Bio-Coat for Reinforced Earth Material
Researchers in Universiti Sains Malaysia developed Bio-Coat from oil palm empty fruit bunches as an alternative to commercial geosynthetic and geotextile materials for slope protection, reinforced earth wall and other soil improvement uses.
Project title: Bio-Coat for Reinforced Earth Material
Researchers: Assoc. Prof. Dr. Fauziah Ahmad, Assoc. Prof. Dr. Abdul Khalil Shawkataly, Ahmad Halmi Ghazalli, Dziauddin Zainol Abidin, Azhar Mohamad Noor
In this project, oil palm empty fruit bunches (EFB) mat fibres were impregnated with Acrylonitrile Butadienne Styrene (ABS). The resulting material also popularly known as "Bio-Coat" were then used as reinforced material for geotechnical applications such as reinforced earth wall, slope protection and other geotechnical soil improvement techniques.
Just like the oil palm, the Bio-Coat has many uses in engineering and construction including that of (1)Reinforcement, (2)Drainage, (3)Filtration, (4)Separator and (5)Barrier.
It can also be used in household applications such as; reinforced plants, garden drainage, unpaved road on soft ground, flower pot, garden mat and other landscaping applications. It was found that, the Load-Strain for the Bio-Coat material increased more than 100% compared to commercial geotextiles and geosynthetics material. The Bio-Coat will be a welcome alternative to the construction, geotechnical and landscaping industries. It not only makes good use of material that would have otherwise been discarded as waste, the Bio-Coat strengthens and improves the soil while remaining highly cost effective.

contact with researcher:

Dr. Fauziah Ahmad
Address:
School of Civil Engineering
Engineering Campus
Universiti Sains Malaysia
Penang
Malaysia

Institution:Universiti Sains Malaysia
Telephone:604-5996268
Email:cefahmad@usm.my
Areas of expertise:civil engineering; erosion control

Plant genetics: A vintage genome sequence


A high-quality draft of the grapevine genome sequence is reported in Nature. The analysis of a grapevine line originally derived from Pinot Noir reveals that it contains twice as many enzymes contributing to essential oil and aroma than other sequenced plants, suggesting that it might eventually be possible to trace the diversity of wine flavours down to the genome level.
The French–Italian Public Consortium for Grapevine Genome Characterization sequenced the genome of Vitis vinifera, the fourth sequence produced for a flowering plant and the first for a fruit crop. The authors selected grapevine for their analysis because of its important place in the cultural heritage of humanity, beginning during the Neolithic period. They report that the genes involved in the metabolism of tannins and terpenes – which contribute to a wine’s aromatic features – have been selectively amplified in this genome. They also found an expansion in the family of genes driving the production of resveratrol, the chemical associated with the proposed health benefits of drinking moderate amounts of red wine.
Public access to the grapevine genome sequence should help identify the genes underlying particular agricultural features and domestication traits. This could be of use for not only recognizing which genes are responsible for the characteristic flavours of a wine, but also in speeding up the process of introducing disease-resistant genes, thereby decreasing the need for pesticides.


Author contact:
Patrick Wincker (Genoscope-Centre National de Sequencage and CNRS, Evry, France)
Tel: +33 1 60 87 25 68; E-mail: pwincker@genoscope.cns.fr

Developmental biology: New method sets stem cells apart

Researchers have devised a way to distinguish between two similar, yet vitally different, proliferative cell types found in the developing brain. Their findings should prove useful in stem cell research.
The developing brain contains many different proliferative cell types including neural stem cells (NSCs), which can give rise to many different types of mature brain cell, and neuroblasts, which are more restricted in their fate. But the signalling differences between these two populations are poorly understood.
Nicholas Gaiano and colleagues now show that differences in the Notch signalling pathway — a highly conserved system known to influence cell fate decisions during embryonic and adult life — may account for the variation between the two cell types. The discovery has yielded a method for separating these two cell types in a dish, a feat that should help researchers to characterise them further.

Author contact:
Nicholas Gaiano (Johns Hopkins School of Medicine, Baltimore, MD, USA)
Tel: +1 443 287 4866; E-mail: gaiano@jhmi.edu

BIOTECHNOLOGY : Human embryonic stem cells do a heart good

Heart attacks may respond to treatment with cells derived from human embryonic stem (ES) cells. Charles Murry and colleagues find that rats subjected to experimental heart attacks show improved cardiac function four weeks after receiving a transplant of heart muscle cells generated in a dish from human ES cells.
Human ES cells are considered a promising source of cells for regenerative medicine because, in theory, they can be taken off the laboratory shelf, coaxed into becoming any kind of specialized cell for repairing damaged organs and given to any patient. But many problems must be solved before this vision is reduced to practice.
Murry and colleagues address two critical problems in heart regeneration. First, they improve the efficiency with which ES cells are converted into heart cells. Second, they improve the survival of such heart cells after transplantation into damaged animal hearts using a ‘survival cocktail’—a mixture of chemicals that blocks various causes of cell death. By combining these techniques, they succeeded in slowing the progression of heart failure in the treated animals.

Author contact:
Charles Murry (University of Washington, Seattle, WA, USA)
Tel: +1 206 616 8685; E-mail: murry@u.washington.edu

METHODS : Shedding light on animals’ interiors

Bright far-red fluorescent proteins that emit light at longer wavelengths than typical red fluorescent proteins, improving their usefulness for deep imaging in living animals.
Fluorescent proteins are invaluable tools for many types of biological investigation. The light from the best performing fluorescent proteins, however, has a difficult time penetrating living tissue due to the relatively short wavelengths emitted. This has limited the usefulness of these proteins for in vivo fluorescence imaging of whole animals. But fluorescent proteins that emit longer wavelength light, in the far-red and infrared regions of the spectrum, have so far been difficult to develop.
Dmitriy Chudakov and colleagues previously cloned a bright red fluorescent protein from a sea anemone. They engineered this protein to increase the wavelength of the emitted light while retaining its brightness. These longer wavelengths of light penetrate tissue more efficiently making detection of fluorescence emanating from deep inside an animal easier than with existing fluorescent proteins. The researchers developed two versions of the protein that are best suited for different applications. These will aid many researchers in different fields of biology who can benefit from the improved in vivo imaging performance the proteins offer.

Author contact:
Dmitriy Chudakov (Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia)
Tel: +7 495 429 8020; E-mail: ChudakovDM@mail.ru

New method of immobilising enzyme helps tell left from right
Researchers from Universiti Putra Malaysia have discovered a simple technique to immobilise the enzyme lipase onto a support providing a derivatised enzyme that shows a high capacity to resolve between chiral pairs. This ability aids in the synthesis of specific compounds in its pure form which is very much sought after by the chemical industry
Chirazim™ — a highly enantioselective enzyme

Researchers: Abu Bakar Salleh, Siti Salhah Othman, Mahiran Basri, Mohd Zobir Hussein, Mohd. Basyaruddin Abd. Rahman and Raja Noor Zaliha Abdul Rahman

If we face our hand right towards our hand left, we can say that each is the mirror image of the other. Although they look similar they are not exactly the same as they cannot overlap on top of each other. In the world of compounds, these are known as chiral compounds.
In nature, we have many such chiral pairs designated as the R and S isomer. Of importance, each member of a chiral pair can exhibit different biological properties. The differential effect is caused by the presence of enzymes (biocatalysts) in living cells that are able to recognize and thus react with specific compounds (i.e. even either member of a chiral pair).
The ability to synthesis specific compounds in its pure form is very much sought after by the chemical industry. Pure isomer has specific applications in the medical and agrichemical industry. Mixed products may diminish the effect required, or worse still may lead to detrimental results. Specific examples of isomer in industrial applications include S-ibuprofen, an analgesic agent, R- chlorophenoxy propanoate, a type of herbicide, and a number of R menthol esters that are used as flavour additives in the food and beverage industry.
However, not all enzymes have the capacity to resolve enantiomers. The ability to recognize each compound depends a lot on the shape and conformation of the enzyme molecules, especially that of the active or catalytic site. One way of modifying the conformation of the enzyme is through the process of immobilisation, where an enzyme is attached to a solid support.
There are different types of supports and techniques to immobilize enzymes. These are selected in accordance to the property of the enzymes as well as the ultimate applications. Immobilised enzymes are easy to handle and can be reused.
Chirazim (TM) is a new discovery where lipase, the enzyme was immobilised onto a support via a simple method. The support used was a multi layered hydroxide that can also be easily produced.
Immobilisation resulted in a derivatised enzyme that showed high capacity to resolve S and R isomers. Apart from that the immobilized enzyme is stable to organic solvents and high temperature, suitable characteristics in the synthesis of chiral compounds.

New scaffold supporting our molecular understanding of psychiatric disorders
Researchers establish a causative link between mutations in a single gene and the pathology of psychiatric illnesses
New work in mice indicates that defective function of the molecular ‘scaffold’ protein Disc1 results in behaviors resembling human schizophrenia and depression. Current treatments for these devastating diseases are palliative but not curative.
Prior work hints at a link between Disc1 and psychiatric illness. Some mood disorders in humans are ameliorated by drugs suppressing the function of PDE4B: a protein that binds to molecular scaffolds including Disc1 and metabolizes cAMP, a compound essential for transmission of cellular signals. From studies in humans, scientists are also aware of associations between Disc1 mutations and the incidence of psychiatric illnesses. However, whether these mutations altered Disc1 function, and thus whether Disc1 dysfunction actually contributed to brain pathology, was not determined.
An international group led by Yoichi Gondo, a scientist at RIKEN Genomic Sciences Center in Yokohama, used a mouse model to forge a causative link between alterations in Disc1 function and the pathology of psychiatric disorders. This work was published in a recent issue of Neuron (1).
The researchers used a chemical mutagen to scatter random infrequent mutations throughout the genome of laboratory mice, and extensive DNA sequencing to identify two mice that each contained a distinct mutation predicted to change the sequence of the PDE4B-binding region of Disc1.
Like brains of some patients with mood disorders, brains in mice expressing mutated versions of Disc1 were of small volume (Fig. 1 - Click on link below). However, although both mutated Disc1 proteins exhibited impaired binding to PDE4B, only one Disc1 mutant reduced PDE4B activity.
Mice expressing this Disc1 mutant exhibited behaviour characteristic of depression; these mice displayed reduced sociability and disinterest in pleasurable activities. In contrast, mice expressing the Disc1 mutant that left PDE4B function intact failed to process and respond to distracting stimuli; this behaviour is more reminiscent of humans with schizophrenia. PDE4B inhibitors ameliorated the behaviour only of mice expressing the latter mutant.
Whether mutations having similar consequences on Disc1 function arise naturally in humans is unknown. Nevertheless, these findings reveal a complex role of Disc1 in brain function, and suggest that psychiatric disorders caused by distinct lesions of Disc1 may require different treatments.
“Studies in mouse models should lead to precise molecular diagnostics for psychiatric illness and allow us to develop preventive and therapeutic medicines. The RIKEN mutant mouse library, from where these Disc1 mutant mice were obtained, provides mouse models for the study of many human diseases,” says Gondo.
Reference
1. Clapcote, S.J., Lipina, T.V., Millar, J.K., Mackie, S., Christie, S., Ogawa, F., Lerch, J.P., Trimble, K., Uchiyama, M., Sakuraba, Y., et al. Behavioral phenotypes of Disc1 missense mutations in mice. Neuron 54, 387–402 (2007).

Enzymes lead the way
A protease enzyme called MIG-17 points cells in the right direction during the development of organ
During the growth and development of organs, proteins act from outside the organs to direct the movements of cells. Researchers at the RIKEN Centre for Developmental Biology in Kobe have identified one such protein that is essential for the development of gonads in the nematode roundworm Caenorhabditis elegans (1).
In C. elegans, the gonads grow along the body wall and then turn through 180°, making two U-shaped gonad arms. The movement is directed by two specialized leader cells called ‘distal tip cells’ (DTCs). The researchers found that when they inhibited the activity of a proteolytic enzyme called MIG-17, the DTCs failed to function properly, resulting in misshapen gonads.
”We mutagenized wild-type worms with [a] chemical mutagen and isolated many mutant worms with misshapen gonads,” says group leader Kiyoji Nishiwaki. “The MIG-17 mutant is one of these isolates and was found to encode a protein of the ADAMTS protease family.”
The MIG-17 enzyme is secreted from muscle cells, and is initially folded over to hide an active zinc ion (Fig. 1). The researchers discovered that actions in part of the MIG-17 molecule called the prodomain are essential for moving the molecule to the gonad. However, the prodomain must first be modified by another protein, MIG-23, in a process called glycosylation.
Previous studies had indicated a role for the prodomain in protein folding and secretion, but this is the first time it has been shown to be crucial for targeting the whole MIG-17 molecule to the gonad. “It is possible that prodomain targeting is one of the key strategies employed by ADAMTS proteins to localize to specific tissues,” says Nishiwaki.
Once the MIG-17 molecule reaches the gonadal membrane, an unknown stimulus initiates autocatalytic cleavage of the molecule. The prodomain falls off, leaving the active zinc ion exposed (Fig. 1). “The zinc ion probably degrades a specific substrate in the gonadal membrane and thereby acts in directing DTCs,” explains Nishiwaki.
In humans, mutations in ADAMTS proteins cause various hereditary diseases related to disorders in connective tissues. MIG-17 is most similar to an enzyme called ADAMTS-10 that may have a role in organ development in humans.
“ADAMTS-10 is a causative gene for Weill–Marchesani syndrome [in humans], characterized by short stature, shortness of fingers and toes and eye abnormalities,” says Nishiwaki. “Abnormalities of internal organs may also occur, although this is not examined yet.”

Reference
1. Ihara, S. & Nishiwaki, K. Prodomain-dependent tissue targeting of an ADAMTS protease controls cell migration in Caenorhabditis elegans. The EMBO Journal 26, 2607–2620 (2007).

Observing single cells on the move

Researchers hold a key to studying cancer, wound healing and development

A team of researchers from RIKEN and other Japanese research institutions has developed a flexible technique for studying migration behavior of single cells. It relies on guiding cell movement by creating adhesive pathways through a non-adhesive environment using a light-driven reaction.
With their technique, the researchers are able to study details of the mechanics of how individual cells move. Already, for example, the team has been able to determine that cells which move by extending a broad front known as a lamellipodium travel faster than cells which can only use the much narrower filopodium.
The study is significant as migration of cells is fundamental to important medical processes such as growth and development, wound healing and the spread of cancer. In addition, the new technique allows researchers to guide individual cells into position, thus engineering nerve networks, for instance.
In the past, migration has been investigated using methods involving monolayers of cells. But cells within layers are unavoidably squeezed into different shapes and orientations and contact variable numbers of other cells, all of which affect movement. So the research team from RIKEN’s Discovery Research Institute in Wako, the Japan Science and Technology Agency, and Waseda and Kanagawa universities set about developing a way of studying the motion of individual cells in isolation, free from these influences.
In a recent paper, the researchers describe coating a glass coverslip with a compound to which cells cannot stick1. The chemical nature of this surface can be changed into one to which cells can adhere by exposure to ultraviolet light. And this can be done with great precision.
The team then prepared coverslips with adhesive patches just big enough for a single fibroblast cell (Fig.1). Leading from those cells they created pathways of adhesive surface in two forms—a broad form, the same width as the patch, which could accommodate lamellipodia, and a narrow pathway, one fifth the width, only fit for filopodia.
Movement of the cells could be followed under a conventional fluorescent microscope. When presented with a broad pathway, less than 10% of the cells extended filopodia. And those cells which used filopodia for movement traveled only about 80% as fast as those employing lamellipodia.
“We now want to combine this technique with advanced fluorescent microscope technologies to observe the molecular events in migrating cells,” says one of the project leaders, Jun Nakanishi. “We are also hoping to engineer neuronal networks by applying our technique to control the movement of single cells.”
Reference
1. Nakanishi, J., Kikuchi, Y., Inoue, S., Yamaguchi, K., Takarada, T. & Maeda, M. Spatiotemporal control of migration of single cells on a photoactivatable cell microarray. Journal of the American Chemical Society 129, 6694–6695 (2007).

Investigating a perplexing mystery

Ultrahigh-energy cosmic particles are an intriguing puzzle in high-energy physics, and RIKEN is involved in a project to solve it. On May 16, the RIKEN proposal for the second utilization plan of the Japanese Experiment Module (JEM) on board the International Space Station was accepted, and its kickoff meeting was held on June 6 to 8 at RIKEN, Wako.
The particles have extremely high kinetic energies, as much as 1020 electronvolts, far greater than other cosmic-ray particles. They are also extremely rare—only 11 have been observed in 13 years of searching with the Akeno Giant Air Shower Array (AGASA), which has an effective area as large as the area enclosed by the Yamanote line in the Tokyo Metro. No one knows where they come from, or how they could have that much energy left over after the long journey through intergalactic and interstellar space.
To observe these rare phenomena, a telescope with an extremely wide field of view is needed, and it is being provided by the Extreme Universe Space Observatory (EUSO), to be installed on the JEM on the International Space Station, after JEM is launched in 2008.
Instead of looking out into space like a conventional telescope, EUSO will look down at the Earth from space, searching for streaks of ultraviolet fluorescence and Cerenkov radiation, which cosmic particles produce when they interact with the Earth's atmosphere.
EUSO incorporates a Fresnel lens, a very thin, wide-aperture lens made up of concentric rings, which provides a 60 ° field of view. The lens was made using ultraprecise grinding technology at the RIKEN Ohmori laboratory.
To detect the faint streaks of ultraviolet fluorescence and Cerenkov radiation that the particles produce as they enter the Earth’s atmosphere, EUSO contains 6,000 photomultiplier tubes, which were developed and built in Japan.
EUSO is said to be launched by a Japanese H-IIB rocket and transferred by H-II transfer vehicle (HTV), and it is expected to detect about 1,000 ultrahigh-energy cosmic particles in the five years of its operation. From this data researchers hope to determine whether the particles originated from a single source or occur throughout the universe.

Australia research links obesity, infertility
Australian researchers have found
a fatty diet damages eggs in the ovaries and prevents them
from becoming healthy embryos, a finding they say may explain
why obese women are often infertile.
While obesity has long been suspected of hampering a
woman's ability to conceive, the University of Adelaide
research is said to be the first to find a direct scientific
link.
Researcher Cadence Minge said experiments on female
mice showed that fat has an impact on the egg before it is
even fertilised.
"Consuming a diet of high fat causes damage to eggs
stored in female ovaries," Minge said. "As a result, when
fertilised, these eggs are not able to undergo normal, healthy
development into embryos."
Minge said a protein called peroxisome
proliferator-activated receptor gamma found in the cells that
nourish the egg was the main reason for diet-induced
infertility.
"The behaviour of this protein helps to determine the
way in which the ovaries sense and respond to fats," she said.
"Being able to control this protein will be very
important in the quest to reverse infertility caused by poor
diets."
Minge found that an anti-diabetes drug called
rosglitazone helped counter the protein's impact, resulting in
higher birth weights and better rates of foetal survival in
the mice being studies.
However, she said the drug had side effects and could
not be seen as a "quick-fix" for infertile obese women.

Titanium Oxide to keep dress fresh for ever!
Coimbatore (India): Believe it or not! people would
require only one pair of dress, if Titanium Oxide was applied
in its molecular form on it.
The cloth would not absorb sweat or any external particle
and would retain an everlasting shine.
"Man would require only one pair of T Shirt or any other
dress material, since it would not get dirtied by dust or any
other particle, if the chemical was used by applying
nanotechnology", Dr A Sivathanu Pillai, Chief Controller, R
and D, DRDO, said during an interaction with college students
here.
"You can just wipe off, if tea falls on the shirt. It will
not be absorbed by the shirt. Shining would remain", Pillai,
said, much to the surprise of over 800 students and faculty
members assembled at the function.
Applying of titanium oxide would not cause any harm to the
human skin also, he assured.
DRDO has been conducting researches in nano technology for
quite some time.
However, he jokingly remarked that the revenue of the
textile industry would dip, since people would be happy
with one or two pairs of dresses.

Cholesterol synthesis: Regulation by destruction
-Dangsheng Li

AbstractScientists have found that the degradation of a key enzyme involved in cholesterol synthesis is regulated by a cofactor known as Ufd1

The endoplasmic reticulum (ER) is an organelle responsible for several specialized functions, including the synthesis of some proteins. As a quality control, ER destroys misfolded proteins through a process known as ER-associated degradation. Cells also use this process to degrade the key enzyme, HMG-CoA reductase (HMGCR), which is involved in cholesterol synthesis. Baoliang Song, Boliang Li at the Chinese Academy of Sciences in Shanghai and co-workers1 have found that the degradation of HMGCR is regulated by a cofactor, Ufd1.
An important step in HMGCR degradation is the attachment of a regulatory protein called ubiquitin — a unique tag which marks the HMGCR for destruction. This ubiquitin attachment is catalysed by an ER-residing enzyme. The researchers discovered that Ufd1 binds directly to this enzyme, enhances its ability to tag ubiquitin onto HMGCR, and consequently helps HMGCR degradation. As a result, cells with higher levels of Ufd1 produce less cholesterol and, to compensate, are able to take up more cholesterol from outside the cell.
A high cholesterol level is associated with medical conditions such as heart disease. The finding provides new strategies to lower cholesterol through regulating HMGCR degradation.
The authors of this work are from:
State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.

Controlling basal stem rot disease in palm oil
TrichoGreen is a Trichoderma-infused compost which is also an effective biological control agent against the basal stem rot disease for palm oil. The production process is entirely organic, eliminates the need for burning, and is an excellent form of environmentally-friendly waste management.
Trichogreen, the Biocontrol Agent and Growth Enhancer for the Oil Palm Industry
Faridah Abdullah

The production of TrichoGreen is a recycling process, turning agricultural waste into useful products.
The production process is entirely organic, eliminates the need for burning, and is an excellent form of
environmentally-friendly waste management. The industry is sustainable and can generate downstream activities.
The product was later found to be a good plant growth enhancer as well. The biocontrol property of
Trichoderma is isolate-specific and from extensive in vitro screening, isolate FA 1132 (T. harzianum) was
selected as the best candidate for biocontrol purposes. From nursery trials, TrichoGreen can save as
much as 95% of plants if treatment is given simultaneously to the infected seedlings; the success rate
decreases with increased severity of tissue damage caused to the palm.
The product has been successfully upscaled using a bioreactor, producing x107 propagules/ml within 96
hours, which was then used to prepare inocula and subsequently in its mass production, using palm
pressed fibres (PPF) agrowaste as the feedstock. The PPF were piled into windrows at 50 mt feedstock
per row of 80m x 4m. Together with intermittent supplies of POME (palm oil mill effluents) and scheduled
turnovers in a solid substrate fermentation, the final product of 22mt per windrow at x1011
propagules/kg material, was achieved over 12 to 15 weeks. Field trials over 8 weeks’ treatment thus far
showed that it significantly enhanced growth of the oil palm, followed only by organic compost and
thirdly the routinely-used fertiliser application. Field applications of TrichoGreen on Ganoderma-infected fields are currently on trial and the results are estimated in 2 to 3 years.

Dr. Nayan KANWAL
Email: ndeeps@admin.upm.edu.my

Getting on worms’ nerves

Two devices that help researchers correlate nerve cell activity with behaviour in the living worm.
The microscopic worm C. elegans has a very simple nervous system, with only 302 neurons. However, it is difficult to monitor neuronal activity in worms without either using invasive methods or restraining them in an unphysiological way. Nikos Chronis and colleagues present devices which make it possible to use a microscope to monitor nerve activity in intact, live worms. The key is that the worms are enclosed in tiny channels only slightly bigger than the animals, so that they are free to move to some extent, but restrained sufficiently to allow for imaging of the neurons. The trapped worms can also be stimulated in a very controlled fashion by substances delivered at the tip of the animal’s nose, so that their effect on nerve activity can be recorded.
The researchers used these devices to uncover new information about particular neurons involved in movement and sensation in the worm. This may very well pave the way to ever more sophisticated devices, as well as to devices for monitoring other small organisms in physiological and precisely controlled environments.

Author contact:
Nikos Chronis (University of Michigan, Ann Arbor, MI, USA)
Tel: +1 734 763 0154; E-mail: chronis@umich.edu

A very sociable brain
Brain activity in primates is directly influenced by social context
Human society puts heavy demands on the brain. Neurons must adapt rapidly to contextual changes in the social environment. Researchers at the RIKEN Brain Science Institute in Wako are gaining insight into this ‘social brain function’ by observing Japanese macaque monkeys (1).
“We can understand how our brain recognizes and adapts to social environments by expanding research in primates,” says cognitive neuroscientist Naotaka Fujii, “because the social behavior of monkeys is very similar to that of human children.”
Fujii’s team placed two male monkeys around a square table in chairs that restricted their necks and lower bodies but arms and head free to move. Food was placed in random positions on the table, and the monkeys’ arm and head movements were closely monitored using a 3D motion capture system. Individual neuron activity was measured by inserting electrodes into the parietal cortex, a region of the brain that processes sensory information to determine the locations and movements of objects. In total, 174 neurons were isolated of which 91 were related to specific actions.
When the monkeys were seated opposite one another, they could only reach half the table each, so could not compete with one another. They effectively behaved as if no other monkey was present, and most activated neurons were associated with the monkeys’ own right-arm motion.
However, when the monkeys were seated on adjacent edges of the table, they shared a corner and could fight over food items that were placed there. One monkey appeared to be dominant, taking the food about 90% of the time. The dominant monkey frequently watched the submissive monkey, and became aggressive on the rare occasions that the submissive monkey managed to grab the food “When the monkeys are placed in a conflict situation, they tend to be more active to get the reward, even when they are not hungry,” says Fujii.
Brain activity changed dramatically when this social conflict was introduced. The researchers saw decreased activity in neurons related to the monkeys’ own right-arm movements, and increased activity in neurons related to other stimuli, such as the actions of their competitor’s arms.
“This is the first evidence that neurons are manipulating activity depending on social context at a single cell level,” says Fujii. “However, the parietal cortex may not be the only structure that implements the function. We have to expand recording areas to obtain an entire view of social brain functions.”
Reference

1. Fujii, N., Hihara, S. & Iriki, A. Dynamic social adaptation of motion-related neurons in primate parietal cortex. PLoS ONE [online] 4, e397 (2007) (doi: 10.1371/journal.pone.0000397).

Agriculture:Putting a STOP to acid stress

A transcription protein called STOP1 helps plants to tolerate aluminum ions and protons
Plant growth can be badly stunted by excess ions in the soil. This effect, called acid soil syndrome, can cause severe agricultural yield losses, especially in areas prone to drought. For this reason, a team of researchers from RIKEN and two Japanese universities are working to identify genes that regulate a plant’s tolerance of ions (1).
Much work has been done on aluminum toxicity in plants, but little is known about the genes that control direct tolerance to acid in the form of hydrogen ions, or protons. The researchers prepared thale cress, Arabidopsis thaliana, from seeds treated with ethyl methanesulfonate to introduce random point mutations in their genome. The seeds were cultivated in an acidic (proton-rich) environment, and the researchers looked for seedlings that failed to grow roots.
“We carried out screening using 25,000 seedlings,” says project leader Satoshi Iuchi from the RIKEN BioResources Center in Tsukuba. “Finally we obtained one mutant that had an acid sensitive phenotype.”
The mutant plant, named stop1 (Sensitive TO Proton), was cloned and subjected to DNA sequencing. The sequencing revealed mutations in a part of the genome that encodes a protein called STOP1, consisting of 499 amino acids. The protein contains four ‘zinc-finger’ domains that regulate DNA transcription in the cell nucleus.
The researchers next investigated whether the stop1 mutant strain was sensitive to other toxic ions. It showed no particular sensitivity to cadmium, copper, sodium, lanthanum or manganese, but was extra sensitive to aluminum ions—stop1 plants showed 80–90% reduced root growth when exposed to aluminum, compared to only 30% in control plants.
Arabidopsis is known to tolerate aluminum by excreting malate, an ionized form of malic acid that is regulated by a gene called AtALMT1. This new study confirmed the link—stop1 mutants failed to express AtALMT1 in the toxic aluminum, and did not excrete any malate.
However, when AtALMT1 was deliberately disrupted in the control plants, the proton sensitivity was not affected. Therefore STOP1 must regulate different genes related to proton sensitivity (Fig. 1).
This work puts STOP1 on the expanding list of transcriptional factors that respond to stress and regulate genes to ensure a plant’s survival. Iuchi believes genetic modification of proteins such as STOP1 is the best way to improve farming efficiency. “Large amounts of chemical fertilizer are used in agriculture, which causes problems,” he says. “If enhanced-tolerance plants can be used, chemical fertilizer usage can be reduced.”
Reference1. Iuchi, S., Koyama, H., Iuchi, A., Kobayashi, Y., Kitabayashi, S., Kobayashi, Y., Ikka, T., Hirayama, T., Shinozaki, K. & Kobayashi, M. Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance. Proceedings of the National Academy of Sciences USA 104, 9900–9905 (2007).

Stellar science: A turbulent wake

A stunning ultraviolet image of a turbulent wind wake produced by the binary star Mira offers a new, unprecedented direct measure of the star’s mass loss history.
Stars such as Mira — in the late stages of stellar evolution and with low-to-intermediate mass — return a large fraction of their original mass to the interstellar medium through the dusty, molecular winds they send out. This means they have a direct affect on subsequent star and planet formation in their host galaxy.
D. Christopher Martin and colleagues report the discovery of an ultraviolet-emitting bow shock and turbulent wake extending over 2 degrees on the sky, produced by the interaction of Mira’s stellar wind and the ambient interstellar medium.
The wind wake is a tracer of the last 30,000 years of Mira’s mass loss history. In the past, observations of interactions between Mira-type stellar winds and the interstellar medium have been in the infrared.

CONTACT
D. Christopher Martin (California Institute of Technology, Pasadena, CA, USA)
Tel: +1 626 395 4243; E-mail: cmartin@srl.caltech.edu

Ageing and cancer: Henrietta's legacy

Over fifty years ago, a 31-year-old woman underwent a biopsy for a suspicious cervical mass. Part of the sample went for pathological analysis, but another went to the research laboratory of George and Martha Gey. The patient died from her cancer just 8 months later, and on that day George Gey appeared on American TV announcing the dawn of a new era in medical research. For the first time, he explained, it was possible to grow human cells continuously in culture. And he called the biopsy-derived cell line 'HeLa', in memory of Henrietta Lacks, the unfortunate young mother whose tumour made it all possible.
Since then, researchers have been slowly stripping away the many secrets that endow cancer cells with the gift of immortality. In a review Toren Finkel and colleagues not only offer a historical perspective, but also describe the more recent research linking cancer biology to normal ageing.

CONTACT

Toren Finkel (National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA)
Tel: +1 301 402 4081; E-mail: finkelt@nih.gov

Geology: The creeping San Andreas
Scientists have discovered talc in rock samples drilled through the San Andreas fault, which could explain why this segment of the tectonic boundary experiences such a high rate of creep. The central Californian part of the San Andreas fault very slowly moves or ‘creeps’ along at a rate of up to 28 millimetres a year and is thought to be the weakest zone of the 1,300-kilometre plate boundary between North America and the Pacific. This weakness was proposed to be due to the presence of the metamorphic rock serpentinite, but recent pressure and temperature measurements have shown that serpentinite is actually too strong and unstable to produce the observed conditions.
Diane Moore and Michael Rymer report the discovery of talc in cuttings collected during drilling of the fault zone. This three-kilometre-deep drill hole — part of the San Andreas Fault Observatory at Depth (SAFOD) — is located near Parkfield in central California. Instruments have been installed across the fault to record data near the source of earthquakes, and rock and fluid samples have been collected to help scientists evaluate the geological properties that control the seismological behaviour of the fault in the region.
The authors examined the mineral composition of grains of serpentinite collected at three-metre intervals. They found that talc of recent origin had replaced the serpentinite along veins and foliations. The presence of talc in the active trace of the San Andreas fault is significant because talc has a very low shear strength in the temperature range found in the fault. They conclude that talc may therefore provide the connection between serpentinite and creep in the San Andreas fault.

CONTACT
Diane Moore (US Geological Survey, Menlo Park, CA, USA)
Tel: +1 650 329 4825; E-mail: dmoore@usgs.gov

Christopher Wibberley (Universite de Nice - Sophia Antipolis, Valbonne, France) N&V author
Tel: +33 4 92 94 26 32; E-mail: wibbs@geoazur.unice.fr

Social mammals: Drive him away or let him stay
Female spotted hyaenas are the determining force behind building a healthy clan. Research shows that female mate-choice is the main factor behind which group males begin their sexual career. Males that responded best to the female preferences had the highest long-term reproductive success.
Dispersal has a significant impact on lifetime reproductive success, and in group-living animals it is usually male biased. Oliver Höner and colleagues use microsatellite DNA profiling in their study and show that the responses of male hyaenas to female mate-choice rules mean that there are no specific kin discrimination mechanisms needed to avoid inbreeding. This is the first empirical study to demonstrate that male dispersal is the result of an adaptive response to female mate-choice.

CONTACT

Oliver Höner (Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany)
Tel: +49 30 5168 516; E-mail: hoener@izw-berlin.de

Carotene from Crude Palm Oil
Palm oil is rich in carotene. However current commercial production of edible oil results in the loss of carotenes. Now, researchers have found a way to recover carotenes from crude palm oil.
Carotenes are yellow to orange pigments found in carrots, leafy vegetables, milk fat and egg yolk. The a- and b-carotenes are associated with synthesis of vitamin A in the liver and may offer some protection against cancer as well.
Commercially, carotenes are used in food coloration, vitamin supplements, pharmaceutical and cosmetic products. Although palm oil is rich in carotenes (about 600 parts per million), carotenes are destroyed or discarded by bleaching and stripping operations in the oil refining process. Commercial production of carotenes by chemical conversion of crude palm oil (CPO) results in loss of edible oil.
This recovery method involves adsorption chromatography by synthetic polymer adsorbent. By employing this method, carotenes were concentrated up to 100,000 ppm in a two step chromatography operation.
The basic component is the chromatography column which is packed with a synthetic porous polymer adsorbent. Of several adsorbents tested, one adsorbent was found which could adsorb the carotene from CPO by the chromatographic column, allowing the oil to pass through. The solvents used to elute out both oil and carotene are non-toxic, can be removed by an evaporator and are considered safe for use in producing edible oil.
Using this process, palm carotene was successfully concentrated to about 160 times its original concentration in CPO. More than 90% of the oil was removed without altering the triglyceride profile of the oil. By manipulating the column temperature and CPO loading onto the column, 85% of carotenes were recovered. Only a chromatographic column needs to be inserted in the present palm oil refining process. The addition of an evaporator and a distillation column for solvent removal and solvent regeneration would enable the solvent to be recycled and save cost.

Researcher: Badlishah Sham Baharin
Department of Food Technology
Faculty of Food Science and Technology
Universiti Putra Malaysia
43400 UPM, Serdang, Selangor
Malaysia
Tel: +603 8946 8394, +6012 914 4984
Fax: +603 8942 3552
E-mail: badli@fsb.upm.edu.my

and
Dr. Nayan KANWAL
Email: ndeeps@admin.upm.edu.my

A sponge to soak up regulatory RNAs

Genetically encoded inhibitors that soak up microRNAs in mammalian. MicroRNAs provides valuable insights into their function during normal development and disease.
MicroRNAs, unlike longer messenger RNAs (mRNAs), do not contain information for making a protein, but their short, 21 nucleotide, sequences specifically regulate mRNA expression. MicroRNAs bind to partly complementary sequences on their target mRNAs and as a consequence the mRNA is either marked for decay or protein translation is inhibited. Overexpression of certain microRNAs has been linked to cancer and other diseases and a better understanding of their action is therefore important.
Philip Sharp and colleagues have developed a tool to specifically block microRNAs. The principle of their system is based on soaking up all the microRNAs with a complementary decoy sequence, so the mRNA can express its protein unhindered. In contrast to previously described chemically synthesized microRNA inhibitors, these microRNA sponges are genetically encoded. They are provided to the cell either in form of a plasmid or they are stably integrated into the genome of a cell. This provides a much higher level of control over the amount of microRNA sponges a cell produces and allows microRNA action in a specific cell or tissue type to be studied.

Author contact:
Philip Sharp (Massachusetts Institute of Technology, Cambridge, MA, USA)
Tel: +1 617 253 6421; E-mail: sharppa@mit.edu

Signalling flies to sleep
A particular signalling pathway is shown to be important in regulation and maintenance of sleep. Fruit fly Drosophila may be a good model in which to identify the molecular pathways involved in sleep regulation.
Fruit flies (and other insects) undergo a process that is biologically similar to sleep in mammals, including immobility and additional ‘catch-up’ sleep following sleep deprivation. Ralph Greenspan and colleagues demonstrate that the activation of the epidermal growth factor receptor, which is known to be involved in natural 24 hour rhythms, led to an increase in sleep. Blocking activity in this signalling pathway led to a decrease in sleep and difficulty in catching up on sleep after deprivation. This regulation occurred in a region of the fly brain that is developmentally and functionally similar to the hypothalamus in mammals – the part of our brain that controls sleep.
Using this type of experimental approach may make it easier and faster for scientists to identify additional molecules required for the induction and/or maintenance of sleep. Drug companies might then be able to use this information to design better sleep aids.

Author contact:

Ralph Greenspan (The Neurosciences Institute, San Diego, CA, USA)
Tel: +1 858 626 2075; E-mail: greenspan@nsi.edu

Positive selection during human evolution

Sequences in the human genome that have undergone positive selection are found in abundance in regions that regulate the expression of genes involved in neural or nutritional processes. Some of the first large-scale evidence that the evolution of some human-specific traits can be traced to changes in gene regulatory (promoter) regions.
Cognitive, behavioural and dietary differences are among the most obvious differences between humans and the great apes. Although one might expect that genes involved in these processes would show evidence of positive natural selection in humans since the most recent common ancestor of humans and chimpanzees, there is little evidence to support this.
Ralph Haygood and colleagues compared probable promoter regions for more than 6,000 genes in the human, chimpanzee and macaque genomes. They generated statistics to identify those promoters that likely had undergone positive selection in the human genome. At least 250 such promoters were found. Although they represent several functional categories, prominent among them are promoters linked to genes involved in neural development and function, including axon guidance, synapse formation and neurotransmission in the brain. Nutrition-related genes include a large number involved in glucose metabolism.

Author contact:
Ralph Haygood (Duke University, Durham, NC, USA)
Tel: +1 919 668 6249; E-mail: rhaygood@duke.edu

Prevention and treatment of craniosynostosis

Two successful strategies for the prevention and treatment of craniosynostosis – premature fusion of the sutures in the skull. At least one of the approaches may be testable in humans in the near term. Craniosynostosis is caused by the sutures of the skull closing too early in infancy, which affects normal brain and skull growth. It occurs in approximately 1 of every 2,500 live births. Apert syndrome, a rare but quite severe form of craniosynostosis, is caused in most cases by a specific mutation in a cell-surface receptor called FGFR2.
Chu-Xia Deng and colleagues created a mouse model of Apert syndrome that bears one of the most common FGFR2 mutations seen in humans. When these mice were crossed with mice expressing a ‘short hairpin’ RNA molecule specifically designed to block expression of the mutant form of FGFR2, the offspring that carry the FGFR2 mutation developed normally. The authors also report the involvement in the disease of an enzyme called ERK, which is regulated by FGFR2. When they injected a drug that inhibits ERK activity into pregnant mice carrying the FGFR2 mutation, the offspring showed no signs of Apert syndrome. Moreover, when the drug was injected at the onset of the disease during the early postnatal period, at least some of the treated mice maintained a normal appearance, although the treatment’s effectiveness was greater in male than in female mice.
Drugs similar to those used in this study are already being tested in clinical trials as anticancer drugs, and may now have additional applications in the prevention and treatment of birth defects such as craniosynostosis.


Author contact:

Chu-Xia Deng (National Institutes of Health, Bethesda, MD, USA)
Tel: +1 301 402 7225; E-mail: chuxiad@bdg10.niddk.nih.gov

GENETICS : How West Nile virus became dangerous

A single causative mutation has been identified in the virulent strain of West Nile virus that has been responsible for deadly outbreaks of human encephalitis in recent years.
West Nile virus is a mosquito-borne virus that is transmitted between avian hosts and mosquitoes, and until the mid 1990s was associated with only mild infections of humans in Africa and the Middle East. More severe outbreaks of encephalitis were reported in Romania in 1996, and subsequently in Israel, Tunisia, Russia, and North America.
Aaron Brault and colleagues sequenced the genomes of West Nile virus strains that have been sampled globally in recent years, and found that a single mutation in a gene encoding an enzyme called a helicase arose independently on at least three separate occasions in strains associated with outbreaks of disease. When a poorly virulent strain from Kenya was engineered to contain the helicase mutation, it was found to replicate more rapidly and to cause death of inoculated American crows at a much higher rate than that of the original Kenyan virus. The authors also provide evidence that the helicase mutation was positively selected, which they say highlights the potential for viruses like West Nile to adapt rapidly to changing environments, with unpredictable consequences for human health.

Author contact:

Aaron Brault (University of California, Davis, CA, USA)
Tel: +1 530 754 8359; E-mail: acbrault@ucdavis.edu

CHEMICAL BIOLOGY : Natural products in a flask

Despite their complicated chemical structures, some potential drug leads can be created by mixing together enzymes in a flask.Chemicals that occur naturally, such as penicillin, have traditionally been very important sources of drugs. These ‘natural products’ often have very elaborate chemical structures that make them difficult to create by chemical synthesis.
Groups led by Bradley Moore and Christopher Walsh now independently show that two complex natural products, which have potential antibacterial and antitumour activity, can be made by taking the enzymes that normally create these chemicals inside cells and mixing them together outside of a cell. These studies have provided new insight into how these natural products are made and will help further efforts to turn these chemicals into drugs.

Author contacts:
Bradley Moore (University of California, San Diego, CA, USA) Author paper [1]
Tel: +1 858 822 6650; E-mail: bsmoore@ucsd.edu

Christopher Walsh (Harvard Medical School, Boston, MA, USA) Author paper [2]
Tel: +1 617 432 1715; E-mail: christopher_walsh@hms.harvard.edu

Halting the inflammation overload
Researchers discover a key molecule involved in regulating our immune response
Our immune system protects us against microbial pathogens that invade our cells and cause illness. When receptors on the cell surface detect microbes, a cascade of signals and activities within the cell is triggered, resulting in inflammation, which is part of our early defense against pathogens.
Immunologists from the RIKEN Research Center for Allergy and Immunology, Yokohama, and the Harvard School of Public Health, US, recently published a study on the regulation of this system1. Without regulation, an unstoppable immune reaction leads to excessive inflammation, which causes conditions such as asthma and arthritis.
The researchers studied a molecule called NF-κB that contains two different subunits known as p65 and p50 and normally resides in the cytoplasm of cells. When this molecule receives the appropriate signal, it enters the cell nucleus and switches on immunoregulatory genes that encode pro-inflammatory molecules. If the process is not stopped, the immune reaction continues. To terminate this reaction promptly, it is important that the p65 molecule that starts this sequence of events is degraded once it has done its job.
RIKEN’s Tsuneyasu Kaisho and his team have identified a pathway that leads to the degradation of p65. Their work shows that the process involves the specific attachment of the protein molecule ubiquitin to p65 followed by transportation of the ‘ubiquitinated’ p65 to distinct sub-nuclear domains, called nuclear bodies, where it is ultimately degraded by the proteins found there (Fig. 1).
Critically, the researchers have described a factor called PDLIM2 that has two highly important roles in the regulation of the immune response. It helps ubiquitin to bind to p65 and then targets this complex to the appropriate nuclear bodies for degradation.
The team showed that PDLIM2-deficient mouse cells had uncontrolled immune responses due to the constant activity of NF-κB and augmented production of molecules that cause inflammation. In vivo studies showed mice lacking PDLIM2 were more sensitive to stimulation of the immune response than mice with normal levels of the molecule.
Developing treatments for inflammatory and autoimmune diseases by modifying the PDLIM2-mediated pathways to terminate NF-κB p65 activation is the future aim of the team. According to team member, Takashi Tanaka, the next step towards this goal is to clarify how PDLIM2 activity itself is regulated. This is very important for developing a way to modify its activity in living cells, he says.

Reference
1. Tanaka, T., Grusby, M.J. & Kaisho, T. PDLIM2-mediated termination of transcription factor NF-κB activation by intranuclear sequestration and degradation of the p65 subunit. Nature Immunology 8, 584–591 (2007).

A better way to make a muscle?

New revelations about how muscle tissue forms could help scientists develop more effective strategies for therapeutic tissue replacement

Even the mightiest individuals are vulnerable to muscle loss, whether from severe injury, old age, or as a byproduct of disease, and many scientists see the engineering of replacement muscle as a promising solution. Current methods involve the culture of progenitor stem cells, known as myoblasts, for transplantation. These cells in turn fuse and differentiate to form myofibers—mature muscle fibers capable of contraction.
Myoblasts show promise for muscle replacement, but cultured myofibers may be superior for clinical use, and could reduce the risk of tumor formation—a potential hazard with undifferentiated myoblasts. Unfortunately, current strategies for myofiber production have proven inadequate, and myofibers produced from cultured myoblasts tend to be poorly differentiated. “Myoblast transplantation is far ahead of myofiber transplantation,” explains Nobuhiro Morishima, of the RIKEN Discovery Research Institute in Wako. “And one of the reasons for the slow progress of cultured myofiber transplantation is the inefficiency of myofiber formation in culture.”
Previous work by Morishima’s team revealed that differentiation of myoblasts appears to correlate with functional disruption of the endoplasmic reticulum (ER), the cellular organelle responsible for protein folding and processing1. Now the team has used chemicals that directly trigger this condition, known as ‘ER stress’, in cultured myoblasts to better understand the role of this process in muscle development2.
Surprisingly, treated cells responded in different ways; nearly half the treated cells died, via a process known as apoptosis, while the other cells survived and differentiated to form fully functional myofibers. Closer examination revealed that the ‘survivors’ were expressing higher levels of Bcl-xL, a protein known to block apoptosis. Morishima suggests that this process of stress-mediated death may be a means for preventing ‘weak’ cells from forming myofibers, as muscle tissue is routinely exposed to stressful physiological conditions. What remains unclear is how otherwise identical cells end up choosing between two different pathways during differentiation, and Morishima hopes to examine this further in the future.
For now, however, his team is encouraged by the high yield of functioning myofibers that can be generated through this culture method, and they are now attempting to better understand the differentiation process and how to exploit it for biomedical applications. “We would like to answer the question of how the myoblast-differentiating ER stress conditions naturally occur in the body,” he says, “and hopefully we will be able to show the merit of ER stress for myofiber formation in vivo for the advancement of both basic biology and clinical research.”

Reference
1. Nakanishi, K., Sudo, T. & Morishima, N. Endoplasmic reticulum stress signaling transmitted by ATF6 mediates apoptosis during muscle development. Journal of Cell Biology 169, 555–560 (2005).
2. Nakanishi, K., Dohmae, N. & Morishima, N. Endoplasmic reticulum stress increases myofiber formation in vitro. FASEB Journal, published online, 13 April 2007 (doi: 10.1096/fj06-6408com).

Electron theory solves heavy problem

Usual properties of lithium vanadate explained

Today’s high-tech devices would not exist without a good theory to predict how electrons move through semiconductor crystals. But gaps remain in the theory—some insulating materials are erroneously predicted to conduct electricity, for example. Resolving these problems could lead to a more robust theory that enables new breakthroughs in electronics.
As part of this effort, a RIKEN researcher and his colleagues have developed a new theoretical method for predicting how electrons will behave at very low temperatures, called the projective quantum Monte Carlo (PQMC) method, and used it to solve a puzzle about the unusual electrical conductivity, heat capacity and magnetic properties of a material called lithium vanadate (
In a single atom, electrons can only occupy certain energy levels, known as orbitals. But in a crystal made up of trillions of atoms these orbitals smear into bands, each representing a range of energies available to the electrons. In semiconductors, electrons must acquire enough energy to hop into the lowest unoccupied band before they start to flow.
In certain materials, there is a magnetic attraction between the electrons flowing through the conduction band and those which remain trapped on the stationary atoms. This can slow the conduction electrons down, and make the trapped electrons, known as ‘heavy fermions’, behave as if they were much heavier than normal. Lithium vanadate is the first material where electrons residing in a lower orbital, called 3d, are responsible for heavy fermion behavior that appears below about -240 ˚C.
Despite the chilly conditions, there has been hot debate about exactly how this works. Now Ryotaro Arita, of RIKEN’s Discovery Research Institute in Wako, and his colleagues believe they have the answer. The team has combined two established ways of calculating how electrons spread around atoms, and used PQMC to extrapolate the case to very low temperatures.
Their calculations show that the orbitals around the vanadium atoms are subdivided into a lower energy band (a1g) where electrons remain tethered to their parent atoms, while those in an upper level (eg) effectively form a conduction band. The lower band acts as a Mott insulator: such materials do not conduct electricity because the mutual repulsion between neighboring electrons forces them to stick by their parent atoms. This makes the a1g band primarily responsible for the heavy fermion effects seen in LiV2O4.
The team now hopes to refine their theory further to explain other anomalous behavior in metals, insulators and semiconductors, says Arita.

Reference
1. Arita, R., Held, K., Lukoyanov, A. V. & Anisimov V. I. Doped Mott insulator as the origin of heavy-fermion behavior in LiV2O4. Physical Review Letters 98, 166402 (2007).

New real-time, cross platform intelligent network monitoring system
jEnterprise is a real-time continuous network monitoring tool to prevent potential performance degradation or downtime. It provides intelligent troubleshooting and support for new protocols such as IPv6 to ensure coverage at all times and is the world's only cross platform enterprise level distributed network analysis and troubleshooting tool

Project Title: jEnterprise: An Enterprise Intelligent Network Monitoring and Troubleshooting Tool Based on Autonomous Self Managed Mobile Agent

Researchers:
Assoc. Prof. Dr. Sureswaran Ramadass
Azlan Osman
Ahmad Manasrah
Muhammad Fermi Pasha
Saravaneh A/P Supramaniam
Selvakumar Manickam

Network and system administrators have turned to network monitoring and protection tools to ensure smooth operation of networks within the enterprise. Most organization has about 50 to 1000 computers and the numbers are growing.
Imagine one of the computers is flooding the network; the system administrator would then have to investigate each machine to find out which one is causing the problem by making desk-side visits. Such processes are cumbersome, inaccurate and in some cases, take days (even weeks) to pinpoint and solve the problem.
jEnterprise is a real-time, around-the-clock network monitoring tool that continuously monitor enterprise network to prevent potential performance degradation or downtime. It provides intelligent troubleshooting as well as support for new protocols that supports next generation network protocols such as IPv6 to ensure coverage at all times.
jEnterprise will be able to provide global access to remotely monitor any network on any corner of the world tunneling via the Internet. It offers complete monitoring from Physical Layer to Application Layer. The uniqueness of jEnterprise Suite as compared to other tools is that it not only provides a centralized visualization and analysis engine, called jCMC (Centralized Monitoring Console), it also provides an autonomous and intelligent self managed remote agents, called jRemote, to monitor and protect each remote network segment within the organization and a managed intelligent server, called jServer, to collect network data from jRemote agents and perform intelligent analysis. This interesting and unique distributed architecture creates a complete protected environment for the organizations servers, PC and the network.
j-Enterprise is also the world's only cross platform enterprise level distributed network analysis and troubleshooting tool.

Contact :
Assoc. Prof. Dr. Sureswaran Ramadass
National Advanced IPv6 Centre (NAv6)
Universiti Sains Malaysia

Neuroscience: Understanding antidepressants
A glimpse of the mechanism involved in antidepressant block of neurotransmitter transporters in the brain is revealed in a paper.Eric Gouaux and colleagues wanted to understand the previously elusive action of tricyclic antidepressant (TCA), to aid the design of new inhibitors.
In humans, inhibiting sodium-coupled transporters has an important role in the treatment of a broad range of neurological diseases and conditions. Gouaux and his team provide mechanistic insights into how such transport proteins are blocked by solving the structure of a prokayotic homologue, in complex with various TCAs, at high resolution. They identify an extracellular-facing cavity in the protein as the site of TCA action and thus as a site with therapeutic potential.

Contact:
Eric Gouaux (Oregon Health and Science University/HHMI,Portland, OR, USA)
Tel: +1 503 494 5535; E-mail: gouauxe@ohsu.edu

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

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

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

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

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).

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).

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).

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.