75 FR 23221 - Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-03

...] Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological Control Agent for Water Hyacinth AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice. SUMMARY... the severity of water hyacinth infestations. Based on its finding of no significant impact, the Animal...

Mining and integration of pathway diagrams from imaging data.

PubMed

Kozhenkov, Sergey; Baitaluk, Michael

2012-03-01

Pathway diagrams from PubMed and World Wide Web (WWW) contain valuable highly curated information difficult to reach without tools specifically designed and customized for the biological semantics and high-content density of the images. There is currently no search engine or tool that can analyze pathway images, extract their pathway components (molecules, genes, proteins, organelles, cells, organs, etc.) and indicate their relationships. Here, we describe a resource of pathway diagrams retrieved from article and web-page images through optical character recognition, in conjunction with data mining and data integration methods. The recognized pathways are integrated into the BiologicalNetworks research environment linking them to a wealth of data available in the BiologicalNetworks' knowledgebase, which integrates data from >100 public data sources and the biomedical literature. Multiple search and analytical tools are available that allow the recognized cellular pathways, molecular networks and cell/tissue/organ diagrams to be studied in the context of integrated knowledge, experimental data and the literature. BiologicalNetworks software and the pathway repository are freely available at www.biologicalnetworks.org. Supplementary data are available at Bioinformatics online.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

The shortest path is not the one you know: application of biological network resources in precision oncology research.

PubMed

Kuperstein, Inna; Grieco, Luca; Cohen, David P A; Thieffry, Denis; Zinovyev, Andrei; Barillot, Emmanuel

2015-03-01

Several decades of molecular biology research have delivered a wealth of detailed descriptions of molecular interactions in normal and tumour cells. This knowledge has been functionally organised and assembled into dedicated biological pathway resources that serve as an invaluable tool, not only for structuring the information about molecular interactions but also for making it available for biological, clinical and computational studies. With the advent of high-throughput molecular profiling of tumours, close to complete molecular catalogues of mutations, gene expression and epigenetic modifications are available and require adequate interpretation. Taking into account the information about biological signalling machinery in cells may help to better interpret molecular profiles of tumours. Making sense out of these descriptions requires biological pathway resources for functional interpretation of the data. In this review, we describe the available biological pathway resources, their characteristics in terms of construction mode, focus, aims and paradigms of biological knowledge representation. We present a new resource that is focused on cancer-related signalling, the Atlas of Cancer Signalling Networks. We briefly discuss current approaches for data integration, visualisation and analysis, using biological networks, such as pathway scoring, guilt-by-association and network propagation. Finally, we illustrate with several examples the added value of data interpretation in the context of biological networks and demonstrate that it may help in analysis of high-throughput data like mutation, gene expression or small interfering RNA screening and can guide in patients stratification. Finally, we discuss perspectives for improving precision medicine using biological network resources and tools. Taking into account the information about biological signalling machinery in cells may help to better interpret molecular patterns of tumours and enable to put precision oncology into general clinical practice. © The Author 2015. Published by Oxford University Press on behalf of the UK Environmental Mutagen Society. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Access to biologicals in Crohn’s disease in ten European countries

PubMed Central

Péntek, Márta; Lakatos, Peter L; Oorsprong, Talitha; Gulácsi, László; Pavlova, Milena; Groot, Wim; Rencz, Fanni; Brodszky, Valentin; Baji, Petra; Crohn’s Disease Research Group

2017-01-01

AIM To analyze access (availability, affordability and acceptability) to biologicals for Crohn’s disease (CD) in ten European countries and to explore the associations between these dimensions, the uptake of biologicals and economic development. METHODS A questionnaire-based survey combined with desk research was carried out in May 2016. Gastroenterologists from the Czech Republic, France, Germany, Hungary, Latvia, Poland, Romania, Slovakia, Spain and Sweden were invited to participate and provide data on the availability of biologicals/biosimilars, reimbursement criteria, clinical practice and prices, and use of biologicals. An availability score was developed to evaluate the restrictiveness of eligibility and administrative criteria applied in the countries. Affordability was defined as the annual cost of treatment as a share of gross domestic product (GDP) per capita. Correlations with the uptake of biologicals, dimensions of access and GDP per capita were calculated. RESULTS At the time of the survey, infliximab and adalimumab were reimbursed in all ten countries, and vedolizumab was reimbursed in five countries (France, Germany, Latvia, Slovakia, Sweden). Reimbursement criteria were the least strict in Sweden and Germany, and the strictest in Hungary, Poland and Slovakia. Between countries, the annual cost of different biological treatments differed 1.6-3.3-fold. Treatments were the most affordable in Sweden (13%-37% of the GDP per capita) and the least affordable in the Central and Eastern European countries, especially in Hungary (87%-124%) and Romania (141%-277%). Biosimilars made treatments more affordable by driving down the annual costs. The number of patients with CD on biologicals per 100000 population was strongly correlated with GDP per capita (0.91), although substantial differences were found in the uptake among countries with similar economic development. Correlation between the number of patients with CD on biologicals per 100000 population and the availability and affordability was also strong (-0.75, -0.69 respectively). CONCLUSION Substantial inequalities in access to biologicals were largely associated with GDP. To explain differences in access among countries with similar development needs further research on acceptance. PMID:28974896

C. elegans network biology: a beginning.

PubMed Central

Piano, Fabio; Gunsalus, Kristin C; Hill, David E; Vidal, Marc

2006-01-01

The architecture and dynamics of molecular networks can provide an understanding of complex biological processes complementary to that obtained from the in-depth study of single genes and proteins. With a completely sequenced and well-annotated genome, a fully characterized cell lineage, and powerful tools available to dissect development, Caenorhabditis elegans, among metazoans, provides an optimal system to bridge cellular and organismal biology with the global properties of macromolecular networks. This chapter considers omic technologies available for C. elegans to describe molecular networks--encompassing transcriptional and phenotypic profiling as well as physical interaction mapping--and discusses how their individual and integrated applications are paving the way for a network-level understanding of C. elegans biology. PMID:18050437

Survey of Biology Capstone Courses in American and Canadian Higher Education: Requirement, Content, and Skills

ERIC Educational Resources Information Center

Haave, Neil C.

2015-01-01

Capstone experiences have high educational impact with various approaches available for biology. However, no information exists regarding the pervasiveness of capstone courses in Canadian and American biology programs. This study surveyed the prevalence and character of biology capstone courses in the USA and Canada. The survey included a majority…

ZINC: A Free Tool to Discover Chemistry for Biology

PubMed Central

2012-01-01

ZINC is a free public resource for ligand discovery. The database contains over twenty million commercially available molecules in biologically relevant representations that may be downloaded in popular ready-to-dock formats and subsets. The Web site also enables searches by structure, biological activity, physical property, vendor, catalog number, name, and CAS number. Small custom subsets may be created, edited, shared, docked, downloaded, and conveyed to a vendor for purchase. The database is maintained and curated for a high purchasing success rate and is freely available at zinc.docking.org. PMID:22587354

Forty Years of Ebolavirus Molecular Biology: Understanding a Novel Disease Agent Through the Development and Application of New Technologies.

PubMed

Groseth, Allison; Hoenen, Thomas

2017-01-01

Molecular biology is a broad discipline that seeks to understand biological phenomena at a molecular level, and achieves this through the study of DNA, RNA, proteins, and/or other macromolecules (e.g., those involved in the modification of these substrates). Consequently, it relies on the availability of a wide variety of methods that deal with the collection, preservation, inactivation, separation, manipulation, imaging, and analysis of these molecules. As such the state of the art in the field of ebolavirus molecular biology research (and that of all other viruses) is largely intertwined with, if not driven by, advancements in the technical methodologies available for these kinds of studies. Here we review of the current state of our knowledge regarding ebolavirus biology and emphasize the associated methods that made these discoveries possible.

easyDAS: Automatic creation of DAS servers

PubMed Central

2011-01-01

Background The Distributed Annotation System (DAS) has proven to be a successful way to publish and share biological data. Although there are more than 750 active registered servers from around 50 organizations, setting up a DAS server comprises a fair amount of work, making it difficult for many research groups to share their biological annotations. Given the clear advantage that the generalized sharing of relevant biological data is for the research community it would be desirable to facilitate the sharing process. Results Here we present easyDAS, a web-based system enabling anyone to publish biological annotations with just some clicks. The system, available at http://www.ebi.ac.uk/panda-srv/easydas is capable of reading different standard data file formats, process the data and create a new publicly available DAS source in a completely automated way. The created sources are hosted on the EBI systems and can take advantage of its high storage capacity and network connection, freeing the data provider from any network management work. easyDAS is an open source project under the GNU LGPL license. Conclusions easyDAS is an automated DAS source creation system which can help many researchers in sharing their biological data, potentially increasing the amount of relevant biological data available to the scientific community. PMID:21244646

76 FR 77234 - Availability of Draft Vieques Report: An Evaluation of Environmental, Biological, and Health Data...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-12

... From the Island of Vieques, Puerto Rico AGENCY: Agency for Toxic Substances and Disease Registry (ATSDR... Environmental, Biological, and Health Data from the Island of Vieques, Puerto Rico for review and comment. This... health and the residents of Vieques, Puerto Rico. The Draft Vieques Report is available in English and...

76 FR 4859 - Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

...] Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological Control Agent... environmental assessment and finding of no significant impact relative to the control of Asian citrus psyllid... the control of ACP. \\1\\ To view the notice, environmental assessment, finding of no significant impact...

76 FR 42675 - Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-19

...] Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological Control Agent.... SUMMARY: We are advising the public that an environmental assessment and finding of no significant impact... woolly adelgid. Based on its finding of no significant impact, the Animal and Plant Health Inspection...

75 FR 6401 - Medical Devices Regulated by the Center for Biologics Evaluation and Research; Availability of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-09

... premarket approval applications (PMAs) that have been approved by the Center for Biologics Evaluation and Research (CBER). This list is intended to inform the public of the availability through the Internet and... post this information on the Internet at http://www.fda.gov . In addition, the regulations provide that...

Improving oral bioavailability of cyclic peptides by N-methylation.

PubMed

Räder, Andreas F B; Reichart, Florian; Weinmüller, Michael; Kessler, Horst

2018-06-01

The renaissance of peptides in pharmaceutical industry results from their importance in many biological functions. However, low metabolic stability and the lack of oral availability of most peptides is a certain limitation. Whereas metabolic instability may be often overcome by development of small cyclic peptides containing d-amino acids, the very low oral availability of most peptides is a serious limitation for some medicinal applications. The situation is complicated because a twofold optimization - biological activity and oral availability - is required to overcome this problem. Moreover, most simple "rules" for achieving oral availability are not general and are applicable only to limited cases. Many structural modifications for increasing biological activities and metabolic stabilities of cyclic peptides have been described, of which N-alkylation is probably the most common. This mini-review focuses on the effects of N-methylation of cyclic peptides in strategies to optimize bioavailabilities. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Biologic agents for IBD: practical insights.

PubMed

Danese, Silvio; Vuitton, Lucine; Peyrin-Biroulet, Laurent

2015-09-01

Six biologic agents are currently approved for the treatment of IBD: four anti-TNF agents (infliximab, adalimumab, golimumab and certolizumab pegol) and two anti-integrin agents (natalizumab and vedolizumab). In Crohn's disease and ulcerative colitis refractory to standard medications, treatment choice among available biologic agents can be challenging. Several parameters should be taken into account to help physicians through the decision-making process, including the comparative effectiveness and long-term safety profile, availability and labelling in the prescriber's country, international guidelines, and cost, as well as patient preferences (such as the route of administration). Herein, we provide practical insights on the use of biologic agents in IBD. The results of head-to-head trials between biologic agents are eagerly awaited to guide decision-making regarding the choice of first-line biologic agents and to determine whether switching within the same drug class or swapping (switching out of the drug class) is preferable after primary or secondary loss of response to the first biologic agent. In the near future, treatment algorithms might evolve with the launch of new drugs (such as ustekinumab, tofacitinib and etrolizumab) and the increased use of biosimilars.

Sporotrichosis: From KOH to Molecular Biology.

PubMed

Arenas, Roberto; Sánchez-Cardenas, Carlos D; Ramirez-Hobak, Lourdes; Ruíz Arriaga, Leon Felipe; Vega Memije, Ma Elisa

2018-05-23

Sporotrichosis is a cosmopolitan, chronic granulomatous mycosis, acquired by traumatic inoculation and caused by Sporothrix schenckii complex . Several methods of diagnostic are available, from KOH to molecular biology. In this review, we describe from the simplest (clinical diagnosis) to the most advanced diagnostic techniques (molecular biology).

Use of Internet Resources in the Biology Lecture Classroom.

ERIC Educational Resources Information Center

Francis, Joseph W.

2000-01-01

Introduces internet resources that are available for instructional use in biology classrooms. Provides information on video-based technologies to create and capture video sequences, interactive web sites that allow interaction with biology simulations, online texts, and interactive videos that display animated video sequences. (YDS)

Chemical and Biological Terrorism: Current Updates for Nurse Educators.

ERIC Educational Resources Information Center

Veenema, Tener Goodwin

2002-01-01

Describes eight topics related to chemical/biological terrorism for a standalone nursing course or integration into other courses: surveillance systems; identification, communication, and response; chemical agents; biological agents; recognition of covert exposure; patient decontamination and mass triage; availability and safety of therapies; and…

Options for Online Undergraduate Courses in Biology at American Colleges and Universities.

PubMed

Varty, Alison K

I aimed to document the online undergraduate course supply in biology to evaluate how well biology educators are serving the diverse and growing population of online students. I documented online biology course offerings in the 2015-2016 academic year at 96 American colleges and universities. I quantified differences in variety, extent, and availability of courses offered by different kinds of academic institutions and characterized 149 online biology courses offered. Although there was no relationship between an institution's enrollment size and any measure of its online biology offerings, I found significantly more online biology course options at 2-year public compared with 4-year public and 4-year private schools. Courses offered for nonmajors, including students pursuing healthcare-related degrees, were three times as common as those intended for biology majors, who were more likely to be offered hybrid courses with face-to-face laboratories. These data indicate some deficiencies in online biology course options; options for students majoring in biology are limited at all types of institutions examined with a minority of 4-year institutions having any online options in biology. Significant investment of institutional resources in faculty training and technological support are necessary to develop online biology courses that will benefit a larger student population. © 2016 A. K. Varty. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

IBS: an illustrator for the presentation and visualization of biological sequences

PubMed Central

Liu, Wenzhong; Xie, Yubin; Ma, Jiyong; Luo, Xiaotong; Nie, Peng; Zuo, Zhixiang; Lahrmann, Urs; Zhao, Qi; Zheng, Yueyuan; Zhao, Yong; Xue, Yu; Ren, Jian

2015-01-01

Summary: Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. Availability and implementation: The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. Contact: renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26069263

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

PubMed

Yang, Kun; Stracquadanio, Giovanni; Luo, Jingchuan; Boeke, Jef D; Bader, Joel S

2016-03-15

Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder joel.bader@jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Signaling gateway molecule pages—a data model perspective

PubMed Central

Dinasarapu, Ashok Reddy; Saunders, Brian; Ozerlat, Iley; Azam, Kenan; Subramaniam, Shankar

2011-01-01

Summary: The Signaling Gateway Molecule Pages (SGMP) database provides highly structured data on proteins which exist in different functional states participating in signal transduction pathways. A molecule page starts with a state of a native protein, without any modification and/or interactions. New states are formed with every post-translational modification or interaction with one or more proteins, small molecules or class molecules and with each change in cellular location. State transitions are caused by a combination of one or more modifications, interactions and translocations which then might be associated with one or more biological processes. In a characterized biological state, a molecule can function as one of several entities or their combinations, including channel, receptor, enzyme, transcription factor and transporter. We have also exported SGMP data to the Biological Pathway Exchange (BioPAX) and Systems Biology Markup Language (SBML) as well as in our custom XML. Availability: SGMP is available at www.signaling-gateway.org/molecule. Contact: shankar@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21505029

Biological Remediation of Petroleum Contaminants

NASA Astrophysics Data System (ADS)

Kuhad, Ramesh Chander; Gupta, Rishi

Large volumes of hazardous wastes are generated in the form of oily sludges and contaminated soils during crude oil transportation and processing. Although many physical, chemical and biological treatment technologies are available for petroleum contaminants petroleum contaminants in soil, biological methods have been considered the most cost-effective. Practical biological remediation methods typically involve direct use of the microbes naturally occurring in the contaminated environment and/or cultured indigenous or modified microorganisms. Environmental and nutritional factors, including the properties of the soil, the chemical structure of the hydrocarbon(s), oxygen, water, nutrient availability, pH, temperature, and contaminant bioavailability, can significantly affect the rate and the extent of hydrocarbon biodegradation hydrocarbon biodegradation by microorganisms in contaminated soils. This chapter concisely discusses the major aspects of bioremediation of petroleum contaminants.

GENIUS: web server to predict local gene networks and key genes for biological functions.

PubMed

Puelma, Tomas; Araus, Viviana; Canales, Javier; Vidal, Elena A; Cabello, Juan M; Soto, Alvaro; Gutiérrez, Rodrigo A

2017-03-01

GENIUS is a user-friendly web server that uses a novel machine learning algorithm to infer functional gene networks focused on specific genes and experimental conditions that are relevant to biological functions of interest. These functions may have different levels of complexity, from specific biological processes to complex traits that involve several interacting processes. GENIUS also enriches the network with new genes related to the biological function of interest, with accuracies comparable to highly discriminative Support Vector Machine methods. GENIUS currently supports eight model organisms and is freely available for public use at http://networks.bio.puc.cl/genius . genius.psbl@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Development of a biologically based fertilizer, incorporating Bacillus megaterium A6, for improved phosphorus nutrition of oilseed rape.

PubMed

Hu, Xiaojia; Roberts, Daniel P; Xie, Lihua; Maul, Jude E; Yu, Changbing; Li, Yinshui; Zhang, Shujie; Liao, Xing

2013-04-01

Sustainable methods with diminished impact on the environment need to be developed for the production of oilseed rape in China and other regions of the world. A biological fertilizer consisting of Bacillus megaterium A6 cultured on oilseed rape meal improved oilseed rape seed yield (P < 0.0001) relative to the nontreated control in 2 greenhouse pot experiments using natural soil. This treatment resulted in slightly greater yield than oilseed rape meal without strain A6 in 1 of 2 experiments, suggesting a role for strain A6 in improving yield. Strain A6 was capable of solubilizing phosphorus from rock phosphate in liquid culture and produced enzymes capable of mineralizing organic phosphorus (acid phosphatase, phytase) in liquid culture and in the biological fertilizer. The biologically based fertilizer, containing strain A6, improved plant phosphorus nutrition in greenhouse pot experiments resulting in significantly greater available phosphorus in natural soil and in significantly greater plant phosphorus content relative to the nontreated control. Seed yield and available phosphorus in natural soil were significantly greater with a synthetic chemical fertilizer treatment, reduced in phosphorus content, than the biological fertilizer treatment, but a treatment containing the biological fertilizer combined with the synthetic fertilizer provided the significantly greatest seed yield, available phosphorus in natural soil, and plant phosphorus content. These results suggest that the biological fertilizer was capable of improving oilseed rape seed yield, at least in part, through the phosphorus-solubilizing activity of B. megaterium A6.

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems

PubMed Central

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K.; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C.; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com PMID:25887162

Omics Workshop Videocast Available | Office of Cancer Clinical Proteomics Research

Cancer.gov

The Omics Integration in Biology and Medicine Workshop, held on June 19th and 20th is now available for viewing on NIH Videocast: Day 1 and Day 2.  The workshop focused on the emerging field of integrating disparate omic data from genomics, proteomics, glycomics, etc. in order to better understand key biological processes and also improve clinical practice.

Clique Relaxations in Biological and Social Network Analysis Foundations and Algorithms

DTIC Science & Technology

2015-10-26

study of clique relaxation models arising in biological and social networks. This project examines the elementary clique-defining properties... elementary clique-defining properties inherently exploited in the available clique relaxation models and pro- poses a taxonomic framework that not...analyzes the elementary clique-defining properties implicitly exploited in the available clique relaxation models and proposes a taxonomic framework that

Chemical and biological methods to evaluate the availability of heavy metals in soils of the Siena urban area (Italy).

PubMed

Nannoni, Francesco; Protano, Giuseppe

2016-10-15

A biogeochemistry field study was conducted in the Siena urban area (Italy) with the main objective of establishing the relationship between available amounts of heavy metals in soil assessed by a chemical method (soil fractionation) and bioavailability assessed by a biological method (bioaccumulation in earthworm tissues). The total content of traffic-related (Cd, Cu, Pb, Sb, Zn) and geogenic (Co, Cr, Ni, U) heavy metals in uncontaminated and contaminated soils and their concentrations in soil fractions and earthworms were used for this purpose. The bioavailability of heavy metals assessed by earthworms did not always match the availability defined by soil fractionation. Earthworms were a good indicator to assess the bioavailability of Pb and Sb in soil, while due to physiological mechanisms of regulation and excretion, Cd, Cu and Zn tissue levels in these invertebrates gave misleading estimates of their bioavailable pool. No relationship was identified between chemical and biological availability for the geogenic heavy metals, characterized by a narrow range of total contents in soil. The study highlighted that chemical and biological methods should be combined to provide more complete information about heavy element bioavailability in soils. Copyright © 2016 Elsevier B.V. All rights reserved.

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

PubMed

Meyer, Michael J; Geske, Philip; Yu, Haiyuan

2016-05-15

Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

MACBenAbim: A Multi-platform Mobile Application for searching keyterms in Computational Biology and Bioinformatics.

PubMed

Oluwagbemi, Olugbenga O; Adewumi, Adewole; Esuruoso, Abimbola

2012-01-01

Computational biology and bioinformatics are gradually gaining grounds in Africa and other developing nations of the world. However, in these countries, some of the challenges of computational biology and bioinformatics education are inadequate infrastructures, and lack of readily-available complementary and motivational tools to support learning as well as research. This has lowered the morale of many promising undergraduates, postgraduates and researchers from aspiring to undertake future study in these fields. In this paper, we developed and described MACBenAbim (Multi-platform Mobile Application for Computational Biology and Bioinformatics), a flexible user-friendly tool to search for, define and describe the meanings of keyterms in computational biology and bioinformatics, thus expanding the frontiers of knowledge of the users. This tool also has the capability of achieving visualization of results on a mobile multi-platform context. MACBenAbim is available from the authors for non-commercial purposes.

Infusing Outdoor Field Experiences into the Secondary Biology Curriculum.

ERIC Educational Resources Information Center

Owens, Ginny

1984-01-01

To offer students biological field experiences, teachers should use their own basic skills, be enthusiastic motivators, participate in community programs/courses/workshops to acquire additional skills/knowledge for outdoor biological education, plan outdoor excursions with safety considerations in mind, and use available resources for classroom…

Querying Large Biological Network Datasets

ERIC Educational Resources Information Center

Gulsoy, Gunhan

2013-01-01

New experimental methods has resulted in increasing amount of genetic interaction data to be generated every day. Biological networks are used to store genetic interaction data gathered. Increasing amount of data available requires fast large scale analysis methods. Therefore, we address the problem of querying large biological network datasets.…

Managing biological networks by using text mining and computer-aided curation

NASA Astrophysics Data System (ADS)

Yu, Seok Jong; Cho, Yongseong; Lee, Min-Ho; Lim, Jongtae; Yoo, Jaesoo

2015-11-01

In order to understand a biological mechanism in a cell, a researcher should collect a huge number of protein interactions with experimental data from experiments and the literature. Text mining systems that extract biological interactions from papers have been used to construct biological networks for a few decades. Even though the text mining of literature is necessary to construct a biological network, few systems with a text mining tool are available for biologists who want to construct their own biological networks. We have developed a biological network construction system called BioKnowledge Viewer that can generate a biological interaction network by using a text mining tool and biological taggers. It also Boolean simulation software to provide a biological modeling system to simulate the model that is made with the text mining tool. A user can download PubMed articles and construct a biological network by using the Multi-level Knowledge Emergence Model (KMEM), MetaMap, and A Biomedical Named Entity Recognizer (ABNER) as a text mining tool. To evaluate the system, we constructed an aging-related biological network that consist 9,415 nodes (genes) by using manual curation. With network analysis, we found that several genes, including JNK, AP-1, and BCL-2, were highly related in aging biological network. We provide a semi-automatic curation environment so that users can obtain a graph database for managing text mining results that are generated in the server system and can navigate the network with BioKnowledge Viewer, which is freely available at http://bioknowledgeviewer.kisti.re.kr.

Biological degradation of wood-plastic composites (WPC) and strategies for improving the resistance of WPC against biological decay

Treesearch

Anke Schirp; Rebecca E. Ibach; David E. Pendleton; Michael P. Wolcott

2008-01-01

Much of the research on wood-plastic composites (WPC) has focused on formulation development and processing while high biological durability of the material was assumed. The gap between assumption and knowledge in biodeterioration of WPC needs to be reduced. Although some information on the short-term resistance of WPC against biological degradation is available, long-...

Industry Studies 2004: Biotechnology

DTIC Science & Technology

2004-01-01

for biological agent research, development, and production are available on the open market. Since biological weapons are relatively cheap, easy to...growing concern is that non-state actors will acquire and use a biological weapon , the “poor man’s nuclear weapon .” Such action is extremely difficult...to detect and counter. International Protocols and the Need to Control Agents and Technologies - The Biological and Toxin Weapons Convention

The Structure and Function of Biological Networks

ERIC Educational Resources Information Center

Wu, Daniel Duanqing

2010-01-01

Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

Application of ToxCast to evaluate potential biological effects from organic contaminants in Great Lakes tributaries

EPA Science Inventory

With the development of “high throughput” in-vitro biological assays, screening-level information on potential adverse biological effects is available for a rapidly increasing number of chemicals. The U.S. EPA ToxCast program has now evaluated several thousand chemica...

78 FR 59927 - Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology..., Computational, and Systems Biology [External Review Draft]'' (EPA/600/R-13/214A). EPA is also announcing that... Advances in Molecular, Computational, and Systems Biology [External Review Draft]'' is available primarily...

78 FR 68058 - Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-13

... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology..., computational, and systems biology data can better inform risk assessment. This draft document is available for...

Using Information and Communication Technology (ICT) to the Maximum: Learning and Teaching Biology with Limited Digital Technologies

ERIC Educational Resources Information Center

Van Rooy, Wilhelmina S.

2012-01-01

Background: The ubiquity, availability and exponential growth of digital information and communication technology (ICT) creates unique opportunities for learning and teaching in the senior secondary school biology curriculum. Digital technologies make it possible for emerging disciplinary knowledge and understanding of biological processes…

78 FR 5465 - Vaccines and Related Biological Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-25

...] Vaccines and Related Biological Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug...: Vaccines and Related Biological Products Advisory Committee. General Function of the Committee: To provide... virus vaccine for the 2013- 2014 influenza season. FDA intends to make background material available to...

75 FR 2876 - Vaccines and Related Biological Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-19

...] Vaccines and Related Biological Products Advisory Committee; Notice of Meeting AGENCY: Food and Drug...: Vaccines and Related Biological Products Advisory Committee. General Function of the Committee: To provide... virus vaccine for the 2010 - 2011 influenza season. FDA intends to make background material available to...

Climate Change Effects on Stream and River Biological Indicators: A Preliminary Analysis (Final Report)

EPA Science Inventory

EPA announced the availability of the final report,Climate Change Effects on Stream and River Biological Indicators: A Preliminary Analysis. This report is a preliminary assessment that describes how biological indicators are likely to respond to climate change, how wel...

Availability, health-care costs, and utilization patterns of biologics in Taiwan.

PubMed

Hsieh, Chee-Ruey; Liu, Ya-Ming

2012-01-01

To provide an overview of the use of biologics in Taiwan, including the access to new biologics, the impact of this access on the growth of health-care expenditure, and the utilization patterns. We first conducted a market-level analysis to investigate the availability of global biologics in Taiwan as well as the growth and concentration of aggregate spending on biologics. We then conducted a patient-level analysis to investigate the costs and utilization patterns for selected new biologics. We found that the concentration index is such that the 20 leading biologics in Taiwan account for more than 90% of the total spending on biologics. In our patient-level study on four biologics, the annual cost of treatment per patient ranged from NT$100,000 to NT$400,000. The prevalence rate of the user was between 6.5 and 37.2 per 100,000 of population. The treatment costs were inversely related to the prevalence rate of users. We also found that physicians in larger and public hospitals were more likely to prescribe new biologics to their patients compared with their counterparts practicing in smaller and private hospitals. In addition, we found that physicians were more likely to prescribe biologics to patients with more severe diseases and higher comorbidities. We conclude that public spending on biologics in Taiwan is highly targeted toward about 20 products with higher annual expenditures and growth rates and that the utilization of these biologics is targeted at a small number of patients. In addition, the access to these costly biologics is not uniform among patients in a country with universal coverage for prescription drugs. Copyright © 2012 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables

PubMed Central

Pounds, Stan; Cheng, Cheng; Cao, Xueyuan; Crews, Kristine R.; Plunkett, William; Gandhi, Varsha; Rubnitz, Jeffrey; Ribeiro, Raul C.; Downing, James R.; Lamba, Jatinder

2009-01-01

Motivation: In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables. Results: Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis. Availability: Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org. Contact: stanley.pounds@stjude.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:19528086

Mass spectrometry in systems biology an introduction.

PubMed

Dunn, Warwick B

2011-01-01

The qualitative detection, quantification, and structural characterization of analytes in biological systems are important requirements for objectives to be fulfilled in systems biology research. One analytical tool applied to a multitude of systems biology studies is mass spectrometry, particularly for the study of proteins and metabolites. Here, the role of mass spectrometry in systems biology will be assessed, the advantages and disadvantages discussed, and the instrument configurations available described. Finally, general applications will be briefly reviewed. Copyright © 2011 Elsevier Inc. All rights reserved.

42 CFR 491.9 - Provision of services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... center. (iii) Rules for the storage, handling, and administration of drugs and biologicals. (4) These... has available the drugs and biologicals commonly used in life saving procedures, such as analgesics...

42 CFR 491.9 - Provision of services.

Code of Federal Regulations, 2011 CFR

2011-10-01

... center. (iii) Rules for the storage, handling, and administration of drugs and biologicals. (4) These... has available the drugs and biologicals commonly used in life saving procedures, such as analgesics...

How well are you teaching one of the most important biological concepts for humankind? A call to action

USGS Publications Warehouse

Bonar, Scott A.; Fife, Deanna A.; Bonar, John S.

2016-01-01

We represent several generations of biology educators – with teaching experiences beginning in the 1940s and continuing to the present, from elementary school to graduate-level programs. We find the vast array of subjects that biology teachers can now cover both thrilling and mind-boggling. Depending on the grade level, units exist that focus on neurobiology, forensics, DNA analysis, biotechnology, marine biology, and a host of other topics.Although science teachers cover a potpourri of advanced topics, we must ask ourselves – no matter our biology-teaching responsibilities – how well we are teaching carrying capacity, one of the most fundamental biological concepts for our society, knowledge of which becomes more important every day. As biology teachers, most of you know that carrying capacity is defined as the maximum population an environment can sustain, given the amounts of food, habitat, and other resources available. Every environment – from your goldfish bowl to the local forest to planet Earth – can only sustain a set number (weight) of a particular species, based on available resources and space. Currently, most science classes teach …

75 FR 69396 - Availability of an Environmental Assessment for a Biological Control Agent for Arundo donax

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-12

... infestations. The proposed biological control agent, Arundo scale, is one of the most damaging insects to A... feeding on cells that carry out photosynthesis and cellular respiration, resulting over time in gradual... donacis (Hemiptera: Diaspididae), an Insect for Biological Control of Arundo donax (Poaceae) in the...

Development of the Neuron Assessment for Measuring Biology Students' Use of Experimental Design Concepts and Representations

ERIC Educational Resources Information Center

Dasgupta, Annwesa P.; Anderson, Trevor R.; Pelaez, Nancy J.

2016-01-01

Researchers, instructors, and funding bodies in biology education are unanimous about the importance of developing students' competence in experimental design. Despite this, only limited measures are available for assessing such competence development, especially in the areas of molecular and cellular biology. Also, existing assessments do not…

Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems.

PubMed

Boué, Stéphanie; Talikka, Marja; Westra, Jurjen Willem; Hayes, William; Di Fabio, Anselmo; Park, Jennifer; Schlage, Walter K; Sewer, Alain; Fields, Brett; Ansari, Sam; Martin, Florian; Veljkovic, Emilija; Kenney, Renee; Peitsch, Manuel C; Hoeng, Julia

2015-01-01

With the wealth of publications and data available, powerful and transparent computational approaches are required to represent measured data and scientific knowledge in a computable and searchable format. We developed a set of biological network models, scripted in the Biological Expression Language, that reflect causal signaling pathways across a wide range of biological processes, including cell fate, cell stress, cell proliferation, inflammation, tissue repair and angiogenesis in the pulmonary and cardiovascular context. This comprehensive collection of networks is now freely available to the scientific community in a centralized web-based repository, the Causal Biological Network database, which is composed of over 120 manually curated and well annotated biological network models and can be accessed at http://causalbionet.com. The website accesses a MongoDB, which stores all versions of the networks as JSON objects and allows users to search for genes, proteins, biological processes, small molecules and keywords in the network descriptions to retrieve biological networks of interest. The content of the networks can be visualized and browsed. Nodes and edges can be filtered and all supporting evidence for the edges can be browsed and is linked to the original articles in PubMed. Moreover, networks may be downloaded for further visualization and evaluation. Database URL: http://causalbionet.com © The Author(s) 2015. Published by Oxford University Press.

BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications.

PubMed

Cui, Ya; Chen, Xiaowei; Luo, Huaxia; Fan, Zhen; Luo, Jianjun; He, Shunmin; Yue, Haiyan; Zhang, Peng; Chen, Runsheng

2016-06-01

We here present BioCircos.js, an interactive and lightweight JavaScript library especially for biological data interactive visualization. BioCircos.js facilitates the development of web-based applications for circular visualization of various biological data, such as genomic features, genetic variations, gene expression and biomolecular interactions. BioCircos.js and its manual are freely available online at http://bioinfo.ibp.ac.cn/biocircos/ rschen@ibp.ac.cn Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Review of the treatment of psoriatic arthritis with biological agents: choice of drug for initial therapy and switch therapy for non-responders.

PubMed

D'Angelo, Salvatore; Tramontano, Giuseppina; Gilio, Michele; Leccese, Pietro; Olivieri, Ignazio

2017-01-01

Psoriatic arthritis (PsA) is a heterogeneous chronic inflammatory disease with a broad clinical spectrum and variable course. It can involve musculoskeletal structures as well as skin, nails, eyes, and gut. The management of PsA has changed tremendously in the last decade, thanks to an earlier diagnosis, an advancement in pharmacological therapies, and a wider application of a multidisciplinary approach. The commercialization of tumor necrosis factor inhibitors (adalimumab, certolizumab pegol, etanercept, golimumab, and infliximab) as well as interleukin (IL)-12/23 (ustekinumab) and IL-17 (secukinumab) inhibitors is representative of a revolution in the treatment of PsA. No evidence-based strategies are currently available for guiding the rheumatologist to prescribe biological drugs. Several international and national recommendation sets are currently available with the aim to help rheumatologists in everyday clinical practice management of PsA patients treated with biological therapy. Since no specific biological agent has been demonstrated to be more effective than others, the drug choice should be made according to the available safety data, the presence of extra-articular manifestations, the patient's preferences (e.g., administration route), and the drug price. However, future studies directly comparing different biological drugs and assessing the efficacy of treatment strategies specific for PsA are urgently needed.

Biological control of purple loosestrife in North America

Treesearch

Bernd Blossey

1998-01-01

In recent years, interest in a biological method to control problem plants in natural areas in the United States has grown. All federal agencies must comply with standards to reduce the use and dependence on chemical control of weeds. But, biological methodologies are not readily available, nor have they been well-endorsed or financially supported. Despite an excellent...

[Biological availability of zinc lignosulfonate on calcareous soil of north Guoangdong Province].

PubMed

Wang, Dehan; Lin, Huidong; Peng, Junjie; Xiao, Xiongshi; Liao, Zongwen

2004-07-01

Zinc lignosulfonate (Zn-LS) is a kind of organic fertilizers made from the by-products of paper industry. With leach and plot treatments, this paper studied the difference of the biological availability between Zn-LS and an inorganic Zn-fertilizer on calcareous soil of north Guangdong Province. The results indicated that the Zn of Zn-LS was less absorbed by calcareous soil. In soil B, when applying 10 mg x kg(-1) Zn, the dissolved amount of Zn-LS was 65.2% higher than that of inorganic Zn-fertilizer, corn grew well, and its biomass was higher. In soil A, when applying 10 mg x kg(-1) Zn of Zn-LS, the biomass of corn increased by 16.3%, and its Zn content was 81.2% higher. Therefore, biological availability of Zn-LS was better than that of inorganic Zn fertilizer.

BioPartsDB: a synthetic biology workflow web-application for education and research.

PubMed

Stracquadanio, Giovanni; Yang, Kun; Boeke, Jef D; Bader, Joel S

2016-11-15

Synthetic biology has become a widely used technology, and expanding applications in research, education and industry require progress tracking for team-based DNA synthesis projects. Although some vendors are beginning to supply multi-kilobase sequence-verified constructs, synthesis workflows starting with short oligos remain important for cost savings and pedagogical benefit. We developed BioPartsDB as an open source, extendable workflow management system for synthetic biology projects with entry points for oligos and larger DNA constructs and ending with sequence-verified clones. BioPartsDB is released under the MIT license and available for download at https://github.com/baderzone/biopartsdb Additional documentation and video tutorials are available at https://github.com/baderzone/biopartsdb/wiki An Amazon Web Services image is available from the AWS Market Place (ami-a01d07c8). joel.bader@jhu.edu. © The Author 2016. Published by Oxford University Press.

Biological Feasibility of Measles Eradication

PubMed Central

Strebel, Peter

2011-01-01

Recent progress in reducing global measles mortality has renewed interest in measles eradication. Three biological criteria are deemed important for disease eradication: (1) humans are the sole pathogen reservoir; (2) accurate diagnostic tests exist; and (3) an effective, practical intervention is available at reasonable cost. Interruption of transmission in large geographical areas for prolonged periods further supports the feasibility of eradication. Measles is thought by many experts to meet these criteria: no nonhuman reservoir is known to exist, accurate diagnostic tests are available, and attenuated measles vaccines are effective and immunogenic. Measles has been eliminated in large geographical areas, including the Americas. Measles eradication is biologically feasible. The challenges for measles eradication will be logistical, political, and financial. PMID:21666201

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization.

PubMed

Tuikkala, Johannes; Vähämaa, Heidi; Salmela, Pekka; Nevalainen, Olli S; Aittokallio, Tero

2012-03-26

Graph drawing is an integral part of many systems biology studies, enabling visual exploration and mining of large-scale biological networks. While a number of layout algorithms are available in popular network analysis platforms, such as Cytoscape, it remains poorly understood how well their solutions reflect the underlying biological processes that give rise to the network connectivity structure. Moreover, visualizations obtained using conventional layout algorithms, such as those based on the force-directed drawing approach, may become uninformative when applied to larger networks with dense or clustered connectivity structure. We implemented a modified layout plug-in, named Multilevel Layout, which applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks. Using a wide variety of real life biological networks, we carried out a systematic evaluation of the method in comparison with other layout algorithms in Cytoscape. The multilevel approach provided both biologically relevant and visually pleasant layout solutions in most network types, hence complementing the layout options available in Cytoscape. In particular, it could improve drawing of large-scale networks of yeast genetic interactions and human physical interactions. In more general terms, the biological evaluation framework developed here enables one to assess the layout solutions from any existing or future graph drawing algorithm as well as to optimize their performance for a given network type or structure. By making use of the multilevel modular organization when visualizing biological networks, together with the biological evaluation of the layout solutions, one can generate convenient visualizations for many network biology applications.

Tumor Biology and Immunology | Center for Cancer Research

Cancer.gov

Tumor Biology and Immunology The Comparative Brain Tumor Consortium is collaborating with National Center for Advanced Translational Sciences to complete whole exome sequencing on canine meningioma samples. Results will be published and made publicly available.

iBiology: communicating the process of science.

PubMed

Goodwin, Sarah S

2014-08-01

The Internet hosts an abundance of science video resources aimed at communicating scientific knowledge, including webinars, massive open online courses, and TED talks. Although these videos are efficient at disseminating information for diverse types of users, they often do not demonstrate the process of doing science, the excitement of scientific discovery, or how new scientific knowledge is developed. iBiology (www.ibiology.org), a project that creates open-access science videos about biology research and science-related topics, seeks to fill this need by producing videos by science leaders that make their ideas, stories, and experiences available to anyone with an Internet connection. © 2014 Goodwin. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

PubMed

Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

2014-08-15

Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

[Biological monitoring in the molding of plastics and rubbers].

PubMed

Fustinoni, S; Campo, L; Cirla, A M; Cirla, P E; Cutugno, V; Lionetti, C; Martinotti, I; Mossini, E; Foà, V

2007-01-01

This survey was carried out in the molding of plastics and rubbers, in the "Professional Cancer Prevention Project" sponsored by the Lombardy region with the objective of developing and implementing protocols for evaluating exposure to carcinogens through the biological monitoring. The realities of molding the thermoplastic polymer ABS, rubber, and thermosetting plastics containing formaldehyde were examined. The carcinogenic substances identified in these processes were: 1,3-butadiene, acrylonitrile and styrene in molding ABS, polycyclic aromatic hydrocarbons (PAH) in molding rubber, and formaldehyde in molding the thermosetting plastics. Only for some of these substances biological indicators are available. The limited exposure to airborne chemicals in molding ABS and the intrinsic characteristics of biological indicators available for 1-3 butadiene have determined the non applicability of biological monitoring to this situation. The absence of a biological indicator of exposure to formaldehyde has made this situation not investigable. Exposure in the rubber molding was studied in 19 subjects applying the determination not metabolized PAH in urine. The levels of these indicators were similar to those measured in other groups of subjects without occupational exposure to PAH, confirming a low airborne contamination in this workplace.

Evaluation of hierarchical models for integrative genomic analyses.

PubMed

Denis, Marie; Tadesse, Mahlet G

2016-03-01

Advances in high-throughput technologies have led to the acquisition of various types of -omic data on the same biological samples. Each data type gives independent and complementary information that can explain the biological mechanisms of interest. While several studies performing independent analyses of each dataset have led to significant results, a better understanding of complex biological mechanisms requires an integrative analysis of different sources of data. Flexible modeling approaches, based on penalized likelihood methods and expectation-maximization (EM) algorithms, are studied and tested under various biological relationship scenarios between the different molecular features and their effects on a clinical outcome. The models are applied to genomic datasets from two cancer types in the Cancer Genome Atlas project: glioblastoma multiforme and ovarian serous cystadenocarcinoma. The integrative models lead to improved model fit and predictive performance. They also provide a better understanding of the biological mechanisms underlying patients' survival. Source code implementing the integrative models is freely available at https://github.com/mgt000/IntegrativeAnalysis along with example datasets and sample R script applying the models to these data. The TCGA datasets used for analysis are publicly available at https://tcga-data.nci.nih.gov/tcga/tcgaDownload.jsp marie.denis@cirad.fr or mgt26@georgetown.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

FALCON: a toolbox for the fast contextualization of logical networks

PubMed Central

De Landtsheer, Sébastien; Trairatphisan, Panuwat; Lucarelli, Philippe; Sauter, Thomas

2017-01-01

Abstract Motivation Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results We have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. Availability and implementation FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. Contact thomas.sauter@uni.lu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28673016

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

PubMed Central

Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-01-01

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists. Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X. Contact: duccio.cavalieri@unifi.it; sorin@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21653523

Identifying biologically relevant differences between metagenomic communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2010-03-15

Metagenomics is the study of genetic material recovered directly from environmental samples. Taxonomic and functional differences between metagenomic samples can highlight the influence of ecological factors on patterns of microbial life in a wide range of habitats. Statistical hypothesis tests can help us distinguish ecological influences from sampling artifacts, but knowledge of only the P-value from a statistical hypothesis test is insufficient to make inferences about biological relevance. Current reporting practices for pairwise comparative metagenomics are inadequate, and better tools are needed for comparative metagenomic analysis. We have developed a new software package, STAMP, for comparative metagenomics that supports best practices in analysis and reporting. Examination of a pair of iron mine metagenomes demonstrates that deeper biological insights can be gained using statistical techniques available in our software. An analysis of the functional potential of 'Candidatus Accumulibacter phosphatis' in two enhanced biological phosphorus removal metagenomes identified several subsystems that differ between the A.phosphatis stains in these related communities, including phosphate metabolism, secretion and metal transport. Python source code and binaries are freely available from our website at http://kiwi.cs.dal.ca/Software/STAMP CONTACT: beiko@cs.dal.ca Supplementary data are available at Bioinformatics online.

Implementing Best Practices and Validation of Cryopreservation Techniques for Microorganisms

PubMed Central

Smith, David; Ryan, Matthew

2012-01-01

Authentic, well preserved living organisms are basic elements for research in the life sciences and biotechnology. They are grown and utilized in laboratories around the world and are key to many research programmes, industrial processes and training courses. They are vouchers for publications and must be available for confirmation of results, further study or reinvestigation when new technologies become available. These biological resources must be maintained without change in biological resource collections. In order to achieve best practice in the maintenance and provision of biological materials for industry, research and education the appropriate standards must be followed. Cryopreservation is often the best preservation method available to achieve these aims, allowing long term, stable storage of important microorganisms. To promulgate best practice the Organisation for Economic Development and Co-operation (OECD published the best practice guidelines for BRCs. The OECD best practice consolidated the efforts of the UK National Culture Collections, the European Common Access to Biological Resources and Information (CABRI) project consortium and the World Federation for Culture Collections. The paper discusses quality management options and reviews cryopreservation of fungi, describing how the reproducibility and quality of the technique is maintained in order to retain the full potential of fungi. PMID:22629202

Self-organization, embodiment, and biologically inspired robotics.

PubMed

Pfeifer, Rolf; Lungarella, Max; Iida, Fumiya

2007-11-16

Robotics researchers increasingly agree that ideas from biology and self-organization can strongly benefit the design of autonomous robots. Biological organisms have evolved to perform and survive in a world characterized by rapid changes, high uncertainty, indefinite richness, and limited availability of information. Industrial robots, in contrast, operate in highly controlled environments with no or very little uncertainty. Although many challenges remain, concepts from biologically inspired (bio-inspired) robotics will eventually enable researchers to engineer machines for the real world that possess at least some of the desirable properties of biological organisms, such as adaptivity, robustness, versatility, and agility.

New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

PubMed Central

Hamon, Morgan; Hong, Jong Wook

2013-01-01

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

Computational analyses in cognitive neuroscience: in defense of biological implausibility.

PubMed

Dror, I E; Gallogly, D P

1999-06-01

Because cognitive neuroscience researchers attempt to understand the human mind by bridging behavior and brain, they expect computational analyses to be biologically plausible. In this paper, biologically implausible computational analyses are shown to have critical and essential roles in the various stages and domains of cognitive neuroscience research. Specifically, biologically implausible computational analyses can contribute to (1) understanding and characterizing the problem that is being studied, (2) examining the availability of information and its representation, and (3) evaluating and understanding the neuronal solution. In the context of the distinct types of contributions made by certain computational analyses, the biological plausibility of those analyses is altogether irrelevant. These biologically implausible models are nevertheless relevant and important for biologically driven research.

Challenges in vaccinating infants born to mothers taking immunoglobulin biologicals during pregnancy.

PubMed

Ling, Juejing; Koren, Gideon

2016-01-01

While immunoglobulin biologicals are increasingly used during pregnancy, there have been concerns on the immune function and vaccination of infants born to mothers taking immunoglobulin biologicals. In addition to the detection of biologicals in cord blood, cases of severe neonatal neutropenia and fatal dissemination of Bacillus Calmette-Guérin (BCG) have been reported. With increasing number of infants exposed to immunoglobulin biologicals in utero, there is a need to address the challenges in vaccinating these infants. This review summarizes the available evidence to discuss the issues of immunoglobulin biological exposure in utero, neonatal immune function, long-term immune development, and the challenges and strategies of vaccinating newborns and infants who were born to mothers taking biologicals during pregnancy.

Cancer Biology

ERIC Educational Resources Information Center

Dominiecki, Mary E.

2004-01-01

University of Colorado's Virtual Student Fellowship available at and developed by Bakemeier, Richard F. This website is designed to give students applying for a fellowship an overview of basic topics in biology and how they are used by cancer researchers to develop new treatments.

STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Getting Beyond Getting Ready for Pandemic Influenza

DTIC Science & Technology

2009-01-01

more information, see: http://homeland.house.gov/Hearings/index.asp?ID=89. “…Emerging biological threats such as pandemic influenza or weaponized ...which we have no immediately available cure. Work is clearly underway to prepare for such a biological event.10 However, despite the fact that...Nation to fully withstand the impact of such a devastating widespread biological event. Pandemic influenza would destroy the security of our

Similar Mutation Rates but Highly Diverse Mutation Spectra in Ascomycete and Basidiomycete Yeasts

DTIC Science & Technology

2016-12-24

Te, and Michael Lynch Department of Biology , Indiana University, Bloomington, IN *Corresponding author: E-mail: longhongan@gmail.com. Accepted...GBE The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access...fungal mutation spectrum. Supplementary Material Supplementary data are available at Genome Biology and Evolution online. Acknowledgments This research

CPTC and NIST-sponsored Yeast Reference Material Now Publicly Available | Office of Cancer Clinical Proteomics Research

Cancer.gov

The yeast protein extract (RM8323) developed by National Institute of Standards and Technology (NIST) under the auspices of NCI's CPTC initiative is currently available to the public at https://www-s.nist.gov/srmors/view_detail.cfm?srm=8323. The yeast proteome offers researchers a unique biological reference material. RM8323 is the most extensively characterized complex biological proteome and the only one associated with several large-scale studies to estimate protein abundance across a wide concentration range.

Study to Determine the CB (Chemical/Biological) Threat and Define Alternative Crew Protection Systems for the Advanced Attack Helicopter (AAH). Volume 1

DTIC Science & Technology

1980-12-01

NTIS GRA&I DTIC TAR Unannou.nced _ Just if i cat i o Distribution/ Availability Codes Avail and/or Dist Special ii -.- ,-4. ,S... -. UNCLASSIFIED...fighting ability. U Biological agents consist of living micro-organisms including bacteria, rickettsia and viruses . These agents are affected by their...six hours when worn with a protective hood. While virus particles are normally extremely minute, it is assumed in this study that they must be

How-to-Do-It: Teaching Recombinant DNA Technology in High School Biology Courses.

ERIC Educational Resources Information Center

Dixon, Linda

1988-01-01

Reports on the teaching of recombinant DNA technology in high school biology courses. Explains reactions of the public, students, and colleagues to the molecular genetics unit. Indicates equipment, curricular materials, training, workshops, and availability. (RT)

Three Activities To Assist Biology Teachers in Presenting Conceptually Difficult Topics.

ERIC Educational Resources Information Center

Taylor, Neil; Tulip, David

1997-01-01

Outlines three activities for different areas of biology that can serve as motivators for students or as demonstrations. Each activity is easy to organize and uses available materials. Topics include evolution, anaerobic respiration, and heat loss. (DDR)

DETERMINATION OF APPARENT QUANTUM YIELD SPECTRA FOR THE FORMATION OF BIOLOGICALLY LABILE PHOTOPRODUCTS

EPA Science Inventory

Quantum yield spectra for the photochemical formation of biologically labile photoproducts from dissolved organic matter (DOM) have not been available previously, although they would greatly facilitate attempts to model photoproduct formation rates across latitudinal, seasonal, a...

A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization

PubMed Central

2012-01-01

Background Graph drawing is an integral part of many systems biology studies, enabling visual exploration and mining of large-scale biological networks. While a number of layout algorithms are available in popular network analysis platforms, such as Cytoscape, it remains poorly understood how well their solutions reflect the underlying biological processes that give rise to the network connectivity structure. Moreover, visualizations obtained using conventional layout algorithms, such as those based on the force-directed drawing approach, may become uninformative when applied to larger networks with dense or clustered connectivity structure. Methods We implemented a modified layout plug-in, named Multilevel Layout, which applies the conventional layout algorithms within a multilevel optimization framework to better capture the hierarchical modularity of many biological networks. Using a wide variety of real life biological networks, we carried out a systematic evaluation of the method in comparison with other layout algorithms in Cytoscape. Results The multilevel approach provided both biologically relevant and visually pleasant layout solutions in most network types, hence complementing the layout options available in Cytoscape. In particular, it could improve drawing of large-scale networks of yeast genetic interactions and human physical interactions. In more general terms, the biological evaluation framework developed here enables one to assess the layout solutions from any existing or future graph drawing algorithm as well as to optimize their performance for a given network type or structure. Conclusions By making use of the multilevel modular organization when visualizing biological networks, together with the biological evaluation of the layout solutions, one can generate convenient visualizations for many network biology applications. PMID:22448851

Semantic integration of data on transcriptional regulation

PubMed Central

Baitaluk, Michael; Ponomarenko, Julia

2010-01-01

Motivation: Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources. However, there are no resources to integrate these data automatically or to provide a ‘one-stop shop’ experience for users seeking information essential for deciphering and modeling gene regulatory networks. Results: IntegromeDB, a semantic graph-based ‘deep-web’ data integration system that automatically captures, integrates and manages publicly available data concerning transcriptional regulation, as well as other relevant biological information, is proposed in this article. The problems associated with data integration are addressed by ontology-driven data mapping, multiple data annotation and heterogeneous data querying, also enabling integration of the user's data. IntegromeDB integrates over 100 experimental and computational data sources relating to genomics, transcriptomics, genetics, and functional and interaction data concerning gene transcriptional regulation in eukaryotes and prokaryotes. Availability: IntegromeDB is accessible through the integrated research environment BiologicalNetworks at http://www.BiologicalNetworks.org Contact: baitaluk@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20427517

Pine Gene Discovery Project - Final Report - 08/31/1997 - 02/28/2001

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whetten, R. W.; Sederoff, R. R.; Kinlaw, C.

2001-04-30

Integration of pines into the large scope of plant biology research depends on study of pines in parallel with study of annual plants, and on availability of research materials from pine to plant biologists interested in comparing pine with annual plant systems. The objectives of the Pine Gene Discovery Project were to obtain 10,000 partial DNA sequences of genes expressed in loblolly pine, to determine which of those pine genes were similar to known genes from other organisms, and to make the DNA sequences and isolated pine genes available to plant researchers to stimulate integration of pines into the widermore » scope of plant biology research. Those objectives have been completed, and the results are available to the public. Requests for pine genes have been received from a number of laboratories that would otherwise not have included pine in their research, indicating that progress is being made toward the goal of integrating pine research into the larger molecular biology research community.« less

Detecting Rhythms in Time Series with RAIN

PubMed Central

Thaben, Paul F.; Westermark, Pål O.

2014-01-01

A fundamental problem in research on biological rhythms is that of detecting and assessing the significance of rhythms in large sets of data. Classic methods based on Fourier theory are often hampered by the complex and unpredictable characteristics of experimental and biological noise. Robust nonparametric methods are available but are limited to specific wave forms. We present RAIN, a robust nonparametric method for the detection of rhythms of prespecified periods in biological data that can detect arbitrary wave forms. When applied to measurements of the circadian transcriptome and proteome of mouse liver, the sets of transcripts and proteins with rhythmic abundances were significantly expanded due to the increased detection power, when we controlled for false discovery. Validation against independent data confirmed the quality of these results. The large expansion of the circadian mouse liver transcriptomes and proteomes reflected the prevalence of nonsymmetric wave forms and led to new conclusions about function. RAIN was implemented as a freely available software package for R/Bioconductor and is presently also available as a web interface. PMID:25326247

Meta-cognition about biological sex and gender-stereotypic physical appearance: consequences for the assessment of leadership competence.

PubMed

Sczesny, Sabine; Kühnen, Ulrich

2004-01-01

Previous findings are inconsistent with regard to whether men are judged as being more or less competent leaders than women. However, masculine-relative to feminine-looking persons seem to be judged consistently as more competent leaders. Can this different impact of biological sex and physical appearance be due to the disparate availability of meta-cognitive knowledge about both sources? The results of Study 1 indicated that individuals possess meta-cognitive knowledge about a possible biasing influence of persons' biological sex, but not for their physical appearance. In Study 2, participants judged the leadership competence of a male versus female stimulus person with either masculine or feminine physical appearance. In addition, the available cognitive capacity was manipulated. When high capacity was available, participants corrected for the influence of stimulus persons' sex, but they fell prey to this influence under cognitive load. However, the effect of physical appearance was not moderated by cognitive capacity.

Can Man Control His Biological Evolution? A Symposium on Genetic Engineering. Man's Responsibility to His Future

ERIC Educational Resources Information Center

Hoagland, Hudson

1972-01-01

Biological evolution can be carried out in the laboratory. With new knowledge available in genetics, possibilities are raised that genetic characters can be transferred in the future to embryos according to a predetermined plan. (PS)

Survey of techniques used to preserve biological materials

NASA Technical Reports Server (NTRS)

Feinler, E. J.; Hubbard, R. W.

1972-01-01

The techniques used to preserve biological materials are documented and summarized. The report is presented in a handbook format that categorizes the most important preservation techniques available, and includes a representative sampling of the thousands of applications of these techniques to biological materials and organisms. Details of the information coverage and method of approach are outlined. Data are given in tabular form, and an index and extensive bibliography are included.

Design and analysis of large-scale biological rhythm studies: a comparison of algorithms for detecting periodic signals in biological data

PubMed Central

Deckard, Anastasia; Anafi, Ron C.; Hogenesch, John B.; Haase, Steven B.; Harer, John

2013-01-01

Motivation: To discover and study periodic processes in biological systems, we sought to identify periodic patterns in their gene expression data. We surveyed a large number of available methods for identifying periodicity in time series data and chose representatives of different mathematical perspectives that performed well on both synthetic data and biological data. Synthetic data were used to evaluate how each algorithm responds to different curve shapes, periods, phase shifts, noise levels and sampling rates. The biological datasets we tested represent a variety of periodic processes from different organisms, including the cell cycle and metabolic cycle in Saccharomyces cerevisiae, circadian rhythms in Mus musculus and the root clock in Arabidopsis thaliana. Results: From these results, we discovered that each algorithm had different strengths. Based on our findings, we make recommendations for selecting and applying these methods depending on the nature of the data and the periodic patterns of interest. Additionally, these results can also be used to inform the design of large-scale biological rhythm experiments so that the resulting data can be used with these algorithms to detect periodic signals more effectively. Contact: anastasia.deckard@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24058056

Glycosylation Is a Major Regulator of Phenylpropanoid Availability and Biological Activity in Plants

PubMed Central

Le Roy, Julien; Huss, Brigitte; Creach, Anne; Hawkins, Simon; Neutelings, Godfrey

2016-01-01

The phenylpropanoid pathway in plants is responsible for the biosynthesis of a huge amount of secondary metabolites derived from phenylalanine and tyrosine. Both flavonoids and lignins are synthesized at the end of this very diverse metabolic pathway, as well as many intermediate molecules whose precise biological functions remain largely unknown. The diversity of these molecules can be further increased under the action of UDP-glycosyltransferases (UGTs) leading to the production of glycosylated hydroxycinnamates and related aldehydes, alcohols and esters. Glycosylation can change phenylpropanoid solubility, stability and toxic potential, as well as influencing compartmentalization and biological activity. (De)-glycosylation therefore represents an extremely important regulation point in phenylpropanoid homeostasis. In this article we review recent knowledge on the enzymes involved in regulating phenylpropanoid glycosylation status and availability in different subcellular compartments. We also examine the potential link between monolignol glycosylation and lignification by exploring co-expression of lignin biosynthesis genes and phenolic (de)glycosylation genes. Of the different biological roles linked with their particular chemical properties, phenylpropanoids are often correlated with the plant's stress management strategies that are also regulated by glycosylation. UGTs can for instance influence the resistance of plants during infection by microorganisms and be involved in the mechanisms related to environmental changes. The impact of flavonoid glycosylation on the color of flowers, leaves, seeds and fruits will also be discussed. Altogether this paper underlies the fact that glycosylation and deglycosylation are powerful mechanisms allowing plants to regulate phenylpropanoid localisation, availability and biological activity. PMID:27303427

DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates

PubMed Central

Peng, Hao; Yang, Yifan; Zhe, Shandian; Wang, Jian; Gribskov, Michael; Qi, Yuan

2017-01-01

Abstract Motivation High-throughput mRNA sequencing (RNA-Seq) is a powerful tool for quantifying gene expression. Identification of transcript isoforms that are differentially expressed in different conditions, such as in patients and healthy subjects, can provide insights into the molecular basis of diseases. Current transcript quantification approaches, however, do not take advantage of the shared information in the biological replicates, potentially decreasing sensitivity and accuracy. Results We present a novel hierarchical Bayesian model called Differentially Expressed Isoform detection from Multiple biological replicates (DEIsoM) for identifying differentially expressed (DE) isoforms from multiple biological replicates representing two conditions, e.g. multiple samples from healthy and diseased subjects. DEIsoM first estimates isoform expression within each condition by (1) capturing common patterns from sample replicates while allowing individual differences, and (2) modeling the uncertainty introduced by ambiguous read mapping in each replicate. Specifically, we introduce a Dirichlet prior distribution to capture the common expression pattern of replicates from the same condition, and treat the isoform expression of individual replicates as samples from this distribution. Ambiguous read mapping is modeled as a multinomial distribution, and ambiguous reads are assigned to the most probable isoform in each replicate. Additionally, DEIsoM couples an efficient variational inference and a post-analysis method to improve the accuracy and speed of identification of DE isoforms over alternative methods. Application of DEIsoM to an hepatocellular carcinoma (HCC) dataset identifies biologically relevant DE isoforms. The relevance of these genes/isoforms to HCC are supported by principal component analysis (PCA), read coverage visualization, and the biological literature. Availability and implementation The software is available at https://github.com/hao-peng/DEIsoM Contact pengh@alumni.purdue.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28595376

Alignment-free protein interaction network comparison

PubMed Central

Ali, Waqar; Rito, Tiago; Reinert, Gesine; Sun, Fengzhu; Deane, Charlotte M.

2014-01-01

Motivation: Biological network comparison software largely relies on the concept of alignment where close matches between the nodes of two or more networks are sought. These node matches are based on sequence similarity and/or interaction patterns. However, because of the incomplete and error-prone datasets currently available, such methods have had limited success. Moreover, the results of network alignment are in general not amenable for distance-based evolutionary analysis of sets of networks. In this article, we describe Netdis, a topology-based distance measure between networks, which offers the possibility of network phylogeny reconstruction. Results: We first demonstrate that Netdis is able to correctly separate different random graph model types independent of network size and density. The biological applicability of the method is then shown by its ability to build the correct phylogenetic tree of species based solely on the topology of current protein interaction networks. Our results provide new evidence that the topology of protein interaction networks contains information about evolutionary processes, despite the lack of conservation of individual interactions. As Netdis is applicable to all networks because of its speed and simplicity, we apply it to a large collection of biological and non-biological networks where it clusters diverse networks by type. Availability and implementation: The source code of the program is freely available at http://www.stats.ox.ac.uk/research/proteins/resources. Contact: w.ali@stats.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161230

Comparison of sediments and organisms in identifying sources of biologically available trace metal contamination

USGS Publications Warehouse

Thomson, E.A.; Luoma, S.N.; Johansson, C.E.; Cain, D.J.

1984-01-01

Sediments and an indicator organism (Macoma balthica, a deposit-feeding bivalve) were used to assess the relative importance of secondary sewage, urban runoff, a landfill containing metal-enriched ash wastes and a yacht harbor in contributing to Ag, Cu and Zn enrichment in South San Francisco Bay. Spatial gradients in sediments and organisms showed Cu and Ag enrichment originated from sewage discharge, whereas Zn enrichment originated from both sewage and urban runoff. Elevated concentrations of Cu in the sediments of the yacht harbor resulted from a high abundance of fine particles. The biological availability of Cu, Ag and Zn did not coincide with metal enrichment in sediments. The availability of Cu and Ag was greatest nearest the sewage outfall and greater in winter and spring than in summer. The availability of Zn in urban runoff appeared to be lower than the availability of Zn associated with sewage.

International Conference on Harmonisation; Electronic Transmission of Postmarket Individual Case Safety Reports for Drugs and Biologics, Excluding Vaccines; Availability of Food and Drug Administration Regional Implementation Specifications for ICH E2B(R3) Reporting to the Food and Drug Administration Adverse Event Reporting System. Notice of Availability.

PubMed

2016-06-23

The Food and Drug Administration (FDA) is announcing the availability of its FDA Adverse Event Reporting System (FAERS) Regional Implementation Specifications for the International Conference on Harmonisation (ICH) E2B(R3) Specification. FDA is making this technical specifications document available to assist interested parties in electronically submitting individual case safety reports (ICSRs) (and ICSR attachments) to the Center for Drug Evaluation and Research (CDER) and the Center for Biologics Evaluation and Research (CBER). This document, entitled "FDA Regional Implementation Specifications for ICH E2B(R3) Implementation: Postmarket Submission of Individual Case Safety Reports (ICSRs) for Drugs and Biologics, Excluding Vaccines" supplements the "E2B(R3) Electronic Transmission of Individual Case Safety Reports (ICSRs) Implementation Guide--Data Elements and Message Specification" final guidance for industry and describes FDA's technical approach for receiving ICSRs, for incorporating regionally controlled terminology, and for adding region-specific data elements when reporting to FAERS.

iTools: a framework for classification, categorization and integration of computational biology resources.

PubMed

Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

2008-05-28

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

PubMed Central

Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

2008-01-01

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu. PMID:18509477

Bacteriophage vehicles for phage display: biology, mechanism, and application.

PubMed

Ebrahimizadeh, Walead; Rajabibazl, Masoumeh

2014-08-01

The phage display technique is a powerful tool for selection of various biological agents. This technique allows construction of large libraries from the antibody repertoire of different hosts and provides a fast and high-throughput selection method. Specific antibodies can be isolated based on distinctive characteristics from a library consisting of millions of members. These features made phage display technology preferred method for antibody selection and engineering. There are several phage display methods available and each has its unique merits and application. Selection of appropriate display technique requires basic knowledge of available methods and their mechanism. In this review, we describe different phage display techniques, available bacteriophage vehicles, and their mechanism.

Community College Biology Lesson Index.

ERIC Educational Resources Information Center

Manteuffel, Mary S., Comp.; Herrick, Kathie, Comp.

This catalog contains lesson descriptions of the available biology lessons on PLATO IV, compiled to assist instructors in planning their curricula. Information is provided for 87 lessons in the following areas: introductory material on experimental tools and techniques; chemical basis of life; cellular structure and function; reproduction and…

Community College Biology Lesson Catalogue.

ERIC Educational Resources Information Center

Herrick, Kathie G.

This catalog contains descriptions of the available biology lessons on PLATO IV, compiled to assist instructors in planning their curricula. Information is provided for 87 lessons in the following areas: experimental tools and techniques; chemical basis of life; cellular structure and function; bioenergetics - enzymes and cellular metabolism;…

Biological control of livestock pests: Pathogens

USDA-ARS?s Scientific Manuscript database

Interest in biological methods for livestock and poultry pest management is largely motivated by the development of resistance to most of the available synthetic pesticides by the major pests. There also has been a marked increase in organic systems, and those that promote animal welfare by reducing...

Bottom-up GGM algorithm for constructing multiple layered hierarchical gene regulatory networks

USDA-ARS?s Scientific Manuscript database

Multilayered hierarchical gene regulatory networks (ML-hGRNs) are very important for understanding genetics regulation of biological pathways. However, there are currently no computational algorithms available for directly building ML-hGRNs that regulate biological pathways. A bottom-up graphic Gaus...

Soilcrust Photo Gallery

Science.gov Websites

Soil Crust Home Crust 101 Advanced Gallery References CCERS Site Links updated: January 30, 2008 images representative of Biological Soil Crusts on the Colorado Plateau. TIF downloads are available for 1 - Open spaces covered by biological soil crusts, a highly specialized community of cyanobacteria

9 CFR 102.6 - Conditional licenses.

Code of Federal Regulations, 2011 CFR

2011-01-01

... PRODUCTS § 102.6 Conditional licenses. In order to meet an emergency condition, limited market, local...) of this part, issue a conditional U.S. Veterinary Biological Product License to an establishment... available, the Administrator shall either reissue the U.S. Veterinary Biological Product License or allow it...

50 CFR 223.203 - Anadromous fish.

Code of Federal Regulations, 2011 CFR

2011-10-01

... identifiably unique biological and life history traits. Populations may be aggregated for management purposes... units, describe how the management units are defined, given biological and life history traits, so as to... impacts. (E) Provide for effective monitoring and adaptive management. (F) Use the best available science...

A benchmark for statistical microarray data analysis that preserves actual biological and technical variance.

PubMed

De Hertogh, Benoît; De Meulder, Bertrand; Berger, Fabrice; Pierre, Michael; Bareke, Eric; Gaigneaux, Anthoula; Depiereux, Eric

2010-01-11

Recent reanalysis of spike-in datasets underscored the need for new and more accurate benchmark datasets for statistical microarray analysis. We present here a fresh method using biologically-relevant data to evaluate the performance of statistical methods. Our novel method ranks the probesets from a dataset composed of publicly-available biological microarray data and extracts subset matrices with precise information/noise ratios. Our method can be used to determine the capability of different methods to better estimate variance for a given number of replicates. The mean-variance and mean-fold change relationships of the matrices revealed a closer approximation of biological reality. Performance analysis refined the results from benchmarks published previously.We show that the Shrinkage t test (close to Limma) was the best of the methods tested, except when two replicates were examined, where the Regularized t test and the Window t test performed slightly better. The R scripts used for the analysis are available at http://urbm-cluster.urbm.fundp.ac.be/~bdemeulder/.

BioPAX – A community standard for pathway data sharing

PubMed Central

Demir, Emek; Cary, Michael P.; Paley, Suzanne; Fukuda, Ken; Lemer, Christian; Vastrik, Imre; Wu, Guanming; D’Eustachio, Peter; Schaefer, Carl; Luciano, Joanne; Schacherer, Frank; Martinez-Flores, Irma; Hu, Zhenjun; Jimenez-Jacinto, Veronica; Joshi-Tope, Geeta; Kandasamy, Kumaran; Lopez-Fuentes, Alejandra C.; Mi, Huaiyu; Pichler, Elgar; Rodchenkov, Igor; Splendiani, Andrea; Tkachev, Sasha; Zucker, Jeremy; Gopinath, Gopal; Rajasimha, Harsha; Ramakrishnan, Ranjani; Shah, Imran; Syed, Mustafa; Anwar, Nadia; Babur, Ozgun; Blinov, Michael; Brauner, Erik; Corwin, Dan; Donaldson, Sylva; Gibbons, Frank; Goldberg, Robert; Hornbeck, Peter; Luna, Augustin; Murray-Rust, Peter; Neumann, Eric; Reubenacker, Oliver; Samwald, Matthias; van Iersel, Martijn; Wimalaratne, Sarala; Allen, Keith; Braun, Burk; Whirl-Carrillo, Michelle; Dahlquist, Kam; Finney, Andrew; Gillespie, Marc; Glass, Elizabeth; Gong, Li; Haw, Robin; Honig, Michael; Hubaut, Olivier; Kane, David; Krupa, Shiva; Kutmon, Martina; Leonard, Julie; Marks, Debbie; Merberg, David; Petri, Victoria; Pico, Alex; Ravenscroft, Dean; Ren, Liya; Shah, Nigam; Sunshine, Margot; Tang, Rebecca; Whaley, Ryan; Letovksy, Stan; Buetow, Kenneth H.; Rzhetsky, Andrey; Schachter, Vincent; Sobral, Bruno S.; Dogrusoz, Ugur; McWeeney, Shannon; Aladjem, Mirit; Birney, Ewan; Collado-Vides, Julio; Goto, Susumu; Hucka, Michael; Le Novère, Nicolas; Maltsev, Natalia; Pandey, Akhilesh; Thomas, Paul; Wingender, Edgar; Karp, Peter D.; Sander, Chris; Bader, Gary D.

2010-01-01

BioPAX (Biological Pathway Exchange) is a standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data (http://www.biopax.org). Pathway data captures our understanding of biological processes, but its rapid growth necessitates development of databases and computational tools to aid interpretation. However, the current fragmentation of pathway information across many databases with incompatible formats presents barriers to its effective use. BioPAX solves this problem by making pathway data substantially easier to collect, index, interpret and share. BioPAX can represent metabolic and signaling pathways, molecular and genetic interactions and gene regulation networks. BioPAX was created through a community process. Through BioPAX, millions of interactions organized into thousands of pathways across many organisms, from a growing number of sources, are available. Thus, large amounts of pathway data are available in a computable form to support visualization, analysis and biological discovery. PMID:20829833

Monitoring biological diversity: strategies, tools, limitations, and challenges

USGS Publications Warehouse

Beever, E.A.

2006-01-01

Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity will likely be most successful when based upon clearly articulated goals and objectives and may be enhanced by including several key steps in the process. Ideally, monitoring of biological diversity will measure not only composition, but also structure and function at the spatial and temporal scales of interest. Although biodiversity monitoring has several key limitations as well as numerous theoretical and practical challenges, many tools and strategies are available to address or overcome such challenges; I summarize several of these. Due to the diversity of spatio-temporal scales and comprehensiveness encompassed by existing definitions of biological diversity, an effective monitoring design will reflect the desired sampling domain of interest and its key stressors, available funding, legal requirements, and organizational goals.

IBS: an illustrator for the presentation and visualization of biological sequences.

PubMed

Liu, Wenzhong; Xie, Yubin; Ma, Jiyong; Luo, Xiaotong; Nie, Peng; Zuo, Zhixiang; Lahrmann, Urs; Zhao, Qi; Zheng, Yueyuan; Zhao, Yong; Xue, Yu; Ren, Jian

2015-10-15

Biological sequence diagrams are fundamental for visualizing various functional elements in protein or nucleotide sequences that enable a summarization and presentation of existing information as well as means of intuitive new discoveries. Here, we present a software package called illustrator of biological sequences (IBS) that can be used for representing the organization of either protein or nucleotide sequences in a convenient, efficient and precise manner. Multiple options are provided in IBS, and biological sequences can be manipulated, recolored or rescaled in a user-defined mode. Also, the final representational artwork can be directly exported into a publication-quality figure. The standalone package of IBS was implemented in JAVA, while the online service was implemented in HTML5 and JavaScript. Both the standalone package and online service are freely available at http://ibs.biocuckoo.org. renjian.sysu@gmail.com or xueyu@hust.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Sharing and executing linked data queries in a collaborative environment.

PubMed

García Godoy, María Jesús; López-Camacho, Esteban; Navas-Delgado, Ismael; Aldana-Montes, José F

2013-07-01

Life Sciences have emerged as a key domain in the Linked Data community because of the diversity of data semantics and formats available through a great variety of databases and web technologies. Thus, it has been used as the perfect domain for applications in the web of data. Unfortunately, bioinformaticians are not exploiting the full potential of this already available technology, and experts in Life Sciences have real problems to discover, understand and devise how to take advantage of these interlinked (integrated) data. In this article, we present Bioqueries, a wiki-based portal that is aimed at community building around biological Linked Data. This tool has been designed to aid bioinformaticians in developing SPARQL queries to access biological databases exposed as Linked Data, and also to help biologists gain a deeper insight into the potential use of this technology. This public space offers several services and a collaborative infrastructure to stimulate the consumption of biological Linked Data and, therefore, contribute to implementing the benefits of the web of data in this domain. Bioqueries currently contains 215 query entries grouped by database and theme, 230 registered users and 44 end points that contain biological Resource Description Framework information. The Bioqueries portal is freely accessible at http://bioqueries.uma.es. Supplementary data are available at Bioinformatics online.

Supervised normalization of microarrays

PubMed Central

Mecham, Brigham H.; Nelson, Peter S.; Storey, John D.

2010-01-01

Motivation: A major challenge in utilizing microarray technologies to measure nucleic acid abundances is ‘normalization’, the goal of which is to separate biologically meaningful signal from other confounding sources of signal, often due to unavoidable technical factors. It is intuitively clear that true biological signal and confounding factors need to be simultaneously considered when performing normalization. However, the most popular normalization approaches do not utilize what is known about the study, both in terms of the biological variables of interest and the known technical factors in the study, such as batch or array processing date. Results: We show here that failing to include all study-specific biological and technical variables when performing normalization leads to biased downstream analyses. We propose a general normalization framework that fits a study-specific model employing every known variable that is relevant to the expression study. The proposed method is generally applicable to the full range of existing probe designs, as well as to both single-channel and dual-channel arrays. We show through real and simulated examples that the method has favorable operating characteristics in comparison to some of the most highly used normalization methods. Availability: An R package called snm implementing the methodology will be made available from Bioconductor (http://bioconductor.org). Contact: jstorey@princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20363728

The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.

PubMed

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J; Inzé, Dirk; Van de Peer, Yves

2013-03-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein-protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies.

Atmospheric energy for subsurface life on Mars?

NASA Technical Reports Server (NTRS)

Weiss, B. P.; Yung, Y. L.; Nealson, K. H.

2000-01-01

The location and density of biologically useful energy sources on Mars will limit the biomass, spatial distribution, and organism size of any biota. Subsurface Martian organisms could be supplied with a large energy flux from the oxidation of photochemically produced atmospheric H(2) and CO diffusing into the regolith. However, surface abundance measurements of these gases demonstrate that no more than a few percent of this available flux is actually being consumed, suggesting that biological activity driven by atmospheric H(2) and CO is limited in the top few hundred meters of the subsurface. This is significant because the available but unused energy is extremely large: for organisms at 30-m depth, it is 2,000 times previous estimates of hydrothermal and chemical weathering energy and far exceeds the energy derivable from other atmospheric gases. This also implies that the apparent scarcity of life on Mars is not attributable to lack of energy. Instead, the availability of liquid water may be a more important factor limiting biological activity because the photochemical energy flux can only penetrate to 100- to 1,000-m depth, where most H(2)O is probably frozen. Because both atmospheric and Viking lander soil data provide little evidence for biological activity, the detection of short-lived trace gases will probably be a better indicator of any extant Martian life.

Atmospheric energy for subsurface life on Mars?

PubMed

Weiss, B P; Yung, Y L; Nealson, K H

2000-02-15

The location and density of biologically useful energy sources on Mars will limit the biomass, spatial distribution, and organism size of any biota. Subsurface Martian organisms could be supplied with a large energy flux from the oxidation of photochemically produced atmospheric H(2) and CO diffusing into the regolith. However, surface abundance measurements of these gases demonstrate that no more than a few percent of this available flux is actually being consumed, suggesting that biological activity driven by atmospheric H(2) and CO is limited in the top few hundred meters of the subsurface. This is significant because the available but unused energy is extremely large: for organisms at 30-m depth, it is 2,000 times previous estimates of hydrothermal and chemical weathering energy and far exceeds the energy derivable from other atmospheric gases. This also implies that the apparent scarcity of life on Mars is not attributable to lack of energy. Instead, the availability of liquid water may be a more important factor limiting biological activity because the photochemical energy flux can only penetrate to 100- to 1,000-m depth, where most H(2)O is probably frozen. Because both atmospheric and Viking lander soil data provide little evidence for biological activity, the detection of short-lived trace gases will probably be a better indicator of any extant Martian life.

An introduction to deep learning on biological sequence data: examples and solutions.

PubMed

Jurtz, Vanessa Isabell; Johansen, Alexander Rosenberg; Nielsen, Morten; Almagro Armenteros, Jose Juan; Nielsen, Henrik; Sønderby, Casper Kaae; Winther, Ole; Sønderby, Søren Kaae

2017-11-15

Deep neural network architectures such as convolutional and long short-term memory networks have become increasingly popular as machine learning tools during the recent years. The availability of greater computational resources, more data, new algorithms for training deep models and easy to use libraries for implementation and training of neural networks are the drivers of this development. The use of deep learning has been especially successful in image recognition; and the development of tools, applications and code examples are in most cases centered within this field rather than within biology. Here, we aim to further the development of deep learning methods within biology by providing application examples and ready to apply and adapt code templates. Given such examples, we illustrate how architectures consisting of convolutional and long short-term memory neural networks can relatively easily be designed and trained to state-of-the-art performance on three biological sequence problems: prediction of subcellular localization, protein secondary structure and the binding of peptides to MHC Class II molecules. All implementations and datasets are available online to the scientific community at https://github.com/vanessajurtz/lasagne4bio. skaaesonderby@gmail.com. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Economic value of biological control in integrated pest management of managed plant systems.

PubMed

Naranjo, Steven E; Ellsworth, Peter C; Frisvold, George B

2015-01-07

Biological control is an underlying pillar of integrated pest management, yet little focus has been placed on assigning economic value to this key ecosystem service. Setting biological control on a firm economic foundation would help to broaden its utility and adoption for sustainable crop protection. Here we discuss approaches and methods available for valuation of biological control of arthropod pests by arthropod natural enemies and summarize economic evaluations in classical, augmentative, and conservation biological control. Emphasis is placed on valuation of conservation biological control, which has received little attention. We identify some of the challenges of and opportunities for applying economics to biological control to advance integrated pest management. Interaction among diverse scientists and stakeholders will be required to measure the direct and indirect costs and benefits of biological control that will allow farmers and others to internalize the benefits that incentivize and accelerate adoption for private and public good.

On Crowd-verification of Biological Networks

PubMed Central

Ansari, Sam; Binder, Jean; Boue, Stephanie; Di Fabio, Anselmo; Hayes, William; Hoeng, Julia; Iskandar, Anita; Kleiman, Robin; Norel, Raquel; O’Neel, Bruce; Peitsch, Manuel C.; Poussin, Carine; Pratt, Dexter; Rhrissorrakrai, Kahn; Schlage, Walter K.; Stolovitzky, Gustavo; Talikka, Marja

2013-01-01

Biological networks with a structured syntax are a powerful way of representing biological information generated from high density data; however, they can become unwieldy to manage as their size and complexity increase. This article presents a crowd-verification approach for the visualization and expansion of biological networks. Web-based graphical interfaces allow visualization of causal and correlative biological relationships represented using Biological Expression Language (BEL). Crowdsourcing principles enable participants to communally annotate these relationships based on literature evidences. Gamification principles are incorporated to further engage domain experts throughout biology to gather robust peer-reviewed information from which relationships can be identified and verified. The resulting network models will represent the current status of biological knowledge within the defined boundaries, here processes related to human lung disease. These models are amenable to computational analysis. For some period following conclusion of the challenge, the published models will remain available for continuous use and expansion by the scientific community. PMID:24151423

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

TinkerCell: modular CAD tool for synthetic biology.

PubMed

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2009-10-29

Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API). TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at http://www.tinkercell.com. An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled and analyzed computationally. TinkerCell can readily accept third-party algorithms, allowing it to serve as a platform for testing different methods relevant to synthetic biology.

TinkerCell: modular CAD tool for synthetic biology

PubMed Central

Chandran, Deepak; Bergmann, Frank T; Sauro, Herbert M

2009-01-01

Background Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. Using a CAD application, it would be possible to construct models using available biological "parts" and directly generate the DNA sequence that represents the model, thus increasing the efficiency of design and construction of synthetic networks. Results An application named TinkerCell has been developed in order to serve as a CAD tool for synthetic biology. TinkerCell is a visual modeling tool that supports a hierarchy of biological parts. Each part in this hierarchy consists of a set of attributes that define the part, such as sequence or rate constants. Models that are constructed using these parts can be analyzed using various third-party C and Python programs that are hosted by TinkerCell via an extensive C and Python application programming interface (API). TinkerCell supports the notion of a module, which are networks with interfaces. Such modules can be connected to each other, forming larger modular networks. TinkerCell is a free and open-source project under the Berkeley Software Distribution license. Downloads, documentation, and tutorials are available at . Conclusion An ideal CAD application for engineering biological systems would provide features such as: building and simulating networks, analyzing robustness of networks, and searching databases for components that meet the design criteria. At the current state of synthetic biology, there are no established methods for measuring robustness or identifying components that fit a design. The same is true for databases of biological parts. TinkerCell's flexible modeling framework allows it to cope with changes in the field. Such changes may involve the way parts are characterized or the way synthetic networks are modeled and analyzed computationally. TinkerCell can readily accept third-party algorithms, allowing it to serve as a platform for testing different methods relevant to synthetic biology. PMID:19874625

Biana: a software framework for compiling biological interactions and analyzing networks

PubMed Central

2010-01-01

Background The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. Results We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. Conclusions BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules. PMID:20105306

Biana: a software framework for compiling biological interactions and analyzing networks.

PubMed

Garcia-Garcia, Javier; Guney, Emre; Aragues, Ramon; Planas-Iglesias, Joan; Oliva, Baldo

2010-01-27

The analysis and usage of biological data is hindered by the spread of information across multiple repositories and the difficulties posed by different nomenclature systems and storage formats. In particular, there is an important need for data unification in the study and use of protein-protein interactions. Without good integration strategies, it is difficult to analyze the whole set of available data and its properties. We introduce BIANA (Biologic Interactions and Network Analysis), a tool for biological information integration and network management. BIANA is a Python framework designed to achieve two major goals: i) the integration of multiple sources of biological information, including biological entities and their relationships, and ii) the management of biological information as a network where entities are nodes and relationships are edges. Moreover, BIANA uses properties of proteins and genes to infer latent biomolecular relationships by transferring edges to entities sharing similar properties. BIANA is also provided as a plugin for Cytoscape, which allows users to visualize and interactively manage the data. A web interface to BIANA providing basic functionalities is also available. The software can be downloaded under GNU GPL license from http://sbi.imim.es/web/BIANA.php. BIANA's approach to data unification solves many of the nomenclature issues common to systems dealing with biological data. BIANA can easily be extended to handle new specific data repositories and new specific data types. The unification protocol allows BIANA to be a flexible tool suitable for different user requirements: non-expert users can use a suggested unification protocol while expert users can define their own specific unification rules.

Authentic Research Experience and "Big Data" Analysis in the Classroom: Maize Response to Abiotic Stress.

PubMed

Makarevitch, Irina; Frechette, Cameo; Wiatros, Natalia

2015-01-01

Integration of inquiry-based approaches into curriculum is transforming the way science is taught and studied in undergraduate classrooms. Incorporating quantitative reasoning and mathematical skills into authentic biology undergraduate research projects has been shown to benefit students in developing various skills necessary for future scientists and to attract students to science, technology, engineering, and mathematics disciplines. While large-scale data analysis became an essential part of modern biological research, students have few opportunities to engage in analysis of large biological data sets. RNA-seq analysis, a tool that allows precise measurement of the level of gene expression for all genes in a genome, revolutionized molecular biology and provides ample opportunities for engaging students in authentic research. We developed, implemented, and assessed a series of authentic research laboratory exercises incorporating a large data RNA-seq analysis into an introductory undergraduate classroom. Our laboratory series is focused on analyzing gene expression changes in response to abiotic stress in maize seedlings; however, it could be easily adapted to the analysis of any other biological system with available RNA-seq data. Objective and subjective assessment of student learning demonstrated gains in understanding important biological concepts and in skills related to the process of science. © 2015 I. Makarevitch et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Broadening Participation in Biology Education Research: Engaging Community College Students and Faculty.

PubMed

Schinske, Jeffrey N; Balke, Virginia L; Bangera, M Gita; Bonney, Kevin M; Brownell, Sara E; Carter, Robert S; Curran-Everett, Douglas; Dolan, Erin L; Elliott, Samantha L; Fletcher, Linnea; Gonzalez, Beatriz; Gorga, Joseph J; Hewlett, James A; Kiser, Stacey L; McFarland, Jenny L; Misra, Anjali; Nenortas, Apryl; Ngeve, Smith M; Pape-Lindstrom, Pamela A; Seidel, Shannon B; Tuthill, Matthew C; Yin, Yue; Corwin, Lisa A

2017-01-01

Nearly half of all undergraduates are enrolled at community colleges (CCs), including the majority of U.S. students who represent groups underserved in the sciences. Yet only a small minority of studies published in discipline-based education research journals address CC biology students, faculty, courses, or authors. This marked underrepresentation of CC biology education research (BER) limits the availability of evidence that could be used to increase CC student success in biology programs. To address this issue, a diverse group of stakeholders convened at the Building Capacity for Biology Education Research at Community Colleges meeting to discuss how to increase the prevalence of CC BER and foster participation of CC faculty as BER collaborators and authors. The group identified characteristics of CCs that make them excellent environments for studying biology teaching and learning, including student diversity and institutional cultures that prioritize teaching, learning, and assessment. The group also identified constraints likely to impede BER at CCs: limited time, resources, support, and incentives, as well as misalignment between doing research and CC faculty identities as teachers. The meeting culminated with proposing strategies for faculty, administrators, journal editors, scientific societies, and funding agencies to better support CC BER. © 2017 J. N. Schinske et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Traditional schemes for treatment of psoriatic arthritis.

PubMed

McHugh, Neil J

2009-08-01

Prior to the availability of biologic agents such as anti-tumor necrosis factor (TNF), traditional treatment schemes for psoriatic arthritis were not extensively evaluated. While it appears that the newer forms of treatment are more effective, conventional agents still need to be scrutinized with similar methodology and will still have a role in those patients with less progressive disease, in combination with biologic agents, and in patients where biologics are not tolerated or have failed.

BicPAMS: software for biological data analysis with pattern-based biclustering.

PubMed

Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

2017-02-02

Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the possibility to: 1) parametrically customize the structure, coherency and quality of biclusters; 2) analyze large-scale biological networks; and 3) tackle the restrictive assumptions placed by state-of-the-art biclustering algorithms. These contributions are shown to be key for an adequate, complete and user-assisted unsupervised analysis of biological data. BicPAMS and its tutorial available in http://www.bicpams.com .

Web-based software tool for constraint-based design specification of synthetic biological systems.

PubMed

Oberortner, Ernst; Densmore, Douglas

2015-06-19

miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system-the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology ( www.eugenecad.org ).

Detection of biological warfare agents using ultra violet-laser induced fluorescence LIDAR

NASA Astrophysics Data System (ADS)

Joshi, Deepti; Kumar, Deepak; Maini, Anil K.; Sharma, Ramesh C.

This review has been written to highlight the threat of biological warfare agents, their types and detection. Bacterial biological agent Bacillus anthracis (bacteria causing the disease anthrax) which is most likely to be employed in biological warfare is being discussed in detail. Standoff detection of biological warfare agents in aerosol form using Ultra violet-Laser Induced Fluorescence (UV-LIF) spectroscopy method has been studied. Range-resolved detection and identification of biological aerosols by both nano-second and non-linear femto-second LIDAR is also discussed. Calculated received fluorescence signal for a cloud of typical biological agent Bacillus globigii (Simulants of B. anthracis) at a location of ˜5.0 km at different concentrations in presence of solar background radiation has been described. Overview of current research efforts in internationally available working UV-LIF LIDAR systems are also mentioned briefly.

The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.

PubMed

Gifford, Lida K; Carter, Lester G; Gabanyi, Margaret J; Berman, Helen M; Adams, Paul D

2012-06-01

The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.

Population biology of the Florida manatee: An overview

USGS Publications Warehouse

O'Shea, Thomas J.; Ackerman, B.B.; O'Shea, Thomas J.; Ackerman, B.B.; Percival, H. Franklin

1995-01-01

In the following overview we discuss progress toward meeting the three objectives of the 1992 workshop: to provide a synthesis of existing information about manatee population biology; to evaluate the strengths and weaknesses of current data sets and approaches to research on manatee population biology; and to provide recommendations for research. We discuss progress in six topics that were assigned to working groups at the workshop: aerial survey and estimation of population size, reproduction, age structure, mortality, photoidentification and estimation of survival, and integration and modeling of population data. The overview includes recommendations by working group participants (*2 0'Shea et al. 1992). This workshop on manatee population biology was the most recent conference on the topic since 1978 (*BrowneIl and Rails 1981). Partly as a result of recommendations made at the 1978 workshop, several long-term population-related research projects were established. Therefore, we also measure progress in relation to knowledge available at the time of the earlier workshop. Finally, we provide a brief synopsis of pertinent new information on manatee population biology that became available between the 1992 workshop and publication of the proceedings and our conclusions about the status of the Florida manatee.

Informatics for maize research: What is possible, and what is practical?

USDA-ARS?s Scientific Manuscript database

The informatics tools and technologies developed to address problems in fields outside of biology often drive what becomes available to biologists. Within the biological sciences, research groups have made headway implementing tools to solve problems of interest to maize researchers, but we do not ...

A Comparative Evaluation of Videodiscs for General Biology.

ERIC Educational Resources Information Center

Ralph, Charles L.

1995-01-01

Provides a brief profile of the currently available videodiscs for general biology, with comparable information for each. An introduction discusses benefits and problems associated with videodisc use in the classroom. Profiles contain information on description, good and bad features, still images, animations and movies, audio, software,…

AIBS Educational Review, Vol. 5, No. 2.

ERIC Educational Resources Information Center

Dodge, Richard A., Ed.

This publication, published quarterly by the American Institute of Biological Sciences, focuses on biology education in colleges and universities. Included in this issue are articles dealing with adapting available materials to an individualized instructional format, science seminars for liberal arts freshmen, the role of physiology in anatomy…

76 FR 13597 - Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-14

... Significant Impact for a Biological Control Agent for Hawkweeds AGENCY: Animal and Plant Health Inspection... Inspection Service (APHIS) has prepared an environmental assessment and finding of no significant impact... / Monday, March 14, 2011 / Notices#0;#0; [[Page 13597

Supporting read-across using biological data.

PubMed

Zhu, Hao; Bouhifd, Mounir; Donley, Elizabeth; Egnash, Laura; Kleinstreuer, Nicole; Kroese, E Dinant; Liu, Zhichao; Luechtefeld, Thomas; Palmer, Jessica; Pamies, David; Shen, Jie; Strauss, Volker; Wu, Shengde; Hartung, Thomas

2016-01-01

Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA's ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment.

Tapping the Power of Crustacean Transcriptomics to Address Grand Challenges in Comparative Biology: An Introduction to the Symposium.

PubMed

Mykles, Donald L; Burnett, Karen G; Durica, David S; Stillman, Jonathon H

2016-12-01

Crustaceans, and decapods in particular (i.e., crabs, shrimp, and lobsters), are a diverse and ecologically and commercially important group of organisms. Understanding responses to abiotic and biotic factors is critical for developing best practices in aquaculture and assessing the effects of changing environments on the biology of these important animals. A relatively small number of decapod crustacean species have been intensively studied at the molecular level; the availability, experimental tractability, and economic relevance factor into the selection of a particular species as a model. Transcriptomics, using high-throughput next generation sequencing (NGS, coupled with RNA sequencing or RNA-seq) is revolutionizing crustacean biology. The 11 symposium papers in this volume illustrate how RNA-seq is being used to study stress response, molting and limb regeneration, immunity and disease, reproduction and development, neurobiology, and ecology and evolution. This symposium occurred on the 10th anniversary of the symposium, "Genomic and Proteomic Approaches to Crustacean Biology", held at the Society for Integrative and Comparative Biology 2006 meeting. Two participants in the 2006 symposium, the late Paul Gross and David Towle, were recognized as leaders who pioneered the use of molecular techniques that would ultimately foster the transcriptomics research reviewed in this volume. RNA-seq is a powerful tool for hypothesis-driven research, as well as an engine for discovery. It has eclipsed the technologies available in 2006, such as microarrays, expressed sequence tags, and subtractive hybridization screening, as the millions of "reads" from NGS enable researchers to de novo assemble a comprehensive transcriptome without a complete genome sequence. The symposium series concludes with a policy paper that gives an overview of the resources available and makes recommendations for developing better tools for functional annotation and pathway and network analysis in organisms in which the genome is not available or is incomplete. © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

BioNSi: A Discrete Biological Network Simulator Tool.

PubMed

Rubinstein, Amir; Bracha, Noga; Rudner, Liat; Zucker, Noga; Sloin, Hadas E; Chor, Benny

2016-08-05

Modeling and simulation of biological networks is an effective and widely used research methodology. The Biological Network Simulator (BioNSi) is a tool for modeling biological networks and simulating their discrete-time dynamics, implemented as a Cytoscape App. BioNSi includes a visual representation of the network that enables researchers to construct, set the parameters, and observe network behavior under various conditions. To construct a network instance in BioNSi, only partial, qualitative biological data suffices. The tool is aimed for use by experimental biologists and requires no prior computational or mathematical expertise. BioNSi is freely available at http://bionsi.wix.com/bionsi , where a complete user guide and a step-by-step manual can also be found.

Inhalation delivery of protein therapeutics.

PubMed

Kane, Colleen; O'Neil, Karyn; Conk, Michelle; Picha, Kristen

2013-04-01

Inhaled therapeutics are used routinely to treat a variety of pulmonary diseases including asthma, COPD and cystic fibrosis. In addition, biological therapies represent the fastest growing segment of approved pharmaceuticals. However, despite the increased availability of biological therapies, nearly all inhaled therapeutics are small molecule drugs with only a single inhaled protein therapeutic approved. There remains a significant unmet need for therapeutics in pulmonary diseases, and biological therapies with potential to alter disease progression represent a significant opportunity to treat these challenging diseases. This review provides a background into efforts to develop inhaled biological therapies and highlights some of the associated challenges. In addition, we speculate on the ideal properties of a biologic therapy for inhaled delivery.

Systems biology for molecular life sciences and its impact in biomedicine.

PubMed

Medina, Miguel Ángel

2013-03-01

Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

Inferring Causes of Biological Impairment in the Clear Fork Watershed, West Virginia (Final)

EPA Science Inventory

EPA announced the availability of the final report, Inferring Causes of Biological Impairment in the Clear Fork Watershed, West Virginia. This study illustrates a causal assessment in a watershed using the US EPA stressor identification process described on the www.epa....

76 FR 4360 - Guidance for Industry on Process Validation: General Principles and Practices; Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-25

... elements of process validation for the manufacture of human and animal drug and biological products... process validation for the manufacture of human and animal drug and biological products, including APIs. This guidance describes process validation activities in three stages: In Stage 1, Process Design, the...

75 FR 14565 - NIST Summer Institute for Middle School Science Teachers; Availability of Funds

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-26

...), including, but not limited to, earth science, physical science, chemistry, physics, and/or biology. This... science, physical science, chemistry, physics and/or biology. NIST will award funding that will support... instruction in general science fields including earth science, physical science, chemistry, physics, and/or...

Index of A/T's in Science.

ERIC Educational Resources Information Center

Bonney, Catherine

This monograph presents an annotated index of auto-tutorial materials in science education available to middle and secondary schools in the Newark School District. Materials relevant to the study of the biological sciences enable the students to become more familiar with Biology Statistics, Cytology, Marine Field Trips, Use of Microscopes,…

Occupational Orientation: Applied Biological and Agricultural Occupations. Experimental Curriculum Materials.

ERIC Educational Resources Information Center

Illinois State Office of Education, Springfield.

These experimental curriculum materials, from one of five clusters developed for the occupational orientation program in Illinois, include a series of learning activity packages (LAPs) designed to acquaint the student with the wide range of occupational choices available in the applied biological and agricultural occupations. The 30 LAPs, each…

Modeling Mendel's Laws on Inheritance in Computational Biology and Medical Sciences

ERIC Educational Resources Information Center

Singh, Gurmukh; Siddiqui, Khalid; Singh, Mankiran; Singh, Satpal

2011-01-01

The current research article is based on a simple and practical way of employing the computational power of widely available, versatile software MS Excel 2007 to perform interactive computer simulations for undergraduate/graduate students in biology, biochemistry, biophysics, microbiology, medicine in college and university classroom setting. To…

Teaching Field Biology with Photography

ERIC Educational Resources Information Center

Jenkins, Ronald L.; Howell, W. Mike; Davenport, L. J.; Wood, Linda F.

2003-01-01

Photography makes an easy and excellent tool for teaching field biology courses, allowing students to study nature without harming it. This photographic technique is used in capturing images of vertebrates, invertebrates, and plants during class field trips, then making these images available for students to identify and study from a departmental…

Best practices for the use and exchange of invertebrate biological control genetic resources relevant for food and agriculture

USDA-ARS?s Scientific Manuscript database

Biological control is an important and environmentally preferred management option for invasive insect pests and weeds. Implementation of new international regulations governing exchange of genetic materials impacts the availability of candidate biocontrol agents, and exchange policies need to be ca...

Photographic catalog of Platygastroidea (Hymenoptera) in the Institute of Ecology and Biological Resources (Hanoi, Vietnam)

USDA-ARS?s Scientific Manuscript database

All holotypes of Platygastroidea housed in the Institute of Ecology and Biological Resources were photographed and these images are now publicly available online, as are images of most species represented in this collection by paratypes alone. Following examination of these specimens, the following ...

Biology Students Building Computer Simulations Using StarLogo TNG

ERIC Educational Resources Information Center

Smith, V. Anne; Duncan, Ishbel

2011-01-01

Confidence is an important issue for biology students in handling computational concepts. This paper describes a practical in which honours-level bioscience students simulate complex animal behaviour using StarLogo TNG, a freely-available graphical programming environment. The practical consists of two sessions, the first of which guides students…

Biological control of aflatoxin is effective and economical in Mississippi field trials

USDA-ARS?s Scientific Manuscript database

Aflatoxin contamination of corn is a major grain quality issue and can be a major economic limiting factor to Mississippi corn farmers. Biological control products based on aflatoxin non-producing strains of Aspergillus flavus are commercially available to prevent the contamination of corn with afl...

INTERACTIONS BETWEEN PHOTOCHEMICAL AND MICROBIAL DECOMPOSITION IN MODIFYING THE BIOLOGICAL AVAILABILITY AND OPTICAL PROPERTIES OF ESTUARINE DISSOLVED ORGANIC MATTER

EPA Science Inventory

Direct photodecomposition and photochemically-mediated bacterial degradation (via photochemical modification of otherwise refractory DOM into biologically labile forms) provide
important pathways for the loss of dissolved organic matter in coastal waters. Here we report
lab...

75 FR 70010 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-16

.... Specificity of acyl transfer from 2- mercaptobenzamide thioesters to the HIV-1 nucleocapsid protein. J Am Chem...) images and de-magnifies the surface of the diffractive grating into a biological sample that causes an... would predominantly be for research in biological imaging. The device provides the ability to image a...

Observations on root disease of container whitebark pine seedlings treated with biological controls

Treesearch

R. Kasten Dumroese

2008-01-01

I observed that whitebark pine (Pinus albicaulis Engelm. [Pinaceae]) germinants treated with biological controls, one commercially available (Trichoderma harzianum strain T-22), and the other being studied for potential efficacy (Fusarium oxysporum isolate Q12), experienced less seedling mortality caused by root disease than did a...

78 FR 19714 - User Fees and Refunds for Premarket Approval Applications and Device Biologics License...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-02

...] User Fees and Refunds for Premarket Approval Applications and Device Biologics License Applications... availability of the guidance entitled ``User Fees and Refunds for Premarket Approval Applications (PMAs) and... for single copies of the guidance document entitled ``User Fees and Refunds for Premarket Approval...

Follow-on biologics: data exclusivity and the balance between innovation and competition.

PubMed

Grabowski, Henry

2008-06-01

Legislation to create a regulatory pathway for follow-on biologics is currently being considered by the United States Congress. A critical issue in this respect is the period of data exclusivity for innovator companies before a follow-on competitor can rely in part on data obtained for an original biologic for an abbreviated approval. Given the nature of patents on biologics, the period of data exclusivity is anticipated to have a key role in determining how quickly follow-on competitors emerge, and consequently also on the time available for originator companies to recoup their investment. With this issue in mind, this article discusses factors influencing return on investment on biologic research and development. A break-even analysis for a representative portfolio of biologics provides support for a substantial data exclusivity period.

Risk analysis for veterinary biologicals released into the environment.

PubMed

Silva, S V; Samagh, B S; Morley, R S

1995-12-01

All veterinary biologicals licensed in Canada must be shown to be pure, potent, safe and effective. A risk-based approach is used to evaluate the safety of all biologicals, whether produced by conventional methods or by molecular biological techniques. Traditionally, qualitative risk assessment methods have been used for this purpose. More recently, quantitative risk assessment has become available for complex issues. The quantitative risk assessment method uses "scenario tree analysis' to predict the likelihood of various outcomes and their respective impacts. The authors describe the quantitative risk assessment approach which is used within the broader context of risk analysis (i.e. risk assessment, risk management and risk communication) to develop recommendations for the field release of veterinary biologicals. The general regulatory framework for the licensing of veterinary biologicals in Canada is also presented.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

PubMed

Egea, Jose A; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro F; MacNamara, Aidan; Danciu, Diana-Patricia; Banga, Julio R; Saez-Rodriguez, Julio

2014-05-10

Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

PubMed Central

2014-01-01

Background Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. Results We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. Conclusions MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods. PMID:24885957

Protect and Defend: Adequacy of the Department of Defense Role Prescribed in the Federal Response to a Chemical or Biological Attack Against the Homeland

DTIC Science & Technology

2002-05-31

fermenters , centrifuges, driers, milling equipment, and safety products-- for a biological weapon is the least difficult barrier for a terrorist to...number of people with biotechnical training but also an increase in the availability of tools, supplies, and equipment such as fermenters and...108 A biological production facility would include fermenters , milling equipment, centrifuges, and drivers. This is the same equipment needed to

Neuro-symbolic representation learning on biological knowledge graphs.

PubMed

Alshahrani, Mona; Khan, Mohammad Asif; Maddouri, Omar; Kinjo, Akira R; Queralt-Rosinach, Núria; Hoehndorf, Robert

2017-09-01

Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are applicable to graph-structured data are becoming available, but have not yet widely been applied and evaluated on structured biological knowledge. Results: We develop a novel method for feature learning on biological knowledge graphs. Our method combines symbolic methods, in particular knowledge representation using symbolic logic and automated reasoning, with neural networks to generate embeddings of nodes that encode for related information within knowledge graphs. Through the use of symbolic logic, these embeddings contain both explicit and implicit information. We apply these embeddings to the prediction of edges in the knowledge graph representing problems of function prediction, finding candidate genes of diseases, protein-protein interactions, or drug target relations, and demonstrate performance that matches and sometimes outperforms traditional approaches based on manually crafted features. Our method can be applied to any biological knowledge graph, and will thereby open up the increasing amount of Semantic Web based knowledge bases in biology to use in machine learning and data analytics. https://github.com/bio-ontology-research-group/walking-rdf-and-owl. robert.hoehndorf@kaust.edu.sa. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Utility of biological sensor tags in animal conservation.

PubMed

Wilson, A D M; Wikelski, M; Wilson, R P; Cooke, S J

2015-08-01

Electronic tags (both biotelemetry and biologging platforms) have informed conservation and resource management policy and practice by providing vital information on the spatial ecology of animals and their environments. However, the extent of the contribution of biological sensors (within electronic tags) that measure an animal's state (e.g., heart rate, body temperature, and details of locomotion and energetics) is less clear. A literature review revealed that, despite a growing number of commercially available state sensor tags and enormous application potential for such devices in animal biology, there are relatively few examples of their application to conservation. Existing applications fell under 4 main themes: quantifying disturbance (e.g., ecotourism, vehicular and aircraft traffic), examining the effects of environmental change (e.g., climate change), understanding the consequences of habitat use and selection, and estimating energy expenditure. We also identified several other ways in which sensor tags could benefit conservation, such as determining the potential efficacy of management interventions. With increasing sensor diversity of commercially available platforms, less invasive attachment techniques, smaller device sizes, and more researchers embracing such technology, we suggest that biological sensor tags be considered a part of the necessary toolbox for conservation. This approach can measure (in real time) the state of free-ranging animals and thus provide managers with objective, timely, relevant, and accurate data to inform policy and decision making. © 2015 Society for Conservation Biology.

Biocellion: accelerating computer simulation of multicellular biological system models

PubMed Central

Kang, Seunghwa; Kahan, Simon; McDermott, Jason; Flann, Nicholas; Shmulevich, Ilya

2014-01-01

Motivation: Biological system behaviors are often the outcome of complex interactions among a large number of cells and their biotic and abiotic environment. Computational biologists attempt to understand, predict and manipulate biological system behavior through mathematical modeling and computer simulation. Discrete agent-based modeling (in combination with high-resolution grids to model the extracellular environment) is a popular approach for building biological system models. However, the computational complexity of this approach forces computational biologists to resort to coarser resolution approaches to simulate large biological systems. High-performance parallel computers have the potential to address the computing challenge, but writing efficient software for parallel computers is difficult and time-consuming. Results: We have developed Biocellion, a high-performance software framework, to solve this computing challenge using parallel computers. To support a wide range of multicellular biological system models, Biocellion asks users to provide their model specifics by filling the function body of pre-defined model routines. Using Biocellion, modelers without parallel computing expertise can efficiently exploit parallel computers with less effort than writing sequential programs from scratch. We simulate cell sorting, microbial patterning and a bacterial system in soil aggregate as case studies. Availability and implementation: Biocellion runs on x86 compatible systems with the 64 bit Linux operating system and is freely available for academic use. Visit http://biocellion.com for additional information. Contact: seunghwa.kang@pnnl.gov PMID:25064572

Visualising associations between paired ‘omics’ data sets

PubMed Central

2012-01-01

Background Each omics platform is now able to generate a large amount of data. Genomics, proteomics, metabolomics, interactomics are compiled at an ever increasing pace and now form a core part of the fundamental systems biology framework. Recently, several integrative approaches have been proposed to extract meaningful information. However, these approaches lack of visualisation outputs to fully unravel the complex associations between different biological entities. Results The multivariate statistical approaches ‘regularized Canonical Correlation Analysis’ and ‘sparse Partial Least Squares regression’ were recently developed to integrate two types of highly dimensional ‘omics’ data and to select relevant information. Using the results of these methods, we propose to revisit few graphical outputs to better understand the relationships between two ‘omics’ data and to better visualise the correlation structure between the different biological entities. These graphical outputs include Correlation Circle plots, Relevance Networks and Clustered Image Maps. We demonstrate the usefulness of such graphical outputs on several biological data sets and further assess their biological relevance using gene ontology analysis. Conclusions Such graphical outputs are undoubtedly useful to aid the interpretation of these promising integrative analysis tools and will certainly help in addressing fundamental biological questions and understanding systems as a whole. Availability The graphical tools described in this paper are implemented in the freely available R package mixOmics and in its associated web application. PMID:23148523

Macro- and microscale fluid flow systems for endothelial cell biology.

PubMed

Young, Edmond W K; Simmons, Craig A

2010-01-21

Recent advances in microfluidics have brought forth new tools for studying flow-induced effects on mammalian cells, with important applications in cardiovascular, bone and cancer biology. The plethora of microscale systems developed to date demonstrate the flexibility of microfluidic designs, and showcase advantages of the microscale that are simply not available at the macroscale. However, the majority of these systems will likely not achieve widespread use in the biological laboratory due to their complexity and lack of user-friendliness. To gain widespread acceptance in the biological research community, microfluidics engineers must understand the needs of cell biologists, while biologists must be made aware of available technology. This review provides a critical evaluation of cell culture flow (CCF) systems used to study the effects of mechanical forces on endothelial cells (ECs) in vitro. To help understand the need for various designs of CCF systems, we first briefly summarize main properties of ECs and their native environments. Basic principles of various macro- and microscale systems are described and evaluated. New opportunities are uncovered for developing technologies that have potential to both improve efficiency of experimentation as well as answer important biological questions that otherwise cannot be tackled with existing systems. Finally, we discuss some of the unresolved issues related to microfluidic cell culture, suggest possible avenues of investigation that could resolve these issues, and provide an outlook for the future of microfluidics in biological research.

Synthetic biology era: Improving antibiotic's world.

PubMed

Guzmán-Trampe, Silvia; Ceapa, Corina D; Manzo-Ruiz, Monserrat; Sánchez, Sergio

2017-06-15

The emergence of antibiotic-resistant pathogen microorganisms is problematic in the context of the current spectrum of available medication. The poor specificity and the high toxicity of some available molecules have made imperative the search for new strategies to improve the specificity and to pursue the discovery of novel compounds with increased bioactivity. Using living cells as platforms, synthetic biology has counteracted this problem by offering novel pathways to create synthetic systems with improved and desired functions. Among many other biotechnological approaches, the advances in synthetic biology have made it possible to design and construct novel biological systems in order to look for new drugs with increased bioactivity. Advancements have also been made in the redesigning of RNA and DNA molecules in order to engineer antibiotic clusters for antibiotic overexpression. As for the production of these antibacterial compounds, yeasts and filamentous fungi as well as gene therapy are utilized to enhance protein solubility. Specific delivery is achieved by creating chimeras using plant genes into bacterial hosts. Some of these synthetic systems are currently in clinical trials, proving the proficiency of synthetic biology in terms of both pharmacological activities as well as an increase in the biosafety of treatments. It is possible that we may just be seeing the tip of the iceberg, and synthetic biology applications will overpass expectations beyond our present knowledge. Copyright © 2017. Published by Elsevier Inc.

Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark.

PubMed

Klein, Max; Sharma, Rati; Bohrer, Chris H; Avelis, Cameron M; Roberts, Elijah

2017-01-15

Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology. Source code is licensed under the Apache 2.0 open source license and is available at the project website: https://www.assembla.com/spaces/roberts-lab-public/wiki/Biospark CONTACT: eroberts@jhu.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

PubMed Central

Diaz Acosta, B.

2011-01-01

The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

sbv IMPROVER: Modern Approach to Systems Biology.

PubMed

Guryanova, Svetlana; Guryanova, Anna

2017-01-01

The increasing amount and variety of data in biosciences call for innovative methods of visualization, scientific verification, and pathway analysis. Novel approaches to biological networks and research quality control are important because of their role in development of new products, improvement, and acceleration of existing health policies and research for novel ways of solving scientific challenges. One such approach is sbv IMPROVER. It is a platform that uses crowdsourcing and verification to create biological networks with easy public access. It contains 120 networks built in Biological Expression Language (BEL) to interpret data from PubMed articles with high-quality verification available for free on the CBN database. Computable, human-readable biological networks with a structured syntax are a powerful way of representing biological information generated from high-density data. This article presents sbv IMPROVER, a crowd-verification approach for the visualization and expansion of biological networks.

Evolution of activities in international biological standardization since the early days of the Health Organisation of the League of Nations.

PubMed

Sizaret, P

1988-01-01

The main activities in international biological standardization during the 18 years that followed the first international biological standardization meeting in London in 1921 were concerned with expressing the potencies of test preparations in comparison with reference materials. After the Second World War, however, it became clear that the testing of biological substances against international reference materials was only one among several measures for obtaining safe and potent products. The activities in international biological standardization were therefore widened so that, by the strict observance of specific manufacturing and control requirements, it was possible to gain further in safety and efficacy. At the end of 1987, 42 international requirements for biological substances were available and were being used as national requirements, sometimes after minor modification, by the majority of WHO's Member States. This is of utmost importance for the worldwide use of safe and potent biological products, including vaccines.

Materials and methods for delivery of biological drugs

NASA Astrophysics Data System (ADS)

Zelikin, Alexander N.; Ehrhardt, Carsten; Healy, Anne Marie

2016-11-01

Biological drugs generated via recombinant techniques are uniquely positioned due to their high potency and high selectivity of action. The major drawback of this class of therapeutics, however, is their poor stability upon oral administration and during subsequent circulation. As a result, biological drugs have very low bioavailability and short therapeutic half-lives. Fortunately, tools of chemistry and biotechnology have been developed into an elaborate arsenal, which can be applied to improve the pharmacokinetics of biological drugs. Depot-type release systems are available to achieve sustained release of drugs over time. Conjugation to synthetic or biological polymers affords long circulating formulations. Administration of biological drugs through non-parenteral routes shows excellent performance and the first products have reached the market. This Review presents the main accomplishments in this field and illustrates the materials and methods behind existing and upcoming successful formulations and delivery strategies for biological drugs.

Detection of biological warfare agents using ultra violet-laser induced fluorescence LIDAR.

PubMed

Joshi, Deepti; Kumar, Deepak; Maini, Anil K; Sharma, Ramesh C

2013-08-01

This review has been written to highlight the threat of biological warfare agents, their types and detection. Bacterial biological agent Bacillus anthracis (bacteria causing the disease anthrax) which is most likely to be employed in biological warfare is being discussed in detail. Standoff detection of biological warfare agents in aerosol form using Ultra violet-Laser Induced Fluorescence (UV-LIF) spectroscopy method has been studied. Range-resolved detection and identification of biological aerosols by both nano-second and non-linear femto-second LIDAR is also discussed. Calculated received fluorescence signal for a cloud of typical biological agent Bacillus globigii (Simulants of B. anthracis) at a location of ~5.0 km at different concentrations in presence of solar background radiation has been described. Overview of current research efforts in internationally available working UV-LIF LIDAR systems are also mentioned briefly. Copyright © 2013 Elsevier B.V. All rights reserved.

cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

PubMed Central

Johnson, Graham T.; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

2014-01-01

cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of models and with recipes and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators, and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org. PMID:25437435

KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

PubMed Central

2014-01-01

Background The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. Description KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data. KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. Conclusions KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects. The web application implemented using Ruby on Rails framework is freely available for web access at http://kimosys.org, along with its full documentation. PMID:25115331

FALCON: a toolbox for the fast contextualization of logical networks.

PubMed

De Landtsheer, Sébastien; Trairatphisan, Panuwat; Lucarelli, Philippe; Sauter, Thomas

2017-11-01

Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. We have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. thomas.sauter@uni.lu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Bayesian network prior: network analysis of biological data using external knowledge

PubMed Central

Isci, Senol; Dogan, Haluk; Ozturk, Cengizhan; Otu, Hasan H.

2014-01-01

Motivation: Reverse engineering GI networks from experimental data is a challenging task due to the complex nature of the networks and the noise inherent in the data. One way to overcome these hurdles would be incorporating the vast amounts of external biological knowledge when building interaction networks. We propose a framework where GI networks are learned from experimental data using Bayesian networks (BNs) and the incorporation of external knowledge is also done via a BN that we call Bayesian Network Prior (BNP). BNP depicts the relation between various evidence types that contribute to the event ‘gene interaction’ and is used to calculate the probability of a candidate graph (G) in the structure learning process. Results: Our simulation results on synthetic, simulated and real biological data show that the proposed approach can identify the underlying interaction network with high accuracy even when the prior information is distorted and outperforms existing methods. Availability: Accompanying BNP software package is freely available for academic use at http://bioe.bilgi.edu.tr/BNP. Contact: hasan.otu@bilgi.edu.tr Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24215027

PubChemSR: A search and retrieval tool for PubChem

PubMed Central

Hur, Junguk; Wild, David J

2008-01-01

Background Recent years have seen an explosion in the amount of publicly available chemical and related biological information. A significant step has been the emergence of PubChem, which contains property information for millions of chemical structures, and acts as a repository of compounds and bioassay screening data for the NIH Roadmap. There is a strong need for tools designed for scientists that permit easy download and use of these data. We present one such tool, PubChemSR. Implementation PubChemSR (Search and Retrieve) is a freely available desktop application written for Windows using Microsoft .NET that is designed to assist scientists in search, retrieval and organization of chemical and biological data from the PubChem database. It employs SOAP web services made available by NCBI for extraction of information from PubChem. Results and Discussion The program supports a wide range of searching techniques, including queries based on assay or compound keywords and chemical substructures. Results can be examined individually or downloaded and exported in batch for use in other programs such as Microsoft Excel. We believe that PubChemSR makes it straightforward for researchers to utilize the chemical, biological and screening data available in PubChem. We present several examples of how it can be used. PMID:18482452

BinQuasi: a peak detection method for ChIP-sequencing data with biological replicates.

PubMed

Goren, Emily; Liu, Peng; Wang, Chao; Wang, Chong

2018-04-19

ChIP-seq experiments that are aimed at detecting DNA-protein interactions require biological replication to draw inferential conclusions, however there is no current consensus on how to analyze ChIP-seq data with biological replicates. Very few methodologies exist for the joint analysis of replicated ChIP-seq data, with approaches ranging from combining the results of analyzing replicates individually to joint modeling of all replicates. Combining the results of individual replicates analyzed separately can lead to reduced peak classification performance compared to joint modeling. Currently available methods for joint analysis may fail to control the false discovery rate at the nominal level. We propose BinQuasi, a peak caller for replicated ChIP-seq data, that jointly models biological replicates using a generalized linear model framework and employs a one-sided quasi-likelihood ratio test to detect peaks. When applied to simulated data and real datasets, BinQuasi performs favorably compared to existing methods, including better control of false discovery rate than existing joint modeling approaches. BinQuasi offers a flexible approach to joint modeling of replicated ChIP-seq data which is preferable to combining the results of replicates analyzed individually. Source code is freely available for download at https://cran.r-project.org/package=BinQuasi, implemented in R. pliu@iastate.edu or egoren@iastate.edu. Supplementary material is available at Bioinformatics online.

The Potential of Text Mining in Data Integration and Network Biology for Plant Research: A Case Study on Arabidopsis[C][W

PubMed Central

Van Landeghem, Sofie; De Bodt, Stefanie; Drebert, Zuzanna J.; Inzé, Dirk; Van de Peer, Yves

2013-01-01

Despite the availability of various data repositories for plant research, a wealth of information currently remains hidden within the biomolecular literature. Text mining provides the necessary means to retrieve these data through automated processing of texts. However, only recently has advanced text mining methodology been implemented with sufficient computational power to process texts at a large scale. In this study, we assess the potential of large-scale text mining for plant biology research in general and for network biology in particular using a state-of-the-art text mining system applied to all PubMed abstracts and PubMed Central full texts. We present extensive evaluation of the textual data for Arabidopsis thaliana, assessing the overall accuracy of this new resource for usage in plant network analyses. Furthermore, we combine text mining information with both protein–protein and regulatory interactions from experimental databases. Clusters of tightly connected genes are delineated from the resulting network, illustrating how such an integrative approach is essential to grasp the current knowledge available for Arabidopsis and to uncover gene information through guilt by association. All large-scale data sets, as well as the manually curated textual data, are made publicly available, hereby stimulating the application of text mining data in future plant biology studies. PMID:23532071

Atmospheric energy for subsurface life on Mars?

PubMed Central

Weiss, Benjamin P.; Yung, Yuk L.; Nealson, Kenneth H.

2000-01-01

The location and density of biologically useful energy sources on Mars will limit the biomass, spatial distribution, and organism size of any biota. Subsurface Martian organisms could be supplied with a large energy flux from the oxidation of photochemically produced atmospheric H2 and CO diffusing into the regolith. However, surface abundance measurements of these gases demonstrate that no more than a few percent of this available flux is actually being consumed, suggesting that biological activity driven by atmospheric H2 and CO is limited in the top few hundred meters of the subsurface. This is significant because the available but unused energy is extremely large: for organisms at 30-m depth, it is 2,000 times previous estimates of hydrothermal and chemical weathering energy and far exceeds the energy derivable from other atmospheric gases. This also implies that the apparent scarcity of life on Mars is not attributable to lack of energy. Instead, the availability of liquid water may be a more important factor limiting biological activity because the photochemical energy flux can only penetrate to 100- to 1,000-m depth, where most H2O is probably frozen. Because both atmospheric and Viking lander soil data provide little evidence for biological activity, the detection of short-lived trace gases will probably be a better indicator of any extant Martian life. PMID:10660689

Systems biology of cancer biomarker detection.

PubMed

Mitra, Sanga; Das, Smarajit; Chakrabarti, Jayprokas

2013-01-01

Cancer systems-biology is an ever-growing area of research due to explosion of data; how to mine these data and extract useful information is the problem. To have an insight on carcinogenesis one need to systematically mine several resources, such as databases, microarray and next-generation sequences. This review encompasses management and analysis of cancer data, databases construction and data deposition, whole transcriptome and genome comparison, analysing results from high throughput experiments to uncover cellular pathways and molecular interactions, and the design of effective algorithms to identify potential biomarkers. Recent technical advances such as ChIP-on-chip, ChIP-seq and RNA-seq can be applied to get epigenetic information transformed into a high-throughput endeavour to which systems biology and bioinformatics are making significant inroads. The data from ENCODE and GENCODE projects available through UCSC genome browser can be considered as benchmark for comparison and meta-analysis. A pipeline for integrating next generation sequencing data, microarray data, and putting them together with the existing database is discussed. The understanding of cancer genomics is changing the way we approach cancer diagnosis and treatment. To give a better understanding of utilizing available resources' we have chosen oral cancer to show how and what kind of analysis can be done. This review is a computational genomic primer that provides a bird's eye view of computational and bioinformatics' tools currently available to perform integrated genomic and system biology analyses of several carcinoma.

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

PubMed Central

Misirli, Goksel; Hallinan, Jennifer S.; Yu, Tommy; Lawson, James R.; Wimalaratne, Sarala M.; Cooling, Michael T.; Wipat, Anil

2011-01-01

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21296753

Data archiving and availability in an era of open science.

PubMed

Baker, Edward N

2017-01-01

The importance of preserving and making available the original experimental data underlying biological structural models is discussed, both for crystallography, where the raw data images pose particular challenges, and for other structure determination techniques.

BioCIDER: a Contextualisation InDEx for biological Resources discovery

PubMed Central

Horro, Carlos; Cook, Martin; Attwood, Teresa K.; Brazas, Michelle D.; Hancock, John M.; Palagi, Patricia; Corpas, Manuel; Jimenez, Rafael

2017-01-01

Abstract Summary The vast, uncoordinated proliferation of bioinformatics resources (databases, software tools, training materials etc.) makes it difficult for users to find them. To facilitate their discovery, various services are being developed to collect such resources into registries. We have developed BioCIDER, which, rather like online shopping ‘recommendations’, provides a contextualization index to help identify biological resources relevant to the content of the sites in which it is embedded. Availability and Implementation BioCIDER (www.biocider.org) is an open-source platform. Documentation is available online (https://goo.gl/Klc51G), and source code is freely available via GitHub (https://github.com/BioCIDER). The BioJS widget that enables websites to embed contextualization is available from the BioJS registry (http://biojs.io/). All code is released under an MIT licence. Contact carlos.horro@earlham.ac.uk or rafael.jimenez@elixir-europe.org or manuel@repositive.io PMID:28407033

Bipartite graphs in systems biology and medicine: a survey of methods and applications.

PubMed

Pavlopoulos, Georgios A; Kontou, Panagiota I; Pavlopoulou, Athanasia; Bouyioukos, Costas; Markou, Evripides; Bagos, Pantelis G

2018-04-01

The latest advances in high-throughput techniques during the past decade allowed the systems biology field to expand significantly. Today, the focus of biologists has shifted from the study of individual biological components to the study of complex biological systems and their dynamics at a larger scale. Through the discovery of novel bioentity relationships, researchers reveal new information about biological functions and processes. Graphs are widely used to represent bioentities such as proteins, genes, small molecules, ligands, and others such as nodes and their connections as edges within a network. In this review, special focus is given to the usability of bipartite graphs and their impact on the field of network biology and medicine. Furthermore, their topological properties and how these can be applied to certain biological case studies are discussed. Finally, available methodologies and software are presented, and useful insights on how bipartite graphs can shape the path toward the solution of challenging biological problems are provided.

Telomere Biology in Metazoa

PubMed Central

Gomes, Nuno M.V.; Shay, Jerry W.; Wright, Woodring E.

2010-01-01

In this review we present critical overview of some of the available literature on the fundamental biology of telomeres and telomerase in Metazoan. With the exception of Nematodes and Arthropods, the (TTAGGG)n sequence is conserved in most Metazoa. Available data shows that telomerase-based end maintenance is a very ancient mechanism in unicellular and multicellular organisms. In invertebrates, fish, amphibian, and reptiles persistent telomerase activity in somatic tissues might allow the maintenance of the extensive regenerative potentials of these species. Telomerase repression among birds and many mammals suggests that, as humans, they may use replicative aging as a tumor protection mechanism. PMID:20655915

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

PubMed Central

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J.; Ball, Catherine A.

2010-01-01

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows. Contact: rshankar@stanford.edu PMID:20733062

Web servicing the biological office.

PubMed

Szugat, Martin; Güttler, Daniel; Fundel, Katrin; Sohler, Florian; Zimmer, Ralf

2005-09-01

Biologists routinely use Microsoft Office applications for standard analysis tasks. Despite ubiquitous internet resources, information needed for everyday work is often not directly and seamlessly available. Here we describe a very simple and easily extendable mechanism using Web Services to enrich standard MS Office applications with internet resources. We demonstrate its capabilities by providing a Web-based thesaurus for biological objects, which maps names to database identifiers and vice versa via an appropriate synonym list. The client application ProTag makes these features available in MS Office applications using Smart Tags and Add-Ins. http://services.bio.ifi.lmu.de/prothesaurus/

Space Biology in the 21st century

NASA Technical Reports Server (NTRS)

Halstead, Thora W.; Krauss, Robert W.

1990-01-01

Space Biology is poised to make significant contributions to science in the next century. A carefully crafted, but largely ground-based, program in the United States has evolved major questions that require answers through experiments in space. Science, scientists, and the new long-term spacecrafts designed by NASA will be available for the first time to mount a serious Space Biology effort. The scientific challenge is of such importance that success will provide countless benefits to biologically dependent areas such as medicine, food, and commerce in the decades ahead. The international community is rapidly expanding its role in this field. The United States should generate the resources that will allow progress in Space Biology to match the recognized progress made in aeronautics and the other space sciences.

[Principles of management in biological infections].

PubMed

Płusa, Tadeusz

2012-11-01

The effectiveness of the management in respiratory infection is depending on the nature of the biological pathogen and the immune status of the patient. For this reason, providing assistance to victims the organ function support, similarly as defining the pathogen and targeted antibiotic therapy should be applied. Available diagnostic tests provide rapid ability to identify the pathogen and antibiotics are able to control infection. Lack of efficacy of treatment may indicate the diversity of the pathogen than previously known and raises suspicion of biological warfare pathogen.

Computational challenges in modeling gene regulatory events.

PubMed

Pataskar, Abhijeet; Tiwari, Vijay K

2016-10-19

Cellular transcriptional programs driven by genetic and epigenetic mechanisms could be better understood by integrating "omics" data and subsequently modeling the gene-regulatory events. Toward this end, computational biology should keep pace with evolving experimental procedures and data availability. This article gives an exemplified account of the current computational challenges in molecular biology.

Physiological Aging and Exercise.

ERIC Educational Resources Information Center

Osness, Wayne

This paper explores the nature of the aging process by providing an overview of the available evidence relating to the body systems that are most critical to biological function. Each system is treated separately to more clearly describe various aspects of the aging process and then integrated in a discussion of the theories of biological aging.…

Short-term C mineralization (aka the flush of CO2) as an indicator of soil biological health

USDA-ARS?s Scientific Manuscript database

Soil biological activity is a key component of soil health assessments, as it (a) indicates soil nutrient cycling capacity from various organic matter sources to inorganic availability, (b) relates to soil structural conditions, (c) informs about the potential to harbor biodiversity in soil, and (d)...

In vitro testing of biological control agents on A1 and A2 isolates of Phytophthora ramorum

Treesearch

Marianne Elliott; Simon Shamoun

2008-01-01

Biological control products were tested in vitro with six isolates of Phytophthora ramorum. These isolates were geographically diverse and were selected based on their pathogenicity to detached Rhododendron leaves. In addition to five commercially available biocontrol products, nine species of Trichoderma were tested. The in vitro...

Chapter 7. Management strategies for dwarf mistletoes: Biological, chemical, and genetic approaches

Treesearch

S. F. Shamoun; L. E. DeWald

2002-01-01

The opportunity and need for management of mistletoe populations with biological, chemical, and genetic approaches are greatest for application to the dwarf mistletoes. Although much information is available on these management strategies (see reviews by Hawksworth 1972, Knutson 1978), significant research and development are still required for these to become...

Which Beak Fits the Bill? An Activity Examining Adaptation, Natural Selection and Evolution

ERIC Educational Resources Information Center

Darling, Randi

2014-01-01

Evolution is a unifying concept within biology. In fact, Dobzhansky, a noted evolutionary biologist, argued, "Nothing in biology makes sense except in the light of evolution" (Dobzhansky, 1973). However, often students have misconceptions about evolution. There are a number of available activities where students use tools (representing…

Forest soil biology-timber harvesting relationships: a perspective

Treesearch

M. F. Jurgensen; M. J. Larsen; A. E. Harvey

1979-01-01

Timber harvesting has a pronounced effect on the soil microflora by wood removal and changing properties. This paper gives a perspective on soil biology-harvesting relationships with emphasis on the northern Rocky Mountain region. Of special significance to forest management operations are the effects of soil micro-organisms on: the availability of soil nutrients,...

Issues and Trends in Higher Education Biology Fieldwork

ERIC Educational Resources Information Center

Smith, Debbie

2004-01-01

This paper describes the outcomes of a two-day Higher Education focus group meeting at Blencathra Field Centre, Cumbria, in November 2003. A review of the current status of fieldwork in undergraduate courses was undertaken. The data available indicates that although the number of students enrolling in Biological Science courses has increased, in…

Faculty Research Productivity 1972-1988: Development and Application of Constant Units of Measure.

ERIC Educational Resources Information Center

Bieber, Jeffery P.; Blackburn, Robert T.

1993-01-01

This study investigated changes in publishing opportunities by college/university faculty between 1972 and 1988 in three disciplines: biology, philosophy, and English. Changes in amount of publishing space available and numbers of individuals competing for that space indicated inflation rates for all three fields (especially biology) requiring…

Biological invasion by Myrica faya alters ecosystem development in Hawaii

NASA Technical Reports Server (NTRS)

Vitousek, Peter M.; Walker, Lawrence R.; Whiteaker, Louis D.; Mueller-Dombois, Dieter; Matson, Pamela A.

1987-01-01

The exotic nitrogen-fixing tree Myrica faya invades young volcanic sites where the growth of native plants is limited by a lack of nitrogen. Myrica quadruples the amount of nitrogen entering certain sites and increases the overall biological availability of nitrogen, thereby altering the nature of ecosystem development after volcanic eruptions.

78 FR 19492 - Draft Guidance for Industry on Formal Meetings Between FDA and Biosimilar Biological Product...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-01

... DEPARTMENT OF HEALTH AND HUMAN SERVICES Food and Drug Administration [Docket No. FDA-2013-D-0286] Draft Guidance for Industry on Formal Meetings Between FDA and Biosimilar Biological Product Sponsors or... Drug Administration (FDA) is announcing the availability of a draft guidance for industry entitled...

Genetic characterization for intraspecific hybridization of an exotic parasitoid prior its introduction for classical biological control

USDA-ARS?s Scientific Manuscript database

The successful establishment of an exotic parasitoid in the context of classical biological control of insect pests depends upon its adaptability to the new environment. In theory, intraspecific hybridization may improve the success of the establishment as a result of an increase in the available ge...

Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels.

PubMed

Caspeta, Luis; Nielsen, Jens

2013-05-01

Recently genome sequence data have become available for Aspergillus and Pichia species of industrial interest. This has stimulated the use of systems biology approaches for large-scale analysis of the molecular and metabolic responses of Aspergillus and Pichia under defined conditions, which has resulted in much new biological information. Case-specific contextualization of this information has been performed using comparative and functional genomic tools. Genomics data are also the basis for constructing genome-scale metabolic models, and these models have helped in the contextualization of knowledge on the fundamental biology of Aspergillus and Pichia species. Furthermore, with the availability of these models, the engineering of Aspergillus and Pichia is moving from traditional approaches, such as random mutagenesis, to a systems metabolic engineering approach. Here we review the recent trends in systems biology of Aspergillus and Pichia species, highlighting the relevance of these developments for systems metabolic engineering of these organisms for the production of hydrolytic enzymes, biofuels and chemicals from biomass. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Radiofrequency ablation of liver tumors (I): biological background.

PubMed

Vanagas, Tomas; Gulbinas, Antanas; Pundzius, Juozas; Barauskas, Giedrius

2010-01-01

Majority of patients suffering from liver tumors are not candidates for surgery. Currently, minimal invasive techniques have become available for local destruction of hepatic tumors. Radiofrequency ablation is based on biological response to tissue hyperthermia. The aim of this article is to review available biological data on tissue destruction mechanisms. Experimental evidence shows that tissue injury following thermal ablation occurs in two distinct phases. The initial phase is direct injury, which is determined by energy applied, tumor biology, and tumor microenvironment. The temperature varies along the ablation zone and this is reflected by different morphological changes in affected tissues. The local hyperthermia alters metabolism, exacerbates tissue hypoxia, and increases thermosensitivity. The second phase - indirect injury - is observed after the cessation of heat stimulus. This phase represents a balance of several promoting and inhibiting mechanisms, such as induction of apoptosis, heat shock proteins, Kupffer cell activation, stimulation of the immune response, release of cytokines, and ischemia-reperfusion injury. A deeper understanding of the underlying mechanisms may possibly lead to refinements in radiofrequency ablation technology, resulting in advanced local tumor control and prolonged overall survival.

Recommendations for incorporating biologicals into management of moderate to severe plaque psoriasis: individualized patient approaches.

PubMed

Langley, Richard G; Ho, Vincent; Lynde, Charles; Papp, Kim A; Poulin, Yves; Shear, Neil; Toole, Jack; Zip, Catherine

2006-01-01

Psoriasis is a T-cell mediated skin disease that affects approximately 2% of the population worldwide. Despite the prevalence of the disease and long-standing efforts to develop strategies to treat it, there is a need for safe and effective therapies to treat psoriasis, particularly the more severe forms. Biological agents such as alefacept, efalizumab, etanercept, and infliximab have been recognized as a class of treatment distinct from other forms of therapy in the treatment algorithm of psoriasis. Recent national and international consensus meetings have developed statements that position biological agents as an important addition to the treatment armamentarium for moderate to severe psoriasis, along with phototherapy and traditional systemic agents. There has been consensus that treatment should be individualized to each patient's needs and circumstances. Biological agents offer the hope of safe, effective, long-term management of moderate to severe psoriasis. As new agents receive approval from Health Canada, the available range of therapeutic options for treating this chronic disease will broaden. A Canadian Psoriasis Expert Panel recently convened in February 2005 to analyze, based on a series of clinical case scenarios, the indications, contraindications, and considerations for and against each of the four biological agents, derived from product labelling, where available, and from the efficacy and safety data from phase 3 and earlier clinical trials, as well as post-marketing reports. The Panel has formulated a set of recommendations for incorporating these biological agents into the current treatment paradigm of moderate to severe plaque psoriasis and has identified the preferred biological agents for each patient based on individual needs and circumstances.

The use and QA of biologically related models for treatment planning: short report of the TG-166 of the therapy physics committee of the AAPM.

PubMed

Allen Li, X; Alber, Markus; Deasy, Joseph O; Jackson, Andrew; Ken Jee, Kyung-Wook; Marks, Lawrence B; Martel, Mary K; Mayo, Charles; Moiseenko, Vitali; Nahum, Alan E; Niemierko, Andrzej; Semenenko, Vladimir A; Yorke, Ellen D

2012-03-01

Treatment planning tools that use biologically related models for plan optimization and/or evaluation are being introduced for clinical use. A variety of dose-response models and quantities along with a series of organ-specific model parameters are included in these tools. However, due to various limitations, such as the limitations of models and available model parameters, the incomplete understanding of dose responses, and the inadequate clinical data, the use of biologically based treatment planning system (BBTPS) represents a paradigm shift and can be potentially dangerous. There will be a steep learning curve for most planners. The purpose of this task group is to address some of these relevant issues before the use of BBTPS becomes widely spread. In this report, the authors (1) discuss strategies, limitations, conditions, and cautions for using biologically based models and parameters in clinical treatment planning; (2) demonstrate the practical use of the three most commonly used commercially available BBTPS and potential dosimetric differences between biologically model based and dose-volume based treatment plan optimization and evaluation; (3) identify the desirable features and future directions in developing BBTPS; and (4) provide general guidelines and methodology for the acceptance testing, commissioning, and routine quality assurance (QA) of BBTPS.

Field Markup Language: biological field representation in XML.

PubMed

Chang, David; Lovell, Nigel H; Dokos, Socrates

2007-01-01

With an ever increasing number of biological models available on the internet, a standardized modeling framework is required to allow information to be accessed or visualized. Based on the Physiome Modeling Framework, the Field Markup Language (FML) is being developed to describe and exchange field information for biological models. In this paper, we describe the basic features of FML, its supporting application framework and its ability to incorporate CellML models to construct tissue-scale biological models. As a typical application example, we present a spatially-heterogeneous cardiac pacemaker model which utilizes both FML and CellML to describe and solve the underlying equations of electrical activation and propagation.

An interdepartmental Ph.D. program in computational biology and bioinformatics: the Yale perspective.

PubMed

Gerstein, Mark; Greenbaum, Dov; Cheung, Kei; Miller, Perry L

2007-02-01

Computational biology and bioinformatics (CBB), the terms often used interchangeably, represent a rapidly evolving biological discipline. With the clear potential for discovery and innovation, and the need to deal with the deluge of biological data, many academic institutions are committing significant resources to develop CBB research and training programs. Yale formally established an interdepartmental Ph.D. program in CBB in May 2003. This paper describes Yale's program, discussing the scope of the field, the program's goals and curriculum, as well as a number of issues that arose in implementing the program. (Further updated information is available from the program's website, www.cbb.yale.edu.)

Detecting subnetwork-level dynamic correlations.

PubMed

Yan, Yan; Qiu, Shangzhao; Jin, Zhuxuan; Gong, Sihong; Bai, Yun; Lu, Jianwei; Yu, Tianwei

2017-01-15

The biological regulatory system is highly dynamic. The correlations between many functionally related genes change over different biological conditions. Finding dynamic relations on the existing biological network may reveal important regulatory mechanisms. Currently no method is available to detect subnetwork-level dynamic correlations systematically on the genome-scale network. Two major issues hampered the development. The first is gene expression profiling data usually do not contain time course measurements to facilitate the analysis of dynamic relations, which can be partially addressed by using certain genes as indicators of biological conditions. Secondly, it is unclear how to effectively delineate subnetworks, and define dynamic relations between them. Here we propose a new method named LANDD (Liquid Association for Network Dynamics Detection) to find subnetworks that show substantial dynamic correlations, as defined by subnetwork A is concentrated with Liquid Association scouting genes for subnetwork B. The method produces easily interpretable results because of its focus on subnetworks that tend to comprise functionally related genes. Also, the collective behaviour of genes in a subnetwork is a much more reliable indicator of underlying biological conditions compared to using single genes as indicators. We conducted extensive simulations to validate the method's ability to detect subnetwork-level dynamic correlations. Using a real gene expression dataset and the human protein-protein interaction network, we demonstrate the method links subnetworks of distinct biological processes, with both confirmed relations and plausible new functional implications. We also found signal transduction pathways tend to show extensive dynamic relations with other functional groups. The R package is available at https://cran.r-project.org/web/packages/LANDD CONTACTS: yunba@pcom.edu, jwlu33@hotmail.com or tianwei.yu@emory.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine).

PubMed

Wong, Darren C J; Sweetman, Crystal; Drew, Damian P; Ford, Christopher M

2013-12-16

Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis) whereby the recovered sub-networks reconfirm established plant gene functions and also identify novel associations. Together, we present valuable insights into grapevine transcriptional regulation by developing network models applicable to researchers in their prioritisation of gene candidates, for on-going study of biological processes related to grapevine development, metabolism and stress responses.

Managing biological diversity

USGS Publications Warehouse

Samson, Fred B.; Knopf, Fritz L.

1993-01-01

Biological diversity is the variety of life and accompanying ecological processes (Off. Technol. Assess. 1987, Wilcove and Samson 1987, Keystone 1991). Conservation of biological diversity is a major environmental issue (Wilson 1988, Counc. Environ. Quality 1991). The health and future of the earth's ecological systems (Lubchenco et al. 1991), global climate change (Botkin 1990), and an ever-increasing rate in loss of species, communities, and ecological systems (Myers 1990) are among issues drawing biological diversity to the mainstream of conservation worldwide (Int. Union Conserv. Nat. and Nat. Resour. [IUCN] et al. 1991). The legal mandate for conserving biological diversity is now in place (Carlson 1988, Doremus 1991). More than 19 federal laws govern the use of biological resources in the United States (Rein 1991). The proposed National Biological Diversity Conservation and Environmental Research Act (H.R. 585 and S.58) notes the need for a national biological diversity policy, would create a national center for biological diversity research, and recommends a federal interagency strategy for ecosystem conservation. There are, however, hard choices ahead for the conservation of biological diversity, and biologists are grappling with how to set priorities in research and management (Roberts 1988). We sense disillusion among field biologists and managers relative to how to operationally approach the seemingly overwhelming charge of conserving biological diversity. Biologists also need to respond to critics like Hunt (1991) who suggest a tree farm has more biological diversity than an equal area of old-growth forest. At present, science has played only a minor role in the conservation of biological diversity (Weston 1992) with no unified approach available to evaluate strategies and programs that address the quality and quantity of biological diversity (Murphy 1990, Erwin 1992). Although actions to conserve biological diversity need to be clearly defined by viewing issues across biological, spatial, and temporal scales (Knopf and Smith 1992), natural resource managers find much conflicting information in the literature on strategies and programs for the conservation of biological diversity (Ehrlich 1992). Moreover, recommendations provided in much of the published information available for planning or decisions not only can be debated but may prove counterproductive if implemented. Current operational efforts beg for clearer focus on fundamental concepts central to daily decisions that impact native biological diversity. Recognizing that many biologists would provide different council and at the risk of oversimplification, we offer the following 4 topical issues as fundamental guidance to wise conservation action. These recommendations are based on our collective experiences working within conservation agencies since our original, collaborative essay (Samson and Knopf 1982). They are offered as initial, rather than authoritative, steps to better align research and management decisions with what we perceive as the critical issues in conserving biological diversity at the landscape and ecosystem levels of resolution.

Set membership experimental design for biological systems.

PubMed

Marvel, Skylar W; Williams, Cranos M

2012-03-21

Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. The practicability of our approach is illustrated with a case study. This study shows that our approach is able to 1) identify candidate measurement time points that maximize information corresponding to biologically relevant metrics and 2) determine the number at which additional measurements begin to provide insignificant information. This framework can be used to balance the availability of resources with the addition of one or more measurement time points to improve the predictability of resulting models.

Set membership experimental design for biological systems

PubMed Central

2012-01-01

Background Experimental design approaches for biological systems are needed to help conserve the limited resources that are allocated for performing experiments. The assumptions used when assigning probability density functions to characterize uncertainty in biological systems are unwarranted when only a small number of measurements can be obtained. In these situations, the uncertainty in biological systems is more appropriately characterized in a bounded-error context. Additionally, effort must be made to improve the connection between modelers and experimentalists by relating design metrics to biologically relevant information. Bounded-error experimental design approaches that can assess the impact of additional measurements on model uncertainty are needed to identify the most appropriate balance between the collection of data and the availability of resources. Results In this work we develop a bounded-error experimental design framework for nonlinear continuous-time systems when few data measurements are available. This approach leverages many of the recent advances in bounded-error parameter and state estimation methods that use interval analysis to generate parameter sets and state bounds consistent with uncertain data measurements. We devise a novel approach using set-based uncertainty propagation to estimate measurement ranges at candidate time points. We then use these estimated measurements at the candidate time points to evaluate which candidate measurements furthest reduce model uncertainty. A method for quickly combining multiple candidate time points is presented and allows for determining the effect of adding multiple measurements. Biologically relevant metrics are developed and used to predict when new data measurements should be acquired, which system components should be measured and how many additional measurements should be obtained. Conclusions The practicability of our approach is illustrated with a case study. This study shows that our approach is able to 1) identify candidate measurement time points that maximize information corresponding to biologically relevant metrics and 2) determine the number at which additional measurements begin to provide insignificant information. This framework can be used to balance the availability of resources with the addition of one or more measurement time points to improve the predictability of resulting models. PMID:22436240

Analysis of undergraduate cell biology contents in Brazilian public universities.

PubMed

Mermelstein, Claudia; Costa, Manoel Luis

2017-04-01

The enormous amount of information available in cell biology has created a challenge in selecting the core concepts we should be teaching our undergraduates. One way to define a set of essential core ideas in cell biology is to analyze what a specific cell biology community is teaching their students. Our main objective was to analyze the cell biology content currently being taught in Brazilian universities. We collected the syllabi of cell biology courses from public universities in Brazil and analyzed the frequency of cell biology topics in each course. We also compared the Brazilian data with the contents of a major cell biology textbook. Our analysis showed that while some cell biology topics such as plasma membrane and cytoskeleton was present in ∼100% of the Brazilian curricula analyzed others such as cell signaling and cell differentiation were present in only ∼35%. The average cell biology content taught in the Brazilian universities is quite different from what is presented in the textbook. We discuss several possible explanations for these observations. We also suggest a list with essential cell biology topics for any biological or biomedical undergraduate course. The comparative discussion of cell biology topics presented here could be valuable in other educational contexts. © 2017 The Authors. Cell Biology International Published by John Wiley & Sons Ltd on behalf of International Federation of Cell Biology.

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2010-01-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

A powerful toolkit for synthetic biology: Over 3.8 billion years of evolution.

PubMed

Rothschild, Lynn J

2010-04-01

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested.

Reproductive biology of the pampas deer (Ozotoceros bezoarticus): a review

PubMed Central

Ungerfeld, Rodolfo; González-Pensado, Solana; Bielli, Alejandro; Villagrán, Matías; Olazabal, Daniel; Pérez, William

2008-01-01

The pampas deer (Ozotoceros bezoarticus) is a South American grazing deer which is in extreme danger of extinction. Very little is known about the biology of the pampas deer. Moreover, most information has not been published in peer-reviewed scientific journals, and is only available in local publications, theses, etc. Therefore, our aim was to update and summarize the available information regarding the reproductive biology of the pampas deer. Moreover, in most sections, we have also included new, unpublished information. Detailed descriptions are provided of the anatomy of both the female and the male reproductive tract, puberty onset, the oestrous cycle and gestational length. Birthing and the early postpartum period are described, as are maternal behaviour and early fawn development, seasonal distribution of births, seasonal changes in male reproduction and antler cycle, reproductive behaviour, semen collection, and cryopreservation. Finally, an overview is given and future directions of research are proposed. PMID:18534014

diffuStats: an R package to compute diffusion-based scores on biological networks.

PubMed

Picart-Armada, Sergio; Thompson, Wesley K; Buil, Alfonso; Perera-Lluna, Alexandre

2018-02-01

Label propagation and diffusion over biological networks are a common mathematical formalism in computational biology for giving context to molecular entities and prioritizing novel candidates in the area of study. There are several choices in conceiving the diffusion process-involving the graph kernel, the score definitions and the presence of a posterior statistical normalization-which have an impact on the results. This manuscript describes diffuStats, an R package that provides a collection of graph kernels and diffusion scores, as well as a parallel permutation analysis for the normalized scores, that eases the computation of the scores and their benchmarking for an optimal choice. The R package diffuStats is publicly available in Bioconductor, https://bioconductor.org, under the GPL-3 license. sergi.picart@upc.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Genetics on the Fly: A Primer on the Drosophila Model System

PubMed Central

Hales, Karen G.; Korey, Christopher A.; Larracuente, Amanda M.; Roberts, David M.

2015-01-01

Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly’s tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism’s natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones. PMID:26564900

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

A postdoctoral position is available in Dr. Efsun Arda’s Developmental Genomics Group within the Laboratory of Receptor Biology and Gene Expression Branch at the National Cancer Institute (NCI), National Institutes of Health (NIH). Our research is focused on understanding the regulatory networks that govern pancreas cell identity and function in the context of diabetes and cancer. The lab is highly interdisciplinary and uses state-of-the-art technologies to address outstanding questions in human pancreas biology. The appointment is renewed annually upon performance evaluation for a maximum of five years. The candidate will be fully funded by a competitive intramural Center for Cancer Research (CCR) fellowship. Other fellowship opportunities outside NIH are also available and applications will be supported. CCR provides a highly collaborative, enabling environment for research fellows with more than 40 core facilities ranging from bioinformatics and computing, chemistry and structural biology, flow cytometry, genomics, imaging and microscopy, pharmacology, proteomics and single cell analysis.

Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics.

PubMed

Womack, Ryan P

2015-01-01

This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined. The study finds that data sharing practices are still relatively rare in these disciplines' top journals, but that the disciplines have markedly different practices. Biology top journals share original data at the highest rate, and physics top journals share at the lowest rate. Overall, the study finds that within the top journals, only 13% of articles with original data published in 2014 make the data available to others.

Research Data in Core Journals in Biology, Chemistry, Mathematics, and Physics

PubMed Central

Womack, Ryan P.

2015-01-01

This study takes a stratified random sample of articles published in 2014 from the top 10 journals in the disciplines of biology, chemistry, mathematics, and physics, as ranked by impact factor. Sampled articles were examined for their reporting of original data or reuse of prior data, and were coded for whether the data was publicly shared or otherwise made available to readers. Other characteristics such as the sharing of software code used for analysis and use of data citation and DOIs for data were examined. The study finds that data sharing practices are still relatively rare in these disciplines’ top journals, but that the disciplines have markedly different practices. Biology top journals share original data at the highest rate, and physics top journals share at the lowest rate. Overall, the study finds that within the top journals, only 13% of articles with original data published in 2014 make the data available to others. PMID:26636676

Kinetic Modeling using BioPAX ontology

PubMed Central

Ruebenacker, Oliver; Moraru, Ion. I.; Schaff, James C.; Blinov, Michael L.

2010-01-01

Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways Exchange (BioPAX) format. However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation. The current standard for kinetic modeling is the System Biology Markup Language (SBML), but only a small number of models are available in SBML format in public repositories. Additionally, reusing and merging SBML models presents a significant challenge, because often each element has a value only in the context of the given model, and information encoding biological meaning is absent. We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell), including improved conversion to SBML (for use with other simulation tools that support this format). PMID:20862270

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Wolin laboratory has recently moved to the National Cancer Institute as part of a new initiative in RNA Biology. A fully funded postdoctoral position is available in the areas of noncoding RNA function, RNA surveillance pathways, and the mechanisms by which defects in RNA decay pathways contribute to diseases such as cancer and autoimmunity. We use mammalian cells and bacteria as complementary systems, and projects in both systems are available. Our group is part of the newly formed RNA Biology Laboratory in the Center for Cancer Research. We are part of the Center of Cancer Research’s RNA Initiative, which includes more than 50 laboratories evenly split between the Frederick and Bethesda campuses of the National Cancer Institute. The environment is highly collaborative and collegial, with the ability to interact with a wide range of scientists. The position is ideal for motivated candidates who are seeking additional training in RNA biology.

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

Tripal: a construction toolkit for online genome databases.

PubMed

Ficklin, Stephen P; Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net.

Tripal: a construction toolkit for online genome databases

PubMed Central

Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E.; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E.; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net PMID:21959868

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text.

PubMed

Baroukh, Caroline; Jenkins, Sherry L; Dannenfelser, Ruth; Ma'ayan, Avi

2011-10-13

Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications.

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text

PubMed Central

2011-01-01

Background Word-clouds recently emerged on the web as a solution for quickly summarizing text by maximizing the display of most relevant terms about a specific topic in the minimum amount of space. As biologists are faced with the daunting amount of new research data commonly presented in textual formats, word-clouds can be used to summarize and represent biological and/or biomedical content for various applications. Results Genes2WordCloud is a web application that enables users to quickly identify biological themes from gene lists and research relevant text by constructing and displaying word-clouds. It provides users with several different options and ideas for the sources that can be used to generate a word-cloud. Different options for rendering and coloring the word-clouds give users the flexibility to quickly generate customized word-clouds of their choice. Methods Genes2WordCloud is a word-cloud generator and a word-cloud viewer that is based on WordCram implemented using Java, Processing, AJAX, mySQL, and PHP. Text is fetched from several sources and then processed to extract the most relevant terms with their computed weights based on word frequencies. Genes2WordCloud is freely available for use online; it is open source software and is available for installation on any web-site along with supporting documentation at http://www.maayanlab.net/G2W. Conclusions Genes2WordCloud provides a useful way to summarize and visualize large amounts of textual biological data or to find biological themes from several different sources. The open source availability of the software enables users to implement customized word-clouds on their own web-sites and desktop applications. PMID:21995939

Improving clustering with metabolic pathway data.

PubMed

Milone, Diego H; Stegmayer, Georgina; López, Mariana; Kamenetzky, Laura; Carrari, Fernando

2014-04-10

It is a common practice in bioinformatics to validate each group returned by a clustering algorithm through manual analysis, according to a-priori biological knowledge. This procedure helps finding functionally related patterns to propose hypotheses for their behavior and the biological processes involved. Therefore, this knowledge is used only as a second step, after data are just clustered according to their expression patterns. Thus, it could be very useful to be able to improve the clustering of biological data by incorporating prior knowledge into the cluster formation itself, in order to enhance the biological value of the clusters. A novel training algorithm for clustering is presented, which evaluates the biological internal connections of the data points while the clusters are being formed. Within this training algorithm, the calculation of distances among data points and neurons centroids includes a new term based on information from well-known metabolic pathways. The standard self-organizing map (SOM) training versus the biologically-inspired SOM (bSOM) training were tested with two real data sets of transcripts and metabolites from Solanum lycopersicum and Arabidopsis thaliana species. Classical data mining validation measures were used to evaluate the clustering solutions obtained by both algorithms. Moreover, a new measure that takes into account the biological connectivity of the clusters was applied. The results of bSOM show important improvements in the convergence and performance for the proposed clustering method in comparison to standard SOM training, in particular, from the application point of view. Analyses of the clusters obtained with bSOM indicate that including biological information during training can certainly increase the biological value of the clusters found with the proposed method. It is worth to highlight that this fact has effectively improved the results, which can simplify their further analysis.The algorithm is available as a web-demo at http://fich.unl.edu.ar/sinc/web-demo/bsom-lite/. The source code and the data sets supporting the results of this article are available at http://sourceforge.net/projects/sourcesinc/files/bsom.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

PubMed Central

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

Treatment preferences of originator versus biosimilar drugs in Crohn's disease; discrete choice experiment among gastroenterologists.

PubMed

Baji, Petra; Gulácsi, László; Lovász, Barbara D; Golovics, Petra A; Brodszky, Valentin; Péntek, Márta; Rencz, Fanni; Lakatos, Péter L

2016-01-01

To explore preferences of gastroenterologists for biosimilar drugs in Crohn's disease. Discrete choice experiment was carried out involving 51 Hungarian gastroenterologists in May 2014. The following attributes were used to describe hypothetical choice sets: 1) type of the treatment (biosimilar/originator), 2) severity of disease, 3) availability of continuous medicine supply, 4) frequency of the efficacy check-ups. Multinomial logit model was used to differentiate between three attitude types: 1) always opting for the originator, 2) willing to consider biosimilar for biological-naïve patients only, 3) willing to consider biosimilar treatment for both types of patients. Conditional logit model was used to estimate the probabilities of choosing a given profile. Men, senior consultants, working in inflammatory bowel disease center and treating more patients were more likely willing to consider biosimilar for biological-naïve patients only. Treatment type (originator/biosimilar) was the most important determinant of choice for patients already treated with biologicals, and the availability of continuous medicine supply in case of biological-naïve patients. The probabilities of choosing the biosimilar with all the benefits offered over the originator under current reimbursement conditions are 89% versus 11% for new patients, and 44% versus 56% for patients already treated with biological. For gastroenterologist, the continuous medical supply would be one of the major benefits of biosimilars. However, benefits offered in the scenarios do not compensate for the change from the originator to the biosimilar treatment of patients already treated with biologicals.

t4 report1

PubMed Central

Zhu, Hao; Bouhifd, Mounir; Kleinstreuer, Nicole; Kroese, E. Dinant; Liu, Zhichao; Luechtefeld, Thomas; Pamies, David; Shen, Jie; Strauss, Volker; Wu, Shengde; Hartung, Thomas

2016-01-01

Summary Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA’s ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment. PMID:26863516

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

PubMed

Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

2016-06-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

Options for Online Undergraduate Courses in Biology at American Colleges and Universities

PubMed Central

Varty, Alison K.

2016-01-01

I aimed to document the online undergraduate course supply in biology to evaluate how well biology educators are serving the diverse and growing population of online students. I documented online biology course offerings in the 2015–2016 academic year at 96 American colleges and universities. I quantified differences in variety, extent, and availability of courses offered by different kinds of academic institutions and characterized 149 online biology courses offered. Although there was no relationship between an institution’s enrollment size and any measure of its online biology offerings, I found significantly more online biology course options at 2-year public compared with 4-year public and 4-year private schools. Courses offered for nonmajors, including students pursuing healthcare-related degrees, were three times as common as those intended for biology majors, who were more likely to be offered hybrid courses with face-to-face laboratories. These data indicate some deficiencies in online biology course options; options for students majoring in biology are limited at all types of institutions examined with a minority of 4-year institutions having any online options in biology. Significant investment of institutional resources in faculty training and technological support are necessary to develop online biology courses that will benefit a larger student population. PMID:27856546

Computational challenges in modeling gene regulatory events

PubMed Central

Pataskar, Abhijeet; Tiwari, Vijay K.

2016-01-01

ABSTRACT Cellular transcriptional programs driven by genetic and epigenetic mechanisms could be better understood by integrating “omics” data and subsequently modeling the gene-regulatory events. Toward this end, computational biology should keep pace with evolving experimental procedures and data availability. This article gives an exemplified account of the current computational challenges in molecular biology. PMID:27390891

A Modular Approach to Teaching Mathematical Modeling in Biotechnology in the Undergraduate Curriculum

ERIC Educational Resources Information Center

Larripa, Kamila R.; Mazzag, Borbala

2016-01-01

Our paper describes a solution we found to a still existing need to develop mathematical modeling courses for undergraduate biology majors. Some challenges of such courses are: (i) relatively limited exposure of biology students to higher-level mathematical and computational concepts; (ii) availability of texts that can give a flavor of how…

Bioengineering/Biophysicist Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

A post-doctoral fellow position is available in the Tissue Morphodynamics Unit headed by Dr. Kandice Tanner at the National Cancer Institute. The Tanner lab combines biophysical and cell biological approaches to understand the interplay between tissue architecture and metastasis. We use a combination of imaging modalities, cell biology and animal models. It is expected that as

RADIOISOTOPE TECHNIQUES FOR INSTRUCTION IN THE BIOLOGICAL SCIENCES, A LIST OF ANNOTATED REFERENCES.

ERIC Educational Resources Information Center

HURLBURT, EVELYN M.

REFERENCES TO BIOLOGICAL EXPERIMENTS THAT EMPHASIZE THE USE OF RADIOISOTOPES AS TRACERS ARE INCLUDED IN THIS ANNOTATED BIBLIOGRAPHY. MATERIALS INCLUDED ARE CONSIDERED TO BE READILY AVAILABLE AND WERE PUBLISHED AFTER 1960. SECTION I IS COMPOSED OF SELECTED SOURCES. ENTRIES INCLUDE (1) COMPLETE CITATIONS, (2) A BRIEF ANNOTATION, AND (3) LISTS OF…

History of fire in eastern oak forests and implications for restoration

Treesearch

Justin L. Hart; Megan L. Buchanan

2012-01-01

Our understanding of long-term fire history in the eastern United States is derived from the interpretation of a variety of archives. While cultural records are available for some sites, biological archives are most frequently used to reconstruct long-term historical fire regimes. The three most commonly used biological archives in eastern oak forests include: the...

Bioengineering/Biophysicist Post-doctoral Fellow | Center for Cancer Research

Cancer.gov

A post-doctoral fellow position is available in the Tissue Morphodynamics Unit headed by Dr. Kandice Tanner at the National Cancer Institute. The Tanner lab combines biophysical and cell biological approaches to understand the interplay between tissue architecture and metastasis. We use a combination of imaging modalities, cell biology and animal models. It is expected that as

Cyberbiosecurity: From Naive Trust to Risk Awareness.

PubMed

Peccoud, Jean; Gallegos, Jenna E; Murch, Randall; Buchholz, Wallace G; Raman, Sanjay

2018-01-01

The cyber-physical nature of biotechnology raises unprecedented security concerns. Computers can be compromised by encoding malware in DNA sequences, and biological threats can be synthesized using publicly available data. Trust within the biotechnology community creates vulnerabilities at the interface between cyberspace and biology. Awareness is a prerequisite to managing these risks. Copyright © 2017 Elsevier Ltd. All rights reserved.

TENTATIVE RECOMMENDATIONS FOR THE UNDERGRADUATE MATHEMATICS PROGRAM OF STUDENTS IN THE BIOLOGICAL MANAGEMENT AND SOCIAL SCIENCES.

ERIC Educational Resources Information Center

DUREN, WILLIAM L.

THIS REPORT DESCRIBES A PROGRAM FOR THE UNDERGRADUATE MATHEMATICAL PREPARATION OF STUDENTS IN THE BIOLOGICAL, MANAGEMENT, AND SOCIAL SCIENCES (BMSS). THE COMMITTEE RECOMMENDS A SEQUENCE OF COURSES WHICH IS DESIGNED TO PROVIDE VARIED TRAINING IN MATHEMATICS IN THE LIMITED TIME BMSS STUDENTS HAVE AVAILABLE. OF SPECIAL IMPORTANCE ARE ELEMENTARY…

Causal Assessment of Biological Impairment in the Bogue Homo River, Mississippi Using the U.S. EPA’s Stressor Identification Methodology (Final)

EPA Science Inventory

EPA announced the availability of the final report, Causal Assessment of Biological Impairment in the Bogue Homo River, Mississippi Using the U.S. EPA’s Stressor Identification Methodology. This assessment is taken from more than 700 court ordered assessments of the cau...

Computing Platforms for Big Biological Data Analytics: Perspectives and Challenges.

PubMed

Yin, Zekun; Lan, Haidong; Tan, Guangming; Lu, Mian; Vasilakos, Athanasios V; Liu, Weiguo

2017-01-01

The last decade has witnessed an explosion in the amount of available biological sequence data, due to the rapid progress of high-throughput sequencing projects. However, the biological data amount is becoming so great that traditional data analysis platforms and methods can no longer meet the need to rapidly perform data analysis tasks in life sciences. As a result, both biologists and computer scientists are facing the challenge of gaining a profound insight into the deepest biological functions from big biological data. This in turn requires massive computational resources. Therefore, high performance computing (HPC) platforms are highly needed as well as efficient and scalable algorithms that can take advantage of these platforms. In this paper, we survey the state-of-the-art HPC platforms for big biological data analytics. We first list the characteristics of big biological data and popular computing platforms. Then we provide a taxonomy of different biological data analysis applications and a survey of the way they have been mapped onto various computing platforms. After that, we present a case study to compare the efficiency of different computing platforms for handling the classical biological sequence alignment problem. At last we discuss the open issues in big biological data analytics.

Modeling Co-evolution of Speech and Biology.

PubMed

de Boer, Bart

2016-04-01

Two computer simulations are investigated that model interaction of cultural evolution of language and biological evolution of adaptations to language. Both are agent-based models in which a population of agents imitates each other using realistic vowels. The agents evolve under selective pressure for good imitation. In one model, the evolution of the vocal tract is modeled; in the other, a cognitive mechanism for perceiving speech accurately is modeled. In both cases, biological adaptations to using and learning speech evolve, even though the system of speech sounds itself changes at a more rapid time scale than biological evolution. However, the fact that the available acoustic space is used maximally (a self-organized result of cultural evolution) is constant, and therefore biological evolution does have a stable target. This work shows that when cultural and biological traits are continuous, their co-evolution may lead to cognitive adaptations that are strong enough to detect empirically. Copyright © 2016 Cognitive Science Society, Inc.

Biological Control Strategies for Mosquito Vectors of Arboviruses.

PubMed

Huang, Yan-Jang S; Higgs, Stephen; Vanlandingham, Dana L

2017-02-10

Historically, biological control utilizes predatory species and pathogenic microorganisms to reduce the population of mosquitoes as disease vectors. This is particularly important for the control of mosquito-borne arboviruses, which normally do not have specific antiviral therapies available. Although development of resistance is likely, the advantages of biological control are that the resources used are typically biodegradable and ecologically friendly. Over the past decade, the advancement of molecular biology has enabled optimization by the manipulation of genetic materials associated with biological control agents. Two significant advancements are the discovery of cytoplasmic incompatibility induced by Wolbachia bacteria, which has enhanced replacement programs, and the introduction of dominant lethal genes into local mosquito populations through the release of genetically modified mosquitoes. As various arboviruses continue to be significant public health threats, biological control strategies have evolved to be more diverse and become critical tools to reduce the disease burden of arboviruses.

BioInt: an integrative biological object-oriented application framework and interpreter.

PubMed

Desai, Sanket; Burra, Prasad

2015-01-01

BioInt, a biological programming application framework and interpreter, is an attempt to equip the researchers with seamless integration, efficient extraction and effortless analysis of the data from various biological databases and algorithms. Based on the type of biological data, algorithms and related functionalities, a biology-specific framework was developed which has nine modules. The modules are a compilation of numerous reusable BioADTs. This software ecosystem containing more than 450 biological objects underneath the interpreter makes it flexible, integrative and comprehensive. Similar to Python, BioInt eliminates the compilation and linking steps cutting the time significantly. The researcher can write the scripts using available BioADTs (following C++ syntax) and execute them interactively or use as a command line application. It has features that enable automation, extension of the framework with new/external BioADTs/libraries and deployment of complex work flows.

Bridging Physics and Biology Using Resistance and Axons

NASA Astrophysics Data System (ADS)

Dyer, Joshua M.

2014-11-01

When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics.1 A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology. Despite this impression held by students, there have been calls for better physics education for future physicians and life scientists.2,3 Research is being performed to improve physics classes and labs by linking topics in biology and physics.4,5 Described here is a laboratory experiment covering the topics of resistance of materials and circuits/Kirchhoff's laws in a biology context with their direct application to neurons, axons, and electrical impulse transmission within animals. This experiment will also demonstrate the mechanism believed to cause multiple sclerosis. The apparatus was designed with low-cost and readily available materials in mind.

Biological Control Strategies for Mosquito Vectors of Arboviruses

PubMed Central

Huang, Yan-Jang S.; Higgs, Stephen; Vanlandingham, Dana L.

2017-01-01

Historically, biological control utilizes predatory species and pathogenic microorganisms to reduce the population of mosquitoes as disease vectors. This is particularly important for the control of mosquito-borne arboviruses, which normally do not have specific antiviral therapies available. Although development of resistance is likely, the advantages of biological control are that the resources used are typically biodegradable and ecologically friendly. Over the past decade, the advancement of molecular biology has enabled optimization by the manipulation of genetic materials associated with biological control agents. Two significant advancements are the discovery of cytoplasmic incompatibility induced by Wolbachia bacteria, which has enhanced replacement programs, and the introduction of dominant lethal genes into local mosquito populations through the release of genetically modified mosquitoes. As various arboviruses continue to be significant public health threats, biological control strategies have evolved to be more diverse and become critical tools to reduce the disease burden of arboviruses. PMID:28208639

Proteomics Improves the New Understanding of Honeybee Biology.

PubMed

Hora, Zewdu Ararso; Altaye, Solomon Zewdu; Wubie, Abebe Jemberie; Li, Jianke

2018-04-11

The honeybee is one of the most valuable insect pollinators, playing a key role in pollinating wild vegetation and agricultural crops, with significant contribution to the world's food production. Although honeybees have long been studied as model for social evolution, honeybee biology at the molecular level remained poorly understood until the year 2006. With the availability of the honeybee genome sequence and technological advancements in protein separation, mass spectrometry, and bioinformatics, aspects of honeybee biology such as developmental biology, physiology, behavior, neurobiology, and immunology have been explored to new depths at molecular and biochemical levels. This Review comprehensively summarizes the recent progress in honeybee biology using proteomics to study developmental physiology, task transition, and physiological changes in some of the organs, tissues, and cells based on achievements from the authors' laboratory in this field. The research advances of honeybee proteomics provide new insights for understanding of honeybee biology and future research directions.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2014-02-06

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

The pharmacology and toxicology of three new biologic agents used in pulmonary medicine.

PubMed

Albertson, T E; Walby, W F; Allen, R P; Tharratt, R S

1995-01-01

Biological agents have played an important role in the evolution of modern medical therapeutics. Recent advances in biologicals have in part been stimulated by the biotechnology revolution seen over the last several years. Toxicologists need to be aware of the proposed mechanisms and approved and experimental uses of these new biologic agents. Further, controversies about their use, efficacy, cost issues and potential toxicities should be known. Often these drugs are designed for small patient populations thus limiting the availability of human toxicological data bases. This paper reviews the pharmacology and toxicology of three new biologics (recombinant human DNase I, alpha 1-protease inhibitor, and nitric oxide). These agents appear to have important roles in treating specific diseases or disease states seen in pulmonary medicine.

Saint: a lightweight integration environment for model annotation.

PubMed

Lister, Allyson L; Pocock, Matthew; Taschuk, Morgan; Wipat, Anil

2009-11-15

Saint is a web application which provides a lightweight annotation integration environment for quantitative biological models. The system enables modellers to rapidly mark up models with biological information derived from a range of data sources. Saint is freely available for use on the web at http://www.cisban.ac.uk/saint. The web application is implemented in Google Web Toolkit and Tomcat, with all major browsers supported. The Java source code is freely available for download at http://saint-annotate.sourceforge.net. The Saint web server requires an installation of libSBML and has been tested on Linux (32-bit Ubuntu 8.10 and 9.04).

Computational biology for ageing

PubMed Central

Wieser, Daniela; Papatheodorou, Irene; Ziehm, Matthias; Thornton, Janet M.

2011-01-01

High-throughput genomic and proteomic technologies have generated a wealth of publicly available data on ageing. Easy access to these data, and their computational analysis, is of great importance in order to pinpoint the causes and effects of ageing. Here, we provide a description of the existing databases and computational tools on ageing that are available for researchers. We also describe the computational approaches to data interpretation in the field of ageing including gene expression, comparative and pathway analyses, and highlight the challenges for future developments. We review recent biological insights gained from applying bioinformatics methods to analyse and interpret ageing data in different organisms, tissues and conditions. PMID:21115530

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

A post-doctoral fellowship is currently available for productive, highly-motivated, and energetic individuals in the Inflammation and Tumorigenesis Section of Dr. Yinling Hu at the NCI-Frederick campus.  A dynamic research environment and outstanding resources are available for enthusiastic individuals.  Requirements include a Ph.D., M.D., or equivalent degree and experience in Immunology, Molecular Biology, and/or Signaling Research. Candidate must have excellent verbal, written communication and organizational skills, and the ability to handle multiple projects simultaneously. The project will be to investigate mechanisms of IKK/NF-kB-involved lung and skin carcinogenesis/cancer biology, tumor initiating cells, and therapy by using mouse genetic modified mouse models.

Bioavailability and dissolution of different formulations of oxytetracycline preparations.

PubMed Central

Hart, A; Barber, H E; Calvey, T N

1975-01-01

1 The concentration of oxytetracycline in plasma was studied by microbiological assay after oral administration of five different preparations of the antibiotic. None of these preparations had been studied previously. 2 There was a statistically significant correlation between the time required for 50% dissolution at pH 2 and biological availability, as assessed by the peak plasma level or the area under the plasma concentration-time curve. 3 The mean bioavailability of oxytetracycline was greatest with preparations of the hydrochloride, and with film-coated tablets of the dihydrate. In contrast, sugar-coated tablets of oxytetracycline dihydrate were associated with poorer dissolution characteristics and reduced biological availability. PMID:10944

Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research

PubMed Central

Benfey, Philip N.; Bennett, Malcolm; Schiefelbein, John

2010-01-01

Summary Prior to the availability of the genome sequence, the root of Arabidopsis had attracted a small but ardent group of researchers drawn to its accessibility and developmental simplicity. Roots are easily observed when grown on the surface of nutrient agar media, facilitating analysis of responses to stimuli such as gravity and touch. Developmental biologists were attracted to the simple radial organization of primary root tissues, which form a series of concentric cylinders around the central vascular tissue. Equally attractive was the mode of propagation, with stem cells at the tip giving rise to progeny that were confined to cell files. These properties of root development reduced the normal four-dimensional problem of development (three spatial dimensions and time) to a two-dimensional problem, with cell type on the radial axis and developmental time along the longitudinal axis. The availability of the complete Arabidopsis genome sequence has dramatically accelerated traditional genetic research on root biology, and has also enabled entirely new experimental strategies to be applied. Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology. PMID:20409273

SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.

PubMed

Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines

2017-06-24

Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.

Behavioural biomarkers and mobile mental health: a new paradigm.

PubMed

Hidalgo-Mazzei, Diego; Young, Allan H; Vieta, Eduard; Colom, Francesc

2018-05-06

Over recent decades, the field of psychiatry has allocated a vast amount of resources and efforts to make available more accurate and objective methods to diagnose, assess and monitor treatment outcomes in psychiatric disorders. Despite the optimism and some significant progress in biological markers, it has become increasingly evident that they are failing to meet initial expectations due to their lack of specificity, inconsistent reliability and limited availability. On the other hand, there is an increasingly emerging evidence of mobile technologies' feasibility to measure mental illness activity. Moreover, taking into account its widespread use, availability and potential to capture behavioural markers, mobile-connected technologies could be strong candidates to fill and complement-at least at some degree-the gaps that biological markers couldn't. This represents an especially interesting opportunity to reform our current diagnostic system using a bottom-up research methodology based on digital and biological markers data instead of the classical traditional top-down approach. Therefore, the field might benefit of further exploring this promising -and increasingly evidence-based- pathway as well as other auspicious alternatives in order to attain a more holistic and integrative approach in research, which could ultimately impact real-world clinical practice.

BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations

PubMed Central

Ghaffarizadeh, Ahmadreza; Friedman, Samuel H.; Macklin, Paul

2016-01-01

Motivation: Computational models of multicellular systems require solving systems of PDEs for release, uptake, decay and diffusion of multiple substrates in 3D, particularly when incorporating the impact of drugs, growth substrates and signaling factors on cell receptors and subcellular systems biology. Results: We introduce BioFVM, a diffusive transport solver tailored to biological problems. BioFVM can simulate release and uptake of many substrates by cell and bulk sources, diffusion and decay in large 3D domains. It has been parallelized with OpenMP, allowing efficient simulations on desktop workstations or single supercomputer nodes. The code is stable even for large time steps, with linear computational cost scalings. Solutions are first-order accurate in time and second-order accurate in space. The code can be run by itself or as part of a larger simulator. Availability and implementation: BioFVM is written in C ++ with parallelization in OpenMP. It is maintained and available for download at http://BioFVM.MathCancer.org and http://BioFVM.sf.net under the Apache License (v2.0). Contact: paul.macklin@usc.edu. Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26656933

The SwissLipids knowledgebase for lipid biology

PubMed Central

Liechti, Robin; Hyka-Nouspikel, Nevila; Niknejad, Anne; Gleizes, Anne; Götz, Lou; Kuznetsov, Dmitry; David, Fabrice P.A.; van der Goot, F. Gisou; Riezman, Howard; Bougueleret, Lydie; Xenarios, Ioannis; Bridge, Alan

2015-01-01

Motivation: Lipids are a large and diverse group of biological molecules with roles in membrane formation, energy storage and signaling. Cellular lipidomes may contain tens of thousands of structures, a staggering degree of complexity whose significance is not yet fully understood. High-throughput mass spectrometry-based platforms provide a means to study this complexity, but the interpretation of lipidomic data and its integration with prior knowledge of lipid biology suffers from a lack of appropriate tools to manage the data and extract knowledge from it. Results: To facilitate the description and exploration of lipidomic data and its integration with prior biological knowledge, we have developed a knowledge resource for lipids and their biology—SwissLipids. SwissLipids provides curated knowledge of lipid structures and metabolism which is used to generate an in silico library of feasible lipid structures. These are arranged in a hierarchical classification that links mass spectrometry analytical outputs to all possible lipid structures, metabolic reactions and enzymes. SwissLipids provides a reference namespace for lipidomic data publication, data exploration and hypothesis generation. The current version of SwissLipids includes over 244 000 known and theoretically possible lipid structures, over 800 proteins, and curated links to published knowledge from over 620 peer-reviewed publications. We are continually updating the SwissLipids hierarchy with new lipid categories and new expert curated knowledge. Availability: SwissLipids is freely available at http://www.swisslipids.org/. Contact: alan.bridge@isb-sib.ch Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25943471

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology.

PubMed

Cankorur-Cetinkaya, Ayca; Dias, Joao M L; Kludas, Jana; Slater, Nigel K H; Rousu, Juho; Oliver, Stephen G; Dikicioglu, Duygu

2017-06-01

Multiple interacting factors affect the performance of engineered biological systems in synthetic biology projects. The complexity of these biological systems means that experimental design should often be treated as a multiparametric optimization problem. However, the available methodologies are either impractical, due to a combinatorial explosion in the number of experiments to be performed, or are inaccessible to most experimentalists due to the lack of publicly available, user-friendly software. Although evolutionary algorithms may be employed as alternative approaches to optimize experimental design, the lack of simple-to-use software again restricts their use to specialist practitioners. In addition, the lack of subsidiary approaches to further investigate critical factors and their interactions prevents the full analysis and exploitation of the biotechnological system. We have addressed these problems and, here, provide a simple-to-use and freely available graphical user interface to empower a broad range of experimental biologists to employ complex evolutionary algorithms to optimize their experimental designs. Our approach exploits a Genetic Algorithm to discover the subspace containing the optimal combination of parameters, and Symbolic Regression to construct a model to evaluate the sensitivity of the experiment to each parameter under investigation. We demonstrate the utility of this method using an example in which the culture conditions for the microbial production of a bioactive human protein are optimized. CamOptimus is available through: (https://doi.org/10.17863/CAM.10257).

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

Towards BioDBcore: a community-defined information specification for biological databases

PubMed Central

Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

2011-01-01

The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

Literature-based cheminformatics for research in chemical toxicity

EPA Science Inventory

PubMed is the largest freely available source of published literature available online with access to 27 million citations (as of October 2017). Contained within the literature is an abundance of information about the activity of chemicals in biological systems. Literature inform...

The Importance of Biological Databases in Biological Discovery.

PubMed

Baxevanis, Andreas D; Bateman, Alex

2015-06-19

Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed. Copyright © 2015 John Wiley & Sons, Inc.

The Texas Adoption Project: adopted children and their intellectual resemblance to biological and adoptive parents.

PubMed

Horn, J M

1983-04-01

Intelligence test scores were obtained from parents and children in 300 adoptive families and compared with similar measures available for the biological mothers of the same adopted children. Results supported the hypothesis that genetic variability is an important influence in the development of individual differences for intelligence. The most salient finding was that adopted children resemble their biological mothers more than they resemble the adoptive parents who reared them from birth. A small subset of the oldest adopted children did not resemble their biological mothers. The suggestion that the influence of genes declines with age is treated with caution since other adoption studies report a trend in the opposite direction.

Tadpoles: the Biology of Anuran Larvae

USGS Publications Warehouse

McDiarmid, R.W.; Altig, R.

1999-01-01

The recent alarming declines in amphibian populations worldwide and the suitability of amphibians for use in answering research questions in disciplines as diverse as molecular systematics, animal behavior, ecology, and evolutionary biology have focused enormous attention on tadpoles. Yet despite this growing interest, relatively little is known about these fascinating creatures. n this invaluable reference, leading experts on tadpole biology relate what we currently know about tadpoles and what we might learn from them in the future. Tadpoles provides detailed summaries of tadpole morphology, development, behavior, ecology, and environmental physiology; explores the evolutionary consequences of the tadpole stage; synthesizes available information on their biodiversity, and presents a standardized terminology and an exhaustive literature review of tadpole biology.

Biology on the outer planets. [life possibility in atmospheres and moons

NASA Technical Reports Server (NTRS)

Young, R. S.; Macelroy, R. D.

1976-01-01

A brief review is given of information on the structure and composition of the outer planets and the organic reactions that may be occurring on them. The possibility of life arising or surviving in the atmospheres of these planets is considered, and the problem of contamination during future unmanned missions is assessed. Atmospheric models or available atmospheric data are reviewed for Jupiter, Saturn, Uranus, Neptune, Pluto, the Galilean satellites, and Titan. The presence of biologically interesting gases on Jupiter and Saturn is discussed, requirements for life on Jupiter are summarized, and possible sources of biological energy are examined. Proposals are made for protecting these planets and satellites from biological contamination by spacecraftborne terrestrial organisms.

Relations between intuitive biological thinking and biological misconceptions in biology majors and nonmajors.

PubMed

Coley, John D; Tanner, Kimberly

2015-03-02

Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems--teleological, essentialist, and anthropocentric thinking--that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. © 2015 J. D. Coley and K. Tanner. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Are Dutch Hospitals Prepared for Chemical, Biological, or Radionuclear Incidents? A Survey Study.

PubMed

Mortelmans, Luc J M; Gaakeer, Menno I; Dieltiens, Greet; Anseeuw, Kurt; Sabbe, Marc B

2017-10-01

Introduction Being one of Europe's most densely populated countries, and having multiple nuclear installations, a heavy petrochemical industry, and terrorist targets, the Netherlands is at-risk for chemical, biological, or radionuclear (CBRN) incidents. Recent world and continental events show that this threat is real and that authorities may be underprepared. Hypothesis The hypothesis of this study is that Dutch hospitals are underprepared to deal with these incidents. A descriptive, cross-sectional study was performed. All 93 Dutch hospitals with an emergency department (ED) were sent a link to an online survey on different aspects of CBRN preparedness. Besides specific hospital information, information was obtained on the hospital's disaster planning; risk perception; and availability of decontamination units, personal protective equipment (PPE), antidotes, radiation detection, infectiologists, isolation measures, and staff training. Response rate was 67%. Sixty-two percent of participating hospitals were estimated to be at-risk for CBRN incidents. Only 40% had decontamination facilities and 32% had appropriate PPE available for triage and decontamination teams. Atropine was available in high doses in all hospitals, but specific antidotes that could be used for treating victims of CBRN incidents, such as hydroxycobolamine, thiosulphate, Prussian blue, Diethylenetriaminepentaacetic acid (DTPA), or pralidoxime, were less frequently available (74%, 65%, 18%, 14%, and 42%, respectively). Six percent of hospitals had radioactive detection equipment with an alarm function and 22.5% had a nuclear specialist available 24/7 in case of disasters. Infectiologists were continuously available in 60% of the hospitals. Collective isolation facilities were present in 15% of the hospitals. There is a serious lack of hospital preparedness for CBRN incidents in The Netherlands. Mortelmans LJM , Gaakeer MI , Dieltiens G , Anseeuw K , Sabbe MB . Are Dutch hospitals prepared for chemical, biological, or radionuclear incidents? A survey study. Prehosp Disaster Med. 2017;32(5):483-491.

Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

PubMed Central

Li, Le; Yip, Kevin Y.

2016-01-01

Currently most terms and term-term relationships in Gene Ontology (GO) are defined manually, which creates cost, consistency and completeness issues. Recent studies have demonstrated the feasibility of inferring GO automatically from biological networks, which represents an important complementary approach to GO construction. These methods (NeXO and CliXO) are unsupervised, which means 1) they cannot use the information contained in existing GO, 2) the way they integrate biological networks may not optimize the accuracy, and 3) they are not customized to infer the three different sub-ontologies of GO. Here we present a semi-supervised method called Unicorn that extends these previous methods to tackle the three problems. Unicorn uses a sub-tree of an existing GO sub-ontology as training part to learn parameters in integrating multiple networks. Cross-validation results show that Unicorn reliably inferred the left-out parts of each specific GO sub-ontology. In addition, by training Unicorn with an old version of GO together with biological networks, it successfully re-discovered some terms and term-term relationships present only in a new version of GO. Unicorn also successfully inferred some novel terms that were not contained in GO but have biological meanings well-supported by the literature.Availability: Source code of Unicorn is available at http://yiplab.cse.cuhk.edu.hk/unicorn/. PMID:27976738

Just-in-Time Teaching in Biology: Creating an Active Learner Classroom Using the Internet

ERIC Educational Resources Information Center

Marrs, Kathleen A.; Novak, Gregor

2004-01-01

Just-in-Time Teaching (ITT) is a teaching and learning approach that combines the best features of traditional in-class instruction with the communication and resource potential available via the Web. We describe here how ITT can be used to teach biology to undergraduate and graduate level students, both science majors as well as non science…

Evaluation of establishment of Cyphocleonus achates and its potential impact on spotted knapweed

Treesearch

Nancy Sturdevant; Sandy Kegley; Yvette Ortega; Dean Pearson

2006-01-01

Environmental characteristics of a site may greatly influence the establishment and impact of biological control agents on the target weed. A biological control agent that is highly successful in one region may be virtually ineffective in another (Gurr and Wratten 2000). To maximize the use of limited availability of agents and financial resources, we should...

Cooperative Project To Develop a Database of Discipline-Specific Workbook Exercises for Agricultural and Biological Engineering, Entomology, and Biological Sciences Courses.

ERIC Educational Resources Information Center

Ellsbury, Susan H.; And Others

A two-part text, "Science Resources: A Self-Paced Instructional Workbook," was designed to provide science students at Mississippi State University with: (1) instruction on basic library usage and reference tools common to most scientific disciplines; (2) materials adapted to specific disciplines; and (3) services available to them from the…

ARTS: automated randomization of multiple traits for study design.

PubMed

Maienschein-Cline, Mark; Lei, Zhengdeng; Gardeux, Vincent; Abbasi, Taimur; Machado, Roberto F; Gordeuk, Victor; Desai, Ankit A; Saraf, Santosh; Bahroos, Neil; Lussier, Yves

2014-06-01

Collecting data from large studies on high-throughput platforms, such as microarray or next-generation sequencing, typically requires processing samples in batches. There are often systematic but unpredictable biases from batch-to-batch, so proper randomization of biologically relevant traits across batches is crucial for distinguishing true biological differences from experimental artifacts. When a large number of traits are biologically relevant, as is common for clinical studies of patients with varying sex, age, genotype and medical background, proper randomization can be extremely difficult to prepare by hand, especially because traits may affect biological inferences, such as differential expression, in a combinatorial manner. Here we present ARTS (automated randomization of multiple traits for study design), which aids researchers in study design by automatically optimizing batch assignment for any number of samples, any number of traits and any batch size. ARTS is implemented in Perl and is available at github.com/mmaiensc/ARTS. ARTS is also available in the Galaxy Tool Shed, and can be used at the Galaxy installation hosted by the UIC Center for Research Informatics (CRI) at galaxy.cri.uic.edu. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.

PubMed

Mazandu, Gaston K; Chimusa, Emile R; Mbiyavanga, Mamana; Mulder, Nicola J

2016-02-01

Gene Ontology (GO) semantic similarity measures are being used for biological knowledge discovery based on GO annotations by integrating biological information contained in the GO structure into data analyses. To empower users to quickly compute, manipulate and explore these measures, we introduce A-DaGO-Fun (ADaptable Gene Ontology semantic similarity-based Functional analysis). It is a portable software package integrating all known GO information content-based semantic similarity measures and relevant biological applications associated with these measures. A-DaGO-Fun has the advantage not only of handling datasets from the current high-throughput genome-wide applications, but also allowing users to choose the most relevant semantic similarity approach for their biological applications and to adapt a given module to their needs. A-DaGO-Fun is freely available to the research community at http://web.cbio.uct.ac.za/ITGOM/adagofun. It is implemented in Linux using Python under free software (GNU General Public Licence). gmazandu@cbio.uct.ac.za or Nicola.Mulder@uct.ac.za Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Effects of small particle numbers on long-term behaviour in discrete biochemical systems

PubMed Central

Ibrahim, Bashar; Dittrich, Peter

2014-01-01

Motivation: The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state. Results: We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. Availability and implementation: http://www.biosys.uni-jena.de/Services.html. Contact: bashar.ibrahim@uni-jena.de or dittrich@minet.uni-jena.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25161236

Air pollution particles and iron homeostasis | Science ...

EPA Pesticide Factsheets

Background: The mechanism underlying biological effects of particles deposited in the lung has not been defined. Major Conclusions: A disruption in iron homeostasis follows exposure of cells to all particulate matter including air pollution particles. Following endocytosis, functional groups at the surface of retained particle complex iron available in the cell. In response to a reduction in concentrations of requisite iron, a functional deficiency can result intracellularly. Superoxide production by the cell exposed to a particle increases ferrireduction which facilitates import of iron with the objective being the reversal of the metal deficiency. Failure to resolve the functional iron deficiency following cell exposure to particles activates kinases and transcription factors resulting in a release of inflammatory mediators and inflammation. Tissue injury is the end product of this disruption in iron homeostasis initiated by the particle exposure. Elevation of available iron to the cell precludes deficiency of the metal and either diminishes or eliminates biological effects.General Significance: Recognition of the pathway for biological effects after particle exposure to involve a functional deficiency of iron suggests novel therapies such as metal supplementation (e.g. inhaled and oral). In addition, the demonstration of a shared mechanism of biological effects allows understanding the common clinical, physiological, and pathological presentation fol

Accelerated telomere attrition is associated with relative household income, diet and inflammation in the pSoBid cohort.

PubMed

Shiels, Paul G; McGlynn, Liane M; MacIntyre, Alan; Johnson, Paul C D; Batty, G David; Burns, Harry; Cavanagh, Jonathan; Deans, Kevin A; Ford, Ian; McConnachie, Alex; McGinty, Agnes; McLean, Jennifer S; Millar, Keith; Sattar, Naveed; Tannahill, Carol; Velupillai, Yoga N; Packard, Chris J

2011-01-01

It has previously been hypothesized that lower socio-economic status can accelerate biological ageing, and predispose to early onset of disease. This study investigated the association of socio-economic and lifestyle factors, as well as traditional and novel risk factors, with biological-ageing, as measured by telomere length, in a Glasgow based cohort that included individuals with extreme socio-economic differences. A total of 382 blood samples from the pSoBid study were available for telomere analysis. For each participant, data was available for socio-economic status factors, biochemical parameters and dietary intake. Statistical analyses were undertaken to investigate the association between telomere lengths and these aforementioned parameters. The rate of age-related telomere attrition was significantly associated with low relative income, housing tenure and poor diet. Notably, telomere length was positively associated with LDL and total cholesterol levels, but inversely correlated to circulating IL-6. These data suggest lower socio-economic status and poor diet are relevant to accelerated biological ageing. They also suggest potential associations between elevated circulating IL-6, a measure known to predict cardiovascular disease and diabetes with biological ageing. These observations require further study to tease out potential mechanistic links.

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

PubMed Central

2010-01-01

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, Microsoft.NET and R programming environments and offers flexible query and broad data- retrieval methods. Data retrieval can be customized to client needs and the API offers a framework to construct and manipulate user-defined networks. The design principles can be used as a template to build programmable interfaces for other biological databases. The API software and tutorials are available at http://www.metnetonline.org/api. PMID:21083943

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

PubMed

Gabanyi, Margaret J; Adams, Paul D; Arnold, Konstantin; Bordoli, Lorenza; Carter, Lester G; Flippen-Andersen, Judith; Gifford, Lida; Haas, Juergen; Kouranov, Andrei; McLaughlin, William A; Micallef, David I; Minor, Wladek; Shah, Raship; Schwede, Torsten; Tao, Yi-Ping; Westbrook, John D; Zimmerman, Matthew; Berman, Helen M

2011-07-01

The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org ) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI's high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.

Quantitative cell biology: the essential role of theory.

PubMed

Howard, Jonathon

2014-11-05

Quantitative biology is a hot area, as evidenced by the recent establishment of institutes, graduate programs, and conferences with that name. But what is quantitative biology? What should it be? And how can it contribute to solving the big questions in biology? The past decade has seen very rapid development of quantitative experimental techniques, especially at the single-molecule and single-cell levels. In this essay, I argue that quantitative biology is much more than just the quantitation of these experimental results. Instead, it should be the application of the scientific method by which measurement is directed toward testing theories. In this view, quantitative biology is the recognition that theory and models play critical roles in biology, as they do in physics and engineering. By tying together experiment and theory, quantitative biology promises a deeper understanding of underlying mechanisms, when the theory works, or to new discoveries, when it does not. © 2014 Howard. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Integrating publicly-available data to generate computationally-predicted adverse outcome pathways for hepatic steatosis

EPA Science Inventory

The adverse outcome pathway (AOP) framework provides a way of organizing knowledge related to the key biological events that result in a particular health outcome. For the majority of environmental chemicals, the availability of curated pathways characterizing potential toxicity ...

75 FR 7522 - United States Section; Notice of Availability of the Final Environmental Impact Statement, Flood...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-19

... Final EIS: Biological resources, cultural resources, water resources, land use, socioeconomic resources... INTERNATIONAL BOUNDARY AND WATER COMMISSION, UNITED STATES AND MEXICO United States Section..., International Boundary and Water Commission (USIBWC). ACTION: Notice of Availability of Final Environmental...

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

PubMed Central

Villaverde, Alejandro F.; Banga, Julio R.

2014-01-01

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology? PMID:24307566

Systems biology of human atherosclerosis.

PubMed

Shalhoub, Joseph; Sikkel, Markus B; Davies, Kerry J; Vorkas, Panagiotis A; Want, Elizabeth J; Davies, Alun H

2014-01-01

Systems biology describes a holistic and integrative approach to understand physiology and pathology. The "omic" disciplines include genomics, transcriptomics, proteomics, and metabolic profiling (metabonomics and metabolomics). By adopting a stance, which is opposing (yet complimentary) to conventional research techniques, systems biology offers an overview by assessing the "net" biological effect imposed by a disease or nondisease state. There are a number of different organizational levels to be understood, from DNA to protein, metabolites, cells, organs and organisms, even beyond this to an organism's context. Systems biology relies on the existence of "nodes" and "edges." Nodes are the constituent part of the system being studied (eg, proteins in the proteome), while the edges are the way these constituents interact. In future, it will be increasingly important to collaborate, collating data from multiple studies to improve data sets, making them freely available and undertaking integrative analyses.

USSR Space Life Sciences Digest, issue 14

NASA Technical Reports Server (NTRS)

Hooke, Lydia Razran; Teeter, Ronald; Radtke, Mike; Rowe, Joseph

1988-01-01

This is the fourteenth issue of NASA's USSR Space Life Sciences Digest. It contains abstracts of 32 papers recently published in Russian language periodicals and bound collections and of three new Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. Also included is a review of a recent Soviet conference on Space Biology and Aerospace Medicine. Current Soviet life sciences titles available in English are cited. The materials included in this issue have been identified as relevant to the following areas of aerospace medicine and space biology: adaptation, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, gastrointestinal systems, habitability and environment effects, human performance, immunology, life support systems, mathematical modeling, metabolism, musculoskeletal system, neurophysiology, nutrition, operational medicine, perception, personnel selection, psychology, radiobiology, and space biology and medicine.

SynBioSS-aided design of synthetic biological constructs.

PubMed

Kaznessis, Yiannis N

2011-01-01

We present walkthrough examples of using SynBioSS to design, model, and simulate synthetic gene regulatory networks. SynBioSS stands for Synthetic Biology Software Suite, a platform that is publicly available with Open Licenses at www.synbioss.org. An important aim of computational synthetic biology is the development of a mathematical modeling formalism that is applicable to a wide variety of simple synthetic biological constructs. SynBioSS-based modeling of biomolecular ensembles that interact away from the thermodynamic limit and not necessarily at steady state affords for a theoretical framework that is generally applicable to known synthetic biological systems, such as bistable switches, AND gates, and oscillators. Here, we discuss how SynBioSS creates links between DNA sequences and targeted dynamic phenotypes of these simple systems. Copyright © 2011 Elsevier Inc. All rights reserved.

Advanced Applications of Next-Generation Sequencing Technologies to Orchid Biology.

PubMed

Yeh, Chuan-Ming; Liu, Zhong-Jian; Tsai, Wen-Chieh

2018-01-01

Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current next-generation sequencing platforms, many of which are already used in plant laboratories. The third part summarizes the state of orchid transcriptome and genome sequencing and illustrates current achievements. The genetic sequences currently obtained will not only provide a broad scope for the study of orchid biology, but also serves as a starting point for uncovering the mystery of orchid evolution.

Statistical approach for selection of biologically informative genes.

PubMed

Das, Samarendra; Rai, Anil; Mishra, D C; Rai, Shesh N

2018-05-20

Selection of informative genes from high dimensional gene expression data has emerged as an important research area in genomics. Many gene selection techniques have been proposed so far are either based on relevancy or redundancy measure. Further, the performance of these techniques has been adjudged through post selection classification accuracy computed through a classifier using the selected genes. This performance metric may be statistically sound but may not be biologically relevant. A statistical approach, i.e. Boot-MRMR, was proposed based on a composite measure of maximum relevance and minimum redundancy, which is both statistically sound and biologically relevant for informative gene selection. For comparative evaluation of the proposed approach, we developed two biological sufficient criteria, i.e. Gene Set Enrichment with QTL (GSEQ) and biological similarity score based on Gene Ontology (GO). Further, a systematic and rigorous evaluation of the proposed technique with 12 existing gene selection techniques was carried out using five gene expression datasets. This evaluation was based on a broad spectrum of statistically sound (e.g. subject classification) and biological relevant (based on QTL and GO) criteria under a multiple criteria decision-making framework. The performance analysis showed that the proposed technique selects informative genes which are more biologically relevant. The proposed technique is also found to be quite competitive with the existing techniques with respect to subject classification and computational time. Our results also showed that under the multiple criteria decision-making setup, the proposed technique is best for informative gene selection over the available alternatives. Based on the proposed approach, an R Package, i.e. BootMRMR has been developed and available at https://cran.r-project.org/web/packages/BootMRMR. This study will provide a practical guide to select statistical techniques for selecting informative genes from high dimensional expression data for breeding and system biology studies. Published by Elsevier B.V.

Development of the Neuron Assessment for Measuring Biology Students' Use of Experimental Design Concepts and Representations.

PubMed

Dasgupta, Annwesa P; Anderson, Trevor R; Pelaez, Nancy J

2016-01-01

Researchers, instructors, and funding bodies in biology education are unanimous about the importance of developing students' competence in experimental design. Despite this, only limited measures are available for assessing such competence development, especially in the areas of molecular and cellular biology. Also, existing assessments do not measure how well students use standard symbolism to visualize biological experiments. We propose an assessment-design process that 1) provides background knowledge and questions for developers of new "experimentation assessments," 2) elicits practices of representing experiments with conventional symbol systems, 3) determines how well the assessment reveals expert knowledge, and 4) determines how well the instrument exposes student knowledge and difficulties. To illustrate this process, we developed the Neuron Assessment and coded responses from a scientist and four undergraduate students using the Rubric for Experimental Design and the Concept-Reasoning Mode of representation (CRM) model. Some students demonstrated sound knowledge of concepts and representations. Other students demonstrated difficulty with depicting treatment and control group data or variability in experimental outcomes. Our process, which incorporates an authentic research situation that discriminates levels of visualization and experimentation abilities, shows potential for informing assessment design in other disciplines. © 2016 A. P. Dasgupta et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.

PubMed

Pounds, Stan; Cheng, Cheng; Cao, Xueyuan; Crews, Kristine R; Plunkett, William; Gandhi, Varsha; Rubnitz, Jeffrey; Ribeiro, Raul C; Downing, James R; Lamba, Jatinder

2009-08-15

In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables. Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis. Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org.

CONTAMINATED SEDIMENT TESTING WITH THE BIVLVE, MULINIA LATERLALIS: CULTURE REFINEMENT FOR ORGANISM AVAILABILITY

EPA Science Inventory

Availability of test species for estuarine benthic assessment is limited; therefore, a method was developed by the U.S. Environmental Protection Agency for utilizing the dwarf surf clam, Mulinia lateralis, to identify adverse biological effects of bulk estuarine sediments. A mult...

TECHNOLOGY VERIFICATION OF COMMERCIALLY AVAILABLE METHODS FOR DECONTAMINATION OF INDOOR SURFACES CONTAMINATED WITH BIOLOGICAL OR CHEMICAL AGENTS

EPA Science Inventory

To support the Nation's Homeland Security Program, this U.S. Environmental Protection Agency (EPA) Environmental Technology Verification (ETV) project is conducted to verify the performance of commercially available products, methods, and equipment for decontamination of hard and...

CONTAMINATED SEDIMENT TESTING WITH THE BIVALVE, MULINA LATERALIS: CULTURE REFINEMENT FOR ORGANISM AVAILABILITY

EPA Science Inventory

Availability of test species for estuarine benthic assessment is limited; therefore, a method was developed by the U.S. Environmental Protection Agency for using the dwarf surf clam (Mulinia lateralis) to identify adverse biological effects of bulk estuarine sediments. A multilab...

78 FR 20667 - Government-Owned Inventions; Availability for Licensing

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-05

..., et al. Visualization of biological texture using correlation coefficient images. J Biomed Opt. 2006.... Development Stage: Early-stage In vitro data available Inventors: Paolo Lusso and David J. Auerbach (NIAID... algorithms to visualize regions of statistical similarity in the image have been developed. Though the...

Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

PubMed

Brohée, Sylvain; Barriot, Roland; Moreau, Yves

2010-09-01

In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

Semantic integration of data on transcriptional regulation.

PubMed

Baitaluk, Michael; Ponomarenko, Julia

2010-07-01

Experimental and predicted data concerning gene transcriptional regulation are distributed among many heterogeneous sources. However, there are no resources to integrate these data automatically or to provide a 'one-stop shop' experience for users seeking information essential for deciphering and modeling gene regulatory networks. IntegromeDB, a semantic graph-based 'deep-web' data integration system that automatically captures, integrates and manages publicly available data concerning transcriptional regulation, as well as other relevant biological information, is proposed in this article. The problems associated with data integration are addressed by ontology-driven data mapping, multiple data annotation and heterogeneous data querying, also enabling integration of the user's data. IntegromeDB integrates over 100 experimental and computational data sources relating to genomics, transcriptomics, genetics, and functional and interaction data concerning gene transcriptional regulation in eukaryotes and prokaryotes. IntegromeDB is accessible through the integrated research environment BiologicalNetworks at http://www.BiologicalNetworks.org baitaluk@sdsc.edu Supplementary data are available at Bioinformatics online.

PyDREAM: high-dimensional parameter inference for biological models in python.

PubMed

Shockley, Erin M; Vrugt, Jasper A; Lopez, Carlos F; Valencia, Alfonso

2018-02-15

Biological models contain many parameters whose values are difficult to measure directly via experimentation and therefore require calibration against experimental data. Markov chain Monte Carlo (MCMC) methods are suitable to estimate multivariate posterior model parameter distributions, but these methods may exhibit slow or premature convergence in high-dimensional search spaces. Here, we present PyDREAM, a Python implementation of the (Multiple-Try) Differential Evolution Adaptive Metropolis [DREAM(ZS)] algorithm developed by Vrugt and ter Braak (2008) and Laloy and Vrugt (2012). PyDREAM achieves excellent performance for complex, parameter-rich models and takes full advantage of distributed computing resources, facilitating parameter inference and uncertainty estimation of CPU-intensive biological models. PyDREAM is freely available under the GNU GPLv3 license from the Lopez lab GitHub repository at http://github.com/LoLab-VU/PyDREAM. c.lopez@vanderbilt.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool.

PubMed

Auerbach, Raymond K; Chen, Bin; Butte, Atul J

2013-08-01

Biological analysis has shifted from identifying genes and transcripts to mapping these genes and transcripts to biological functions. The ENCODE Project has generated hundreds of ChIP-Seq experiments spanning multiple transcription factors and cell lines for public use, but tools for a biomedical scientist to analyze these data are either non-existent or tailored to narrow biological questions. We present the ENCODE ChIP-Seq Significance Tool, a flexible web application leveraging public ENCODE data to identify enriched transcription factors in a gene or transcript list for comparative analyses. The ENCODE ChIP-Seq Significance Tool is written in JavaScript on the client side and has been tested on Google Chrome, Apple Safari and Mozilla Firefox browsers. Server-side scripts are written in PHP and leverage R and a MySQL database. The tool is available at http://encodeqt.stanford.edu. abutte@stanford.edu Supplementary material is available at Bioinformatics online.

Evaluation of Commercially-Available Equipment for the ...

EPA Pesticide Factsheets

Report The Underground Transport Restoration (UTR) project is an inter-agency effort. This effort aims to improve the capability for transit systems to quickly and efficiently recover from a biological contamination incident by refining existing methods, tools and protocols for characterization, clean-up, and clearance of contamination in physical structures (i.e., tunnels, stations) and rolling stock (i.e., subway trains). The aim was to evaluate existing sampling, characterization, and decontamination technologies through experimentation, table-top exercises and operational demonstrations to develop guidance and decision frameworks and support tools through interactions of local, state and federal partners. In this investigation, a survey of commercially-available or fielded equipment was conducted and resulted in three pieces of identified equipment that could be used or rapidly modified for use in dispensing liquid chemicals to decontaminate surfaces following a biological contamination incident. documenting lab-scale testing, field-scale testing, and an equipment demonstration of commercial equipment used to decontaminate subway infrastructure following a biological incident.

GenSSI 2.0: multi-experiment structural identifiability analysis of SBML models.

PubMed

Ligon, Thomas S; Fröhlich, Fabian; Chis, Oana T; Banga, Julio R; Balsa-Canto, Eva; Hasenauer, Jan

2018-04-15

Mathematical modeling using ordinary differential equations is used in systems biology to improve the understanding of dynamic biological processes. The parameters of ordinary differential equation models are usually estimated from experimental data. To analyze a priori the uniqueness of the solution of the estimation problem, structural identifiability analysis methods have been developed. We introduce GenSSI 2.0, an advancement of the software toolbox GenSSI (Generating Series for testing Structural Identifiability). GenSSI 2.0 is the first toolbox for structural identifiability analysis to implement Systems Biology Markup Language import, state/parameter transformations and multi-experiment structural identifiability analysis. In addition, GenSSI 2.0 supports a range of MATLAB versions and is computationally more efficient than its previous version, enabling the analysis of more complex models. GenSSI 2.0 is an open-source MATLAB toolbox and available at https://github.com/genssi-developer/GenSSI. thomas.ligon@physik.uni-muenchen.de or jan.hasenauer@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online.

Advances in chemical labeling of proteins in living cells.

PubMed

Yan, Qi; Bruchez, Marcel P

2015-04-01

The pursuit of quantitative biological information via imaging requires robust labeling approaches that can be used in multiple applications and with a variety of detectable colors and properties. In addition to conventional fluorescent proteins, chemists and biologists have come together to provide a range of approaches that combine dye chemistry with the convenience of genetic targeting. This hybrid-tagging approach amalgamates the rational design of properties available through synthetic dye chemistry with the robust biological targeting available with genetic encoding. In this review, we discuss the current range of approaches that have been exploited for dye targeting or for targeting and activation and some of the recent applications that are uniquely permitted by these hybrid-tagging approaches.

Intergenerational Transmission of Internalizing Problems: Effects of Parental and Grandparental Major Depressive Disorder on Child Behavior

ERIC Educational Resources Information Center

Pettit, Jeremy W.; Olino, Thomas M.; Roberts, Robert E.; Seeley, John R.; Lewinsohn, Peter M.

2008-01-01

Effects of lifetime histories of grandparental (G1) and parental (G2) major depressive disorder (MDD) on children's (G3) internalizing problems were investigated among 267 G3 children (ages 2-18 years) who received Child Behavior Checklist (CBCL) ratings and had diagnostic data available on 267 biological G2 parents and 527 biological G1…

Proceedings, XV U.S. Department of Agriculture interagency research forum on gypsy moth and other invasive species 2004

Treesearch

Kurt W., ed. Gottschalk

2005-01-01

Contains 61 abstracts and papers of oral and poster presentations on gypsy moth and other invasive species biology, molecular biology, ecology, impacts, and management presented at the annual U. S. Department of Agriculture Interagency Research Forum on Gypsy Moth and Other Invasive Species. The online version contains two additional papers that were not available at...

geneLAB: Expanding the Impact of NASA's Biological Research in Space

NASA Technical Reports Server (NTRS)

Rayl, Nicole; Smith, Jeffrey D.

2014-01-01

The geneLAB project is designed to leverage the value of large 'omics' datasets from molecular biology projects conducted on the ISS by making these datasets available, citable, discoverable, interpretable, reusable, and reproducible. geneLAB will create a collaboration space with an integrated set of tools for depositing, accessing, analyzing, and modeling these diverse datasets from spaceflight and related terrestrial studies.

Evaluation of Carpet Steam and Heat Cleaners as Biological Sampling Devices

DTIC Science & Technology

2016-05-01

to develop this approach into a valuable, readily available sampling capability and to evaluate its applicability for decontamination . 15. SUBJECT...Center, Research Triangle Park, NC) for their critical review of the test plan and the final report; and  Debbie Sheppard (U.S. Army Edgewood Chemical ...established to further examine and enhance the capabilities for sampling, decontaminating , and clearing biologically contaminated areas, including the

Fundamental Investigations of the Tribological Properties of Biological Interfaces

DTIC Science & Technology

2005-10-01

In spite of a wide range of applications of this commercially available copolymer (BASF Co.) for other fields outside tribology, the information on...lubrication for alumina. Si-PEG has found a variety of applications , especially in the biological field , due mainly to the protein resistance of PEG...Zurich, 13.7.04, Surface functionalization for tribological and biomaterials applications Presentations- Contributed * Xiaoping Yan, Scott, S. Perry

Evaluation of Teachers' Activities in the Use of Animated Instructional Resource Materials in Biology Teaching in Senior Secondary Schools in Bauchi State Nigeria

ERIC Educational Resources Information Center

Kwasu, I. A.; Abubakar; Ema, E.

2015-01-01

This paper presents a profile on how teachers in senior secondary schools in Bauchi state Nigeria utilise animated instructional resource (AIR) in the teaching of biology. A structured questionnaire used to generate data on the availability, accessibility and application of the AIR for classroom instruction by teachers. The instrument for data…

Source or Sink? The Role of Soil and Water Borne Inoculum in the Dispersal of Phytophthora ramorum in Oregon Tanoak Forests

Treesearch

E. Peterson; E. Hansen; J. Hulbert

2014-01-01

Management of invasive species requires confidence in the detection methods used to assess expanding distributions, as well as an understanding of the dominant modes of spread. Lacking this basic biological information, during early stages of invasion management choices are often driven by available resources and the biology of closely related species. Such has been...

Biological phosphorus removal in wastewater treatment.

PubMed

Timmerman, M W

1984-09-01

Several commercially available systems claim to remove phosphate biologically from municipal wastewater. Techniques such as scanning electron microscopy, transmission electron microscopy and 31P nuclear magnetic resonance (NMR) have demonstrated that the phosphate removed is stored within bacterial cells as polyphosphate. Acinetobacter species are usually isolated from phosphate-removing systems although there is a great deal of evidence which casts doubt on the exclusive role of these organisms.

Variation in Citational Practice in a Corpus of Student Biology Papers: From Parenthetical Plonking to Intertextual Storytelling

ERIC Educational Resources Information Center

Swales, John M.

2014-01-01

This is a corpus-based study of a key aspect of academic writing in one discipline (biology) by final-year undergraduates and first-, second-, and third-year graduate students. The papers come from the Michigan Corpus of Upper-level Student Papers, a freely available electronic database. The principal aim of the study is to examine the extent of…

Zebrafish Melanoma.

PubMed

Kaufman, Charles K

2016-01-01

Melanoma skin cancer is a potentially deadly disease in humans and has remained extremely difficult to treat once it has metastasized. In just the last 10 years, a number of models of melanoma have been developed in the zebrafish that are biologically faithful to the human disease and have already yielded important insights into the fundamental biology of melanoma and offered new potential avenues for treatment. With the diversity and breadth of the molecular genetic tools available in the zebrafish, these melanoma models will continue to be refined and expanded upon to keep pace with the rapidly evolving field of melanoma biology.

Availability: A Metric for Nucleic Acid Strand Displacement Systems.

PubMed

Olson, Xiaoping; Kotani, Shohei; Padilla, Jennifer E; Hallstrom, Natalya; Goltry, Sara; Lee, Jeunghoon; Yurke, Bernard; Hughes, William L; Graugnard, Elton

2017-01-20

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks.

Manipulation of biological samples using micro and nano techniques.

PubMed

Castillo, Jaime; Dimaki, Maria; Svendsen, Winnie Edith

2009-01-01

The constant interest in handling, integrating and understanding biological systems of interest for the biomedical field, the pharmaceutical industry and the biomaterial researchers demand the use of techniques that allow the manipulation of biological samples causing minimal or no damage to their natural structure. Thanks to the advances in micro- and nanofabrication during the last decades several manipulation techniques offer us the possibility to image, characterize and manipulate biological material in a controlled way. Using these techniques the integration of biomaterials with remarkable properties with physical transducers has been possible, giving rise to new and highly sensitive biosensing devices. This article reviews the different techniques available to manipulate and integrate biological materials in a controlled manner either by sliding them along a surface (2-D manipulation), by grapping them and moving them to a new position (3-D manipulation), or by manipulating and relocating them applying external forces. The advantages and drawbacks are mentioned together with examples that reflect the state of the art of manipulation techniques for biological samples (171 references).

Agent-based modelling in synthetic biology.

PubMed

Gorochowski, Thomas E

2016-11-30

Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

Passive Antibody Administration (Immediate Immunity) as a Specific Defense Against Biological Weapons

PubMed Central

2002-01-01

The potential threat of biological warfare with a specific agent is proportional to the susceptibility of the population to that agent. Preventing disease after exposure to a biological agent is partially a function of the immunity of the exposed individual. The only available countermeasure that can provide immediate immunity against a biological agent is passive antibody. Unlike vaccines, which require time to induce protective immunity and depend on the host’s ability to mount an immune response, passive antibody can theoretically confer protection regardless of the immune status of the host. Passive antibody therapy has substantial advantages over antimicrobial agents and other measures for postexposure prophylaxis, including low toxicity and high specific activity. Specific antibodies are active against the major agents of bioterrorism, including anthrax, smallpox, botulinum toxin, tularemia, and plague. This article proposes a biological defense initiative based on developing, producing, and stockpiling specific antibody reagents that can be used to protect the population against biological warfare threats. PMID:12141970

USSR Space Life Sciences Digest, issue 9

NASA Technical Reports Server (NTRS)

Hooke, Lydia Razran; Radtke, Mike; Teeter, Ronald; Rowe, Joseph E.

1987-01-01

This is the ninth issue of NASA's USSR Space Lifes Sciences Digest. It contains abstracts of 46 papers recently published in Russian language periodicals and bound collections and of a new Soviet monograph. Selected abstracts are illustrated with figures and tables from the original. Additional features include reviews of a Russian book on biological rhythms and a description of the papers presented at a conference on space biology and medicine. A special feature describes two paradigms frequently cited in Soviet space life sciences literature. Information about English translations of Soviet materials available to readers is provided. The abstracts included in this issue have been identified as relevant to 28 areas of aerospace medicine and space biology. These areas are: adaptation, biological rhythms, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, gastrointestinal system, genetics, habitability and environment effects, hematology, human performance, immunology, life support systems, mathematical modeling, metabolism, microbiology, morphology and cytology, musculoskeletal system, nutrition, neurophysiology, operational medicine, perception, personnel selection, psychology, radiobiology, and space biology and medicine.

Cell biology of the Koji mold Aspergillus oryzae.

PubMed

Kitamoto, Katsuhiko

2015-01-01

Koji mold, Aspergillus oryzae, has been used for the production of sake, miso, and soy sauce for more than one thousand years in Japan. Due to the importance, A. oryzae has been designated as the national micro-organism of Japan (Koku-kin). A. oryzae has been intensively studied in the past century, with most investigations focusing on breeding techniques and developing methods for Koji making for sake brewing. However, the understanding of fundamental biology of A. oryzae remains relatively limited compared with the yeast Saccharomyces cerevisiae. Therefore, we have focused on studying the cell biology including live cell imaging of organelles, protein vesicular trafficking, autophagy, and Woronin body functions using the available genomic information. In this review, I describe essential findings of cell biology of A. oryzae obtained in our study for a quarter of century. Understanding of the basic biology will be critical for not its biotechnological application, but also for an understanding of the fundamental biology of other filamentous fungi.

Evolving Strategies for the Incorporation of Bioinformatics Within the Undergraduate Cell Biology Curriculum

PubMed Central

Honts, Jerry E.

2003-01-01

Recent advances in genomics and structural biology have resulted in an unprecedented increase in biological data available from Internet-accessible databases. In order to help students effectively use this vast repository of information, undergraduate biology students at Drake University were introduced to bioinformatics software and databases in three courses, beginning with an introductory course in cell biology. The exercises and projects that were used to help students develop literacy in bioinformatics are described. In a recently offered course in bioinformatics, students developed their own simple sequence analysis tool using the Perl programming language. These experiences are described from the point of view of the instructor as well as the students. A preliminary assessment has been made of the degree to which students had developed a working knowledge of bioinformatics concepts and methods. Finally, some conclusions have been drawn from these courses that may be helpful to instructors wishing to introduce bioinformatics within the undergraduate biology curriculum. PMID:14673489

Biologic agents in the management of Hodgkin lymphoma.

PubMed

Rashidi, Armin; Bartlett, Nancy L

2015-05-01

The advent of biologic approaches for the treatment of solid tumors and hematologic malignancies has been a major accomplishment in oncology and a rapidly growing field of clinical and translational research in cancer therapeutics. Classical Hodgkin lymphoma (HL) is no exception. Although the investigation of biologic therapies in HL started decades ago, it has only recently flourished, largely because of the development of new monoclonal antibody drug conjugates and checkpoint inhibitors. Biologic therapies represent a potent treatment option that have produced durable remissions even in patients who have had multiple relapses or with refractory disease. This article reviews 8 major classes of biologic approaches that have been investigated in HL: monoclonal antibodies, immunotoxins, antibody-drug conjugates, radioimmunotherapy, adoptive immunotherapy, immunomodulators, chimeric antigen receptor T cells, and checkpoint inhibitors. An armamentarium of biologic therapies for HL that are well tolerated and potentially more effective is expected to be available in the near future. Copyright © 2015 by the National Comprehensive Cancer Network.

Node fingerprinting: an efficient heuristic for aligning biological networks.

PubMed

Radu, Alex; Charleston, Michael

2014-10-01

With the continuing increase in availability of biological data and improvements to biological models, biological network analysis has become a promising area of research. An emerging technique for the analysis of biological networks is through network alignment. Network alignment has been used to calculate genetic distance, similarities between regulatory structures, and the effect of external forces on gene expression, and to depict conditional activity of expression modules in cancer. Network alignment is algorithmically complex, and therefore we must rely on heuristics, ideally as efficient and accurate as possible. The majority of current techniques for network alignment rely on precomputed information, such as with protein sequence alignment, or on tunable network alignment parameters, which may introduce an increased computational overhead. Our presented algorithm, which we call Node Fingerprinting (NF), is appropriate for performing global pairwise network alignment without precomputation or tuning, can be fully parallelized, and is able to quickly compute an accurate alignment between two biological networks. It has performed as well as or better than existing algorithms on biological and simulated data, and with fewer computational resources. The algorithmic validation performed demonstrates the low computational resource requirements of NF.

What is biological physics?

NASA Astrophysics Data System (ADS)

Moss, Frank

1997-11-01

The question arises in a number of contexts from the editorial policies of our journals to the decisions and priorities of agencies that financially support scientific research. What kinds of papers should Physical Review E and Physical Review Letters accept within this category? What constitutes success in choosing which projects to fund? Do biological physicists discover new physics, or new biology, or do they simply make their considerable instrumental and analytical talents available to the biologists(see for example, V.A. Parsegian, Physics Today), July 1997 p. 23 and a Counterpoint by R. H. Austin, ibid p. 27.? And are there bridges to medical science? Are there now some questions in biological and medical science that cannot be creditably addressed without contemporary physics? And what does it mean that the president has ventured that the next five decades will be the age of biology as opposed to the last (which he described as the age of physics)? These questions seem interesting (at least to those who call themselves biological physicists) and may be gaining significance in view of the fact that what we loosely describe as biological physics as a field seems to be growing.

76 FR 81467 - Availability of an Environmental Assessment for Field Testing Swine Influenza Vaccine, RNA

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-28

...] Availability of an Environmental Assessment for Field Testing Swine Influenza Vaccine, RNA AGENCY: Animal and... Vaccine, RNA. The environmental assessment, which is based on a risk analysis prepared to assess the risks... veterinary biological product: Requester: Harrisvaccines, Inc. Product: Swine Influenza Vaccine, RNA. Field...

CamOptimus: a tool for exploiting complex adaptive evolution to optimize experiments and processes in biotechnology

PubMed Central

Cankorur-Cetinkaya, Ayca; Dias, Joao M. L.; Kludas, Jana; Slater, Nigel K. H.; Rousu, Juho; Dikicioglu, Duygu

2017-01-01

Multiple interacting factors affect the performance of engineered biological systems in synthetic biology projects. The complexity of these biological systems means that experimental design should often be treated as a multiparametric optimization problem. However, the available methodologies are either impractical, due to a combinatorial explosion in the number of experiments to be performed, or are inaccessible to most experimentalists due to the lack of publicly available, user-friendly software. Although evolutionary algorithms may be employed as alternative approaches to optimize experimental design, the lack of simple-to-use software again restricts their use to specialist practitioners. In addition, the lack of subsidiary approaches to further investigate critical factors and their interactions prevents the full analysis and exploitation of the biotechnological system. We have addressed these problems and, here, provide a simple‐to‐use and freely available graphical user interface to empower a broad range of experimental biologists to employ complex evolutionary algorithms to optimize their experimental designs. Our approach exploits a Genetic Algorithm to discover the subspace containing the optimal combination of parameters, and Symbolic Regression to construct a model to evaluate the sensitivity of the experiment to each parameter under investigation. We demonstrate the utility of this method using an example in which the culture conditions for the microbial production of a bioactive human protein are optimized. CamOptimus is available through: (https://doi.org/10.17863/CAM.10257). PMID:28635591

The biology of small, introduced populations, with special reference to biological control

PubMed Central

Fauvergue, Xavier; Vercken, Elodie; Malausa, Thibaut; Hufbauer, Ruth A

2012-01-01

Populations are introduced into novel environments in different contexts, one being the biological control of pests. Despite intense efforts, less than half introduced biological control agents establish. Among the possible approaches to improve biological control, one is to better understand the processes that underpin introductions and contribute to ecological and evolutionary success. In this perspective, we first review the demographic and genetic processes at play in small populations, be they stochastic or deterministic. We discuss the theoretical outcomes of these different processes with respect to individual fitness, population growth rate, and establishment probability. Predicted outcomes differ subtly in some cases, but enough so that the evaluating results of introductions have the potential to reveal which processes play important roles in introduced populations. Second, we attempt to link the theory we have discussed with empirical data from biological control introductions. A main result is that there are few available data, but we nonetheless report on an increasing number of well-designed, theory-driven, experimental approaches. Combining demography and genetics from both theoretical and empirical perspectives highlights novel and exciting avenues for research on the biology of small, introduced populations, and great potential for improving both our understanding and practice of biological control. PMID:22949919

Synthetic biology and metabolic engineering.

PubMed

Stephanopoulos, Gregory

2012-11-16

Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.

EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes.

PubMed

Danaci, Hasan Fehmi; Cetin-Atalay, Rengul; Atalay, Volkan

2018-03-26

Visualizing large-scale data produced by the high throughput experiments as a biological graph leads to better understanding and analysis. This study describes a customized force-directed layout algorithm, EClerize, for biological graphs that represent pathways in which the nodes are associated with Enzyme Commission (EC) attributes. The nodes with the same EC class numbers are treated as members of the same cluster. Positions of nodes are then determined based on both the biological similarity and the connection structure. EClerize minimizes the intra-cluster distance, that is the distance between the nodes of the same EC cluster and maximizes the inter-cluster distance, that is the distance between two distinct EC clusters. EClerize is tested on a number of biological pathways and the improvement brought in is presented with respect to the original algorithm. EClerize is available as a plug-in to cytoscape ( http://apps.cytoscape.org/apps/eclerize ).

A basis for a visual language for describing, archiving and analyzing functional models of complex biological systems

PubMed Central

Cook, Daniel L; Farley, Joel F; Tapscott, Stephen J

2001-01-01

Background: We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. Results: We outline here a conceptual basis for designing such a language and describe BioD, a prototype language that we have used to explore the utility and feasibility of this approach to functional biology. Using example models, we demonstrate that a rather limited lexicon of icons and arrows suffices to describe complex cell-biological systems as discrete models that can be posted and linked on the internet. Conclusions: Given available computer and internet technology, BioD may be implemented as an extensible, multidisciplinary language that can be used to archive functional systems knowledge and be extended to support both qualitative and quantitative functional analysis. PMID:11305940

Synthetic biology: advancing the design of diverse genetic systems

PubMed Central

Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

2013-01-01

A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

It’s More Than Stamp Collecting: How Genome Sequencing Can Unify Biological Research

PubMed Central

Richards, Stephen

2015-01-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, whilst the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to “Big Science” survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. PMID:26003218

It's more than stamp collecting: how genome sequencing can unify biological research.

PubMed

Richards, Stephen

2015-07-01

The availability of reference genome sequences, especially the human reference, has revolutionized the study of biology. However, while the genomes of some species have been fully sequenced, a wide range of biological problems still cannot be effectively studied for lack of genome sequence information. Here, I identify neglected areas of biology and describe how both targeted species sequencing and more broad taxonomic surveys of the tree of life can address important biological questions. I enumerate the significant benefits that would accrue from sequencing a broader range of taxa, as well as discuss the technical advances in sequencing and assembly methods that would allow for wide-ranging application of whole-genome analysis. Finally, I suggest that in addition to 'big science' survey initiatives to sequence the tree of life, a modified infrastructure-funding paradigm would better support reference genome sequence generation for research communities most in need. Copyright © 2015 Elsevier Ltd. All rights reserved.

Parameter estimation using meta-heuristics in systems biology: a comprehensive review.

PubMed

Sun, Jianyong; Garibaldi, Jonathan M; Hodgman, Charlie

2012-01-01

This paper gives a comprehensive review of the application of meta-heuristics to optimization problems in systems biology, mainly focussing on the parameter estimation problem (also called the inverse problem or model calibration). It is intended for either the system biologist who wishes to learn more about the various optimization techniques available and/or the meta-heuristic optimizer who is interested in applying such techniques to problems in systems biology. First, the parameter estimation problems emerging from different areas of systems biology are described from the point of view of machine learning. Brief descriptions of various meta-heuristics developed for these problems follow, along with outlines of their advantages and disadvantages. Several important issues in applying meta-heuristics to the systems biology modelling problem are addressed, including the reliability and identifiability of model parameters, optimal design of experiments, and so on. Finally, we highlight some possible future research directions in this field.

Visualizing time-related data in biology, a review

PubMed Central

Secrier, Maria; Schneider, Reinhard

2014-01-01

Time is of the essence in biology as in so much else. For example, monitoring disease progression or the timing of developmental defects is important for the processes of drug discovery and therapy trials. Furthermore, an understanding of the basic dynamics of biological phenomena that are often strictly time regulated (e.g. circadian rhythms) is needed to make accurate inferences about the evolution of biological processes. Recent advances in technologies have enabled us to measure timing effects more accurately and in more detail. This has driven related advances in visualization and analysis tools that try to effectively exploit this data. Beyond timeline plots, notable attempts at more involved temporal interpretation have been made in recent years, but awareness of the available resources is still limited within the scientific community. Here, we review some advances in biological visualization of time-driven processes and consider how they aid data analysis and interpretation. PMID:23585583

Light microscopy applications in systems biology: opportunities and challenges

PubMed Central

2013-01-01

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology. PMID:23578051

Establishing a national biological laboratory safety and security monitoring program.

PubMed

Blaine, James W

2012-12-01

The growing concern over the potential use of biological agents as weapons and the continuing work of the Biological Weapons Convention has promoted an interest in establishing national biological laboratory biosafety and biosecurity monitoring programs. The challenges and issues that should be considered by governments, or organizations, embarking on the creation of a biological laboratory biosafety and biosecurity monitoring program are discussed in this article. The discussion focuses on the following questions: Is there critical infrastructure support available? What should be the program focus? Who should be monitored? Who should do the monitoring? How extensive should the monitoring be? What standards and requirements should be used? What are the consequences if a laboratory does not meet the requirements or is not willing to comply? Would the program achieve the results intended? What are the program costs? The success of a monitoring program can depend on how the government, or organization, responds to these questions.

Neural system modeling and simulation using Hybrid Functional Petri Net.

PubMed

Tang, Yin; Wang, Fei

2012-02-01

The Petri net formalism has been proved to be powerful in biological modeling. It not only boasts of a most intuitive graphical presentation but also combines the methods of classical systems biology with the discrete modeling technique. Hybrid Functional Petri Net (HFPN) was proposed specially for biological system modeling. An array of well-constructed biological models using HFPN yielded very interesting results. In this paper, we propose a method to represent neural system behavior, where biochemistry and electrical chemistry are both included using the Petri net formalism. We built a model for the adrenergic system using HFPN and employed quantitative analysis. Our simulation results match the biological data well, showing that the model is very effective. Predictions made on our model further manifest the modeling power of HFPN and improve the understanding of the adrenergic system. The file of our model and more results with their analysis are available in our supplementary material.

Using Petri Net Tools to Study Properties and Dynamics of Biological Systems

PubMed Central

Peleg, Mor; Rubin, Daniel; Altman, Russ B.

2005-01-01

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats. PMID:15561791

EcoFlex: A Multifunctional MoClo Kit for E. coli Synthetic Biology.

PubMed

Lai, Hung-En; Moore, Simon; Polizzi, Karen; Freemont, Paul

2018-01-01

Development of advanced synthetic biology tools is always in demand since they act as a platform technology to enable rapid prototyping of biological constructs in a high-throughput manner. EcoFlex is a modular cloning (MoClo) kit for Escherichia coli and is based on the Golden Gate principles, whereby Type IIS restriction enzymes (BsaI, BsmBI, BpiI) are used to construct modular genetic elements (biological parts) in a bottom-up approach. Here, we describe a collection of plasmids that stores various biological parts including promoters, RBSs, terminators, ORFs, and destination vectors, each encoding compatible overhangs allowing hierarchical assembly into single transcription units or a full-length polycistronic operon or biosynthetic pathway. A secondary module cloning site is also available for pathway optimization, in order to limit library size if necessary. Here, we show the utility of EcoFlex using the violacein biosynthesis pathway as an example.

Relations among Functional Systems in Behavior Analysis

PubMed Central

Thompson, Travis

2007-01-01

This paper proposes that an organism's integrated repertoire of operant behavior has the status of a biological system, similar to other biological systems, like the nervous, cardiovascular, or immune systems. Evidence from a number of sources indicates that the distinctions between biological and behavioral events is often misleading, engendering counterproductive explanatory controversy. A good deal of what is viewed as biological (often thought to be inaccessible or hypothetical) can become publicly measurable variables using currently available and developing technologies. Moreover, such endogenous variables can serve as establishing operations, discriminative stimuli, conjoint mediating events, and maintaining consequences within a functional analysis of behavior and need not lead to reductionistic explanation. I suggest that explanatory misunderstandings often arise from conflating different levels of analysis and that behavior analysis can extend its reach by identifying variables operating within a functional analysis that also serve functions in other biological systems. PMID:17575907

Tissue regeneration during tissue expansion and choosing an expander

PubMed Central

Agrawal, K.; Agrawal, S.

2012-01-01

This paper reviews the various aspects of tissue regeneration during the process of tissue expansion. “Creep” and mechanical and biological “stretch” are responsible for expansion. During expansion, the epidermis thickens, the dermis thins out, vascularity improves, significant angiogenesis occurs, hair telogen phase becomes shorter and the peripheral nerves, vessels and muscle fibres lengthen. Expansion is associated with molecular changes in the tissue. Almost all these biological changes are reversible after the removal of the expander.This study is also aimed at reviewing the difficulty in deciding the volume and dimension of the expander for a defect. Basic mathematical formulae and the computer programmes for calculating the dimension of tissue expanders, although available in the literature, are not popular. A user-friendly computer programme based on the easily available Microsoft Excel spread sheet has been introduced. When we feed the area of defect and base dimension of the donor area or tissue expander, this programme calculates the volume and height of the expander. The shape of the expander is decided clinically based on the availability of the donor area and the designing of the future tissue movement. Today, tissue expansion is better understood biologically and mechanically. Clinical judgement remains indispensable in choosing the size and shape of the tissue expander. PMID:22754146

BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks

PubMed Central

Rialle, Stéphanie; Felicori, Liza; Dias-Lopes, Camila; Pérès, Sabine; El Atia, Sanaâ; Thierry, Alain R.; Amar, Patrick; Molina, Franck

2010-01-01

Motivation: Synthetic biology studies how to design and construct biological systems with functions that do not exist in nature. Biochemical networks, although easier to control, have been used less frequently than genetic networks as a base to build a synthetic system. To date, no clear engineering principles exist to design such cell-free biochemical networks. Results: We describe a methodology for the construction of synthetic biochemical networks based on three main steps: design, simulation and experimental validation. We developed BioNetCAD to help users to go through these steps. BioNetCAD allows designing abstract networks that can be implemented thanks to CompuBioTicDB, a database of parts for synthetic biology. BioNetCAD enables also simulations with the HSim software and the classical Ordinary Differential Equations (ODE). We demonstrate with a case study that BioNetCAD can rationalize and reduce further experimental validation during the construction of a biochemical network. Availability and implementation: BioNetCAD is freely available at http://www.sysdiag.cnrs.fr/BioNetCAD. It is implemented in Java and supported on MS Windows. CompuBioTicDB is freely accessible at http://compubiotic.sysdiag.cnrs.fr/ Contact: stephanie.rialle@sysdiag.cnrs.fr; franck.molina@sysdiag.cnrs.fr Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20628073

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology[OPEN

PubMed Central

Waese, Jamie; Fan, Jim; Yu, Hans; Fucile, Geoffrey; Shi, Ruian; Cumming, Matthew; Town, Chris; Stuerzlinger, Wolfgang

2017-01-01

A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research. PMID:28808136

Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

PubMed

Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

2017-03-01

Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

An exploration of student experiences of using biology podcasts in nursing training

PubMed Central

2013-01-01

Background Students regard biological science as one of the most difficult components of the nursing curriculum. However, a good understanding of this area is essential for effective nursing practice. The aim of this study was to explore nursing students’ perceptions of the usefulness of supplementary biology podcasts for their learning. Methods Biological science podcasts (n = 9) were made available to first-year nursing students (n = 189) as supplementary learning tools. On completion of their first year, students were asked to complete a survey which investigated the frequency of their podcast use, reasons for use and their perception of the usefulness of podcasts as a learning tool. 153 of these students participated in the survey study (80.9%). Two focus groups were conducted with students (n = 6) to gain a detailed understanding of student experiences of the usefulness of the podcasts for their learning. Results Survey data demonstrated that most students (71%) accessed at least one podcast. The majority of students who reported accessing podcasts agreed that they were useful as learning tools (83%), revision aids (83%) and that they helped promote understanding of course materials (72%). Focus group participants discussed how they found podcasts especially useful in terms of revision. Students valued being able to repeatedly access the lecture materials, and appreciated having access to podcasts from a range of lecturers. Focus group members discussed the benefits of live recordings, in terms of valuing the information gleaned from questions asked during the lecture sessions, although there were concerns about the level of background noise in live recordings. Lack of awareness of the availability of podcasts was an issue raised by participants in both the survey component and the focus groups and this negatively impacted on podcast use. Conclusions Nursing students found the availability of biology podcasts helpful for their learning. Successful implementation of these tools to support learning requires teaching staff to understand and promote the importance of these tools. PMID:23360078

Differential Nutrient Limitation of Soil Microbial Biomass and Metabolic Quotients (qCO2): Is There a Biological Stoichiometry of Soil Microbes?

PubMed Central

Hartman, Wyatt H.; Richardson, Curtis J.

2013-01-01

Background Variation in microbial metabolism poses one of the greatest current uncertainties in models of global carbon cycling, and is particularly poorly understood in soils. Biological Stoichiometry theory describes biochemical mechanisms linking metabolic rates with variation in the elemental composition of cells and organisms, and has been widely observed in animals, plants, and plankton. However, this theory has not been widely tested in microbes, which are considered to have fixed ratios of major elements in soils. Methodology/Principal Findings To determine whether Biological Stoichiometry underlies patterns of soil microbial metabolism, we compiled published data on microbial biomass carbon (C), nitrogen (N), and phosphorus (P) pools in soils spanning the global range of climate, vegetation, and land use types. We compared element ratios in microbial biomass pools to the metabolic quotient qCO2 (respiration per unit biomass), where soil C mineralization was simultaneously measured in controlled incubations. Although microbial C, N, and P stoichiometry appeared to follow somewhat constrained allometric relationships at the global scale, we found significant variation in the C∶N∶P ratios of soil microbes across land use and habitat types, and size-dependent scaling of microbial C∶N and C∶P (but not N∶P) ratios. Microbial stoichiometry and metabolic quotients were also weakly correlated as suggested by Biological Stoichiometry theory. Importantly, we found that while soil microbial biomass appeared constrained by soil N availability, microbial metabolic rates (qCO2) were most strongly associated with inorganic P availability. Conclusions/Significance Our findings appear consistent with the model of cellular metabolism described by Biological Stoichiometry theory, where biomass is limited by N needed to build proteins, but rates of protein synthesis are limited by the high P demands of ribosomes. Incorporation of these physiological processes may improve models of carbon cycling and understanding of the effects of nutrient availability on soil C turnover across terrestrial and wetland habitats. PMID:23526933

CEBS object model for systems biology data, SysBio-OM.

PubMed

Xirasagar, Sandhya; Gustafson, Scott; Merrick, B Alex; Tomer, Kenneth B; Stasiewicz, Stanley; Chan, Denny D; Yost, Kenneth J; Yates, John R; Sumner, Susan; Xiao, Nianqing; Waters, Michael D

2004-09-01

To promote a systems biology approach to understanding the biological effects of environmental stressors, the Chemical Effects in Biological Systems (CEBS) knowledge base is being developed to house data from multiple complex data streams in a systems friendly manner that will accommodate extensive querying from users. Unified data representation via a single object model will greatly aid in integrating data storage and management, and facilitate reuse of software to analyze and display data resulting from diverse differential expression or differential profile technologies. Data streams include, but are not limited to, gene expression analysis (transcriptomics), protein expression and protein-protein interaction analysis (proteomics) and changes in low molecular weight metabolite levels (metabolomics). To enable the integration of microarray gene expression, proteomics and metabolomics data in the CEBS system, we designed an object model, Systems Biology Object Model (SysBio-OM). The model is comprehensive and leverages other open source efforts, namely the MicroArray Gene Expression Object Model (MAGE-OM) and the Proteomics Experiment Data Repository (PEDRo) object model. SysBio-OM is designed by extending MAGE-OM to represent protein expression data elements (including those from PEDRo), protein-protein interaction and metabolomics data. SysBio-OM promotes the standardization of data representation and data quality by facilitating the capture of the minimum annotation required for an experiment. Such standardization refines the accuracy of data mining and interpretation. The open source SysBio-OM model, which can be implemented on varied computing platforms is presented here. A universal modeling language depiction of the entire SysBio-OM is available at http://cebs.niehs.nih.gov/SysBioOM/. The Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. The database and interface are being built to implement the model and will be available for public use at http://cebs.niehs.nih.gov.

Determination of suitable chemical extraction methods for the available iron content of brown forest soils in Turkey

NASA Astrophysics Data System (ADS)

Adiloglu, Aydin

2006-09-01

The aim of this research was to determine the available iron (Fe) content of brown forest soils of Edirne Province and the most suitable chemical extraction method. Eight chemical extraction methods (the 0.005 M DTPA + 0.01 M CaCl2 + 0.1 MTEA, 0.05 M HCl + 0.012 M H2SO4, 1 M NH4OAc (pH: 4.8), 0.01 M EDTA + 1 M NH4OAc, 1 M MgCl2, 0.01 M EDTA + 1 M (NH4)2CO3, 0.005 M DTPA + 1 M NH4HCO3, and 0.001 M EDDHA methods) and six biological indices (the dry matter yield, Fe concentration, Fe uptake, relative dry matter yield, relative Fe concentration, and relative Fe uptake) were compared. The biological indices were determined with barley (Hordeum vulgare L.) grown under greenhouse conditions. At the end of the experiment, the highest correlation coefficients (r) were determined to be between the 0.005 M DTPA + 0.01 M CaCl2 + 0.1 M TEA method and the biological indices and between the 0.005 M DTPA + 1 M NH4HCO3 method and the biological indices. The corresponding correlation coefficients (r) for the 0.005 M DTPA + 0.01 M CaCl2 + 0.1 M TEA method and the six biological indices were 0.621**, 0.823**, 0.810** 0.433**, 0.558**, and 0.640**, respectively. For the 0.005 M DTPA + 1 M NH4HCO3 method, these coefficients were equal to 0.618**, 0.520**, 0.679**, 0.521**, 0.492**, and 0.641**, respectively (** indicate the validity of the relationships at p < 0.01) These extraction methods, out of all the methods tested, were suggested for the determination of the available Fe content of the brown forest soils.

Synergistic Synthetic Biology: Units in Concert

PubMed Central

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications. PMID:25022769

Synergistic Synthetic Biology: Units in Concert.

PubMed

Trosset, Jean-Yves; Carbonell, Pablo

2013-01-01

Synthetic biology aims at translating the methods and strategies from engineering into biology in order to streamline the design and construction of biological devices through standardized parts. Modular synthetic biology devices are designed by means of an adequate elimination of cross-talk that makes circuits orthogonal and specific. To that end, synthetic constructs need to be adequately optimized through in silico modeling by choosing the right complement of genetic parts and by experimental tuning through directed evolution and craftsmanship. In this review, we consider an additional and complementary tool available to the synthetic biologist for innovative design and successful construction of desired circuit functionalities: biological synergies. Synergy is a prevalent emergent property in biological systems that arises from the concerted action of multiple factors producing an amplification or cancelation effect compared with individual actions alone. Synergies appear in domains as diverse as those involved in chemical and protein activity, polypharmacology, and metabolic pathway complementarity. In conventional synthetic biology designs, synergistic cross-talk between parts and modules is generally attenuated in order to verify their orthogonality. Synergistic interactions, however, can induce emergent behavior that might prove useful for synthetic biology applications, like in functional circuit design, multi-drug treatment, or in sensing and delivery devices. Synergistic design principles are therefore complementary to those coming from orthogonal design and may provide added value to synthetic biology applications. The appropriate modeling, characterization, and design of synergies between biological parts and units will allow the discovery of yet unforeseeable, novel synthetic biology applications.

2014 update of the Consensus Statement of the Spanish Society of Rheumatology on the use of biological therapies in rheumatoid arthritis.

PubMed

Sanmartí, Raimon; García-Rodríguez, Susana; Álvaro-Gracia, José María; Andreu, José Luis; Balsa, Alejandro; Cáliz, Rafael; Fernández-Nebro, Antonio; Ferraz-Amaro, Iván; Gómez-Reino, Juan Jesús; González-Álvaro, Isidoro; Martín-Mola, Emilio; Martínez-Taboada, Víctor Manuel; Ortiz, Ana M; Tornero, Jesús; Marsal, Sara; Moreno-Muelas, José Vicente

2015-01-01

To establish recommendations for the management of patients with rheumatoid arthritis (RA) to serve as a reference for all health professionals involved in the care of these patients, and focusing on the role of available synthetic and biologic disease-modifying antirheumatic drugs (DMARDs). Consensual recommendations were agreed on by a panel of 14 experts selected by the Spanish Society of Rheumatology (SER). The available scientific evidence was collected by updating three systematic reviews (SR) used for the EULAR 2013 recommendations. A new SR was added to answer an additional question. The literature review of the scientific evidence was made by the SER reviewer's group. The level of evidence and the degree of recommendation was classified according to the Oxford Centre for Evidence-Based Medicine system. A Delphi panel was used to evaluate the level of agreement between panellists (strength of recommendation). Thirteen recommendations for the management of adult RA were emitted. The therapeutic objective should be to treat patients in the early phases of the disease with the aim of achieving clinical remission, with methotrexate playing a central role in the therapeutic strategy of RA as the reference synthetic DMARD. Indications for biologic DMARDs were updated and the concept of the optimization of biologicals was introduced. We present the fifth update of the SER recommendations for the management of RA with synthetic and biologic DMARDs. Copyright © 2015 Elsevier España, S.L.U. All rights reserved.

Improving integrative searching of systems chemical biology data using semantic annotation.

PubMed

Chen, Bin; Ding, Ying; Wild, David J

2012-03-08

Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

Petunia, Your Next Supermodel?

PubMed Central

Vandenbussche, Michiel; Chambrier, Pierre; Rodrigues Bento, Suzanne; Morel, Patrice

2016-01-01

Plant biology in general, and plant evo–devo in particular would strongly benefit from a broader range of available model systems. In recent years, technological advances have facilitated the analysis and comparison of individual gene functions in multiple species, representing now a fairly wide taxonomic range of the plant kingdom. Because genes are embedded in gene networks, studying evolution of gene function ultimately should be put in the context of studying the evolution of entire gene networks, since changes in the function of a single gene will normally go together with further changes in its network environment. For this reason, plant comparative biology/evo–devo will require the availability of a defined set of ‘super’ models occupying key taxonomic positions, in which performing gene functional analysis and testing genetic interactions ideally is as straightforward as, e.g., in Arabidopsis. Here we review why petunia has the potential to become one of these future supermodels, as a representative of the Asterid clade. We will first detail its intrinsic qualities as a model system. Next, we highlight how the revolution in sequencing technologies will now finally allows exploitation of the petunia system to its full potential, despite that petunia has already a long history as a model in plant molecular biology and genetics. We conclude with a series of arguments in favor of a more diversified multi-model approach in plant biology, and we point out where the petunia model system may further play a role, based on its biological features and molecular toolkit. PMID:26870078

Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces.

PubMed

Bordner, Andrew J; Gorin, Andrey A

2008-05-12

Protein-protein interactions are ubiquitous and essential for all cellular processes. High-resolution X-ray crystallographic structures of protein complexes can reveal the details of their function and provide a basis for many computational and experimental approaches. Differentiation between biological and non-biological contacts and reconstruction of the intact complex is a challenging computational problem. A successful solution can provide additional insights into the fundamental principles of biological recognition and reduce errors in many algorithms and databases utilizing interaction information extracted from the Protein Data Bank (PDB). We have developed a method for identifying protein complexes in the PDB X-ray structures by a four step procedure: (1) comprehensively collecting all protein-protein interfaces; (2) clustering similar protein-protein interfaces together; (3) estimating the probability that each cluster is relevant based on a diverse set of properties; and (4) combining these scores for each PDB entry in order to predict the complex structure. The resulting clusters of biologically relevant interfaces provide a reliable catalog of evolutionary conserved protein-protein interactions. These interfaces, as well as the predicted protein complexes, are available from the Protein Interface Server (PInS) website (see Availability and requirements section). Our method demonstrates an almost two-fold reduction of the annotation error rate as evaluated on a large benchmark set of complexes validated from the literature. We also estimate relative contributions of each interface property to the accurate discrimination of biologically relevant interfaces and discuss possible directions for further improving the prediction method.

Biological pathways of exposure and ecotoxicity values for uranium and associated radionuclides: Chapter D in Hydrological, geological, and biological site characterization of breccia pipe uranium deposits in Northern Arizona

USGS Publications Warehouse

Hinck, Jo E.; Linder, Greg L.; Finger, Susan E.; Little, Edward E.; Tillitt, Donald E.; Kuhne, Wendy

2010-01-01

This chapter compiles available chemical and radiation toxicity information for plants and animals from the scientific literature on naturally occurring uranium and associated radionuclides. Specifically, chemical and radiation hazards associated with radionuclides in the uranium decay series including uranium, thallium, thorium, bismuth, radium, radon, protactinium, polonium, actinium, and francium were the focus of the literature compilation. In addition, exposure pathways and a food web specific to the segregation areas were developed. Major biological exposure pathways considered were ingestion, inhalation, absorption, and bioaccumulation, and biota categories included microbes, invertebrates, plants, fishes, amphibians, reptiles, birds, and mammals. These data were developed for incorporation into a risk assessment to be conducted as part of an environmental impact statement for the Bureau of Land Management, which would identify representative plants and animals and their relative sensitivities to exposure of uranium and associated radionuclides. This chapter provides pertinent information to aid in the development of such an ecological risk assessment but does not estimate or derive guidance thresholds for radionuclides associated with uranium. Previous studies have not attempted to quantify the risks to biota caused directly by the chemical or radiation releases at uranium mining sites, although some information is available for uranium mill tailings and uranium mine closure activities. Research into the biological impacts of uranium exposure is strongly biased towards human health and exposure related to enriched or depleted uranium associated with the nuclear energy industry rather than naturally occurring uranium associated with uranium mining. Nevertheless, studies have reported that uranium and other radionuclides can affect the survival, growth, and reproduction of plants and animals. Exposure to chemical and radiation hazards is influenced by a plant’s or an animal’s life history and surrounding environment. Various species of plants, invertebrates, fishes, amphibians, reptiles, birds, and mammals found in the segregation areas that are considered species of concern by State and Federal agencies were included in the development of the site-specific food web. The utilization of subterranean habitats (burrows in uranium-rich areas, burrows in waste rock piles or reclaimed mining areas, mine tunnels) in the seasonally variable but consistently hot, arid environment is of particular concern in the segregation areas. Certain species of reptiles, amphibians, birds, and mammals in the segregation areas spend significant amounts of time in burrows where they can inhale or ingest uranium and other radionuclides through digging, eating, preening, and hibernating. Herbivores may also be exposed though the ingestion of radionuclides that have been aerially deposited on vegetation. Measured tissues concentrations of uranium and other radionuclides are not available for any species of concern in the segregation areas. The sensitivity of these animals to uranium exposure is unknown based on the existing scientific literature, and species-specific uranium presumptive effects levels were only available for two endangered fish species known to inhabit the segregation areas. Overall, the chemical toxicity data available for biological receptors of concern were limited, although chemical and radiation toxicity guidance values are available from several sources. However, caution should be used when directly applying these values to northern Arizona given the unique habitat and life history strategies of biological receptors in the segregation areas and the fact that some guidance values are based on models rather than empirical (laboratory or field) data. No chemical toxicity information based on empirical data is available for reptiles, birds, or wild mammals; therefore, the risks associated with uranium and other radionuclides are unknown for these biota.

The role of adalimumab in rheumatic and autoimmune disorders: comparison with other biologic agents

PubMed Central

Reimold, Andreas M

2012-01-01

Adalimumab (ADA) is a biologic medication that dampens inflammatory pathways by binding to the cytokine tumor necrosis factor alpha. The US Food and Drug Administration has approved ADA as a medication for use in rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis, Crohn’s disease, psoriasis, and juvenile idiopathic arthritis. This year marks 10 years of clinical experience with ADA. Long-term extension studies of some of the initial clinical trials, as well as data from large patient registries, are demonstrating ongoing benefit for responders. Potential side effects such as increased risk of infection, lymphoma, congestive heart failure, and demyelination continue to be examined, as the available data are not unanimous in showing an increase in incidence. In balancing both the advantages and the disadvantages of using ADA, the drug’s overall effectiveness and its availability for use in patients with hepatic or renal comorbidities are weighed against the high cost. ADA is expected to have a leading role in the treatment of rheumatoid arthritis and other inflammatory conditions for years to come. Future studies will need to address the optimal sequence of disease-modifying antirheumatic drugs and biologics to use, combinations of disease-modifying antirheumatic drugs and biologics, and head-to-head comparisons of biologics in clinical trials. For those who go into clinical remission on an anti-tumor necrosis factor medication, unanswered questions remain about identifying the patients who can maintain the remission off all drugs, or at least off injected medication. Given the cost of biologic drugs, even studies that increase the interval between drug doses in well-controlled patients could provide financial benefits. PMID:27790010

The Future is Now – Biologics for Non-Infectious Pediatric Anterior Uveitis

PubMed Central

Lerman, Melissa A.; Rabinovich, C. Egla

2015-01-01

Anterior uveitis (AU), inflammation of the iris, choroid, or ciliary body, can cause significant eye morbidity, including visual loss. In the pediatric age group, the most common underlying diagnosis for AU is juvenile idiopathic associated uveitis and idiopathic AU, which are the focus of this paper. AU is often resistant to medications such as topical corticosteroids and methotrexate. In the past 15 years, biologic agents (biologics) have transformed treatment. In this review, we discuss those in widespread use and those with more theoretical applications for anterior uveitis. Tumor Necrosis Factor alpha inhibitors (anti-TNFα) have been available the longest and are used widely to treat pediatric uveitis. The effects of anti-TNFα in children are described mostly in small retrospective case series. Together, the literature suggests that the majority of children treated with anti-TNFα achieve decreased uveitis activity and reduce corticosteroid burden. However, many will have disease flares even on treatment. Only a few small studies directly compare outcomes between alternate anti-TNFα (infliximab and adalimumab). The use of different uveitis grading systems, inclusion criteria, and outcome measures, makes cross-study comparisons difficult. Whether the achievement and maintenance of inactive disease occurs more frequently with certain anti-TNFα remains controversial. Newer biologics that modulate the immune system differently (e.g., interfere with TH17 activation through IL-17a and IL-6 blockade, limit T lymphocyte costimulation, and deplete B lymphocytes), have shown promise for uveitis. Studies of these agents are small and include mostly adults. Additional biologics are also being explored to treat uveitis. With their advent, we are hopeful that outcomes will ultimately be improved for children with AU. With many biologics available, much work remains to identify the optimal inflammatory pathway to target in AU. PMID:25893479

The Future Is Now: Biologics for Non-Infectious Pediatric Anterior Uveitis.

PubMed

Lerman, Melissa A; Rabinovich, C Egla

2015-08-01

Anterior uveitis (AU), inflammation of the iris, choroid or ciliary body, can cause significant eye morbidity, including visual loss. In the pediatric age group, the most common underlying diagnosis for AU is juvenile idiopathic associated uveitis and idiopathic AU, which are the focus of this paper. AU is often resistant to medications such as topical corticosteroids and methotrexate. In the past 15 years, biologic agents (biologics) have transformed treatment. In this review, we discuss those in widespread use and those with more theoretical applications for anterior uveitis. Tumor necrosis factor alpha inhibitors (anti-TNFα) have been available the longest and are used widely to treat pediatric uveitis. The effects of anti-TNFα in children are described mostly in small retrospective case series. Together, the literature suggests that the majority of children treated with anti-TNFα achieve decreased uveitis activity and reduced corticosteroid burden. However, many will have disease flares even on treatment. Only a few small studies directly compare outcomes between alternate anti-TNFα (infliximab and adalimumab). The use of different uveitis grading systems, inclusion criteria, and outcome measures makes cross-study comparisons difficult. Whether the achievement and maintenance of inactive disease occurs more frequently with certain anti-TNFα remains controversial. Newer biologics that modulate the immune system differently (e.g., interfere with Th17 activation through IL-17a and IL-6 blockade, limit T lymphocyte costimulation, and deplete B lymphocytes), have shown promise for uveitis. Studies of these agents are small and include mostly adults. Additional biologics are also being explored to treat uveitis. With their advent, we are hopeful that outcomes will ultimately be improved for children with AU. With many biologics available, much work remains to identify the optimal inflammatory pathway to target in AU.

Predicting Student Success in a Major's Introductory Biology Course via Logistic Regression Analysis of Scientific Reasoning Ability and Mathematics Scores

ERIC Educational Resources Information Center

Thompson, E. David; Bowling, Bethany V.; Markle, Ross E.

2018-01-01

Studies over the last 30 years have considered various factors related to student success in introductory biology courses. While much of the available literature suggests that the best predictors of success in a college course are prior college grade point average (GPA) and class attendance, faculty often require a valuable predictor of success in…

Selective turn-on fluorescent probes for imaging hydrogen sulfide in living cells.

PubMed

Montoya, Leticia A; Pluth, Michael D

2012-05-16

Hydrogen sulfide (H(2)S) is an important biological messenger but few biologically-compatible methods are available for its detection. Here we report two bright fluorescent probes that are selective for H(2)S over cysteine, glutathione and other reactive sulfur, nitrogen, and oxygen species. Both probes are demonstrated to detect H(2)S in live cells. This journal is © The Royal Society of Chemistry 2012

The role of drug profiles as similarity metrics: applications to repurposing, adverse effects detection and drug-drug interactions.

PubMed

Vilar, Santiago; Hripcsak, George

2017-07-01

Explosion of the availability of big data sources along with the development in computational methods provides a useful framework to study drugs' actions, such as interactions with pharmacological targets and off-targets. Databases related to protein interactions, adverse effects and genomic profiles are available to be used for the construction of computational models. In this article, we focus on the description of biological profiles for drugs that can be used as a system to compare similarity and create methods to predict and analyze drugs' actions. We highlight profiles constructed with different biological data, such as target-protein interactions, gene expression measurements, adverse effects and disease profiles. We focus on the discovery of new targets or pathways for drugs already in the pharmaceutical market, also called drug repurposing, in the interaction with off-targets responsible for adverse reactions and in drug-drug interaction analysis. The current and future applications, strengths and challenges facing all these methods are also discussed. Biological profiles or signatures are an important source of data generation to deeply analyze biological actions with important implications in drug-related studies. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Extending gene ontology with gene association networks.

PubMed

Peng, Jiajie; Wang, Tao; Wang, Jixuan; Wang, Yadong; Chen, Jin

2016-04-15

Gene ontology (GO) is a widely used resource to describe the attributes for gene products. However, automatic GO maintenance remains to be difficult because of the complex logical reasoning and the need of biological knowledge that are not explicitly represented in the GO. The existing studies either construct whole GO based on network data or only infer the relations between existing GO terms. None is purposed to add new terms automatically to the existing GO. We proposed a new algorithm 'GOExtender' to efficiently identify all the connected gene pairs labeled by the same parent GO terms. GOExtender is used to predict new GO terms with biological network data, and connect them to the existing GO. Evaluation tests on biological process and cellular component categories of different GO releases showed that GOExtender can extend new GO terms automatically based on the biological network. Furthermore, we applied GOExtender to the recent release of GO and discovered new GO terms with strong support from literature. Software and supplementary document are available at www.msu.edu/%7Ejinchen/GOExtender jinchen@msu.edu or ydwang@hit.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The biological safety of condom material can be determined using an in vitro cell culture system.

PubMed

Motsoane, N A; Pretorius, E; Bester, M J; Becker, P J

2001-01-01

Latex products have long been recognized as a cause of latex protein allergy. The increased usage of latex gloves, with the consequent increased occurrence of latex allergies appears to have escalated with increasing awareness of the transmission of HIV-AIDS and other infections. The use of condoms as a means to prevent the transmission of STD's (sexually transmitted diseases) and HIV-AIDS has been widely promoted. Although extensive testing is done to evaluate the physical quality of condoms, no information is available regarding the biological safety of condoms. This study was undertaken to determine the effects of short-term exposure to physiological levels of condom surface material on cell viability (MTT assay) and cell growth (crystal violet assay). A direct contact cell culture testing method (FDA test method F813-83 used to evaluate the cytotoxic potential of medical materials and devices) was used. The modified test method was found to be a sensitive test system for the evaluation of the biological safety of condoms. This study reveals the importance of evaluating the biological safety of all condoms that are commercially available, because of the potential health risk that may be associated with prolonged use of certain types of condoms.

Energy as a Constraint on Habitability in the Subsurface

NASA Astrophysics Data System (ADS)

Hoehler, T.

2008-12-01

All living things must obtain energy from the environment to grow, to maintain a metabolic steady state, or simply to preserve viability. The availability of energy sources in the environment thus represents a key factor in determining the size, distribution, and activity of biological populations, and ultimately constrains the possibility for life itself. Lacking the abundant energy provided by solar radiation or the products of oxygenic photosynthesis, life in subsurface environments may be limited by energy availability as much as any other factor. The biological requirement for energy is expressed in two dimensions - analogous to the power and voltage requirements of electrical devices - and consideration and quantification of these requirements establishes quantitative boundary conditions on subsurface habitability. The magnitude of these requirements depends significantly on physicochemical environment, as does the provision of biologically-accessible energy from subsurface sources. With this conceptual basis, we are developing an 'energy balance' model that is designed to ultimately predict the habitability of a given environment, with respect to a given metabolism, in quantitative terms (as 'biomass density potential'). The model will develop from conceptual to quantitative as experimental and observational work constrains and quantifies, in natural populations adapted to low energy conditions, the magnitude of the biological energy requirements and the impacts of physicochemical environmental conditions on energy demand and supply.

A Problem-Sorting Task Detects Changes in Undergraduate Biological Expertise over a Single Semester.

PubMed

Hoskinson, Anne-Marie; Maher, Jessica Middlemis; Bekkering, Cody; Ebert-May, Diane

2017-01-01

Calls for undergraduate biology reform share similar goals: to produce people who can organize, use, connect, and communicate about biological knowledge. Achieving these goals requires students to gain disciplinary expertise. Experts organize, access, and apply disciplinary knowledge differently than novices, and expertise is measurable. By asking introductory biology students to sort biological problems, we investigated whether they changed how they organized and linked biological ideas over one semester of introductory biology. We administered the Biology Card Sorting Task to 751 students enrolled in their first or second introductory biology course focusing on either cellular-molecular or organismal-population topics, under structured or unstructured sorting conditions. Students used a combination of superficial, deep, and yet-uncharacterized ways of organizing and connecting biological knowledge. In some cases, this translated to more expert-like ways of organizing knowledge over a single semester, best predicted by whether students were enrolled in their first or second semester of biology and by the sorting condition completed. In addition to illuminating differences between novices and experts, our results show that card sorting is a robust way of detecting changes in novices' biological expertise-even in heterogeneous populations of novice biology students over the time span of a single semester. © 2017 A.-M. Hoskinson et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License(http://creativecommons.org/licenses/by-nc-sa/3.0).

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs

PubMed Central

Weeding, Emma; Houle, Jason

2010-01-01

Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications. PMID:20639523

Investigating Novice and Expert Conceptions of Genetically Modified Organisms.

PubMed

Potter, Lisa M; Bissonnette, Sarah A; Knight, Jonathan D; Tanner, Kimberly D

2017-01-01

The aspiration of biology education is to give students tools to apply knowledge learned in the classroom to everyday life. Genetic modification is a real-world biological concept that relies on an in-depth understanding of the molecular behavior of DNA and proteins. This study investigated undergraduate biology students' conceptions of genetically modified organisms (GMOs) when probed with real-world, molecular and cellular, and essentialist cues, and how those conceptions compared across biology expertise. We developed a novel written assessment tool and administered it to 120 non-biology majors, 154 entering biology majors, 120 advanced biology majors (ABM), and nine biology faculty. Results indicated that undergraduate biology majors rarely included molecular and cellular rationales in their initial explanations of GMOs. Despite ABM demonstrating that they have much of the biology knowledge necessary to understand genetic modification, they did not appear to apply this knowledge to explaining GMOs. Further, this study showed that all undergraduate student populations exhibited evidence of essentialist thinking while explaining GMOs, regardless of their level of biology training. Finally, our results suggest an association between scientifically accurate ideas and the application of molecular and cellular rationales, as well as an association between misconceptions and essentialist rationales. © 2017 L. M. Potter et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Use of lactose against the deadly biological toxin ricin.

PubMed

Nagatsuka, Takehiro; Uzawa, Hirotaka; Ohsawa, Isaac; Seto, Yasuo; Nishida, Yoshihiro

2010-04-01

Developing a technology for detecting and decontaminating biological toxins is needed. Ricin from Ricinus communis is a highly poisonous toxin; it was formerly used for an assassination in London and in postal attacks in the United States. Ricin is readily available from castor beans and could be used as a biological agent. We propose using glycotechnology against the illegal use of ricin. Lactose (a natural ligand of this toxin) was incorporated into polyacrylamide-based glycopolymers at variable sugar densities (18-100%) and evaluated with surface plasmon resonance (SPR) spectroscopy and the real agent, ricin. Glycopolymers (18-65% lactose densities) effectively interfered with the toxin-lactoside adhesion event (>99% efficiency within 20 min). This supported the notion of using the mammary sugar lactose against a deadly biological toxin.

Microtools for single-cell analysis in biopharmaceutical development and manufacturing.

PubMed

Love, Kerry Routenberg; Bagh, Sangram; Choi, Jonghoon; Love, J Christopher

2013-05-01

Biologic drugs are promoting growth in the biopharmaceutical industry. Despite the clinical benefits of these drugs, the time and costs required to bring new biologics to market still are substantial. Three key challenges, among others, persist in the development of biologic drugs: namely, establishing product similarity, product toxicity, and global accessibility. New classes of microtools that facilitate the isolation and interrogation of single cells have the potential to impact each of these challenges. This opinion considers recent examples of microtools with demonstrated or potential utility to address problems in these areas. Integrating these advanced technologies into the development of new biologics could greatly reduce time and costs required to bring alternative products to market, and thus expand their global availability. Copyright © 2013 Elsevier Ltd. All rights reserved.

Elemental and isotopic imaging of biological samples using NanoSIMS.

PubMed

Kilburn, Matt R; Clode, Peta L

2014-01-01

With its low detection limits and the ability to analyze most of the elements in the periodic table, secondary ion mass spectrometry (SIMS) represents one of the most versatile in situ analytical techniques available, and recent developments have resulted in significant advantages for the use of imaging mass spectrometry in biological and biomedical research. Increases in spatial resolution and sensitivity allow detailed interrogation of samples at relevant scales and chemical concentrations. Advances in dynamic SIMS, specifically with the advent of NanoSIMS, now allow the tracking of stable isotopes within biological systems at subcellular length scales, while static SIMS combines subcellular imaging with molecular identification. In this chapter, we present an introduction to the SIMS technique, with particular reference to NanoSIMS, and discuss its application in biological and biomedical research.

Convergence between biological, behavioural and genetic determinants of obesity.

PubMed

Ghosh, Sujoy; Bouchard, Claude

2017-12-01

Multiple biological, behavioural and genetic determinants or correlates of obesity have been identified to date. Genome-wide association studies (GWAS) have contributed to the identification of more than 100 obesity-associated genetic variants, but their roles in causal processes leading to obesity remain largely unknown. Most variants are likely to have tissue-specific regulatory roles through joint contributions to biological pathways and networks, through changes in gene expression that influence quantitative traits, or through the regulation of the epigenome. The recent availability of large-scale functional genomics resources provides an opportunity to re-examine obesity GWAS data to begin elucidating the function of genetic variants. Interrogation of knockout mouse phenotype resources provides a further avenue to test for evidence of convergence between genetic variation and biological or behavioural determinants of obesity.

Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization.

PubMed

Whitaker, William B; Sandoval, Nicholas R; Bennett, Robert K; Fast, Alan G; Papoutsakis, Eleftherios T

2015-06-01

Synthetic methylotrophy is the development of non-native methylotrophs that can utilize methane and methanol as sole carbon and energy sources or as co-substrates with carbohydrates to produce metabolites as biofuels and chemicals. The availability of methane (from natural gas) and its oxidation product, methanol, has been increasing, while prices have been decreasing, thus rendering them as attractive fermentation substrates. As they are more reduced than most carbohydrates, methane and methanol, as co-substrates, can enhance the yields of biologically produced metabolites. Here we discuss synthetic biology and metabolic engineering strategies based on the native biology of aerobic methylotrophs for developing synthetic strains grown on methanol, with Escherichia coli as the prototype. Copyright © 2015. Published by Elsevier Ltd.

Gap analysis on the biology of Mediterranean marine fishes

PubMed Central

Dimarchopoulou, Donna; Stergiou, Konstantinos I.

2017-01-01

We estimated the current level of knowledge concerning several biological characteristics of the Mediterranean marine fishes by carrying out a gap analysis based on information extracted from the literature, aiming to identify research trends and future needs in the field of Mediterranean fish biology that can be used in stock assessments, ecosystem modeling and fisheries management. Based on the datasets that emerged from the literature review, there is no information on any biological characteristic for 43% (n = 310) of the Mediterranean fish species, whereas for an additional 15% (n = 109) of them there is information about just one characteristic. The gap between current and desired knowledge (defined here as having information on most biological characteristics for at least half of the Mediterranean marine fishes) is smaller in length-weight relationships, which have been studied for 43% of the species, followed by spawning (39%), diet (29%), growth (25%), maturity (24%), lifespan (19%) and fecundity (17%). The gap is larger in natural mortality for which information is very scarce (8%). European hake (Merluccius merluccius), red mullet (Mullus barbatus), annular seabream (Diplodus annularis), common pandora (Pagellus erythrinus), European anchovy (Engraulis encrasicolus), European pilchard (Sardina pilchardus) and bogue (Boops boops) were the most studied species, while sharks and rays were among the least studied ones. Only 25 species were fully studied, i.e. there was available information on all their biological characteristics. The knowledge gaps per characteristic varied among the western, central and eastern Mediterranean subregions. The number of available records per species was positively related to total landings, while no relationship emerged with its maximum reported length, trophic level and commercial value. Future research priorities that should be focused on less studied species (e.g. sharks and rays) and mortality/fecundity instead of length-weight relationships, as well as the economy of scientific sampling (using the entire catch to acquire data on as many biological characteristics as possible) are discussed. PMID:28407022

Preclinical assessment of abuse liability of biologics: In defense of current regulatory control policies.

PubMed

Gauvin, David V; Zimmermann, Zachary J; Baird, Theodore J

2015-10-01

Current regulatory policies of both the US Food and Drug Administration and Drug Enforcement Administration do not delineate automatic exceptions for biologics with respect to preclinical assessments for abuse liability of all new entities. As defined in current guidance documents and drug control policies, an exception may be given upon thorough review of available data, therapeutic target and in consultation with the Controlled Substances Staff within the Center for Drug Evaluation and Research of the FDA, but a blanket exception for all biological entities is not currently available. We review the abuse liability testing of four known biologics with definitive positive abuse liability signals in the three core abuse liability assays, self-administration, drug discrimination, and dependence potential described in the FDA draft guidance document. Interestingly, while all four examplars have positive abuse liability signals in all three assays, two of these biologics are controlled under the Comprehensive Drug Abuse and Control Act (CSA, 1970) and the other two are not currently controlled. Admittedly, these four biologics are small molecule entities. However, there is no reference to "molecular size" in the legally-binding statutory definition of biologics under the FD&C act or in the Controlled Substances Act. Neither of these drug control policy mandates have a bifurcated control status in which to make exceptions based solely on molecular size. With the current pharmaceutical focus on new technologies, such as "Trojan Horses", targeting the active transport of large molecule entities directly into the CNS, an argument to automatically exempt new molecular entities solely on molecular size is untenable. We argue that for the safety and health of general public the current regulatory control status be maintained until definitive criteria for exceptions can be identified and amended to both the FD&CA and CSA, if warranted. Copyright © 2015 Elsevier Inc. All rights reserved.

Gap analysis on the biology of Mediterranean marine fishes.

PubMed

Dimarchopoulou, Donna; Stergiou, Konstantinos I; Tsikliras, Athanassios C

2017-01-01

We estimated the current level of knowledge concerning several biological characteristics of the Mediterranean marine fishes by carrying out a gap analysis based on information extracted from the literature, aiming to identify research trends and future needs in the field of Mediterranean fish biology that can be used in stock assessments, ecosystem modeling and fisheries management. Based on the datasets that emerged from the literature review, there is no information on any biological characteristic for 43% (n = 310) of the Mediterranean fish species, whereas for an additional 15% (n = 109) of them there is information about just one characteristic. The gap between current and desired knowledge (defined here as having information on most biological characteristics for at least half of the Mediterranean marine fishes) is smaller in length-weight relationships, which have been studied for 43% of the species, followed by spawning (39%), diet (29%), growth (25%), maturity (24%), lifespan (19%) and fecundity (17%). The gap is larger in natural mortality for which information is very scarce (8%). European hake (Merluccius merluccius), red mullet (Mullus barbatus), annular seabream (Diplodus annularis), common pandora (Pagellus erythrinus), European anchovy (Engraulis encrasicolus), European pilchard (Sardina pilchardus) and bogue (Boops boops) were the most studied species, while sharks and rays were among the least studied ones. Only 25 species were fully studied, i.e. there was available information on all their biological characteristics. The knowledge gaps per characteristic varied among the western, central and eastern Mediterranean subregions. The number of available records per species was positively related to total landings, while no relationship emerged with its maximum reported length, trophic level and commercial value. Future research priorities that should be focused on less studied species (e.g. sharks and rays) and mortality/fecundity instead of length-weight relationships, as well as the economy of scientific sampling (using the entire catch to acquire data on as many biological characteristics as possible) are discussed.

75 FR 28233 - Availability of an Environmental Assessment for a Biological Control Agent for Asian Citrus Psyllid

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-20

... DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service [Docket No. APHIS-2010-0028...: Animal and Plant Health Inspection Service, USDA. ACTION: Notice of availability and request for comments. SUMMARY: We are advising the public that the Animal and Plant Health Inspection Service has prepared an...

77 FR 55171 - Approval and Promulgation of Air Quality Implementation Plans; Maryland; Deferral for CO2

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-07

... consider your comment. Electronic files should avoid the use of special characters, any form of encryption... copy form. Publicly available docket materials are available either electronically in www.regulations... biologically-based materials other than fossil fuels and mineral sources of carbon. Examples of ``biogenic CO 2...

Emergency Response

EPA Pesticide Factsheets

Information for first responders, industry, federal, state and local governments on EPA's role and available resources for response to oil spills, chemical, biological, radiological releases, and large-scale national emergencies.

CellML metadata standards, associated tools and repositories

PubMed Central

Beard, Daniel A.; Britten, Randall; Cooling, Mike T.; Garny, Alan; Halstead, Matt D.B.; Hunter, Peter J.; Lawson, James; Lloyd, Catherine M.; Marsh, Justin; Miller, Andrew; Nickerson, David P.; Nielsen, Poul M.F.; Nomura, Taishin; Subramanium, Shankar; Wimalaratne, Sarala M.; Yu, Tommy

2009-01-01

The development of standards for encoding mathematical models is an important component of model building and model sharing among scientists interested in understanding multi-scale physiological processes. CellML provides such a standard, particularly for models based on biophysical mechanisms, and a substantial number of models are now available in the CellML Model Repository. However, there is an urgent need to extend the current CellML metadata standard to provide biological and biophysical annotation of the models in order to facilitate model sharing, automated model reduction and connection to biological databases. This paper gives a broad overview of a number of new developments on CellML metadata and provides links to further methodological details available from the CellML website. PMID:19380315

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

Synthetic biology: insights into biological computation.

PubMed

Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

2016-04-18

Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and biotechnological applications, but also affords a greater understanding of biological systems.

The Math-Biology Values Instrument: Development of a Tool to Measure Life Science Majors' Task Values of Using Math in the Context of Biology.

PubMed

Andrews, Sarah E; Runyon, Christopher; Aikens, Melissa L

2017-01-01

In response to calls to improve the quantitative training of undergraduate biology students, there have been increased efforts to better integrate math into biology curricula. One challenge of such efforts is negative student attitudes toward math, which are thought to be particularly prevalent among biology students. According to theory, students' personal values toward using math in a biological context will influence their achievement and behavioral outcomes, but a validated instrument is needed to determine this empirically. We developed the Math-Biology Values Instrument (MBVI), an 11-item college-level self--report instrument grounded in expectancy-value theory, to measure life science students' interest in using math to understand biology, the perceived usefulness of math to their life science career, and the cost of using math in biology courses. We used a process that integrates multiple forms of validity evidence to show that scores from the MBVI can be used as a valid measure of a student's value of math in the context of biology. The MBVI can be used by instructors and researchers to help identify instructional strategies that influence math-biology values and understand how math-biology values are related to students' achievement and decisions to pursue more advanced quantitative-based courses. © 2017 S. E. Andrews et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Using the Biology Card Sorting Task to Measure Changes in Conceptual Expertise during Postsecondary Biology Education.

PubMed

Bissonnette, Sarah A; Combs, Elijah D; Nagami, Paul H; Byers, Victor; Fernandez, Juliana; Le, Dinh; Realin, Jared; Woodham, Selina; Smith, Julia I; Tanner, Kimberly D

2017-01-01

While there have been concerted efforts to reform undergraduate biology toward teaching students to organize their conceptual knowledge like experts, there are few tools that attempt to measure this. We previously developed the Biology Card Sorting Task (BCST), designed to probe how individuals organize their conceptual biological knowledge. Previous results showed the BCST could differentiate between different populations, namely non-biology majors (NBM) and biology faculty (BF). In this study, we administered the BCST to three additional populations, using a cross-sectional design: entering biology majors (EBM), advanced biology majors (ABM), and biology graduate students (BGS). Intriguingly, ABM did not initially sort like experts any more frequently than EBM. However, once the deep-feature framework was revealed, ABM were able to sort like experts more readily than did EBM. These results are consistent with the conclusion that biology education enables advanced biology students to use an expert-like conceptual framework. However, these results are also consistent with a process of "selection," wherein students who persist in the major may have already had an expert-like conceptual framework to begin with. These results demonstrate the utility of the BCST in measuring differences between groups of students over the course of their undergraduate education. © 2017 S. A. Bissonnette et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Ontology- and graph-based similarity assessment in biological networks.

PubMed

Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

2010-10-15

A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different 'guilt-by-association' analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a 'semantic similarity' space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. http://rosalind.infj.ulst.ac.uk/SimTrek.html francisco.azuaje@crp-sante.lu Supplementary data are available at Bioinformatics online.

iBiology: communicating the process of science

PubMed Central

Goodwin, Sarah S.

2014-01-01

The Internet hosts an abundance of science video resources aimed at communicating scientific knowledge, including webinars, massive open online courses, and TED talks. Although these videos are efficient at disseminating information for diverse types of users, they often do not demonstrate the process of doing science, the excitement of scientific discovery, or how new scientific knowledge is developed. iBiology (www.ibiology.org), a project that creates open-access science videos about biology research and science-related topics, seeks to fill this need by producing videos by science leaders that make their ideas, stories, and experiences available to anyone with an Internet connection. PMID:25080124

Possible application of a nematophagous fungus as a biological control agent of parasitic nematodes on commercial sheep farms in South Africa.

PubMed

Faedo, M; Krecek, R C

2002-03-01

Biological control of parasitic nematodes of livestock is currently under development and represents another tool that may be integrated into helminth parasite control strategies. This paper presents a brief introduction to commercial sheep farming in South Africa and currently available nematode parasite control methods. These include the FAMACHA clinical assay, strategies of pasture management, dilution of resistant worm species by introduction of susceptible worms, breed resistant sheep and nutritional supplementation. The purpose of this paper is to outline the principles of biological control using nematophagous fungi and how it may be applied on sheep farms in South Africa.

SBEToolbox: A Matlab Toolbox for Biological Network Analysis

PubMed Central

Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J.

2013-01-01

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases. PMID:24027418

SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

PubMed

Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

2013-01-01

We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013.

PubMed

Verspoor, Karin; Shatkay, Hagit; Hirschman, Lynette; Blaschke, Christian; Valencia, Alfonso

2015-01-15

The ISMB Special Interest Group on Linking Literature, Information and Knowledge for Biology (BioLINK) organized a one-day workshop at ISMB/ECCB 2013 in Berlin, Germany. The theme of the workshop was 'Roles for text mining in biomedical knowledge discovery and translational medicine'. This summary reviews the outcomes of the workshop. Meeting themes included concept annotation methods and applications, extraction of biological relationships and the use of text-mined data for biological data analysis. All articles are available at http://biolinksig.org/proceedings-online/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Integrative structure modeling with the Integrative Modeling Platform.

PubMed

Webb, Benjamin; Viswanath, Shruthi; Bonomi, Massimiliano; Pellarin, Riccardo; Greenberg, Charles H; Saltzberg, Daniel; Sali, Andrej

2018-01-01

Building models of a biological system that are consistent with the myriad data available is one of the key challenges in biology. Modeling the structure and dynamics of macromolecular assemblies, for example, can give insights into how biological systems work, evolved, might be controlled, and even designed. Integrative structure modeling casts the building of structural models as a computational optimization problem, for which information about the assembly is encoded into a scoring function that evaluates candidate models. Here, we describe our open source software suite for integrative structure modeling, Integrative Modeling Platform (https://integrativemodeling.org), and demonstrate its use. © 2017 The Protein Society.

[Small compounds libraries: a research tool for chemical biology].

PubMed

Florent, Jean-Claude

2013-01-01

Obtaining and screening collections of small molecules remain a challenge for biologists. Recent advances in analytical techniques and instrumentation now make screening possible in academia. The history of the creation of such public or commercial collections and their accessibility is related. It shows that there is interest for an academic laboratory involved in medicinal chemistry, chemogenomics or "chemical biology" to organize its own collection and make it available through existing networks such as the French National chimiothèque or the European partner network "European Infrastructure of open screening platforms for Chemical Biology" EU-OpenScreen under construction. © Société de Biologie, 2013.

Development of practical methods for removal of radiological, biological, and chemical contaminants from water supplies. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Woodward, R.L.; Robeck, G.G.

1958-06-01

Laboratory and engineering studies were conducted to determine the design criteria and cost estimated of providing and operating devices to protect against radiological, biological and chemical warfare agents that may contaminate shore based Naval water supplies. Small disposable columns of mixed cation-anion exchange resins will remove the soluble radionuclides enough to suffice for immediate drinking and culinary purposes. Chemical warfare agents are so numerous and varied that it is not feasible to provide a single protective device to cope with them. Chlorination with free available chlorine residuals of 1 mg liter will handle most biological warfare agents.

Trends in Occupational Exposure to Styrene in the European Glass Fibre-Reinforced Plastics Industry

PubMed Central

Van Rooij, J. G. M.; Kasper, A.; Triebig, G.; Werner, P.; Kromhout, H.

2008-01-01

Aim: This study presents temporal trends of styrene exposure for workers in the European glass fibre-reinforced plastics (GRP) industry during the period 1966–2002. Methods: Data of personal styrene exposure measurements were retrieved from reports, databases and peer-reviewed papers. Only sources with descriptive statistics of personal measurements were accepted. The styrene exposure data cover personal air samples and biological monitoring data, that is, urinary styrene metabolites (mandelic acid and/or phenylglyoxylic acid) and styrene in blood. Means of series of measurements were categorized by year, country, production process, job and sampling strategy. Linear mixed models were used to identify temporal trends and factors affecting exposure levels. Results: Personal exposure measurements were available from 60 reports providing data on 24145 1–8-h time-weighted average shift personal air samples. Available data of biological exposure indicators included measurements of mandelic acid in post-shift urine (6361 urine samples being analysed). Trend analyses of the available styrene exposure data showed that the average styrene concentration in the breathing zone of open-mould workers in the European GRP industry has decreased on average by 5.3% per year during the period 1966–1990 and by only 0.4% annually in the period after 1990. The highest exposures were measured in Southern Europe and the lowest exposures in Northern Europe with Central Europe in between. Biological indicators of styrene (mandelic acid in post-shift urine) showed a somewhat steeper decline (8.9%), most likely because urine samples were collected in companies that showed a stronger decrease of styrene exposure in air than GRP companies where no biological measurements were carried out. PMID:18550625

An algorithm for automated layout of process description maps drawn in SBGN

PubMed Central

Genc, Begum; Dogrusoz, Ugur

2016-01-01

Motivation: Evolving technology has increased the focus on genomics. The combination of today’s advanced techniques with decades of molecular biology research has yielded huge amounts of pathway data. A standard, named the Systems Biology Graphical Notation (SBGN), was recently introduced to allow scientists to represent biological pathways in an unambiguous, easy-to-understand and efficient manner. Although there are a number of automated layout algorithms for various types of biological networks, currently none specialize on process description (PD) maps as defined by SBGN. Results: We propose a new automated layout algorithm for PD maps drawn in SBGN. Our algorithm is based on a force-directed automated layout algorithm called Compound Spring Embedder (CoSE). On top of the existing force scheme, additional heuristics employing new types of forces and movement rules are defined to address SBGN-specific rules. Our algorithm is the only automatic layout algorithm that properly addresses all SBGN rules for drawing PD maps, including placement of substrates and products of process nodes on opposite sides, compact tiling of members of molecular complexes and extensively making use of nested structures (compound nodes) to properly draw cellular locations and molecular complex structures. As demonstrated experimentally, the algorithm results in significant improvements over use of a generic layout algorithm such as CoSE in addressing SBGN rules on top of commonly accepted graph drawing criteria. Availability and implementation: An implementation of our algorithm in Java is available within ChiLay library (https://github.com/iVis-at-Bilkent/chilay). Contact: ugur@cs.bilkent.edu.tr or dogrusoz@cbio.mskcc.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26363029

densityCut: an efficient and versatile topological approach for automatic clustering of biological data

PubMed Central

Ding, Jiarui; Shah, Sohrab; Condon, Anne

2016-01-01

Motivation: Many biological data processing problems can be formalized as clustering problems to partition data points into sensible and biologically interpretable groups. Results: This article introduces densityCut, a novel density-based clustering algorithm, which is both time- and space-efficient and proceeds as follows: densityCut first roughly estimates the densities of data points from a K-nearest neighbour graph and then refines the densities via a random walk. A cluster consists of points falling into the basin of attraction of an estimated mode of the underlining density function. A post-processing step merges clusters and generates a hierarchical cluster tree. The number of clusters is selected from the most stable clustering in the hierarchical cluster tree. Experimental results on ten synthetic benchmark datasets and two microarray gene expression datasets demonstrate that densityCut performs better than state-of-the-art algorithms for clustering biological datasets. For applications, we focus on the recent cancer mutation clustering and single cell data analyses, namely to cluster variant allele frequencies of somatic mutations to reveal clonal architectures of individual tumours, to cluster single-cell gene expression data to uncover cell population compositions, and to cluster single-cell mass cytometry data to detect communities of cells of the same functional states or types. densityCut performs better than competing algorithms and is scalable to large datasets. Availability and Implementation: Data and the densityCut R package is available from https://bitbucket.org/jerry00/densitycut_dev. Contact: condon@cs.ubc.ca or sshah@bccrc.ca or jiaruid@cs.ubc.ca Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153661

Actual evapotranspiration and deficit: Biologically meaningful correlates of vegetation distribution across spatial scales

USGS Publications Warehouse

Stephenson, N.L.

1998-01-01

Correlative approaches to understanding the climatic controls of vegetation distribution have exhibited at least two important weaknesses: they have been conceptually divorced across spatial scales, and their climatic parameters have not necessarily represented aspects of climate of broad physiological importance to plants. Using examples from the literature and from the Sierra Nevada of California, I argue that two water balance parameters-actual evapotranspiration (AET) and deficit (D)-are biologically meaningful, are well correlated with the distribution of vegetation types, and exhibit these qualities over several orders of magnitude of spatial scale (continental to local). I reach four additional conclusions. (1) Some pairs of climatic parameters presently in use are functionally similar to AET and D; however, AET and D may be easier to interpret biologically. (2) Several well-known climatic parameters are biologically less meaningful or less important than AET and D, and consequently are poorer correlates of the distribution of vegetation types. Of particular interest, AET is a much better correlate of the distributions of coniferous and deciduous forests than minimum temperature. (3) The effects of evaporative demand and water availability on a site's water balance are intrinsically different. For example, the 'dry' experienced by plants on sunward slopes (high evaporative demand) is not comparable to the 'dry' experienced by plants on soils with low water-holding capacities (low water availability), and these differences are reflected in vegetation patterns. (4) Many traditional topographic moisture scalars-those that additively combine measures related to evaporative demand and water availability are not necessarily meaningful for describing site conditions as sensed by plants; the same holds for measured soil moisture. However, using AET and D in place of moisture scalars and measured soil moisture can solve these problems.

Exploration for the Biological Control of Flowering Rush, Butomus umbellatus

DTIC Science & Technology

2015-06-01

control of flowering rush, Butomus umbellatus P. Häfliger, R. Leiner, C. Baan, A. Martins, S. Soukou, D. Sjolie, I. Toševski and H.L...2014 to 00-06-2015 4. TITLE AND SUBTITLE Exploration for the Biological Control of Flowering Rush, Butomus umbellatus 5a. CONTRACT NUMBER W911NF-14...AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Flowering rush (Butomus umbellatus

Ruggedized Portable Instrumentation Package for Marine Mammal Evoked Potential Hearing Measurements (DURIP)

DTIC Science & Technology

2011-09-30

NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) Hawaii Institute of Marine Biology,Marine Mammal...Program Hawaii Institute of Marine Biology P.O. Box 1106 Kailua, Hawaii 96734 phone: (808) 247-5297 fax: (808) 247-5831 email: nachtiga...portable equipment was used at the Hilo Stranding Center to obtain the audiograms. Ready and available for RIMPAC excercises. 2 IMPACT

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

PubMed

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Creating Successful Campus Partnerships for Teaching Communication in Biology Courses and Labs.

PubMed

Hall, Susanne E; Birch, Christina

2018-01-01

Creating and teaching successful writing and communication assignments for biology undergraduate students can be challenging for faculty trying to balance the teaching of technical content. The growing body of published research and scholarship on effective teaching of writing and communication in biology can help inform such work, but there are also local resources available to support writing within biology courses that may be unfamiliar to science faculty and instructors. In this article, we discuss common on-campus resources biology faculty can make use of when incorporating writing and communication into their teaching. We present the missions, histories, and potential collaboration outcomes of three major on-campus writing resources: writing across the curriculum and writing in the disciplines initiatives (WAC/WID), writing programs, and writing centers. We explain some of the common misconceptions about these resources in order to help biology faculty understand their uses and limits, and we offer guiding questions faculty might ask the directors of these resources to start productive conversations. Collaboration with these resources will likely save faculty time and effort on curriculum development and, more importantly, will help biology students develop and improve their critical reading, writing, and communication skills.

Creating Successful Campus Partnerships for Teaching Communication in Biology Courses and Labs

PubMed Central

Hall, Susanne E.; Birch, Christina

2018-01-01

Creating and teaching successful writing and communication assignments for biology undergraduate students can be challenging for faculty trying to balance the teaching of technical content. The growing body of published research and scholarship on effective teaching of writing and communication in biology can help inform such work, but there are also local resources available to support writing within biology courses that may be unfamiliar to science faculty and instructors. In this article, we discuss common on-campus resources biology faculty can make use of when incorporating writing and communication into their teaching. We present the missions, histories, and potential collaboration outcomes of three major on-campus writing resources: writing across the curriculum and writing in the disciplines initiatives (WAC/WID), writing programs, and writing centers. We explain some of the common misconceptions about these resources in order to help biology faculty understand their uses and limits, and we offer guiding questions faculty might ask the directors of these resources to start productive conversations. Collaboration with these resources will likely save faculty time and effort on curriculum development and, more importantly, will help biology students develop and improve their critical reading, writing, and communication skills. PMID:29904537

Parasitoids of Queensland Fruit Fly Bactrocera tryoni in Australia and Prospects for Improved Biological Control

PubMed Central

Zamek, Ashley L.; Spinner, Jennifer E.; Micallef, Jessica L.; Gurr, Geoff M.; Reynolds, Olivia L.

2012-01-01

This review draws together available information on the biology, methods for study, and culturing of hymenopteran parasitoids of the Queensland fruit fly, Bactrocera tryoni, and assesses prospects for improving biological control of this serious pest. Augmentative release of the native and naturalised Australian parasitoids, especially the braconid Diachasmimorpha tryoni, may result in better management of B. tryoni in some parts of Australia. Mass releases are an especially attractive option for areas of inland eastern Australia around the Fruit Fly Exclusion Zone that produces B. tryoni-free fruits for export. Diachasmimorpha tryoni has been successful in other locations such as Hawaii for the biological control of other fruit fly species. Biological control could contribute to local eradication of isolated outbreaks and more general suppression and/or eradication of the B. tryoni population in endemic areas. Combining biological control with the use of sterile insect technique offers scope for synergy because the former is most effective at high pest densities and the latter most economical when the pest becomes scarce. Recommendations are made on methods for culturing and study of four B. tryoni parasitoids present in Australia along with research priorities for optimising augmentative biological control of B. tryoni. PMID:26466726

Defining the "like" in "begetting the like": The development of inductive inference in the domain of biology

NASA Astrophysics Data System (ADS)

Lo, Ya-Fen

There are evidences that very young children consider linguistic labels when making similarity judgment and inductive inferences. However, it remains unclear how labels contribute to young children's similarity judgment and inductive inferences. It has been demonstrated that labels facilitate categorical memberships about objects in young children's similarity judgment and inductive inferences. It is also suggested that young children should rely on several sources of information when making similarity judgment and inductive inferences. Three experiments were conducted to examine these interpretations, in which biological information, labeling information, and perceptual similarity information were varied in a systematic manner. Three- to eleven-year-old children were asked to judge which of two Test animals a baby animals would share biological properties with. In Experiment 1, preschool children demonstrated a basic understanding of the importance of biological information for generalizing biological properties. In Experiment 2, when the labeling information became available, young children relied on linguistic labels rather than on biological information when generalizing biological properties. At the same time, 9- to 11-year-old children relied consistently on biological information. Experiment 3 supported the results of Experiment 2 and suggested that in addition to labels, perceptual similarity also contributed to children's inductive inferences.

PathVisio 3: an extendable pathway analysis toolbox.

PubMed

Kutmon, Martina; van Iersel, Martijn P; Bohler, Anwesha; Kelder, Thomas; Nunes, Nuno; Pico, Alexander R; Evelo, Chris T

2015-02-01

PathVisio is a commonly used pathway editor, visualization and analysis software. Biological pathways have been used by biologists for many years to describe the detailed steps in biological processes. Those powerful, visual representations help researchers to better understand, share and discuss knowledge. Since the first publication of PathVisio in 2008, the original paper was cited more than 170 times and PathVisio was used in many different biological studies. As an online editor PathVisio is also integrated in the community curated pathway database WikiPathways. Here we present the third version of PathVisio with the newest additions and improvements of the application. The core features of PathVisio are pathway drawing, advanced data visualization and pathway statistics. Additionally, PathVisio 3 introduces a new powerful extension systems that allows other developers to contribute additional functionality in form of plugins without changing the core application. PathVisio can be downloaded from http://www.pathvisio.org and in 2014 PathVisio 3 has been downloaded over 5,500 times. There are already more than 15 plugins available in the central plugin repository. PathVisio is a freely available, open-source tool published under the Apache 2.0 license (http://www.apache.org/licenses/LICENSE-2.0). It is implemented in Java and thus runs on all major operating systems. The code repository is available at http://svn.bigcat.unimaas.nl/pathvisio. The support mailing list for users is available on https://groups.google.com/forum/#!forum/wikipathways-discuss and for developers on https://groups.google.com/forum/#!forum/wikipathways-devel.

Biological treatment strategies for disc degeneration: potentials and shortcomings

PubMed Central

Nerlich, Andreas G.; Boos, Norbert

2006-01-01

Recent advances in molecular biology, cell biology and material sciences have opened a new emerging field of techniques for the treatment of musculoskeletal disorders. These new treatment modalities aim for biological repair of the affected tissues by introducing cell-based tissue replacements, genetic modifications of resident cells or a combination thereof. So far, these techniques have been successfully applied to various tissues such as bone and cartilage. However, application of these treatment modalities to cure intervertebral disc degeneration is in its very early stages and mostly limited to experimental studies in vitro or in animal studies. We will discuss the potential and possible shortcomings of current approaches to biologically cure disc degeneration by gene therapy or tissue engineering. Despite the increasing number of studies examining the therapeutic potential of biological treatment strategies, a practicable solution to routinely cure disc degeneration might not be available in the near future. However, knowledge gained from these attempts might be applied in a foreseeable future to cure the low back pain that often accompanies disc degeneration and therefore be beneficial for the patient. PMID:16983559

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

PubMed Central

Tohsato, Yukako; Ho, Kenneth H. L.; Kyoda, Koji; Onami, Shuichi

2016-01-01

Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis. Results: We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. Availability and Implementation: SSBD is accessible at http://ssbd.qbic.riken.jp. Contact: sonami@riken.jp PMID:27412095

Bone effects of biologic drugs in rheumatoid arthritis.

PubMed

Corrado, Addolorata; Neve, Anna; Maruotti, Nicola; Cantatore, Francesco Paolo

2013-01-01

Biologic agents used in the treatment of rheumatoid arthritis (RA) are able to reduce both disease activity and radiographic progression of joint disease. These drugs are directed against several proinflammatory cytokines (TNF α , IL-6, and IL-1) which are involved both in the pathogenesis of chronic inflammation and progression of joint structural damage and in systemic and local bone loss typically observed in RA. However, the role of biologic drugs in preventing bone loss in clinical practice has not yet clearly assessed. Many clinical studies showed a trend to a positive effect of biologic agents in preventing systemic bone loss observed in RA. Although the suppression of inflammation is the main goal in the treatment of RA and the anti-inflammatory effects of biologic drugs exert a positive effect on bone metabolism, the exact relationship between the prevention of bone loss and control of inflammation has not been clearly established, and if the available biologic drugs against TNF α , IL-1, and IL-6 can exert their effect on systemic and local bone loss also through a direct mechanism on bone cell metabolism is still to be clearly defined.

Application of ToxCast to evaluate potential biological effects ...

EPA Pesticide Factsheets

With the development of “high throughput” in-vitro biological assays, screening-level information on potential adverse biological effects is available for a rapidly increasing number of chemicals. The U.S. EPA ToxCast program has now evaluated several thousand chemicals with more than 800 assays. The original intent of this data was to evaluate potential for human health effects, but it is now being extended to environmental health evaluations. The R package ToxEval was developed as a screening tool to use ToxCast results for evaluation of potential adverse biological effects from trace organic chemicals in water samples. Using ToxEval, trace organic chemical data from water samples and passive samplers collected at 57 Great Lakes tributaries from 2010-2013 were examined to determine the tributaries with the greatest potential for adverse biological effects with prioritization of the most influential contaminants. Results are being used as part of the Great Lakes Restoration Initiative to focus current and future investigations that will help understand likely adverse outcome pathways in biological organisms, and to formulate possible remediation strategies. not applicable

Functional Genomics Assistant (FUGA): a toolbox for the analysis of complex biological networks

PubMed Central

2011-01-01

Background Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context. Findings We present Functional Genomics Assistant (FUGA) - an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology. Conclusion FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at http://code.google.com/p/fuga. PMID:22035155

Graphics processing units in bioinformatics, computational biology and systems biology.

PubMed

Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

2017-09-01

Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

Promoting microbiology education through the iGEM synthetic biology competition.

PubMed

Kelwick, Richard; Bowater, Laura; Yeoman, Kay H; Bowater, Richard P

2015-08-01

Synthetic biology has developed rapidly in the 21st century. It covers a range of scientific disciplines that incorporate principles from engineering to take advantage of and improve biological systems, often applied to specific problems. Methods important in this subject area include the systematic design and testing of biological systems and, here, we describe how synthetic biology projects frequently develop microbiology skills and education. Synthetic biology research has huge potential in biotechnology and medicine, which brings important ethical and moral issues to address, offering learning opportunities about the wider impact of microbiological research. Synthetic biology projects have developed into wide-ranging training and educational experiences through iGEM, the International Genetically Engineered Machines competition. Elements of the competition are judged against specific criteria and teams can win medals and prizes across several categories. Collaboration is an important element of iGEM, and all DNA constructs synthesized by iGEM teams are made available to all researchers through the Registry for Standard Biological Parts. An overview of microbiological developments in the iGEM competition is provided. This review is targeted at educators that focus on microbiology and synthetic biology, but will also be of value to undergraduate and postgraduate students with an interest in this exciting subject area. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The similarity of life across the universe.

PubMed

Cockell, Charles S

2016-05-15

Is the hypothesis correct that if life exists elsewhere in the universe, it would have forms and structures unlike anything we could imagine? From the subatomic level in cellular energy acquisition to the assembly and even behavior of organisms at the scale of populations, life on Earth exhibits characteristics that suggest it is a universal norm for life at all levels of hierarchy. These patterns emerge from physical and biochemical limitations. Their potentially universal nature is supported by recent data on the astrophysical abundance and availability of carbon compounds and water. Within these constraints, biochemical and biological variation is certainly possible, but it is limited. If life exists elsewhere, life on Earth, rather than being a contingent product of one specific experiment in biological evolution, is likely to reflect common patterns for the assembly of living matter. © 2016 Cockell. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Computational biology in the cloud: methods and new insights from computing at scale.

PubMed

Kasson, Peter M

2013-01-01

The past few years have seen both explosions in the size of biological data sets and the proliferation of new, highly flexible on-demand computing capabilities. The sheer amount of information available from genomic and metagenomic sequencing, high-throughput proteomics, experimental and simulation datasets on molecular structure and dynamics affords an opportunity for greatly expanded insight, but it creates new challenges of scale for computation, storage, and interpretation of petascale data. Cloud computing resources have the potential to help solve these problems by offering a utility model of computing and storage: near-unlimited capacity, the ability to burst usage, and cheap and flexible payment models. Effective use of cloud computing on large biological datasets requires dealing with non-trivial problems of scale and robustness, since performance-limiting factors can change substantially when a dataset grows by a factor of 10,000 or more. New computing paradigms are thus often needed. The use of cloud platforms also creates new opportunities to share data, reduce duplication, and to provide easy reproducibility by making the datasets and computational methods easily available.

An efficient method to identify differentially expressed genes in microarray experiments

PubMed Central

Qin, Huaizhen; Feng, Tao; Harding, Scott A.; Tsai, Chung-Jui; Zhang, Shuanglin

2013-01-01

Motivation Microarray experiments typically analyze thousands to tens of thousands of genes from small numbers of biological replicates. The fact that genes are normally expressed in functionally relevant patterns suggests that gene-expression data can be stratified and clustered into relatively homogenous groups. Cluster-wise dimensionality reduction should make it feasible to improve screening power while minimizing information loss. Results We propose a powerful and computationally simple method for finding differentially expressed genes in small microarray experiments. The method incorporates a novel stratification-based tight clustering algorithm, principal component analysis and information pooling. Comprehensive simulations show that our method is substantially more powerful than the popular SAM and eBayes approaches. We applied the method to three real microarray datasets: one from a Populus nitrogen stress experiment with 3 biological replicates; and two from public microarray datasets of human cancers with 10 to 40 biological replicates. In all three analyses, our method proved more robust than the popular alternatives for identification of differentially expressed genes. Availability The C++ code to implement the proposed method is available upon request for academic use. PMID:18453554

Relapsing polychondritis: A 2016 update on clinical features, diagnostic tools, treatment and biological drug use.

PubMed

Mathian, Alexis; Miyara, Makoto; Cohen-Aubart, Fleur; Haroche, Julien; Hie, Miguel; Pha, Micheline; Grenier, Philippe; Amoura, Zahir

2016-04-01

Relapsing polychondritis (RP) is a very rare autoimmune disease characterised by a relapsing inflammation of the cartilaginous tissues (joints, ears, nose, intervertebral discs, larynx, trachea and cartilaginous bronchi), which may progress to long-lasting atrophy and/or deformity of the cartilages. Non-cartilaginous tissues may also be affected, such as the eyes, heart, aorta, inner ear and skin. RP has a long and unpredictable course. Because no randomised therapeutic trials are available, the treatment of RP remains mainly empirical. Minor forms of the disease can be treated with non-steroidal anti-inflammatory drugs, whereas more severe forms are treated with systemic corticosteroids. Life-threatening diseases and corticosteroid-dependent or resistant diseases are an indication for immunosuppressant therapy such as methotrexate, azathioprine, mycophenolate mofetil and cyclophosphamide. Biologics could be given as second-line treatment in patients with an active disease despite the use of steroids and immunosuppressive drugs. Although the biologics represent new potential treatment for RP, very scarce information is available to draw any firm conclusion on their use in RP. Copyright © 2016 Elsevier Ltd. All rights reserved.

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

PubMed

Marchetti, Luca; Manca, Vincenzo

2015-04-15

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Probabilistic representation of gene regulatory networks.

PubMed

Mao, Linyong; Resat, Haluk

2004-09-22

Recent experiments have established unambiguously that biological systems can have significant cell-to-cell variations in gene expression levels even in isogenic populations. Computational approaches to studying gene expression in cellular systems should capture such biological variations for a more realistic representation. In this paper, we present a new fully probabilistic approach to the modeling of gene regulatory networks that allows for fluctuations in the gene expression levels. The new algorithm uses a very simple representation for the genes, and accounts for the repression or induction of the genes and for the biological variations among isogenic populations simultaneously. Because of its simplicity, introduced algorithm is a very promising approach to model large-scale gene regulatory networks. We have tested the new algorithm on the synthetic gene network library bioengineered recently. The good agreement between the computed and the experimental results for this library of networks, and additional tests, demonstrate that the new algorithm is robust and very successful in explaining the experimental data. The simulation software is available upon request. Supplementary material will be made available on the OUP server.

A knowledge base of the chemical compounds of intermediary metabolism.

PubMed

Karp, P D

1992-08-01

This paper describes a publicly available knowledge base of the chemical compounds involved in intermediary metabolism. We consider the motivations for constructing a knowledge base of metabolic compounds, the methodology by which it was constructed, and the information that it currently contains. Currently the knowledge base describes 981 compounds, listing for each: synonyms for its name, a systematic name, CAS registry number, chemical formula, molecular weight, chemical structure and two-dimensional display coordinates for the structure. The Compound Knowledge Base (CompoundKB) illustrates several methodological principles that should guide the development of biological knowledge bases. I argue that biological datasets should be made available in multiple representations to increase their accessibility to end users, and I present multiple representations of the CompoundKB (knowledge base, relational data base and ASN. 1 representations). I also analyze the general characteristics of these representations to provide an understanding of their relative advantages and disadvantages. Another principle is that the error rate of biological data bases should be estimated and documented-this analysis is performed for the CompoundKB.

The Economic Impact of Biosimilars on Chronic Immune-Mediated Inflammatory Diseases.

PubMed

Pentek, Marta; Zrubka, Zsombor; Gulacsi, Laszlo

2017-01-01

Biological drugs represent highly effective but costly treatments for chronic immunemediated inflammatory diseases posing substantial burden on health care budgets. Introduction of biosimilars since 2013 has brought forward the potential of market competition, and as a societal benefit, the hope of increased access at a lower cost. We aim to provide a descriptive review on economic aspects and market changes related to the introduction of biosimilar drugs. Our focus is on chronic immune-mediated inflammatory conditions in rheumatology, gastroenterology and dermatology. Based on available literature data, we discuss the determinants of access to biological treatment, summarize the available health economic evidences with special focus on cost-utility and budget impact analyses. Market penetration of biosimilars and their overall impact on biological markets are analyzed. Biosimilar markets are country specific due to differences in the regulatory and reimbursement systems. Cost-utility analyses suggest, that given the lower price of biosimilars, formerly established biological treatment sequence practices and the eligibility criteria for biological treatment deserve reconsideration. Budget impact analyses forecasted significant budget savings in various diagnoses and countries, providing opportunity for the treatment of more patients. Biosimilars may contribute to better patient-access and provide savings to governments. To increase their acceptability, further clinical evidences and real world experiences are needed, as well as education of physicians and patients. The high biosimilar penetration rates in Norway, Denmark and Poland suggest that policies which support interchanging from the reference product may be important drivers of biosimilar uptake. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

An energy balance concept for habitability.

PubMed

Hoehler, Tori M

2007-12-01

Habitability can be formulated as a balance between the biological demand for energy and the corresponding potential for meeting that demand by transduction of energy from the environment into biological process. The biological demand for energy is manifest in two requirements, analogous to the voltage and power requirements of an electrical device, which must both be met if life is to be supported. These requirements exhibit discrete (non-zero) minima whose magnitude is set by the biochemistry in question, and they are increased in quantifiable fashion by (i) deviations from biochemically optimal physical and chemical conditions and (ii) energy-expending solutions to problems of resource limitation. The possible rate of energy transduction is constrained by (i) the availability of usable free energy sources in the environment, (ii) limitations on transport of those sources into the cell, (iii) upper limits on the rate at which energy can be stored, transported, and subsequently liberated by biochemical mechanisms (e.g., enzyme saturation effects), and (iv) upper limits imposed by an inability to use "power" and "voltage" at levels that cause material breakdown. A system is habitable when the realized rate of energy transduction equals or exceeds the biological demand for energy. For systems in which water availability is considered a key aspect of habitability (e.g., Mars), the energy balance construct imposes additional, quantitative constraints that may help to prioritize targets in search-for-life missions. Because the biological need for energy is universal, the energy balance construct also helps to constrain habitability in systems (e.g., those envisioned to use solvents other than water) for which little constraint currently exists.

Geological and Chemical Factors that Impacted the Biological Utilization of Cobalt in the Archean Eon

NASA Astrophysics Data System (ADS)

Moore, Eli K.; Hao, Jihua; Prabhu, Anirudh; Zhong, Hao; Jelen, Ben I.; Meyer, Mike; Hazen, Robert M.; Falkowski, Paul G.

2018-03-01

The geosphere and biosphere coevolved and influenced Earth's biological and mineralogical diversity. Changing redox conditions influenced the availability of different transition metals, which are essential components in the active sites of oxidoreductases, proteins that catalyze electron transfer reactions across the tree of life. Despite its relatively low abundance in the environment, cobalt (Co) is a unique metal in biology due to its importance to a wide range of organisms as the metal center of vitamin B12 (aka cobalamin, Cbl). Cbl is vital to multiple methyltransferase enzymes involved in energetically favorable metabolic pathways. It is unclear how Co availability is linked to mineral evolution and weathering processes. Here we examine important biological functions of Co, as well as chemical and geological factors that may have influenced the utilization of Co early in the evolution of life. Only 66 natural minerals are known to contain Co as an essential element. However, Co is incorporated as a minor element in abundant rock-forming minerals, potentially representing a reliable source of Co as a trace element in marine systems due to weathering processes. We developed a mineral weathering model that indicates that dissolved Co was potentially more bioavailable in the Archean ocean under low S conditions than it is today. Mineral weathering, redox chemistry, Co complexation with nitrogen-containing organics, and hydrothermal environments were crucial in the incorporation of Co in primitive metabolic pathways. These chemical and geological characteristics of Co can inform the biological utilization of other trace metals in early forms of life.

biochem4j: Integrated and extensible biochemical knowledge through graph databases.

PubMed

Swainston, Neil; Batista-Navarro, Riza; Carbonell, Pablo; Dobson, Paul D; Dunstan, Mark; Jervis, Adrian J; Vinaixa, Maria; Williams, Alan R; Ananiadou, Sophia; Faulon, Jean-Loup; Mendes, Pedro; Kell, Douglas B; Scrutton, Nigel S; Breitling, Rainer

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and-crucially-the relationships between them. Such a resource should be extensible, such that newly discovered relationships-for example, those between novel, synthetic enzymes and non-natural products-can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists.

biochem4j: Integrated and extensible biochemical knowledge through graph databases

PubMed Central

Batista-Navarro, Riza; Dunstan, Mark; Jervis, Adrian J.; Vinaixa, Maria; Ananiadou, Sophia; Faulon, Jean-Loup; Kell, Douglas B.

2017-01-01

Biologists and biochemists have at their disposal a number of excellent, publicly available data resources such as UniProt, KEGG, and NCBI Taxonomy, which catalogue biological entities. Despite the usefulness of these resources, they remain fundamentally unconnected. While links may appear between entries across these databases, users are typically only able to follow such links by manual browsing or through specialised workflows. Although many of the resources provide web-service interfaces for computational access, performing federated queries across databases remains a non-trivial but essential activity in interdisciplinary systems and synthetic biology programmes. What is needed are integrated repositories to catalogue both biological entities and–crucially–the relationships between them. Such a resource should be extensible, such that newly discovered relationships–for example, those between novel, synthetic enzymes and non-natural products–can be added over time. With the introduction of graph databases, the barrier to the rapid generation, extension and querying of such a resource has been lowered considerably. With a particular focus on metabolic engineering as an illustrative application domain, biochem4j, freely available at http://biochem4j.org, is introduced to provide an integrated, queryable database that warehouses chemical, reaction, enzyme and taxonomic data from a range of reliable resources. The biochem4j framework establishes a starting point for the flexible integration and exploitation of an ever-wider range of biological data sources, from public databases to laboratory-specific experimental datasets, for the benefit of systems biologists, biosystems engineers and the wider community of molecular biologists and biological chemists. PMID:28708831

Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures

PubMed Central

Stanton, Kelly Patrick; Parisi, Fabio; Strino, Francesco; Rabin, Neta; Asp, Patrik; Kluger, Yuval

2013-01-01

Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated data sets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles. Furthermore, data representations that allow comparisons of genomic signals from different platforms and across species enhance our ability to leverage these large repositories. Here, we present a signal processing approach that characterizes protein–chromatin interaction patterns at length scales of several kilobases. This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals. We used 806 publicly available ChIP-seq experiments and showed that Arpeggio profiles with similar spectral densities shared biological properties. Arpeggio profiles of ChIP-seq data sets revealed characteristics that are not easily detected by standard peak finders. They also allowed us to relate sequencing data sets from different genomes, experimental platforms and protocols. Arpeggio is freely available at http://sourceforge.net/p/arpeggio/wiki/Home/. PMID:23873955

Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures.

PubMed

Stanton, Kelly Patrick; Parisi, Fabio; Strino, Francesco; Rabin, Neta; Asp, Patrik; Kluger, Yuval

2013-09-01

Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated data sets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles. Furthermore, data representations that allow comparisons of genomic signals from different platforms and across species enhance our ability to leverage these large repositories. Here, we present a signal processing approach that characterizes protein-chromatin interaction patterns at length scales of several kilobases. This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals. We used 806 publicly available ChIP-seq experiments and showed that Arpeggio profiles with similar spectral densities shared biological properties. Arpeggio profiles of ChIP-seq data sets revealed characteristics that are not easily detected by standard peak finders. They also allowed us to relate sequencing data sets from different genomes, experimental platforms and protocols. Arpeggio is freely available at http://sourceforge.net/p/arpeggio/wiki/Home/.

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Unicellular eukaryotes as models in cell and molecular biology: critical appraisal of their past and future value.

PubMed

Simon, Martin; Plattner, Helmut

2014-01-01

Unicellular eukaryotes have been appreciated as model systems for the analysis of crucial questions in cell and molecular biology. This includes Dictyostelium (chemotaxis, amoeboid movement, phagocytosis), Tetrahymena (telomere structure, telomerase function), Paramecium (variant surface antigens, exocytosis, phagocytosis cycle) or both ciliates (ciliary beat regulation, surface pattern formation), Chlamydomonas (flagellar biogenesis and beat), and yeast (S. cerevisiae) for innumerable aspects. Nowadays many problems may be tackled with "higher" eukaryotic/metazoan cells for which full genomic information as well as domain databases, etc., were available long before protozoa. Established molecular tools, commercial antibodies, and established pharmacology are additional advantages available for higher eukaryotic cells. Moreover, an increasing number of inherited genetic disturbances in humans have become elucidated and can serve as new models. Among lower eukaryotes, yeast will remain a standard model because of its peculiarities, including its reduced genome and availability in the haploid form. But do protists still have a future as models? This touches not only the basic understanding of biology but also practical aspects of research, such as fund raising. As we try to scrutinize, due to specific advantages some protozoa should and will remain favorable models for analyzing novel genes or specific aspects of cell structure and function. Outstanding examples are epigenetic phenomena-a field of rising interest. © 2014 Elsevier Inc. All rights reserved.

Extracting microRNA-gene relations from biomedical literature using distant supervision

PubMed Central

Clarke, Luka A.; Couto, Francisco M.

2017-01-01

Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text. MicroRNA regulation is an important biological process due to its close association with human diseases. The proposed method, IBRel, is based on distantly supervised multi-instance learning. We evaluated IBRel on three datasets, and the results were compared with a co-occurrence approach as well as a supervised machine learning algorithm. While supervised learning outperformed on two of those datasets, IBRel obtained an F-score 28.3 percentage points higher on the dataset for which there was no training set developed specifically. To demonstrate the applicability of IBRel, we used it to extract 27 miRNA-gene relations from recently published papers about cystic fibrosis. Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at https://github.com/AndreLamurias/IBRel. PMID:28263989

Extracting microRNA-gene relations from biomedical literature using distant supervision.

PubMed

Lamurias, Andre; Clarke, Luka A; Couto, Francisco M

2017-01-01

Many biomedical relation extraction approaches are based on supervised machine learning, requiring an annotated corpus. Distant supervision aims at training a classifier by combining a knowledge base with a corpus, reducing the amount of manual effort necessary. This is particularly useful for biomedicine because many databases and ontologies have been made available for many biological processes, while the availability of annotated corpora is still limited. We studied the extraction of microRNA-gene relations from text. MicroRNA regulation is an important biological process due to its close association with human diseases. The proposed method, IBRel, is based on distantly supervised multi-instance learning. We evaluated IBRel on three datasets, and the results were compared with a co-occurrence approach as well as a supervised machine learning algorithm. While supervised learning outperformed on two of those datasets, IBRel obtained an F-score 28.3 percentage points higher on the dataset for which there was no training set developed specifically. To demonstrate the applicability of IBRel, we used it to extract 27 miRNA-gene relations from recently published papers about cystic fibrosis. Our results demonstrate that our method can be successfully used to extract relations from literature about a biological process without an annotated corpus. The source code and data used in this study are available at https://github.com/AndreLamurias/IBRel.

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology.

PubMed

Waese, Jamie; Fan, Jim; Pasha, Asher; Yu, Hans; Fucile, Geoffrey; Shi, Ruian; Cumming, Matthew; Kelley, Lawrence A; Sternberg, Michael J; Krishnakumar, Vivek; Ferlanti, Erik; Miller, Jason; Town, Chris; Stuerzlinger, Wolfgang; Provart, Nicholas J

2017-08-01

A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an "app" on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research. © 2017 American Society of Plant Biologists. All rights reserved.

Impact of Release Rates on the Effectiveness of Augmentative Biological Control Agents

PubMed Central

Crowder, David W.

2007-01-01

To access the effect of augmentative biological control agents, 31 articles were reviewed that investigated the impact of release rates of 35 augmentative biological control agents on the control of 42 arthropod pests. In 64% of the cases, the release rate of the biological control agent did not significantly affect the density or mortality of the pest insect. Results where similar when parasitoidsor predators were utilized as the natural enemy. Within any order of natural enemy, there were more cases where release rates did not affect augmentative biological control than cases where release rates were significant. There were more cases in which release rates did not affect augmentative biological control when pests were from the orders Hemiptera, Acari, or Diptera, but not with pests from the order Lepidoptera. In most cases, there was an optimal release rate that produced effective control of a pest species. This was especially true when predators were used as a biological control agent. Increasing the release rate above the optimal rate did not improve control of the pest and thus would be economically detrimental. Lower release rates were of ten optimal when biological control was used in conjunction with insecticides. In many cases, the timing and method of biological control applications were more significant factors impacting the effectiveness of biological control than the release rate. Additional factors that may limit the relative impact of release rates include natural enemy fecundity, establishment rates, prey availability, dispersal, and cannibalism. PMID:20307240

Management of Rheumatoid Arthritis Patients with Interstitial Lung Disease: Safety of Biological Antirheumatic Drugs and Assessment of Pulmonary Fibrosis

PubMed Central

Mori, Shunsuke

2015-01-01

Interstitial lung disease (ILD) is one of the major causes of morbidity and mortality of patients with rheumatoid arthritis (RA). Accompanying the increased number of reports on the development or exacerbation of ILD in RA patients following therapy with biological disease-modifying antirheumatic drugs (DMARDs), RA-associated ILD (RA-ILD) has aroused renewed interest. Although such cases have been reported mainly in association with the use of tumor necrosis factor inhibitors, the use of other biological DMARDs has also become a matter of concern. Nevertheless, it is difficult to establish a causative relationship between the use of biological DMARDs and either the development or exacerbation of ILD. Such pulmonary complications may occur in the natural course of RA regardless of the use of biological DMARDs. Since rheumatologists currently aim to achieve remission in RA patients, the administration of biological DMARDs is increasing, even for those with RA-ILD. However, there are no reliable, evidence-based guidelines for deciding whether biological DMARDs can be safely introduced and continued in RA-ILD patients. A standardized staging system for pulmonary conditions of RA-ILD patients is needed when making therapeutic decisions at baseline and monitoring during biological DMARD therapy. Based on the available information regarding the safety of biological DMARDs and the predictive factors for a worse prognosis, this review discusses candidate parameters for risk evaluation of ILD in RA patients who are scheduled to receive biological antirheumatic therapy. PMID:26401101

Biological aerosol background characterization

NASA Astrophysics Data System (ADS)

Blatny, Janet; Fountain, Augustus W., III

2011-05-01

To provide useful information during military operations, or as part of other security situations, a biological aerosol detector has to respond within seconds or minutes to an attack by virulent biological agents, and with low false alarms. Within this time frame, measuring virulence of a known microorganism is extremely difficult, especially if the microorganism is of unknown antigenic or nucleic acid properties. Measuring "live" characteristics of an organism directly is not generally an option, yet only viable organisms are potentially infectious. Fluorescence based instruments have been designed to optically determine if aerosol particles have viability characteristics. Still, such commercially available biological aerosol detection equipment needs to be improved for their use in military and civil applications. Air has an endogenous population of microorganisms that may interfere with alarm software technologies. To design robust algorithms, a comprehensive knowledge of the airborne biological background content is essential. For this reason, there is a need to study ambient live bacterial populations in as many locations as possible. Doing so will permit collection of data to define diverse biological characteristics that in turn can be used to fine tune alarm algorithms. To avoid false alarms, improving software technologies for biological detectors is a crucial feature requiring considerations of various parameters that can be applied to suppress alarm triggers. This NATO Task Group will aim for developing reference methods for monitoring biological aerosol characteristics to improve alarm algorithms for biological detection. Additionally, they will focus on developing reference standard methodology for monitoring biological aerosol characteristics to reduce false alarm rates.

75 FR 17929 - Vaccines and Related Biological Products Advisory Committee; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-08

... detection methods not currently applied for the characterization of cell substrates, viral seeds, and other... May 7, 2010, in the morning, the committee will review and discuss available data regarding the... material available to the public no later than 2 business days before the meeting. If FDA is unable to post...

78 FR 40162 - Endangered and Threatened Wildlife and Plants; Notice of Availability of a Technical/Agency Draft...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-07-03

...-FF04E00000] Endangered and Threatened Wildlife and Plants; Notice of Availability of a Technical/Agency Draft... recovery potential. Restoring an endangered or threatened animal or plant to the point where it is again a... about the species' biology, and magnitude of threats. Therefore, this recovery plan only establishes...

Chemical and biological nonproliferation program. FY99 annual report

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2000-03-01

This document is the first of what will become an annual report documenting the progress made by the Chemical and Biological Nonproliferation Program (CBNP). It is intended to be a summary of the program's activities that will be of interest to both policy and technical audiences. This report and the annual CBNP Summer Review Meeting are important vehicles for communication with the broader chemical and biological defense and nonproliferation communities. The Chemical and Biological Nonproliferation Program Strategic Plan is also available and provides additional detail on the program's context and goals. The body of the report consists of an overviewmore » of the program's philosophy, goals and recent progress in the major program areas. In addition, an appendix is provided with more detailed project summaries that will be of interest to the technical community.« less

Investigating biological activity spectrum for novel quinoline analogues.

PubMed

Musiol, Robert; Jampilek, Josef; Kralova, Katarina; Richardson, Des R; Kalinowski, Danuta; Podeszwa, Barbara; Finster, Jacek; Niedbala, Halina; Palka, Anna; Polanski, Jaroslaw

2007-02-01

The lack of the wide spectrum of biological data is an important obstacle preventing the efficient molecular design. Quinoline derivatives are known to exhibit a variety of biological effects. In the current publication, we tested a series of novel quinoline analogues for their photosynthesis-inhibiting activity (the inhibition of photosynthetic electron transport in spinach chloroplasts (Spinacia oleracea L.) and the reduction of chlorophyll content in Chlorella vulgaris Beij.). Moreover, antiproliferative activity was measured using SK-N-MC neuroepithelioma cell line. We described the structure-activity relationships (SAR) between the chemical structure and biological effects of the synthesized compounds. We also measured the lipophilicity of the novel compounds by means of the RP-HPLC and illustrate the relationships between the RP-HPLC retention parameter logK (the logarithm of capacity factor K) and logP data calculated by available programs.

Evolution across the Curriculum: Microbiology

PubMed Central

Burmeister, Alita R.; Smith, James J.

2016-01-01

An integrated understanding of microbiology and evolutionary biology is essential for students pursuing careers in microbiology and healthcare fields. In this Perspective, we discuss the usefulness of evolutionary concepts and an overall evolutionary framework for students enrolled in microbiology courses. Further, we propose a set of learning goals for students studying microbial evolution concepts. We then describe some barriers to microbial evolution teaching and learning and encourage the continued incorporation of evidence-based teaching practices into microbiology courses at all levels. Next, we review the current status of microbial evolution assessment tools and describe some education resources available for teaching microbial evolution. Successful microbial evolution education will require that evolution be taught across the undergraduate biology curriculum, with a continued focus on applications and applied careers, while aligning with national biology education reform initiatives. Journal of Microbiology & Biology Education PMID:27158306

Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations

PubMed Central

Liao, David; Tlsty, Thea D.

2014-01-01

The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely ‘empirical’ equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods for in vitro and in vivo experiments. PMID:25097752

Neutron Imaging at the Oak Ridge National Laboratory: Application to Biological Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bilheux, Hassina Z; Cekanova, Maria; Bilheux, Jean-Christophe

2014-01-01

The Oak Ridge National Laboratory Neutron Sciences Directorate (NScD) has recently installed a neutron imaging beamline at the High Flux Isotope Reactor (HFIR) cold guide hall. The CG-1D beamline supports a broad range of user research spanning from engineering to material research, energy storage, additive manufacturing, vehicle technologies, archaeology, biology, and plant physiology. The beamline performance (spatial resolution, field of view, etc.) and its utilization for biological research are presented. The NScD is also considering a proposal to build the VENUS imaging beamline (beam port 10) at the Spallation Neutron Source (SNS). Unlike CG-1D which provides cold neutrons, VENUS willmore » offer a broad range of neutron wavelengths, from epithermal to cold, and enhanced contrast mechanisms. This new capability will also enable the imaging of thicker biological samples than is currently available at CG-1D. A brief overview of the VENUS capability for biological research is discussed.« less

When galectins recognize glycans: from biochemistry to physiology and back again.

PubMed

Di Lella, Santiago; Sundblad, Victoria; Cerliani, Juan P; Guardia, Carlos M; Estrin, Dario A; Vasta, Gerardo R; Rabinovich, Gabriel A

2011-09-20

In the past decade, increasing efforts have been devoted to the study of galectins, a family of evolutionarily conserved glycan-binding proteins with multifunctional properties. Galectins function, either intracellularly or extracellularly, as key biological mediators capable of monitoring changes occurring on the cell surface during fundamental biological processes such as cellular communication, inflammation, development, and differentiation. Their highly conserved structures, exquisite carbohydrate specificity, and ability to modulate a broad spectrum of biological processes have captivated a wide range of scientists from a wide spectrum of disciplines, including biochemistry, biophysics, cell biology, and physiology. However, in spite of enormous efforts to dissect the functions and properties of these glycan-binding proteins, limited information about how structural and biochemical aspects of these proteins can influence biological functions is available. In this review, we aim to integrate structural, biochemical, and functional aspects of this bewildering and ancient family of glycan-binding proteins and discuss their implications in physiologic and pathologic settings. © 2011 American Chemical Society

PROPER: global protein interaction network alignment through percolation matching.

PubMed

Kazemi, Ehsan; Hassani, Hamed; Grossglauser, Matthias; Pezeshgi Modarres, Hassan

2016-12-12

The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PPI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch .

The Minorities Affairs Committee of the American Society for Cell Biology-Fostering the Professional Development of Scientists from Underrepresented Minority Backgrounds.

PubMed

Segarra, Verónica A; Carrero-Martínez, Franklin; Shugart, Erika

2017-01-01

As part of its mission, the American Society for Cell Biology (ASCB) works to increase diversity in the scientific workforce, in part through the work of its Minorities Affairs Committee. It is for this reason that the ASCB was happy to welcome the special September 2016 issue of CBE-Life Sciences Education ( LSE ) focused on broadening participation. As a response to this special issue, we update our ASCB community and LSE readership on the society's efforts to broaden participation of underrepresented minorities in the biological sciences. © 2017 V. A. Segarra et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 485

NASA Technical Reports Server (NTRS)

1999-01-01

This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP-1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes-subject and author are included after the abstract section.

AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

PubMed Central

Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2016-01-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

Biosimilars in inflammatory bowel disease: A review of post-marketing experience.

PubMed

Deiana, Simona; Gabbani, Tommaso; Annese, Vito

2017-01-14

Biologic compounds are obtained from living organisms or cell cultures by means of biotechnology methods. A similar biologic drug, commonly called biosimilar, is a product copied by a native approved biologic drug whose license has expired. Biosimilar drugs usually are marketed at a lower price and provide important financial savings for public healthcare systems. Some differences between biosimilars and original biologic drugs might exist but they are acceptable if they fall within defined "boundaries of tolerance": differences in some features between the two molecules are considered important only if clinical relevant. Considering that the efficacy of the innovator biologic drug has already been established, the clinical studies required for approval of a biosimilar could be reduced compared with those required for the approval of the originator. In this review, real life data available in inflammatory bowel disease patients treated with biosimilars are reported, documenting in general satisfactory outcomes, sustained efficacy and no sign of increased immunogenicity, although, further controlled data are awaited.

Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 506

NASA Technical Reports Server (NTRS)

2000-01-01

This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP#2000-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes- subject and author are included after the abstract section.

Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 494

NASA Technical Reports Server (NTRS)

1999-01-01

This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth's atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes--subject and author are included after the abstract section.

An overview of computational life science databases & exchange formats of relevance to chemical biology research.

PubMed

Smalter Hall, Aaron; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2013-03-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities.

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes.

PubMed

Hassani-Pak, Keywan; Rawlings, Christopher

2017-06-13

Genetics and "omics" studies designed to uncover genotype to phenotype relationships often identify large numbers of potential candidate genes, among which the causal genes are hidden. Scientists generally lack the time and technical expertise to review all relevant information available from the literature, from key model species and from a potentially wide range of related biological databases in a variety of data formats with variable quality and coverage. Computational tools are needed for the integration and evaluation of heterogeneous information in order to prioritise candidate genes and components of interaction networks that, if perturbed through potential interventions, have a positive impact on the biological outcome in the whole organism without producing negative side effects. Here we review several bioinformatics tools and databases that play an important role in biological knowledge discovery and candidate gene prioritization. We conclude with several key challenges that need to be addressed in order to facilitate biological knowledge discovery in the future.

Aerospace Medicine and Biology: A Continuing Bibliography with Indexes. Supplement 496

NASA Technical Reports Server (NTRS)

2000-01-01

This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP#2000-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth#s atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes#subject and author are included after the abstract section.

Mixed-Methods Design in Biology Education Research: Approach and Uses.

PubMed

Warfa, Abdi-Rizak M

Educational research often requires mixing different research methodologies to strengthen findings, better contextualize or explain results, or minimize the weaknesses of a single method. This article provides practical guidelines on how to conduct such research in biology education, with a focus on mixed-methods research (MMR) that uses both quantitative and qualitative inquiries. Specifically, the paper provides an overview of mixed-methods design typologies most relevant in biology education research. It also discusses common methodological issues that may arise in mixed-methods studies and ways to address them. The paper concludes with recommendations on how to report and write about MMR. © 2016 L. A.-R. M. Warfa. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Guidelines for biological treatment of substance use and related disorders, part 1: Alcoholism, first revision.

PubMed

Soyka, Michael; Kranzler, Henry R; Hesselbrock, Victor; Kasper, Siegfried; Mutschler, Jochen; Möller, Hans-Jürgen

2017-03-01

These practice guidelines for the biological treatment of alcohol use disorders are an update of the first edition, published in 2008, which was developed by an international Task Force of the World Federation of Societies of Biological Psychiatry (WFSBP). For this 2016 revision, we performed a systematic review (MEDLINE/PUBMED database, Cochrane Library) of all available publications pertaining to the biological treatment of alcoholism and extracted data from national guidelines. The Task Force evaluated the identified literature with respect to the strength of evidence for the efficacy of each medication and subsequently categorised it into six levels of evidence (A-F) and five levels of recommendation (1-5). Thus, the current guidelines provide a clinically and scientifically relevant, evidence-based update of our earlier recommendations. These guidelines are intended for use by clinicians and practitioners who evaluate and treat people with alcohol use disorders and are primarily concerned with the biological treatment of adults with such disorders.

Aerospace Medicine and Biology: A Continuing Bibliography With Indexes. Supplement 499

NASA Technical Reports Server (NTRS)

2000-01-01

This supplemental issue of Aerospace Medicine and Biology, A Continuing Bibliography with Indexes (NASA/SP#1999-7011) lists reports, articles, and other documents recently announced in the NASA STI Database. In its subject coverage, Aerospace Medicine and Biology concentrates on the biological, physiological, psychological, and environmental effects to which humans are subjected during and following simulated or actual flight in the Earth#s atmosphere or in interplanetary space. References describing similar effects on biological organisms of lower order are also included. Such related topics as sanitary problems, pharmacology, toxicology, safety and survival, life support systems, exobiology, and personnel factors receive appropriate attention. Applied research receives the most emphasis, but references to fundamental studies and theoretical principles related to experimental development also qualify for inclusion. Each entry in the publication consists of a standard bibliographic citation accompanied, in most cases, by an abstract. The NASA CASI price code table, addresses of organizations, and document availability information are included before the abstract section. Two indexes-subject and author are included after the abstract section.

Comparative systems biology between human and animal models based on next-generation sequencing methods.

PubMed

Zhao, Yu-Qi; Li, Gong-Hua; Huang, Jing-Fei

2013-04-01

Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

Availability: A Metric for Nucleic Acid Strand Displacement Systems

PubMed Central

2016-01-01

DNA strand displacement systems have transformative potential in synthetic biology. While powerful examples have been reported in DNA nanotechnology, such systems are plagued by leakage, which limits network stability, sensitivity, and scalability. An approach to mitigate leakage in DNA nanotechnology, which is applicable to synthetic biology, is to introduce mismatches to complementary fuel sequences at key locations. However, this method overlooks nuances in the secondary structure of the fuel and substrate that impact the leakage reaction kinetics in strand displacement systems. In an effort to quantify the impact of secondary structure on leakage, we introduce the concepts of availability and mutual availability and demonstrate their utility for network analysis. Our approach exposes vulnerable locations on the substrate and quantifies the secondary structure of fuel strands. Using these concepts, a 4-fold reduction in leakage has been achieved. The result is a rational design process that efficiently suppresses leakage and provides new insight into dynamic nucleic acid networks. PMID:26875531

Triage, monitoring, and treatment of mass casualty events involving chemical, biological, radiological, or nuclear agents

PubMed Central

Ramesh, Aruna C.; Kumar, S.

2010-01-01

In a mass casualty situation due to chemical, biological, radiological, or nuclear (CBRN) event, triage is absolutely required for categorizing the casualties in accordance with medical care priorities. Dealing with a CBRN event always starts at the local level. Even before the detection and analysis of agents can be undertaken, zoning, triage, decontamination, and treatment should be initiated promptly. While applying the triage system, the available medical resources and maximal utilization of medical assets should be taken into consideration by experienced triage officers who are most familiar with the natural course of the injury presented and have detailed information on medical assets. There are several triage systems that can be applied to CBRN casualties. With no one standardized system globally or nationally available, it is important for deploying a triage and decontamination system which is easy to follow and flexible to the available medical resources, casualty number, and severity of injury. PMID:21829319

Data Integration and Mining for Synthetic Biology Design.

PubMed

Mısırlı, Göksel; Hallinan, Jennifer; Pocock, Matthew; Lord, Phillip; McLaughlin, James Alastair; Sauro, Herbert; Wipat, Anil

2016-10-21

One aim of synthetic biologists is to create novel and predictable biological systems from simpler modular parts. This approach is currently hampered by a lack of well-defined and characterized parts and devices. However, there is a wealth of existing biological information, which can be used to identify and characterize biological parts, and their design constraints in the literature and numerous biological databases. However, this information is spread among these databases in many different formats. New computational approaches are required to make this information available in an integrated format that is more amenable to data mining. A tried and tested approach to this problem is to map disparate data sources into a single data set, with common syntax and semantics, to produce a data warehouse or knowledge base. Ontologies have been used extensively in the life sciences, providing this common syntax and semantics as a model for a given biological domain, in a fashion that is amenable to computational analysis and reasoning. Here, we present an ontology for applications in synthetic biology design, SyBiOnt, which facilitates the modeling of information about biological parts and their relationships. SyBiOnt was used to create the SyBiOntKB knowledge base, incorporating and building upon existing life sciences ontologies and standards. The reasoning capabilities of ontologies were then applied to automate the mining of biological parts from this knowledge base. We propose that this approach will be useful to speed up synthetic biology design and ultimately help facilitate the automation of the biological engineering life cycle.

Quantitative biology: where modern biology meets physical sciences.

PubMed

Shekhar, Shashank; Zhu, Lian; Mazutis, Linas; Sgro, Allyson E; Fai, Thomas G; Podolski, Marija

2014-11-05

Quantitative methods and approaches have been playing an increasingly important role in cell biology in recent years. They involve making accurate measurements to test a predefined hypothesis in order to compare experimental data with predictions generated by theoretical models, an approach that has benefited physicists for decades. Building quantitative models in experimental biology not only has led to discoveries of counterintuitive phenomena but has also opened up novel research directions. To make the biological sciences more quantitative, we believe a two-pronged approach needs to be taken. First, graduate training needs to be revamped to ensure biology students are adequately trained in physical and mathematical sciences and vice versa. Second, students of both the biological and the physical sciences need to be provided adequate opportunities for hands-on engagement with the methods and approaches necessary to be able to work at the intersection of the biological and physical sciences. We present the annual Physiology Course organized at the Marine Biological Laboratory (Woods Hole, MA) as a case study for a hands-on training program that gives young scientists the opportunity not only to acquire the tools of quantitative biology but also to develop the necessary thought processes that will enable them to bridge the gap between these disciplines. © 2014 Shekhar, Zhu, Mazutis, Sgro, Fai, and Podolski. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Soilcrust References

Science.gov Websites

Soil Crust Home Crust 101 Advanced Gallery References CCERS Site Links Updated: April 24, 2006 References The complete biological soil crust reference list is available in three formats: HTML Version

Comprehensive, comprehensible, distributed and intelligent databases: current status.

PubMed

Frishman, D; Heumann, K; Lesk, A; Mewes, H W

1998-01-01

It is only a matter of time until a user will see not many but one integrated database of information for molecular biology. Is this true? Is it a good thing? Why will it happen? Where are we now? What developments are fostering and what developments are impeding progress towards this end? A list of WWW resources devoted to database issues in molecular biology is available at http://www.mips.biochem.mpg.de frishman@mips.biochem.mpg.de

LEGO® Bricks as Building Blocks for Centimeter-Scale Biological Environments: The Case of Plants

PubMed Central

Lind, Kara R.; Sizmur, Tom; Benomar, Saida; Miller, Anthony; Cademartiri, Ludovico

2014-01-01

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil. PMID:24963716

LEGO® bricks as building blocks for centimeter-scale biological environments: the case of plants.

PubMed

Lind, Kara R; Sizmur, Tom; Benomar, Saida; Miller, Anthony; Cademartiri, Ludovico

2014-01-01

LEGO bricks are commercially available interlocking pieces of plastic that are conventionally used as toys. We describe their use to build engineered environments for cm-scale biological systems, in particular plant roots. Specifically, we take advantage of the unique modularity of these building blocks to create inexpensive, transparent, reconfigurable, and highly scalable environments for plant growth in which structural obstacles and chemical gradients can be precisely engineered to mimic soil.

Remote sensing and extractable biological resources

NASA Technical Reports Server (NTRS)

Cronin, L. E.

1972-01-01

The nature and quantity of extractable biological resources available in the Chesapeake Bay are discussed. The application of miniaturized radio sensors to track the movement of fish and birds is described. The specific uses of remote sensors for detecting and mapping areas of algae, red tide, thermal pollution, and vegetation beds are presented. The necessity for obtaining information on the physical, chemical, and meteorological features of the entire bay in order to provide improved resources management is emphasized.

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

PubMed Central

Kuleshov, Maxim V.; Jones, Matthew R.; Rouillard, Andrew D.; Fernandez, Nicolas F.; Duan, Qiaonan; Wang, Zichen; Koplev, Simon; Jenkins, Sherry L.; Jagodnik, Kathleen M.; Lachmann, Alexander; McDermott, Michael G.; Monteiro, Caroline D.; Gundersen, Gregory W.; Ma'ayan, Avi

2016-01-01

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr. PMID:27141961

Recent developments of ion sources for life-science studies at the Heavy Ion Medical Accelerator in Chiba (invited)

NASA Astrophysics Data System (ADS)

Kitagawa, A.; Drentje, A. G.; Fujita, T.; Muramatsu, M.; Fukushima, K.; Shiraishi, N.; Suzuki, T.; Takahashi, K.; Takasugi, W.; Biri, S.; Rácz, R.; Kato, Y.; Uchida, T.; Yoshida, Y.

2016-02-01

With about 1000-h of relativistic high-energy ion beams provided by Heavy Ion Medical Accelerator in Chiba, about 70 users are performing various biology experiments every year. A rich variety of ion species from hydrogen to xenon ions with a dose rate of several Gy/min is available. Carbon, iron, silicon, helium, neon, argon, hydrogen, and oxygen ions were utilized between 2012 and 2014. Presently, three electron cyclotron resonance ion sources (ECRISs) and one Penning ion source are available. Especially, the two frequency heating techniques have improved the performance of an 18 GHz ECRIS. The results have satisfied most requirements for life-science studies. In addition, this improved performance has realized a feasible solution for similar biology experiments with a hospital-specified accelerator complex.

Biological phosphorus cycling in dryland regions

USGS Publications Warehouse

Belnap, Jayne; Bunemann, Else; Oberson, Astrid; Frossard, Emmanuel

2011-01-01

The relatively few studies done on phosphorus (P) cycling in arid and semiarid lands (drylands) show many factors that distinguish P cycling in drylands from that in more mesic regions. In drylands, most biologically relevant P inputs and losses are from the deposition and loss of dust. Horizontal and vertical redistribution of P is an important process. P is concentrated at the soil surface and thus vulnerable to loss via erosion. High pH and CaCO3 limit P bioavailability, and low rainfall limits microbe and plant ability to free abiotically bound P via exudates, thus making it available for uptake. Many invasive plants are able to access recalcitrant P more effectively than are native plants. As P availability depends on soil moisture and temperature, climate change is expected to have large impacts on P cycling

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

PubMed

Lan, Haidong; Chan, Yuandong; Xu, Kai; Schmidt, Bertil; Peng, Shaoliang; Liu, Weiguo

2016-07-19

Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level fine-grained parallelism. Furthermore, we re-organize the sequence datasets and use Xeon Phi shuffle operations to improve I/O efficiency. Evaluations show that our method achieves a peak overall performance up to 220 GCUPS for scanning real protein sequence databanks on a single node consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of sequence length and size, and number of compute nodes for both database scanning and multiple sequence alignment. Furthermore, the achieved performance is highly competitive in comparison to optimized Xeon Phi and GPU implementations. Our implementation is available at https://github.com/turbo0628/LSDBS-mpi .

Biological sequence compression algorithms.

PubMed

Matsumoto, T; Sadakane, K; Imai, H

2000-01-01

Today, more and more DNA sequences are becoming available. The information about DNA sequences are stored in molecular biology databases. The size and importance of these databases will be bigger and bigger in the future, therefore this information must be stored or communicated efficiently. Furthermore, sequence compression can be used to define similarities between biological sequences. The standard compression algorithms such as gzip or compress cannot compress DNA sequences, but only expand them in size. On the other hand, CTW (Context Tree Weighting Method) can compress DNA sequences less than two bits per symbol. These algorithms do not use special structures of biological sequences. Two characteristic structures of DNA sequences are known. One is called palindromes or reverse complements and the other structure is approximate repeats. Several specific algorithms for DNA sequences that use these structures can compress them less than two bits per symbol. In this paper, we improve the CTW so that characteristic structures of DNA sequences are available. Before encoding the next symbol, the algorithm searches an approximate repeat and palindrome using hash and dynamic programming. If there is a palindrome or an approximate repeat with enough length then our algorithm represents it with length and distance. By using this preprocessing, a new program achieves a little higher compression ratio than that of existing DNA-oriented compression algorithms. We also describe new compression algorithm for protein sequences.

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT)

PubMed Central

Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

2016-01-01

Abstract Background During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CTvlab) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. New information The Micro-CTvlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CTvlab can be accessed either on a normal computer or through a dedicated version for mobile devices. PMID:27956848

Micro-CTvlab: A web based virtual gallery of biological specimens using X-ray microtomography (micro-CT).

PubMed

Keklikoglou, Kleoniki; Faulwetter, Sarah; Chatzinikolaou, Eva; Michalakis, Nikitas; Filiopoulou, Irene; Minadakis, Nikos; Panteri, Emmanouela; Perantinos, George; Gougousis, Alexandros; Arvanitidis, Christos

2016-01-01

During recent years, X-ray microtomography (micro-CT) has seen an increasing use in biological research areas, such as functional morphology, taxonomy, evolutionary biology and developmental research. Micro-CT is a technology which uses X-rays to create sub-micron resolution images of external and internal features of specimens. These images can then be rendered in a three-dimensional space and used for qualitative and quantitative 3D analyses. However, the online exploration and dissemination of micro-CT datasets are rarely made available to the public due to their large size and a lack of dedicated online platforms for the interactive manipulation of 3D data. Here, the development of a virtual micro-CT laboratory (Micro-CT vlab ) is described, which can be used by everyone who is interested in digitisation methods and biological collections and aims at making the micro-CT data exploration of natural history specimens freely available over the internet. The Micro-CT vlab offers to the user virtual image galleries of various taxa which can be displayed and downloaded through a web application. With a few clicks, accurate, detailed and three-dimensional models of species can be studied and virtually dissected without destroying the actual specimen. The data and functions of the Micro-CT vlab can be accessed either on a normal computer or through a dedicated version for mobile devices.

Novel and rare prenyllipids - Occurrence and biological activity.

PubMed

Szymańska, Renata; Kruk, Jerzy

2018-01-01

The data presented indicate that there is a variety of unique prenyllipids, often of very limited taxonomic distribution, whose origin, biosynthesis, metabolism and biological function deserves to be elucidated. These compounds include tocoenols, tocochromanol esters, tocochromanol acids, plastoquinones and ubiquinones. Additionally, based on the available data, it can be assumed that there are still unrecognized prenyllipids, like prenylquinols fatty acid esters of the hydroquinone ring, including prenylquinol phosphates, and others, whose biological function might be of great importance. Our knowledge of these compounds is not only important from the scientific point of view, but may also be of practical significance to medicine, pharmacy or cosmetics. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Chemical regulators of plant hormones and their applications in basic research and agriculture.

PubMed

Jiang, Kai; Asami, Tadao

2018-04-20

Plant hormones are small molecules that play versatile roles in regulating plant growth, development, and responses to the environment. Classic methodologies, including genetics, analytic chemistry, biochemistry, and molecular biology, have contributed to the progress in plant hormone studies. In addition, chemical regulators of plant hormone functions have been important in such studies. Today, synthetic chemicals, including plant growth regulators, are used to study and manipulate biological systems, collectively referred to as chemical biology. Here, we summarize the available chemical regulators and their contributions to plant hormone studies. We also pose questions that remain to be addressed in plant hormone studies and that might be solved with the help of chemical regulators.

Utility of QR codes in biological collections

PubMed Central

Diazgranados, Mauricio; Funk, Vicki A.

2013-01-01

Abstract The popularity of QR codes for encoding information such as URIs has increased exponentially in step with the technological advances and availability of smartphones, digital tablets, and other electronic devices. We propose using QR codes on specimens in biological collections to facilitate linking vouchers’ electronic information with their associated collections. QR codes can efficiently provide such links for connecting collections, photographs, maps, ecosystem notes, citations, and even GenBank sequences. QR codes have numerous advantages over barcodes, including their small size, superior security mechanisms, increased complexity and quantity of information, and low implementation cost. The scope of this paper is to initiate an academic discussion about using QR codes on specimens in biological collections. PMID:24198709