The Genetic Network for Temporal Expression in Drosophila Neurogenesis

Precise temporal coordination of gene expression is crucial for many developmental processes. One central question in developmental biology is how such coordinated expression patterns are robustly controlled. During embryonic development of the Drosophila central nervous system, neural stem cells called neuroblasts express a group of genes in a definite order, which leads to the diversity of cell types. We produced all possible regulatory networks of these genes and examined their expression dynamics numerically. From the analysis, we identified requisite regulations and predicted an unknown factor to reproduce known expression profiles caused by loss-of-function or overexpression of the genes in vivo, as well as in the wild type. Following this, we evaluated the stability of the actual Drosophila network for sequential expression. This network shows the highest robustness against parameter variations and gene expression fluctuations among the possible networks that reproduce the expression profiles. We propose a regulatory module composed of three types of regulations that is responsible for precise sequential expression. This study suggests that the Drosophila network for sequential expression has evolved to generate the robust temporal expression for neuronal specification. Visit the PLoS Computational Biology portal for complete study findings

In vivo trans-specific gene silencing in fungal cells by in planta expression of a double-stranded RNA

The genetic interference phenomenon [RNA interference (RNAi)] was described in Caenorhabditis elegans in which double-stranded RNA (dsRNA) induces individual sequence-specific posttranscriptional gene silencing. The spreading silencing effect has been demonstrated, in which the interference is observed in a broad region of the animal after the injection of dsRNA into the extracellular body cavity. Fire et al. demonstrated that RNAi abolished expression of targeted genes in C. elegans by injecting dsRNA. Subsequently, others have shown that the effect also occurs when C. elegans is fed the bacterium Escherichia coli, which transcribes the recombinant dsRNA. It also results from simply soaking the animals in dsRNA preparations. Data obtained from in vivo and in vitro studies are now being used to engineer resistance against parasitic nematodes in transgenic plants. Cellular boundaries play a pivotal role in this integration by maintaining a level of cell autonomy while enabling communication between cells for coordinated gene expression and metabolism. In vascular plants, trafficking of RNAi molecules occurs between cells and systemically throughout the plant. Such RNA trafficking breaks the boundaries of our traditional thinking of RNAs as functioning solely within the cells in which they are produced, and ushers in a new frontier of plant biology. Intercellular and systemic movement occurs via plasmodesmata, which provide the continuity of cytoplasm and endoplasmic reticulum between adjacent cells and the phloem. Analyses of vascular exudates from oilseed rape (Brassica napus) showed that phloem sap contained a large number of small (sm)RNAs, predominantly of 21 and 24 nucleotides in length. 

In addition, RNAi signals can spread systemically throughout a plant, even across graft junctions from transgenic stocks to non-transgenic scions. Moreover, recent experiments described by Tomilov et al. demonstrated that the movement of RNAi molecules between a parasite and its host plants. The gus silencing signal generated by lettuce roots was functional in its parasite Triphysaria versicolor, translocating across the haustorium interface. In nematodes gene silencing may also be triggered by a diet composed of transgene-encoded RNAi plants. The same phenomenon has been observed in herbivorous insects fed on a plant engineered to express dsRNAs targeting vital insect genes. Visit the BMC Biology home page for complete research details

7th Annual Biotechnology and Bioinformatics Symposium - Preview (BIOT 2010)

The Symposium's objective is to showcase the state of the art research and development activities in the area of genome sequencing and annotation, functional and computational genomics, and transcriptomics. The other areas of bioinformatics and biotechnology are also welcome. The Symposium brings together scientists in multiple disciplines such as computer scientists, engineers, and researchers from biotechnology, bioinformatics, and the medical research community, and promote future interdisciplinary activity and research in these areas. We encourage graduate and post doctoral students to submit their contributions either as complete papers or as poster presentations.

 

Each field that BIOT attracts has its own tradition. For example, in computer science, it is customary to require the submission of full papers for review several months prior to a conference or symposium. Conferences in other disciplines generally require that an abstract or extended abstract be submitted for review. The organizing committee of BIOT understands these differences, and the speakers will be invited from both accepted papers and abstracts. Accepted papers and abstracts will be printed in the conference proceedings. Abstracts for poster presentation are also accepted. Visit the conference portal for complete speaker and agenda details

Mre11 Nuclease

Mre11 is at the heart of one of the major processes that fixes double-strand breaks in DNA. This method is called homologous recombination, because it relies on having at least two similar copies of the genome in the cell. It uses one copy of the genome as a template to reconstruct the broken copy. Because it uses an intact DNA to guide the repair, it is very accurate. Mre11 finds the broken ends of the DNA and gets this whole process started. Mre11 is a composed of two identical subunits, which associate to form a complex with a groove down the center. The two arms of the complex (extending to right and left here) bind to DNA, positioning the broken DNA strands (the short pieces of DNA used for the structure analysis are shown in red and yellow). Then, the nuclease domains in the center of the protein trim the ends of the DNA and make them ready for repair. Mre11 acts as part of a larger complex of proteins, including the long protein Rad50 that forms a tether between the broken strands and the rest of the chromosomes.
Researchers at JCSG have solved the structure of Mre11 from the eubacterium Thermatoga maritima, as part of their large structural genomics effort to determine the structure of all proteins from this organism. The structure was instrumental in determining the function of the protein. It was postulated to be a nuclease based on its sequence, but its identification as Mre11 nuclease was only made after the structure was solved, since its sequence is quite different from the sequences of Mre11 nucleases from organisms in other kingdoms. Comparison of theThermatoga enzyme with the one from the archaeon Pyrococcus furiosus showed that they have similar domain structures and active sites, but differences in their fine structures may cause them to interact differently with particular types of damaged DNA. By comparing these two structures, researchers will be able to pinpoint the structural features that are important for DNA recognition and interaction of Mre11 with its partners in homologous recombination. Click on the image below for an interactive Jmol that compares the two structures. See the PSI Structural Genomics Knowledgebase for complete details

Gene Ontology Annotation (GOA) Database - Available for Download

The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI) and is a central dataset for other major multi-species databases; such as Ensembl and NCBI. 

GOA has been a member of the GO Consortium since 2001, and is responsible for the integration and release of GO annotations to the human, chicken and cow proteomes. Because of the multi-species nature of the UniProtKB, GOA also assists in the curation of another 200,000 species. This involves electronic annotation and the integration of high-quality manual GO annotation from all GO Consortium model organism groups and specialist groups. This effort ensures that the GOA dataset remain a key reference and a comprehensive source of GO annotation for all species. Download the complete GOA dataset via the EMBL-EBI web site

Defining the RNA polymerase III transcriptome: Genome-wide localization of RNA polymerase III

Researchers view of the RNA polymerase III (Pol III) transcription machinery in mammalian cells arises mostly from studies of the RN5S (5S) gene, the Ad2 VAI gene, and the RNU6 (U6) gene, as paradigms for genes with type 1, 2, and 3 promoters. Recruitment of Pol III onto these genes requires prior binding of well-characterized transcription factors. Technical limitations in dealing with repeated genomic units, typically found at mammalian Pol III genes, have so far hampered genome-wide studies of the Pol III transcription machinery and transcriptome. We have localized, genome-wide, Pol III and some of its transcription factors. Our results reveal broad usage of the known Pol III transcription machinery and define a minimal Pol III transcriptome in dividing IMR90hTert fibroblasts. This transcriptome consists of some 500 actively transcribed genes including a few dozen candidate novel genes, of which we confirmed nine as Pol III transcription units by additional methods. It does not contain any of the microRNA genes previously described as transcribed by Pol III, but reveals two other microRNA genes, MIR886 (hsa-mir-886) and MIR1975 (RNY5, hY5, hsa-mir-1975), which are genuine Pol III transcription units. Read the complete study findings via the Genome Research portal

Structural Characteristics of Novel Protein Folds

Folds are the basic building blocks of protein structures. Understanding the emergence of novel protein folds is an important step towards understanding the rules governing the evolution of protein structure and function and for developing tools for protein structure modeling and design. We explored the frequency of occurrences of an exhaustively classified library of supersecondary structural elements (Smotifs), in protein structures, in order to identify features that would define a fold as novel compared to previously known structures. We found that a surprisingly small set of Smotifs is sufficient to describe all known folds. Furthermore, novel folds do not require novel Smotifs, but rather are a new combination of existing ones. Novel folds can be typified by the inclusion of a relatively higher number of rarely occurring Smotifs in their structures and, to a lesser extent, by a novel topological combination of commonly occurring Smotifs. When investigating the structural features of Smotifs, we found that the top 10% of most frequent ones have a higher fraction of internal contacts, while some of the most rare motifs are larger, and contain a longer loop region. Visit the PLoS Computational Biology portal for complete research findings

A Tagging-via-substrate Approach to Detect the Farnesylated Proteome Using Two-dimensional Electrophoresis Coupled with Western Blotting

Prenylation is a post-translational modification critical for the proper function of multiple physiologically important proteins, including small G-proteins, such as Ras. Methods allowing rapid and selective detection of protein farnesylation and geranylgeranylation are fundamental for the understanding of prenylated protein function and for monitoring efficacy of drugs such as farnesyltransferase inhibitors (FTIs). Although the natural substrates for prenyltransferases are farnesyl pyrophosphate and geranylgeranyl pyrophosphate, farnesyltransferase has been shown to incorporate isoprenoid analogues into protein substrates. In this study, protein prenyltransferase targets were labeled using anilinogeraniol, the alcohol precursor to the unnatural farnesyl pyrophosphate analogue 8-anilinogeranyl diphosphate in a tagging-via-substrate approach. Antibodies specific for the anilinogeranyl moiety were used to detect the anilinogeranyl-modified proteins. Coupling this highly effective labeling/detection method with two-dimensional electrophoresis and subsequent Western blotting allowed simple, rapid analysis of the complex farnesylated proteome. For example, this method elucidated the differential effects induced by two chemically distinct FTIs, BMS-214,662 and L-778,123. Although both FTIs strongly inhibited farnesylation of many proteins such as Lamins, NAP1L1, N-Ras, and H-Ras, only the dual prenylation inhibitor L-778,123 blocked prenylation of Pex19, RhoB, K-Ras, Cdc42, and Rap1. This snapshot approach has significant advantages over traditional techniques, including radiolabeling, anti-farnesyl antibodies, or mass spectroscopy, and enables dynamic analysis of the farnesylated proteome. Visit the MCP web site for complete research findings

Gramene Announces Scholarships for Groups Underrepresented in Science to Learn How to Use Bioinformatics and Genomics Resources

The creators of the Gramene Resource for Comparative Grass Genomics and OpenHelix announced the availability of scholarships to colleges and universities serving underrepresented minorities for full access to over 85 online tutorial suites on bioinformatics and genomics resources. The program is partially funded by the National Science Foundation (NSF).

“An ongoing goal for Gramene, our institutions, and the NSF, has been to provide opportunities for advancement and training to underrepresented groups in science,” said Dr. Doreen Ware, of Cold Spring Harbor Laboratory and Principal Investigator of Gramene, “So we are excited to be able to offer individual and institution scholarships to an extensive and valuable catalog of online training on genomics resources.” Recipients will have access to the OpenHelix catalog of tutorial suites on a wide range of bioinformatics and genomics resources, including Gramene, PlantGDB, NCBI tools such as Entrez Gene, BLAST and PubMed and many more. Each tutorial suite includes a 45-60 minute, online, self-run, narrated introductory tutorial on how to use a specific resource. The tutorial suite also includes PowerPoint slides, slide handouts and exercises which can be used as reference material or to build classroom content.

“The study of genomics has affected just about every area of life sciences, so learning how to access and interpret genomic data is critical to research success,” said Scott Lathe, Chief Executive Officer of OpenHelix, “With the convenience and broad accessibility of online training, we hope these scholarships will help in leveling access to this important training and further the potential and ongoing careers of the recipients.”

International Cancer Genome Consortium plans to sequence 25,000 cancer genomes

The International Cancer Genome Consortium (ICGC) today set out its bold plan to decode the genomes from 25,000 cancer samples and create a resource of freely available data that will help cancer researchers around the world. The document outlines research design and projects as well as the important ethical framework for this science. The ICGC also announced that new members have joined the consortium. 

New projects in Italy and the European Union will contribute to efforts already underway in Australia, Canada, China, France, Germany, India, Japan, Spain, the United Kingdom, and the United States. Funded projects will examine more than 10,000 tumors for cancer types found around the globe that affect a diversity of organs including blood, brain, breast, colon, kidney, liver, lung, pancreas, stomach, oral cavity and ovary. Published today in the journal Nature is a paper written by over 200 authors participating in ICGC projects. The paper describes how the projects will proceed, outlining the ethical framework, study design and policies. ICGC leaders will also present progress on their projects at the annual conference of the American Association for Cancer Research in Washington DC, April 17-21, 2010. Studies of breast, liver, and pancreatic cancer have already generated datasets which are now available on the ICGC website at www.icgc.org. The genomic analyses of the tumors were conducted by ICGC members in the U.K. (breast cancer), Japan (liver cancer), and Australia and Canada (pancreatic cancer). The data are housed in the Data Coordination Center which is hosted by the Ontario Institute for Cancer Research in Toronto.

Deterministic graph-theoretic algorithm for detecting modules in biological interaction networks

An approach for module identification, Modules of Networks (MoNet), introduced an intuitive module definition and clear detection method using edges ranked by the Girvan-Newman algorithm. Modules from a yeast network showed significant association with biological processes, indicating the method's utility; however, systematic bias leads to varied results across trials. MoNet modules also exclude some network regions. To address these shortcomings, we developed a deterministic version of the Girvan-Newman algorithm and a new agglomerative algorithm, Deterministic Modularization of Networks (dMoNet). dMoNet simultaneously processes structurally equivalent edges while preserving intuitive foundations of the MoNet algorithm and generates modules with full network coverage. Go to the Bioinformatics Research and Applications portal for in-depth findings

A CTCF-independent role for cohesin in tissue-specific transcription

The cohesin protein complex holds sister chromatids in dividing cells together and is essential for chromosome segregation. Recently, cohesin has been implicated in mediating transcriptional insulation, via its interactions with CTCF. Here, we show in different cell types that cohesin functionally behaves as a tissue-specific transcriptional regulator, independent of CTCF binding. By performing matched genome-wide binding assays (ChIP-seq) in human breast cancer cells (MCF-7), we discovered thousands of genomic sites that share cohesin and estrogen receptor alpha (ER) yet lack CTCF binding. By use of human hepatocellular carcinoma cells (HepG2), we found that liver-specific transcription factors colocalize with cohesin independently of CTCF at liver-specific targets that are distinct from those found in breast cancer cells. Furthermore, estrogen-regulated genes are preferentially bound by both ER and cohesin, and functionally, the silencing of cohesin caused aberrant re-entry of breast cancer cells into cell cycle after hormone treatment. We combined chromosomal interaction data in MCF-7 cells with our cohesin binding data to show that cohesin is highly enriched at ER-bound regions that capture inter-chromosomal loop anchors. Together, our data show that cohesin cobinds across the genome with transcription factors independently of CTCF, plays a functional role in estrogen-regulated transcription, and may help to mediate tissue-specific transcriptional responses via long-range chromosomal interactions. See the current issue of Genome Research for complete details

Origin and fate of pseudogenes in hemiascomycetes: a comparative analysis

Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation. Characterization of pseudogenes is important to understand genome dynamics and evolution, and its significance increases when several genomes of related organisms can be compared. Among yeasts, only the genome of the S. cerevisiae reference strain has been analyzed so far for pseudogenes. Researchers present here the first comparative analysis of pseudogenes within the fully sequenced and annotated genomes of eight yeast species, spanning the entire phylogenetic range of Hemiascomycetes. A total of 871 pseudogenes were found, out of which mutational degradation patterns and consequences on the genetic repertoire of each species could be identified. We found that most pseudogenes in yeasts originate from mutational degradation of gene copies formed after species-specific duplications but duplications of pseudogenes themselves are also encountered. In all yeasts, except in Y. lipolytica, pseudogenes tend to cluster in subtelomeric regions where they can outnumber the number of functional genes from 3 to 16 times. Pseudogenes are generally not conserved between the yeast species studied (except in two cases), consistent with their large evolutionary distances, but tend to be conserved among S. cerevisiae strains. Reiterated pseudogenization of some genes is often observed in different lineages and may affect functions essential in S. cerevisiae, which are, therefore, lost in other species. Although a variety of functions are affected by pseudogenization, there is a bias towards functions involved in the adaptation of the yeasts to their environment, and towards genes of unknown functions.  Our work illustrates for the first time the formation of pseudogenes in different branches of hemiascomycetous yeasts, showing their limited conservation and how they testify for the adaptation of the yeasts functional repertoires. Visit BMC Genetics for compete study findings

Genomes of citrus canker pathogens decoded (VBI)

An international team of scientists from Brazil and the United States have completed the draft genome sequences of two strains of the Xanthomonas bacteria that cause citrus canker. Citrus canker, a belligerent disease that has plagued plant growers in parts of the United States, South America, and Asia, causes millions of dollars in lost revenue every year for farmers of citrus crops such as oranges, limes, and grapefruit. The genomic information obtained by these sequencing projects, which is described in the journal BMC Genomics, suggests possible intervention targets for further experimental investigation.

João Setubal, Associate Professor at the Virginia Bioinformatics Institute and the Department of Computer Science at Virginia Tech, commented: "Citrus canker, which is found in different citrus plants, is effectively a single disease that is spawned by one of three strains of certain species of the Xanthomonas bacterium. The genome sequence of the most virulent of the citrus canker pathogens, Xanthomonas citri subsp. citri, was completed in 2002, and this was a big step forward in understanding the disease. The two new sequences will provide a welcome boost to citrus canker studies."

Citrus canker has proved difficult to combat despite concerted national disease eradication efforts. The disease produces lesions, blisters, and holes in the stems, leaves, and fruit of citrus crops. While the bacterial infection of the plant is not harmful to humans, the fruit becomes damaged and infection can lead to leaf loss and premature dropping of fruit. The availability of the genome sequences for the two additional bacterial strains that cause citrus canker means that scientists can now use key similarities and differences between the three related genomic sequences to zero in on the molecular basis of citrus canker.

Prevalence of liver fibrosis and risk factors in a general population using non-invasive biomarkers (FibroTest)

FibroTest and elastography have been validated as biomarkers of liver fibrosis in the most frequent chronic liver diseases and in the fibrosis screening of patients with diabetes. One challenge was to use them for estimating the prevalence of fibrosis, identifying independent risk factors and to propose screening strategies in the general population. Researchers prospectively studied 7,463 consecutive subjects aged 40 years or older. Subjects with presumed advanced fibrosis (FibroTest greater than 0.48) were re-investigated in a tertiary center.

The sample characteristics were similar to those of the French population. FibroTest was interpretable in 99.6%. The prevalence of presumed fibrosis was 2.8%, (209/7,463), including cirrhosis in 0.3% (25/7,463); 105/209 (50%) subjects with presumed fibrosis accepted re-investigation. Fibrosis was confirmed in 50, still suspected in 27, indeterminate in 25 and not confirmed with false positive FibroTest or false negative elastography in 3 subjects. False negative rate of FibroTest estimated using elastography was 0.4% (3/766). The attributable causes for confirmed fibrosis were both alcoholic and nonalcoholic fatty liver disease (NAFLD) in 66%, NAFLD in 13%, alcohol in 9%, HCV in 6%, and other in 6%. Factors independently associated (all P<0.003) with confirmed fibrosis were age, male gender, waist circumference, HCV antibody and alcohol consumption estimated using carbohydrate-deficient transferrin, enabling efficient screening-oriented strategies to be compared and proposed. Biomarkers have permitted to estimate prevalence of advanced fibrosis around 2.8% in a general population aged 40 years or older, and several risk factors which may be used for the validation of selective or non-selective screening strategies. Visit the BMC Gastroenterology web site for in-depth stidy findings

Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets

Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein is natively unfolded requires laborious experimental investigations, then reliable sequence-only methods for predicting whether a sequence corresponds to a folded or to an unfolded protein are of interest in fundamental and applicative studies. Many proteins have amino acidic compositions compatible both with the folded and unfolded status, and belong to a twilight zone between order and disorder. This makes difficult a dichotomic classification of protein sequences into folded and natively unfolded ones. In this work we propose an operational method to identify proteins belonging to the twilight zone by combining into a consensus score good performing single predictors of folding.

In this methodological paper dichotomic folding indexes are considered: hydrophobicity-charge, mean packing, mean pairwise energy, Poodle-W and a new global index, that is called here gVSL2, based on the local disorder predictor VSL2. The performance of these indexes is evaluated on different datasets, in particular on a new dataset composed by 2369 folded and 81 natively unfolded proteins. Poodle-W, gVSL2 and mean pairwise energy have good performance and stability in all the datasets considered and are combined into a strictly unanimous combination score SSU, that leaves proteins unclassified when the consensus of all combined indexes is not reached. The unclassified proteins: i) belong to an overlap region in the vector space of amino acidic compositions occupied by both folded and unfolded proteins; ii) are composed by approximately the same number of order-promoting and disorder-promoting amino acids; iii) have a mean flexibility intermediate between that of folded and that of unfolded proteins.

Results show that proteins unclassified by SSU belong to the twilight zone. Proteins left unclassified by the consensus score SSU reasonably have physical properties intermediate between those of folded and those of natively unfolded proteins and their structural properties and evolutionary history are worth to be investigated.

Fowlpox virus recombinants expressing HPV-16 E6 and E7 oncogenes

Around half million new cases of cervical cancer arise each year, making the development of an effective therapeutic vaccine against HPV a high priority. As the E6 and E7 oncoproteins are expressed in all HPV-16 tumour cells, vaccines expressing these proteins might clear an already established tumour and support the treatment of HPV-related precancerous lesions. Three different immunisation regimens were tested in a pre-clinical trial in rabbits to evaluate the humoral and cell-mediated responses of a putative HPV-16 vaccine. Fowlpoxvirus (FP) recombinants separately expressing the HPV-16 E6 (FPE6) and E7 (FPE7) transgenes were used for priming, followed by E7 protein boosting.
 

All of the protocols were effective in eliciting a high antibody response. This was also confirmed by interleukin-4 production, which increased after simultaneous priming with both FPE6 and FPE7 and after E7 protein boost. A cell-mediated immune response was also detected in most of the animals. These results establish a preliminary profile for the therapy with the combined use of avipox recombinants, which may represent safer immunogens than vaccinia-based vectors in immuno-compromised individuals, as they express the transgenes in most mammalian cells in the absence of a productive replication. Visit the Journal of Translational Medicine portal for complete study details

The Asparaginyl Hydroxylase Factor Inhibiting HIF-1α Is an Essential Regulator of Metabolism

Factor inhibiting HIF-1α (FIH) is an asparaginyl hydroxylase. Hydroxylation of HIF-α proteins by FIH blocks association of HIFs with the transcriptional coactivators CBP/p300, thus inhibiting transcriptional activation. We have created mice with a null mutation in the FIH gene and found that it has little or no discernable role in mice in altering classical aspects of HIF function, e.g., angiogenesis, erythropoiesis, or development. Rather, it is an essential regulator of metabolism: mice lacking FIH exhibit reduced body weight, elevated metabolic rate, hyperventilation, and improved glucose and lipid homeostasis and are resistant to high-fat-diet-induced weight gain and hepatic steatosis. Neuron-specific loss of FIH phenocopied some of the major metabolic phenotypes of the global null animals: those mice have reduced body weight, increased metabolic rate, and enhanced insulin sensitivity and are also protected against high-fat-diet-induced weight gain. These results demonstrate that FIH acts to a significant degree through the nervous system to regulate metabolism. Read the current issue of Cell Metabolism for i-depth research details

Gene Expression and Genetic Variation in Response to Endoplasmic Reticulum Stress

The accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) results in the condition called “ER stress,” which induces the unfolded protein response (UPR), a complex cellular process that includes changes in expression of many genes. Failure to restore homeostasis in the ER is associated with human diseases. To identify the underlying changes in gene expression in response to ER stress, we induced ER stress in human B cells and then measured gene expression at ten time points. We followed up those results by studying cells from 60 unrelated people. We rediscovered genes that were known to play a role in the ER-stress response and uncovered several thousand genes that are not known to be involved. 

Two of these are VLDLR and INHBE, which showed significant increase in expression after ER stress in B cells and in primary fibroblasts. To study the links between UPR and disease susceptibility, we identified ER-stress-responsive genes that are associated with human diseases and assessed individual differences in the ER-stress response. Many of the UPR genes are associated with Mendelian disorders, such as Wolfram syndrome, and complex diseases, including amyotrophic lateral sclerosis and diabetes. Data from two independent samples showed extensive individual variability in ER-stress response. Additional analyses with monozygotic twins revealed significant correlations within twin pairs in their responses to ER stress, thus showing evidence for heritable variation among individuals. These results have implications for basic understanding of ER function and its role in disease susceptibility. Visit the American Jounral of Human Genetics web site for complete study findings

Bacterial teichoic acid polymerase TagF provides insights into membrane association and catalysis

Teichoic acid polymers are composed of polyol-phosphate units and form a major component of Gram-positive bacterial cell walls. These anionic compounds perform a multitude of important roles in bacteria and are synthesized by monotopic membrane proteins of the TagF polymerase family. We have determined the structure of Staphylococcus epidermidis TagF to 2.7-Å resolution from a construct that includes both the membrane-targeting region and the glycerol-phosphate polymerase domains. TagF possesses a helical region for interaction with the lipid bilayer, placing the active site at a suitable distance for access to the membrane-bound substrate. Characterization of active-site residue variants and analysis of a CDP-glycerol substrate complex suggest a mechanism for polymer synthesis. With the importance of teichoic acid in Gram-positive physiology, this elucidation of the molecular details of TagF function provides a critical new target in the development of novel anti-infectives. The Nature Structural and Molecular Biology web site provide in-depth study results

Restriction Site Tiling Analysis: Accurate discovery and quantitative genotyping of genome-wide polymorphisms using nucleotide arrays

High-throughput genotype data can be used to identify genes important for local adaptation in wild populations, phenotypes in lab stocks, or disease-related traits in human medicine. Here we advance microarray-based genotyping for population genomics with Restriction Site Tiling Analysis. The approach simultaneously discovers polymorphisms and provides quantitative genotype data at 10,000s of loci. It is highly accurate and free from ascertainment bias. We apply the approach to uncover genomic differentiation in the purple sea urchin. 

Uncovering the genetic underpinnings of adaptive evolution is key to understanding the evolutionary processes that generate biodiversity. The combined use of genome scans and population genetic analyses has been applied in both model and non-model organisms to discover and document the role of specific genes in adaptive evolution. Surveys of hundreds to thousands of genome-wide markers identified from single nucleotide polymorphism (SNP) databases, microarray-based SNP survey methods, or sequences have been applied in humans, yeast, dogs, the malaria parasite Plasmodium falciparum, Drosophila, and Arabidopsis. Based on massive sequencing efforts to identify polymorphisms, these approaches have led to insightful evaluation of genetic adaptation. However, these data sets can be complicated by ascertainment bias and have historically required a large investment in SNP development.Visit the Genome Biology portal for complete research findings

Cytometry of chromatin bound Mcm6 and PCNA identifies two states in G1 that are separated functionally by the G1 restriction point

Cytometric measurements of DNA content and chromatin-bound Mcm2 have demonstrated bimodal patterns of expression in G1. These patterns, the replication licensing function of Mcm proteins, and a correlation between Mcm loading and cell cycle commitment for cells re-entering the cell cycle, led us to test the idea that cells expressing a defined high level of chromatin-bound Mcm6 in G1 are committed - i.e., past the G1 restriction point. We developed a cell-based assay for tightly-bound PCNA (PCNA*) and Mcm6 (Mcm6*), DNA content, and a mitotic marker to clearly define G1, S, G2, and M phases of the cell cycle. hTERT-BJ1, hTERT-RPE-1, and Molt4 cells were extracted with Triton X-100 followed by methanol fixation, stained with antibodies and DAPI, then measured by cytometry.

Bivariate analysis of cytometric data demonstrated complex patterns with distinct clustering for all combinations of the 4 variables. In G1, cells clustered in two groups characterized by low and high Mcm6* expression. Serum starvation and release experiments showed that residence in the high group was in late G1, just prior to S phase. Kinetic experiments, employing serum withdrawal, and stathmokinetic analysis with aphidicolin, mimosine or nocodazole demonstrated that cells with high levels of Mcm6* cycled with the committed phases of the cell cycle (S, G2, and M).

A multivariate assay for Mcm6*, PCNA*, DNA content, and a mitotic marker provides analysis capable of estimating the fraction of pre and post-restriction point G1 cells and supports the idea that there are at least two states in G1 defined by levels of chromatin bound Mcm proteins.

Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program

The epigenome changes that underlie cellular differentiation in developing organisms are poorly understood. To gain insights into how pancreatic beta-cells are programmed, we profiled key histone methylations and transcripts in embryonic stem cells, multipotent progenitors of the nascent embryonic pancreas, purified beta-cells, and 10 differentiated tissues. We report that despite their endodermal origin, beta-cells show a transcriptional and active chromatin signature that is most similar to ectoderm-derived neural tissues. 

In contrast, the beta-cell signature of trimethylated H3K27, a mark of Polycomb-mediated repression, clusters with pancreatic progenitors, acinar cells and liver, consistent with the epigenetic transmission of this mark from endoderm progenitors to their differentiated cellular progeny. We also identified two H3K27 methylation events that arise in the beta-cell lineage after the pancreatic progenitor stage. One is a wave of cell-selective de novo H3K27 trimethylation in non-CpG island genes. Another is the selective loss of H3K27me3-repressed chromatin in a core program of neural developmental regulators that enables a convergence of the gene activity state of beta-cells with that of neural cells. These findings reveal a dynamic regulation of Polycomb repression programs that shape the identity of differentiated beta-cells.

Global Entrainment of Transcriptional Systems to Periodic Inputs

The activities of living organisms are governed by complex sets of biochemical reactions. Often, entrainment to certain external signals helps control the timing and sequencing of reactions. An important open problem is to understand the onset of entrainment and under what conditions it can be ensured in the presence of uncertainties, noise, and environmental variations. In this paper, we focus mainly on transcriptional systems, modeled by Ordinary Differential Equations. These are basic building blocks for more complex biochemical systems. However, the results that we obtain are of more generality. To illustrate this generality, and to emphasize the use of our techniques in synthetic biology, we discuss the entrainment of a Repressilator circuit and the synchronization of a network of Repressilators. We answer the following two questions: 1) What are the dynamical mechanisms that ensure the entrainment to periodic inputs in transcriptional modules? 2) Starting from natural systems, what properties can be used to design novel synthetic biological circuits that can be entrained? For some biological systems which are always “in contact” with a continuously changing environment, entrainment may be a “desired” property. Thus, answering the above two questions is of fundamental importance. While entrainment may appear obvious at first thought, it is not a generic property of nonlinear dynamical systems. The main result of our paper shows that, even if the transcriptional modules are modeled by nonlinear ODEs, they can be entrained by any (positive) periodic signal. Surprisingly, such a property is preserved if the system parameters are varied: entrainment is obtained independently of the particular biochemical conditions. We prove that combinations of the above transcriptional module also show the same property. Finally, we show how the developed tools can be applied to design synthetic biochemical systems guaranteed to exhibit entrainment. Review the complete article via the PLoS web site

IntEnz 59 and Rhea Database Releases

UniProt 2010_04 and Reactome 32 have been used for cross-references. This release includes preliminary EC numbers issued by UniProt, as well as a new sub-subclass (EC 1.7.5). IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME resource. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

Rhea is a reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions. We have populated the database with the reactions found in the EC list (and in the IntEnz and ENZYME databases), extending it with additional known reactions of biological interest. While the main focus of Rhea is enzyme-catalysed reactions, other biochemical reactions (including those that are often termed "spontaneous") also are included. Visit the EMBL portal for complete details

The Collapse of Cancer Metastases Hypothesis PRW -- The Announcement of New Study Results

The announcement of new study results -- Sergey N. Rumyantsev Director of research, Andent Inc. For the last 50 years the prevailing paradigm in cancer origin, pathogenesis, prevention and treatment has been based upon the rarely questioned ‘somatic mutation hypothesis’. This hypothesis states that (1) cancer primarily occurs in individuals over 40 years of age from a single somatic cell that has accumulated multiple DNA mutations in genes that control proliferation and the cell cycle, (2) cancer is a disease of the control of cell proliferation that leads to (3) the formation of a maternal tumor and (4) subsequent spread (metastasis) of cancer maternal cells outside the primary site to form daughter tumors in distant locations in the body. The recent cancer epidemic, characterized by the aggressive increase in the prevalence of cancer among human populations, is outside of the scope of the ‘somatic mutation hypothesis’ calling into question the premise of this hypothesis.

According to the conventional paradigm, cancer cells metastasize from a maternal tumor through the bloodstream or the lymphatic system; however, this process has not been proven or fully elucidated. In reality we observe the non-simultaneous appearance of several identical tumors in different parts of a diseased body. The details of the supposed metastasis remain hypothetical and mysterious. The lack of evidence of the metastatic pathway prevents effective interventions for cancer healing and prevention.

In contrast to the hypothesis of mutant maternal tumor and its subsequent metastasis, recent evidence revealed that potentially cancerous cell clones do not appear in a body as a result of specific mutation of a somatic cell. The clone is of innate origin formed by heterozygous interbreeding. This leads to genetic admixture between ethnic groups that have developed in ecologically different environments. As a result, differences may exist in the molecular composition of physiological regulators in these individuals. The clone appears in some persons’ bodies as a result of cross-fertilization of parents with genetically incongruent regulators of cell dividing and tissue growth. That is why the highest incidence of cancer is observed in the ethnically mixed populations. This heterozygous clone is formed and distributed in the offspring’s body before its birth and exists for many decades within the body in a dormant state. The period of dormancy is terminated according to a specific program of the clone ontogenesis. At this time, the clone demonstrates hereditary immunity against the body’s prevailing regulators of cell reproduction and begins to multiply uncontrollably, thus initiating the cancerous growth.

RURO and Sidus BioData Introduce High Performance, Ultra-Secure US & EU GxP Certified Hosting

RURO, Inc. announced that it has partnered with Sidus BioData to offer GLP/GMP certified hosting services for FreezerPro, ezColony, Sciency and LIMS 247 products. Sidus BioData provides a centralized FDA/HIPAA compliant Data Center in Annapolis, Maryland for regulated companies. The Tier 2 Annapolis Data Center has been qualified in accordance with FDA regulations.

According to Vlad Lebedev, System Architect, RURO, "Clients will benefit from a cooperative model that eliminates the need to maintain a costly internal Data Center. We provide a plug-and-play US/EU GxP compliance program that allows access to the latest technology, significantly reduces IT costs and most importantly, allows funding and resources to be focused on core business activities. A small to medium sized biotechnology company now has the resources and security of large pharma with a fraction of the investment."

 A small to medium sized biotechnology company now has the resources and security of large pharma with a fraction of the investment. "The combination of RURO products and our US & EU GxP hosting is a cost-effective solution that dramatically expands the reach of enterprise class lab management and productivity technology, which is welcome news in today’s economic environment. Whether your company is subject to 21 CFR Part 11, Eudralex Vol. 4 Annex 11, the QSR or the cGMP's - our fully qualified compliant cloud is ready to host your data." stated Cathy Shaw, Marketing Director, Sidus Group.

Cloud Computing, IaaS PaaS, SaaS Market Strategies, Shares & Forecasts, Worldwide (2010-2016)

Research and Markets announced the addition of WinterGreen Research, Inc.'s new report "Cloud Computing Stack Layers IaaS PaaS, SaaS Market Strategies, Shares, and Forecasts, Worldwide, 2010-2016" to their offering.

Applications and infrastructure markets come together to make information technology delivery a utility. On demand systems scale to meet the needs of users and users only pay for the capacity they use. Strategies relate to different ways to position software, hardware and services for the most effective product set. The 2010 study has 737 pages, 206 tables and figures.IBM is the market leader in SOA Platform as a Service (PaaS) with 73% market share. Oracle / BEA /Sun participate in the market with 6% share, Microsoft with 5% share in 2009.

The popularity of the on-demand deployment model has increased significantly. Systems provide security, response time, and service availability. SaaS software as a service application is widely known by the salesforce.com computing model illustrates. Business applications and computing models have matured and adoption has become an issue for every IT department. Platform as a service (PaaS) and infrastructure as a service (IaaS) have joined SaaS as compelling aspects of cloud computing applications and infrastructure services.

An organization's application development team and the application portfolio need to be managed as a piecemeal part of the IT infrastructure. It is generally managed on an application by application basis. Applications represent a major source of IT value and are a large IT cost component. The major management objectives for this critical area of applications implementation include improving service-oriented architecture (SOA) adoption, increasing Software Development Life Cycle (SDLC) efficiency, improving cost management, and reducing ineffective spending. The fundamental aspect of applications implementation relates to flexibility. The ability to be responsive to changing market conditions is central to the modern IT management task and the desire for systems that support that is anticipated to spur rapid growth of cloud computing. SOA services oriented architecture forms the base for achieving that capability.

Protein folding stability and dynamics imaged in a living cell

Biomolecular dynamics and stability are predominantly investigated in vitro and extrapolated to explain function in the living cell. We present fast relaxation imaging (FreI), which combines fluorescence microscopy and temperature jumps to probe biomolecular dynamics and stability inside a single living cell with high spatiotemporal resolution. We demonstrated the method by measuring the reversible fast folding kinetics as well as folding thermodynamics of a fluorescence resonance energy transfer (FRET) probe-labeled phosphoglycerate kinase construct in two human cell lines. Comparison with in vitro experiments at 23–49 °C showed that the cell environment influences protein stability and folding rate. FReI should also be applicable to the study of protein-protein interactions and heat-shock responses as well as to comparative studies of cell populations or whole organisms. See the April 2010 issue of Nature Methods for in-depth research results

Chromosome 9p21 SNPs Associated with Multiple Disease Phenotypes Correlate with ANRIL Expression

Single nucleotide polymorphisms (SNPs) on chromosome 9p21 are associated with coronary artery disease, diabetes, and multiple cancers. Risk SNPs are mainly non-coding, suggesting that they influence expression and may act in cis. We examined the association between 56 SNPs in this region and peripheral blood expression of the three nearest genes CDKN2A, CDKN2B, and ANRIL using total and allelic expression in two populations of healthy volunteers: 177 British Caucasians and 310 mixed-ancestry South Africans. Total expression of the three genes was correlated (P<0.05), suggesting that they are co-regulated. SNP associations mapped by allelic and total expression were similar (r = 0.97, P = 4.8×10−99), but the power to detect effects was greater for allelic expression. The proportion of expression variance attributable to cis-acting effects was 8% for CDKN2A, 5% for CDKN2B, and 20% for ANRIL. SNP associations were similar in the two populations (r = 0.94, P = 10−72). Multiple SNPs were independently associated with expression of each gene (P<0.05 after correction for multiple testing), suggesting that several sites may modulate disease susceptibility. Individual SNPs correlated with changes in expression up to 1.4-fold for CDKN2A, 1.3-fold for CDKN2B, and 2-fold for ANRIL. Risk SNPs for coronary disease, stroke, diabetes, melanoma, and glioma were all associated with allelic expression of ANRIL (all P<0.05 after correction for multiple testing), while association with the other two genes was only detectable for some risk SNPs. SNPs had an inverse effect on ANRIL and CDKN2B expression, supporting a role of antisense transcription in CDKN2B regulation. Our study suggests that modulation of ANRIL expression mediates susceptibility to several important human diseases. Review the PLoS Genetics web site for full research findings

The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to their 5' termini

As a part of an initiative aimed at a large-scale comparative analysis of fungal mitochondrial genomes, we determined the complete DNA sequence of the mitochondrial genome of the yeast Candida subhashii and found that it exhibits a number of peculiar features. First, the mitochondrial genome is represented by linear double-stranded DNA molecules of uniform length (29,795-bp), with an unusually high content of guanine and cytosine residues (52.7%). Second, the coding sequences lack introns; thus, the genome has a relatively compact organization. Third, the termini of the linear molecules consist of long inverted repeats and seem to contain a protein covalently bound to terminal nucleotides at the 5' ends. 

This architecture resembles the telomeres in a number of linear viral and plasmid DNA genomes classified as invertrons, in which the terminal proteins serve as specific primers for the initiation of DNA synthesis. Finally, although the mitochondrial genome of C. subhashii contains essentially the same set of genes as other closely related pathogenic Candida species, we identified additional open reading frames coding for two homologs of the family B protein-priming DNA polymerases and an unknown protein. The terminal structures and the genes for DNA polymerases are reminiscent of linear mitochondrial plasmids, indicating that this genome architecture might have emerged from fortuitous recombination between an ancestral, presumably circular, mitochondrial genome and an invertron-like element.

How the young brigade mapped the TB genome

When nearly 400 motivated students, with the help of a few faculty and scientists, get together voluntarily and work single-mindedly, solving any complex problem can turn out to be child's play. These students, with a few exceptions, were trying to solve a complex problem during their free time after attending classes or studying for an exam. They spent more than six hours every day for four months to achieve their goal. That the entire exercise was done through online interaction did not in any way cause any problems. They succeeded though some of them had never studied bioinformatics, so essential for such work. What is significant is that some were only doing their under-graduation.

The fact that there would be no monetary gain from solving the mega scientific puzzle had little bearing. Many of the students had never read a peer-reviewed paper published in journals like Science and Nature. That, in a nutshell, is the story of how the young brigade went about mapping the TB genome in just four months despite many limitations.

The TB genome contains nearly 4,000 genes. The functions of nearly 1,500 genes were not known. And a flood of information contained in hundreds of published peer-reviewed papers was to be culled out. And for those genes that were not annotated (functions not known), the predicted functions were computationally extrapolated by them. Quality checks were done onsite by students and their Principal Investigators (PI). The TB gene map was finally produced by combining the already annotated genes and those that were computationally extrapolated.