Systems biology approach provides insulin resistance insights (UC San Diego)

Researchers from the University of California, San Diego recently offered the sharpest-yet picture of how core biochemical pathways in skeletal muscle cells and fat cells are altered in people who suffer from insulin resistance—a primary defect in type 2 diabetes and obesity. Taking a systems biology approach, the bioengineers and medical researchers also determined how a common class of drugs for treating insulin resistance—TZDs—alter these same core pathways. This led the team to uncover previously unknown effects of TZDs and insights that could lead to improved drug therapies for insulin resistance.

The team—led by investigators from the UC San Diego Jacobs School of Engineering and School of Medicine—recently published their findings in the journal Proceedings of the National Academy of Sciences (PNAS).

"When you are insulin resistant, your metabolism suffers. If you take a TZD for your insulin resistance, will the drug fix the dysfunction in muscle and fat tissues? Will these changes be functionally related to drug efficacy? These are some of the questions we addressed in our new study," say UC San Diego faculty members Dr. Shankar Subramaniam and Dr. Dorothy Sears, co-corresponding authors of the new paper. The collaborative project involved Dr. Subramaniam's Bioinformatics and Systems Biology laboratory in the Department of Bioengineering at the Jacobs School of Engineering, Dr. Sears and her colleagues in the Department of Medicine, and Pfizer, Inc. Visit the UC san Diego press room for complete research findings

First-ever blueprint of a minimal cell more complex than expected (EMBL)

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 today 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. Visit the EMBL portal for complete details

Systems biology approach provides insulin resistance insights

Researchers from the University of California, San Diego recently offered the sharpest-yet picture of how core biochemical pathways in skeletal muscle cells and fat cells are altered in people who suffer from insulin resistance—a primary defect in type 2 diabetes and obesity. Taking a systems biology approach, the bioengineers and medical researchers also determined how a common class of drugs for treating insulin resistance—TZDs—alter these same core pathways. This led the team to uncover previously unknown effects of TZDs and insights that could lead to improved drug therapies for insulin resistance.

The team—led by investigators from the UC San Diego Jacobs School of Engineering and School of Medicine—recently published their findings in the journal Proceedings of the National Academy of Sciences (PNAS).

"When you are insulin resistant, your metabolism suffers. If you take a TZD for your insulin resistance, will the drug fix the dysfunction in muscle and fat tissues? Will these changes be functionally related to drug efficacy? These are some of the questions we addressed in our new study," say UC San Diego faculty members Dr. Shankar Subramaniam and Dr. Dorothy Sears, co-corresponding authors of the new paper. The collaborative project involved Dr. Subramaniam's Bioinformatics and Systems Biology laboratory in the Department of Bioengineering at the Jacobs School of Engineering, Dr. Sears and her colleagues in the Department of Medicine, and Pfizer, Inc.

Circadian KaiC Phosphorylation: A Multi-Layer Network (PLoS)

Circadian KaiC phosphorylation in cyanobacteria reconstituted in vitro recently initiates a series of studies experimentally and theoretically to explore its mechanism. In this paper, we report a dynamic diversity in hexameric KaiC phosphoforms using a multi-layer reaction network based on the nonequivalence of the dual phosphorylation sites (S431 and T432) in each KaiC subunit. These diverse oscillatory profiles can generate a kaleidoscopic phase modulation pattern probably responsible for the genome-wide transcription rhythms directly and/or indirectly in cyanobacteria. Particularly, our model reveals that a single KaiC hexamer is an energy-based, phosphorylation-dependent and self-regulated circadian oscillator modulated by KaiA and KaiB. We suggest that T432 is the main regulator for the oscillation amplitude, while S431 is the major phase regulator. S431 and T432 coordinately control the phosphorylation period.

Robustness of the Kai network was examined by mixing samples in different phases, and varying protein concentrations and temperature. Similar results were obtained regardless of the deterministic or stochastic method employed. Therefore, the dynamic diversities and robustness of Kai oscillator make it a qualified core pacemaker that controls the cellular processes in cyanobacteria pervasively and accurately. Visit the PLoS portal to review the abstract or order this article

TGen Drug Development (TD2) establishes European footprint

TGen Drug Development (TD2) and the Institut Paoli-Calmettes (IPC) have forged a strategic alliance that will enable both to maximize their worldwide contributions in the treatment of cancer patients. The partnership between TD2, a Scottsdale subsidiary of the Phoenix-based Translational Genomics Research Institute (TGen), and Marseille, France-based IPC’s comprehensive cancer center will enable both non-profit institutes to speed research discoveries to patients with cancer.
Both organizations will expand their clinical research network to evaluate new therapies in the U.S. and Europe in an effort to more quickly introduce new drugs into clinical trials. Teams from both TD2 and IPC will focus their efforts on discovering molecular alterations within cancers and finding biomarkers that will help identify new therapeutic targets that can be used to tailor treatments for individual patients. The TGen portal provides full details of this partnership

A curated online resource for protein function and structure based on evolutionary constraint analyses (Genome Research)

ProPhylER (Protein Phylogeny and Evolutionary Rates) is a next-generation curated proteome resource that uses comparative sequence analysis to predict constraint and mutation impact for eukaryotic proteins. Its purpose is to inform any research program for which protein function and structure are relevant, by the predictive power of evolutionary constraint analyses. ProPhylER currently has nearly 9000 clusters of related proteins, including more than 200,000 sequences. It serves data via two interfaces.

The “ProPhylER Interface” displays predictive analyses in sequence space; the “CrystalPainter” maps evolutionary constraints onto solved protein structures. Here we summarize ProPhylER's data content and analysis pipeline, demonstrate the use of ProPhylER's interfaces, and evaluate ProPhylER's unique regional analysis of evolutionary constraint. The high accuracy of ProPhylER's regional analysis complements the high resolution of its single-site analysis to effectively guide and inform structure–function investigations and predict the impact of polymorphisms. Review the entire abstract or purchase this article via the Genome Research portal

Beyond genomics, biologists and engineers decode the next frontier (Molecular & Cellular Proteomics)

A team of Princeton biologists and engineers has dramatically improved the speed and accuracy of measuring an enigmatic set of proteins that influences almost every aspect of how cells and tissues function. The new method offers a long-sought tool for studying stem cells, cancer and other problems of fundamental importance to biology and medicine. The research allows scientists an unprecedented look at a special class of proteins called histones, which are at the core of every chromosome and control the way instructions in DNA are carried out. Despite rapid progress in understanding the information encoded in DNA and genes, scientists have achieved much less insight into the so-called "histone code," which determines why a gene in one cell functions differently than the same gene in another cell.

"We take a cutting-edge approach to a field that has been using more or less the same techniques for the past 15 years," said Benjamin Garcia, assistant professor of molecular biology, who supervised the experimental aspects of the study.

The technique reduces by a factor of 100 the time it takes to analyze histones, while requiring far less sample material and achieving much more nuanced results than existing methods, said Christodoulos Floudas, the Stephen C. Macaleer '63 Professor in Engineering and Applied Science, who oversaw computational aspects of the research. Review the complete study findings via the Princeton School of Engeering and Applied Science or Molecular and Cellular Proteomics portals: www.mcponline.org

Cross-country runabouts - immune cells on the move (Max Planck Institute)

Scientists from the Max Planck Institute (MPI) of Biochemistry in Martinsried near Munich, Germany, have now deciphered the mechanism that illustrates how these mobile cells move on diverse surfaces. "Similar to a car, these cells have an engine, a clutch and wheels which provide the necessary friction," explains Michael Sixt, a research group leader at the MPI of Biochemistry. The results, which were developed in cooperation with colleagues from the MPI for Metals Research in Stuttgart, Germany, have now been published in Nature Cell Biology.

White blood cells, also called leukocytes or immune cells, fight infections in the human body in many different ways. As defence cells, they are able to invade infected tissues, detect and eliminate pathogens. Also foreign structures and wreckage of the body’s own cells are disposed of with their help. To cope with these tasks, the cells move a hundred fold faster than other cell types. Thereby, immune cells follow certain attractants which are released by the body’s own cells or the pathogens. Energy transfer on a molecular level Cells have to generate the necessary energy from the inside in order to move forward. This task is carried out by the cytoskeleton, a network of proteins which stretches through the cell’s complete interior. It can expand and form finger-like extensions and likewise retract them.

However, this deformation is not enough to make a cell move. "Similar to a car, the energy has to be transferred onto the street," says Dr. Sixt. "We need a clutch and wheels." For this purpose, every cell carries special cell anchors on their surface: the integrins. These proteins span the envelope of the cells and are directly connected to the cell’s cytoskeleton. On the outside, these anchors can stick to other cells and tissues and thus form a connection to the outside world. "The connection between the cytoskeleton and the integrin matches the clutch, the connection between the integrin and the outside world corresponds to the grasp of the wheels." says Dr. Sixt. Reivew the full press release via the MPI portal or in the current issue of Nature Cell Biology: www.nature.com/ncb/index.html

In-solution Method for Streamlining Next-Generation Genome Sequencing Shown to be Uniform

Researchers from the Moores University of California San Diego (UCSD) Cancer Center, The Scripps Institute, and Agilent Technologies have shown that “solution enrichment,” followed by next generation sequencing is highly accurate and reproducible, and it can make large scale population studies economically feasible without upfront expenditure for capital equipment. The researchers sequenced the exons and potential regulatory elements of 622 genes distributed across the genome that are candidate intervals for playing a role in healthy aging. They also included three contiguous genomic intervals containing variants associated with age-related diseases for a total of 3.6Mb using only standard molecular biology equipment and the Agilent SureSelect Target Enrichment System. They were able to call known SNPs with 99.7% accuracy, as well as tens of novel variants, the vast majority of them heterozygotes.

The researchers performed the sequencing on an Illumina Genome Analyzer and used SureSelect capture probes in-solution manufactured by Agilent Technologies for target enrichment. The article states that, in recent years, genome-wide association studies have identified “compelling” associations between more than 350 locations along the human genome and common complex traits. But a much larger number of samples must be analyzed to move beyond statistical associations to pinpoint the exact causes of these traits. The article explains that current methods of DNA sequencing cost too much for such large-scale population studies. The authors write, “Next-generation sequencing technologies and their increased capacity have made it feasible to efficiently sequence hundreds of megabases of DNA. However, the current costs for sequencing entire human genomes make this approach prohibitively expensive for population studies.”

“SureSelect is a very scalable capture method,” said Olivier Harismendy, Ph.D., project scientist at the Moores UCSD Cancer Center. “It allows you to process multiple samples simultaneously. All you need is already in your lab: a 96-well plate, a magnet and a multichannel pipetter, and here is your high-throughput.” Download the complete study findings by clicking on the title to this article

Petascale computing tools could provide deeper insight into genomics (Georgia Tech)

Technological advances in high-throughput DNA sequencing have opened up the possibility of determining how living things are related by analyzing the ways in which their genes have been rearranged on chromosomes. However, inferring such evolutionary relationships from rearrangement events is computationally intensive on even the most advanced computing systems available today.

Research recently funded by the American Recovery and Reinvestment Act of 2009 aims to develop computational tools that will utilize next-generation petascale computers to understand genomic evolution. The four-year $1 million project, supported by the National Science Foundation's PetaApps program, was awarded to a team of universities that includes the Georgia Institute of Technology, the University of South Carolina and The Pennsylvania State University.

"Genome sequences are now available for many organisms, but making biological sense of the genomic data requires high-performance computing methods and an evolutionary perspective, whether you are trying to understand how genes of new functions arise, why genes are organized as they are in chromosomes, or why these arrangements are subject to change," said lead investigator David A. Bader, a professor in the Computational Science and Engineering Division of Georgia Tech's College of Computing.

Cancer research gets into the groove (Broad Institute)

Uncovering the molecular basis of cancer can be a double-edged sword. With decades of research and recent advances in cancer genomics, physicians may have a better idea of what genetic mutations cause a patient’s cancer. But, in many cases, they have no way of targeting the root cause, resorting instead to chemotherapy that kills dividing cells indiscriminately and brings a host of dangerous side effects.

One reason for this frustrating situation is that the driving many cancers are notoriously difficult to target with drugs. The out-of-control cell growth that defines cancer results from runaway growth genes activated by regulator proteins, known as transcription factors, that sit on DNA and turn genes on and off. Transcription factors are often mutated in cancer, but scientists have been largely unable to design or find drugs capable of blocking the proteins.

A creative method of targeting these gene regulators has recently been applied to cancer by a multi-institutional collaboration of researchers from the Broad Institute’s Chemical Biology Program, Dana-Farber Cancer Institute, Harvard University, and Brigham and Women’s Hospital. By combining advances in chemistry, chemical biology and genomics, the scientists have devised a way to generate unique molecules that target transcription factors, and can serve as both valuable research tools and prototypes for new cancer medicines. The new work, led in part by co-senior author Jay Bradner, also a chemical biologist and oncologist at the Dana-Farber Cancer Institute and an associate member of the Broad Institute of MIT and Harvard, appears in the November 12 issue of Nature.

Inferring tumor progression from genomic heterogeneity (Genome Research)

Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors.

SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (I) monogenomic and (II) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that heterogeneity can be ascribed to few clonal subpopulations, rather than a series of gradual intermediates. By comparing multiple subpopulations from different anatomic locations we have inferred pathways of cancer progression and the organization of tumor growth. visit the Genome Research portal for complete article details

Interactions between Connected Half-Sarcomeres Produce Emergent Mechanical Behavior in a Mathematical Model of Muscle (PLoS)

Most reductionist theories of muscle attribute a fiber's mechanical properties to the scaled behavior of a single half-sarcomere. Mathematical models of this type can explain many of the known mechanical properties of muscle but have to incorporate a passive mechanical component that becomes ~300% stiffer in activating conditions to reproduce the force response elicited by stretching a fast mammalian muscle fiber. The available experimental data suggests that titin filaments, which are the mostly likely source of the passive component, become at most ~30% stiffer in saturating Ca2+ solutions. The work described in this manuscript used computer modeling to test an alternative systems theory that attributes the stretch response of a mammalian fiber to the composite behavior of a collection of half-sarcomeres. The principal finding was that the stretch response of a chemically permeabilized rabbit psoas fiber could be reproduced with a framework consisting of 300 half-sarcomeres arranged in 6 parallel myofibrils without requiring titin filaments to stiffen in activating solutions.

Ablation of inter-myofibrillar links in the computer simulations lowered isometric force values and lowered energy absorption during a stretch. This computed behavior mimics effects previously observed in experiments using muscles from desmin-deficient mice in which the connections between Z-disks in adjacent myofibrils are presumably compromised. The current simulations suggest that muscle fibers exhibit emergent properties that reflect interactions between half-sarcomeres and are not properties of a single half-sarcomere in isolation. It is therefore likely that full quantitative understanding of a fiber's mechanical properties requires detailed analysis of a complete fiber system and cannot be achieved by focusing solely on the properties of a single half-sarcomere. Review the complete article via the PLoS web site

New imagining technique could lead to better antibiotics and cancer drugs (AgriLife News)

A recently devised method of imaging the chemical communication and warfare between microorganisms could lead to new antibiotics, antifungal, antiviral and anti-cancer drugs, said a Texas AgriLife Research scientist.

"Translating metabolic exchange with imaging mass spectrometry," was published Nov. 8 in Nature Chemical Biology, a prominent scientific journal. The article describes a technique developed by a collaborative team that includes Dr. Paul Straight, AgriLife Research scientist in the department of biochemistry and biophysics at Texas A&M University in College Station, Dr. Pieter Dorrestein, Yu-Liang Yang and Yuquan Xu, all at the University of California, San Diego. "Microorganisms encode in their genomes the capacity to produce many small molecules that are potential new antibiotics," Straight said. "Because we do not understand the circumstances under which those molecules are produced in the environment, we see only a small fraction of them in the laboratory."

An example is the antibiotic erythromycin, which is often prescribed for people who are allergic to penicillin, Straight said.

"We know that Saccharopolyspora erythraea, the bacteria from which erythromycin is derived, encodes the capacity to produce numerous other small molecules that might be potentially valuable drugs," he said. "Conventional microbial culture and drug discovery techniques uncovered erythromycin. Other potentially useful metabolites may require some unconventional methods for identification." Read the article via AgriLife News or the Nature Chemical Biology journal

Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype (Genome Research)

Whereas most nontyphoidal Salmonella (NTS) are associated with gastroenteritis, there has been a dramatic increase in reports of NTS-associated invasive disease in sub-Saharan Africa. Salmonella enterica serovar Typhimurium isolates are responsible for a significant proportion of the reported invasive NTS in this region. Multilocus sequence analysis of invasive S. Typhimurium from Malawi and Kenya identified a dominant type, designated ST313, which currently is rarely reported outside of Africa. Whole-genome sequencing of a multiple drug resistant (MDR) ST313 NTS isolate, D23580, identified a distinct prophage repertoire and a composite genetic element encoding MDR genes located on a virulence-associated plasmid.

Further, there was evidence of genome degradation, including pseudogene formation and chromosomal deletions, when compared with other S. Typhimurium genome sequences. Some of this genome degradation involved genes previously implicated in virulence of S. Typhimurium or genes for which the orthologs in S. Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field. Review the full abstract or order this article the Genome Research portal

First draft of the pig genome (Wellcome Trust Sanger Institute)

A global collaborative has produced a first draft of the genome of a domesticated pig, an achievement that will lead to insights in agriculture, medicine, conservation and evolution. A red-haired Duroc pig from a farm at the University of Illinois will now be among the growing list of domesticated animals that have had their genomes sequenced. Researchers announced the achievement today at a meeting at the Wellcome Trust Sanger Institute in Hinxton, England.

"The pig is a unique animal that is important for food and that is used as an animal model for human disease," said Larry Schook, a University of Illinois professor of biomedical sciences and leader of the sequencing project. "And because the native wild animals are still in existence, it is a really exciting animal to look at to learn about the genomic effects of domestication,"he said.

The Duroc is one of five major breeds used in pork production around the world and is one of about 200 breeds of domesticated pigs. There are also numerous varieties of wild boar, the non-domesticated pigs that are believed to have originated in Eurasia. The sequencing project involved an international team of scientists and genome-sequencing centres. The USDA National Institute of Food and Agriculture, formerly the Cooperative State Research, Education and Extension Service, provided £6 million (US$ 10 million) in initial funding, requiring that this be the only pig genome-sequencing project in the world, that it be a public-private partnership and a global collaborative effort, with significant financial or in-kind support from the other participating agencies and stakeholders.

UK-Singapore Symposium on p53: The Next 30 Years (November 25-26 in Singapore)

Held under the auspices of the "UK-Singapore Partners in Science" Programme, Prof Sir David Lane of Agency for Science, Technology and Research (A*STAR) and Dr Chandra Verma of A*STAR's Bioinformatics Institute (BII) are pleased to co-organise a 2-day UK-Singapore Symposium on p53: The Next 30 Years.

Since its discovery 30 years ago, the p53 gene has proved a source of continuous fascination and intellectual surprises. First described as a host protein binding to viral oncogenes, p53 flirted briefly with being an oncogene itself. But in 1990, it was found to be a tumour suppressor gene mutated in over half of all human cancers. Germ line mutations in p53 are responsible for the "Li-Fraumeni " cancer family syndrome. Mutations in p53 have proved to be the perfect "smoking gun" in epidemiological studies of human cancer causation, and polymorphisms in p53 and it regulators affect cancer incidence and aging in man. A sequence specific DNA binding protein and highly regulated transcription factor induced by DNA damage p53 was reborn as the "Guardian of the Genome". Efforts in Singapore have recently identified all the chromosomal DNA binding sites for p53 and highlighted the role of newly discovered p53 isoforms in development.

47,000 papers later, much is known but much more is still to be learnt. Enormous efforts are now being made to develop p53 based therapeutics, and indeed p53 gene therapy is now in widespread use in China for the treatment of Head and Neck cancer. The activity of p53 is regulated by a ubiquitin E3 ligase MDM2 and its partner protein MDM4 and new drugs that activate p53 by blocking MDM2 activity are now in clinical trial. Visit the conference portal by clicking on the title to this article

Horse genome sequence and analysis published in Science (c/o Broad Institute)

An international team of researchers has decoded the genome of the domestic horseEquus caballus, revealing a genome structure with remarkable similarities to humans and morethan 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. Visit the Broad Institute or Science magazine portals for complete details

DNA barcodes: Creative new uses span health, fraud, smuggling (CBOL)

The scientific ability to quickly and accurately identify species through DNA "barcoding" is being embraced and applied by a growing legion of global authorities – from medical and agricultural researchers to police and customs authorities to palaeontologists and others.

Some 350 experts from 50 nations gathering in Mexico for their 3rd global meeting will outline the latest creative applications of DNA barcoding, including projects to sequence ancient plant and animal remains extracted from northern permafrost cores. Using new techniques to identify species from degraded DNA, the results could reveal how life on Earth responded to global climate change in ages past. Meanwhile, by analyzing the DNA of gut contents, scientists have started unravelling secrets of what eats what in the animal world.

The International Barcode of Life Project, headquartered in Guelph, Canada, where barcoding was pioneered, will present new research showing that eight bat species feed on over 300 types of insect – one of the largest food webs ever revealed. This extension of DNA barcoding to unravel complex dynamics in the wild is an exciting new research field with important conservation implications.

"DNA barcoding is opening a new window into the relations between hunter and prey in the wild and how diets may be changing due to climate change," says Scott Miller, Acting Under Secretary for Science at the Smithsonian Institution and Chair of the Consortium for the Barcode of Life (CBOL). See the complete press release via EurekAlert

Predictable dynamic program of timing of DNA replication in human cells

The organization of mammalian DNA replication is poorly understood. We have produced high-resolution dynamic maps of the timing of replication in human erythroid, mesenchymal, and embryonic stem (ES) cells using TimEX, a method that relies on gaussian convolution of massive, highly redundant determinations of DNA copy-number variations during S phase to produce replication timing profiles. We first obtained timing maps of 3% of the genome using high-density oligonucleotide tiling arrays and then extended the TimEX method genome-wide using massively parallel sequencing. We show that in untransformed human cells, timing of replication is highly regulated and highly synchronous, and that many genomic segments are replicated in temporal transition regions devoid of initiation, where replication forks progress unidirectionally from origins that can be hundreds of kilobases away.

Absence of initiation in one transition region is shown at the molecular level by single molecule analysis of replicated DNA (SMARD). Comparison of ES and erythroid cells replication patterns revealed that these cells replicate about 20% of their genome in different quarters of S phase. Importantly, we detected a strong inverse relationship between timing of replication and distance to the closest expressed gene. This relationship can be used to predict tissue-specific timing of replication profiles from expression data and genomic annotations. We also provide evidence that early origins of replication are preferentially located near highly expressed genes, that mid-firing origins are located near moderately expressed genes, and that late-firing origins are located far from genes.

Pathogen protection & virulence: Fungal membrane protein revealed (VBI)

Researchers at the Virginia Bioinformatics Institute (VBI) at Virginia Tech and Montana State University have discovered a fungal protein that plays a key role in causing disease in plants and animals and which also shields the pathogen from oxidative stress. The researchers have found that the fungal protein TmpL is critical for the infection of host tissue and helps these pathogens regulate oxidative stress responses that are caused by the presence of destructive reactive oxygen species, a natural feature of the adaptive response to infection.

Dr. Chris Lawrence, Associate Professor at VBI and the Department of Biological Sciences at Virginia Tech and leader of the project, remarked: “The critical roles of reactive oxygen species in fungal development and virulence have been well established over the past half century. However little is known about how these molecules are produced or how the balance is achieved between their cell signaling roles on the one hand and their potentially destructive properties on the other. I believe we now have a unique opportunity to study a common fungal disease-associated mechanism in plants and animals that appears to be inextricably linked to the oxidative stress of the host-pathogen environment.”

The scientists looked at two different fungal pathogens: Alternaria brassicicola, which causes widespread damage in crops like canola, cabbage and broccoli, and Aspergillus fumigatus, a human pathogen that often leads to fatal disease in immunocompromised patients. Infection with A. fumigatus can lead to invasive pulmonary aspergillosis, the leading cause of death due to invasive fungal infections in humans. Visit VBI's portal for complete study findings

Researchers identify drug candidate for treating spinal muscular atrophy (CSHL)

A chemical cousin of the common antibiotic tetracycline might be useful in treating spinal muscular atrophy (SMA), a currently incurable disease that is the leading genetic cause of death in infants. This is the finding of a research collaboration involving Adrian Krainer, Ph.D., of Cold Spring Harbor Laboratory (CSHL) and scientists from Paratek Pharmaceuticals and Rosalind Franklin University of Medicine and Science.

SMA is caused by mutations in a gene called Survival of Motor Neuron 1 (SMN1), resulting in a decrease in the levels of SMN protein in the motor neurons of the spinal cord – the cells that control muscle activity. Without the protein, these neurons degenerate, and infants born with the mutations progressively lose the ability to move, swallow, and breathe. There are no approved therapies for the treatment of SMA, which affects approximately 1 in 6,000 babies born in the United States.

The new molecule boosts the levels of SMN protein in cells by fixing a mistake in a cellular processing mechanism called RNA splicing. In a study that will appear in the journal Science Translational Medicine on November 4th, the scientists report this fix in both mouse models of SMA, as well as in cells isolated from SMA patients.

Unlike previously identified molecules that stimulate SMN production, the tetracycline-like compound is a unique therapeutic candidate in that it is a small molecule that specifically alters RNA splicing by directly targeting the splicing reaction.

Scientists launch effort to sequence the DNA of 10,000 vertebrates (HHMI)

Scientists have an ambitious new strategy for untangling the evolutionary history of humans and their biological relatives: Create a genetic menagerie made of the DNA of more than 10,000 vertebrate species. The plan, proposed by an international consortium of scientists, is to obtain, preserve, and sequence the DNA of approximately one species for each genus of living mammals, birds, reptiles, amphibians, and fish.

"Understanding the evolution of the vertebrates is one of the greatest detective stories in science," said David Haussler, a Howard Hughes Medical Institute investigator at the University of California, Santa Cruz (UCSC). "No one has ever really known how the elephant got its trunk, or how the leopard got its spots. This project will lay the foundation for work that will answer those questions and many others."

Known as the Genome 10K Project, the approximately $50 million initiative is "tremendously exciting science that will have great benefits for human and animal health," Haussler said. "Within our lifetimes, we could get a glimpse of the genetic changes that have given rise to some of the most diverse life forms on the planet." Haussler is one of the lead authors of an article, published online November 5, 2009, in the Journal of Heredity, that outlines the project. The other lead authors include Stephen J. O'Brien, chief of the Laboratory of Genomic Diversity at the National Cancer Institute, and Oliver A. Ryder, director of genetics at the San Diego Zoo's Institute for Conservation Research and adjunct professor of biology at the University of California, San Diego. Coauthors and additional authors, who together make up a group called the Genome 10K Community of Scientists (G10KCOS), include geneticists, paleontologists, ecologists, conservationists, and other scientists representing major zoos, museums, research centers, and universities around the world. Visit the HHMI new room for complete project details

Bimolecular Affinity Purification (BAP): Tandem Affinity Purification Using Two Protein Baits (CSHP)

The introduction of high-throughput laboratory methods has greatly increased the pace of research into the genetics of complex diseases. Instead of focusing only on one or a few coding variants in a small sample of individuals, the ability to accurately and efficiently genotype many individuals and to cover more of the variation within individual genes has resulted in genetic studies with greater statistical power. "Laboratory Methods for High-Throughput Genotyping," from Howard Edenberg and Yunlong Liu at the University of Indiana presents an overview of the commonly used methods for high-throughput single-nucleotide polymorphism (SNP) genotyping for different stages of genetic studies and briefly reviews some of the high-throughput sequencing methods just coming into use. The authors also discuss recent developments in "next-generation" sequencing that will enable other kinds of studies. The article is excerpted from the recently published Genetics of Complex Human Diseases laboratory manual. It is featured in the November issue of Cold Spring Harbor Protocols.

The tandem affinity purification (TAP) procedure was pioneered in yeast for the purpose of purifying and characterizing protein complexes and has since been adapted for use in many organisms, including mammalian systems. The TAP procedure involves two sequential affinity purification steps to avoid non-specific protein interactions, a common problem in identifying proteins in complexes. "Bimolecular Affinity Purification (BAP): Tandem Affinity Purification Using Two Protein Baits," from Ezra Burstein and colleagues presents a variation on the TAP procedure in which the affinity moieties are placed on two different proteins of a molecular complex to isolate or detect components present in the complex. This variation, called bimolecular affinity purification (BAP), is suited for the identification of specific molecular complexes marked by the presence of two known components. The article is freely accessible on the website for Cold Spring Harbor Protocols. Download the full article by clicking on the title to this article

2 genes cooperate to cause aggressive leukemia (University of Gothenburg)

Two genes, each one of which is known to cause cancer on its own, together can lead to aggressive leukaemia. This is the conclusion from new research carried out on gene-modified mice at the Sahlgrenska Academy at the University of Gothenburg, Sweden. The discovery has surprised scientists, and may lead to new treatments.

The two genes are often present in mutated form in acute leukaemias, but the mutations rarely occur together. Scientists have previously believed that the two mutated genes have exactly the same function: each one alone will lead to increased activity of a carcinogenic protein known as "RAS". This protein, in turn, causes blood cells to proliferate more rapidly.

"This is a surprising discovery that suggests that there is a mechanism behind the development of cancer that has not yet been recognised. It opens the way for new methods of fighting blood cancer cells with NF1 mutations", says Associate professor Martin Bergö, who leads the research at the Wallenberg Laboratory at the Sahlgrenska Academy.

One of the genes codes for the RAS protein, which is a known accelerator for cell proliferation in several forms of cancer. The other gene codes for a protein known as "NF1", which is known to reduce the activity of the RAS protein. Visit the University of Gothenburg's portal for complete study findings

Caliper Life Sciences and SRU Biosystems to Offer Services for Cell-based and Biochemical Assays

SRU Biosystems today announced that Caliper Life Sciences will use SRU Biosystems’ label-free BIND^®technology to offer new functional assays as part of its Discovery Alliances and Services. The label-free BIND technology, developed by SRU Biosystems, provides researchers with a new ultra-high throughput screening and profiling system for cell-based and biochemical assays. BIND technology for cell-based assays offers an orthogonal screening tool to access new hits and lead molecules that are not detected by other systems, including compounds that undergo G-protein switching, non-G protein coupled pathways, inverse and partial agonists, and receptor desensitization. The screening platform is robust and can be applied to both over-expressed and endogenous receptors, and can be used with low numbers of primary cells. The technology can also used for receptor profiling on native cells, due to the high sensitivity of the response. Lastly, the BIND technology provides a way to easily screen Gi-coupled GPCR targets and ion channels, which have been traditionally difficult to assess.

“Caliper Life Sciences is an excellent partner for SRU. They are uniquely positioned to offer BIND technology as a contract service to the biotechnology and pharmaceutical communities. They have tremendous knowledge utilizing innovative technologies to advance drug discovery and will provide an outstanding new service to the drug discovery industry,” said Rick Wagner, Ph.D., President and CEO of SRU Biosystems.

SRU Biosystems’ label-free BIND technology has extraordinary sensitivity and application flexibility. It can be used for complex cellular assays such as GPCR pathway analysis, ion channel assays and cell adhesion assays; as well as biochemical assays, such as protein-protein binding, enzyme assays, and fragment and small molecule screening. These applications have been utilized in exploring assay development, 1536-well high throughput screening, and lead profiling. SRU anticipates a continued expansion of its label-free BIND products, creating new assay capabilities.