2 were unknown.
In a recent paper in the Proceedings of the National Academy of Sciences (1), the researchers from RIKEN’s Center for Developmental Biology in Kobe and their colleagues describe how they used carefully engineered transgenic mice to demonstrate the critical role of the transcription factor Foxa2 in regulating Otx2. In laboratory studies, they also showed that the Foxa2 protein is needed for the production of at least two Wnt antagonists. Through these actions Foxa2 controls the establishment of the A–P axis.
Similar genes and compounds also exist in the pufferfish, fugu (Fig. 1 - Click on link). In fact, the group found, the fugu equivalent of Foxa2 can actually work in mice. According to the researchers, this shows how tightly the whole regulatory system has been conserved in the evolution of higher vertebrates from the bony fishes.
Reference
Developmental biologists from RIKEN working with Japanese and Canadian colleagues have located an important gene that regulates the establishment of the head-to-tail or anterior-to-posterior (A–P) axis in mice. The future development of the whole embryo is orientated to this point of reference.
The A–P axis appears before the emergence of the three primary germ layers of body tissue during the process known as gastrulation, when the primitive ball of cells called the blastula folds in on itself to form the more complex, layered structure of the gastrula. Before gastrulation, there are only two types of tissue—epiblast from which the animal proper develops and visceral endoderm (VE) that forms all of the support structures such as blood vessels and nutrient cells.
The establishment of the A–P axis involves interplay between the VE cells and the underlying epiblast. In particular, a group of VE cells furthest from where embryonic structure attaches to the uterus migrates to close to where the head will develop in the epiblast. At the same time VE cells near the posterior end of the axis switch on a gene, Wnt, that produces a compound necessary to initiate gastrulation. In contrast, the VE cells at the head end or anterior visceral endoderm (AVE) produce compounds which block Wnt.
Earlier work has shown that the developmental gene known as Otx2 is critical in the generation and function of the AVE. In mutants lacking Otx2 there is no migration of VE cells to form the AVE and a key antagonist to Wnt is not produced. But the factors that regulated Otx2 were unknown.
In a recent paper in the Proceedings of the National Academy of Sciences (1), the researchers from RIKEN’s Center for Developmental Biology in Kobe and their colleagues describe how they used carefully engineered transgenic mice to demonstrate the critical role of the transcription factor Foxa2 in regulating Otx2. In laboratory studies, they also showed that the Foxa2 protein is needed for the production of at least two Wnt antagonists. Through these actions Foxa2 controls the establishment of the A–P axis.
Similar genes and compounds also exist in the pufferfish, fugu (Fig. 1 - Click on link). In fact, the group found, the fugu equivalent of Foxa2 can actually work in mice. According to the researchers, this shows how tightly the whole regulatory system has been conserved in the evolution of higher vertebrates from the bony fishes.
Reference
Playing tag highlights genetic disorder
A team of Japanese scientists led by Akimitsu Okamoto from the RIKEN Frontier Research System, Wako, has developed a new method for tagging a particular DNA base responsible for causing cancer.
Cytosine, a common DNA base, is reacted to add a methyl group to form methylcytosine during many biological processes. This process, known as methylation, is important for gene regulation, and DNA and protein stability. Further, excessive methylation of cytosine has been shown to result in cancer. The development of simple techniques to detect methylcytosine is therefore of great interest to scientists.
Although conventional methods have many advantages, they also have problems. Current methods cannot differentiate between cytosine and methylcytosine; they also destroy the DNA sample and are time-consuming. The latest technique by Okamoto and co-workers is selective for methylcytosine, fast and allows easy detection1.
The technique takes advantage of the easy oxidation of methylcytosine and uses three, specially designed, components to enable detection. When the reaction takes place, the methylcytosine forms a stable complex with an oxidant, potassium osmate, and a rate-enhancing ligand. The ligand, a bipyridine derivative, can then react further to bond with a variety of fluorescent or electrochemical tags allowing routine detection of the complex (Fig. 1 - Click on link below).
This conceptually new approach to methylcytosine detection takes just six hours to complete. Importantly, the key complex only forms between the methylcytosine and the ligand. This leaves the cytosine in the sample untouched and allows a clear distinction to be made. In addition, methylcytosines in single-stranded DNA efficiently formed the complex, whereas complexation of methylcytosines in a DNA duplex was suppressed. This result implies that the technique could also provide sequence-specific results giving detailed and accurate information of the methylated sites.
Okamoto explains that there is still more work to be done. Unfortunately, the information gained from the sequence-specific studies is limited as a consequence of the competing reaction with thymine, another DNA base. Also, the signal intensities and sensitivities are a little too weak to be useful on small sample sizes at this time.
Okamoto and his team are now striving to improve their technique so it can be used routinely in clinics with standard fluorescence or electronic signal analyzers. This technique is based on easy-to-use chemistry and Okamoto says, “Because the total process finishes in a few hours, this technique may make it possible to design machines that automate a series of processes from purification of samples to analysis.”
Reference
A team of Japanese scientists led by Akimitsu Okamoto from the RIKEN Frontier Research System, Wako, has developed a new method for tagging a particular DNA base responsible for causing cancer.
Cytosine, a common DNA base, is reacted to add a methyl group to form methylcytosine during many biological processes. This process, known as methylation, is important for gene regulation, and DNA and protein stability. Further, excessive methylation of cytosine has been shown to result in cancer. The development of simple techniques to detect methylcytosine is therefore of great interest to scientists.
Although conventional methods have many advantages, they also have problems. Current methods cannot differentiate between cytosine and methylcytosine; they also destroy the DNA sample and are time-consuming. The latest technique by Okamoto and co-workers is selective for methylcytosine, fast and allows easy detection1.
The technique takes advantage of the easy oxidation of methylcytosine and uses three, specially designed, components to enable detection. When the reaction takes place, the methylcytosine forms a stable complex with an oxidant, potassium osmate, and a rate-enhancing ligand. The ligand, a bipyridine derivative, can then react further to bond with a variety of fluorescent or electrochemical tags allowing routine detection of the complex (Fig. 1 - Click on link below).
This conceptually new approach to methylcytosine detection takes just six hours to complete. Importantly, the key complex only forms between the methylcytosine and the ligand. This leaves the cytosine in the sample untouched and allows a clear distinction to be made. In addition, methylcytosines in single-stranded DNA efficiently formed the complex, whereas complexation of methylcytosines in a DNA duplex was suppressed. This result implies that the technique could also provide sequence-specific results giving detailed and accurate information of the methylated sites.
Okamoto explains that there is still more work to be done. Unfortunately, the information gained from the sequence-specific studies is limited as a consequence of the competing reaction with thymine, another DNA base. Also, the signal intensities and sensitivities are a little too weak to be useful on small sample sizes at this time.
Okamoto and his team are now striving to improve their technique so it can be used routinely in clinics with standard fluorescence or electronic signal analyzers. This technique is based on easy-to-use chemistry and Okamoto says, “Because the total process finishes in a few hours, this technique may make it possible to design machines that automate a series of processes from purification of samples to analysis.”
Reference
Thursday, July 12, 2007
IMMUNOLOGY:Arresting autoimmunity
Working with a mouse version of multiple sclerosis, Gang Pei and colleagues study a protein called beta-arrestin 1, a factor known to regulate gene expression in all cells. Pei’s team reports that beta-arrestin 1 helps promote survival of T lymphocytes, which increases the duration of inflammation. In the absence of beta-arrestin 1 a critical factor required for T lymphocyte survival is not produced. Consistently, T lymphocytes lacking beta-arrestin 1 survive less well and cause much less brain inflammation in a mouse model of multiple sclerosis.
Demonstrating a role for beta-arrestin 1 in prolonging survival of aggressive T lymphocytes associated with autoimmune disease provides a possible target for reducing such diseases. Whether blocking the function of beta-arrestin 1 will help multiple sclerosis patients, however, remains a question for future investigation.
Author contact:
Gang Pei (Shanghai Institutes for Biological Sciences, China)
Tel: +86 21 5492 1371; E-mail: gpei@sibs.ac.cn
Working with a mouse version of multiple sclerosis, Gang Pei and colleagues study a protein called beta-arrestin 1, a factor known to regulate gene expression in all cells. Pei’s team reports that beta-arrestin 1 helps promote survival of T lymphocytes, which increases the duration of inflammation. In the absence of beta-arrestin 1 a critical factor required for T lymphocyte survival is not produced. Consistently, T lymphocytes lacking beta-arrestin 1 survive less well and cause much less brain inflammation in a mouse model of multiple sclerosis.
Demonstrating a role for beta-arrestin 1 in prolonging survival of aggressive T lymphocytes associated with autoimmune disease provides a possible target for reducing such diseases. Whether blocking the function of beta-arrestin 1 will help multiple sclerosis patients, however, remains a question for future investigation.
Author contact:
Gang Pei (Shanghai Institutes for Biological Sciences, China)
Tel: +86 21 5492 1371; E-mail: gpei@sibs.ac.cn
Growth factor reinforces cocaine addiction
Release of a growth factor in the nucleus accumbens – a brain area mediating reward – is necessary for the development and relapse of cocaine addiction.
Addictive drugs are thought to ‘hijack’ reward systems in the brain, causing neurons to be persistently more responsive to drug-associated cues and stressors. David Self and colleagues report that four hours after cocaine self-administration, rats show an increase in brain-derived neurotrophic factor (BDNF) in the nucleus accumbens. Preventing this increase in BDNF reduced cocaine self-administration and the propensity to relapse, whereas giving the rats daily BDNF injections after cocaine self-administration increased cocaine-seeking behaviour and relapse.
Moreover, using mice that were genetically engineered to lack BDNF only in the nucleus accumbens in adulthood, they showed that BDNF release in the nucleus accumbens did not affect the initial rewarding effects of cocaine, but did dramatically alter the development of addiction. If similar mechanisms mediate addiction in humans, these results could suggest possible approaches to addiction treatment.
Author contact:
David Self (University of Texas Southwestern Medical Center, Dallas, TX, USA)
Tel: +1 214 648 1237; E-mail: david.self@utsouthwestern.edu
Release of a growth factor in the nucleus accumbens – a brain area mediating reward – is necessary for the development and relapse of cocaine addiction.
Addictive drugs are thought to ‘hijack’ reward systems in the brain, causing neurons to be persistently more responsive to drug-associated cues and stressors. David Self and colleagues report that four hours after cocaine self-administration, rats show an increase in brain-derived neurotrophic factor (BDNF) in the nucleus accumbens. Preventing this increase in BDNF reduced cocaine self-administration and the propensity to relapse, whereas giving the rats daily BDNF injections after cocaine self-administration increased cocaine-seeking behaviour and relapse.
Moreover, using mice that were genetically engineered to lack BDNF only in the nucleus accumbens in adulthood, they showed that BDNF release in the nucleus accumbens did not affect the initial rewarding effects of cocaine, but did dramatically alter the development of addiction. If similar mechanisms mediate addiction in humans, these results could suggest possible approaches to addiction treatment.
Author contact:
David Self (University of Texas Southwestern Medical Center, Dallas, TX, USA)
Tel: +1 214 648 1237; E-mail: david.self@utsouthwestern.edu
Common genetic risk variant for colorectal cancer
A common variant on chromosome 8 that predisposes to prostate cancer also confers risk of colorectal cancer, according to three studies.Although a few relatively rare mutations have been identified that are associated with colorectal cancer, this is the first evidence for a common genetic risk factor. Colorectal cancer is one of the most commonly diagnosed forms of cancer.
In the first study, Richard Houlston, Ian Tomlinson and colleagues carried out a genome-wide association study for colorectal cancer and identified the most strongly associated variant on chromosome 8 as the same variant that had previously been associated with risk of prostate cancer. In the second study, Thomas Hudson, Malcolm Dunlop and colleagues screened a smaller number of variants across the genome but identified the same one on chromosome 8 as highly associated with colorectal cancer. Finally, Christopher Haiman and colleagues noted that the region on chromosome 8 that was shown to be associated with prostate cancer is also known to be amplified in individuals with colorectal cancer. Given this background they directly assessed the relevant variants in individuals with colorectal cancer and found them to be significantly more frequent than in cancer-free individuals. Haiman and colleagues also note that five other variants in this region that had been associated with prostate cancer were not associated with colorectal cancer, suggesting that the mechanism by which variants in the region contribute to cancer risk may differ depending on the type of cancer.
Author contacts:
Richard Houlston (Institute of Cancer Research, Sutton, UK)
Tel: +44 208 722 4175; E-mail: richard.houlston@icr.ac.uk
Ian Tomlinson (London Research Institute, Cancer Research UK)
Tel: +44 207 269 2884; E-mail: ian.tomlinson@cancer.org.uk Authors paper [7]
Thomas Hudson (The Ontario Institute for Cancer Research, Toronto, Ontario, Canada)
Tel: +1 416 673 6650; E-mail: tom.hudson@oicr.on.ca
Malcolm Dunlop (University of Edinburgh, UK)
Tel: +44 131 467 8439; E-mail: malcolm.dunlop@hgu.mrc.ac.uk Authors paper [8]
Christopher Haiman (University of Southern California, Los Angeles, CA, USA)
Tel: +1 323 865 0429; E-mail: haiman@usc.edu Author paper [9]
A common variant on chromosome 8 that predisposes to prostate cancer also confers risk of colorectal cancer, according to three studies.Although a few relatively rare mutations have been identified that are associated with colorectal cancer, this is the first evidence for a common genetic risk factor. Colorectal cancer is one of the most commonly diagnosed forms of cancer.
In the first study, Richard Houlston, Ian Tomlinson and colleagues carried out a genome-wide association study for colorectal cancer and identified the most strongly associated variant on chromosome 8 as the same variant that had previously been associated with risk of prostate cancer. In the second study, Thomas Hudson, Malcolm Dunlop and colleagues screened a smaller number of variants across the genome but identified the same one on chromosome 8 as highly associated with colorectal cancer. Finally, Christopher Haiman and colleagues noted that the region on chromosome 8 that was shown to be associated with prostate cancer is also known to be amplified in individuals with colorectal cancer. Given this background they directly assessed the relevant variants in individuals with colorectal cancer and found them to be significantly more frequent than in cancer-free individuals. Haiman and colleagues also note that five other variants in this region that had been associated with prostate cancer were not associated with colorectal cancer, suggesting that the mechanism by which variants in the region contribute to cancer risk may differ depending on the type of cancer.
Author contacts:
Richard Houlston (Institute of Cancer Research, Sutton, UK)
Tel: +44 208 722 4175; E-mail: richard.houlston@icr.ac.uk
Ian Tomlinson (London Research Institute, Cancer Research UK)
Tel: +44 207 269 2884; E-mail: ian.tomlinson@cancer.org.uk Authors paper [7]
Thomas Hudson (The Ontario Institute for Cancer Research, Toronto, Ontario, Canada)
Tel: +1 416 673 6650; E-mail: tom.hudson@oicr.on.ca
Malcolm Dunlop (University of Edinburgh, UK)
Tel: +44 131 467 8439; E-mail: malcolm.dunlop@hgu.mrc.ac.uk Authors paper [8]
Christopher Haiman (University of Southern California, Los Angeles, CA, USA)
Tel: +1 323 865 0429; E-mail: haiman@usc.edu Author paper [9]
Nanocrystal shape control
The shape of metal nanocrystals can be accurately controlled by using a small particle of a different metal as a seed.
Peidong Yang and co-authors reacted a platinum nanocube (~13 nanometres each side) with a palladium-based compound to produce core–shell Pt/Pd nanocrystals. By varying the reaction environment, and in particular the amount of NO2, the researchers were able to obtain three different shapes — cubes, cuboctahedra and octahedra.
Many of the physical and chemical properties of nanocrystals depend strongly on their morphology. The authors show, for example, that the catalytic activity of the cubes is quite different from that of the other two types of nanocrystals. The use of seeds represents a clear step towards the development of nanocrystals with well-defined shapes.
Author contact:
Peidong Yang (University of California, Berkley, CA, USA)
Tel: +1 510 643 1545; E-mail: p_yang@berkeley.edu
The shape of metal nanocrystals can be accurately controlled by using a small particle of a different metal as a seed.
Peidong Yang and co-authors reacted a platinum nanocube (~13 nanometres each side) with a palladium-based compound to produce core–shell Pt/Pd nanocrystals. By varying the reaction environment, and in particular the amount of NO2, the researchers were able to obtain three different shapes — cubes, cuboctahedra and octahedra.
Many of the physical and chemical properties of nanocrystals depend strongly on their morphology. The authors show, for example, that the catalytic activity of the cubes is quite different from that of the other two types of nanocrystals. The use of seeds represents a clear step towards the development of nanocrystals with well-defined shapes.
Author contact:
Peidong Yang (University of California, Berkley, CA, USA)
Tel: +1 510 643 1545; E-mail: p_yang@berkeley.edu
new method to detect small changes in human genes
A new method to detect small changes in human genes could lead the way in personalized medicine. The most common type of variation in our genes is a single difference in one of the nucleotide building blocks of the DNA sequence, known as single nucleotide polymorphism (SNP—pronounced ‘snip’). Scientists believe differences in SNPs reveal an individual’s susceptibility to disease, meaning accurate analysis of SNPs would play a key role in diagnostics. These small SNP variations can account for as little as 0.1 per cent of a genome sequence.
SNP diagnostics have recently attracted much attention and several strategies to identify SNPs have been developed in the past few years. Existing methods are often limited by the need to identify large DNA sequences. Now, a team of Japanese researchers led by Akimitsu Okamoto from the RIKEN Frontier Research System, Wako, has used derivatives of the fluorescent dye PRODAN to correctly identify SNPs quickly and efficiently1.
PRODAN, a well-known fluorophore, absorbs and emits light at different wavelengths depending on the polarity of its environment. Okamoto reasoned that similar dyes, which include differing nucleotide components, could be incorporated into DNA structures and ‘report back’ differences in the microenvironment. Such changes in the microenvironment would likely be the result of small changes in the DNA structure and allow detection of sequence variations (Fig. 1 - Click on link below). The team synthesized four variants of the dye, so that all combinations of base matches and mismatches could be investigated.
Once incorporated in a DNA sequence under a variety of conditions, the team calculated the differences between the wavelengths absorbed and emitted by the dye. These differences are known as Stokes shifts. The researchers detected a small Stokes shift when DNA base pairs matched correctly, but a larger shift when there was a mismatch. Therefore, by using various PRODAN-labeled DNA dyes, single nucleotide alterations could be detected. “The use of this DNA probe makes it possible to judge the type of base located at a specific site on the target DNA, simply by mixing the DNA and the dye together. This method is a very powerful assay that does not require enzymes or time-consuming steps, and avoids errors,” says Okamoto.
Okamoto believes that this method of detection is very promising and is working towards making the system suitable for every day use. “I think SNP chips using our probe would make important contributions to cancer diagnosis,” he enthuses.
A new method to detect small changes in human genes could lead the way in personalized medicine. The most common type of variation in our genes is a single difference in one of the nucleotide building blocks of the DNA sequence, known as single nucleotide polymorphism (SNP—pronounced ‘snip’). Scientists believe differences in SNPs reveal an individual’s susceptibility to disease, meaning accurate analysis of SNPs would play a key role in diagnostics. These small SNP variations can account for as little as 0.1 per cent of a genome sequence.
SNP diagnostics have recently attracted much attention and several strategies to identify SNPs have been developed in the past few years. Existing methods are often limited by the need to identify large DNA sequences. Now, a team of Japanese researchers led by Akimitsu Okamoto from the RIKEN Frontier Research System, Wako, has used derivatives of the fluorescent dye PRODAN to correctly identify SNPs quickly and efficiently1.
PRODAN, a well-known fluorophore, absorbs and emits light at different wavelengths depending on the polarity of its environment. Okamoto reasoned that similar dyes, which include differing nucleotide components, could be incorporated into DNA structures and ‘report back’ differences in the microenvironment. Such changes in the microenvironment would likely be the result of small changes in the DNA structure and allow detection of sequence variations (Fig. 1 - Click on link below). The team synthesized four variants of the dye, so that all combinations of base matches and mismatches could be investigated.
Once incorporated in a DNA sequence under a variety of conditions, the team calculated the differences between the wavelengths absorbed and emitted by the dye. These differences are known as Stokes shifts. The researchers detected a small Stokes shift when DNA base pairs matched correctly, but a larger shift when there was a mismatch. Therefore, by using various PRODAN-labeled DNA dyes, single nucleotide alterations could be detected. “The use of this DNA probe makes it possible to judge the type of base located at a specific site on the target DNA, simply by mixing the DNA and the dye together. This method is a very powerful assay that does not require enzymes or time-consuming steps, and avoids errors,” says Okamoto.
Okamoto believes that this method of detection is very promising and is working towards making the system suitable for every day use. “I think SNP chips using our probe would make important contributions to cancer diagnosis,” he enthuses.
Origin of adult blood cells clarified
A research team at the RIKEN Center for Developmental Biology, Kobe, has developed a cell tracing method that unambiguously identifies the yolk sac—an extra-embryonic structure—as a source of blood cells in both the embryo and, later, the adult.
Developmental biologists have debated the original source blood cells in adult mammals for over thirty years. Now, a team led by Igor Samokhvalov at the RIKEN Center for Developmental Biology, Kobe, has developed a cell tracing method that unambiguously identifies the yolk sac—an extra-embryonic structure—as a source of blood cells in both the embryo and, later, the adult.
The yolk sac, which provides the developing embryo with nutrients, is the first extra-embryonic structure to form during embryogenesis. This structure is also the first place of embryonic blood cell formation (hematopoiesis). A central question in developmental biology about hematopoiesis is the role—if any—the yolk sac-derived blood cells play in the development of adult blood cells.
“The origin of [the] hematopoietic [blood] system was always obscure and controversial; this was the reason I became interested in this area of hematology,” says Samokhvalov.
To resolve the controversy, the team labored for two years to develop a cell tracing method to follow yolk sac-derived blood cells through later stages of embryonic development1. The ability to study this development non-invasively through time was critical, says Samokhvalov, because removing cells from tissue introduces stresses that can lead to an inaccurate picture of actual embryonic processes.
The method consists of replacing of one copy of a gene called Runx1, which is essential for blood development, with another gene that produces a protein creating ‘tags’ in the cells and all their progeny. The ‘new’ gene is turned on at the same time Runx1 normally is—at a mere 7.5 days after embryonic development begins.
Tagging the earliest Runx1-expressing yolk sac cells at day 7.5 of development allowed the team to follow these cells’ progeny when they’re incorporated into blood vessel walls (Fig. 1 - Click on link below), and evaluate their long-term contribution to the adult blood system.
So clear were the results, remarks Samokhvalov, that “our work showed direct contribution of [the] yolk sac to adult haematopoiesis”. Indeed, the team’s direct and carefully designed cell tracing methodology eliminated ambiguities that could lead to alternative interpretations.
This work settles the long-standing controversy, marking an important step forward in developmental biology. However, the team’s data do not rule out the possibility of an additional source of haematopoietic stem cells in the embryo.
Samokhvalov’s future plans include determining more precisely the extent of the yolk sac’s participation in adult blood development, and whether another source of haematopoietic stem cells occurs in the embryo itself.
A research team at the RIKEN Center for Developmental Biology, Kobe, has developed a cell tracing method that unambiguously identifies the yolk sac—an extra-embryonic structure—as a source of blood cells in both the embryo and, later, the adult.
Developmental biologists have debated the original source blood cells in adult mammals for over thirty years. Now, a team led by Igor Samokhvalov at the RIKEN Center for Developmental Biology, Kobe, has developed a cell tracing method that unambiguously identifies the yolk sac—an extra-embryonic structure—as a source of blood cells in both the embryo and, later, the adult.
The yolk sac, which provides the developing embryo with nutrients, is the first extra-embryonic structure to form during embryogenesis. This structure is also the first place of embryonic blood cell formation (hematopoiesis). A central question in developmental biology about hematopoiesis is the role—if any—the yolk sac-derived blood cells play in the development of adult blood cells.
“The origin of [the] hematopoietic [blood] system was always obscure and controversial; this was the reason I became interested in this area of hematology,” says Samokhvalov.
To resolve the controversy, the team labored for two years to develop a cell tracing method to follow yolk sac-derived blood cells through later stages of embryonic development1. The ability to study this development non-invasively through time was critical, says Samokhvalov, because removing cells from tissue introduces stresses that can lead to an inaccurate picture of actual embryonic processes.
The method consists of replacing of one copy of a gene called Runx1, which is essential for blood development, with another gene that produces a protein creating ‘tags’ in the cells and all their progeny. The ‘new’ gene is turned on at the same time Runx1 normally is—at a mere 7.5 days after embryonic development begins.
Tagging the earliest Runx1-expressing yolk sac cells at day 7.5 of development allowed the team to follow these cells’ progeny when they’re incorporated into blood vessel walls (Fig. 1 - Click on link below), and evaluate their long-term contribution to the adult blood system.
So clear were the results, remarks Samokhvalov, that “our work showed direct contribution of [the] yolk sac to adult haematopoiesis”. Indeed, the team’s direct and carefully designed cell tracing methodology eliminated ambiguities that could lead to alternative interpretations.
This work settles the long-standing controversy, marking an important step forward in developmental biology. However, the team’s data do not rule out the possibility of an additional source of haematopoietic stem cells in the embryo.
Samokhvalov’s future plans include determining more precisely the extent of the yolk sac’s participation in adult blood development, and whether another source of haematopoietic stem cells occurs in the embryo itself.
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