Protein Engineering Advancing Alzheimer’s Research

No one has yet found a cure or a way to prevent people from developing Alzheimer's disease. Researchers from the Swedish University of Agricultural Sciences, among others, are breaking new ground in biotechnology to find new tools that can help provide new solutions. A protein constructed by these researchers has yielded experimental results that are promising when it comes to stopping the disease. And for the first time, using protein engineering, it seems they have successfully created the oligomer that is believed to trigger the disorder.

Alzheimer's disease is the most common form of dementia. In the 60-64 age group, one percent have the disorder, and among people age 85 and older, 25 percent are affected. At present there is no cure for Alzheimer's. Those who develop it grow gradually worse, and the disease leads to death, often after several years of sickness. Besides the tragedy entailed when people contract Alzheimer's disease, the healthcare involved consumes huge resources.

Symptoms of Alzheimer's disease begin with loss of memory. The disorder is caused by damage to the nerves in the brain. This damage is caused by so-called oligomers of the peptide Aß, which is also found in amyloid plaques, a kind of precipitate, that accumulate in the brain.

At the Swedish University of Agricultural Sciences (SLU) in Uppsala, Sweden, Professor Torleif Härd of the Department of Molecular Biology is directing a research project that is developing new biotechnological tools that could be used to in research and as potential therapies. They are deploying protein engineering, and experiments have yielded highly promising results.

One of the strategies for finding an answer to how Alzheimer's disease could be prevented is based on the idea of adding a protein to the blood, to bind to the Aß peptide there. In this way the Aß peptide becomes harmless, and the disease might be prevented.

The research team has studied how an artificial so-called Affibody protein entirely encases the Aß peptide, thereby preventing the formation of toxic forms.

"Nothing like this has ever been done before, and the results have attracted a great deal of attention," says Torleif Härd. "Our success in also determining the structure of this complex constituted a breakthrough, because it paved the way for new ideas for further research."

Now the SLU scientists, working with teams from the Royal Institute of Technology (KTH) in Stockholm and Affibody AB, are seeking to alter the characteristics of the Affibody protein so it won't be broken down when it enters the blood. The strategy is also being tested in flies, and the preliminary results indicate that the strategy works.

Another strategy involves using protein engineering to stabilize the toxic oligomers that are the cause of nerve cell death and memory loss. Oligomers are a stage halfway between the Aß peptide and amyloid plaques. In the laboratory environment they survive only about 15 minutes, making it impossible to study them. If these oligomers can be stopped, it should be possible to prevent Alzheimer's disease from breaking out. To find out more about the structure and mechanism of these oligomers, scientists need to stabilize them in order to examine them, and this is something the scientists in the project have managed to do: they have create a stable oligomer with the same toxic properties as before.

"We are now busy determining the 3D structure of the oligomer. This is important if we are to be able to further study the molecular mechanisms, and it may lead on to drug development," says Torleif Härd. In collaboration with MIVAC Development AB, they are also investigating the possibility of directly developing a vaccine against the disease.

It Takes Two to Infect: Structural Biologists Shed Light on Mechanism of Invasion Protein

Bacteria are quite creative when infecting the human organism. They invade cells, migrate through the body, avoid an immune response and misuse processes of the host cell for their own purposes. To this end, every bacterium employs its own strategy.

In collaboration with a British research group, structural biologists from the Helmholtz Centre for Infection Research in Braunschweig, Germany, and the University of Bielefeld, Germany, have now elucidated one mechanism of Listeria bacteria.

Two so-called invasion proteins are crucial for infection. Each binds a specific receptor on the surface of human cells, which stimulates the host cell to take up the pathogen. Normally, these receptor molecules exert a different function, for example the regulation of cell growth and wound healing. The group's results have now been published in the current issue of the Journal of Molecular Biology.

Spoiled meat is one of the sources for Listeria infections leading to listeriosis. Pregnant women, newborns and immune compromised people are susceptible for a severe progression of this disease. Firstly, the pathogen breaches the intestinal barrier and thus enters the body. The key for further spreading is the invasion protein internalin B that is located on the bacterial surface. On human cells, internalin B activates a receptor molecule called "Met," thereby signaling the host cell to take up the pathogen. Inside the cell, Listeria uses the host cell's nutrients and is somehow sheltered from an immune response.

Until now, the researchers did not know how the bacterial invasion protein activates the human receptor. To solve this question, the structural biologists from the HZI first analysed the crystal structures of the single internalin B molecule and of its complex bound to human Met. "In X-Ray structural analysis we noticed that in protein crystals two internalin B molecules align characteristically," says Hartmut Niemann, assistant professor at the University of Bielefeld. Professor Dirk Heinz, head of the structural biologists at the HZI, explains: "This gave rise to the idea of a dimer -- two congregated internalin B molecules -- playing a pivotal role in the activation of the Met receptor."

Minor changes in the internalin B molecule confirmed their hypothesis: inhibiting the congregation of two internalin B molecules prevented the activation of Met. On the other hand, strengthening the interaction resulted in particularly strong receptor activation.

These results may lead to the development of new protein drugs in the future. "Met plays a major role in the body, for example during wound healing," says Heinz. "Thanks to the extraordinary ability of the internalin B dimer to strongly activate Met, therapeutics for improved wound healing may result someday."

Brain Scan Study Shows Cocaine Abusers Can Control Cravings

When asked to inhibit their response to a "cocaine-cues" video, active cocaine abusers were, on average, able to suppress activity in brain regions linked to drug craving, according to a new study at the U.S. Department of Energy's Brookhaven National Laboratory. The results, to be published in an upcoming issue of NeuroImage, suggest that clinical interventions designed to strengthen these inhibitory responses could help cocaine abusers stop using drugs and avoid relapse.

"Exposure to drugs or stimuli associated with using drugs is one of the most common factors leading to relapse in drug-addicted individuals," said Nora Volkow, Director of the National Institute on Drug Abuse and lead author on the paper.

"We know from previous studies that drug cues can trigger dramatic changes in the brain that are linked to a strong craving response," added co-author Gene-Jack Wang, Chair of Brookhaven's medical department. "This study provides the first evidence that cocaine abusers retain some ability to cognitively inhibit their craving responses to drug-related cues."

Added Volkow, "Our findings provide enormous hope because they imply that cognitive interventions might be developed to maximize cocaine abusers' success in blocking the drug-craving response to help them avoid relapse."

The scientists used a brain-scanning technique called positron emission tomography (PET) and a radioactively "tagged" form of glucose -- the brain's main fuel -- to measure brain activity in 24 active cocaine abusers during three different conditions:

1. while subjects simply lay in the scanner with eyes open;
2. while subjects watched a "cocaine-cues" video with scenes simulating the purchase, preparation, and smoking of crack cocaine; and
3. while subjects watched the video but were told to try to inhibit their craving response.

Scans were performed in random order and on separate days.In each scan, the PET camera tracked the radioactive signal from the tagged glucose as it was taken up by various regions of the brain. A stronger signal indicates higher metabolic activity in a particular brain region where more glucose is being used. This technique allows scientists to accurately monitor which brain regions are most active and how that activity changes with time or in response to different situations.

The scientists also monitored the research subjects’ heart rate and blood pressure and asked them to describe their level of craving during the scans. Compared with the baseline condition, the cocaine-cues video triggered increases in brain activity in several brain regions associated with drug craving, as well as increases in research subjects’ self-reports of craving.

When the research subjects were asked to inhibit their response to the video, and those scans were compared with the no-inhibition condition, metabolic activity decreased dramatically in brain regions involved in experiencing and anticipating rewards, and in a part of the brain that plays a role in assigning value, or salience, to different stimuli. During inhibition, research subjects also reported lower levels of craving compared with the no-inhibition video condition.

The researchers say the findings have significant clinical implications: “Many current drug treatment programs help addicted individuals predict when and where they might be exposed to drug cues so that they can avoid such situations,” Volkow said. “While this is a very useful strategy, in real-word situations, cues may come up in unexpected ways. Our findings suggest that a clinical strategy that trains cocaine abusers to exert greater cognitive control could help them selectively inhibit the craving response whenever and wherever drug cues are encountered — whether expectedly or unexpectedly.”

Because inhibitory control is crucial for regulating emotions and desires, the findings from this study could have implications for other disorders involving loss of behavioral control, such as gambling and obesity.

This study was supported by the intramural program from the National Institutes of Health Intramural Research Program at the National Institute on Alcohol Abuse and Alcoholism. Brookhaven Lab’s infrastructure for PET imaging and radiotracer development also receive support from the DOE Office of Science.

Birth Control Pill for Men? Scientists Find a Hormonal on-and-Off Switch for Male Fertility

A new research report published in the December 2009 print issue of The FASEB Journal could one day give men similar type of control over their fertility that women have had since the 1960s. That's because scientists have found how and where androgenic hormones work in the testis to control normal sperm production and male fertility. This opens a promising avenue for the development of "the pill" for men.

The discovery also offers hope to those who cannot have children because of low sperm counts. Although the research was conducted in mice, a similar effect is likely to obtain in other mammals, such as humans.

"This study provides a new opportunity to identify how androgens control sperm production, which could provide new insight for the development of new treatments for male infertility and perhaps new male contraceptives," said Michelle Welsh, Ph.D., co-author of the study, from the Centre for Reproductive Biology at The Queen's Medical Research Institute in Edinburgh, UK.

To make this discovery, Welsh and colleagues performed studies in two groups of mice. The first group of mice was normal, but the second group of mice was missing a gene from the peritubular myoid cells in the testis. This gene that was missing codes for the androgen hormone receptor, and when missing, sperm production was significantly decreased when compared to the normal group. The result was infertility.

"Although 'the pill' arguably has been liberating for women since its development in the 1960s, a similar birth control drug for men has been elusive," said Gerald Weissmann, M.D., Editor-in-Chief of The FASEB Journal. "Not only does this research pinpoint androgenic hormones and their cellular receptors as prime targets for the development of new birth control drugs, but it promises to speed the development of new agents to boost sperm production."

Small Hairy Balls Hide Foul-Tasting Healthful Enzymes

Dutch researcher Saskia Lindhoud has discovered a new way to package enzymes by causing charged polymers to form a 'ball of hair' around them. Her approach significantly increases the utility of the enzymes. For example, healthy enzymes with a foul taste can be packaged in such a way that they are released in the stomach without being tasted.

Enzymes are molecules that can trigger specific chemical reactions. They are responsible for the taste of beer, the effectiveness of detergents and the digestion of food in our guts. However, the optimal use of enzymes requires that they do not trigger the chemical reactions too early or too late. Moreover, enzymes are quite sensitive to changes in their environment such as temperature fluctuations and changes in the salt concentration or pH. Enzymes can be protected from such influences by means of a packaging. Lindhoud discovered a new way of doing this well.

Hairy balls

Lindhoud used polyelectrolyte complex micelles for the packaging. These consist of at least two types of molecules that have an opposite charge and of which at least one type has a charged and an uncharged block (diblock copolymer). If these molecules are mixed together then the oppositely charged parts of the molecules form a complex because opposite charges attract. The uncharged parts of the molecules prefer not to be located in the core and stick outwards. This results in the automatic formation of balls with hairs on the outside.

As enzymes are also charged they can be packaged into these hairy balls. Yet unfortunately, particles that consist of just enzymes and diblock copolymers are not very robust. Lindhoud therefore substituted a part of the enzymes with a polymer of the same charge. This improved the stability and robustness of the particles. Moreover, Lindhoud discovered that the enzymes preferred not to be located in the core of the particle but on the boundary of this instead. Adding polymers with the same charge increased the surface of this boundary.

The advantage of enzymes packaged using Lindhoud's approach is the ease with which these can be unpackaged again. This is essential for the effective use of enzymes in industrial applications. Lindhoud's research could therefore do more than improve detergents; it could enable new applications of enzymes. One such possible application is the specific delivery of medicines. Saskia Lindhoud carried out her research with a TOP grant from the NWO Division for the Chemical Sciences. She is now a postdoctoral researcher at the University of Bath.

RNA Network Seen in Live Bacterial Cells for First Time

Scientists who study RNA have faced a formidable roadblock: trying to examine RNA's movements in a living cell when they can't see the RNA. Now, a new technology has given scientists the first look ever at RNA in a live bacteria cell -- a sight that could offer new information about how the molecule moves and works.

Interest in RNA, which plays a key role in manufacturing proteins, has increased in recent years, due in large part to its potential in new drug therapies. RNA localization and movement in bacterial cell are poorly understood. The problem has been finding a way to mark RNA in a living cell so that scientists can track it, says Natasha Broude, a research associate professor at Boston University's Department of Biomedical Engineering.

"You can label any protein within the cell and watch what it is doing," says Broude, a senior researcher on the new study, published in a recent issue of the Proceedings of the National Academy of Sciences. "For RNA it was much more difficult because RNA is more mobile and less stable than both proteins and DNA."

Before now, scientists used green fluorescent protein (GFP) to label RNA in a cell. But proteins were also tagged with GFP and their fluorescence was so bright, it drowned out the glow from the RNA. "The initial idea was to do something to allow us to decrease background fluorescence," Broude says.

In 2007, Broude and her colleagues developed a system to persuade a cell to synthesize protein in two fragments rather than a whole, which made the protein inactive. They then modified an RNA molecule, adding a small tail of RNA sequence that works like a handle, grabbing the fragments and pulling them together, which makes the protein active -- and glow bright green. The scientists can then follow the RNA as it moves through the cell.

"In our case, the protein becomes fluorescent because it binds to RNA," Broude says. "If there is no RNA, we don't see this protein."

In this new work, the team modified this system to allow for the controlled synthesis of RNA -- allowing the researchers to track RNA as soon as it appears in the cell. For the study, they used live Eschericha coli cells, the simplest bacteria model, and a nonfunctional RNA. To monitor the RNA and capture images as it moved through the cell, the team used a sophisticated microscope and detection system developed by colleague Amit Meller, a co-author of the study and associate professor of biological engineering at Boston University. Meller's system made it possible to watch RNA in whole cells with high resolution. Their observations are not only the first of their kind, they also contradict previously held theories about RNA localization, which held that RNA was evenly distributed throughout the cell.

"The first thing we saw is that RNA is localized along mostly the periphery of the cell," Broude says. One possibility for this could be that the middle of the bacterial cell, which is occupied by DNA, is less accessible to the RNA.

The researchers also noted that the RNA appeared to form helical structures resembling those seen in proteins involved in producing the cell's cytoskeleton, which is involved in DNA replication, cell division and other important processes. "They are necessary structural elements which rule all changes in bacterial life," Broude says. "But we need to learn more before we can say anything about the RNA helical structure's function."

With this new technology in place, Broude and her colleagues can learn more about the RNA network they've observed, examine the localization and movement of other types of RNA in live bacterial cells and, ultimately, mammalian cells.

Other study authors included Maria Valencia-Burton, research associate in biomedical engineering, Ankita Shah, undergraduate student, Jason Sutin, graduate student, Azra Borogovac, undergraduate student, and Charles Cantor, professor and director of biomedical engineering, all at Boston University, and Ron McCullough with Sequenom, Inc.

First-Ever Blueprint of 'Minimal Cell' Is More Complex Than Expected

What are the bare essentials of life, the indispensable ingredients required to produce a cell that can survive on its own? Can we describe the molecular anatomy of a cell, and understand how an entire organism functions as a system? These are just some of the questions that scientists in a partnership between the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, and the Centre de Regulacio Genòmica (CRG) in Barcelona, Spain, set out to address.

In three papers published back-to-back in Science, they provide the first comprehensive picture of a minimal cell, based on an extensive quantitative study of the biology of the bacterium that causes atypical pneumonia, Mycoplasma pneumoniae. The study uncovers fascinating novelties relevant to bacterial biology and shows that even the simplest of cells is more complex than expected.

Mycoplasma pneumoniae is a small, single-cell bacterium that causes atypical pneumonia in humans. It is also one of the smallest prokaryotes -- organisms whose cells have no nucleus -- that don't depend on a host's cellular machinery to reproduce. This is why the six research groups which set out to characterize a minimal cell in a project headed by scientists Peer Bork, Anne-Claude Gavin and Luis Serrano chose M. pneumoniae as a model: it is complex enough to survive on its own, but small and, theoretically, simple enough to represent a minimal cell -- and to enable a global analysis.

A network of research groups at EMBL's Structural and Computational Biology Unit and CRG's EMBL-CRG Systems Biology Partnership Unit approached the bacterium at three different levels. One team of scientists described M. pneumoniae's transcriptome, identifying all the RNA molecules, or transcripts, produced from its DNA, under various environmental conditions. Another defined all the metabolic reactions that occurred in it, collectively known as its metabolome, under the same conditions. A third team identified every multi-protein complex the bacterium produced, thus characterising its proteome organisation.

"At all three levels, we found M. pneumoniae was more complex than we expected," says Luis Serrano, co-initiator of the project at EMBL and now head of the Systems Biology Department at CRG.

When studying both its proteome and its metabolome, the scientists found many molecules were multifunctional, with metabolic enzymes catalyzing multiple reactions, and other proteins each taking part in more than one protein complex. They also found that M. pneumoniae couples biological processes in space and time, with the pieces of cellular machinery involved in two consecutive steps in a biological process often being assembled together.

Remarkably, the regulation of this bacterium's transcriptome is much more similar to that of eukaryotes -- organisms whose cells have a nucleus -- than previously thought. As in eukaryotes, a large proportion of the transcripts produced fromM. pneumoniae's DNA are not translated into proteins. And although its genes are arranged in groups as is typical of bacteria, M. pneumoniae doesn't always transcribe all the genes in a group together, but can selectively express or repress individual genes within each group.

Unlike that of other, larger, bacteria, M. pneumoniae's metabolism doesn't appear to be geared towards multiplying as quickly as possible, perhaps because of its pathogenic lifestyle. Another surprise was the fact that, although it has a very small genome, this bacterium is incredibly flexible and readily adjusts its metabolism to drastic changes in environmental conditions. This adaptability and its underlying regulatory mechanisms mean M. pneumoniae has the potential to evolve quickly, and all the above are features it also shares with other, more evolved organisms.

"The key lies in these shared features," explains Anne-Claude Gavin, an EMBL group leader who headed the study of the bacterium's proteome: "Those are the things that not even the simplest organism can do without and that have remained untouched by millions of years of evolution -- the bare essentials of life".

This study required a wide range of expertise, to understand M. pneumoniae's molecular organisation at such different scales and integrate all the resulting information into a comprehensive picture of how the whole organism functions as a system -- an approach called systems biology.

"Within EMBL's Structural and Computational Biology Unit we have a unique combination of methods, and we pooled them all together for this project," says Peer Bork, joint head of the unit, co-initiator of the project, and responsible for the computational analysis. "In partnership with the CRG group we thus could build a complete overall picture based on detailed studies at very different levels." Bork was recently awarded the Royal Society and Académie des Sciences Microsoft Award for the advancement of science using computational methods. Serrano was recently awarded a European Research Council Senior grant.

New Synthetic Molecules Trigger Immune Response To HIV And Prostate Cancer

Researchers at Yale University have developed synthetic molecules capable of enhancing the body's immune response to HIV and HIV-infected cells, as well as to prostate cancer cells. Their findings, published online in theJournal of the American Chemical Society, could lead to novel therapeutic approaches for these diseases.

The molecules -- called "antibody-recruiting molecule targeting HIV" (ARM-H) and "antibody-recruiting molecule targeting prostate cancer" (ARM-P) -- work by binding simultaneously to an antibody already present in the bloodstream and to proteins on HIV, HIV-infected cells or cancer cells. By coating these pathogens in antibodies, the molecules flag them as a threat and trigger the body's own immune response. In the case of ARM-H, by binding to proteins on the outside of the virus, they also prevent healthy human cells from being infected.

"Instead of trying to kill the pathogens directly, these molecules manipulate our immune system to do something it wouldn't ordinarily do," said David Spiegel, Ph.D., M.D., assistant professor of chemistry and the corresponding author of both papers.

Because both HIV and cancer have methods for evading the body's immune system, treatments and vaccinations for the two diseases have proven difficult. Current treatment options for HIV and prostate cancer -- including antiviral drugs, radiation and chemotherapy -- involve severe side effects and are often ineffective against advanced cases. While there are some antibody drugs available, they are difficult to produce in large quantities and are costly. They also must be injected and are accompanied by severe side effects of their own.

By contrast, the ARM-H and ARM-P molecules, which the team has begun testing in mice, are structurally simple, inexpensive to produce, and could in theory be taken in pill form, Spiegel said. And because they are unlikely to target essential biological processes in the body, the side effects could be smaller, he noted.

"This is an entirely new approach to treating these two diseases, which are extraordinarily important in terms of their impact on human health," Spiegel said.

HIV is a global pandemic that affects 33 million people worldwide, while prostate cancer is the second leading cause of cancer-related death among American men, with one out of every six American men expected to develop the disease.

Funding for this research was provided by the National Institutes of Health.

Higher Incidence Of Thyroid Cancer In Volcanic Area Of Sicily

People living in volcanic areas may be at a higher risk for thyroid cancer, according to a new study published online November 5 in the Journal of the National Cancer Institute.

The increasing incidence of thyroid cancer has been attributed to more sensitive screening, but recent evidence indicates that this may not be the only cause. Various environmental factors, such as those associated with volcanoes, have not been excluded as risk factors.

To study this, Gabriella Pellegriti, M.D., Ph.D., of the endocrinology division, University of Catania Medical School, Garibaldi-Nesima Hospital in Italy, and colleagues collected incidence [newly diagnosed cases] of thyroid cancers in Sicily from January 1, 2002 through December 31, 2004 to compare the cancer rates of residents living in the volcanic area of Mt. Etna of Catania with those in the rest of Sicily.

The researchers found that residents of the Catania province had a more than two times higher incidence of papillary thyroid cancer, but not follicular or medullary thyroid cancers, than elsewhere on the island. Also, papillary tumors from patients in Catania more frequently carried the BRAF V600E gene mutation, which has been associated with more aggressive thyroid cancer.

The authors point out that a volcanic environment -- which can produce toxic compounds that are suspended particulate matter and gases and elements that may pollute the water -- may increase the incidence of thyroid cancer; however, the mechanism by which it affects risk is unknown.

"The striking increase in papillary thyroid cancer incidence that was associated with the Etna volcanic environment leads us to suggest that residents of other volcanic areas…could be at increased risk for thyroid cancer and, possibly, of other cancers," the authors write. "Although specific risk factors for thyroid cancer in this volcanic environment are still unknown, identification of these factors could help to better understand the cause(s) of the increasing thyroid cancer incidence in Europe and North America and perhaps to develop prevention measures."

Women Have More Diverse Hand Bacteria Than Men

A new University of Colorado at Boulder study indicates that not only do human hands harbor far higher numbers of bacteria species than previously believed, women have a significantly greater diversity of microbes on their palms than men.

The results have implications for better understanding human bacteria and should help establish a "healthy baseline" to detect microbial community differences on individuals that are associated with a wide variety of human diseases, said CU-Boulder Assistant Professor Noah Fierer, lead study author. A paper on the subject by the CU-Boulder researchers was published online Nov. 3 in the Proceedings of the National Academy of Sciences.

Using powerful gene sequencing techniques, the team found a typical hand in the new study had roughly 150 different species of bacteria living on it, said Fierer of CU-Boulder's ecology and evolutionary biology department. While the researchers detected and identified more than 4,700 different bacteria species across 102 human hands in the study, only five species were shared among all 51 participants.

"The sheer number of bacteria species detected on the hands of the study participants was a big surprise, and so was the greater diversity of bacteria we found on the hands of women," said Fierer. The study also showed that the diversity of bacteria on individual hands was not significantly affected by regular hand washing, he said.

The 332,000 gene sequences obtained by the CU team were nearly 100 times greater than those obtained from other studies of skin bacteria also obtained by sampling the entire DNA of microbe communities, known as "metagenomics." The new CU-Boulder study also confirms that standard skin culturing of human skin bacteria, a technique used by many labs, dramatically underestimates the full extent of microbial diversity, Fierer said.

Co-authors on the PNAS study included Micah Hamady of CU-Boulder's computer science department, Christian Lauber of CU-Boulder's Cooperative Institute for Research in Environmental Sciences and CU-Boulder chemistry and biochemistry Assistant Professor Rob Knight. The study was funded primarily by the National Institutes of Health and the National Science Foundation.

Fierer speculated that skin pH may play a role in the higher bacterial diversity on women's hands, since men generally have more acidic skin, and other research has shown microbes are less diverse in more acidic environments. The findings also could be due to differences in sweat and oil gland production between men and women, the frequency of moisturizer or cosmetics applications, skin thickness or hormone production, he said.

The right and left palms of the same individual shared an average of only 17 percent of the same bacteria types, said Knight. Study volunteers, all CU undergraduates, shared an average of only 13 percent of bacteria species with each other, he said.

Although the composition of bacterial communities on dominant and non-dominant hands of subjects was significantly different, diversity levels were similar, Fierer said. The differences found between dominant and non-dominant hands were likely due to environmental conditions like oil production, salinity, moisture or variable environmental surfaces touched by either hand of an individual, he said.

While some groups of bacteria were less abundant following hand washing, others were more abundant, said Knight, who stressed that regular hand washing with anti-bacterial soap is beneficial. "The vast majority of bacteria are non-pathogenic, and some bacteria even protect against the spread of pathogens," Knight said. "From a public health standpoint, regular hand washing has a very positive effect."

"Although hand washing altered community composition, overall levels of bacterial diversity were unrelated to the time since the last hand washing," wrote the researchers in PNAS. "Either the bacterial colonies rapidly re-establish after hand washing, or washing (as practiced by the students included in this study) does not remove the majority of bacteria taxa found on the skin surface."

The CU-Boulder team used the metagenomic survey to simultaneously analyze all of the bacteria on a given palm surface, said Knight. In simple terms, the effort involved isolating and amplifying tiny bits of microbial DNA, then building complementary DNA strands with a high-powered sequencing machine that allowed the team to identify different families, genera and species of bacteria from the sample.

Knight recently received a $1.1 million NIH grant to develop new computational tools to better understand the composition and dynamics of microbial communities. He has been developing novel methods to tag DNA samples with error-correcting "barcodes" to obtain more accurate sequencing data.

The richness of bacteria types on the palm was three times higher than that found on the forearm and elbow, according to the researchers. The total diversity of hand bacteria appears to match or exceed levels of bacteria colonizing other parts of the body, including the esophagus, the mouth and lower intestine, Fierer said.

"I view humans as 'continents' of microscopic ecological zones with the kind of diversity comparable to deep oceans or tropical jungles," Fierer said. "Today we have the ability to answer large-scale questions about these complex microbial communities and their implications for human health that we weren't even asking six months or a year ago."

Hormone That Affects Finger Length Key To Social Behavior

Research at the universities of Liverpool and Oxford into the finger length of primate species has revealed that cooperative behavior is linked to exposure to hormone levels in the womb.

The hormones, called androgens, are important in the development of masculine characteristics such as aggression and strength. It is also thought that prenatal androgens affect finger length during development in the womb. High levels of androgens, such as testosterone, increase the length of the fourth finger in comparison to the second finger. Scientists used finger ratios as an indicator of the levels of exposure to the hormone and compared this data with social behaviour in primate groups.

The team found that Old World monkeys, such as baboons and rhesus macaques, have a longer fourth finger in comparison to the second finger, which suggests that they have been exposed to high levels of prenatal androgens. These species tend to be highly competitive and promiscuous, which suggests that exposure to a lot of androgens before birth could be linked to the expression of this behaviour.

Other species, such as gibbons and many New World species, have digit ratios that suggest low levels of prenatal androgen exposure. These species were monogamous and less competitive than Old World monkeys.

The results show that Great Apes, such as orangutans and chimpanzees, expressed a different finger ratio. The analysis suggests that early androgen exposure is lower in this groups compared to Old World monkeys. Lower androgen levels could help explain why Great Apes show high levels of male cooperation and tolerance.

Emma Nelson, from the University of Liverpool's School of Archaeology, Classics and Egyptology, explains: "It is thought that prenatal androgens affect the genes responsible for the development of fingers, toes and the reproductive system. High androgen levels from a foetus or mother during pregnancy, may alter gene function and lead to subtle changes in relative digit length and the functioning of the reproductive system. Finger ratios do not change very much after birth and appear to tell us something about how very early androgens affect adult behaviour, particularly behaviour linked to mating and reproduction."

Dr Susanne Shultz, from the Institute of Cognitive and Evolutionary Anthropology at the University of Oxford, said: "Humans are unique in that they live in large multi-male, multi-female groups, but maintain strong bonds and show high levels of group cooperation in both males and females. In most other species males are competitive rather than co-operative. Research from finger ratios may help us understand more clearly the development of human sociality and its evolutionary origins."

This research, published in the American Journal of Physical Anthropology, is supported by the British Academy Centenary Research Project, Lucy to Language -- a multi-disciplinary project that aims to understand the complexities of human social evolution

Map Of Human Bacterial Diversity Shows Wide Interpersonal Differences

A University of Colorado at Boulder team has developed the first atlas of bacterial diversity across the human body, charting wide variations in microbe populations that live in different regions of the human body and which aid us in physiological functions that contribute to our health.

The study showed humans carry "personalized" communities of bacteria around that vary widely from our foreheads and feet to our noses and navels, said CU-Boulder's Rob Knight, senior author on the paper published in the Nov. 6 issue ofScience Express. The researchers found unexpectedly wide variability in bacterial communities from person to person in the study, which included nine healthy volunteers and which targeted 27 specific sites on the body.

"This is the most complete view we have yet of the microbial side of ourselves, one that our group and others will be adding to over the coming years," said Knight an assistant professor in CU-Boulder's chemistry and biochemistry department. "The goal is to find out what is normal for a healthy person, which will provide a baseline for further studies to look at people with diseased states. One of the biggest surprises was how much variation there was from person to person in a healthy group of subjects."

Co-authors on the Science Express study, the online version of the journal Science, included CU-Boulder's Elizabeth Costello, Christian Lauber, Micah Hamady and Noah Fierer, as well as Jeffrey Gordon from the Washington University School of Medicine in St. Louis.

There are an estimated 100 trillion microbes residing on and within each human being that are thought to collectively endow us with the essential traits we rely on for a variety of functions, including the proper development of our immune systems, efficient digestion of key foods and resistance to invasion by lurking microbial pathogens.

The CU-Boulder team looked high and low, analyzing microbial communities in places such as hair on the head, ear canals, nostrils, mouth, lower intestine, and 18 different skin sites ranging from foreheads and armpits, forearms, palms, index fingers, navels, the back of the knees and the soles of the feet. The team used the latest generation of massively parallel DNA sequencers and new computational tools developed at CU-Boulder.

The study subjects were sampled four times each over a three-month period, typically after showering an hour or two earlier. Microbial DNA was then isolated directly from swabs used for sampling each body site, eliminating the standard culturing step. Specific bacterial RNA genes present in the DNA were then amplified using a technique known as PCR and the genes were then sequenced with high-capacity DNA sequencers, said Knight.

The specific bacterial RNA genes amplified from each sample, which were obtained from each body site of each individual, were "tagged" during the PCR step with a sample-specific DNA barcode developed by Knight's group. This allowed the team to pool hundreds of samples together prior to a single sequencing "run," reducing the cost and increasing the speed of the work.

Specific skin sites, as well as hair, nostril and ear canal sites, had the highest levels of variability within individuals over time and were roughly on a par with the human lower intestine, according to the study. The highest diversity skin sites were the forearms, palm, index finger, back of the knee and sole of the foot. The armpits and soles of the feet showed some similarities, perhaps because they are from dark and moist environments, said Fierer.

The mouth cavity showed the least variation in diversity both within individuals and between people, according to the study. The team also found the skin "head group" -- which included forehead, external nose, external ear and hair -- was dominated by one type of bacteria, while sites on the trunk and legs were dominated by a different group.

"We have an immense number of questions to answer," said Fierer, an assistant professor in CU-Boulder's ecology and evolutionary biology department who was a co-author on the study. "Why do healthy people have such different microbial communities? Do we each have distinct microbial signatures at birth, or do they evolve as we age? And how much do they matter? We just don't know yet."

Costello, the first author on the paper who recently accepted a postdoctoral position at Stanford University, likened the analysis of human bacterial communities to charting the growth of newborns. "Just as babies are tracked for weight and height as they grow to see where they fall in relation to normal ranges, we'd like to be able to find out if there are normal ranges of microbial communities for humans that could be tracked over time."

In an intriguing microbial community "transplant" experiment, the team disinfected the forearms and foreheads of some test subjects, then "inoculated" both sites with bacterial communities harvested from the tongue. The tongue bacteria persisted longer on the forearms than foreheads, suggesting some bacterial populations more strongly prefer sebaceous, or oily sites.

"As some others have speculated, it may be that drier areas of the skin like forearms make generally more hospitable landing pads for bacteria," Costello said. The team did not find any significant difference in how easily a person's forehead or forearm could be colonized by his or her own "transplanted" microbes as opposed to those of other people.

"These patterns suggest that the search for microbial factors associated with disease, although difficult to ascertain due to the high intrinsic levels of variability among healthy individuals, may be achieved using broad profiling techniques such as those employed here," the authors wrote in Science Express.

Previous microbial studies of healthy individuals have generally focused on individual body habitats including the lower intestine, skin and mouth. The new study builds on a 2008 CU study on hand bacteria indicating that while more than 4,200 species of bacteria resided on 102 human hands, only about five species were shared by all 51 participants. The 2008 study also showed women had a greater diversity of bacteria on their palms than men.

Knight, also a faculty member in CU-Boulder's computer science department and who is a member of the university's Colorado Initiative in Molecular Biotechnology, said understanding the variation in human microbial communities holds promise for future clinical research.

"If we can better understand this variation, we may be able to begin searching for genetic biomarkers for disease," he said. The CU-Boulder researchers said it might someday be possible to identify sites on the human body that would be amenable to microbial community transplants with either natural or engineered microbial systems that would be beneficial to the health of the host.

The research was funded by the Howard Hughes Medical Institute, the National Institutes of Health, the Bill and Melinda Gates Foundation and the Crohn's and Colitis Foundation of America.

Babies' Language Learning Starts From The Womb

From their very first days, newborns' cries already bear the mark of the language their parents speak, reveals a new study published online on November 5th in Current Biology, a Cell Press publication. The findings suggest that infants begin picking up elements of what will be their first language in the womb, and certainly long before their first babble or coo.

"The dramatic finding of this study is that not only are human neonates capable of producing different cry melodies, but they prefer to produce those melody patterns that are typical for the ambient language they have heard during their fetal life, within the last trimester of gestation," said Kathleen Wermke of the University of Würzburg in Germany. "Contrary to orthodox interpretations, these data support the importance of human infants' crying for seeding language development."

Human fetuses are able to memorize sounds from the external world by the last trimester of pregnancy, with a particular sensitivity to melody contour in both music and language, earlier studies showed. Newborns prefer their mother's voice over other voices and perceive the emotional content of messages conveyed via intonation contours in maternal speech (a.k.a. "motherese"). Their perceptual preference for the surrounding language and their ability to distinguish between different languages and pitch changes are based primarily on melody.

Although prenatal exposure to native language was known to influence newborns' perception, scientists had thought that the surrounding language affected sound production much later, the researchers said. It now appears that isn't so.

Wermke's team recorded and analyzed the cries of 60 healthy newborns, 30 born into French-speaking families and 30 born into German-speaking families, when they were three to five days old. That analysis revealed clear differences in the shape of the newborns' cry melodies, based on their mother tongue.

Specifically, French newborns tend to cry with a rising melody contour, whereas German newborns seem to prefer a falling melody contour in their crying. Those patterns are consistent with characteristic differences between the two languages, Wermke said.

The new data show an extremely early impact of native language, the researchers say. Earlier studies of vocal imitation had shown that infants can match vowel sounds presented to them by adult speakers, but only from 12 weeks on. That skill depends on vocal control that just isn't physically possible much earlier, the researchers explain.

"Imitation of melody contour, in contrast, is merely predicated upon well-coordinated respiratory-laryngeal mechanisms and is not constrained by articulatory immaturity," they write. "Newborns are probably highly motivated to imitate their mother's behavior in order to attract her and hence to foster bonding. Because melody contour may be the only aspect of their mother's speech that newborns are able to imitate, this might explain why we found melody contour imitation at that early age."

The researchers include Birgit Mampe, University of Wurzburg, Wurzburg, Germany; Angela D. Friederici, Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany; Anne Christophe, Ecole Normale Superieure/CNRS, Paris, France; and Kathleen Wermke, University of Wurzburg, Wurzburg, Germany.

Domestic Horse Genome Sequenced

An international team of researchers has decoded the genome of the domestic horse Equus caballus, revealing a genome structure with remarkable similarities to humans and more than one million genetic differences across a variety of horse breeds. In addition to shedding light on a key part of the mammalian branch of the evolutionary tree, the work also provides a critical starting point for mapping disease genes in horses.

"Horses and humans suffer from similar illnesses, so identifying the genetic culprits in horses promises to deepen our knowledge of disease in both organisms," said senior author Kerstin Lindblad-Toh, scientific director of vertebrate genome biology at the Broad Institute of MIT and Harvard and a professor of comparative genomics at Uppsala University in Sweden. "The horse genome sequence is a key enabling resource toward this goal."

For centuries, horses have been close human companions. The animals were first domesticated 4,000 to 6,000 years ago and were harnessed primarily for power and transportation. Over time, as machines have become the chief sources of agricultural and industrial muscle, those roles have shifted to mainly sports and recreational activities.

Predating this coexistence, humans and horses share an evolutionary history that has implications for the health of both species. Like other mammals, the two species share much of the same DNA. Moreover, horses suffer from more than 90 hereditary diseases that show similarities to those in humans. Recognizing the need for genomic tools to foster biomedical research on horses as well as humans, a research consortium led by scientists at the Broad Institute of MIT and Harvard launched a project three years ago to decode the horse's genetic blueprint. The effort was based on a ten-year collaboration among an international group of scientists to exploit genomic technologies for the benefit of equine health known as the Horse Genome Project.

"We are especially grateful to our collaborators in the horse genetics community who participated in this project," said Lindblad-Toh. "We really could not have done this work without them."

To generate a high-quality genome sequence, the researchers analyzed DNA from an adult female Thoroughbred named Twilight. The horse's DNA was decoded using conventional capillary DNA sequencing technology (known as Sanger sequencing) to reveal a genome that is roughly 2.7 billion letters, or nucleotides, in size -- slightly larger than the genome of the domestic dog, and smaller than both the human and cow genomes.

A remarkable feature of the horse genome is the small number of chromosomal rearrangements that have occurred in horses relative to humans. During the course of evolution, parts of chromosomes can get shuffled to other locations in the genome, or they can remain in their original ancestral order, like beads on a string -- a situation known as "synteny." More than half of the horse chromosomes show synteny with a single human chromosome. This is in contrast to dogs, where the figure is less than one-third.

Another intriguing result to emerge from the horse genome analysis pertains to chromosomes and something called the "centromere." If you imagine chromosomes as X-shaped, centromeres are the central constrictions where the arms of the 'X' come together.

More than just a nexus, centromeres ensure that cells inherit copies of each chromosome during cellular division. Despite this essential role, relatively little is known about them. It is clear that they contain highly repetitive DNA sequences, but what is less clear is which comes first, the centromere or its repeats.

Lindblad-Toh and her colleagues, including Elena Giulotto of Pavia University in Italy, were surprised to uncover a region on horse chromosome 11 that contains a developing centromere, already functional, but frozen in a young state. Analyses of this budding centromere revealed no repetitive DNA, suggesting that centromeres appear first and their repeats appear later

"We don't know a lot about centromeres, particularly because they have proven so difficult to analyze by DNA sequencing," said first author Claire Wade, a former researcher at the Broad Institute and the Center for Human Genetic Research at Massachusetts General Hospital who is now a professor at the University of Sydney in Australia. "This result helps address some important questions about how centromeres evolve."

In addition to sequencing the genome of a Thoroughbred horse, the researchers also examined DNA from a variety of other horse breeds, including the American quarter horse, Andalusian, Arabian, Belgian draft horse, Hanoverian, Hakkaido, Icelandic horse, Norwegian fjord horse, and Standardbred breeds. The team surveyed the extent of genetic variation both within and across breeds to create a catalog of more than one million single-letter genetic differences (called "single nucleotide polymorphisms" or SNPs).

In a first proof-of-principle of the power of trait mapping in horses, the researchers harnessed the SNP catalog to localize the candidate mutation in the Leopard Complex or "Appaloosa spotting," in which horses' coats are mottled with striking patches of white, either with or without colored spots. Horses carrying this trait often suffer from a form of night blindness, a disorder that also afflicts humans. The researchers narrowed the list of genetic suspects in horses to 42 associated SNPs, including two candidate mutations residing near a gene involved in pigmentation.

"This demonstrates the utility of the horse for disease gene mapping," said Wade. "By making these resources freely available to the scientific community, we hope that many new results will flow from them in the coming years."

The research was funded by the National Human Genome Research Institute as well as the Dorothy Russell Havemeyer Foundation, the Volkswagen Foundation, the Morris Animal Foundation and the Programmi di Ricerca Scientifica di Rilevante Interesse Nazionale.

Gene Therapy Technique Slows Brain Disease ALD Featured In Movie 'Lorenzo's Oil'

A strategy that combines gene therapy with blood stem cell therapy may be a useful tool for treating a fatal brain disease, French researchers have found.

These findings appear in the 6 November 2009 issue of the journalScience, which is published by AAAS, the nonprofit science society.

In a pilot study of two patients monitored for two years, an international team of researchers slowed the onset of the debilitating brain disease X-linked adrenoleukodystrophy (ALD) using a lentiviral vector to introduce a therapeutic gene into patient's blood cells. Although studies with larger cohorts of patients are needed, these results suggest that gene therapy with lentiviral vectors, which are derived from disabled versions of human immunodeficiency virus (HIV), could potentially become instrumental in treating a broad range of human disorders.

"This is the first time we were able to successfully use an HIV-derived lentivirus vector for gene therapy in humans, and also the first time that a very severe brain disease has been treated with efficacy by gene therapy. We've demonstrated that this HIV-derived lentivirus vector works as was hoped for so many years," said coauthor Patrick Aubourg, professor of pediatrics at University Paris-Descartes and head of a research unit at Inserm-University Paris Descartes.

Featured in the movie "Lorenzo's Oil," ALD is a severe hereditary condition caused by a deficiency of a protein called ALD that is involved in fatty acid degradation. Sufferers steadily lose their myelin sheath, the protective layer that coats nerve fibers in the brain. Without myelin the nerves lose function, leading to increasing physical and mental disability in patients. X-linked ALD, the most common form of the disease, affects boys starting at age 6-8 years of age and death usually occurs before the patients reach adolescence.

Bone marrow transplants typically slow progression of the disease because the donor marrow includes cells that develop into myelin-producing cells. However, finding a matching bone marrow donor can be a challenging and lengthy process, and the procedure carries considerable risks.

Genetically correcting the blood stem cells in the patients' own bone marrow may prove to be a valuable alternative approach when no matched donors are available.

In most gene therapy studies, a working gene is inserted into the genome to replace a dysfunctional, disease-causing gene. A carrier molecule called a vector is used to deliver the therapeutic gene into the patient's cells. Vectors are typically the backbones of viruses that have been genetically altered to carry normal human DNA. Scientists have recently turned to vectors based on the lentivirus genus of retroviruses, which includes HIV. Lentiviral vectors are a type of retrovirus that can infect both dividing and nondividing cells, and are thought to provide long-term and stable gene expression, unlike other retroviruses.

"The HIV-derived lentivirus vector allows expression of the therapeutic gene in principle for life, because the therapeutic gene is inserted in the chromosomes -- the genome. Therefore, cells that derive from the initially corrected cells, stem cells in particular, will continue to express the therapeutic gene forever," said Aubourg.

In the study, blood stem cells were removed from the patients and genetically corrected in the lab, using a lentiviral vector to introduce a working copy of the ALD gene into the cells. The modified cells were then infused back into the patients' after they had received a treatment that destroyed their bone marrow. Two years later, healthy ALD proteins were still detectable in both patients' blood cells. Encouragingly, both patients showed neurological improvement and a delay in disease progression comparable to that seen with bone marrow transplants.

The healthy ALD protein was expressed in about 15 percent of blood cells, yet surprisingly this low level was sufficient to slow brain disease in ALD. "This percentage of correction will not be sufficient for all diseases," warns Aubourg. "There is a lot of work to be done to make this gene therapy vector more powerful, less complicated, and less expensive. This is only the beginning," he said.

Gene therapy is not without serious risks. Like other retrovirus vectors, the HIV-derived lentivirus vector is tasked with inserting the therapeutic gene in the chromosomes of the patients' cells. In a worst case scenario, this action could disturb the biology of the cells and patients could end up with leukemia; this outcome has occurred in past gene therapy trials. "The HIV-derived lentivirus vector basically has this same risk, although the design of the vector makes patients less prone to this side effect," said Aubourg.

This research was funded by INSERM (National Institute of Health and Research Medical), Assistance Publique des Hôpitaux de Paris, PHRC programs, the Deutsche Forchungsgemeinschaft and the German Ministry of Education and Research, the European Leukodystrophy Association, the Association Française contre les Myopathies, the Stop ALD Foundation and University Paris-Descartes.

Related Press Briefing in France: A press conference related to the forthcoming Science paper, "Hematopoietic Stem Cell Gene Therapy with a Lentiviral Vector in X-linked Adrenoleukodystrophy," by Dr. Nathalie Cartier and colleagues is planned for 2:00 p.m. in Paris on Wednesday, 4 November

'Spoonful Of Sugar' Makes The Worms' Life Span Go Down

If worms are any indication, all the sugar in your diet could spell much more than obesity and type 2 diabetes. Researchers reporting in the November issue of Cell Metabolism, a Cell Press publication, say it might also be taking years off your life.

By adding just a small amount of glucose to C. elegans usual fare of straight bacteria, they found the worms lose about 20 percent of their usual life span. They trace the effect to insulin signals, which can block other life-extending molecular players.

Although the findings are in worms, Cynthia Kenyon of the University of California, San Francisco, says there are known to be many similarities between worms and people in the insulin signaling pathways. (As an aside, Kenyon says she read up on low-carb diets and changed her eating habits immediately -- cutting out essentially all starches and desserts -- after making the initial discovery in worms. The discovery was made several years ago, but had not been reported in a peer-reviewed journal until now.)

"In the early 90s, we discovered mutations that could double the normal life span of worms," Kenyon said. Those mutations effected insulin signals. Specifically, a mutation in a gene known as daf-2 slowed aging and doubled life span. That longer life depended on another "FOXO transcription factor" called DAF-16 and the heat shock factor HSF-1.

Now, the researchers show that those same players are also involved in numbering the days of worms who are fed on glucose. In fact, glucose makes no difference to the life span of worms that lack DAF-16 or HSF-1, they show. Glucose also completely prevents the life-extending benefits that would otherwise come with mutations in the daf-2 gene.

Ultimately, worms fed a steady diet containing glucose show a reduction in aquaporin channels that transport glycerol, one of the ingredients in the process by which the body produces its own glucose. "If there is not enough glucose, the body makes it with glycerol," Kenyon explained. That glycerol has to first get where it needs to go, which it does via the aquaporin channels.

Further studies are needed to see if these same effects of sugar can be seen in mice, or even people. But there is reason to think they may.

"Although we do not fully understand the mechanism by which glucose shortens the life span of C. elegans, the fact that the two mammalian aquaporin glycerol-transporting channels are downregulated by insulin raises the possibility that glucose may have a life-span-shortening effect in humans, and, conversely, that a diet with a low glycemic index may extend human life span," the researchers write. Kenyon also points to recent studies that have linked particular FOXO variants to longevity in several human populations, making the pathway the first with clear effects on human aging.

She says the findings may also have implications for drugs now in development for the treatment of diabetes, which are meant to block glucose production by inhibiting glycerol channels. The new findings "raise a flag" that glycerol channels might be doing something else, she says, and that drugs designed to block them might have a downside.

The researchers include Seung-Jae Lee, University of California, San Francisco, CA, Pohang University of Science and Technology, Pohang, Kyungbuk, South Korea; Coleen T. Murphy, University of California, San Francisco, CA; and Cynthia Kenyon, University of California, San Francisco, CA