Algebra adds value to mathematical biology education (VBI)

As mathematics continues to become an increasingly important component in undergraduate biology programs, a more comprehensive understanding of the use of algebraic models is needed by the next generation of biologists to facilitate new advances in the life sciences, according to researchers at Sweet Briar College and the Virginia Bioinformatics Institute (VBI) at Virginia Tech. In the paper, "Mathematical Biology Education: Beyond Calculus," which is featured in the July 31, 2009 issue of Science, VBI Professor Reinhard Laubenbacher and Sweet Briar College Mathematical Sciences Professor Raina Robeva highlight algebraic models as one of the diverse mathematical tools needed in the professional development of up-and-coming life scientists. Despite this critical need, the authors explain, algebraic models have played a less substantial role in undergraduate curricula than other methods.

"Discrete-time algebraic models created from finite-state variables, such as Boolean networks, are increasingly being used to model a variety of biochemical networks, including metabolic, gene regulatory, and signal transduction networks," says Laubenbacher. "Often, researchers do not have enough of the information required to build detailed quantitative models. Algebraic models need less information about the system to be modeled, making them useful for instances where quantitative information may be missing. All the work that goes into building them can then be used to construct detailed kinetic models, when additional information becomes available. In addition, algebraic models are much more intuitive than differential equations models, which makes them more easily accessible to life scientists." Review the complete article on Eureka Alert

New computer simulation helps explain folding in important cellular protein

Most parts of living organisms come packaged with ribbons. The ribbons are proteins—chains of amino acids that must fold into three-dimensional structures to work properly. But when for any reason the ribbons fold incorrectly, bad things can happen, and in humans misfolded-protein disorders include Alzheimer's and Parkinson's diseases. Scientists have for the past three decades tried to understand what makes proteins fold into functional units and why it happens, and several breakthroughs have occurred through computer modeling—a field that dramatically increases analytical speed.

Now, scientists at the University of Georgia have created a two-step computer simulation (using an important process called the Wang-Landau algorithm) that sheds light on how a crucial protein—glycophorin A—becomes an active part of living cells. The new use of Wang-Landau could lead to a better understanding of the controlling mechanisms behind protein folding.
"Our goal is to present the methodology in a clear, self-consistent way, accessible to any scientist with knowledge of Monte Carlo simulations," said David Landau, distinguished research professor of physics at the University of Georgia and director of the Center for Simulational Physics.

The research was just published in The Journal of Chemical Physics. Authors of the paper are Clare Gervais and Thomas Wüst, formerly of UGA and now employed in Switzerland; Landau, and Ying Xu, Regents-Georgia Research Alliance Eminent Scholar and professor of bioinformatics and computational biology, also at UGA. The research was supported by grants from the National Institutes of Health and the National Science Foundation. Landau and Xu are in UGA's Franklin College of Arts and Sciences. Read the complete study results via Eureka Alert

UBC researchers help push for standard DNA barcodes for plants

Two University of British Columbia researchers are part of an international team recommending standards for the DNA barcoding of land plants, a step they hope will lead to a universal system for identifying over 400,000 species, and ultimately boost conservation efforts. Barcodes based on portions of DNA – the taxonomical equivalent to UPC barcodes on products – have already emerged as a viable solution for uniquely identifying species in many animal groups. However, because DNA varies less between plant species, determining which portions of plant DNA to use as a unique identifier has been a thorny issue. The research team, which included scientists from more than 20 institutions around the world, selected two genomic regions – genes referred to as rbcL and matK – as the best candidates from which to generate barcode data. Results of the four-year study are published this week in the Proceedings of the National Academy of Sciences.

"It's a pragmatic first step in solving a complex issue," says UBC botanist and Associate Professor Sean Graham, who conducted research on the project and helped author the study. "We've selected areas of DNA that are available in the vast majority of plants, could easily and accurately be sequenced, and when combined, provide a near-unique signature for barcoding." See the complete press release on EurekaAlert

After dinosaurs, mammals rise but their genomes get smaller

Evidence buried in the chromosomes of animals and plants strongly suggests only one group -- mammals -- have seen their genomes shrink after the dinosaurs' extinction. What's more, that trend continues today, say Indiana University Bloomington scientists in the first issue of a new journal, Genome Biology and Evolution. The scientists' finding might seem counter-intuitive, given that the last 65 million years have seen mammals expand in diversity and number, not to mention dominance in a wide variety of ecological roles. But it is precisely their success in numbers that could have led to the contraction of their genomes.

"Larger population sizes make natural selection more efficient," said IU Bloomington evolutionary biologist Michael Lynch, who led the study. "If we are correct, we have shown how to bring ancient genomic information together with the paleontological record to learn more about the past."

And the present. Lynch says the data he and his colleagues analyzed suggest human genomes are still undergoing a contraction -- though you shouldn't expect to see noticeable changes in our chromosomes for a few million years yet. Lynch's group examined the genomes of seven mammals, eight non-mammalian animals and three plants, specifically with regard for the long terminal repeat (LTR) sequences of transposable elements, a curious sort of "jumping" genetic sequence initially dropped into genomes by viruses. IU School of Informatics (Bloomington) bioinformaticians Mina Rho and Haixu Tang oversaw the survey of mammalian and non-mammalian genomes. Read the complete press release and research findings via the IU portal

Technology on way to forecasting humanity's needs

Much as meteorologists predict the path and intensity of hurricanes, Indiana University's Alessandro Vespignani believes we will one day predict with unprecedented foresight, specificity and scale such things as the economic and social effects of billions of new Internet users in China and India, or the exact location and number of airline flights to cancel around the world in order to halt the spread of a pandemic.

In tomorrow's (July 24) "Perspectives" section of the journal Science, Vespignani writes that advances in complex networks theory and modeling, along with access to new data, will enable humans to achieve true predictive power in areas never before imagined. This capability will be realized as the one wild card in the mix -- the social behavior of large aggregates of humans -- becomes more definable through progress in data gathering, new informatics tools and increases in computational power.

Vespignani is the James H. Rudy Professor of Informatics and adjunct professor of physics and statistics at IU, where he is also the director of the Center for Complex Networks and Systems Research (CNetS) at IU's Pervasive Technology Institute and the IU Bloomington School of Informatics and Computing. Researchers have already shown they can track the movement of as many as 100,000 people at a time over six months using mobile phone data, and use worldwide currency traffic as a proxy for human mobility. There are sensors and tags generating data at micro, one-to-one interaction levels, much as Bluetooth, Global Positioning Systems and WiFi leave behind detailed traces of our lives. Read the complete research findings via the Eureka Alert Bioinformatics portal

Gene linked to increasingly common type of blood cancer (TGen)

California and Arizona researchers have identified a gene variant that carries nearly twice the risk of developing an increasingly common type of blood cancer, according to a study published online today by the science journal Nature Genetics. Investigators at the University of California, Berkeley (UC Berkeley) and at the Translational Genomics Research Institute (TGen) found that mutations in a gene called C6orf15, or STG, are associated with the risk of developing follicular lymphoma. This is a cancer of the body's disease-fighting network whose rates have nearly doubled in the past three decades.

In the first genome-wide association study of non-Hodgkin lymphoma, scientists at UC Berkeley and TGen identified a SNP – a single nucleotide polymorphism – that could determine susceptibility to follicular lymphoma. The SNP, a DNA variant within the more than 3-billion base pairs in the human genome, was identified as rs6457327. The study was led by Dr. Christine Skibola, Associate Adjunct Professor of Environmental Health Sciences at UC Berkeley's School of Public Health, and by Dr. Kevin M. Brown, an Associate Investigator in the Integrated Cancer Genomics Division of TGen, a Phoenix-based, non-profit biomedical research institute. Read the complete study results on the TGen web site

Surviving mass extinction by leading a double life (Institute of Genetics)

Drifting across the world's oceans are a group of unicellular marine microorganisms that are not only a crucial source of food for other marine life — but their fossils, which are found in abundance, provide scientists with an extraordinary record of climatic change and other major events in the history of the earth. Now, planktonic foraminifera — single-celled shell building members of the marine microplankton community — have given up a secret of their very own. A team of experts, including scientists from The University of Nottingham, have presented remarkable evidence that planktonic foraminifera may have survived mass extinction by taking refuge on the sea floor.

Dr Chris Wade from the Institute of Genetics, said: "Using genetic data we have been able to prove that the planktonic species Streptochilus globigerus and the benthic — sediment living — foraminiferan Bolivina variabilis are one and the same biological species. Moreover, geochemical evidence shows that this species actively grows within the open-ocean surface waters, thus occupying both planktonic and benthic domains. Such ecologically-flexible species are eminently suited to the recolonisation of the extinction-susceptible planktonic domain following mass extinctions events, such as the end-Cretaceous event." ead the complete article on the University of Nottingham web site

Integrated Biobank of Luxembourg gears up

A partnership between Luxembourg and the Translational Genomics Research Institute (TGen) begins in earnest this month with the arrival of a new CEO and the advent of a new building for the Integrated Biobank of Luxembourg (IBBL). The IBBL is seen as an international collection, repository, analysis and distribution point for blood, serum, saliva, tumors and other biospecimen samples to assist investigators worldwide in scientific research.

"I think it's fantastic. This project helps Luxembourg with their long-term goals, while providing Arizona with significant investments. At the same time, it holds the promise of furthering scientific investigations on a global basis,'' said Dr. Jeffrey Trent, President and Research Director. "We've already made a lot of progress.''

The IBBL is part of a 140-million-euro effort (more than $190 million) over five years to help turn Luxembourg develop into one of Europe's foremost biomedical centers – one uniquely focused on diagnostic biomarkers. The effort is wide-ranging and dynamic in its goals of improving patient care while lowering healthcare costs. See the TGen web site for complete scientific details

Complete fluke? Genome sequencers crack parasite genome

Researchers have today published the complete genome sequence of the Schistosoma mansoni, a parasitic worm – commonly known as a blood fluke – that causes devastating disease. The World Health Organization ranks schistosomiasis as a neglected disease of the poor, affecting 210 million people in 76 countries, and each year causing 280,000 deaths in sub-Saharan Africa alone. The international team has identified several potential new drug targets and the genome sequence will be invaluable to scientists searching for new methods to treat and eradicate the disease. Schistosomiasis has devastating global impact, yet research has been neglected for years. In part, this is due to the huge challenges that biologists face when studying the organism. Currently, there is only one drug treatment that is used to treat schistosomiasis and – with mounting fears that the parasites will become resistant – researchers have been looking at ways to find new drug targets. Today's publication provides the first steps.

"This genome sequence catapults schistosomiasis research into a new era," says Dr Matthew Berriman of the Wellcome Trust Sanger Institute and first author and co-leader of the study. "It provides a foundation for understanding aspects of the parasite's complex biology as well as a vehicle to immediately identify new targets for drug treatment." See the complete survey results on the Wellcome Trust Sanger Institute web site

Reviews of microbial gene language published in special issue of Trends in Microbiology

Ten articles describing how a universal language to describe genes is bringing benefits to the study of the microbial world have been published in a special issue of Trends in Microbiology, co-edited by Virginia Bioinformatics Institute professor Brett Tyler. The Gene Ontology is a powerful language that gives researchers a shared vocabulary to describe disease-related and beneficial interactions between a microbe and its host. By allowing scientists to link experimental results to a computer-readable language, the Gene Ontology provides scientists with an important bridge between specific experiments that characterize gene function and larger-scale, systems biology efforts to provide a global picture of host-microbe interactions. The Gene Ontology was started in 1998 by a consortium of three databases for the organisms yeast, fruit fly, and mouse. The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium joined the effort in 2004 to focus on microbe-plant associations, which include the many relationships of plants with bacteria, fungi, oomycetes, and nematodes.

Candace Collmer of Wells College, who helped launch PAMGO in 2003, noted: "A crucial step at the beginning of the PAMGO project was the realization that plant pathogenesis is only one possible outcome along a continuum of broadly-defined, symbiotic microbial-host interactions ranging from detrimental to beneficial. Since all are types of intimate interactions, and because microbes initiating these different types have common needs in approaching a host, be it plant or animal, we initially crafted broad terms for describing "symbiont" gene functions in an attempt to highlight these similarities across a diverse set of microbes. For these and the more specific terms that followed, an important contribution of PAMGO to the Gene Ontology was the development of terms that describe the functions of gene products that are made by one organism, for example the microbe, but actually act in a different organism, namely the host." See the Eureka Alert Bioinformatics service has published the press release

Agilent Introduces DNA Capture Microarray to Streamline Next-Gen Sequencing Studies

Agilent Technologies Inc. (NYSE:A) today introduced the SureSelect DNA Capture Array, which easily removes a major bottleneck in small-scale DNA studies by letting scientists sequence only genomic areas of interest with next-generation sequencing (NGS) instruments. Designed for smaller studies, the SureSelect DNA Capture Arrays complement Agilent’s in-solution SureSelect Target Enrichment System, which is designed for medium to large-scale NGS studies of tens through thousands of samples, including automated high-throughput workflows.

“If a lab is doing next-generation sequencing, Agilent offers a portfolio of products that make those experiments run faster, better and/or less expensively,” said Fred Ernani, Ph.D., Agilent emerging genomics applications product manager. “SureSelect DNA Capture Array is well suited for the researcher who needs a cost-effective target enrichment tool for a small number of samples.” See the Agilent press release for complete technical details

New drugs faster from natural compounds: A UC San Diego breakthrough

Researchers have invented computational tools to decode and rapidly determine whether natural compounds collected in oceans and forests are new—or if these pharmaceutically promising compounds have already been described and are therefore not patentable. This University of California, San Diego advance will finally enable scientists to rapidly characterize ring-shaped nonribosomal peptides (NRPs)—a class of natural compounds of intense interest due to their potential to yield or inspire new pharmaceuticals. The study will be published in the July 13 online issue of journal Nature Methods.

"These advances will speed the process by which we discover and describe new and biologically active molecules from organisms such as marine cyanobacteria, also known as blue-green algae. This, in turn, will accelerate the timeline for bringing new experimental therapies into clinical application," said William Gerwick, an author on the paper and a professor with the UC San Diego Scripps Institution of Oceanography Center for Marine Biotechnology and Biomedicine and the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences. See Eureka Alert Bioinformatics for complete results

Mystery E. coli genes essential for survival of many species (BBSRC)

Scientists have shown that E. coli – one of the best known and extensively studied organisms in the world – remains an enigma that may hold the key to human diseases, such as cancer. The team, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and based at the University of Dundee has examined the genome sequence of this workhorse of the laboratory and spotted three previously unknown genes that, it turns out, are essential for the survival of E. coli and one out of the three could also be implicated in cancer or developmental abnormalities in humans. These mystery genes are also found in numerous other creatures, suggesting a vital role for them across many species. The research will be published in the 1 August edition of the Journal of Bacteriology.

The effort over recent years to sequence genomes of various important species has uncovered many previously unknown genes. This has given scientists the opportunity to choose to study these genes now, rather than waiting for them to make themselves known serendipitously e.g. when they are implicated in disease. Professor Tracy Palmer and her colleagues have taken three genes identified through sequencing of the E. coli genome and studied them to discover their significance. See the BBSRC press release for compete study results

Systems biology recommended as a clinical approach to cancer

Four researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech and their colleagues at the Wake Forest University School of Medicine are advocating the use of systems biology as an innovative clinical approach to cancer. This approach could result in the development of improved diagnostic tools and treatment options, as well as potential new drug targets to help combat the many potentially fatal types of the disease. In an upcoming paper in Biochimica et Biophysica Acta, the international journal of biochemistry, biophysics and molecular biology, the team highlights the usefulness of a systems biology approach in developing a comprehensive view of cancer diseases, which will help researchers better understand the complex processes related to cancer progression, diagnosis, and treatment. Systems biology brings together mathematical modeling, simulations, and quantitative experiments, allowing researchers to use the data of one of the approaches to repeatedly define the framework of the other approaches. Biochemical networks are central to biological function, while computer models provide a particularly useful way to understand their workings. Biochemical models are the ideal means to design and predict the effect of interventions, such as cancer treatments.

"One of the goals of this paper is to show the potential benefits that can result from moving the use of systems biology techniques closer to the clinic," explained VBI Professor Reinhard Laubenbacher. "We believe this kind of shift is very possible. For example, mathematical models could integrate patient characteristics to help researchers determine the features of dynamic processes linked to cancer progression, diagnosis, and treatment. Systems biology has an increasingly important role in cancer research and treatment, especially as mathematical modelers, biologists, and clinicians continue working together. Through these transdisciplinary efforts, the needs of the clinic can directly impact work in the laboratory." ee the Eureka lert article for complete details

Scientists identify cholesterol-regulating genes

Scientists at the European Molecular Biology Laboratory (EMBL) and the University of Heidelberg, Germany, have come a step closer to understanding how cholesterol levels are regulated. In a study published today in the journal Cell Metabolism, the researchers identified 20 genes that are involved in this process. Besides giving scientists a better idea of where to look to uncover the mechanisms that ensure cholesterol balance is maintained, the discovery could lead to new treatments for cholesterol-related diseases.

"This finding may open new avenues for designing targeted therapies, for example by looking for small molecules that could impact these genes," says Heiko Runz, whose group at the University Clinic Heidelberg carried out the research together with Rainer Pepperkok's lab at EMBL. High levels of cholesterol in the bloodstream are a major risk factor for atherosclerosis and coronary heart disease, one of the leading causes of death in developed countries today. Nevertheless, cholesterol is an important cellular component: 90% of the cholesterol in our bodies is inside our cells, where it does not cause any harm. Blood cholesterol levels are partly regulated by cells taking up cholesterol from the bloodstream, a process Runz and his colleagues are helping to unveil. See the full Cell Metabolism article for all the details

Research Reveals What Drives Lung Cancer's Spread

A new study by researchers at Memorial Sloan-Kettering Cancer Center (MSKCC) reveals the genetic underpinnings of what causes lung cancer to quickly metastasize, or spread, to the brain and the bone - the two most prominent sites of lung cancer relapse. The study will be published online in the journal Cell on July 2. Researchers discovered that the same cellular pathway that has been shown to be involved with the spread of colorectal cancer is also responsible for providing lung cancer with an enhanced ability to infiltrate and colonize other organs without delay and with little need to adapt to its new environment. This is a dramatic departure from other cancers, like breast cancer, in which recurrences tend to emerge following years of remission, suggesting that such cancer cells initially lack - and need time to acquire - the characteristics and ability to spread to other organs.

The investigators hypothesized that because not all lung tumors have spread before diagnosis and removal, metastasis may depend on some added feature beyond the mutations that initiate these tumors. See the MSKCC press release for complete study results

New e-science service could accelerate cancer research (Biocatalgue.org)

The University of Manchester and the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) have launched a major new e-science resource for biologists – which could accelerate research into treatments for H1N1 flu and cancer.

Biocatalogue.org, a centralised registry of curated life science Web Services, is being officially launched today (Wednesday 1 July) at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology conference (ISMB-ECCB 2009) in Stockholm. This type of systematic access has the potential to significantly accelerate the work of researchers in the medical, agronomical and pharmaceutical fields. The service allows researchers to discover, annotate, register and use biological web-based services. See the Biocatalogue.org web site for further details