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Evolution and Medicine: An Inquiry-Based High School Curriculum Supplement

Evolution: Education and Outreach 2011年第4期4卷 603-612页

作者： Beardsley, Paul M. Stuhlsatz, Molly A.M. Kruse, Rebecca A. Eckstrand, Irene A. Gordon, Shefa D. Odenwald, Ward F. BSCS (Biological Sciences Curriculum Study) 5415 Mark Dabling Blvd Colorado Springs 80918 CO United States National Institute of General Medical Sciences Division of Genetics and Developmental Biology Center for Bioinformatics and Computational Biology 45 Center Drive Bethesda 20892-6200 MD United States National Eye Institute Office of Program Planning and Analysis 9000 Rockville Pike Bethesda 20892-6200 MD United States National Institute of Neurological Disorders and Stroke Neural Cell-Fate Determinants Section Bethesda 20892-6200 MD United States Center for Excellence in Mathematics and Science Teaching and Department of Biological Sciences CEMaST 4-2-515 California State Polytechnic University 3801 W. Temple Ave. Pomona 91768 CA United States

Evolution and Medicine is a curriculum supplement designed by the National Institutes of Health (NIH) and the Biological Sciences Curriculum Study (BSCS) for high school students. The supplement is freely available from NIH's Office of Science Education (OSE) as a part of the NIH curriculum supplement series. Development of the supplement was a collaborative effort that included input from a panel of experts in medicine, evolution, education, and educational technology. In total, the curriculum supplement includes five inquiry-based lessons that are integrated into the BSCS 5E instructional model (based on constructivist learning theory). The goal was to develop a 2-week curriculum to help students understand major concepts of evolution using the dynamic, modern, and relevant context of medicine. A diverse group of students and teachers across the US participated in a formative evaluation of a field test version of the curriculum. High school students made significant learning gains from pretest to posttest, with a relatively large effect size for student understanding of common ancestry and a relatively small effect size for student understanding of natural selection. There was no statistically significant difference in achievement gains between white students and all other racial/ethnic categories. Overall, the evaluation suggests that a curriculum that emphasizes the role of evolution in medicine, uses a constructivist instructional model, and is grounded in inquiry is relatively well-received by teachers and students and shows promise for increasing student learning in evolution. © 2011 Springer Science+Business Media, LLC.

关键词： Common ancestry Evolution Evolution and medicine High school Inquiry Instructional model Natural selection

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MetNetAPI: A flexible method to access and manipulate biological network data from MetNet

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BMC Research Notes 2010年第1期3卷 1-9页

作者： Sucaet, Yves Wurtele, Eve Syrkin Department of Genetics Development and Cell Biology Iowa State University Ames IA 50011 United States Interdepartmental Program in Bioinformatics and Computational Biology Iowa State University Ames IA 50011 United States

Background. Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Results. MetNetAPI is a versatile Application programming Interface (API) to the MetNetDB database. It abstracts, captures and retains operations away from a biological network repository and website. A range of database functions, previously only available online, can be immediately (and independently from the website) applied to a dataset of interest. Data is available in four layers: molecular entities, localized entities (linked to a specific organelle), interactions, and pathways. Navigation between these layers is intuitive (e.g. one can request the molecular entities in a pathway, as well as request in what pathways a specific entity participates). Data retrieval can be customized: Network objects allow the construction of new and integration of existing pathways and interactions, which can be uploaded back to our server. In contrast to webservices, the computational demand on the host server is limited to processing data-related queries only. Conclusions. An API provides several advantages to a systems biology software platform. MetNetAPI illustrates an interface with a central repository of data that represents the complex interrelationships of a metabolic and regulatory network. As an alternative to data-dumps and webservices, it allows access to a current and "live" database and exposes analytical functions to application developers. Yet it only requires limited resources on the server-side (thin server/fat client setup). The API is available for Java, *** and R programming environments and offers flexible query and bro

关键词： Application program Interface Molecular Entity Biological Database Command Line Interface Network Object

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PS2-108. Infection with Hepatitis C down-regulates the expression of cytokine genes in peripheral blood

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Cytokine 2011年第1期56卷 94-94页

作者： Milton W. Taylor Christopher R. Bolen Steven H. Kleinstein Leonid Brodsky Department of Biology Indiana University Bloomington IN 47401 USA 1Interdepartmental Program in Computational Biology and Bioinformatics Yale University 300 George St. Suite 501 New Haven CT 06511 USA Department of Pathology Yale University School of Medicine New Haven CT USA Institute of Evolution University of Haifa Mount Carmel Haifa 31905 Israel

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Characterizing the tumor microenvironmental changes in a network perspective

Characterizing the tumor microenvironmental changes in a net...

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第四届全国生物信息学与系统生物学学术大会

作者：李文婷王瑞孙之荣 Institute of Bioinformatics School of Life SciencesTsinghua University Computational Biology and Bioinformatics Program Institute for Genome Science and PolicyDuke University Medical CenterDurhamNC27705

Alternations in tumor microenvironment are critical in driving tumor development. However,it proves difficult to characterize their molecular components and further relate to important pathological *** using a network approach,we characterized systematic expression changes at multi-gene module levels between colorectal tumors with and without recurrence after surgery and confirmed their association with two critical

关键词： Characterizing the tumor microenvironmental changes in a network perspective

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Dynamic and static analysis of transcriptional regulatory networks in a hierarchical context

Dynamic and static analysis of transcriptional regulatory ne...

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IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)

作者： Nitin Bhardwaj Mark Gerstein Program in Computational Biology and Bioinformatics Yale University New Heaven CT USA Department of Computer Science Yale University New Heaven CT USA

Gene regulatory networks have been shown to share some common aspects with commonplace social governance structures such as hierarchies. Thus, we can get some intuition into their organization by arranging them into well-known hierarchical layouts. Here we study a wide range of regulatory networks (transcriptional, modification and phosphorylation) in a hierarchical context for five evolutionarily diverse species. We specify three levels of regulators - top, middle and bottom - which collectively regulate the non-regulator targets lying in the lowest fourth level, and we define quantities for nodes, levels and entire networks that measure their degree of collaboration and autocratic or democratic character. Overall we show that in all the networks studied, the middle level has the highest collaborative propensity and that co-regulatory partnerships occur most frequently amongst mid-level regulators, an observation that has parallels in efficient corporate settings where middle managers need to interact most to ensure organizational effectiveness. Then to study dynamic effects, superimpose the phenotypic effects of tampering with nodes and edges directly onto the hierarchies. We reconstruct modified hierarchies reflecting changes in the level of regulators within the hierarchy upon deletions or insertions of nodes or edges. Overall, we find that rewiring events that affect upper levels have a more dramatic effect on cell proliferation rate and survival than do those involving lower levels. We also investigate other features connected to the importance of upper-level regulators: expression divergence, back-up copies and expression level.

关键词： Regulators Collaboration Context bioinformatics Biochemistry Molecular biophysics Performance analysis

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Characterization of the retinal proteome during rod photoreceptor genesis

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BMC Research Notes 2010年第1期3卷 1-8页

作者： Barnhill, Alison E Hecker, Laura A Kohutyuk, Oksana Buss, Janice E Honavar, Vasant G Greenlee, Heather West Interdepartmental Neuroscience Program Iowa State University Ames IA United States Department of Biomedical Sciences Iowa State University Ames IA United States Bioinformatics and Computational Biology Program Iowa State University Ames IA United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA United States Department of Computer Science Iowa State University Ames IA United States National Animal Disease Center Ames IA 50010 United States Mayo Clinic Department of Ophthalmology Rochester MN 55905 United States

Background. The process of rod photoreceptor genesis, cell fate determination and differentiation is complex and multi-factorial. Previous studies have defined a model of photoreceptor differentiation that relies on intrinsic changes within the presumptive photoreceptor cells as well as changes in surrounding tissue that are extrinsic to the cell. We have used a proteomics approach to identify proteins that are dynamically expressed in the mouse retina during rod genesis and differentiation. Findings. A series of six developmental ages from E13 to P5 were used to define changes in retinal protein expression during rod photoreceptor genesis and early differentiation. Retinal proteins were separated by isoelectric focus point and molecular weight. Gels were analyzed for changes in protein spot intensity across developmental time. Protein spots that peaked in expression at E17, P0 and P5 were picked from gels for identification. There were 239 spots that were picked for identification based on their dynamic expression during the developmental period of maximal rod photoreceptor genesis and differentiation. Of the 239 spots, 60 of them were reliably identified and represented a single protein. Ten proteins were represented by multiple spots, suggesting they were post-translationally modified. Of the 42 unique dynamically expressed proteins identified, 16 had been previously reported to be associated with the developing retina. Conclusions. Our results represent the first proteomics study of the developing mouse retina that includes prenatal development. We identified 26 dynamically expressed proteins in the developing mouse retina whose expression had not been previously associated with retinal development. © 2010 Greenlee et al.;licensee BioMed Central Ltd.

关键词： Protein Spot Mouse Retina Retinal Development Retinal Protein Probability Base Mowse Score

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Analysis of cancer omics data in a semantic web framework

Analysis of cancer omics data in a semantic web framework

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Workshop on Semantic Web Applications and Tools for Life Sciences 2010, SWAT4LS 2010

作者： Holford, Matthew E. McCusker, James P. Cheung, Kei-Hoi Krauthammer, Michael Interdepartmental Program in Computational Biology and Bioinformatics Yale University New Haven CT United States Department of Pathology Yale University New Haven CT United States Department of Computer Science Yale University New Haven CT United States Center for Medical Informatics Yale University New Haven CT United States Department of Genetics Yale University New Haven CT United States

Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancer cell's molecular state and its response to anti-cancer therapy. To study the problem, we have previously focused on data warehousing technologies and statistical data integration. In this paper, we present recent work on extending our analytical capabilities using Semantic Web technology. A key new component presented here is a SPARQL endpoint to our existing data warehouse. This endpoint allows the merging of observed quantitative data with existing data from semantic knowledge sources such as Gene Ontology (GO). We show how such variegated quantitative and functional data can be integrated and accessed in a universal manner using Semantic Web tools. We also demonstrate how Description Logic (DL) reasoning can be used to infer previously unstated conclusions from existing knowledge bases. As proof of concept, we illustrate the ability of our setup to answer complex queries on resistance of cancer cells to Decitabine, a demethylating agent.

关键词： Semantic Web

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Multistate modeling and simulation for regulatory networks 10

Multistate modeling and simulation for regulatory networks

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Simulation Winter Conference

作者： Zhen Liu Umme Juka Mobassera Clifford A. Shaffer Layne T. Watson Yang Cao Department of Computer Science Virginia Technology Blacksburg VA USA Program in Genetics Bioinformatics and Computational Biology Virginia Technology Blacksburg VA USA Department of Computer Science Department of Mathematics Virginia Technology Blacksburg VA USA

ISBN: (纸本)9781424498642

Many protein regulatory models contain chemical species best represented as having multiple states. Such models stem from the potential for multiple levels of phosphorylation or from the formation of multiprotein complexes. We seek to support such models by augmenting an existing modeling and simulation system. Interactions between multistate species can lead to a combinatorial explosion in the potential state space. This creates a challenge when using Gillespie's stochastic simulation algorithm (SSA). Both the network-free algorithm (NFA) and various rules-based methods have been proposed to more efficiently simulate such models. We show how to further improve NFA to integrate population-based and particle-based features. We then present a population-based scheme for the stochastic simulation of rule-based models. A complexity analysis is presented comparing the proposed simulation methods. We present numerical experiments for two sample models that demonstrate the power of the proposed simulation methods.

关键词： Mathematical model Biological system modeling Numerical models Chemicals Stochastic processes Equations Proteins

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Computing H/D-Exchange rates of single residues from data of proteolytic fragments

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BMC bioinformatics 2010年第1期11卷 1-12页

作者： Althaus, Ernst Canzar, Stefan Ehrler, Carsten Emmett, Mark R. Karrenbauer, Andreas Marshall, Alan G. Meyer-Bäse, Anke Tipton, Jeremiah D. Zhang, Hui-Min Institut für Informatik Fachbereich 08 Staudingerweg 9 55099 Mainz Germany Algorithmic Computational Biology Centrum Wiskunde and Informatica Amsterdam Netherlands Center for Bioinformatics Computer Science Department Saarland University 66041 Saarbrücken Germany Ion Cyclotron Resonance Program National High Magnetic Field Laboratory Florida State University 1800 East Paul Dirac Drive Tallahassee FL 32310-4005 United States Department of Chemistry and Biochemistry Florida State University 95 Chieftain Way Tallahassee FL 32306 United States Institute of Mathematics EPFL Station 8 1015 Lausanne Switzerland Department of Scientific Computing Florida State University Tallahassee FL 32306-4120 United States

Background: Protein conformation and protein/protein interaction can be elucidated by solution-phase Hydrogen/Deuterium exchange (sHDX) coupled to high-resolution mass analysis of the digested protein or protein complex. In sHDX experiments mutant proteins are compared to wild-type proteins or a ligand is added to the protein and compared to the wild-type protein (or mutant). The number of deuteriums incorporated into the polypeptides generated from the protease digest of the protein is related to the solvent accessibility of amide protons within the original protein ***: In this work, sHDX data was collected on a 14.5 T FT-ICR MS. An algorithm was developed based on combinatorial optimization that predicts deuterium exchange with high spatial resolution based on the sHDX data of overlapping proteolytic fragments. Often the algorithm assigns deuterium exchange with single residue ***: With our new method it is possible to automatically determine deuterium exchange with higher spatial resolution than the level of digested fragments. © 2010 Althaus et al;licensee BioMed Central Ltd.

关键词： Proteins

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Genetic correlates of autoreactivity and autoreactive potential in human Ig heavy chains

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Immunome Research 2009年第1期5卷 1-8页

作者： Volpe, Joseph M Kepler, Thomas B Center for Computational Immunology Duke University Durham NC United States Departments of Biostatistics and Bioinformatics and Immunology Duke University Medical Center Durham NC United States Computational Biology and Bioinformatics Graduate Program Institute for Genome Sciences and Policy Duke University Durham NC United States

Background. Immature bone marrow B cells are known to have longer CDR3 than mature peripheral B cells, and this genetic characteristic has been shown to correlate with autoreactivity in these early cells. B-cell Central tolerance eliminates these cells, but it is known that autoreactive B cells nevertheless appear commonly in healthy human blood. We examined over 7,300 Ig genes from Genbank, including those annotated by their discoverers as associated with autoreactivity, to determine the genetic correlates of autoreactivity in mature B cells. Results. We find differential biases in gene segment usage and higher mutation frequency in autoreactivity-associated Ig genes, but the CDR3 lengths do not differ between autoreactive and non-autoreactive Ig genes. The most striking genetic signature of autoreactivity is an increase in the proportion of N-nucleotides relative to germline-encoded nucleotides in CDR3 from autoreactive genes. Conclusion. We hypothesize that peripheral autoreactivity results primarily from somatic mutation, and that the genetic correlates of autoreactivity in mature B-cells are not the same as those for autoreactivity in immature B cells. What is seen in mature autoreactive B cells are the correlates of autoreactive potential, not of autoreactivity per se. The autoreactive potential is higher for V(D)J rearrangements encoded to a large extent by N-nucleotides rather than by the gene segments that, we posit, have been selected in germline evolution for their suppression of autoreactive potential.

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