Biological risk indicators for recurrent non-specific low back pain in adolescents.

Science.gov (United States)

Jones, M A; Stratton, G; Reilly, T; Unnithan, V B

2005-03-01

A matched case-control study was carried out to evaluate biological risk indicators for recurrent non-specific low back pain in adolescents. Adolescents with recurrent non-specific low back pain (symptomatic; n = 28; mean (SD) age 14.9 (0.7) years) and matched controls (asymptomatic; n = 28; age 14.9 (0.7) years) with no history of non-specific low back pain participated. Measures of stature, mass, sitting height, sexual maturity (Tanner self assessment), lateral flexion of the spine, lumbar sagittal plane mobility (modified Schober), hip range of motion (Leighton flexometer), back and hamstring flexibility (sit and reach), and trunk muscle endurance (number of sit ups) were performed using standardised procedures with established reliability. Backward stepwise logistic regression analysis was performed, with the presence/absence of recurrent low back pain as the dependent variable and the biological measures as the independent variables. Hip range of motion, trunk muscle endurance, lumbar sagittal plane mobility, and lateral flexion of the spine were identified as significant risk indicators of recurrent low back pain (plow back pain in a group of adolescents. These risk indicators identify the potential for exercise as a primary or secondary prevention method.

Teaching Methods in Biology Education and Sustainability Education Including Outdoor Education for Promoting Sustainability--A Literature Review

Science.gov (United States)

Jeronen, Eila; Palmberg, Irmeli; Yli-Panula, Eija

2017-01-01

There are very few studies concerning the importance of teaching methods in biology education and environmental education including outdoor education for promoting sustainability at the levels of primary and secondary schools and pre-service teacher education. The material was selected using special keywords from biology and sustainable education…

Biological monitoring of radiation exposure

Science.gov (United States)

Horneck, G.

1998-11-01

Complementary to physical dosimetry, biological dosimetry systems have been developed and applied which weight the different components of environmental radiation according to their biological efficacy. They generally give a record of the accumulated exposure of individuals with high sensitivity and specificity for the toxic agent under consideration. Basically three different types of biological detecting/monitoring systems are available: (i) intrinsic biological dosimeters that record the individual radiation exposure (humans, plants, animals) in measurable units. For monitoring ionizing radiation exposure, in situ biomarkers for genetic (e.g. chromosomal aberrations in human lymphocytes, germ line minisatellite mutation rates) or metabolic changes in serum, plasma and blood (e.g. serum lipids, lipoproteins, lipid peroxides, melatonin, antibody titer) have been used. (ii) Extrinsic biological dosimeters/indicators that record the accumulated dose in biological model systems. Their application includes long-term monitoring of changes in environmental UV radiation and its biological implications as well as dosimetry of personal UV exposure. (iii) Biological detectors/biosensors for genotoxic substances and agents such as bacterial assays (e.g. Ames test, SOS-type test) that are highly sensitive to genotoxins with high specificity. They may be applicable for different aspects in environmental monitoring including the International Space Station.

A method to determine site-specific, anisotropic fracture toughness in biological materials

International Nuclear Information System (INIS)

Bechtle, Sabine; Özcoban, Hüseyin; Yilmaz, Ezgi D.; Fett, Theo; Rizzi, Gabriele; Lilleodden, Erica T.; Huber, Norbert; Schreyer, Andreas; Swain, Michael V.; Schneider, Gerold A.

2012-01-01

Many biological materials are hierarchically structured, with highly anisotropic structures and properties on several length scales. To characterize the mechanical properties of such materials, detailed testing methods are required that allow precise and site-specific measurements on several length scales. We propose a fracture toughness measurement technique based on notched focused ion beam prepared cantilevers of lower and medium micron size scales. Using this approach, site-specific fracture toughness values in dental enamel were determined. The usefulness and challenges of the method are discussed.

Stepfather or biological father? Education-specific pathways of postdivorce fatherhood

Directory of Open Access Journals (Sweden)

Christine Schnor

2017-11-01

Full Text Available Background: Men are commonly assigned the role of economic providers in the family, and education informs about their capacity to fulfil this role. Yet having biological ties to coresident children can determine the man's willingness to step into the provider role. This study investigates how education is linked to fatherhood after divorce, distinguishing between biological father and stepfather positions. Methods: We analysed life course data from 1,111 divorced Belgian men collected in the 'Divorce in Flanders' project. We used descriptive methods of sequence analysis to illustrate the pathways of postdivorce fatherhood. In multinomial logistic regressions, we estimated the likelihood of, firstly, being a father with coresident biological children or/and stepchildren and, secondly, repartnering with a mother and fathering children in this union. Results: Divorced men's family situation depend on their educational levels. More educated men are more often in the role of a resident biological father, whereas the less educated men are more often stepfathers. Men's resident arrangement for first-marriage children, their selection into a new union and the parental status of their new partner help explaining educational differences in post-divorce father positions. Highly educated men live more often with their children from first marriage and repartner more often and especially women without own coresident children, which is beneficial for their transition to a post-divorce birth. Contribution: The findings suggest that both capacity and willingness to support the postdivorce family are lower among the less educated. These education-specific pathways of postdivorce fatherhood are likely to enhance social inequalities.

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

Science.gov (United States)

Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

2016-01-19

Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

Plant synthetic biology.

Science.gov (United States)

Liu, Wusheng; Stewart, C Neal

2015-05-01

Plant synthetic biology is an emerging field that combines engineering principles with plant biology toward the design and production of new devices. This emerging field should play an important role in future agriculture for traditional crop improvement, but also in enabling novel bioproduction in plants. In this review we discuss the design cycles of synthetic biology as well as key engineering principles, genetic parts, and computational tools that can be utilized in plant synthetic biology. Some pioneering examples are offered as a demonstration of how synthetic biology can be used to modify plants for specific purposes. These include synthetic sensors, synthetic metabolic pathways, and synthetic genomes. We also speculate about the future of synthetic biology of plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

The female gametophyte: an emerging model for cell type-specific systems biology in plant development

Directory of Open Access Journals (Sweden)

Marc William Schmid

2015-11-01

Full Text Available Systems biology, a holistic approach describing a system emerging from the interactions of its molecular components, critically depends on accurate qualitative determination and quantitative measurements of these components. Development and improvement of large-scale profiling methods (omics now facilitates comprehensive measurements of many relevant molecules. For multicellular organisms, such as animals, fungi, algae, and plants, the complexity of the system is augmented by the presence of specialized cell types and organs, and a complex interplay within and between them. Cell type-specific analyses are therefore crucial for the understanding of developmental processes and environmental responses. This review first gives an overview of current methods used for large-scale profiling of specific cell types exemplified by recent advances in plant biology. The focus then lies on suitable model systems to study plant development and cell type specification. We introduce the female gametophyte of flowering plants as an ideal model to study fundamental developmental processes. Moreover, the female reproductive lineage is of importance for the emergence of evolutionary novelties such as an unequal parental contribution to the tissue nurturing the embryo or the clonal production of seeds by asexual reproduction (apomixis. Understanding these processes is not only interesting from a developmental or evolutionary perspective, but bears great potential for further crop improvement and the simplification of breeding efforts. We finally highlight novel methods, which are already available or which will likely soon facilitate large-scale profiling of the specific cell types of the female gametophyte in both model and non-model species. We conclude that it may take only few years until an evolutionary systems biology approach toward female gametogenesis may decipher some of its biologically most interesting and economically most valuable processes.

Green mathematics: Benefits of including biological variation in your data analysis

NARCIS (Netherlands)

Tijskens, L.M.M.; Schouten, R.E.; Unuk, T.; Simcic, M.

2015-01-01

Biological variation is omnipresent in nature. It contains useful information that is neglected by the usually applied statistical procedures. To extract this information special procedures have to be applied. Biological variation is seen in properties (e.g. size, colour, firmness), but the

Integrative Biological Chemistry Program Includes the Use of Informatics Tools, GIS and SAS Software Applications

Science.gov (United States)

D'Souza, Malcolm J.; Kashmar, Richard J.; Hurst, Kent; Fiedler, Frank; Gross, Catherine E.; Deol, Jasbir K.; Wilson, Alora

2015-01-01

Wesley College is a private, primarily undergraduate minority-serving institution located in the historic district of Dover, Delaware (DE). The College recently revised its baccalaureate biological chemistry program requirements to include a one-semester Physical Chemistry for the Life Sciences course and project-based experiential learning…

Knowledge Enrichment Analysis for Human Tissue- Specific Genes Uncover New Biological Insights

Directory of Open Access Journals (Sweden)

Gong Xiu-Jun

2012-06-01

Full Text Available The expression and regulation of genes in different tissues are fundamental questions to be answered in biology. Knowledge enrichment analysis for tissue specific (TS and housekeeping (HK genes may help identify their roles in biological process or diseases and gain new biological insights.In this paper, we performed the knowledge enrichment analysis for 17,343 genes in 84 human tissues using Gene Set Enrichment Analysis (GSEA and Hypergeometric Analysis (HA against three biological ontologies: Gene Ontology (GO, KEGG pathways and Disease Ontology (DO respectively.The analyses results demonstrated that the functions of most gene groups are consistent with their tissue origins. Meanwhile three interesting new associations for HK genes and the skeletal muscle tissuegenes are found. Firstly, Hypergeometric analysis against KEGG database for HK genes disclosed that three disease terms (Parkinson’s disease, Huntington’s disease, Alzheimer’s disease are intensively enriched.Secondly, Hypergeometric analysis against the KEGG database for Skeletal Muscle tissue genes shows that two cardiac diseases of “Hypertrophic cardiomyopathy (HCM” and “Arrhythmogenic right ventricular cardiomyopathy (ARVC” are heavily enriched, which are also considered as no relationship with skeletal functions.Thirdly, “Prostate cancer” is intensively enriched in Hypergeometric analysis against the disease ontology (DO for the Skeletal Muscle tissue genes, which is a much unexpected phenomenon.

7 CFR 1755.98 - List of telecommunications specifications included in other 7 CFR parts.

Science.gov (United States)

2010-01-01

... 7 Agriculture 11 2010-01-01 2010-01-01 false List of telecommunications specifications included in... (Continued) RURAL UTILITIES SERVICE, DEPARTMENT OF AGRICULTURE TELECOMMUNICATIONS POLICIES ON SPECIFICATIONS, ACCEPTABLE MATERIALS, AND STANDARD CONTRACT FORMS § 1755.98 List of telecommunications specifications...

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Science.gov (United States)

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

Lysyl oxidase: properties, specificity, and biological roles inside and outside of the cell.

Science.gov (United States)

Kagan, Herbert M; Li, Wande

2003-03-01

Lysyl oxidase (LO) plays a critical role in the formation and repair of the extracellular matrix (ECM) by oxidizing lysine residues in elastin and collagen, thereby initiating the formation of covalent crosslinkages which stabilize these fibrous proteins. Its catalytic activity depends upon both its copper cofactor and a unique carbonyl cofactor and has been shown to extend to a variety of basic globular proteins, including histone H1. Although the three-dimensional structure of LO has yet to be determined, the present treatise offers hypotheses based upon its primary sequence, which may underlie the prominent electrostatic component of its unusual substrate specificity as well as the catalysis-suppressing function of the propeptide domain of prolysyl oxidase. Recent studies have demonstrated that LO appears to function within the cell in a manner, which strongly modifies cellular activity. Newly discovered LO-like proteins also likely play unique roles in biology. Copyright 2002 Wiley-Liss, Inc.

A mathematical model of the accumulation of radionuclides by oysters (C. virginica) aquacultured in the effluent of a nuclear power reactor to include major biological parameters

International Nuclear Information System (INIS)

Hess, C.T.; Smith, C.W.; Price, A.H.

1977-01-01

The uptake, accumulation and loss of radionuclides by the American oyster (C. virginica) aquacultured in the effluent of a nuclear power reactor has been measured monthly for 3 yr at four field stations in the Montsweag Estuary of the Sheepscot River and at a control station in the nearby Damariscotta River Estuary, southern central coastal Maine, U.S.A. A mathematical model for the time variation of the specific activity of the oysters has been developed to include the physical half-lives of the various radionuclides, the biological half-lives of the various radionuclides (biological depuration), the water temperature (oyster hibernation) and shell growth. The resulting first order linear differential equation incorporating these phenomena is driven by the liquid radionuclide effluent release of the Maine Yankee Nuclear Reactor. Comparison of the monthly measurements of the specific activity for 58 Co, 60 Co, 54 Mn, 134 Cs and 137 Cs in oysters with model calculations show close agreement over all ranges of variation observed. A special feature of this mathematical model is its ability to describe the non-chemostatic field situation. (author)

Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris

Science.gov (United States)

Martinez, Jennifer S [Santa Fe, NM; Swanson, Basil I [Los Alamos, NM; Grace, Karen M [Los Alamos, NM; Grace, Wynne K [Los Alamos, NM; Shreve, Andrew P [Santa Fe, NM

2009-06-02

An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

Integrating biological redesign: where synthetic biology came from and where it needs to go.

Science.gov (United States)

Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

2014-03-27

Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

Synthesis of molecules of biological interest labelled with high specific activity tritium

International Nuclear Information System (INIS)

Petillot, Yves

1975-01-01

Labelled molecules are artificial organic compounds possessing one or several radioactive or steady isotopic atoms. Using tritium to label molecules presents several benefits: a raw material easy to obtain with a high purity and at reasonable cost; synthesised labelled molecules displaying high specific activities very interesting in molecular biology; high resolution of radiographies; relatively simple and quick introduction of tritium atoms in complex molecules. Thus, this report for graduation in organic chemistry addresses the synthesis and study of new labelled molecules which belong to families of organic compounds which have fundamental activities in biology: uridine 3 H-5,6 and thymidine 3 H-methyl which are nucleotides which intervene under the form of phosphates in the synthesis of nucleic acids, oestradiol 3 H-2,4,6,7 which is a powerful estrogenic hormone which naturally secreted by the ovary; and noradrenaline 3 H-1,1' and dopamine 3 H-1,2 which are usually secreted by adrenal medulla and have multiple actions on the nervous system

Of arrows and flows. Causality, determination, and specificity in the Central Dogma of molecular biology.

Science.gov (United States)

Fantini, Bernardino

2006-01-01

From its first proposal, the Central Dogma had a graphical form, complete with arrows of different types, and this form quickly became its standard presentation. In different scientific contexts, arrows have different meanings and in this particular case the arrows indicated the flow of information among different macromolecules. A deeper analysis illustrates that the arrows also imply a causal statement, directly connected to the causal role of genetic information. The author suggests a distinction between two different kinds of causal links, defined as 'physical causality' and 'biological determination', both implied in the production of biological specificity.

DC-ATLAS: a systems biology resource to dissect receptor specific signal transduction in dendritic cells.

NARCIS (Netherlands)

Cavalieri, D.; Rivero, D.; Beltrame, L.; Buschow, S.I.; Calura, E.; Rizzetto, L.; Gessani, S.; Gauzzi, M.C.; Reith, W.; Baur, A.; Bonaiuti, R.; Brandizi, M.; Filippo, C. De; D'Oro, U.; Draghici, S.; Dunand-Sauthier, I.; Gatti, E.; Granucci, F.; Gundel, M.; Kramer, M.; Kuka, M.; Lanyi, A.; Melief, C.J.; Montfoort, N. van; Ostuni, R.; Pierre, P.; Popovici, R.; Rajnavolgyi, E.; Schierer, S.; Schuler, G.; Soumelis, V.; Splendiani, A.; Stefanini, I.; Torcia, M.G.; Zanoni, I.; Zollinger, R.; Figdor, C.G.; Austyn, J.M.

2010-01-01

BACKGROUND: The advent of Systems Biology has been accompanied by the blooming of pathway databases. Currently pathways are defined generically with respect to the organ or cell type where a reaction takes place. The cell type specificity of the reactions is the foundation of immunological research,

Modification-specific proteomics in plant biology

DEFF Research Database (Denmark)

Ytterberg, A Jimmy; Jensen, Ole N

2010-01-01

and proteomics. In general, methods for PTM characterization are developed to study yeast and mammalian biology and later adopted to investigate plants. Our point of view is that it is advantageous to enrich for PTMs on the peptide level as part of a quantitative proteomics strategy to not only identify the PTM...

Surgery confounds biology: the predictive value of stage-, grade- and prostate-specific antigen for recurrence after radical prostatectomy as a function of surgeon experience.

Science.gov (United States)

Vickers, Andrew J; Savage, Caroline J; Bianco, Fernando J; Klein, Eric A; Kattan, Michael W; Secin, Fernando P; Guilloneau, Bertrand D; Scardino, Peter T

2011-04-01

Statistical models predicting cancer recurrence after surgery are based on biologic variables. We have shown previously that prostate cancer recurrence is related to both tumor biology and to surgical technique. Here, we evaluate the association between several biological predictors and biochemical recurrence across varying surgical experience. The study included two separate cohorts: 6,091 patients treated by open radical prostatectomy and an independent replication set of 2,298 patients treated laparoscopically. We calculated the odds ratios for biological predictors of biochemical recurrence-stage, Gleason grade and prostate-specific antigen (PSA)-and also the predictive accuracy (area under the curve, AUC) of a multivariable model, for subgroups of patients defined by the experience of their surgeon. In the open cohort, the odds ratio for Gleason score 8+ and advanced pathologic stage, though not PSA or Gleason score 7, increased dramatically when patients treated by surgeons with lower levels of experience were excluded (Gleason 8+: odds ratios 5.6 overall vs. 13.0 for patients treated by surgeons with 1,000+ prior cases; locally advanced disease: odds ratios of 6.6 vs. 12.2, respectively). The AUC of the multivariable model was 0.750 for patients treated by surgeons with 50 or fewer cases compared to 0.849 for patients treated by surgeons with 500 or more. Although predictiveness was lower overall for the independent replication set cohort, the main findings were replicated. Surgery confounds biology. Although our findings have no direct clinical implications, studies investigating biological variables as predictors of outcome after curative resection of cancer should consider the impact of surgeon-specific factors. Copyright © 2010 UICC.

A comparison of biological and cultural evolution.

Science.gov (United States)

Portin, Petter

2015-03-01

This review begins with a definition of biological evolution and a description of its general principles. This is followed by a presentation of the biological basis of culture, specifically the concept of social selection. Further, conditions for cultural evolution are proposed, including a suggestion for language being the cultural replicator corresponding to the concept of the gene in biological evolution. Principles of cultural evolution are put forward and compared to the principles of biological evolution. Special emphasis is laid on the principle of selection in cultural evolution, including presentation of the concept of cultural fitness. The importance of language as a necessary condition for cultural evolution is stressed. Subsequently, prime differences between biological and cultural evolution are presented, followed by a discussion on interaction of our genome and our culture. The review aims at contributing to the present discussion concerning the modern development of the general theory of evolution, for example by giving a tentative formulation of the necessary and sufficient conditions for cultural evolution, and proposing that human creativity and mind reading or theory of mind are motors specific for it. The paper ends with the notion of the still ongoing coevolution of genes and culture.

Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.

Science.gov (United States)

Sen, Dilara; Keung, Albert J

2018-01-01

The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus specificity by considering concentration, affinity, avidity, and sequestration effects.

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

Energy Technology Data Exchange (ETDEWEB)

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Z.

2011-06-18

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. Thus, here we have extensively characterized the CD147 Ig0 domain by elucidating its three-dimensional structure through crystallography and its solution behavior through several biophysical methods that include nuclear magnetic resonance. Furthermore, we have utilized this data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6, which is a well-known contributor to retinoblastoma and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Furthermore, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation.

Specific determination of clinical and toxicological important substances in biological samples by LC-MS

International Nuclear Information System (INIS)

Mitulovic, G.

2001-02-01

This thesis of this dissertation is the specific determination of clinical and toxicological important substances in biological samples by LC-MS. Nicotine was determined in serum after application of nicotine plaster and nicotine nasal spray with HPLC-ESI-MS. Cotinine was determined direct in urine with HPLC-ESI-MS. Short time anesthetics were determined in blood and cytostatics were determined in liquor with HPLC-ESI-MS. (botek)

Biological sex influences learning strategy preference and muscarinic receptor binding in specific brain regions of prepubertal rats.

Science.gov (United States)

Grissom, Elin M; Hawley, Wayne R; Hodges, Kelly S; Fawcett-Patel, Jessica M; Dohanich, Gary P

2013-04-01

According to the theory of multiple memory systems, specific brain regions interact to determine how the locations of goals are learned when rodents navigate a spatial environment. A number of factors influence the type of strategy used by rodents to remember the location of a given goal in space, including the biological sex of the learner. We recently found that prior to puberty male rats preferred a striatum-dependent stimulus-response strategy over a hippocampus-dependent place strategy when solving a dual-solution task, while age-matched females showed no strategy preference. Because the cholinergic system has been implicated in learning strategy and is known to be sexually dimorphic prior to puberty, we explored the relationship between learning strategy and muscarinic receptor binding in specific brain regions of prepubertal males and female rats. We confirmed our previous finding that at 28 days of age a significantly higher proportion of prepubertal males preferred a stimulus-response learning strategy than a place strategy to solve a dual-solution visible platform water maze task. Equal proportions of prepubertal females preferred stimulus-response or place strategies. Profiles of muscarinic receptor binding as assessed by autoradiography varied according to strategy preference. Regardless of biological sex, prepubertal rats that preferred stimulus-response strategy exhibited lower ratios of muscarinic receptor binding in the hippocampus relative to the dorsolateral striatum compared to rats that preferred place strategy. Importantly, much of the variance in this ratio was related to differences in the ventral hippocampus to a greater extent than the dorsal hippocampus. The ratios of muscarinic receptors in the hippocampus relative to the basolateral amygdala also were lower in rats that preferred stimulus-response strategy over place strategy. Results confirm that learning strategy preference varies with biological sex in prepubertal rats with males

Synthetic biology: an emerging engineering discipline.

Science.gov (United States)

Cheng, Allen A; Lu, Timothy K

2012-01-01

Over the past decade, synthetic biology has emerged as an engineering discipline for biological systems. Compared with other substrates, biology poses a unique set of engineering challenges resulting from an incomplete understanding of natural biological systems and tools for manipulating them. To address these challenges, synthetic biology is advancing from developing proof-of-concept designs to focusing on core platforms for rational and high-throughput biological engineering. These platforms span the entire biological design cycle, including DNA construction, parts libraries, computational design tools, and interfaces for manipulating and probing synthetic circuits. The development of these enabling technologies requires an engineering mindset to be applied to biology, with an emphasis on generalizable techniques in addition to application-specific designs. This review aims to discuss the progress and challenges in synthetic biology and to illustrate areas where synthetic biology may impact biomedical engineering and human health.

Structure and function in biology

International Nuclear Information System (INIS)

Hirs, C.H.W.

1976-01-01

A summary is given of the history of the developments of structural chemistry in biology beginning with the work of the bacteriologist Ehrlich leading to a comprehensive examination of the influence of size and configuration on the interaction between specific antibodies and side-chain determinants. Recent developments include the recognition of a higher order of specificity in the interaction of proteins with one another

Radiological/biological/aerosol removal system

Science.gov (United States)

Haslam, Jeffery J

2015-03-17

An air filter replacement system for existing buildings, vehicles, arenas, and other enclosed airspaces includes a replacement air filter for replacing a standard air filter. The replacement air filter has dimensions and air flow specifications that allow it to replace the standard air filter. The replacement air filter includes a filter material that removes radiological or biological or aerosol particles.

Synthetic biology and occupational risk.

Science.gov (United States)

Howard, John; Murashov, Vladimir; Schulte, Paul

2017-03-01

Synthetic biology is an emerging interdisciplinary field of biotechnology that involves applying the principles of engineering and chemical design to biological systems. Biosafety professionals have done an excellent job in addressing research laboratory safety as synthetic biology and gene editing have emerged from the larger field of biotechnology. Despite these efforts, risks posed by synthetic biology are of increasing concern as research procedures scale up to industrial processes in the larger bioeconomy. A greater number and variety of workers will be exposed to commercial synthetic biology risks in the future, including risks to a variety of workers from the use of lentiviral vectors as gene transfer devices. There is a need to review and enhance current protection measures in the field of synthetic biology, whether in experimental laboratories where new advances are being researched, in health care settings where treatments using viral vectors as gene delivery systems are increasingly being used, or in the industrial bioeconomy. Enhanced worker protection measures should include increased injury and illness surveillance of the synthetic biology workforce; proactive risk assessment and management of synthetic biology products; research on the relative effectiveness of extrinsic and intrinsic biocontainment methods; specific safety guidance for synthetic biology industrial processes; determination of appropriate medical mitigation measures for lentiviral vector exposure incidents; and greater awareness and involvement in synthetic biology safety by the general occupational safety and health community as well as by government occupational safety and health research and regulatory agencies.

A novel bench-scale column assay to investigate site-specific nitrification biokinetics in biological rapid sand filters

DEFF Research Database (Denmark)

Tatari, Karolina; Smets, Barth F.; Albrechtsen, Hans-Jørgen

2013-01-01

A bench-scale assay was developed to obtain site-specific nitrification biokinetic information from biological rapid sand filters employed in groundwater treatment. The experimental set-up uses granular material subsampled from a full-scale filter, packed in a column, and operated with controlled...

WE-E-17A-07: Patient-Specific Mathematical Neuro-Oncology: Biologically-Informed Radiation Therapy and Imaging Physics

Energy Technology Data Exchange (ETDEWEB)

Swanson, K; Corwin, D [Northwestern University, Chicago, IL (United States); Rockne, R

2014-06-15

Purpose: To demonstrate a method of generating patient-specific, biologically-guided radiation therapy (RT) plans and to quantify and predict response to RT in glioblastoma. We investigate the biological correlates and imaging physics driving T2-MRI based response to radiation therapy using an MRI simulator. Methods: We have integrated a patient-specific biomathematical model of glioblastoma proliferation, invasion and radiotherapy with a multiobjective evolutionary algorithm for intensity-modulated RT optimization to construct individualized, biologically-guided plans. Patient-individualized simulations of the standard-of-care and optimized plans are compared in terms of several biological metrics quantified on MRI. An extension of the PI model is used to investigate the role of angiogenesis and its correlates in glioma response to therapy with the Proliferation-Invasion-Hypoxia- Necrosis-Angiogenesis model (PIHNA). The PIHNA model is used with a brain tissue phantom to predict tumor-induced vasogenic edema, tumor and tissue density that is used in a multi-compartmental MRI signal equation for generation of simulated T2- weighted MRIs. Results: Applying a novel metric of treatment response (Days Gained) to the patient-individualized simulation results predicted that the optimized RT plans would have a significant impact on delaying tumor progression, with Days Gained increases from 21% to 105%. For the T2- MRI simulations, initial validation tests compared average simulated T2 values for white matter, tumor, and peripheral edema to values cited in the literature. Simulated results closely match the characteristic T2 value for each tissue. Conclusion: Patient-individualized simulations using the combination of a biomathematical model with an optimization algorithm for RT generated biologically-guided doses that decreased normal tissue dose and increased therapeutic ratio with the potential to improve survival outcomes for treatment of glioblastoma. Simulated T2-MRI

WE-E-17A-07: Patient-Specific Mathematical Neuro-Oncology: Biologically-Informed Radiation Therapy and Imaging Physics

International Nuclear Information System (INIS)

Swanson, K; Corwin, D; Rockne, R

2014-01-01

Purpose: To demonstrate a method of generating patient-specific, biologically-guided radiation therapy (RT) plans and to quantify and predict response to RT in glioblastoma. We investigate the biological correlates and imaging physics driving T2-MRI based response to radiation therapy using an MRI simulator. Methods: We have integrated a patient-specific biomathematical model of glioblastoma proliferation, invasion and radiotherapy with a multiobjective evolutionary algorithm for intensity-modulated RT optimization to construct individualized, biologically-guided plans. Patient-individualized simulations of the standard-of-care and optimized plans are compared in terms of several biological metrics quantified on MRI. An extension of the PI model is used to investigate the role of angiogenesis and its correlates in glioma response to therapy with the Proliferation-Invasion-Hypoxia- Necrosis-Angiogenesis model (PIHNA). The PIHNA model is used with a brain tissue phantom to predict tumor-induced vasogenic edema, tumor and tissue density that is used in a multi-compartmental MRI signal equation for generation of simulated T2- weighted MRIs. Results: Applying a novel metric of treatment response (Days Gained) to the patient-individualized simulation results predicted that the optimized RT plans would have a significant impact on delaying tumor progression, with Days Gained increases from 21% to 105%. For the T2- MRI simulations, initial validation tests compared average simulated T2 values for white matter, tumor, and peripheral edema to values cited in the literature. Simulated results closely match the characteristic T2 value for each tissue. Conclusion: Patient-individualized simulations using the combination of a biomathematical model with an optimization algorithm for RT generated biologically-guided doses that decreased normal tissue dose and increased therapeutic ratio with the potential to improve survival outcomes for treatment of glioblastoma. Simulated T2-MRI

BIOLOGY OF HUMAN MALARIA PLASMODIA INCLUDING PLASMODIUM KNOWLESI

Directory of Open Access Journals (Sweden)

Spinello Antinori

2012-03-01

Full Text Available Malaria is a vector-borne infection caused by unicellular parasite of the genus Plasmodium. Plasmodia are obligate intracellular parasites that in humans after a clinically silent replication phase in the liver are able to infect and replicate within the erythrocytes. Four species (P.falciparum, P.malariae, P.ovale and P.vivax are traditionally recognized as responsible of natural infection in human beings but the recent upsurge of P.knowlesi malaria in South-East Asia has led clinicians to consider it as the fifth human malaria parasite. Recent studies in wild-living apes in Africa have revealed that P.falciparum, the most deadly form of human malaria, is not only human-host restricted as previously believed and its phylogenetic lineage is much more complex with new species identified in gorilla, bonobo and chimpanzee. Although less impressive, new data on biology of P.malariae, P.ovale and P.vivax are also emerging and will be briefly discussed in this review.

Teaching Methods in Biology Education and Sustainability Education Including Outdoor Education for Promoting Sustainability—A Literature Review

Directory of Open Access Journals (Sweden)

Eila Jeronen

2016-12-01

Full Text Available There are very few studies concerning the importance of teaching methods in biology education and environmental education including outdoor education for promoting sustainability at the levels of primary and secondary schools and pre-service teacher education. The material was selected using special keywords from biology and sustainable education in several scientific databases. The article provides an overview of 24 selected articles published in peer-reviewed scientific journals from 2006–2016. The data was analyzed using qualitative content analysis. Altogether, 16 journals were selected and 24 articles were analyzed in detail. The foci of the analyses were teaching methods, learning environments, knowledge and thinking skills, psychomotor skills, emotions and attitudes, and evaluation methods. Additionally, features of good methods were investigated and their implications for teaching were emphasized. In total, 22 different teaching methods were found to improve sustainability education in different ways. The most emphasized teaching methods were those in which students worked in groups and participated actively in learning processes. Research points toward the value of teaching methods that provide a good introduction and supportive guidelines and include active participation and interactivity.

Biological Systems Thinking for Control Engineering Design

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D. J. Murray-Smith

2004-01-01

Full Text Available Artificial neural networks and genetic algorithms are often quoted in discussions about the contribution of biological systems thinking to engineering design. This paper reviews work on the neuromuscular system, a field in which biological systems thinking could make specific contributions to the development and design of automatic control systems for mechatronics and robotics applications. The paper suggests some specific areas in which a better understanding of this biological control system could be expected to contribute to control engineering design methods in the future. Particular emphasis is given to the nonlinear nature of elements within the neuromuscular system and to processes of neural signal processing, sensing and system adaptivity. Aspects of the biological system that are of particular significance for engineering control systems include sensor fusion, sensor redundancy and parallelism, together with advanced forms of signal processing for adaptive and learning control. 

Radiation biology in Canada 1962-63

International Nuclear Information System (INIS)

Thacker, D.G.

1963-02-01

A survey of the research projects in radiation biology being carried out in Canada during the fiscal year 1962-63. The report includes the names of the investigators, their location, a brief description of the projects and information on the financial support being provided. A classification of the projects into areas of specific interest is also included. (author)

Hyperpolarized NMR Probes for Biological Assays

Directory of Open Access Journals (Sweden)

Sebastian Meier

2014-01-01

Full Text Available During the last decade, the development of nuclear spin polarization enhanced (hyperpolarized molecular probes has opened up new opportunities for studying the inner workings of living cells in real time. The hyperpolarized probes are produced ex situ, introduced into biological systems and detected with high sensitivity and contrast against background signals using high resolution NMR spectroscopy. A variety of natural, derivatized and designed hyperpolarized probes has emerged for diverse biological studies including assays of intracellular reaction progression, pathway kinetics, probe uptake and export, pH, redox state, reactive oxygen species, ion concentrations, drug efficacy or oncogenic signaling. These probes are readily used directly under natural conditions in biofluids and are often directly developed and optimized for cellular assays, thus leaving little doubt about their specificity and utility under biologically relevant conditions. Hyperpolarized molecular probes for biological NMR spectroscopy enable the unbiased detection of complex processes by virtue of the high spectral resolution, structural specificity and quantifiability of NMR signals. Here, we provide a survey of strategies used for the selection, design and use of hyperpolarized NMR probes in biological assays, and describe current limitations and developments.

Molecular biology - Part II: Beneficial liaisons: Radiobiology meets cellular and molecular biology

International Nuclear Information System (INIS)

Stevenson, Mary Ann; Coleman, C. Norman

1997-01-01

Purpose: The purpose of this course is to familiarize radiation oncologists with the concepts and terminology of molecular and cellular biology that are especially relevant to radiation oncology. The ability of radiation oncologists to remain current with the new discoveries of modern biology is essential to the development of improved therapeutic strategies and, importantly, to the proper balance between investment in technology and biology. Objective: This year, this Refresher Course is part of a three-part ''series'' including Drs. McKenna and Dritschilo. The objective is to provide continuing education for the academic and practicing radiation oncologist, physicist and biologist in the modern biologic concepts of cancer and its treatment. An effort will be made to relate these general concepts to the clinic by providing a broad view as to potential new biological treatments which might enhance the efficacy of radiation therapy. The specific focus of this Course will vary from year to year. Some of the classic radiation biology models which form the basis of clinical practice and laboratory research will be examined and 'newer' models will be presented which take into account the emerging knowledge of cellular and molecular biology. A few techniques in molecular and cellular biology will be described to the extent necessary to understand their basic concepts and their applicability. Aspects of radiation biology which will be covered include cell cycle, radiation-induced changes in the cellular phenotype, and considerations of the effect of the tumor microenvironment. It is not the expectation that the attendees will become experts in the particular subjects presented. Rather, it is the intent to increase their curiosity as to the new knowledge that is emerging and to demonstrate that these seemingly complicated areas can be understood and appreciated with a modicum of the effort

Molecular biology - Part II: Beneficial liaisons: Radiobiology meets cellular and molecular biology

International Nuclear Information System (INIS)

Stevenson, Mary Ann; Coleman, C. Norman

1996-01-01

Purpose: The purpose of this course is to familiarize radiation oncologists with the concepts and terminology of molecular and cellular biology that are especially relevant to radiation oncology. The ability of radiation oncologists to remain current with the new discoveries of modern biology is essential to the development of improved therapeutic strategies and, importantly, to the proper balance between investment in technology and biology. Objective: This year, this Refresher Course is part of a three-part 'series' including Drs. Martin Brown and Amato Giaccia. The objective is to provide continuing education for the academic and practicing radiation oncologist, physicist and biologist in the modern biologic concepts of cancer and its treatment. An effort will be made to relate these general concepts to the clinic by providing a broad view as to potential new biological treatments which might enhance the efficacy of radiation therapy. The specific focus of this Course will vary from year to year. Some of the classic radiation biology models which form the basis of clinical practice and laboratory research will be examined and 'newer' models will be presented which take into account the emerging knowledge of cellular and molecular biology. A few techniques in molecular and cellular biology will be described to the extent necessary to understand their basic concepts and their applicability. Aspects of radiation biology which will be covered include cell cycle, radiation-induced changes in the cellular phenotype, and considerations of the effect of the tumor microenvironment. It is not the expectation that the attendees will become experts in the particular subjects presented. Rather, it is the intent to increase their curiosity as to the new knowledge that is emerging and to demonstrate that these seemingly complicated areas can be understood and appreciated with a modicum of the effort

System biology and the project Encode

Directory of Open Access Journals (Sweden)

M. Yu. Obolenskaya

2014-08-01

Full Text Available The goal of this review is to give an incipient knowledge on the background of system biology, the premises to its assignment as a new branch of biology, its principles, methodology and its great achievements in identification of functional elements of human genome and regulation of their concordant­ and differential activity. The short characteristics of functional elements including the protein-coding sequences and those coding noncoding RNAs, the DNAse 1 hypersensitivity sites and methylated CpG islets, modified histones and specific 3D structure of chromatin, are represented. The topology of transcription factors network with its main motifs, hierar­chy, combination and association of transcription factors and their allelic specificity are highlighted­.

Energy transmission transformer for a wireless capsule endoscope: analysis of specific absorption rate and current density in biological tissue.

Science.gov (United States)

Shiba, Kenji; Nagato, Tomohiro; Tsuji, Toshio; Koshiji, Kohji

2008-07-01

This paper reports on the electromagnetic influences on the analysis of biological tissue surrounding a prototype energy transmission system for a wireless capsule endoscope. Specific absorption rate (SAR) and current density were analyzed by electromagnetic simulator in a model consisting of primary coil and a human trunk including the skin, fat, muscle, small intestine, backbone, and blood. First, electric and magnetic strength in the same conditions as the analytical model were measured and compared to the analytical values to confirm the validity of the analysis. Then, SAR and current density as a function of frequency and output power were analyzed. The validity of the analysis was confirmed by comparing the analytical values with the measured ones. The SAR was below the basic restrictions of the International Commission on Nonionizing Radiation Protection (ICNIRP). At the same time, the results for current density show that the influence on biological tissue was lowest in the 300-400 kHz range, indicating that it was possible to transmit energy safely up to 160 mW. In addition, we confirmed that the current density has decreased by reducing the primary coil's current.

[Use of the 2D:4D digit ratio as a biological marker of specific language disorders].

Science.gov (United States)

Font-Jordà, Antònia; Gamundí, Antoni; Nicolau Llobera, María Cristina; Aguilar-Mediavilla, Eva

2018-04-03

The finding of biological markers of specific language impairment would facilitate their detection and early intervention. In this sense, the 2D:4D finger ratio is considered an indirect indicator of prenatal exposure to testosterone. Previous studies have related it to linguistic competence and aggressive behaviour, and could be a candidate for a biological marker of language impairment. The aim was to compare the value of the 2D:4D ratio in children with Specific Language Impairment (SLI) with those of children with typical language development, as well as to establish to what extent this biological index correlates with the behaviour (linguistic, cognitive, social,...) in both groups. 2D:4D ratio, language, cognition and social behaviour were compared in a group of children with SLI (n=15), with a group of children without language difficulties (n=16) of the same age (between 5-8 years), gender (male), and socio-cultural level. Children with SLI showed significantly higher values of 2D:4D ratio of the right hand, and a negative correlation between this ratio and their linguistic competence. Although the children with SLI showed impaired adaptive abilities, but not more aggressive behaviour, these measurements did not correlate with the 2D:4D index. Nevertheless, social behaviour correlated with language and cognition competence. A higher value of the biological 2D:4D ration (lower intrauterine exposure to testosterone) seems to be associated with language difficulties in boys with SLI, but not with their behavioural difficulties. Their behavioural difficulties seem to be a consequence of their linguistic difficulties and their level of cognition. Copyright © 2018. Publicado por Elsevier España, S.L.U.

Multi trace element analysis of dry biological materials by neutron activation analysis including a chemical group separation

International Nuclear Information System (INIS)

Weers, C.A.

1980-07-01

Multi-element analysis of dry biological material by neutron activation analysis has to include radiochemical separation. The evaporation process is described in terms of the half-volume. The pretreatment of the samples and the development of the destruction-evaporation apparatus are described. The successive adsorption steps with active charcoal, Al 2 O 3 and coprecipitation with Fe(OH) 3 are described. Results obtained for standard reference materials are summarized. (G.T.H.)

A Comprehensive Web-based Platform For Domain-Specific Biological Models

Czech Academy of Sciences Publication Activity Database

Klement, M.; Šafránek, D.; Děd, J.; Pejznoch, A.; Nedbal, Ladislav; Steuer, Ralf; Červený, Jan; Müller, Stefan

2013-01-01

Roč. 299, 25 Dec (2013), s. 61-67 ISSN 1571-0661 R&D Projects: GA MŠk(CZ) EE2.3.20.0256 Institutional support: RVO:67179843 Keywords : biological models * model annotation * systems biology * simulation * database Subject RIV: EH - Ecology, Behaviour

Quantitative analysis of biological responses to low dose-rate γ-radiation, including dose, irradiation time, and dose-rate

International Nuclear Information System (INIS)

Magae, J.; Furukawa, C.; Kawakami, Y.; Hoshi, Y.; Ogata, H.

2003-01-01

Full text: Because biological responses to radiation are complex processes dependent on irradiation time as well as total dose, it is necessary to include dose, dose-rate and irradiation time simultaneously to predict the risk of low dose-rate irradiation. In this study, we analyzed quantitative relationship among dose, irradiation time and dose-rate, using chromosomal breakage and proliferation inhibition of human cells. For evaluation of chromosome breakage we assessed micronuclei induced by radiation. U2OS cells, a human osteosarcoma cell line, were exposed to gamma-ray in irradiation room bearing 50,000 Ci 60 Co. After the irradiation, they were cultured for 24 h in the presence of cytochalasin B to block cytokinesis, cytoplasm and nucleus were stained with DAPI and propidium iodide, and the number of binuclear cells bearing micronuclei was determined by fluorescent microscopy. For proliferation inhibition, cells were cultured for 48 h after the irradiation and [3H] thymidine was pulsed for 4 h before harvesting. Dose-rate in the irradiation room was measured with photoluminescence dosimeter. While irradiation time less than 24 h did not affect dose-response curves for both biological responses, they were remarkably attenuated as exposure time increased to more than 7 days. These biological responses were dependent on dose-rate rather than dose when cells were irradiated for 30 days. Moreover, percentage of micronucleus-forming cells cultured continuously for more than 60 days at the constant dose-rate, was gradually decreased in spite of the total dose accumulation. These results suggest that biological responses at low dose-rate, are remarkably affected by exposure time, that they are dependent on dose-rate rather than total dose in the case of long-term irradiation, and that cells are getting resistant to radiation after the continuous irradiation for 2 months. It is necessary to include effect of irradiation time and dose-rate sufficiently to evaluate risk

HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation

Science.gov (United States)

Carroll, Jeffrey B.; Deik, Amy; Fossale, Elisa; Weston, Rory M.; Guide, Jolene R.; Arjomand, Jamshid; Kwak, Seung; Clish, Clary B.; MacDonald, Marcy E.

2015-01-01

The HTT CAG expansion mutation causes Huntington’s Disease and is associated with a wide range of cellular consequences, including altered metabolism. The mutant allele is expressed widely, in all tissues, but the striatum and cortex are especially vulnerable to its effects. To more fully understand this tissue-specificity, early in the disease process, we asked whether the metabolic impact of the mutant CAG expanded allele in heterozygous B6.HdhQ111/+ mice would be common across tissues, or whether tissues would have tissue-specific responses and whether such changes may be affected by diet. Specifically, we cross-sectionally examined steady state metabolite concentrations from a range of tissues (plasma, brown adipose tissue, cerebellum, striatum, liver, white adipose tissue), using an established liquid chromatography-mass spectrometry pipeline, from cohorts of 8 month old mutant and wild-type littermate mice that were fed one of two different high-fat diets. The differential response to diet highlighted a proportion of metabolites in all tissues, ranging from 3% (7/219) in the striatum to 12% (25/212) in white adipose tissue. By contrast, the mutant CAG-expanded allele primarily affected brain metabolites, with 14% (30/219) of metabolites significantly altered, compared to wild-type, in striatum and 11% (25/224) in the cerebellum. In general, diet and the CAG-expanded allele both elicited metabolite changes that were predominantly tissue-specific and non-overlapping, with evidence for mutation-by-diet interaction in peripheral tissues most affected by diet. Machine-learning approaches highlighted the accumulation of diverse lipid species as the most genotype-predictive metabolite changes in the striatum. Validation experiments in cell culture demonstrated that lipid accumulation was also a defining feature of mutant HdhQ111 striatal progenitor cells. Thus, metabolite-level responses to the CAG expansion mutation in vivo were tissue specific and most evident

HdhQ111 Mice Exhibit Tissue Specific Metabolite Profiles that Include Striatal Lipid Accumulation.

Directory of Open Access Journals (Sweden)

Jeffrey B Carroll

Full Text Available The HTT CAG expansion mutation causes Huntington's Disease and is associated with a wide range of cellular consequences, including altered metabolism. The mutant allele is expressed widely, in all tissues, but the striatum and cortex are especially vulnerable to its effects. To more fully understand this tissue-specificity, early in the disease process, we asked whether the metabolic impact of the mutant CAG expanded allele in heterozygous B6.HdhQ111/+ mice would be common across tissues, or whether tissues would have tissue-specific responses and whether such changes may be affected by diet. Specifically, we cross-sectionally examined steady state metabolite concentrations from a range of tissues (plasma, brown adipose tissue, cerebellum, striatum, liver, white adipose tissue, using an established liquid chromatography-mass spectrometry pipeline, from cohorts of 8 month old mutant and wild-type littermate mice that were fed one of two different high-fat diets. The differential response to diet highlighted a proportion of metabolites in all tissues, ranging from 3% (7/219 in the striatum to 12% (25/212 in white adipose tissue. By contrast, the mutant CAG-expanded allele primarily affected brain metabolites, with 14% (30/219 of metabolites significantly altered, compared to wild-type, in striatum and 11% (25/224 in the cerebellum. In general, diet and the CAG-expanded allele both elicited metabolite changes that were predominantly tissue-specific and non-overlapping, with evidence for mutation-by-diet interaction in peripheral tissues most affected by diet. Machine-learning approaches highlighted the accumulation of diverse lipid species as the most genotype-predictive metabolite changes in the striatum. Validation experiments in cell culture demonstrated that lipid accumulation was also a defining feature of mutant HdhQ111 striatal progenitor cells. Thus, metabolite-level responses to the CAG expansion mutation in vivo were tissue specific and

Numerical Treatment of Two-phase Flow in Porous Media Including Specific Interfacial Area

KAUST Repository

El-Amin, Mohamed

2015-06-01

In this work, we present a numerical treatment for the model of two-phase flow in porous media including specific interfacial area. For numerical discretization we use the cell-centered finite difference (CCFD) method based on the shifting-matrices method which can reduce the time-consuming operations. A new iterative implicit algorithm has been developed to solve the problem under consideration. All advection and advection-like terms that appear in saturation equation and interfacial area equation are treated using upwind schemes. Selected simulation results such as pc–Sw–awn surface, capillary pressure, saturation and specific interfacial area with various values of model parameters have been introduced. The simulation results show a good agreement with those in the literature using either pore network modeling or Darcy scale modeling.

A systems biology approach to the analysis of subset-specific responses to lipopolysaccharide in dendritic cells.

Science.gov (United States)

Hancock, David G; Shklovskaya, Elena; Guy, Thomas V; Falsafi, Reza; Fjell, Chris D; Ritchie, William; Hancock, Robert E W; Fazekas de St Groth, Barbara

2014-01-01

Dendritic cells (DCs) are critical for regulating CD4 and CD8 T cell immunity, controlling Th1, Th2, and Th17 commitment, generating inducible Tregs, and mediating tolerance. It is believed that distinct DC subsets have evolved to control these different immune outcomes. However, how DC subsets mount different responses to inflammatory and/or tolerogenic signals in order to accomplish their divergent functions remains unclear. Lipopolysaccharide (LPS) provides an excellent model for investigating responses in closely related splenic DC subsets, as all subsets express the LPS receptor TLR4 and respond to LPS in vitro. However, previous studies of the LPS-induced DC transcriptome have been performed only on mixed DC populations. Moreover, comparisons of the in vivo response of two closely related DC subsets to LPS stimulation have not been reported in the literature to date. We compared the transcriptomes of murine splenic CD8 and CD11b DC subsets after in vivo LPS stimulation, using RNA-Seq and systems biology approaches. We identified subset-specific gene signatures, which included multiple functional immune mediators unique to each subset. To explain the observed subset-specific differences, we used a network analysis approach. While both DC subsets used a conserved set of transcription factors and major signalling pathways, the subsets showed differential regulation of sets of genes that 'fine-tune' the network Hubs expressed in common. We propose a model in which signalling through common pathway components is 'fine-tuned' by transcriptional control of subset-specific modulators, thus allowing for distinct functional outcomes in closely related DC subsets. We extend this analysis to comparable datasets from the literature and confirm that our model can account for cell subset-specific responses to LPS stimulation in multiple subpopulations in mouse and man.

Building biological foundries for next-generation synthetic biology.

Science.gov (United States)

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

SMRT has tissue-specific isoform profiles that include a form containing one CoRNR box

International Nuclear Information System (INIS)

Short, Stephen; Malartre, Marianne; Sharpe, Colin

2005-01-01

SMRT acts as a corepressor for a range of transcription factors. The amino-terminal part of the protein includes domains that mainly mediate transcriptional repression whilst the carboxy-terminal part includes domains that interact with nuclear receptors using up to three motifs called CoRNR boxes. The region of the SMRT primary transcript encoding the interaction domains is subject to alternative splicing that varies the inclusion of the third CoRNR box. The profile in mice includes an abundant, novel SMRT isoform that possesses just one CoRNR box. Mouse tissues therefore express SMRT isoforms containing one, two or three CoRNR boxes. In frogs, the SMRT isoform profile is tissue-specific. The mouse also shows distinct profiles generated by differential expression levels of the SMRT transcript isoforms. The formation of multiple SMRT isoforms and their tissue-specific regulation indicates a mechanism, whereby cells can define the repertoire of transcription factors regulated by SMRT

Biocompatible Quantum Dots for Biological Applications

Science.gov (United States)

Rosenthal, Sandra J.; Chang, Jerry C.; Kovtun, Oleg; McBride, James R.; Tomlinson, Ian D.

2011-01-01

Semiconductor quantum dots are quickly becoming a critical diagnostic tool for discerning cellular function at the molecular level. Their high brightness, long-lasting, sizetunable, and narrow luminescence set them apart from conventional fluorescence dyes. Quantum dots are being developed for a variety of biologically oriented applications, including fluorescent assays for drug discovery, disease detection, single protein tracking, and intracellular reporting. This review introduces the science behind quantum dots and describes how they are made biologically compatible. Several applications are also included, illustrating strategies toward target specificity, and are followed by a discussion on the limitations of quantum dot approaches. The article is concluded with a look at the future direction of quantum dots. PMID:21276935

The retinal specific CD147 Ig0 domain: from molecular structure to biological activity

Science.gov (United States)

Redzic, Jasmina S.; Armstrong, Geoffrey S.; Isern, Nancy. G.; Jones, David N.M.; Kieft, Jeffrey S.; Eisenmesser, Elan Zohar

2011-01-01

CD147 is a type I transmembrane protein that is involved in inflammatory diseases, cancer progression, and multiple human pathogens utilize CD147 for efficient infection. In several cancers, CD147 expression is so high that it is now used as a prognostic marker. The two primary isoforms of CD147 that are related to cancer progression have been identified, differing in their number of immunoglobulin (Ig)-like domains. These include CD147 Ig1-Ig2 that is ubiquitously expressed in most tissues and CD147 Ig0-Ig1-Ig2 that is retinal specific and implicated in retinoblastoma. However, little is known in regard to the retinal specific CD147 Ig0 domain despite its potential role in retinoblastoma. We present the first crystal structure of the human CD147 Ig0 domain and show that the CD147 Ig0 domain is a crystallographic dimer with an I-type domain structure, which is maintained in solution. Furthermore, we have utilized our structural data together with mutagenesis to probe the biological activity of CD147-containing proteins both with and without the CD147 Ig0 domain within several model cell lines. Our findings reveal that the CD147 Ig0 domain is a potent stimulator of interleukin-6 and suggest that the CD147 Ig0 domain has its own receptor distinct from that of the other CD147 Ig-like domains, CD147 Ig1-Ig2. Finally, we show that the CD147 Ig0 dimer is the functional unit required for activity and can be disrupted by a single point mutation. PMID:21620857

Detection and Characterization of Reactive Oxygen and Nitrogen Species in Biological Systems by Monitoring Species-Specific Products.

Science.gov (United States)

Hardy, Micael; Zielonka, Jacek; Karoui, Hakim; Sikora, Adam; Michalski, Radosław; Podsiadły, Radosław; Lopez, Marcos; Vasquez-Vivar, Jeannette; Kalyanaraman, Balaraman; Ouari, Olivier

2018-05-20

Since the discovery of the superoxide dismutase enzyme, the generation and fate of short-lived oxidizing, nitrosating, nitrating, and halogenating species in biological systems has been of great interest. Despite the significance of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in numerous diseases and intracellular signaling, the rigorous detection of ROS and RNS has remained a challenge. Recent Advances: Chemical characterization of the reactions of selected ROS and RNS with electron paramagnetic resonance (EPR) spin traps and fluorescent probes led to the establishment of species-specific products, which can be used for specific detection of several forms of ROS and RNS in cell-free systems and in cultured cells in vitro and in animals in vivo. Profiling oxidation products from the ROS and RNS probes provides a rigorous method for detection of those species in biological systems. Formation and detection of species-specific products from the probes enables accurate characterization of the oxidative environment in cells. Measurement of the total signal (fluorescence, chemiluminescence, etc.) intensity does not allow for identification of the ROS/RNS formed. It is critical to identify the products formed by using chromatographic or other rigorous techniques. Product analyses should be accompanied by monitoring of the intracellular probe level, another factor controlling the yield of the product(s) formed. More work is required to characterize the chemical reactivity of the ROS/RNS probes, and to develop new probes/detection approaches enabling real-time, selective monitoring of the specific products formed from the probes. Antioxid. Redox Signal. 28, 1416-1432.

The use of biologically based cancer risk models in radiation epidemiology

International Nuclear Information System (INIS)

Krewski, D.; Zielinski, J.M.; Hazelton, W.D.; Garner, M.J.; Moolgavkar, S.H.

2003-01-01

Biologically based risk projection models for radiation carcinogenesis seek to describe the fundamental biological processes involved in neoplastic transformation of somatic cells into malignant cancer cells. A validated biologically based model, whose parameters have a direct biological interpretation, can also be used to extrapolate cancer risks to different exposure conditions with some confidence. In this article, biologically based models for radiation carcinogenesis, including the two-stage clonal expansion (TSCE) model and its extensions, are reviewed. The biological and mathematical bases for such models are described, and the implications of key model parameters for cancer risk assessment examined. Specific applications of versions of the TSCE model to important epidemiologic datasets are discussed, including the Colorado uranium miners' cohort; a cohort of Chinese tin miners; the lifespan cohort of atomic bomb survivors in Hiroshima and Nagasaki; and a cohort of over 200,000 workers included in the National Dose Registry (NDR) of Canada. (author)

Age by Disease Biological Interactions: Implications for Late-Life Depression

Directory of Open Access Journals (Sweden)

Brandon eMcKinney

2012-11-01

Full Text Available Onset of depressive symptoms after the age of 65, or late-life depression (LLD, is common and poses a significant burden on affected individuals, caretakers and society. Evidence suggests a unique biological basis for LLD, but current hypotheses do not account for its pathophysiological complexity. Here we propose a novel etiological framework for LLD, the age-by-disease biological interaction hypothesis, based on the observations that the subset of genes that undergoes lifelong progressive changes in expression is restricted to a specific set of biological processes, and that a disproportionate number of these age-dependent genes have been previously and similarly implicated in neurodegenerative and neuropsychiatric disorders, including depression. The age-by-disease biological interaction hypothesis posits that age-dependent biological processes (i are pushed in LLD-promoting directions by changes in gene expression naturally occurring during brain aging, which (ii directly contribute to pathophysiological mechanisms of LLD, and (iii that individual variability in rates of age-dependent changes determines risk or resiliency to develop age-related disorders, including LLD. We review observations supporting this hypothesis, including consistent and specific age-dependent changes in brain gene expression, and their overlap with neuropsychiatric and neurodegenerative disease pathways. We then review preliminary reports supporting the genetic component of this hypothesis. Other potential biological mediators of age-dependent gene changes are proposed. We speculate that studies examining the relative contribution of these mechanisms to age-dependent changes and related disease mechanisms will not only provide critical information on the biology of normal aging of the human brain, but will inform our understanding our age-dependent diseases, in time fostering the development of new interventions for prevention and treatment of age-dependent diseases

Recent progress of task-specific ionic liquids in chiral resolution and extraction of biological samples and metal ions.

Science.gov (United States)

Wu, Datong; Cai, Pengfei; Zhao, Xiaoyong; Kong, Yong; Pan, Yuanjiang

2018-01-01

Ionic liquids have been functionalized for modern applications. The functional ionic liquids are also called task-specific ionic liquids. Various task-specific ionic liquids with certain groups have been constructed and exploited widely in the field of separation. To take advantage of their properties in separation science, task-specific ionic liquids are generally used in techniques such as liquid-liquid extraction, solid-phase extraction, gas chromatography, high-performance liquid chromatography, and capillary electrophoresis. This review mainly covers original research papers published in the last five years, and we will focus on task-specific ionic liquids as the chiral selectors in chiral resolution and as extractant or sensor for biological samples and metal ion purification. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

AC Calorimetric Design for Dynamic of Biological Materials

OpenAIRE

Shigeo Imaizumi

2006-01-01

We developed a new AC calorimeter for the measurement of dynamic specific heat capacity in liquids, including aqueous suspensions of biological materials. This method has several advantages. The first is that a high-resolution measurement of heat capacity, inmillidegrees, can be performed as a function of temperature, even with a very small sample. Therefore, AC calorimeter is a powerful tool to study critical behavior a tphase transition in biological materials. The second advantage is that ...

Hemodynamic Evaluation of a Biological and Mechanical Aortic Valve Prosthesis Using Patient-Specific MRI-Based CFD.

Science.gov (United States)

Hellmeier, Florian; Nordmeyer, Sarah; Yevtushenko, Pavlo; Bruening, Jan; Berger, Felix; Kuehne, Titus; Goubergrits, Leonid; Kelm, Marcus

2018-01-01

Modeling different treatment options before a procedure is performed is a promising approach for surgical decision making and patient care in heart valve disease. This study investigated the hemodynamic impact of different prostheses through patient-specific MRI-based CFD simulations. Ten time-resolved MRI data sets with and without velocity encoding were obtained to reconstruct the aorta and set hemodynamic boundary conditions for simulations. Aortic hemodynamics after virtual valve replacement with a biological and mechanical valve prosthesis were investigated. Wall shear stress (WSS), secondary flow degree (SFD), transvalvular pressure drop (TPD), turbulent kinetic energy (TKE), and normalized flow displacement (NFD) were evaluated to characterize valve-induced hemodynamics. The biological prostheses induced significantly higher WSS (medians: 9.3 vs. 8.6 Pa, P = 0.027) and SFD (means: 0.78 vs. 0.49, P = 0.002) in the ascending aorta, TPD (medians: 11.4 vs. 2.7 mm Hg, P = 0.002), TKE (means: 400 vs. 283 cm 2 /s 2 , P = 0.037), and NFD (means: 0.0994 vs. 0.0607, P = 0.020) than the mechanical prostheses. The differences between the prosthesis types showed great inter-patient variability, however. Given this variability, a patient-specific evaluation is warranted. In conclusion, MRI-based CFD offers an opportunity to assess the interactions between prosthesis and patient-specific boundary conditions, which may help in optimizing surgical decision making and providing additional guidance to clinicians. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.

MO-DE-207B-03: Improved Cancer Classification Using Patient-Specific Biological Pathway Information Via Gene Expression Data

Energy Technology Data Exchange (ETDEWEB)

Young, M; Craft, D [Massachusetts General Hospital and Harvard Medical School, Boston, MA (United States)

2016-06-15

Purpose: To develop an efficient, pathway-based classification system using network biology statistics to assist in patient-specific response predictions to radiation and drug therapies across multiple cancer types. Methods: We developed PICS (Pathway Informed Classification System), a novel two-step cancer classification algorithm. In PICS, a matrix m of mRNA expression values for a patient cohort is collapsed into a matrix p of biological pathways. The entries of p, which we term pathway scores, are obtained from either principal component analysis (PCA), normal tissue centroid (NTC), or gene expression deviation (GED). The pathway score matrix is clustered using both k-means and hierarchical clustering, and a clustering is judged by how well it groups patients into distinct survival classes. The most effective pathway scoring/clustering combination, per clustering p-value, thus generates various ‘signatures’ for conventional and functional cancer classification. Results: PICS successfully regularized large dimension gene data, separated normal and cancerous tissues, and clustered a large patient cohort spanning six cancer types. Furthermore, PICS clustered patient cohorts into distinct, statistically-significant survival groups. For a suboptimally-debulked ovarian cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00127) showed significant improvement over that of a prior gene expression-classified study (p = .0179). For a pancreatic cancer set, the pathway-classified Kaplan-Meier survival curve (p = .00141) showed significant improvement over that of a prior gene expression-classified study (p = .04). Pathway-based classification confirmed biomarkers for the pyrimidine, WNT-signaling, glycerophosphoglycerol, beta-alanine, and panthothenic acid pathways for ovarian cancer. Despite its robust nature, PICS requires significantly less run time than current pathway scoring methods. Conclusion: This work validates the PICS method to improve

Biological Variation and Reference Change Value Data for Serum Neuron-Specific Enolase in a Turkish Population.

Science.gov (United States)

Matyar, Selcuk; Goruroglu Ozturk, Ozlem; Ziyanoglu Karacor, Esin; Yuzbasioglu Ariyurek, Sedefgul; Sahin, Gulhan; Kibar, Filiz; Yaman, Akgun; Inal, Tamer

2016-11-01

Neuron-specific enolase (NSE) is a recognized biomarker for the assessment of cerebral injury in neurological disorders. This study aims to report a definitive assessment of the biological variation (BV) components of this biomarker, including within-subject BV (CVI), between-subject BV (CVG), index of individuality (II), and reference change value (RCV), in a cohort of Turkish participants using an experimental protocol. Six blood specimens were collected from each of the 13 apparently healthy volunteers (seven women, six men; ranging in age from 23 to 36) on the same day, every 2 weeks for 2 months. Serum specimens were stored at -20°C until analysis. Neuron-specific enolase levels were evaluated in serum samples using an electrochemiluminescence (ECLIA) immunoassay kit with a Roche Cobas e 411 auto-analyser. ANOVA test was used to calculate the variations. The CVI and CVG for NSE were 21.5% and 28.8%, respectively. Analytical variation (CVA) was calculated as 10.2%. Additionally, II and RCV were calculated as 0.74 and 66% (95% confident interval, CI), respectively. As the performance index (PI) was found to be less than 2 (PI = 0.95), it is concluded that the NSE measurements have a desirable performance for analytical imprecision. Since the II was found to be less than 1 (II: 0.74), the reference values will be of little use. Thus, RCV would provide better information for deciding whether a significant change has occurred. © 2016 Wiley Periodicals, Inc.

Developmental biology, the stem cell of biological disciplines

OpenAIRE

Gilbert, Scott F.

2017-01-01

Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines.” Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, ...

Relations between Intuitive Biological Thinking and Biological Misconceptions in Biology Majors and Nonmajors

Science.gov (United States)

Coley, John D.; Tanner, Kimberly

2015-01-01

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. PMID:25713093

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Science.gov (United States)

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grünberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H; Myers, Chris; Sauro, Herbert; Wipat, Anil

2018-04-02

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL) Version 2.2.0

KAUST Repository

Cox, Robert Sidney

2018-04-04

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year\\'s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL Version 2.2.0

Directory of Open Access Journals (Sweden)

Cox Robert Sidney

2018-04-01

Full Text Available Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL) Version 2.2.0

KAUST Repository

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grunberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H.; Myers, Chris; Sauro, Herbert; Wipat, Anil

2018-01-01

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Mammalian synthetic biology for studying the cell.

Science.gov (United States)

Mathur, Melina; Xiang, Joy S; Smolke, Christina D

2017-01-02

Synthetic biology is advancing the design of genetic devices that enable the study of cellular and molecular biology in mammalian cells. These genetic devices use diverse regulatory mechanisms to both examine cellular processes and achieve precise and dynamic control of cellular phenotype. Synthetic biology tools provide novel functionality to complement the examination of natural cell systems, including engineered molecules with specific activities and model systems that mimic complex regulatory processes. Continued development of quantitative standards and computational tools will expand capacities to probe cellular mechanisms with genetic devices to achieve a more comprehensive understanding of the cell. In this study, we review synthetic biology tools that are being applied to effectively investigate diverse cellular processes, regulatory networks, and multicellular interactions. We also discuss current challenges and future developments in the field that may transform the types of investigation possible in cell biology. © 2017 Mathur et al.

Developmental biology, the stem cell of biological disciplines.

Science.gov (United States)

Gilbert, Scott F

2017-12-01

Developmental biology (including embryology) is proposed as "the stem cell of biological disciplines." Genetics, cell biology, oncology, immunology, evolutionary mechanisms, neurobiology, and systems biology each has its ancestry in developmental biology. Moreover, developmental biology continues to roll on, budding off more disciplines, while retaining its own identity. While its descendant disciplines differentiate into sciences with a restricted set of paradigms, examples, and techniques, developmental biology remains vigorous, pluripotent, and relatively undifferentiated. In many disciplines, especially in evolutionary biology and oncology, the developmental perspective is being reasserted as an important research program.

Toxicity of silver nanoparticles in biological systems: Does the complexity of biological systems matter?

Science.gov (United States)

Vazquez-Muñoz, Roberto; Borrego, Belen; Juárez-Moreno, Karla; García-García, Maritza; Mota Morales, Josué D; Bogdanchikova, Nina; Huerta-Saquero, Alejandro

2017-07-05

Currently, nanomaterials are more frequently in our daily life, specifically in biomedicine, electronics, food, textiles and catalysis just to name a few. Although nanomaterials provide many benefits, recently their toxicity profiles have begun to be explored. In this work, the toxic effects of silver nanoparticles (35nm-average diameter and Polyvinyl-Pyrrolidone-coated) on biological systems of different levels of complexity was assessed in a comprehensive and comparatively way, through a variety of viability and toxicological assays. The studied organisms included viruses, bacteria, microalgae, fungi, animal and human cells (including cancer cell lines). It was found that biological systems of different taxonomical groups are inhibited at concentrations of silver nanoparticles within the same order of magnitude. Thus, the toxicity of nanomaterials on biological/living systems, constrained by their complexity, e.g. taxonomic groups, resulted contrary to the expected. The fact that cells and virus are inhibited with a concentration of silver nanoparticles within the same order of magnitude could be explained considering that silver nanoparticles affects very primitive cellular mechanisms by interacting with fundamental structures for cells and virus alike. Copyright © 2017 Elsevier B.V. All rights reserved.

Accelerator produced nuclides for use in biology and medicine. A bibliography, 1939--1973

International Nuclear Information System (INIS)

Christman, D.R.; Karlstrom, K.I.; Fowler, J.; Lambrecht, R.; Wolf, A.P.

1975-04-01

A bibliography of more than 1300 references on accelerator-produced nuclides for use in biology and medicine is presented. The information is arranged by subject and by specific nuclide. An author index is included. Appendices are provided of medical uses of specific elements and of radioisotopes not included in the main bibliography. (U.S.)

Perspective Biological Markers for Autism Spectrum Disorders: Advantages of the Use of Receiver Operating Characteristic Curves in Evaluating Marker Sensitivity and Specificity

Directory of Open Access Journals (Sweden)

Provvidenza M. Abruzzo

2015-01-01

Full Text Available Autism Spectrum Disorders (ASD are a heterogeneous group of neurodevelopmental disorders. Recognized causes of ASD include genetic factors, metabolic diseases, toxic and environmental factors, and a combination of these. Available tests fail to recognize genetic abnormalities in about 70% of ASD children, where diagnosis is solely based on behavioral signs and symptoms, which are difficult to evaluate in very young children. Although it is advisable that specific psychotherapeutic and pedagogic interventions are initiated as early as possible, early diagnosis is hampered by the lack of nongenetic specific biological markers. In the past ten years, the scientific literature has reported dozens of neurophysiological and biochemical alterations in ASD children; however no real biomarker has emerged. Such literature is here reviewed in the light of Receiver Operating Characteristic (ROC analysis, a very valuable statistical tool, which evaluates the sensitivity and the specificity of biomarkers to be used in diagnostic decision making. We also apply ROC analysis to some of our previously published data and discuss the increased diagnostic value of combining more variables in one ROC curve analysis. We also discuss the use of biomarkers as a tool for advancing our understanding of nonsyndromic ASD.

Simulation of E. coli gene regulation including overlapping cell cycles, growth, division, time delays and noise.

Directory of Open Access Journals (Sweden)

Ruoyu Luo

Full Text Available Due to the complexity of biological systems, simulation of biological networks is necessary but sometimes complicated. The classic stochastic simulation algorithm (SSA by Gillespie and its modified versions are widely used to simulate the stochastic dynamics of biochemical reaction systems. However, it has remained a challenge to implement accurate and efficient simulation algorithms for general reaction schemes in growing cells. Here, we present a modeling and simulation tool, called 'GeneCircuits', which is specifically developed to simulate gene-regulation in exponentially growing bacterial cells (such as E. coli with overlapping cell cycles. Our tool integrates three specific features of these cells that are not generally included in SSA tools: 1 the time delay between the regulation and synthesis of proteins that is due to transcription and translation processes; 2 cell cycle-dependent periodic changes of gene dosage; and 3 variations in the propensities of chemical reactions that have time-dependent reaction rates as a consequence of volume expansion and cell division. We give three biologically relevant examples to illustrate the use of our simulation tool in quantitative studies of systems biology and synthetic biology.

DNA Fingerprinting To Improve Data Collection Efficiency and Yield in a Host-Specificity Test of a Weed Biological Control Candidate

Science.gov (United States)

An open-field test was conducted in southern France to assess the host-specificity of Ceratapion basicorne, a candidate for biological control of yellow starthistle (Centaurea solstitialis; YST). Test plants were infested by naturally occurring populations of C. basicorne but were also exposed to s...

The diversification of developmental biology.

Science.gov (United States)

Crowe, Nathan; Dietrich, Michael R; Alomepe, Beverly S; Antrim, Amelia F; ByrneSim, Bay Lauris; He, Yi

2015-10-01

In the 1960s, "developmental biology" became the dominant term to describe some of the research that had previously been included under the rubrics of embryology, growth, morphology, and physiology. As scientific societies formed under this new label, a new discipline took shape. Historians, however, have a number of different perspectives on what changes led to this new field of developmental biology and how the field itself was constituted during this period. Using the General Embryological Information Service, a global index of post-World War II development-related research, we have documented and visualized significant changes in the kinds of research that occurred as this new field formed. In particular, our analysis supports the claim that the transition toward developmental biology was marked by a growth in new topics and forms of research. Although many historians privilege the role of molecular biology and/or the molecularization of biology in general during this formative period, we have found that the influence of molecular biology is not sufficient to account for the wide range of new research that constituted developmental biology at the time. Overall, our work creates a robust characterization of the changes that occurred with regard to research on growth and development in the decades following World War II and provides a context for future work on the specific drivers of those changes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Radiation biology as a basis for multidisciplinary cancer therapy

International Nuclear Information System (INIS)

Hosoya, N.

2017-01-01

The research field of radiation biology has progressed greatly thanks to the advances in molecular biology. DNA in the cell nucleus is the principal target of radiation. The biological effect of radiation can be determined by how the DNA damage is processed in the cell. In order to prevent deleterious biological effects due to DNA damage, the cells possess a system termed 'DNA damage response'. The DNA damage response finally induces cell cycle arrest, activation of DNA repair pathways, or cell death. If accurately repaired, DNA damage will result in survival of cells with no biological effects. If inaccurately repaired, DNA damage may result in survival of cells exhibiting genetic alterations, which can lead to the development of various diseases including cancer. If unrepaired, fatal DNA damage such as the DNA double-strand break will result in cell depth. Since radiation therapy and chemotherapy are designed to specifically kill cancer cells by inducing DNA double-strand breaks, it is important to take advantage of cancer-specific abnormalities in DNA damage response. In this review, I describe the impact of targeting DNA damage response in cancer therapy and show how progress in radiation biology has contributed to the development of novel therapeutic strategies. (author)

Optimization of biological and instrumental detection of explosives and ignitable liquid residues including canines, SPME/ITMS and GC/MSn

Science.gov (United States)

Furton, Kenneth G.; Harper, Ross J.; Perr, Jeannette M.; Almirall, Jose R.

2003-09-01

A comprehensive study and comparison is underway using biological detectors and instrumental methods for the rapid detection of ignitable liquid residues (ILR) and high explosives. Headspace solid phase microextraction (SPME) has been demonstrated to be an effective sampling method helping to identify active odor signature chemicals used by detector dogs to locate forensic specimens as well as a rapid pre-concentration technique prior to instrumental detection. Common ignitable liquids and common military and industrial explosives have been studied including trinitrotoluene, tetryl, RDX, HMX, EGDN, PETN and nitroglycerine. This study focuses on identifying volatile odor signature chemicals present, which can be used to enhance the level and reliability of detection of ILR and explosives by canines and instrumental methods. While most instrumental methods currently in use focus on particles and on parent organic compounds, which are often involatile, characteristic volatile organics are generally also present and can be exploited to enhance detection particularly for well-concealed devices. Specific examples include the volatile odor chemicals 2-ethyl-1-hexanol and cyclohexanone, which are readily available in the headspace of the high explosive composition C-4; whereas, the active chemical cyclo-1,3,5-trimethylene-2,4,6-trinitramine (RDX) is not. The analysis and identification of these headspace 'fingerprint' organics is followed by double-blind dog trials of the individual components using certified teams in an attempt to isolate and understand the target compounds to which dogs are sensitive. Studies to compare commonly used training aids with the actual target explosive have also been undertaken to determine their suitability and effectiveness. The optimization of solid phase microextraction (SPME) combined with ion trap mobility spectrometry (ITMS) and gas chromatography/mass spectrometry/mass spectrometry (GC/MSn) is detailed including interface development

Synthetic biological networks

International Nuclear Information System (INIS)

Archer, Eric; Süel, Gürol M

2013-01-01

Despite their obvious relationship and overlap, the field of physics is blessed with many insightful laws, while such laws are sadly absent in biology. Here we aim to discuss how the rise of a more recent field known as synthetic biology may allow us to more directly test hypotheses regarding the possible design principles of natural biological networks and systems. In particular, this review focuses on synthetic gene regulatory networks engineered to perform specific functions or exhibit particular dynamic behaviors. Advances in synthetic biology may set the stage to uncover the relationship of potential biological principles to those developed in physics. (review article)

Specific biological properties of Listeria innocua spp. isolated in Primorye Territory

Directory of Open Access Journals (Sweden)

E. A. Zaitseva

2017-01-01

Full Text Available Rationale: Most cases of listeriosis are caused by the pathogenic Listeria monocytogenes. Some cases of isolation of L.  innocua with pathogenicity factors from foods have been published, as well as on the cases of the disease in humans caused by this species. Aim: To assess biological properties including potential pathogenicity of L.  innocua, isolated from food and environmental objects. Materials and methods: We performed microbiological study of L. innocua cultures isolated from foods (n = 35 and environmental objects (n = 15 on the territory of Primorye Territory (Russian Federation, as well as assessment of their sensitivity to antibiotics. Results: The studied L.  innocua cultures showed stable phenotypic features of their biological properties, such as morphology, typical colony growth on the medium with characteristic odor of fermented milk, blue or blue-green luminescence induced by inclined light, presence of catalase activity and absence of the oxidase activity. Only 38 ± 6.9% of L.  innocua demonstrated movements at T 22 °С. L.  innocua cultures did not ferment mannitol (100% of cultures; they degraded ramnose to its acid without gas (70 ± 6.5% and degraded xylose (42.8 ± 7%. Listeria isolated from vegetables and environmental objects could ferment ramnose (92.8 ± 7.2% of the studied cultures and xylose (28.5 ± 12.5% more frequently than L. innocua isolated from meat and fish foods. L.  innocua demonstrated variable biochemical activities towards mannose (92 ± 3.8%, saccharose (85.7 ± 7.8% and melesitose (76.2 ± 9.5%. L. innocua cultures with hemolytic activity (34 ± 6.7% (α or β  type were isolated, more commonly from fish products. All Listeria irrespective of their isolation source showed lipase activity. L.  innocua cultures from foods and environmental objects were highly sensitive to antimicrobials from the following classes: penicillins (ampicillin, carbenicillin, combined amoxicillin and clavulanic

Evolutionary cell biology: two origins, one objective.

Science.gov (United States)

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

2014-12-02

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

Mathematical models in biology bringing mathematics to life

CERN Document Server

Ferraro, Maria; Guarracino, Mario

2015-01-01

This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

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

Science.gov (United States)

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).

Interpretation of biological-rate coefficients derived from radionuclide content, radionuclide concentration and specific activity experiments

International Nuclear Information System (INIS)

Vanderploeg, H.A.; Booth, R.S.

1976-01-01

Rigorous expressions are derived for the biological-rate coefficients (BRCs) determined from time-dependent measurements of three different dependent variables of radionuclide tracer experiments. These variables, which apply to a single organism, are radionuclide content, radionuclide concentration and specific activity. The BRCs derived from these variables have different mathematical expressions and, for high growth rates, their numerical values can be quite different. The precise mathematical expressions for the BRCs are presented here to aid modelers in selecting the correct parameters for their models and to aid experiments in interpreting their results. The usefulness of these three variables in quantifying elemental uptakes and losses by organisms is discussed. (U.K.)

Promoting microbiology education through the iGEM synthetic biology competition.

Science.gov (United States)

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.

Prostaglandins and their receptors in insect biology

Directory of Open Access Journals (Sweden)

David eStanley

2011-12-01

Full Text Available We treat the biological significance of prostaglandins (PGs and their known receptors in insect biology. PGs and related eicosanoids are oxygenated derivatives of arachidonic acid (AA and two other C20 polyunsaturated fatty acids. PGs are mostly appreciated in the context of biomedicine, but a growing body of literature indicates the biological significance of these compounds extends throughout the animal kingdom, and possibly beyond. PGs act in several crucial areas of insect biology. In reproduction, a specific PG, PGE2, releases oviposition behavior in most crickets and a few other insect species; PGs also mediate events in egg development in some species, which may represent all insects. PGs play major roles in modulating fluid secretion in Malpighian tubules, rectum and salivary glands, although, again, this has been studied in only a few insect species that may represent the Class. Insect immunity is a very complex defense system. PGs and other eicosanoids mediate a large number of immune reactions to infection and invasion. The actions of most PGs are mediated by specific receptors. Biomedical research has discovered a great deal of knowledge about PG receptors in mammals, including their structures, pharmacology, molecular biology and cellular locations. Studies of PG receptors in insects lag behind the biomedical background, however, recent results hold the promise of accelerated research in this area. A PG receptor has been identified in a class of lepidopteran hemocytes and experimentally linked to the release of prophenoloxidase. We conclude that research into PGs and their receptors in insects will lead to important advances in our understanding of insect biology.

Specific balance training included in an endurance-resistance exercise program improves postural balance in elderly patients undergoing haemodialysis.

Science.gov (United States)

Frih, Bechir; Mkacher, Wajdi; Jaafar, Hamdi; Frih, Ameur; Ben Salah, Zohra; El May, Mezry; Hammami, Mohamed

2018-04-01

The purpose of this study was to evaluate the effects of 6 months of specific balance training included in endurance-resistance program on postural balance in haemodialysis (HD) patients. Forty-nine male patients undergoing HD were randomly assigned to an intervention group (balance training included in an endurance-resistance training, n = 26) or a control group (resistance-endurance training only, n = 23). Postural control was assessed using six clinical tests; Timed Up and Go test, Tinetti Mobility Test, Berg Balance Scale, Unipodal Stance test, Mini-Balance Evaluation Systems Test and Activities Balance Confidence scale. All balance measures increased significantly after the period of rehabilitation training in the intervention group. Only the Timed Up and Go, Berg Balance Scale, Mini-Balance Evaluation Systems Test and Activities Balance Confidence scores were improved in the control group. The ranges of change in these tests were greater in the balance training group. In HD patients, specific balance training included in a usual endurance-resistance training program improves static and dynamic balance better than endurance-resistance training only. Implications for rehabilitation Rehabilitation using exercise in haemodialysis patients improved global mobility and functional abilities. Specific balance training included in usual endurance resistance training program could lead to improved static and dynamic balance.

Structured population models in biology and epidemiology

CERN Document Server

Ruan, Shigui

2008-01-01

This book consists of six chapters written by leading researchers in mathematical biology. These chapters present recent and important developments in the study of structured population models in biology and epidemiology. Topics include population models structured by age, size, and spatial position; size-structured models for metapopulations, macroparasitc diseases, and prion proliferation; models for transmission of microparasites between host populations living on non-coincident spatial domains; spatiotemporal patterns of disease spread; method of aggregation of variables in population dynamics; and biofilm models. It is suitable as a textbook for a mathematical biology course or a summer school at the advanced undergraduate and graduate level. It can also serve as a reference book for researchers looking for either interesting and specific problems to work on or useful techniques and discussions of some particular problems.

Reproductive Biology Including Evidence for Superfetation in the European Badger Meles meles (Carnivora: Mustelidae.

Directory of Open Access Journals (Sweden)

Leigh A L Corner

Full Text Available The reproductive biology of the European badger (Meles meles is of wide interest because it is one of the few mammal species that show delayed implantation and one of only five which are suggested to show superfetation as a reproductive strategy. This study aimed to describe the reproductive biology of female Irish badgers with a view to increasing our understanding of the process of delayed implantation and superfetation. We carried out a detailed histological examination of the reproductive tract of 264 female badgers taken from sites across 20 of the 26 counties in the Republic of Ireland. The key results show evidence of multiple blastocysts at different stages of development present simultaneously in the same female, supporting the view that superfetation is relatively common in this population of badgers. In addition we present strong evidence that the breeding rate in Irish badgers is limited by failure to conceive, rather than failure at any other stages of the breeding cycle. We show few effects of age on breeding success, suggesting no breeding suppression by adult females in this population. The study sheds new light on this unusual breeding strategy of delayed implantation and superfetation, and highlights a number of significant differences between the reproductive biology of female Irish badgers and those of Great Britain and Swedish populations.

Plant biology in the future.

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Bazzaz, F A

2001-05-08

In the beginning of modern plant biology, plant biologists followed a simple model for their science. This model included important branches of plant biology known then. Of course, plants had to be identified and classified first. Thus, there was much work on taxonomy, genetics, and physiology. Ecology and evolution were approached implicitly, rather than explicitly, through paleobotany, taxonomy, morphology, and historical geography. However, the burgeoning explosion of knowledge and great advances in molecular biology, e.g., to the extent that genes for specific traits can be added (or deleted) at will, have created a revolution in the study of plants. Genomics in agriculture has made it possible to address many important issues in crop production by the identification and manipulation of genes in crop plants. The current model of plant study differs from the previous one in that it places greater emphasis on developmental controls and on evolution by differential fitness. In a rapidly changing environment, the current model also explicitly considers the phenotypic variation among individuals on which selection operates. These are calls for the unity of science. In fact, the proponents of "Complexity Theory" think there are common algorithms describing all levels of organization, from atoms all the way to the structure of the universe, and that when these are discovered, the issue of scaling will be greatly simplified! Plant biology must seriously contribute to, among other things, meeting the nutritional needs of the human population. This challenge constitutes a key part of the backdrop against which future evolution will occur. Genetic engineering technologies are and will continue to be an important component of agriculture; however, we must consider the evolutionary implications of these new technologies. Meeting these demands requires drastic changes in the undergraduate curriculum. Students of biology should be trained in molecular, cellular, organismal

Biology and hemodynamics of aneurismal vasculopathies

International Nuclear Information System (INIS)

Pereira, Vitor Mendes; Brina, Olivier; Gonzalez, Ana Marcos; Narata, Ana Paula; Ouared, Rafik; Karl-Olof, Lovblad

2013-01-01

Aneurysm vasculopathies represents a group of vascular disorders that share a common morphological diagnosis: a vascular dilation, the aneurysm. They can have a same etiology and a different clinical presentation or morphology, or have different etiology and very similar anatomical geometry. The biology of the aneurysm formation is a complex process that will be a result of an endogenous predisposition and epigenetic factors later on including the intracranial hemodynamics. We describe the biology of saccular aneurysms, its growth and rupture, as well as, current concepts of hemodynamics derived from application of computational flow dynamics on patient specific vascular models. Furthermore, we describe different aneurysm phenotypes and its extremely variability on morphological and etiological presentation

Updating biological bases of social behavior.

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O'Connor, Thomas G

2014-09-01

This month's collation of papers deals with social behaviors that operationalize key constructs in fields covered by the journal, including attachment theory and parenting; emotional regulation; psychopathology of several forms; general and specific cognitive abilities. Notably, many examples are offered of how these social behaviors link with biology. That is an obvious and important direction for clinical research insofar as it helps to erase a perceptual chasm and artificial duality between 'behavior' and 'biology'. But, although it must be the case that social behavior has biological connections of one sort or other, identifying reliable connections with practical application has proved to be a non-trivial challenge. In particular, the challenge seems to be in measuring social behavior meaningfully enough that it could be expected to have a biological pulse, and in measuring biological markers systematically enough that emergent-downstream effects would surface. Associations are not especially uncommon, but it has been a frustrating task in constructing a practically broad model from a bricolage of scattered and disconnected parts and findings in the literature. Several reports in this issue offer contrasts that may help move along this line of study. © 2014 Association for Child and Adolescent Mental Health.

Information technology developments within the national biological information infrastructure

Science.gov (United States)

Cotter, G.; Frame, M.T.

2000-01-01

Looking out an office window or exploring a community park, one can easily see the tremendous challenges that biological information presents the computer science community. Biological information varies in format and content depending whether or not it is information pertaining to a particular species (i.e. Brown Tree Snake), or a specific ecosystem, which often includes multiple species, land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993. The NBII is designed to address these issues on a National scale within the United States, and through international partnerships abroad. This paper discusses current computer science efforts within the National Biological Information Infrastructure Program and future computer science research endeavors that are needed to address the ever-growing issues related to our Nation's biological concerns.

Other relevant biological papers

International Nuclear Information System (INIS)

Shimizu, M.

1989-01-01

A considerable number of CRESP-relevant papers concerning deep-sea biology and radioecology have been published. It is the purpose of this study to call attention to them. They fall into three general categories. The first is papers of general interest. They are mentioned only briefly, and include text references to the global bibliography at the end of the volume. The second are papers that are not only mentioned and referenced, but for various reasons are described in abstract form. The last is a list of papers compiled by H.S.J. Roe specifically for this volume. They are listed in bibliographic form, and are also included in the global bibliography at the end of the volume

Deciphering cancer heterogeneity: the biological space

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Stephanie eRoessler

2014-04-01

Full Text Available Most lethal solid tumors including hepatocellular carcinoma (HCC are considered incurable due to extensive heterogeneity in clinical presentation and tumor biology. Tumor heterogeneity may result from different cells of origin, patient ethnicity, etiology, underlying disease and diversity of genomic and epigenomic changes which drive tumor development. Cancer genomic heterogeneity thereby impedes treatment options and poses a significant challenge to cancer management. Studies of the HCC genome have revealed that although various genomic signatures identified in different HCC subgroups share a common prognosis, each carries unique molecular changes which are linked to different sets of cancer hallmarks whose misregulation has been proposed by Hanahan and Weinberg to be essential for tumorigenesis. We hypothesize that these specific sets of cancer hallmarks collectively occupy different tumor biological space representing the misregulation of different biological processes. In principle, a combination of different cancer hallmarks can result in new convergent molecular networks that are unique to each tumor subgroup and represent ideal druggable targets. Due to the ability of the tumor to adapt to external factors such as treatment or changes in the tumor microenvironment, the tumor biological space is elastic. Our ability to identify distinct groups of cancer patients with similar tumor biology who are most likely to respond to a specific therapy would have a significant impact on improving patient outcome. It is currently a challenge to identify a particular hallmark or a newly emerged convergent molecular network for a particular tumor. Thus, it is anticipated that the integration of multiple levels of data such as genomic mutations, somatic copy number aberration, gene expression, proteomics, and metabolomics, may help us grasp the tumor biological space occupied by each individual, leading to improved therapeutic intervention and outcome.

Synthetic Biology and the Translational Imperative.

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Heidari Feidt, Raheleh; Ienca, Marcello; Elger, Bernice Simone; Folcher, Marc

2017-12-18

Advances at the interface between the biological sciences and engineering are giving rise to emerging research fields such as synthetic biology. Harnessing the potential of synthetic biology requires timely and adequate translation into clinical practice. However, the translational research enterprise is currently facing fundamental obstacles that slow down the transition of scientific discoveries from the laboratory to the patient bedside. These obstacles including scarce financial resources and deficiency of organizational and logistic settings are widely discussed as primary impediments to translational research. In addition, a number of socio-ethical considerations inherent in translational research need to be addressed. As the translational capacity of synthetic biology is tightly linked to its social acceptance and ethical approval, ethical limitations may-together with financial and organizational problems-be co-determinants of suboptimal translation. Therefore, an early assessment of such limitations will contribute to proactively favor successful translation and prevent the promising potential of synthetic biology from remaining under-expressed. Through the discussion of two case-specific inventions in synthetic biology and their associated ethical implications, we illustrate the socio-ethical challenges ahead in the process of implementing synthetic biology into clinical practice. Since reducing the translational lag is essential for delivering the benefits of basic biomedical research to society at large and promoting global health, we advocate a moral obligation to accelerating translational research: the "translational imperative."

Specific methanogenic activity (SMA of industrial sludge from the aerobic and anaerobic biological treatment

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Danieli Schneiders

2013-08-01

Full Text Available In this study, specific methanogenic activity (SMA tests were performed on textile sludge and food industry sludge. The textile sludge from an activated sludge was collected at the entrance of the secondary biologic clarifier and the food sludge was collected in a UASB reactor. Once collected, the sludges were characterized and tested for SMA. It was found that the microrganisms present in the food sludge had SMA of 0.17 gCOD-CH4 gSSV.d-1 and 337.05 mL of methane production, while the microrganisms of the textile sludge presented 0.10 gCOD-CH4 gSSV.d-1 of SMA and 3.04 mL of methane production. Therefore, the food sludge was more suitable to be used as a starting inoculum in UASB.

Botulinum Neurotoxins: Biology, Pharmacology, and Toxicology.

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Pirazzini, Marco; Rossetto, Ornella; Eleopra, Roberto; Montecucco, Cesare

2017-04-01

The study of botulinum neurotoxins (BoNT) is rapidly progressing in many aspects. Novel BoNTs are being discovered owing to next generation sequencing, but their biologic and pharmacological properties remain largely unknown. The molecular structure of the large protein complexes that the toxin forms with accessory proteins, which are included in some BoNT type A1 and B1 pharmacological preparations, have been determined. By far the largest effort has been dedicated to the testing and validation of BoNTs as therapeutic agents in an ever increasing number of applications, including pain therapy. BoNT type A1 has been also exploited in a variety of cosmetic treatments, alone or in combination with other agents, and this specific market has reached the size of the one dedicated to the treatment of medical syndromes. The pharmacological properties and mode of action of BoNTs have shed light on general principles of neuronal transport and protein-protein interactions and are stimulating basic science studies. Moreover, the wide array of BoNTs discovered and to be discovered and the production of recombinant BoNTs endowed with specific properties suggest novel uses in therapeutics with increasing disease/symptom specifity. These recent developments are reviewed here to provide an updated picture of the biologic mechanism of action of BoNTs, of their increasing use in pharmacology and in cosmetics, and of their toxicology. Copyright © 2017 by The Author(s).

Organization and Biology of the Porcine Serum Amyloid A (SAA) Gene Cluster: Isoform Specific Responses to Bacterial Infection

DEFF Research Database (Denmark)

Olsen, Helle G; Skovgaard, Kerstin; Nielsen, Ole L

2013-01-01

Serum amyloid A (SAA) is a prominent acute phase protein. Although its biological functions are debated, the wide species distribution of highly homologous SAA proteins and their uniform behavior in response to injury or inflammation in itself suggests a significant role for this protein. The pig...... is increasingly being used as a model for the study of inflammatory reactions, yet only little is known about how specific SAA genes are regulated in the pig during acute phase responses and other responses induced by pro-inflammatory host mediators. We designed SAA gene specific primers and quantified the gene...... expression of porcine SAA1, SAA2, SAA3, and SAA4 by reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) in liver, spleen, and lung tissue from pigs experimentally infected with the Gram-negative swine specific bacterium Actinobacillus pleuropneumoniae, as well as from pigs experimentally...

Radiochemical tracers in marine biology

International Nuclear Information System (INIS)

Petrocelli, S.R.; Anderson, J.W.; Neff, J.M.

1977-01-01

Tracers have been used in a great variety of experimentation. More recently, labeled materials have been applied in marine biological research. Some of the existing tracer techniques have been utilized directly, while others have been modified to suit the specific needs of marine biologists. This chapter describes some of the uses of tracers in marine biological research. It also mentions the problems encountered as well as offering possible solutions and discusses further applications of these techniques. Only pertinent references are cited and additional information may be obtained by consulting these references. Due to their relative ease of maintenance, freshwater species are also utilized in studies which involve radiotracer techniques. Since most of these techniques e directly applicable to marine species, some of these studies will also be included

Stochastic narrow escape in molecular and cellular biology analysis and applications

CERN Document Server

Holcman, David

2015-01-01

This book covers recent developments in the non-standard asymptotics of the mathematical narrow escape problem in stochastic theory, as well as applications of the narrow escape problem in cell biology. The first part of the book concentrates on mathematical methods, including advanced asymptotic methods in partial equations, and is aimed primarily at applied mathematicians and theoretical physicists who are interested in biological applications. The second part of the book is intended for computational biologists, theoretical chemists, biochemists, biophysicists, and physiologists. It includes a summary of output formulas from the mathematical portion of the book and concentrates on their applications in modeling specific problems in theoretical molecular and cellular biology. Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small sp...

Site-specific distribution of claudin-based paracellular channels with roles in biological fluid flow and metabolism.

Science.gov (United States)

Tanaka, Hiroo; Tamura, Atsushi; Suzuki, Koya; Tsukita, Sachiko

2017-10-01

The claudins are a family of membrane proteins with at least 27 members in humans and mice. The extracellular regions of claudin proteins play essential roles in cell-cell adhesion and the paracellular barrier functions of tight junctions (TJs) in epithelial cell sheets. Furthermore, the extracellular regions of some claudins function as paracellular channels in the paracellular barrier that allow the selective passage of water, ions, and/or small organic solutes across the TJ in the extracellular space. Structural analyses have revealed a common framework of transmembrane, cytoplasmic, and extracellular regions among the claudin-based paracellular barriers and paracellular channels; however, differences in the claudins' extracellular regions, such as their charges and conformations, determine their properties. Among the biological systems that involve fluid flow and metabolism, it is noted that hepatic bile flow, renal Na + reabsorption, and intestinal nutrient absorption are dynamically regulated via site-specific distributions of paracellular channel-forming claudins in tissue. Here, we focus on how site-specific distributions of claudin-2- and claudin-15-based paracellular channels drive their organ-specific functions in the liver, kidney, and intestine. © 2017 New York Academy of Sciences.

PathJam: a new service for integrating biological pathway information

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Glez-Peña Daniel

2010-03-01

Full Text Available Biological pathways are crucial to much of the scientific research today including the study of specific biological processes related with human diseases. PathJam is a new comprehensive and freely accessible web-server application integrating scattered human pathway annotation from several public sources. The tool has been designed for both (i being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii giving support to the development of new integrative pathway applications. PathJam’s unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized RESTful API.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

Biology of Schwann cells.

Science.gov (United States)

Kidd, Grahame J; Ohno, Nobuhiko; Trapp, Bruce D

2013-01-01

The fundamental roles of Schwann cells during peripheral nerve formation and regeneration have been recognized for more than 100 years, but the cellular and molecular mechanisms that integrate Schwann cell and axonal functions continue to be elucidated. Derived from the embryonic neural crest, Schwann cells differentiate into myelinating cells or bundle multiple unmyelinated axons into Remak fibers. Axons dictate which differentiation path Schwann cells follow, and recent studies have established that axonal neuregulin1 signaling via ErbB2/B3 receptors on Schwann cells is essential for Schwann cell myelination. Extracellular matrix production and interactions mediated by specific integrin and dystroglycan complexes are also critical requisites for Schwann cell-axon interactions. Myelination entails expansion and specialization of the Schwann cell plasma membrane over millimeter distances. Many of the myelin-specific proteins have been identified, and transgenic manipulation of myelin genes have provided novel insights into myelin protein function, including maintenance of axonal integrity and survival. Cellular events that facilitate myelination, including microtubule-based protein and mRNA targeting, and actin based locomotion, have also begun to be understood. Arguably, the most remarkable facet of Schwann cell biology, however, is their vigorous response to axonal damage. Degradation of myelin, dedifferentiation, division, production of axonotrophic factors, and remyelination all underpin the substantial regenerative capacity of the Schwann cells and peripheral nerves. Many of these properties are not shared by CNS fibers, which are myelinated by oligodendrocytes. Dissecting the molecular mechanisms responsible for the complex biology of Schwann cells continues to have practical benefits in identifying novel therapeutic targets not only for Schwann cell-specific diseases but other disorders in which axons degenerate. Copyright © 2013 Elsevier B.V. All rights

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge.

Science.gov (United States)

Zhang, Yuji

2015-01-01

Molecular networks act as the backbone of molecular activities within cells, offering a unique opportunity to better understand the mechanism of diseases. While network data usually constitute only static network maps, integrating them with time course gene expression information can provide clues to the dynamic features of these networks and unravel the mechanistic driver genes characterizing cellular responses. Time course gene expression data allow us to broadly "watch" the dynamics of the system. However, one challenge in the analysis of such data is to establish and characterize the interplay among genes that are altered at different time points in the context of a biological process or functional category. Integrative analysis of these data sources will lead us a more complete understanding of how biological entities (e.g., genes and proteins) coordinately perform their biological functions in biological systems. In this paper, we introduced a novel network-based approach to extract functional knowledge from time-dependent biological processes at a system level using time course mRNA sequencing data in zebrafish embryo development. The proposed method was applied to investigate 1α, 25(OH)2D3-altered mechanisms in zebrafish embryo development. We applied the proposed method to a public zebrafish time course mRNA-Seq dataset, containing two different treatments along four time points. We constructed networks between gene ontology biological process categories, which were enriched in differential expressed genes between consecutive time points and different conditions. The temporal propagation of 1α, 25-Dihydroxyvitamin D3-altered transcriptional changes started from a few genes that were altered initially at earlier stage, to large groups of biological coherent genes at later stages. The most notable biological processes included neuronal and retinal development and generalized stress response. In addition, we also investigated the relationship among

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

Science.gov (United States)

Tien, Shin-Ming; Hsu, Chih-Yuan; Chen, Bor-Sen

2016-01-01

Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

Engineering Bacteria to Search for Specific Concentrations of Molecules by a Systematic Synthetic Biology Design Method.

Directory of Open Access Journals (Sweden)

Shin-Ming Tien

Full Text Available Bacteria navigate environments full of various chemicals to seek favorable places for survival by controlling the flagella's rotation using a complicated signal transduction pathway. By influencing the pathway, bacteria can be engineered to search for specific molecules, which has great potential for application to biomedicine and bioremediation. In this study, genetic circuits were constructed to make bacteria search for a specific molecule at particular concentrations in their environment through a synthetic biology method. In addition, by replacing the "brake component" in the synthetic circuit with some specific sensitivities, the bacteria can be engineered to locate areas containing specific concentrations of the molecule. Measured by the swarm assay qualitatively and microfluidic techniques quantitatively, the characteristics of each "brake component" were identified and represented by a mathematical model. Furthermore, we established another mathematical model to anticipate the characteristics of the "brake component". Based on this model, an abundant component library can be established to provide adequate component selection for different searching conditions without identifying all components individually. Finally, a systematic design procedure was proposed. Following this systematic procedure, one can design a genetic circuit for bacteria to rapidly search for and locate different concentrations of particular molecules by selecting the most adequate "brake component" in the library. Moreover, following simple procedures, one can also establish an exclusive component library suitable for other cultivated environments, promoter systems, or bacterial strains.

Pragmatic information in biology and physics.

Science.gov (United States)

Roederer, Juan G

2016-03-13

I will show how an objective definition of the concept of information and the consideration of recent results about information processing in the human brain help clarify some fundamental aspects of physics and biology. Rather than attempting to define information ab initio, I introduce the concept of interaction between material bodies as a primary concept. Two distinct categories can be identified: (i) interactions which can always be reduced to a superposition of physical interactions (forces) between elementary constituents; and (ii) interactions between complex bodies which cannot be expressed as a superposition of interactions between parts, and in which patterns and forms (in space and/or time) play the determining role. Pragmatic information is then defined as the link between a given pattern and the ensuing pattern-specific change. I will show that pragmatic information is a biological concept; it plays no active role in the purely physical domain-it only does so when a living organism intervenes. The consequences for physics (including foundations of quantum mechanics) and biology (including brain function) will be discussed. This will include speculations about three fundamental transitions, from the quantum to the classical domain, from natural inanimate to living systems, and from subhuman to human brain information-processing operations, introduced here in their direct connection with the concept of pragmatic information. © 2016 The Author(s).

The growing role of biologics and biosimilars in the United States: Perspectives from the APhA Biologics and Biosimilars Stakeholder Conference.

Science.gov (United States)

Crespi-Lofton, Judy; Skelton, Jann B

participants identified issues, they discussed strategies to address these concerns, including the need to enhance the education of pharmacists, prescribers, and patients regarding biologic products, including biosimilars and FOBs; the passage of state laws and regulations that do not impede the use of biosimilars, including interchangeable biosimilars; the use of product-specific tracking information in electronic health records and surveillance systems; bidirectional communication among pharmacists, prescribers, and other members of the care team to support pharmacovigilance and the maintenance of accurate patient records; and the development of evidence-based third-party payer policies. Patient access to safe and cost-effective treatments is an important goal for the health care system. As the availability and use of biosimilars, including those determined to be interchangeable, increases, their potential to lower costs and improve patient access to treatment grows. However, the extent of such growth is, in part, dependent on various stakeholders' decisions to provide, pay for, or use these products in a safe and thoughtful manner. Ongoing stakeholder collaboration, educational activities, and review of current government or payer policies are required to optimize the uptake of biological products, including biosimilars. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Analysis of general and specific combining abilities of popcorn populations, including selfed parents

Directory of Open Access Journals (Sweden)

José Marcelo Soriano Viana

2003-12-01

Full Text Available Estimation of general and specific combining ability effects in a diallel analysis of cross-pollinating populations, including the selfed parents, is presented in this work. The restrictions considered satisfy the parametric values of the GCA and SCA effects. The method is extended to self-pollinating populations (suitable for other species, without the selfed parents. The analysis of changes in population means due to inbreeding (sensitivity to inbreeding also permits to assess the predominant direction of dominance deviations and the relative genetic variability in each parent population. The methodology was used to select popcorn populations for intra- and inter-population breeding programs and for hybrid production, developed at the Federal University of Viçosa, MG, Brazil. Two yellow pearl grain popcorn populations were selected.

Psoriasis : implications of biologics

NARCIS (Netherlands)

Lecluse, L.L.A.

2010-01-01

Since the end of 2004 several specific immunomodulating therapies: ‘biologic response modifiers’ or ‘biologics’ have been registered for moderate to severe psoriasis in Europe. This thesis is considering the implications of the introduction of the biologics for psoriasis patients, focusing on safety

Marine molecular biology: An emerging field of biological sciences

Digital Repository Service at National Institute of Oceanography (India)

Thakur, N.L.; Jain, R.; Natalio, F.; Hamer, B.; Thakur, A.N.; Muller, W.E.G.

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies...

Species-Specific Thiol-Disulfide Equilibrium Constant: A Tool To Characterize Redox Transitions of Biological Importance.

Science.gov (United States)

Mirzahosseini, Arash; Somlyay, Máté; Noszál, Béla

2015-08-13

Microscopic redox equilibrium constants, a new species-specific type of physicochemical parameters, were introduced and determined to quantify thiol-disulfide equilibria of biological significance. The thiol-disulfide redox equilibria of glutathione with cysteamine, cysteine, and homocysteine were approached from both sides, and the equilibrium mixtures were analyzed by quantitative NMR methods to characterize the highly composite, co-dependent acid-base and redox equilibria. The directly obtained, pH-dependent, conditional constants were then decomposed by a new evaluation method, resulting in pH-independent, microscopic redox equilibrium constants for the first time. The 80 different, microscopic redox equilibrium constant values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress.

Analysis of biological spectrum of Divčibare flora

Directory of Open Access Journals (Sweden)

Popović Ivana

2006-01-01

Full Text Available One of the essential analyses which is performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of Divčibare flora. The study results are in correlation with the results of the analysis of the biological spectrum of the flora of Serbia and the Balkan Peninsula.

Site-specific confocal fluorescence imaging of biological microstructures in a turbid medium

International Nuclear Information System (INIS)

Saloma, Caesar; Palmes-Saloma, Cynthia; Kondoh, Hisato

1998-01-01

Normally transparent biological structures in a turbid medium are imaged using a laser confocal microscope and multiwavelength site-specific fluorescence labelling. The spatial filtering capability of the detector pinhole in the confocal microscope limits the number of scattered fluorescent photons that reach the photodetector. Simultaneous application of different fluorescent markers on the same sample site minimizes photobleaching by reducing the excitation time for each marker. A high-contrast grey-level image is also produced by summing confocal images of the same site taken at different fluorescence wavelengths. Monte Carlo simulations are performed to obtain the quantitative behaviour of confocal fluorescence imaging in turbid media. Confocal images of the following samples were also obtained: (i) 15 μm diameter fluorescent spheres placed 1.16 mm deep beneath an aqueous suspension of 0.0823 μm diameter polystyrene latex spheres, and (ii) hindbrain of a whole-mount mouse embryo (age 10 days) that was stained to fluoresce at 515 nm and 580 nm peak wavelengths. Expression of RNA transcripts of a gene within the embryo hindbrain was detected by a fluorescence-based whole-mount in situ hybridization procedure that we recently tested. (author)

Experiences of Students with Specific Learning Disorder (Including ADHD) in Online College Degree Programs: A Phenomenological Study

Science.gov (United States)

Bunch, Seleta LeAnn

2016-01-01

Enrollment in online degree programs is rapidly expanding due to the convenience and affordability offered to students and improvements in technology. The purpose of this hermeneutical phenomenological study was to understand the shared experiences of students with documented specific learning disorders (including Attention-Deficit/Hyperactivity…

Beneficial liaisons: radiobiology meets cellular and molecular biology

International Nuclear Information System (INIS)

Stevenson, Mary Ann; Coleman, C. Norman

1995-01-01

Purpose: The purpose of this course is to familiarize radiation oncologists with the concepts and terminology and molecular and cellular biology that are especially relevant to radiation oncology. The ability of radiation oncologists to remain current with the new discoveries of modern biology is essential to the development of improved therapeutic strategies and, importantly, to the proper balance between investment in technology and biology. Objective: This year, this Refresher Course is part of a three-part ''series'' including Drs. Martin Brown and Amato Giaccia. The objective is to provide continuing education for the academic and practicing radiation oncologist, physicist and biologist in the modern biologic concepts of cancer and its treatment. An effort will be made to relate these general concepts to the clinic by providing a broad view as to potential new biological treatments which might enhance the efficacy of radiation therapy. The specific focus of this Course will vary from year to year. Some of the classic radiation biology models which form the basis of clinical practice and laboratory research will be examined and 'newer' models will be presented which take into account the emerging knowledge of cellular and molecular biology. A few techniques in molecular and cellular biology will be described to the extent necessary to understand their basic concepts and their applicability. Aspects of radiation biology which will be covered include cell cycle, radiation-induced changes in the cellular phenotype, and considerations of the effect of the tumor microenvironment. It is not the expectation that the attendees will become experts in the particular subjects presented. Rather, it is the intent to increase their curiosity as to the new knowledge that is emerging and to demonstrate that these seemingly complicated areas can be understood and appreciated with a modicum of the effort

Method to detect biological particles

International Nuclear Information System (INIS)

Giaever, I.

1976-01-01

A medical-diagnostic method to detect immunological as well as other specific reactions is described. According to the invention, first reactive particles (e.g. antibodies) are adsorbed on the surface of a solid, non-reactive substrate. The coated substrate is subjected to a solution which one assumes to contain the second biological particles (e.g. antigens) which are specific to the first and form complexes with these. A preferential radioactive labelling (e.g. with iodine 125) of the second biological particle is then directly or indirectly carried out. Clearage follows labelling in order to separate the second biological particles from the first ones. A specific splitting agent can selectively break the bond of both types of particle. The splitting agent solution is finally separated off and its content is investigated for the presence of labelling. (VJ) [de

Carotenoids in Adipose Tissue Biology and Obesity.

Science.gov (United States)

Bonet, M Luisa; Canas, Jose A; Ribot, Joan; Palou, Andreu

2016-01-01

Cell, animal and human studies dealing with carotenoids and carotenoid derivatives as nutritional regulators of adipose tissue biology with implications for the etiology and management of obesity and obesity-related metabolic diseases are reviewed. Most studied carotenoids in this context are β-carotene, cryptoxanthin, astaxanthin and fucoxanthin, together with β-carotene-derived retinoids and some other apocarotenoids. Studies indicate an impact of these compounds on essential aspects of adipose tissue biology including the control of adipocyte differentiation (adipogenesis), adipocyte metabolism, oxidative stress and the production of adipose tissue-derived regulatory signals and inflammatory mediators. Specific carotenoids and carotenoid derivatives restrain adipogenesis and adipocyte hypertrophy while enhancing fat oxidation and energy dissipation in brown and white adipocytes, and counteract obesity in animal models. Intake, blood levels and adipocyte content of carotenoids are reduced in human obesity. Specifically designed human intervention studies in the field, though still sparse, indicate a beneficial effect of carotenoid supplementation in the accrual of abdominal adiposity. In summary, studies support a role of specific carotenoids and carotenoid derivatives in the prevention of excess adiposity, and suggest that carotenoid requirements may be dependent on body composition.

Cardiovascular safety of biologic therapies for the treatment of RA.

Science.gov (United States)

Greenberg, Jeffrey D; Furer, Victoria; Farkouh, Michael E

2011-11-15

Cardiovascular disease represents a major source of extra-articular comorbidity in patients with rheumatoid arthritis (RA). A combination of traditional cardiovascular risk factors and RA-related factors accounts for the excess risk in RA. Among RA-related factors, chronic systemic inflammation has been implicated in the pathogenesis and progression of atherosclerosis. A growing body of evidence--mainly derived from observational databases and registries--suggests that specific RA therapies, including methotrexate and anti-TNF biologic agents, can reduce the risk of future cardiovascular events in patients with RA. The cardiovascular profile of other biologic therapies for the treatment of RA has not been adequately studied, including of investigational drugs that improve systemic inflammation but alter traditional cardiovascular risk factors. In the absence of large clinical trials adequately powered to detect differences in cardiovascular events between biologic drugs in RA, deriving firm conclusions on cardiovascular safety is challenging. Nevertheless, observational research using large registries has emerged as a promising approach to study the cardiovascular risk of emerging RA biologic therapies.

Models for synthetic biology.

Science.gov (United States)

Kaznessis, Yiannis N

2007-11-06

Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

Merkel Cell Carcinomas Arising in Autoimmune Disease Affected Patients Treated with Biologic Drugs, Including Anti-TNF.

Science.gov (United States)

Rotondo, John Charles; Bononi, Ilaria; Puozzo, Andrea; Govoni, Marcello; Foschi, Valentina; Lanza, Giovanni; Gafà, Roberta; Gaboriaud, Pauline; Touzé, Françoise Antoine; Selvatici, Rita; Martini, Fernanda; Tognon, Mauro

2017-07-15

Purpose: The purpose of this investigation was to characterize Merkel cell carcinomas (MCC) arisen in patients affected by autoimmune diseases and treated with biologic drugs. Experimental Design: Serum samples from patients with MCC were analyzed for the presence and titer of antibodies against antigens of the oncogenic Merkel cell polyomavirus (MCPyV). IgG antibodies against the viral oncoproteins large T (LT) and small T (ST) antigens and the viral capsid protein-1 were analyzed by indirect ELISA. Viral antigens were recombinant LT/ST and virus-like particles (VLP), respectively. MCPyV DNA sequences were studied using PCR methods in MCC tissues and in peripheral blood mononuclear cells (PBMC). Immunohistochemical (IHC) analyses were carried out in MCC tissues to reveal MCPyV LT oncoprotein. Results: MCPyV DNA sequences identified in MCC tissues showed 100% homology with the European MKL-1 strain. PBMCs from patients tested MCPyV-negative. Viral DNA loads in the three MCC tissues were in the 0.1 to 30 copy/cell range. IgG antibodies against LT/ST were detected in patients 1 and 3, whereas patient 2 did not react to the MCPyV LT/ST antigen. Sera from the three patients with MCC contained IgG antibodies against MCPyV VP1. MCC tissues tested MCPyV LT-antigen-positive in IHC assays, with strong LT expression with diffuse nuclear localization. Normal tissues tested MCPyV LT-negative when employed as control. Conclusions: We investigated three new MCCs in patients affected by rheumatologic diseases treated with biologic drugs, including TNF. A possible cause-effect relationship between pharmacologic immunosuppressive treatment and MCC onset is suggested. Indeed, MCC is associated with MCPyV LT oncoprotein activity. Clin Cancer Res; 23(14); 3929-34. ©2017 AACR . ©2017 American Association for Cancer Research.

Has Modern Biology Entered the Mouth? The Clinical Impact of Biological Research.

Science.gov (United States)

Baum, Bruce J.

1991-01-01

Three areas of biological research that are beginning to have an impact on clinical medicine are examined, including molecular biology, cell biology, and biotechnology. It is concluded that oral biologists and educators must work cooperatively to bring rapid biological and biomedical advances into dental training in a meaningful way. (MSE)

System and method for deriving a process-based specification

Science.gov (United States)

Hinchey, Michael Gerard (Inventor); Rash, James Larry (Inventor); Rouff, Christopher A. (Inventor)

2009-01-01

A system and method for deriving a process-based specification for a system is disclosed. The process-based specification is mathematically inferred from a trace-based specification. The trace-based specification is derived from a non-empty set of traces or natural language scenarios. The process-based specification is mathematically equivalent to the trace-based specification. Code is generated, if applicable, from the process-based specification. A process, or phases of a process, using the features disclosed can be reversed and repeated to allow for an interactive development and modification of legacy systems. The process is applicable to any class of system, including, but not limited to, biological and physical systems, electrical and electro-mechanical systems in addition to software, hardware and hybrid hardware-software systems.

Personalized disease-specific protein corona influences the therapeutic impact of graphene oxide

Science.gov (United States)

Hajipour, Mohammad Javad; Raheb, Jamshid; Akhavan, Omid; Arjmand, Sareh; Mashinchian, Omid; Rahman, Masoud; Abdolahad, Mohammad; Serpooshan, Vahid; Laurent, Sophie; Mahmoudi, Morteza

2015-05-01

The hard corona, the protein shell that is strongly attached to the surface of nano-objects in biological fluids, is recognized as the first layer that interacts with biological objects (e.g., cells and tissues). The decoration of the hard corona (i.e., the type, amount, and conformation of the attached proteins) can define the biological fate of the nanomaterial. Recent developments have revealed that corona decoration strongly depends on the type of disease in human patients from which the plasma is obtained as a protein source for corona formation (referred to as the `personalized protein corona'). In this study, we demonstrate that graphene oxide (GO) sheets can trigger different biological responses in the presence of coronas obtained from various types of diseases. GO sheets were incubated with plasma from human subjects with different diseases/conditions, including hypofibrinogenemia, blood cancer, thalassemia major, thalassemia minor, rheumatism, fauvism, hypercholesterolemia, diabetes, and pregnancy. Identical sheets coated with varying protein corona decorations exhibited significantly different cellular toxicity, apoptosis, and uptake, reactive oxygen species production, lipid peroxidation and nitrogen oxide levels. The results of this report will help researchers design efficient and safe, patient-specific nano biomaterials in a disease type-specific manner for clinical and biological applications.The hard corona, the protein shell that is strongly attached to the surface of nano-objects in biological fluids, is recognized as the first layer that interacts with biological objects (e.g., cells and tissues). The decoration of the hard corona (i.e., the type, amount, and conformation of the attached proteins) can define the biological fate of the nanomaterial. Recent developments have revealed that corona decoration strongly depends on the type of disease in human patients from which the plasma is obtained as a protein source for corona formation (referred

Nonlinear dynamics in biological systems

CERN Document Server

Carballido-Landeira, Jorge

2016-01-01

This book presents recent research results relating to applications of nonlinear dynamics, focusing specifically on four topics of wide interest: heart dynamics, DNA/RNA, cell mobility, and proteins. The book derives from the First BCAM Workshop on Nonlinear Dynamics in Biological Systems, held in June 2014 at the Basque Center of Applied Mathematics (BCAM). At this international meeting, researchers from different but complementary backgrounds, including molecular dynamics, physical chemistry, bio-informatics and biophysics, presented their most recent results and discussed the future direction of their studies using theoretical, mathematical modeling and experimental approaches. Such was the level of interest stimulated that the decision was taken to produce this publication, with the organizers of the event acting as editors. All of the contributing authors are researchers working on diverse biological problems that can be approached using nonlinear dynamics. The book will appeal especially to applied math...

Polyfunctional Specific Response to Echinococcus Granulosus Associates to the Biological Activity of the Cysts.

Directory of Open Access Journals (Sweden)

Linda Petrone

2015-11-01

Full Text Available Cystic echinococcosis (CE is a complex disease caused by Echinococcus granulosus (E.granulosus, and its immunophatogenesis is still not clearly defined. A peculiar feature of chronic CE is the coexistence of Th1 and Th2 responses. It has been suggested that Th1 cytokines are related to disease resistance, whereas Th2 cytokines are related to disease susceptibility and chronicity. The aim of this study was to evaluate, by multi-parametric flow cytometry (FACS, the presence of CE specific immune signatures.We enrolled 54 subjects with suspected CE; 42 of them had a confirmed diagnosis, whereas 12 were classified as NO-CE. Based on the ultrasonography images, CE patients were further categorized as being in "active stages" (25 and "inactive stages" (17. The ability of CD4+ T-cells to produce IFN-γ, IL-2, TNF-α, Th2 cytokines or IL-10 was assessed by FACS on antigen-specific T-cells after overnight stimulation with Antigen B (AgB of E.granulosus. Cytokine profiles were evaluated in all the enrolled subjects. The results show that none of the NO-CE subjects had a detectable AgB-specific response. Among the CE patients, the frequency and proportions of AgB-specific CD4+ T-cells producing IL-2+TNF-α+Th2+ or TNF-α+Th2+ were significantly increased in the "active stages" group compared to the "inactive stages" group. Moreover, an increased proportion of the total polyfunctional subsets, as triple-and double-functional CD4 T-cells, was found in CE patients with active disease. The response to the mitogen, used as a control stimulus to evaluate the immune competence status, was characterized by the same cytokine subsets in all the subjects enrolled, independent of CE.We demonstrate, for the first time to our knowledge, that polyfunctional T-cell subsets as IL-2+TNF-α+Th2+ triple-positive and TNF-α+Th2+ double-positive specific T-cells associate with cyst biological activity. These results contribute to increase knowledge of CE immunophatogenesis and

Using systems and structure biology tools to dissect cellular phenotypes.

Science.gov (United States)

Floratos, Aris; Honig, Barry; Pe'er, Dana; Califano, Andrea

2012-01-01

The Center for the Multiscale Analysis of Genetic Networks (MAGNet, http://magnet.c2b2.columbia.edu) was established in 2005, with the mission of providing the biomedical research community with Structural and Systems Biology algorithms and software tools for the dissection of molecular interactions and for the interaction-based elucidation of cellular phenotypes. Over the last 7 years, MAGNet investigators have developed many novel analysis methodologies, which have led to important biological discoveries, including understanding the role of the DNA shape in protein-DNA binding specificity and the discovery of genes causally related to the presentation of malignant phenotypes, including lymphoma, glioma, and melanoma. Software tools implementing these methodologies have been broadly adopted by the research community and are made freely available through geWorkbench, the Center's integrated analysis platform. Additionally, MAGNet has been instrumental in organizing and developing key conferences and meetings focused on the emerging field of systems biology and regulatory genomics, with special focus on cancer-related research.

The Biology of Cancer Exosomes: Insights and New Perspectives.

Science.gov (United States)

Ruivo, Carolina F; Adem, Bárbara; Silva, Miguel; Melo, Sónia A

2017-12-01

Exosomes are a subclass of extracellular vesicles involved in intercellular communication that are released by all cell types, including cancer cells. Cancer exosomes carry malignant information in the form of proteins, lipids, and nucleic acids that can reprogram recipient cells. Exosomes have emerged as putative biological mediators in cancer contributing to major steps of disease progression. A leading role exists for cancer exosomes in specific aspects of tumor progression: modulation of immune response, tumor microenvironment reprogramming, and metastasis. This review will address the functions attributed to cancer exosomes in these three aspects of cancer biology, highlighting recent advances and potential limitations. Finally, we explore alternative strategies to develop better models to study cancer exosomes biology. Cancer Res; 77(23); 6480-8. ©2017 AACR . ©2017 American Association for Cancer Research.

Integrated Biological Control

International Nuclear Information System (INIS)

JOHNSON, A.R.

2002-01-01

Biological control is any activity taken to prevent, limit, clean up, or remediate potential environmental, health and safety, or workplace quality impacts from plants, animals, or microorganisms. At Hanford the principal emphasis of biological control is to prevent the transport of radioactive contamination by biological vectors (plants, animals, or microorganisms), and where necessary, control and clean up resulting contamination. Other aspects of biological control at Hanford include industrial weed control (e.g.; tumbleweeds), noxious weed control (invasive, non-native plant species), and pest control (undesirable animals such as rodents and stinging insects; and microorganisms such as molds that adversely affect the quality of the workplace environment). Biological control activities may be either preventive (apriori) or in response to existing contamination spread (aposteriori). Surveillance activities, including ground, vegetation, flying insect, and other surveys, and apriori control actions, such as herbicide spraying and placing biological barriers, are important in preventing radioactive contamination spread. If surveillance discovers that biological vectors have spread radioactive contamination, aposteriori control measures, such as fixing contamination, followed by cleanup and removal of the contamination to an approved disposal location are typical response functions. In some cases remediation following the contamination cleanup and removal is necessary. Biological control activities for industrial weeds, noxious weeds and pests have similar modes of prevention and response

Predicting tissue-specific expressions based on sequence characteristics

KAUST Repository

Paik, Hyojung; Ryu, Tae Woo; Heo, Hyoungsam; Seo, Seungwon; Lee, Doheon; Hur, Cheolgoo

2011-01-01

In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

Predicting tissue-specific expressions based on sequence characteristics

KAUST Repository

Paik, Hyojung

2011-04-30

In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

Propulsion of swimming microrobots inspired by metachronal waves in ciliates: from biology to material specifications

International Nuclear Information System (INIS)

Palagi, Stefano; Mazzolai, Barbara; Beccai, Lucia; Jager, Edwin WH

2013-01-01

The quest for swimming microrobots originates from possible applications in medicine, especially involving navigation in bodily fluids. Swimming microorganisms have become a source of inspiration because their propulsion mechanisms are effective in the low-Reynolds number regime. In this study, we address a propulsion mechanism inspired by metachronal waves, i.e. the spontaneous coordination of cilia leading to the fast swimming of ciliates. We analyse the biological mechanism (referring to its particular embodiment in Paramecium caudatum), and we investigate the contribution of its main features to the swimming performance, through a three-dimensional finite-elements model, in order to develop a simplified, yet effective artificial design. We propose a bioinspired propulsion mechanism for a swimming microrobot based on a continuous cylindrical electroactive surface exhibiting perpendicular wave deformations travelling longitudinally along its main axis. The simplified propulsion mechanism is conceived specifically for microrobots that embed a micro-actuation system capable of executing the bioinspired propulsion (self-propelled microrobots). Among the available electroactive polymers, we select polypyrrole as the possible actuation material and we assess it for this particular embodiment. The results are used to appoint target performance specifications for the development of improved or new electroactive materials to attain metachronal-waves-like propulsion. (paper)

Propulsion of swimming microrobots inspired by metachronal waves in ciliates: from biology to material specifications.

Science.gov (United States)

Palagi, Stefano; Jager, Edwin W H; Mazzolai, Barbara; Beccai, Lucia

2013-12-01

The quest for swimming microrobots originates from possible applications in medicine, especially involving navigation in bodily fluids. Swimming microorganisms have become a source of inspiration because their propulsion mechanisms are effective in the low-Reynolds number regime. In this study, we address a propulsion mechanism inspired by metachronal waves, i.e. the spontaneous coordination of cilia leading to the fast swimming of ciliates. We analyse the biological mechanism (referring to its particular embodiment in Paramecium caudatum), and we investigate the contribution of its main features to the swimming performance, through a three-dimensional finite-elements model, in order to develop a simplified, yet effective artificial design. We propose a bioinspired propulsion mechanism for a swimming microrobot based on a continuous cylindrical electroactive surface exhibiting perpendicular wave deformations travelling longitudinally along its main axis. The simplified propulsion mechanism is conceived specifically for microrobots that embed a micro-actuation system capable of executing the bioinspired propulsion (self-propelled microrobots). Among the available electroactive polymers, we select polypyrrole as the possible actuation material and we assess it for this particular embodiment. The results are used to appoint target performance specifications for the development of improved or new electroactive materials to attain metachronal-waves-like propulsion.

Mechanical Biological Treatment

DEFF Research Database (Denmark)

Bilitewski, B-; Oros, Christiane; Christensen, Thomas Højlund

2011-01-01

The basic processes and technologies of composting and anaerobic digestion, as described in the previous chapters, are usually used for specific or source-separated organic waste flows. However, in the 1990s mechanical biological waste treatment technologies (MBT) were developed for unsorted...... or residual waste (after some recyclables removed at the source). The concept was originally to reduce the amount of waste going to landfill, but MBT technologies are today also seen as plants recovering fuel as well as material fractions. As the name suggests the technology combines mechanical treatment...... technologies (screens, sieves, magnets, etc.) with biological technologies (composting, anaerobic digestion). Two main technologies are available: Mechanical biological pretreatment (MBP), which first removes an RDF fraction and then biologically treats the remaining waste before most of it is landfilled...

Optimal Conventional and Semi-Natural Treatments for the Upper Yakima Spring Chinook Salmon Supplementation Project, Treatment Definitions and Descriptions, and Biological Specifications for Facility Design, Final Report 1999

International Nuclear Information System (INIS)

Hager, Robert C.; Costello, Ronald J.

1999-01-01

This report describes the Yakima Fisheries Project facilities (Cle Elum Hatchery and acclimation satellites) which provide the mechanism to conduct state-of-the-art research for addressing questions about spring chinook supplementation strategies. The definition, descriptions, and specifications for the Yakima spring chinook supplementation program permit evaluation of alternative fish culture techniques that should yield improved methods and procedures to produce wild-like fish with higher survival that can be used to rebuild depleted spring chinook stocks of the Columbia River Basin. The definition and description of three experimental treatments, Optimal Conventional (OCT), Semi-Natural (SNT), Limited Semi-Natural (LSNT), and the biological specifications for facilities have been completed for the upper Yakima spring chinook salmon stock of the Yakima Fisheries Project. The task was performed by the Biological Specifications Work Group (BSWG) represented by Yakama Indian Nation, Washington Department of Fish and Wildlife, National Marine Fisheries Service, and Bonneville Power Administration. The control and experimental variables of the experimental treatments (OCT, SNT, and LSNT) are described in sufficient detail to assure that the fish culture facilities will be designed and operated as a production scale laboratory to produce and test supplemented upper Yakima spring chinook salmon. Product specifications of the treatment groups are proposed to serve as the generic templates for developing greater specificity for measurements of product attributes. These product specifications will be used to monitor and evaluate treatment effects, with respect to the biological response variables (post release survival, long-term fitness, reproductive success and ecological interactions)

Biologic Constraints on Modelling Virus Assembly

Directory of Open Access Journals (Sweden)

Robert L. Garcea

2008-01-01

Full Text Available The mathematic modelling of icosahedral virus assembly has drawn increasing interest because of the symmetric geometry of the outer shell structures. Many models involve equilibrium expressions of subunit binding, with reversible subunit additions forming various intermediate structures. The underlying assumption is that a final lowest energy state drives the equilibrium toward assembly. In their simplest forms, these models have explained why high subunit protein concentrations and strong subunit association constants can result in kinetic traps forming off pathway partial and aberrant structures. However, the cell biology of virus assembly is exceedingly complex. The biochemistry and biology of polyoma and papillomavirus assembly described here illustrates many of these specific issues. Variables include the use of cellular ‘chaperone’ proteins as mediators of assembly fidelity, the coupling of assembly to encapsidation of a specific nucleic acid genome, the use of cellular structures as ‘workbenches’ upon which assembly occurs, and the underlying problem of making a capsid structure that is metastable and capable of rapid disassembly upon infection. Although formidable to model, incorporating these considerations could advance the relevance of mathematical models of virus assembly to the real world.

Predicting the biological condition of streams: Use of geospatial indicators of natural and anthropogenic characteristics of watersheds

Science.gov (United States)

Carlisle, D.M.; Falcone, J.; Meador, M.R.

2009-01-01

We developed and evaluated empirical models to predict biological condition of wadeable streams in a large portion of the eastern USA, with the ultimate goal of prediction for unsampled basins. Previous work had classified (i.e., altered vs. unaltered) the biological condition of 920 streams based on a biological assessment of macroinvertebrate assemblages. Predictor variables were limited to widely available geospatial data, which included land cover, topography, climate, soils, societal infrastructure, and potential hydrologic modification. We compared the accuracy of predictions of biological condition class based on models with continuous and binary responses. We also evaluated the relative importance of specific groups and individual predictor variables, as well as the relationships between the most important predictors and biological condition. Prediction accuracy and the relative importance of predictor variables were different for two subregions for which models were created. Predictive accuracy in the highlands region improved by including predictors that represented both natural and human activities. Riparian land cover and road-stream intersections were the most important predictors. In contrast, predictive accuracy in the lowlands region was best for models limited to predictors representing natural factors, including basin topography and soil properties. Partial dependence plots revealed complex and nonlinear relationships between specific predictors and the probability of biological alteration. We demonstrate a potential application of the model by predicting biological condition in 552 unsampled basins across an ecoregion in southeastern Wisconsin (USA). Estimates of the likelihood of biological condition of unsampled streams could be a valuable tool for screening large numbers of basins to focus targeted monitoring of potentially unaltered or altered stream segments. ?? Springer Science+Business Media B.V. 2008.

"Biology Education"--An Emerging Interdisciplinary Area of Research

Science.gov (United States)

Rutledge, Michael

2013-01-01

The growing number of faculty positions in biology education, the formation of professional societies focused specifically on biology education, and the increasing number of publications in biology education over the past decade

Sources and basic threats of biological safety

International Nuclear Information System (INIS)

Nazarova, O.D.

2010-01-01

Full text: Biological safety of any state is connected with development of its public protection against biological weapons and opportunity to prevent bio terrorist attacks. That's why in modern social-economic and geo-political conditions, the problem of biological safety strengthening become significant, which is connected with migration process globalization, development of bio-technology and dramatically increased risk of pathogenic germ infections proliferation, which can be used as biological weapon. Despite of undertaken efforts by world community on full prohibition of biological weapon, its proliferation in the world still takes place. Biology revolution during second and third millennium lead to development not only biotechnology but new achievements in medicine, agriculture and other fields of economy, but also created scientific and research preconditions for development of advanced biological means of mass destruction, that make it more attractive for achieving superiority and assigned targets: low developments costs, opportunity to create it by one small laboratory with two-three high qualified specialists bio technologists; tremendous impact effect: one substance gram can contain from one till one hundreds quintillions (10"1"8 - 10"2"0) active pathogen molecules and in case if they belong to amplificated RNA and DNA, each molecule getting to organism, will multiply and contaminate environment (the last one is its principal difference from chemical weapon); bypass of organism immunological barriers and specific vaccinations; unusual clinic finding, hard diagnosis; weakness of traditional medications and treatment methods; lack of material destruction; opportunity of tight-lipped developments; opportunity of tight-lipped application; opportunity of delayed effect; opportunity of selective influence on specific population (by use of genetic, climatic and cultural specifications of race, nations and nationalities). Above mentioned specifications create

Carbon nanotubes for biological and biomedical applications

International Nuclear Information System (INIS)

Yang Wenrong; Thordarson, Pall; Gooding, J Justin; Ringer, Simon P; Braet, Filip

2007-01-01

Ever since the discovery of carbon nanotubes, researchers have been exploring their potential in biological and biomedical applications. The recent expansion and availability of chemical modification and bio-functionalization methods have made it possible to generate a new class of bioactive carbon nanotubes which are conjugated with proteins, carbohydrates, or nucleic acids. The modification of a carbon nanotube on a molecular level using biological molecules is essentially an example of the 'bottom-up' fabrication principle of bionanotechnology. The availability of these biomodified carbon nanotube constructs opens up an entire new and exciting research direction in the field of chemical biology, finally aiming to target and to alter the cell's behaviour at the subcellular or molecular level. This review covers the latest advances of bio-functionalized carbon nanotubes with an emphasis on the development of functional biological nano-interfaces. Topics that are discussed herewith include methods for biomodification of carbon nanotubes, the development of hybrid systems of carbon nanotubes and biomolecules for bioelectronics, and carbon nanotubes as transporters for a specific delivery of peptides and/or genetic material to cells. All of these current research topics aim at translating these biotechnology modified nanotubes into potential novel therapeutic approaches. (topical review)

To Demonstrate the Specificity of an Enzymatic Method for Plasma Paracetamol Estimation.

Science.gov (United States)

O'Mullane, John A.

1987-01-01

Describes an experiment designed to introduce biochemistry students to the specificity of an analytical method which uses an enzyme to quantitate its substrate. Includes the use of toxicity charts together with the concept of the biological half-life of a drug. (TW)

Toward the First Data Acquisition Standard in Synthetic Biology.

Science.gov (United States)

Sainz de Murieta, Iñaki; Bultelle, Matthieu; Kitney, Richard I

2016-08-19

This paper describes the development of a new data acquisition standard for synthetic biology. This comprises the creation of a methodology that is designed to capture all the data, metadata, and protocol information associated with biopart characterization experiments. The new standard, called DICOM-SB, is based on the highly successful Digital Imaging and Communications in Medicine (DICOM) standard in medicine. A data model is described which has been specifically developed for synthetic biology. The model is a modular, extensible data model for the experimental process, which can optimize data storage for large amounts of data. DICOM-SB also includes services orientated toward the automatic exchange of data and information between modalities and repositories. DICOM-SB has been developed in the context of systematic design in synthetic biology, which is based on the engineering principles of modularity, standardization, and characterization. The systematic design approach utilizes the design, build, test, and learn design cycle paradigm. DICOM-SB has been designed to be compatible with and complementary to other standards in synthetic biology, including SBOL. In this regard, the software provides effective interoperability. The new standard has been tested by experiments and data exchange between Nanyang Technological University in Singapore and Imperial College London.

Imaging specific cellular glycan structures using glycosyltransferases via click chemistry.

Science.gov (United States)

Wu, Zhengliang L; Person, Anthony D; Anderson, Matthew; Burroughs, Barbara; Tatge, Timothy; Khatri, Kshitij; Zou, Yonglong; Wang, Lianchun; Geders, Todd; Zaia, Joseph; Sackstein, Robert

2018-02-01

Heparan sulfate (HS) is a polysaccharide fundamentally important for biologically activities. T/Tn antigens are universal carbohydrate cancer markers. Here, we report the specific imaging of these carbohydrates using a mesenchymal stem cell line and human umbilical vein endothelial cells (HUVEC). The staining specificities were demonstrated by comparing imaging of different glycans and validated by either removal of target glycans, which results in loss of signal, or installation of target glycans, which results in gain of signal. As controls, representative key glycans including O-GlcNAc, lactosaminyl glycans and hyaluronan were also imaged. HS staining revealed novel architectural features of the extracellular matrix (ECM) of HUVEC cells. Results from T/Tn antigen staining suggest that O-GalNAcylation is a rate-limiting step for O-glycan synthesis. Overall, these highly specific approaches for HS and T/Tn antigen imaging should greatly facilitate the detection and functional characterization of these biologically important glycans. © The Author(s) 2017. Published by Oxford University Press.

New trends in the use of biological response modifiers for treatment of malignant neoplasm

International Nuclear Information System (INIS)

Saad, Sherif Y.

2002-01-01

Biological response modifiers are critical controllers of cell division and hence tissue, growth, migration development and differentiation. The family of biological response modifiers includes interferons, tumor necrosis factor, interleukins, colony stimulating factors and hematopoietic growth factors as well as tumor vaccines and monoclonal antibodies. Biological response modifiers have important roles in cancer development and progression, control of cell replication and apoptosis and modulation of immune reactions such as sensitization. This article reviews the biology, pharmacology and clinical application of biological response modifiers in oncology. The antitumor activity of biological response modifiers may be augmented immune response including activation of natural killer lymphocytes and enhanced expression of cell surface antigens (MHC I and II). Combination of biological therapy with chemotherapy improves the response of those tumors refractory to conventional therapies. Colony stimulating factors are used for manipulating immune system to fight against cancer and to prevent chemotherapy-induced neutropenia. Recent advances in tumor immunology, most notably the identification of genes encoding for cancer regression antigens, have paved the way for the development of a variety of novel and specific vaccines and monoclonal antibody approaches. These approaches are discussed from a therapeutic perspective. (author)

Nonlinear optical polarization analysis in chemistry and biology

CERN Document Server

Simpson, Garth J

2017-01-01

This rigorous yet accessible guide presents a molecular-based description of nonlinear optical polarization analysis of chemical and biological assemblies. It includes discussion of the most common nonlinear optical microscopy and interfacial measurements used for quantitative analysis, specifically second harmonic generation (SHG), two-photon excited fluorescence (2PEF), vibrational sum frequency generation (SFG), and coherent anti-Stokes Raman spectroscopy/stimulated Raman spectroscopy (CARS/SRS). A linear algebra mathematical framework is developed, allowing step-wise systematic connections to be made between the observable measurements and the molecular response. Effects considered include local field corrections, the molecular orientation distribution, rotations between the molecular frame, the local frame and the laboratory frame, and simplifications from molecular and macromolecular symmetry. Specific examples are provided throughout the book, working from the common and relatively simple case studies ...

Mathematical modeling of biological processes

CERN Document Server

Friedman, Avner

2014-01-01

This book on mathematical modeling of biological processes includes a wide selection of biological topics that demonstrate the power of mathematics and computational codes in setting up biological processes with a rigorous and predictive framework. Topics include: enzyme dynamics, spread of disease, harvesting bacteria, competition among live species, neuronal oscillations, transport of neurofilaments in axon, cancer and cancer therapy, and granulomas. Complete with a description of the biological background and biological question that requires the use of mathematics, this book is developed for graduate students and advanced undergraduate students with only basic knowledge of ordinary differential equations and partial differential equations; background in biology is not required. Students will gain knowledge on how to program with MATLAB without previous programming experience and how to use codes in order to test biological hypothesis.

The fusion of biology, computer science, and engineering: towards efficient and successful synthetic biology.

Science.gov (United States)

Linshiz, Gregory; Goldberg, Alex; Konry, Tania; Hillson, Nathan J

2012-01-01

Synthetic biology is a nascent field that emerged in earnest only around the turn of the millennium. It aims to engineer new biological systems and impart new biological functionality, often through genetic modifications. The design and construction of new biological systems is a complex, multistep process, requiring multidisciplinary collaborative efforts from "fusion" scientists who have formal training in computer science or engineering, as well as hands-on biological expertise. The public has high expectations for synthetic biology and eagerly anticipates the development of solutions to the major challenges facing humanity. This article discusses laboratory practices and the conduct of research in synthetic biology. It argues that the fusion science approach, which integrates biology with computer science and engineering best practices, including standardization, process optimization, computer-aided design and laboratory automation, miniaturization, and systematic management, will increase the predictability and reproducibility of experiments and lead to breakthroughs in the construction of new biological systems. The article also discusses several successful fusion projects, including the development of software tools for DNA construction design automation, recursive DNA construction, and the development of integrated microfluidics systems.

The application of biological motion research: biometrics, sport, and the military.

Science.gov (United States)

Steel, Kylie; Ellem, Eathan; Baxter, David

2015-02-01

The body of research that examines the perception of biological motion is extensive and explores the factors that are perceived from biological motion and how this information is processed. This research demonstrates that individuals are able to use relative (temporal and spatial) information from a person's movement to recognize factors, including gender, age, deception, emotion, intention, and action. The research also demonstrates that movement presents idiosyncratic properties that allow individual discrimination, thus providing the basis for significant exploration in the domain of biometrics and social signal processing. Medical forensics, safety garments, and victim selection domains also have provided a history of research on the perception of biological motion applications; however, a number of additional domains present opportunities for application that have not been explored in depth. Therefore, the purpose of this paper is to present an overview of the current applications of biological motion-based research and to propose a number of areas where biological motion research, specific to recognition, could be applied in the future.

Guidelines for measuring the physical, chemical, and biological condition of wilderness ecosystems

Science.gov (United States)

Douglas G Fox; J. Christopher Bernabo; Betsy Hood

1987-01-01

Guidelines include a large number of specific measures to characterize the existing condition of wilderness resources. Measures involve the atmospheric environment, water chemistry and biology, geology and soils, and flora. Where possible, measures are coordinated with existing long-term monitoring programs. Application of the measures will allow more effective...

Analysis of complex networks from biology to linguistics

CERN Document Server

Dehmer, Matthias

2009-01-01

Mathematical problems such as graph theory problems are of increasing importance for the analysis of modelling data in biomedical research such as in systems biology, neuronal network modelling etc. This book follows a new approach of including graph theory from a mathematical perspective with specific applications of graph theory in biomedical and computational sciences. The book is written by renowned experts in the field and offers valuable background information for a wide audience.

Radiation physics, biophysics, and radiation biology

International Nuclear Information System (INIS)

Hall, E.J.; Zaider, M.

1993-05-01

Research at the Center for Radiological Research is a multidisciplenary blend of physics, chemistry and biology aimed at understanding the mechanisms involved in the health problems resulting from human exposure to ionizing radiations. The focus is increased on biochemistry and the application of the techniques of molecular biology to the problems of radiation biology. Research highlights of the program from the past year are described. A mathematical model describing the production of single-strand and double-strand breaks in DNA as a function radiation quality has been completed. For the first time Monte Carlo techniques have been used to obtain directly the spatial distribution of DNA moieties altered by radiation. This information was obtained by including the transport codes a realistic description of the electronic structure of DNA. We have investigated structure activity relationships for the potential oncogenicity of a new generation of bioreductive drugs that function as hypoxic cytotoxins. Experimental and theoretical investigation of the inverse dose rate effect, whereby medium LET radiations actually produce an c effect when the dose is protracted, is now at a point where the basic mechanisms are reasonably understood and the complex interplay between dose, dose rate and radiation quality which is necessary for the effect to be present can now be predicted at least in vitro. In terms of early radiobiological damage, a quantitative link has been established between basic energy deposition and locally multiply damaged sites, the radiochemical precursor of DNA double strand breaks; specifically, the spatial and energy deposition requirements necessary to form LMDs have been evaluated. For the first time, a mechanically understood ''biological fingerprint'' of high-LET radiation has been established. Specifically measurement of the ratio of inter-to intra-chromosomal aberrations produces a unique signature from alpha-particles or neutrons

Radiation physics, biophysics, and radiation biology

Energy Technology Data Exchange (ETDEWEB)

Hall, E.J.; Zaider, M.

1993-05-01

Research at the Center for Radiological Research is a multidisciplenary blend of physics, chemistry and biology aimed at understanding the mechanisms involved in the health problems resulting from human exposure to ionizing radiations. The focus is increased on biochemistry and the application of the techniques of molecular biology to the problems of radiation biology. Research highlights of the program from the past year are described. A mathematical model describing the production of single-strand and double-strand breaks in DNA as a function radiation quality has been completed. For the first time Monte Carlo techniques have been used to obtain directly the spatial distribution of DNA moieties altered by radiation. This information was obtained by including the transport codes a realistic description of the electronic structure of DNA. We have investigated structure activity relationships for the potential oncogenicity of a new generation of bioreductive drugs that function as hypoxic cytotoxins. Experimental and theoretical investigation of the inverse dose rate effect, whereby medium LET radiations actually produce an c effect when the dose is protracted, is now at a point where the basic mechanisms are reasonably understood and the complex interplay between dose, dose rate and radiation quality which is necessary for the effect to be present can now be predicted at least in vitro. In terms of early radiobiological damage, a quantitative link has been established between basic energy deposition and locally multiply damaged sites, the radiochemical precursor of DNA double strand breaks; specifically, the spatial and energy deposition requirements necessary to form LMDs have been evaluated. For the first time, a mechanically understood biological fingerprint'' of high-LET radiation has been established. Specifically measurement of the ratio of inter-to intra-chromosomal aberrations produces a unique signature from alpha-particles or neutrons.

Flexible automated approach for quantitative liquid handling of complex biological samples.

Science.gov (United States)

Palandra, Joe; Weller, David; Hudson, Gary; Li, Jeff; Osgood, Sarah; Hudson, Emily; Zhong, Min; Buchholz, Lisa; Cohen, Lucinda H

2007-11-01

A fully automated protein precipitation technique for biological sample preparation has been developed for the quantitation of drugs in various biological matrixes. All liquid handling during sample preparation was automated using a Hamilton MicroLab Star Robotic workstation, which included the preparation of standards and controls from a Watson laboratory information management system generated work list, shaking of 96-well plates, and vacuum application. Processing time is less than 30 s per sample or approximately 45 min per 96-well plate, which is then immediately ready for injection onto an LC-MS/MS system. An overview of the process workflow is discussed, including the software development. Validation data are also provided, including specific liquid class data as well as comparative data of automated vs manual preparation using both quality controls and actual sample data. The efficiencies gained from this automated approach are described.

Future arrangements for Great Britain's gas quality specifications. Government Response (including Summary of Responses) to consultation on future arrangements for Great Britain's gas quality specifications

International Nuclear Information System (INIS)

2007-01-01

Last year the Government consulted on GB's future gas quality specifications. The background is that some streams of imported gases have an energy content that exceeds the upper limit specified in GB's current gas quality regulations. The policy issue was whether to stick with the current regulated specifications, but at the cost of having to process imported gas to bring it within those specifications; or, at some time after 2020, to adjust those specifications, but at the cost of having to check (and potentially change) approximately 45m domestic gas appliances in 22m households, to ensure that they are capable of burning the high energy gas safely (and with a residual safety risk that some appliances are missed). The Consultation Document sought views on the proposal (backed up by the Partial Regulatory Impact Assessment) to adopt the 'no change' option. In the light of the responses, this is what the Government now proposes. The associated Impact Assessment estimates the total net benefit of the 'no change' option at UK Pounds 1.5bn - 14bn, with a best estimate of UK Pounds 8bn (NPV, 2005). The risks for gas prices and security of supply (included in the Impact Assessment) are judged to be small. The Government proposes a 'forward plan', consisting of support for Ofgem's work on maximising the commercial flexibilities for the GB gas market to handle gases of different specifications, whilst continuing to engage in EU discussions on the gas quality issue. (Author)

[Is there a "biology of violence"?].

Science.gov (United States)

Karli, Pierre

2004-01-01

Human violence does not stem from any specific biological substrate. As affective processes play a pre-eminent role in the elaboration and evolution of social interactions, a "biology of violence" draws essentially upon the concepts, methods and techniques of "affective neuroscience".

Optimal Conventional and Semi-Natural Treatments for the Upper Yakima Spring Chinook Salmon Supplementation Project; Treatment Definitions and Descriptions and Biological Specifications for Facility Design, 1995-1999 Final Report.

Energy Technology Data Exchange (ETDEWEB)

Hager, Robert C. (Hatchery Operations Consulting); Costello, Ronald J. (Mobrand Biometrics, Inc., Vashon Island, WA)

1999-10-01

This report describes the Yakima Fisheries Project facilities (Cle Elum Hatchery and acclimation satellites) which provide the mechanism to conduct state-of-the-art research for addressing questions about spring chinook supplementation strategies. The definition, descriptions, and specifications for the Yakima spring chinook supplementation program permit evaluation of alternative fish culture techniques that should yield improved methods and procedures to produce wild-like fish with higher survival that can be used to rebuild depleted spring chinook stocks of the Columbia River Basin. The definition and description of three experimental treatments, Optimal Conventional (OCT), Semi-Natural (SNT), Limited Semi-Natural (LSNT), and the biological specifications for facilities have been completed for the upper Yakima spring chinook salmon stock of the Yakima Fisheries Project. The task was performed by the Biological Specifications Work Group (BSWG) represented by Yakama Indian Nation, Washington Department of Fish and Wildlife, National Marine Fisheries Service, and Bonneville Power Administration. The control and experimental variables of the experimental treatments (OCT, SNT, and LSNT) are described in sufficient detail to assure that the fish culture facilities will be designed and operated as a production scale laboratory to produce and test supplemented upper Yakima spring chinook salmon. Product specifications of the treatment groups are proposed to serve as the generic templates for developing greater specificity for measurements of product attributes. These product specifications will be used to monitor and evaluate treatment effects, with respect to the biological response variables (post release survival, long-term fitness, reproductive success and ecological interactions).

Marine molecular biology: an emerging field of biological sciences.

Science.gov (United States)

Thakur, Narsinh L; Jain, Roopesh; Natalio, Filipe; Hamer, Bojan; Thakur, Archana N; Müller, Werner E G

2008-01-01

An appreciation of the potential applications of molecular biology is of growing importance in many areas of life sciences, including marine biology. During the past two decades, the development of sophisticated molecular technologies and instruments for biomedical research has resulted in significant advances in the biological sciences. However, the value of molecular techniques for addressing problems in marine biology has only recently begun to be cherished. It has been proven that the exploitation of molecular biological techniques will allow difficult research questions about marine organisms and ocean processes to be addressed. Marine molecular biology is a discipline, which strives to define and solve the problems regarding the sustainable exploration of marine life for human health and welfare, through the cooperation between scientists working in marine biology, molecular biology, microbiology and chemistry disciplines. Several success stories of the applications of molecular techniques in the field of marine biology are guiding further research in this area. In this review different molecular techniques are discussed, which have application in marine microbiology, marine invertebrate biology, marine ecology, marine natural products, material sciences, fisheries, conservation and bio-invasion etc. In summary, if marine biologists and molecular biologists continue to work towards strong partnership during the next decade and recognize intellectual and technological advantages and benefits of such partnership, an exciting new frontier of marine molecular biology will emerge in the future.

Biological desulfurisation

Energy Technology Data Exchange (ETDEWEB)

Arena, B.J. [UOP LLC (United States); Benschop, A.; Janssen, A. [Paques Natural Solutions (Netherlands); Kijlstra, S. [Shell Global Solutions (Netherlands)

2001-03-01

This article focuses on the biological THIOPAQ process for removing hydrogen sulphide from refinery gases and recovering elemental sulphur. Details are given of the process which absorbs hydrogen sulphide-containing gas in alkaline solution prior to oxidation of the dissolved sulphur to elemental sulphur in a THIOPAQ aerobic biological reactor, with regeneration of the caustic solution. Sulphur handling options including sulphur wash, the drying of the sulphur cake, and sulphur smelting by pressure liquefaction are described. Agricultural applications of the biologically recovered sulphur, and application of the THIOPAQ process to sulphur recovery are discussed.

MAK and BAT values list 2017. Maximum permissible concentrations at the place of work and biological tolerance values for working materials

International Nuclear Information System (INIS)

2017-01-01

The MAK and BAT values list 2017 includes the maximum permissible concentrations at the place of work and biological tolerance values for working materials. The following working materials are covered: carcinogenic working materials, sensitizing materials and aerosols. The report discusses the restriction of exposure peaks, skin resorption, MAK (maximum working place concentration) values during pregnancy, germ cell mutagens and specific working materials. Importance and application of BAT (biological working material tolerance) values, list of materials, carcinogens, biological guide values and reference values are also included.

MAK and BAT values list 2016. Maximum permissible concentrations at the place of work and biological tolerance values for working materials

International Nuclear Information System (INIS)

2016-01-01

The MAK and BAT values list 2016 includes the maximum permissible concentrations at the place of work and biological tolerance values for working materials. The following working materials are covered: carcinogenic working materials, sensitizing materials and aerosols. The report discusses the restriction of exposure peaks, skin resorption, MAK (maximum working place concentration) values during pregnancy, germ cell mutagens and specific working materials. Importance and application of BAT (biological working material tolerance) values, list of materials, carcinogens, biological guide values and reference values are also included.

Synthetic biology era: Improving antibiotic's world.

Science.gov (United States)

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.

Dual Causality and the Autonomy of Biology.

Science.gov (United States)

Bock, Walter J

2017-03-01

Ernst Mayr's concept of dual causality in biology with the two forms of causes (proximate and ultimate) continues to provide an essential foundation for the philosophy of biology. They are equivalent to functional (=proximate) and evolutionary (=ultimate) causes with both required for full biological explanations. The natural sciences can be classified into nomological, historical nomological and historical dual causality, the last including only biology. Because evolutionary causality is unique to biology and must be included for all complete biological explanations, biology is autonomous from the physical sciences.

An overview of bioinformatics methods for modeling biological pathways in yeast.

Science.gov (United States)

Hou, Jie; Acharya, Lipi; Zhu, Dongxiao; Cheng, Jianlin

2016-03-01

The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particular, discovery of biological pathways in yeast has become an important forefront in systems biology, which aims to understand the interactions among molecules within a cell leading to certain cellular processes in response to a specific environment. While the existing theoretical and experimental approaches enable the investigation of well-known pathways involved in metabolism, gene regulation and signal transduction, bioinformatics methods offer new insights into computational modeling of biological pathways. A wide range of computational approaches has been proposed in the past for reconstructing biological pathways from high-throughput datasets. Here we review selected bioinformatics approaches for modeling biological pathways inS. cerevisiae, including metabolic pathways, gene-regulatory pathways and signaling pathways. We start with reviewing the research on biological pathways followed by discussing key biological databases. In addition, several representative computational approaches for modeling biological pathways in yeast are discussed. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Synthetic biology for microbial heavy metal biosensors.

Science.gov (United States)

Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

2018-02-01

Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

Environmental philosophy 2.0: ethics and conservation biology for the 21st century.

Science.gov (United States)

Odenbaugh, Jay

2014-03-01

In this essay, I critically engage Sahotra Sarkar's Environmental Philosophy. The several topics include the conceptual foundations of conservation biology and traditional philosophy of science, naturalism and its implications, and ethical theory and specifically the status of human welfare. Copyright © 2013 Elsevier Ltd. All rights reserved.

Site-Specific Infrared Probes of Proteins

Science.gov (United States)

Ma, Jianqiang; Pazos, Ileana M.; Zhang, Wenkai; Culik, Robert M.; Gai, Feng

2015-01-01

Infrared spectroscopy has played an instrumental role in studying a wide variety of biological questions. However, in many cases it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and/or environmental information in a site-specific manner. To overcome this limitation, many recent efforts have been dedicated to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural and/or environmental properties. In this Review, we highlight some recent advancements of this rapidly growing research area. PMID:25580624

Substantiation of Biological Assets Classification Indexes for Enhancing Their Accounting Efficiency

OpenAIRE

Rayisa Tsyhan; Olha Chubka

2013-01-01

Present day national agricultural companies sell their products in both domestic and foreign markets which has a significant impact on specifics of biological assets accounting. The article offers biological assets classification provided in the Practical Guide to Accounting for Biological Assets and, besides, specifications proposed by various scientists. Based on the analysis, biological assets classification has been supplemented with new classification factors and their appropriateness ha...

Leveraging biology interest to broaden participation in the geosciences

Science.gov (United States)

Perin, S.; Conner, L.; Oxtoby, L.

2017-12-01

It has been well documented that female participation in the geoscience workforce is low. By contrast, the biology workforce has largely reached gender parity. These trends are rooted in patterns of interest among youth. Specifically, girls tend to like biology and value social and societal connections to science (Brotman & Moore 2008). Our NSF-funded project, "BRIGHT Girls," offers two-week summer academies to high school-aged girls, in which the connections between the geosciences and biology are made explicit. We are conducting qualitative research to trace the girls' identity work during this intervention. Using team-based video interaction analysis, we are finding that the fabric of the academy allows girls to "try on" new possible selves in science. Our results imply that real-world, interdisciplinary programs that include opportunities for agency and authentic science practice may be a fruitful approach for broadening participation in the geosciences.

Biological Movement and Laws of Physics.

Science.gov (United States)

Latash, Mark L

2017-07-01

Living systems may be defined as systems able to organize new, biology-specific, laws of physics and modify their parameters for specific tasks. Examples include the force-length muscle dependence mediated by the stretch reflex, and the control of movements with modification of the spatial referent coordinates for salient performance variables. Low-dimensional sets of referent coordinates at a task level are transformed to higher-dimensional sets at lower hierarchical levels in a way that ensures stability of performance. Stability of actions can be controlled independently of the actions (e.g., anticipatory synergy adjustments). Unintentional actions reflect relaxation processes leading to drifts of corresponding referent coordinates in the absence of changes in external load. Implications of this general framework for movement disorders, motor development, motor skill acquisition, and even philosophy are discussed.

Biology task group

International Nuclear Information System (INIS)

Anon.

1981-01-01

The accomplishments of the task group studies over the past year are reviewed. The purposes of biological investigations, in the context of subseabed disposal, are: an evaluation of the dose to man; an estimation of effects on the ecosystem; and an estimation of the influence of organisms on and as barriers to radionuclide migration. To accomplish these ends, the task group adopted the following research goals: (1) acquire more data on biological accumulation of specific radionuclides, such as those of Tc, Np, Ra, and Sr; (2) acquire more data on transfer coefficients from sediment to organism; (3) Calculate mass transfer rates, construct simple models using them, and estimate collective dose commitment; (4) Identify specific pathways or transfer routes, determine the rates of transfer, and make dose limit calculations with simple models; (5) Calculate dose rates to and estimate irradiation effects on the biota as a result of waste emplacement, by reference to background irradiation calculations. (6) Examine the effect of the biota on altering sediment/water radionuclide exchange; (7) Consider the biological data required to address different accident scenarios; (8) Continue to provide the basic biological information for all of the above, and ensure that the system analysis model is based on the most realistic and up-to-date concepts of marine biologists; and (9) Ensure by way of free exchange of information that the data used in any model are the best currently available

Radionuclide biological half-life values for terrestrial and aquatic wildlife

International Nuclear Information System (INIS)

Beresford, N.A.; Beaugelin-Seiller, K.; Burgos, J.; Cujic, M.; Fesenko, S.; Kryshev, A.; Pachal, N.; Real, A.; Su, B.S.; Tagami, K.; Vives i Batlle, J.; Vives-Lynch, S.; Wells, C.; Wood, M.D.

2015-01-01

The equilibrium concentration ratio is typically the parameter used to estimate organism activity concentrations within wildlife dose assessment tools. Whilst this is assumed to be fit for purpose, there are scenarios such as accidental or irregular, fluctuating, releases from licensed facilities when this might not be the case. In such circumstances, the concentration ratio approach may under- or over-estimate radiation exposure depending upon the time since the release. To carrying out assessments for such releases, a dynamic approach is needed. The simplest and most practical option is representing the uptake and turnover processes by first-order kinetics, for which organism- and element-specific biological half-life data are required. In this paper we describe the development of a freely available international database of radionuclide biological half-life values. The database includes 1907 entries for terrestrial, freshwater, riparian and marine organisms. Biological half-life values are reported for 52 elements across a range of wildlife groups (marine = 9, freshwater = 10, terrestrial = 7 and riparian = 3 groups). Potential applications and limitations of the database are discussed. - Highlights: • 1907 biological half-life values have been collated for wildlife species. • Data cover 52 elements. • 27 marine, freshwater, riparian and terrestrial organisms are included.

Quantum Biology

Directory of Open Access Journals (Sweden)

Alessandro Sergi

2009-06-01

Full Text Available A critical assessment of the recent developmentsof molecular biology is presented.The thesis that they do not lead to a conceptualunderstanding of life and biological systems is defended.Maturana and Varela's concept of autopoiesis is briefly sketchedand its logical circularity avoided by postulatingthe existence of underlying living processes,entailing amplification from the microscopic to the macroscopic scale,with increasing complexity in the passage from one scale to the other.Following such a line of thought, the currently accepted model of condensed matter, which is based on electrostatics and short-ranged forces,is criticized. It is suggested that the correct interpretationof quantum dispersion forces (van der Waals, hydrogen bonding, and so onas quantum coherence effects hints at the necessity of includinglong-ranged forces (or mechanisms for them incondensed matter theories of biological processes.Some quantum effects in biology are reviewedand quantum mechanics is acknowledged as conceptually important to biology since withoutit most (if not all of the biological structuresand signalling processes would not even exist. Moreover, it is suggested that long-rangequantum coherent dynamics, including electron polarization,may be invoked to explain signal amplificationprocess in biological systems in general.

TH-A-BRD-01: Radiation Biology for Radiation Therapy Physicists

International Nuclear Information System (INIS)

Orton, C; Borras, C; Carlson, D

2014-01-01

Mechanisms by which radiation kills cells and ways cell damage can be repaired will be reviewed. The radiobiological parameters of dose, fractionation, delivery time, dose rate, and LET will be discussed. The linear-quadratic model for cell survival for high and low dose rate treatments and the effect of repopulation will be presented and discussed. The rationale for various radiotherapy techniques such as conventional fractionation, hyperfractionation, hypofractionation, and low and high dose rate brachytherapy, including permanent implants, will be presented. The radiobiological principles underlying radiation protection guidelines and the different radiation dosimetry terms used in radiation biology and in radiation protection will be reviewed. Human data on radiation induced cancer, including increases in the risk of second cancers following radiation therapy, as well as data on radiation induced tissue reactions, such as cardiovascular effects, for follow up times up to 20–40 years, published by ICRP, NCRP and BEIR Committees, will be examined. The latest risk estimates per unit dose will be presented. Their adoption in recent radiation protection standards and guidelines and their impact on patient and workers safety in radiotherapy will be discussed. Biologically-guided radiotherapy (BGRT) provides a systematic method to derive prescription doses that integrate patient-specific information about tumor and normal tissue biology. Treatment individualization based on patient-specific biology requires the identification of biological objective functions to facilitate the design and comparison of competing treatment modalities. Biological objectives provide a more direct approach to plan optimization instead of relying solely on dose-based surrogates and can incorporate factors that alter radiation response, such as DNA repair, tumor hypoxia, and relative biological effectiveness. We review concepts motivating biological objectives and provide examples of how

TH-A-BRD-01: Radiation Biology for Radiation Therapy Physicists

Energy Technology Data Exchange (ETDEWEB)

Orton, C [Wayne State University, Grosse Pointe, MI (United States); Borras, C [Radiological Physics and Health Services, Washington, DC (United States); Carlson, D [Yale University School of Medicine, New Haven, CT (United States)

2014-06-15

Mechanisms by which radiation kills cells and ways cell damage can be repaired will be reviewed. The radiobiological parameters of dose, fractionation, delivery time, dose rate, and LET will be discussed. The linear-quadratic model for cell survival for high and low dose rate treatments and the effect of repopulation will be presented and discussed. The rationale for various radiotherapy techniques such as conventional fractionation, hyperfractionation, hypofractionation, and low and high dose rate brachytherapy, including permanent implants, will be presented. The radiobiological principles underlying radiation protection guidelines and the different radiation dosimetry terms used in radiation biology and in radiation protection will be reviewed. Human data on radiation induced cancer, including increases in the risk of second cancers following radiation therapy, as well as data on radiation induced tissue reactions, such as cardiovascular effects, for follow up times up to 20–40 years, published by ICRP, NCRP and BEIR Committees, will be examined. The latest risk estimates per unit dose will be presented. Their adoption in recent radiation protection standards and guidelines and their impact on patient and workers safety in radiotherapy will be discussed. Biologically-guided radiotherapy (BGRT) provides a systematic method to derive prescription doses that integrate patient-specific information about tumor and normal tissue biology. Treatment individualization based on patient-specific biology requires the identification of biological objective functions to facilitate the design and comparison of competing treatment modalities. Biological objectives provide a more direct approach to plan optimization instead of relying solely on dose-based surrogates and can incorporate factors that alter radiation response, such as DNA repair, tumor hypoxia, and relative biological effectiveness. We review concepts motivating biological objectives and provide examples of how

Classification of Recombinant Biologics in the EU

DEFF Research Database (Denmark)

Klein, Kevin; De Bruin, Marie L; Broekmans, Andre W

2015-01-01

BACKGROUND AND OBJECTIVE: Biological medicinal products (biologics) are subject to specific pharmacovigilance requirements to ensure that biologics are identifiable by brand name and batch number in adverse drug reaction (ADR) reports. Since Member States collect ADR data at the national level...... of biologics by national authorities responsible for ADR reporting. METHODS: A sample list of recombinant biologics from the European Medicines Agency database of European Public Assessment Reports was created to analyze five Member States (Belgium, the Netherlands, Spain, Sweden, and the UK) according...

Two Dogmas of Biology

Directory of Open Access Journals (Sweden)

Leonore Fleming

2017-01-01

Full Text Available The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology.

Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

Science.gov (United States)

Culbertson, Jennifer; Kirby, Simon

2016-01-01

The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

More Ideas for Monitoring Biological Experiments with the BBC Computer: Absorption Spectra, Yeast Growth, Enzyme Reactions and Animal Behaviour.

Science.gov (United States)

Openshaw, Peter

1988-01-01

Presented are five ideas for A-level biology experiments using a laboratory computer interface. Topics investigated include photosynthesis, yeast growth, animal movements, pulse rates, and oxygen consumption and production by organisms. Includes instructions specific to the BBC computer system. (CW)

Unaffected perceptual thresholds for biological and non-biological form-from-motion perception in autism spectrum conditions.

Directory of Open Access Journals (Sweden)

Ayse Pinar Saygin

2010-10-01

Full Text Available Perception of biological motion is linked to the action perception system in the human brain, abnormalities within which have been suggested to underlie impairments in social domains observed in autism spectrum conditions (ASC. However, the literature on biological motion perception in ASC is heterogeneous and it is unclear whether deficits are specific to biological motion, or might generalize to form-from-motion perception.We compared psychophysical thresholds for both biological and non-biological form-from-motion perception in adults with ASC and controls. Participants viewed point-light displays depicting a walking person (Biological Motion, a translating rectangle (Structured Object or a translating unfamiliar shape (Unstructured Object. The figures were embedded in noise dots that moved similarly and the task was to determine direction of movement. The number of noise dots varied on each trial and perceptual thresholds were estimated adaptively. We found no evidence for an impairment in biological or non-biological object motion perception in individuals with ASC. Perceptual thresholds in the three conditions were almost identical between the ASC and control groups.Impairments in biological motion and non-biological form-from-motion perception are not across the board in ASC, and are only found for some stimuli and tasks. We discuss our results in relation to other findings in the literature, the heterogeneity of which likely relates to the different tasks performed. It appears that individuals with ASC are unaffected in perceptual processing of form-from-motion, but may exhibit impairments in higher order judgments such as emotion processing. It is important to identify more specifically which processes of motion perception are impacted in ASC before a link can be made between perceptual deficits and the higher-level features of the disorder.

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

Directory of Open Access Journals (Sweden)

Sette Alessandro

2005-05-01

Full Text Available Abstract Background Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM. This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP and proteasomal cleavage of protein sequences. Results Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1 the output generated is easy to interpret, (2 input and output are both quantitative, (3 specific computational strategies to handle experimental noise are built in, (4 the algorithm is designed to effectively handle bounded experimental data, (5 experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6 it is possible to incorporate pair interactions between positions of a sequence. Conclusion Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.

The Importance of Biological Databases in Biological Discovery.

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Gross Benjamin E

2006-11-01

Full Text Available Abstract 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.

A Unifying Theory of Biological Function.

Science.gov (United States)

van Hateren, J H

2017-01-01

A new theory that naturalizes biological function is explained and compared with earlier etiological and causal role theories. Etiological (or selected effects) theories explain functions from how they are caused over their evolutionary history. Causal role theories analyze how functional mechanisms serve the current capacities of their containing system. The new proposal unifies the key notions of both kinds of theories, but goes beyond them by explaining how functions in an organism can exist as factors with autonomous causal efficacy. The goal-directedness and normativity of functions exist in this strict sense as well. The theory depends on an internal physiological or neural process that mimics an organism's fitness, and modulates the organism's variability accordingly. The structure of the internal process can be subdivided into subprocesses that monitor specific functions in an organism. The theory matches well with each intuition on a previously published list of intuited ideas about biological functions, including intuitions that have posed difficulties for other theories.

Challenges in resonant cavity biosensor design: collection efficiency and specificity

Science.gov (United States)

Armani, Andrea M.; Mehrabani, Simin; Sun, Victoria; McBirney, Samantha; Hawk, Rasheeda M.; Gungor, Eda; Lee, Michele

2014-03-01

Optical cavities have successfully demonstrated the ability to detect a wide range of analytes with exquisite sensitivity. However, optimizing other parameters of the system, such as collection efficiency and specificity, have remained elusive. This presentation will discuss some of the recent work in this area, including 3D COMSOL Multiphysics models including mass transfer and binding kinetics of different cavity geometries and covalent attachment methods for a wide range of biological and synthetic moieties. A few representative experimental demonstrations will also be presented.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Science.gov (United States)

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

Systems Biology Markup Language (SBML Level 2 Version 5: Structures and Facilities for Model Definitions

Directory of Open Access Journals (Sweden)

Hucka Michael

2015-06-01

Full Text Available Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Human biological monitoring of occupational genotoxic exposures

DEFF Research Database (Denmark)

Knudsen, Lisbeth E.; Sorsa, M

1993-01-01

Human biological monitoring is a valuable tool for exposure assessment in groups of persons occupationally exposed to genotoxic agents. If the monitoring activity covers genetic material the term genetic monitoring is used. The methods used for genetic monitoring are either substance specific, e......) occupational exposure limit value of styrene in ambient air. The consideration of ethical issues in human genetic monitoring is an important but often overlooked aspect. This includes the scientific and preventional relevance of performing a test on individuals, pre- and post study information of donors...

Chemical biology based on target-selective degradation of proteins and carbohydrates using light-activatable organic molecules.

Science.gov (United States)

Toshima, Kazunobu

2013-05-01

Proteins and carbohydrates play crucial roles in a wide range of biological processes, including serious diseases. The development of novel and innovative methods for selective control of specific proteins and carbohydrates functions has attracted much attention in the field of chemical biology. In this account article, the development of novel chemical tools, which can degrade target proteins and carbohydrates by irradiation with a specific wavelength of light under mild conditions without any additives, is introduced. This novel class of photochemical agents promise bright prospects for finding not only molecular-targeted bioprobes for understanding of the structure-activity relationships of proteins and carbohydrates but also novel therapeutic drugs targeting proteins and carbohydrates.

A model for firm-specific strategic wisdom : including illustrations and 49 guiding questions

NARCIS (Netherlands)

van Straten, Roeland Peter

2017-01-01

This PhD thesis provides an answer to the question ‘How may one think strategically’. It does so by presenting a new prescriptive ‘Model for Firm-Specific Strategic Wisdom’. This Model aims to guide any individual strategist in his or her thinking from a state of firm-specific ‘ignorance’ to a state

Cameroon Journal of Experimental Biology

African Journals Online (AJOL)

The Cameroon Journal of Experimental Biology is the official journal of the Cameroon Forum for Biological Sciences (CAFOBIOS). It is an interdisciplinary journal for the publication of original research papers, short communications and review articles in all fields of experimental biology including biochemistry, physiology, ...

A Critical Perspective on Synthetic Biology

OpenAIRE

Michel Morange

2009-01-01

Synthetic biology emerged around 2000 as a new biological discipline. It shares with systems biology the same modular vision of organisms, but is more concerned with applications than with a better understanding of the functioning of organisms. A herald of this new discipline is Craig Venter who aims to create an artificial microorganism with the minimal genome compatible with life and to implement into it different 'functional modules' to generate new micro-organisms adapted to specific task...

Biological therapeutics

National Research Council Canada - National Science Library

Greenstein, Ben; Brook, Daniel A

2011-01-01

This introductory textbook covers all the main categories of biological medicines, including vaccines, hormonal preparations, drugs for rheumatoid arthritis and other connective tissue diseases, drugs...

Designing a 'neotissue' using the principles of biology, chemistry and engineering.

Science.gov (United States)

Nannaparaju, Madhusudhan; Oragui, Emeka; Khan, Wasim S

2012-01-01

The traditional methods of treating musculoskeletal injuries and disorders are not completely effective and have several limitations. Tissue engineering involves using the principles of biology, chemistry and engineering to design a 'neotissue' that augments a malfunctioning in vivo tissue. The main requirements for functional engineered tissue include reparative cellular components that proliferate on a scaffold grown within a bioreactor that provides specific biochemical and physical signals to regulate cell differentiation and tissue assembly. In this review we provide an overview of the biology of common musculoskeletal tissue and discuss their common pathologies. We also describe the commonly used stem cells, scaffolds and bioreactors and evaluate their role in issue engineering.

Biological effects of ionizing radiation - changing worker attitudes

International Nuclear Information System (INIS)

Johnson, N.; Schenley, C.

1989-01-01

Training Resources and Data Exchange (TRADE) Radiation Protection Training Special Interest Group has taken an innovative approach to providing DOE contractors with radiation worker training material information. Newly-hired radiation workers may be afraid to work near radiation and long-term radiation workers may become indifferent to the biological hazard of radiation. Commercially available training material is often presented at an inappropriate technical level or in an uninteresting style. These training problems have been addressed in the DOE system through development of a training videotape and supporting material package entitled Understanding Ionizing Radiation and its Biological Effects. The training package, developed and distributed by TRADE specifically to meet the needs of DOE contractor facilities, contains the videotape and accompanying paper supporting materials designed to assist the instructor. Learning objectives, presentation suggestion for the instructor, trainee worksheets, guided discussion questions, and trainee self-evaluation sheets are included in the training package. DOE contractors have agreed that incorporating this training module into radiation worker training programs enhances the quality of the training and increase worker understanding of the biological effects of ionizing radiation

Context-specific protein network miner - an online system for exploring context-specific protein interaction networks from the literature

KAUST Repository

Chowdhary, Rajesh

2012-04-06

Background: Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis. Results: We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality. Conclusions: CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/. © 2012 Chowdhary et al.

Context-specific protein network miner - an online system for exploring context-specific protein interaction networks from the literature

KAUST Repository

Chowdhary, Rajesh; Tan, Sin Lam; Zhang, Jinfeng; Karnik, Shreyas; Bajic, Vladimir B.; Liu, Jun S.

2012-01-01

Background: Protein interaction networks (PINs) specific within a particular context contain crucial information regarding many cellular biological processes. For example, PINs may include information on the type and directionality of interaction (e.g. phosphorylation), location of interaction (i.e. tissues, cells), and related diseases. Currently, very few tools are capable of deriving context-specific PINs for conducting exploratory analysis. Results: We developed a literature-based online system, Context-specific Protein Network Miner (CPNM), which derives context-specific PINs in real-time from the PubMed database based on a set of user-input keywords and enhanced PubMed query system. CPNM reports enriched information on protein interactions (with type and directionality), their network topology with summary statistics (e.g. most densely connected proteins in the network; most densely connected protein-pairs; and proteins connected by most inbound/outbound links) that can be explored via a user-friendly interface. Some of the novel features of the CPNM system include PIN generation, ontology-based PubMed query enhancement, real-time, user-queried, up-to-date PubMed document processing, and prediction of PIN directionality. Conclusions: CPNM provides a tool for biologists to explore PINs. It is freely accessible at http://www.biotextminer.com/CPNM/. © 2012 Chowdhary et al.

Philosophy of Systems and Synthetic Biology

DEFF Research Database (Denmark)

Green, Sara

2017-01-01

This entry aims to clarify how systems and synthetic biology contribute to and extend discussions within philosophy of science. Unlike fields such as developmental biology or molecular biology, systems and synthetic biology are not easily demarcated by a focus on a specific subject area or level...... of organization. Rather, they are characterized by the development and application of mathematical, computational, and synthetic modeling strategies in response to complex problems and challenges within the life sciences. Proponents of systems and synthetic biology often stress the necessity of a perspective...... that goes beyond the scope of molecular biology and genetic engineering, respectively. With the emphasis on systems and interaction networks, the approaches explicitly engage in one of the oldest philosophical discussions on the relationship between parts and wholes, or between reductionism and holism...

THE BIOLOGICAL CYCLE OF SUNFLOWER BROOMRAPE

Directory of Open Access Journals (Sweden)

DUCA Maria

2013-12-01

Full Text Available Orobanchaceae is a dicot family, which consists of annual and perennial plants distributing from tropical to subarctic regions, predominately in temperate regions. Broomrape (Orobanche cumana Wallr. = Orobanche cernua Loefl. is a parasitic angiosperm that has been causing a great deal of damage to sunflower production in many countries, including Republic of Moldova. This parasitic angiosperm depends entirely on the host for its supply of water and nutrients. A thorough understanding of its biology, including detailed knowledge of the specific mechanisms of parasitism, is needed in order to develop novel control methods. Some main developmental steps are described for the root parasites: seed conditioning and germination, haustorium formation, penetration into host tissues, maturation of the parasite plant, and seed production. All these stages were studied in artificial and natural conditions.

External irradiation facilities open for biological studies - progress in july 2005

International Nuclear Information System (INIS)

Gaillard-Lecanu, E.; Authier, N.; Verrey, B.; Bailly, I.; Bordy, J.M.; Coffigny, H.; Cortela, L.; Duval, D.; Leplat, J.J.; Poncy, J.L.; Testard, I.; Thuret, J.Y.

2005-01-01

The Life Science Division of the Atomic Energy Commission is making an inventory of the various radiation sources accessible for investigation on the biological effects of ionizing radiation. In this field, a wide range of studies is being carried out at the Life Science Division, attempting to characterize the kind of lesions with their early biological consequences (on the various cell compartments) and their late biological consequences (deterministic or stochastic effects), in relation to the radiation type and dose, especially at low doses. Several experimental models are available: plants, bacteria, eukaryotic cells from yeast up to mammalian cells and in vivo studies, mostly on rodents, in order to characterize the somatic late effects and the hereditary effects. Due to the significant cost of these facilities, also to their specific properties (nature of the radiation, dose and dose rate, possible accuracy of the irradiation at the molecular level), the closeness is no longer the only criteria for biologists to make a choice. The current evolution is to set up irradiation infrastructures combining ionizing radiation sources themselves and specific tools dedicated to biological studies: cell or molecular biology laboratories, animal facilities. The purpose, in this new frame, is to provide biologists with the most suitable facilities, and, if possible, to change these facilities according to requirements in radiobiology. In this report, the basics of interactions of ionizing radiation with biological tissues are briefly introduced, followed by a presentation of some of the facilities available for radiobiological studies especially at CEA. This panorama is not a comprehensive one, new data will be included as they advance, whether reporting existing facilities or if a new one is developed. (authors)

Using biological networks to improve our understanding of infectious diseases

Directory of Open Access Journals (Sweden)

Nicola J. Mulder

2014-08-01

Full Text Available Infectious diseases are the leading cause of death, particularly in developing countries. Although many drugs are available for treating the most common infectious diseases, in many cases the mechanism of action of these drugs or even their targets in the pathogen remain unknown. In addition, the key factors or processes in pathogens that facilitate infection and disease progression are often not well understood. Since proteins do not work in isolation, understanding biological systems requires a better understanding of the interconnectivity between proteins in different pathways and processes, which includes both physical and other functional interactions. Such biological networks can be generated within organisms or between organisms sharing a common environment using experimental data and computational predictions. Though different data sources provide different levels of accuracy, confidence in interactions can be measured using interaction scores. Connections between interacting proteins in biological networks can be represented as graphs and edges, and thus studied using existing algorithms and tools from graph theory. There are many different applications of biological networks, and here we discuss three such applications, specifically applied to the infectious disease tuberculosis, with its causative agent Mycobacterium tuberculosis and host, Homo sapiens. The applications include the use of the networks for function prediction, comparison of networks for evolutionary studies, and the generation and use of host–pathogen interaction networks.

Aspartate and glutamate mimetic structures in biologically active compounds.

Science.gov (United States)

Stefanic, Peter; Dolenc, Marija Sollner

2004-04-01

Glutamate and aspartate are frequently recognized as key structural elements for the biological activity of natural peptides and synthetic compounds. The acidic side-chain functionality of both the amino acids provides the basis for the ionic interaction and subsequent molecular recognition by specific receptor sites that results in the regulation of physiological or pathophysiological processes in the organism. In the development of new biologically active compounds that possess the ability to modulate these processes, compounds offering the same type of interactions are being designed. Thus, using a peptidomimetic design approach, glutamate and aspartate mimetics are incorporated into the structure of final biologically active compounds. This review covers different bioisosteric replacements of carboxylic acid alone, as well as mimetics of the whole amino acid structure. Amino acid analogs presented include those with different distances between anionic moieties, and analogs with additional functional groups that result in conformational restriction or alternative interaction sites. The article also provides an overview of different cyclic structures, including various cycloalkane, bicyclic and heterocyclic analogs, that lead to conformational restriction. Higher di- and tripeptide mimetics in which carboxylic acid functionality is incorporated into larger molecules are also reviewed. In addition to the mimetic structures presented, emphasis in this article is placed on their steric and electronic properties. These mimetics constitute a useful pool of fragments in the design of new biologically active compounds, particularly in the field of RGD mimetics and excitatory amino acid agonists and antagonists.

Urine: Waste product or biologically active tissue?

Science.gov (United States)

2018-03-01

Historically, urine has been viewed primarily as a waste product with little biological role in the overall health of an individual. Increasingly, data suggest that urine plays a role in human health beyond waste excretion. For example, urine might act as an irritant and contribute to symptoms through interaction with-and potential compromise of-the urothelium. To explore the concept that urine may be a vehicle for agents with potential or occult bioactivity and to discuss existing evidence and novel research questions that may yield insight into such a role, the National Institute of Diabetes and Digestive and Kidney Disease invited experts in the fields of comparative evolutionary physiology, basic science, nephrology, urology, pediatrics, metabolomics, and proteomics (among others) to a Urinology Think Tank meeting on February 9, 2015. This report reflects ideas that evolved from this meeting and current literature, including the concept of urine quality, the biological, chemical, and physical characteristics of urine, including the microbiota, cells, exosomes, pH, metabolites, proteins, and specific gravity (among others). Additionally, the manuscript presents speculative, and hopefully testable, ideas about the functional roles of urine constituents in health and disease. Moving forward, there are several questions that need further understanding and pursuit. There were suggestions to consider actively using various animal models and their biological specimens to elaborate on basic mechanistic information regarding human bladder dysfunction. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Learning Biology with Plant Pathology.

Science.gov (United States)

Carroll, Juliet E.

This monograph contains 10 plant pathology experiments that were written to correspond to portions of a biology curriculum. Each experiment is suitable to a biology topic and designed to encourage exploration of those biological concepts being taught. Experiments include: (1) The Symptoms and Signs of Disease; (2) Koch's Postulates; (3)…

Potentials of single-cell biology in identification and validation of disease biomarkers.

Science.gov (United States)

Niu, Furong; Wang, Diane C; Lu, Jiapei; Wu, Wei; Wang, Xiangdong

2016-09-01

Single-cell biology is considered a new approach to identify and validate disease-specific biomarkers. However, the concern raised by clinicians is how to apply single-cell measurements for clinical practice, translate the message of single-cell systems biology into clinical phenotype or explain alterations of single-cell gene sequencing and function in patient response to therapies. This study is to address the importance and necessity of single-cell gene sequencing in the identification and development of disease-specific biomarkers, the definition and significance of single-cell biology and single-cell systems biology in the understanding of single-cell full picture, the development and establishment of whole-cell models in the validation of targeted biological function and the figure and meaning of single-molecule imaging in single cell to trace intra-single-cell molecule expression, signal, interaction and location. We headline the important role of single-cell biology in the discovery and development of disease-specific biomarkers with a special emphasis on understanding single-cell biological functions, e.g. mechanical phenotypes, single-cell biology, heterogeneity and organization of genome function. We have reason to believe that such multi-dimensional, multi-layer, multi-crossing and stereoscopic single-cell biology definitely benefits the discovery and development of disease-specific biomarkers. © 2016 The Authors. Journal of Cellular and Molecular Medicine published by John Wiley & Sons Ltd and Foundation for Cellular and Molecular Medicine.

Biological activities of Lavandula angustifolia essential oil

OpenAIRE

Bílková, Zuzana

2013-01-01

Zuzana Bílková, Biological activities of Lavandula angustifolia essential oil, Thesis, Charles University in Prague, Faculty of Pharmacy in Hradec Králové, thesis author: PharmDr. Jan Martin, PhD., Hradec Králové, 2013, 72 pages. The thesis called "Biological activities of Lavandula angustifolia essential oil" is interested in biological activities of Lavandula angustifolia essential oil, specifically antifungal, antioxidant, anti-inflammatory, cytotoxicity, nematicidal and repellency activit...

Virtual lesions of the IFG abolish response facilitation for biological and non-biological cues

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Roger D Newman-Norlund

2010-03-01

Full Text Available Humans are faster to perform a given action following observation of that same action. Converging evidence suggests that the human mirror neuron system (MNS plays an important role in this phenomenon. However, the specificity of the neural mechanisms governing this effect remain controversial. Specialist theories of imitation suggest that biological cues are maximally capable of eliciting imitative facilitation. Generalist models, on the other hand, posit a broader role for the MNS in linking visual stimuli with appropriate responses. In the present study, we investigated the validity of these two theoretical approaches by disrupting the left and right inferior frontal gyrus (IFG during the preparation of congruent (imitative and incongruent (complementary actions cued by either biological (hand or non-biological (static dot stimuli. Delivery of TMS over IFG abolished imitative response facilitation. Critically, this effect was identical whether actions were cued by biological or non-biological stimuli. This finding argues against theories of imitation in which biological stimuli are treated preferentially and stresses the notion of the IFG as a vital center of general perception-action coupling in the human brain.

Quantum biological information theory

CERN Document Server

Djordjevic, Ivan B

2016-01-01

This book is a self-contained, tutorial-based introduction to quantum information theory and quantum biology. It serves as a single-source reference to the topic for researchers in bioengineering, communications engineering, electrical engineering, applied mathematics, biology, computer science, and physics. The book provides all the essential principles of the quantum biological information theory required to describe the quantum information transfer from DNA to proteins, the sources of genetic noise and genetic errors as well as their effects. Integrates quantum information and quantum biology concepts; Assumes only knowledge of basic concepts of vector algebra at undergraduate level; Provides a thorough introduction to basic concepts of quantum information processing, quantum information theory, and quantum biology; Includes in-depth discussion of the quantum biological channel modelling, quantum biological channel capacity calculation, quantum models of aging, quantum models of evolution, quantum models o...

Towards a Unified Understanding of Lithium Action in Basic Biology and its Significance for Applied Biology.

Science.gov (United States)

Jakobsson, Eric; Argüello-Miranda, Orlando; Chiu, See-Wing; Fazal, Zeeshan; Kruczek, James; Nunez-Corrales, Santiago; Pandit, Sagar; Pritchet, Laura

2017-12-01

Lithium has literally been everywhere forever, since it is one of the three elements created in the Big Bang. Lithium concentration in rocks, soil, and fresh water is highly variable from place to place, and has varied widely in specific regions over evolutionary and geologic time. The biological effects of lithium are many and varied. Based on experiments in which animals are deprived of lithium, lithium is an essential nutrient. At the other extreme, at lithium ingestion sufficient to raise blood concentration significantly over 1 mM/, lithium is acutely toxic. There is no consensus regarding optimum levels of lithium intake for populations or individuals-with the single exception that lithium is a generally accepted first-line therapy for bipolar disorder, and specific dosage guidelines for sufferers of that condition are generally agreed on. Epidemiological evidence correlating various markers of social dysfunction and disease vs. lithium level in drinking water suggest benefits of moderately elevated lithium compared to average levels of lithium intake. In contrast to other biologically significant ions, lithium is unusual in not having its concentration in fluids of multicellular animals closely regulated. For hydrogen ions, sodium ions, potassium ions, calcium ions, chloride ions, and magnesium ions, blood and extracellular fluid concentrations are closely and necessarily regulated by systems of highly selective channels, and primary and secondary active transporters. Lithium, while having strong biological activity, is tolerated over body fluid concentrations ranging over many orders of magnitude. The lack of biological regulation of lithium appears due to lack of lithium-specific binding sites and selectivity filters. Rather lithium exerts its myriad physiological and biochemical effects by competing for macromolecular sites that are relatively specific for other cations, most especially for sodium and magnesium. This review will consider what is known

Colloquium paper: uniquely human evolution of sialic acid genetics and biology.

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Varki, Ajit

2010-05-11

Darwinian evolution of humans from our common ancestors with nonhuman primates involved many gene-environment interactions at the population level, and the resulting human-specific genetic changes must contribute to the "Human Condition." Recent data indicate that the biology of sialic acids (which directly involves less than 60 genes) shows more than 10 uniquely human genetic changes in comparison with our closest evolutionary relatives. Known outcomes are tissue-specific changes in abundant cell-surface glycans, changes in specificity and/or expression of multiple proteins that recognize these glycans, and novel pathogen regimes. Specific events include Alu-mediated inactivation of the CMAH gene, resulting in loss of synthesis of the Sia N-glycolylneuraminic acid (Neu5Gc) and increase in expression of the precursor N-acetylneuraminic acid (Neu5Ac); increased expression of alpha2-6-linked Sias (likely because of changed expression of ST6GALI); and multiple changes in SIGLEC genes encoding Sia-recognizing Ig-like lectins (Siglecs). The last includes binding specificity changes (in Siglecs -5, -7, -9, -11, and -12); expression pattern changes (in Siglecs -1, -5, -6, and -11); gene conversion (SIGLEC11); and deletion or pseudogenization (SIGLEC13, SIGLEC14, and SIGLEC16). A nongenetic outcome of the CMAH mutation is human metabolic incorporation of foreign dietary Neu5Gc, in the face of circulating anti-Neu5Gc antibodies, generating a novel "xeno-auto-antigen" situation. Taken together, these data suggest that both the genes associated with Sia biology and the related impacts of the environment comprise a relative "hot spot" of genetic and physiological changes in human evolution, with implications for uniquely human features both in health and disease.

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses.

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Konstantin Yarygin

Full Text Available The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequencing data tends to extract only a little of the information concerning the metabolic potential and often omits specific functions. A meta-analysis of the available data with an emphasis on biomedically relevant gene groups can unveil new global trends in the gut microbiota. As a step toward the reuse of metagenomic data, we developed a method for the quantitative profiling of user-defined groups of genes in human gut metagenomes. This method is based on the quick analysis of a gene coverage matrix obtained by pre-mapping the metagenomic reads to a global gut microbial catalogue. The method was applied to profile the abundance of several gene groups related to antibiotic resistance, phages, biosynthesis clusters and carbohydrate degradation in 784 metagenomes from healthy populations worldwide and patients with inflammatory bowel diseases and obesity. We discovered country-wise functional specifics in gut resistome and virome compositions. The most distinct features of the disease microbiota were found for Crohn's disease, followed by ulcerative colitis and obesity. Profiling of the genes belonging to crAssphage showed that its abundance varied across the world populations and was not associated with clinical status. We demonstrated temporal resilience of crAssphage and the influence of the sample preparation protocol on its detected abundance. Our approach offers a convenient method to add value to accumulated "shotgun" metagenomic data by helping researchers state and assess novel biological hypotheses.

Carbohydrate/glycan-binding specificity of legume lectins in respect to their proposed biological functions

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Márcio Viana Ramos

2000-01-01

Full Text Available The lectins, proteins which specifically recognize carbohydrate moieties, have been extensively studied in many biochemical and structural aspects in order to establish the molecular basis of this non-catalytic event. On the other hand, their clinical and agricultural potentials have been growing fast. Although lectins, mainly those from legume plants, had been investigated for biological properties, studies about the physiological functions of lectins are scarce in literature. Therefore, despite the accumulated data on lectins (as proteins, the role played by these signalizing molecules is poorly discussed. In the light of our accumulated results on legume lectins, specially those obtained from plants belonging to the Diocleinae sub-tribe and available data in literature, we discuss here the main hypothesis of their functions according to their carbohydrate/glycan-binding specificity.As lectinas, proteinas que especificamente reconhecem estruturas que contém carboidratos, têm sido extensivamente estudadas em muitos aspectos bioquímicos e estruturais, objetivando estabelecer as bases moleculares deste evento não-catalítico. Por outro lado, os potenciais clínicos e agriculturais destas proteínas têm crescido rapidamente. Embora as lectinas, principalmente aquelas de legumes tenham sido bastante investigadas em suas propriedades biológicas, estudos sobre as funcões fisiológicas de lectinas são escassos na literatura. Além disto, a despeito da quantidade de dados acumulados sobre lectinas (como proteínas, o papel desempenhado por estas moléculas de sinalização é pobremente discutido. Valendo-se de nossos estudos sobre lectinas de leguminosas, principalmente da sub-tribo Diocleinae, e outros dados presentes na literatura, discutimos aqui, as principais hipóteses de suas funções com base na especificidade por carboidratos e glicanos complexos.

Paleoreconstruction by biological markers

Energy Technology Data Exchange (ETDEWEB)

Seifert, W K; Moldowan, J M

1981-06-01

During diagenesis and conversion of the original lipid fraction of biological systems to petroleum hydrocarbons, the following four basic events needed for paleoreconstruction may be monitored by biological markers: (1) sourcing, (2) maturation, (3) migration and (4) biodegradation. Actual cases of applying biological markers to petroleum exploration problems in different parts of the world are demonstrated. Cretaceous- and Phosphoria-sourced oils in the Wyoming Thrust Belt can be distinguished from one another by high quality source fingerprinting of biomarker terpanes using gas chromatography mass spectrometry. Identification of recently discovered biological markers, head-to-head isoprenoids, allows source differentiation between some oils from Sumatra. The degree of crude oil maturation in basins from California, Alaska, Russia, Wyoming and Louisiana can be assessed by specific biomarker ratios (20S/20R sterane epimers). Field evidence from such interpretation is augmented by laboratory pyrolysis of the rock. Extensive migration is documented by biomarkers in several oils. Biological marker results are consistent with the geological setting and add a dimension in assisting the petroleum explorationist towar paleoreconstruction.

Synthetic biology and its alternatives. Descartes, Kant and the idea of engineering biological machines.

Science.gov (United States)

Kogge, Werner; Richter, Michael

2013-06-01

The engineering-based approach of synthetic biology is characterized by an assumption that 'engineering by design' enables the construction of 'living machines'. These 'machines', as biological machines, are expected to display certain properties of life, such as adapting to changing environments and acting in a situated way. This paper proposes that a tension exists between the expectations placed on biological artefacts and the notion of producing such systems by means of engineering; this tension makes it seem implausible that biological systems, especially those with properties characteristic of living beings, can in fact be produced using the specific methods of engineering. We do not claim that engineering techniques have nothing to contribute to the biotechnological construction of biological artefacts. However, drawing on Descartes's and Kant's thinking on the relationship between the organism and the machine, we show that it is considerably more plausible to assume that distinctively biological artefacts emerge within a paradigm different from the paradigm of the Cartesian machine that underlies the engineering approach. We close by calling for increased attention to be paid to approaches within molecular biology and chemistry that rest on conceptions different from those of synthetic biology's engineering paradigm. Copyright © 2013 Elsevier Ltd. All rights reserved.

Systems Biology Modeling of the Radiation Sensitivity Network: A Biomarker Discovery Platform

International Nuclear Information System (INIS)

Eschrich, Steven; Zhang Hongling; Zhao Haiyan; Boulware, David; Lee, Ji-Hyun; Bloom, Gregory; Torres-Roca, Javier F.

2009-01-01

Purpose: The discovery of effective biomarkers is a fundamental goal of molecular medicine. Developing a systems-biology understanding of radiosensitivity can enhance our ability of identifying radiation-specific biomarkers. Methods and Materials: Radiosensitivity, as represented by the survival fraction at 2 Gy was modeled in 48 human cancer cell lines. We applied a linear regression algorithm that integrates gene expression with biological variables, including ras status (mut/wt), tissue of origin and p53 status (mut/wt). Results: The biomarker discovery platform is a network representation of the top 500 genes identified by linear regression analysis. This network was reduced to a 10-hub network that includes c-Jun, HDAC1, RELA (p65 subunit of NFKB), PKC-beta, SUMO-1, c-Abl, STAT1, AR, CDK1, and IRF1. Nine targets associated with radiosensitization drugs are linked to the network, demonstrating clinical relevance. Furthermore, the model identified four significant radiosensitivity clusters of terms and genes. Ras was a dominant variable in the analysis, as was the tissue of origin, and their interaction with gene expression but not p53. Overrepresented biological pathways differed between clusters but included DNA repair, cell cycle, apoptosis, and metabolism. The c-Jun network hub was validated using a knockdown approach in 8 human cell lines representing lung, colon, and breast cancers. Conclusion: We have developed a novel radiation-biomarker discovery platform using a systems biology modeling approach. We believe this platform will play a central role in the integration of biology into clinical radiation oncology practice.

Designing and testing a classroom curriculum to teach preschoolers about the biology of physical activity: The respiration system as an underlying biological causal mechanism

Science.gov (United States)

Ewing, Tracy S.

The present study examined young children's understanding of respiration and oxygen as a source of vital energy underlying physical activity. Specifically, the purpose of the study was to explore whether a coherent biological theory, characterized by an understanding that bodily parts (heart and lungs) and processes (oxygen in respiration) as part of a biological system, can be taught as a foundational concept to reason about physical activity. The effects of a biology-based intervention curriculum designed to teach preschool children about bodily functions as a part of the respiratory system, the role of oxygen as a vital substance and how physical activity acts an energy source were examined. Participants were recruited from three private preschool classrooms (two treatment; 1 control) in Southern California and included a total of 48 four-year-old children (30 treatment; 18 control). Findings from this study suggested that young children could be taught relevant biological concepts about the role of oxygen in respiratory processes. Children who received biology-based intervention curriculum made significant gains in their understanding of the biology of respiration, identification of physical and sedentary activities. In addition these children demonstrated that coherence of conceptual knowledge was correlated with improved accuracy at activity identification and reasoning about the inner workings of the body contributing to endurance. Findings from this study provided evidence to support the benefits of providing age appropriate but complex coherent biological instruction to children in early childhood settings.

Remarks on the Foundations of Biology

Directory of Open Access Journals (Sweden)

Seán Ó Nualláin

2008-10-01

Full Text Available p class="MsoNormal"span style="font-size: 12pt"This paper attempts, inevitably briefly, aspannbsp; /spanre-categorization and partial resolution of some foundational issues in biology.spannbsp; /spanAn initialspannbsp; /spanground-clearing exercise extends the notion of causality in biology from merely the efficient cause to include also final and formal causality./span/p p class="MsoNormal"span style="font-size: 12pt"The HGPspannbsp; /spancan be looked on as an attempt to ground explanation of the phenotype in terms of an efficient cause rooted in a gene.spannbsp; /spanThis notion gives rise to the first section discussing the computational metaphor and epigenesis and suggesting ways to extend this metaphor. The extended notion of causality alluded to above is necessary, but not sufficient, to demarcate a specific explanatory realm for the biological.spannbsp; /spanWhile the universe can ultimately, perhaps,be explainedspannbsp; /spanby quantum fluctuations being computed through the laws of nature, the origin of life remains a mystery.spannbsp;nbsp; /spanThe ground-clearing exercise refers to coincidences that motivate the cosmological anthropic /span/p p class="MsoNormal"span style="font-size: 12pt"principle, before raising an alert about the possibility of similar thermodynamic laws facilitating the emergence of life./span/p p class="MsoNormal"span style="font-size: 12pt"nbsp;/span/p p class="MsoNormal"span style="font-size: 12pt"Life itself seems to involve symbolic operations that can be described by the grammatical rules within tightly -defined limits of complexity.spannbsp;nbsp; /spanThe nascent field of biosemiotics has extended this argument, often in a Peircean direction.spannbsp; /spanYet, even here, the task involved needs to be specified. Is the organism creating proteins to launch an immune counter-attack ?spannbsp;nbsp; /spanAlternatively, is a pluripotent stem cell generating an entire organism?spannbsp; /spanWe consider what

Use of Biologics in Private Practice: Nine Years of Lessons and Learning.

Science.gov (United States)

Correa-Selm, Lilia M; Alamgir, Mahin; Rao, Babar K

2017-03-01

Over a decade ago, the FDA approved biologics for psoriasis, which changed how the disease is treated and, in most cases, has a significant positive impact on the lives of patients. Side effects primarily identified during the investigational and research phase led to the development of specific guidelines for treatment. The treatment guidelines have been amended to incorporate better understandings of side-effects over the years that the disease has been treated. In this study, we focused on a chart review that included assessing the current guidelines and their alignment with modern patient management and the recent side effects presented. This life-cycle evaluation included over 100 patients, management of their treatment, laboratory abnormalities, criteria for choosing or changing to a different biologic, and the effects of the treatments management throughout the years. The review identified some recommended changes in the application and treatment of psoriasis with biologics. To further evidence our findings, we hope to expand this study to a larger scale with more patients. J Drugs Dermatol. 2017;16(3):215-217..

Biological Effects of Neutron and Proton Irradiations. Vol. II. Proceedings of the Symposium on Biological Effects of Neutron Irradiations

International Nuclear Information System (INIS)

1964-01-01

During recent years the interest in biological effects caused by neutrons has been increasing steadily as a result of the rapid development of neutron technology and the great number of neutron sources being used. Neutrons, because of their specific physical characteristics and biological effects, form a special type of radiation hazard but, at the same time, are a prospective tool for applied radiobiology. This Symposium, held in Brookhaven at the invitation of the United States Government from 7-11 October 1963, provided an opportunity for scientists to discuss the experimental information at present available on the biological action of neutrons and to evaluate future possibilities. It was a sequel to the Symposium on Neutron Detection, Dosimetry and Standardization, which was organized by the International Atomic Energy Agency in December 1962 at Harwell. The Symposium was attended by 128 participants from 17 countries and 6 international organizations. Fifty-four papers were presented. The following subjects were discussed in various sessions: (1) Dosimetry. Estimation of absorbed dose of neutrons in biological material. (2) Biological effects of high-energy protons. (3) Cellular and genetic effects. (4) Pathology of neutron irradiation, including acute and chronic radiation syndromes (mortality, anatomical and histological changes, biochemical and metabolic disturbances) and delayed consequences. (5) Relative biological effectiveness of neutrons evaluated by different biological tests. A Panel on Biophysical Considerations in Neutron Experimentation, with special emphasis on informal discussions, was organized during the Symposium. The views of the Panel are recorded in Volume II of the Proceedings. Many reports were presented on the important subject of the relative effectiveness of the biological action of neutrons, as well as on the general pathology of neutron irradiation and the cellular and genetic effects related to it. Three survey papers considered

Systems biology in critical-care nursing.

Science.gov (United States)

Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

2011-01-01

Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

3D-printed biological organs: medical potential and patenting opportunity.

Science.gov (United States)

Yoo, Seung-Schik

2015-05-01

Three-dimensional (3D) bioprinting has emerged as a new disruptive technology that may address the ever-increasing demand for organ transplants. 3D bioprinting offers many technical features that allow for building functional biological tissue constructs by dispensing the individual or group of cells into specific locations along with various types of bio-scaffold materials and extracellular matrices, and thus, may provide flexibility needed for on-demand individualized construction of biological organs. Several key classes of 3D bioprinting techniques are reviewed, including potential medical and industrial applications. Several unanswered engineering components for the ultimate creation of printed biological organs are also discussed. The complicated nature of the human organs, in addition to the legal and ethical requirements for safe implantation into the human body, would require significant research and development to produce marketable bioprinted organs. This also suggests the possibility for further patenting and licensing opportunities from different sectors of the economy.

A Comparative Analysis of Numbers and Biology Content Domains between Turkey and the USA

Science.gov (United States)

Incikabi, Lutfi; Ozgelen, Sinan; Tjoe, Hartono

2012-01-01

This study aimed to compare Mathematics and Science programs focusing on TIMSS content domains of Numbers and Biology that produced the largest achievement gap among students from Turkey and the USA. Specifically, it utilized the content analysis method within Turkish and New York State (NYS) frameworks. The procedures of study included matching…

Biophysics and systems biology.

Science.gov (United States)

Noble, Denis

2010-03-13

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

Constructing the 'gender-specific body': A critical discourse analysis of publications in the field of gender-specific medicine.

Science.gov (United States)

Annandale, Ellen; Hammarström, Anne

2011-11-01

Gender-specific medicine, a new and increasingly influential ethos within medical research and practice, has received little critical attention to date. The objective of this article is to critically examine the attributes of gender-specific medicine as imparted by its advocates. Through a critical discourse analysis of its two leading academic journals, we identify five interrelated discourses: of male/female difference; of hegemonic biology; of men's disadvantages; of biological and social reductionism; and of the fragmented body. Together these comprise a master discourse of the 'gender-specific body'. The discourse of the 'gender-specific body' is discussed in relation to the current neoliberal political agenda which frames healthcare as a market good and locates health and illness in individual bodies rather than in the wider social arrangements of society. We argue that the 'gender-specific body' threatens not only to turn back the clock to a vision of the biological body as fixed and determinate, but to extend this ever deeper into the social imagination. Lost in the process is any meaningful sense of the human body as a relatively open system which develops in interaction with its social world. We propose that, as it gains momentum, the 'gender-specific body' is likely progressively to circumscribe our thinking about the health of women and men in potentially problematic ways.

Physics and biology

International Nuclear Information System (INIS)

Frauenfelder, H.

1988-01-01

The author points out that the coupling between physics and biology is becoming closer as time goes on. He tries to show that physical studies on biological systems not only yield insight into biology but also provide results of interest to physics. Biological systems are extremly complex system. Ideally one would like to understand the behavior of such systems in terms of the behavior of its constituent atoms. Since in small organisms this may be 10 20 atoms, it is clear these are not simple many-body systems. He reviews the basic elements of cells and then considers the broader questions of structure, complexity, and function, which must be looked at on levels from the cell to the organism. Despite the vast amount of observational material already in existence, biophysics and biological physics are only at a beginning. We can expect that physics will continue to interact strongly with biology. Actually, the connection also includes chemistry and mathematics. New tools that become available in physics will continue to be applied to biological problems. We can expect that the flow of information will not be one way; biological systems will provide new information on many old and new parts of physics, from reaction theory and transport phenomena to complexity, cooperativity, and nonlinear processes

Impaired Perception of Biological Motion in Parkinson’s Disease

Science.gov (United States)

Jaywant, Abhishek; Shiffrar, Maggie; Roy, Serge; Cronin-Golomb, Alice

2016-01-01

Objective We examined biological motion perception in Parkinson’s disease (PD). Biological motion perception is related to one’s own motor function and depends on the integrity of brain areas affected in PD, including posterior superior temporal sulcus. If deficits in biological motion perception exist, they may be specific to perceiving natural/fast walking patterns that individuals with PD can no longer perform, and may correlate with disease-related motor dysfunction. Method 26 non-demented individuals with PD and 24 control participants viewed videos of point-light walkers and scrambled versions that served as foils, and indicated whether each video depicted a human walking. Point-light walkers varied by gait type (natural, parkinsonian) and speed (0.5, 1.0, 1.5 m/s). Participants also completed control tasks (object motion, coherent motion perception), a contrast sensitivity assessment, and a walking assessment. Results The PD group demonstrated significantly less sensitivity to biological motion than the control group (pperception (p=.02, Cohen’s d=.68). There was no group difference in coherent motion perception. Although individuals with PD had slower walking speed and shorter stride length than control participants, gait parameters did not correlate with biological motion perception. Contrast sensitivity and coherent motion perception also did not correlate with biological motion perception. Conclusion PD leads to a deficit in perceiving biological motion, which is independent of gait dysfunction and low-level vision changes, and may therefore arise from difficulty perceptually integrating form and motion cues in posterior superior temporal sulcus. PMID:26949927

Sex matters: The effects of biological sex on adipose tissue biology and energy metabolism

Directory of Open Access Journals (Sweden)

Teresa G. Valencak

2017-08-01

Full Text Available Adipose tissue is a complex and multi-faceted organ. It responds dynamically to internal and external stimuli, depending on the developmental stage and activity of the organism. The most common functional subunits of adipose tissue, white and brown adipocytes, regulate and respond to endocrine processes, which then determine metabolic rate as well as adipose tissue functions. While the molecular aspects of white and brown adipose biology have become clearer in the recent past, much less is known about sex-specific differences in regulation and deposition of adipose tissue, and the specific role of the so-called pink adipocytes during lactation in females. This review summarises the current understanding of adipose tissue dynamics with a focus on sex-specific differences in adipose tissue energy metabolism and endocrine functions, focussing on mammalian model organisms as well as human-derived data. In females, pink adipocytes trans-differentiate during pregnancy from subcutaneous white adipocytes and are responsible for milk-secretion in mammary glands. Overlooking biological sex variation may ultimately hamper clinical treatments of many aspects of metabolic disorders. Keywords: Body fatness, Adipose tissue, Sex-specific differences, Adipokines, Adipocytes, Obesity, Energy metabolism

Continuing training program in radiation protection in biological research centers

International Nuclear Information System (INIS)

Escudero, R.; Hidalgo, R.M.; Usera, F.; Macias, M.T.; Mirpuri, E.; Perez, J.; Sanchez, A.

2008-01-01

The use of ionizing radiation in biological research has many specific characteristics. A great variety of radioisotopic techniques involve unsealed radioactive sources, and their use not only carries a risk of irradiation, but also a significant risk of contamination. Moreover, a high proportion of researchers are in training and the labor mobility rate is therefore high. Furthermore, most newly incorporated personnel have little or no previous training in radiological protection, since most academic qualifications do not include training in this discipline. In a biological research center, in addition to personnel whose work is directly associated with the radioactive facility (scientific-technical personnel, operators, supervisors), there are also groups of support personnel The use of ionizing radiation in biological research has many specific characteristics. A great variety of radioisotopic techniques involve unsealed radioactive sources, and their use not only carries a risk of irradiation, but also a significant risk of contamination. Moreover, a high proportion of researchers are in training and the labor mobility rate is therefore high. Furthermore, most newly incorporated personnel have little or no previous training in radiological protection, since most academic qualifications do not include training in this discipline. In a biological research center, in addition to personnel whose work is directly associated with the radioactive facility (scientific-technical personnel, operators, supervisors), there are also groups of support personnel maintenance and instrumentation workers, cleaners, administrative personnel, etc. who are associated with the radioactive facility indirectly. These workers are affected by the work in the radioactive facility to varying degrees, and they therefore also require information and training in radiological protection tailored to their level of interaction with the installation. The aim of this study was to design a

Synthetic Biology and Personalized Medicine

Science.gov (United States)

Jain, K.K.

2013-01-01

Synthetic biology, application of synthetic chemistry to biology, is a broad term that covers the engineering of biological systems with structures and functions not found in nature to process information, manipulate chemicals, produce energy, maintain cell environment and enhance human health. Synthetic biology devices contribute not only to improve our understanding of disease mechanisms, but also provide novel diagnostic tools. Methods based on synthetic biology enable the design of novel strategies for the treatment of cancer, immune diseases metabolic disorders and infectious diseases as well as the production of cheap drugs. The potential of synthetic genome, using an expanded genetic code that is designed for specific drug synthesis as well as delivery and activation of the drug in vivo by a pathological signal, was already pointed out during a lecture delivered at Kuwait University in 2005. Of two approaches to synthetic biology, top-down and bottom-up, the latter is more relevant to the development of personalized medicines as it provides more flexibility in constructing a partially synthetic cell from basic building blocks for a desired task. PMID:22907209

Standard biological parts knowledgebase.

Directory of Open Access Journals (Sweden)

Michal Galdzicki

2011-02-01

Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org. The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org. SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL, a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Standard Biological Parts Knowledgebase

Science.gov (United States)

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

Standard biological parts knowledgebase.

Science.gov (United States)

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Evolutionary cell biology: functional insight from "endless forms most beautiful".

Science.gov (United States)

Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

2015-12-15

In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. © 2015 Richardson et al. 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).

Biological detector and method

Science.gov (United States)

Sillerud, Laurel; Alam, Todd M; McDowell, Andrew F

2013-02-26

A biological detector includes a conduit for receiving a fluid containing one or more magnetic nanoparticle-labeled, biological objects to be detected and one or more permanent magnets or electromagnet for establishing a low magnetic field in which the conduit is disposed. A microcoil is disposed proximate the conduit for energization at a frequency that permits detection by NMR spectroscopy of whether the one or more magnetically-labeled biological objects is/are present in the fluid.

Integrating biological and social values when prioritizing places for biodiversity conservation.

Science.gov (United States)

Whitehead, Amy L; Kujala, Heini; Ives, Christopher D; Gordon, Ascelin; Lentini, Pia E; Wintle, Brendan A; Nicholson, Emily; Raymond, Christopher M

2014-08-01

The consideration of information on social values in conjunction with biological data is critical for achieving both socially acceptable and scientifically defensible conservation planning outcomes. However, the influence of social values on spatial conservation priorities has received limited attention and is poorly understood. We present an approach that incorporates quantitative data on social values for conservation and social preferences for development into spatial conservation planning. We undertook a public participation GIS survey to spatially represent social values and development preferences and used species distribution models for 7 threatened fauna species to represent biological values. These spatially explicit data were simultaneously included in the conservation planning software Zonation to examine how conservation priorities changed with the inclusion of social data. Integrating spatially explicit information about social values and development preferences with biological data produced prioritizations that differed spatially from the solution based on only biological data. However, the integrated solutions protected a similar proportion of the species' distributions, indicating that Zonation effectively combined the biological and social data to produce socially feasible conservation solutions of approximately equivalent biological value. We were able to identify areas of the landscape where synergies and conflicts between different value sets are likely to occur. Identification of these synergies and conflicts will allow decision makers to target communication strategies to specific areas and ensure effective community engagement and positive conservation outcomes. © 2014 Society for Conservation Biology.

Metabolomics: Definitions and Significance in Systems Biology.

Science.gov (United States)

Klassen, Aline; Faccio, Andréa Tedesco; Canuto, Gisele André Baptista; da Cruz, Pedro Luis Rocha; Ribeiro, Henrique Caracho; Tavares, Marina Franco Maggi; Sussulini, Alessandra

2017-01-01

Nowadays, there is a growing interest in deeply understanding biological mechanisms not only at the molecular level (biological components) but also the effects of an ongoing biological process in the organism as a whole (biological functionality), as established by the concept of systems biology. Within this context, metabolomics is one of the most powerful bioanalytical strategies that allow obtaining a picture of the metabolites of an organism in the course of a biological process, being considered as a phenotyping tool. Briefly, metabolomics approach consists in identifying and determining the set of metabolites (or specific metabolites) in biological samples (tissues, cells, fluids, or organisms) under normal conditions in comparison with altered states promoted by disease, drug treatment, dietary intervention, or environmental modulation. The aim of this chapter is to review the fundamentals and definitions used in the metabolomics field, as well as to emphasize its importance in systems biology and clinical studies.

Rethinking biology instruction: The application of DNR-based instruction to the learning and teaching of biology

Science.gov (United States)

Maskiewicz, April Lee

Educational studies report that secondary and college level students have developed only limited understandings of the most basic biological processes and their interrelationships from typical classroom experiences. Furthermore, students have developed undesirable reasoning schemes and beliefs that directly affect how they make sense of and account for biological phenomena. For these reasons, there exists a need to rethink instructional practices in biology. This dissertation discusses how the principles of Harel's (1998, 2001) DNR-based instruction in mathematics could be applied to the teaching and learning of biology. DNR is an acronym for the three foundational principles of the system: Duality, Necessity, and Repeated-reasoning. This study examines the application of these three principles to ecology instruction. Through clinical and teaching interviews, I developed models of students' existing ways of understanding in ecology and inferred their ways of thinking. From these models a hypothetical learning trajectory was developed for 16 college level freshmen enrolled in a 10-week ecology teaching experiment. Through cyclical, interpretive analysis I documented and analyzed the evolution of the participants' progress. The results provide empirical evidence to support the claim that the DNR principles are applicable to ecology instruction. With respect to the Duality Principle, helping students develop specific ways of understanding led to the development of model-based reasoning---a way of thinking and the cognitive objective guiding instruction. Through carefully structured problem solving tasks, the students developed a biological understanding of the relationship between matter cycling, energy flow, and cellular processes such as photosynthesis and respiration, and used this understanding to account for observable phenomena in nature. In the case of intellectual necessity, the results illuminate how problem situations can be developed for biology learners

Hazard identification and risk assessment for biologics targeting the immune system.

Science.gov (United States)

Weir, Andrea B

2008-01-01

Biologic pharmaceuticals include a variety of products, such as monoclonal antibodies, fusion proteins and cytokines. Products in those classes include immunomodulatory biologics, which are intended to enhance or diminish the activity of the immune system. Immunomodulatory biologics have been approved by the U.S. FDA for a variety of indications, including cancer and inflammatory conditions. Prior to gaining approval for marketing, sponsoring companies for all types of products must demonstrate a product's safety in toxicology studies conducted in animals and show safety and efficacy in clinical trials conducted in patients. The overall goal of toxicology studies, which applies to immunomodulatory and other product types, is to identify the hazards that products pose to humans. Because biologics are generally highly selective for specific targets (receptors/epitopes), conducting toxicology studies in animal models with the target is essential. Such animals are referred to as pharmacologically relevant. Endpoints routinely included in toxicology studies, such as hematology, organ weight and histopathology, can be used to assess the effect of a product on the structure of the immune system. Additionally, specialized endpoints, such as immunophenotyping and immune function tests, can be used to define effects of immunomodulatory products on the immune system. Following hazard identification, risks posed to patients are assessed and managed. Risks can be managed through clinical trial design and risk communication, a practice that applies to immunomodulatory and other product types. Examples of risk management in clinical trial design include establishing a safe starting dose, defining the appropriate patient population and establishing appropriate patient monitoring. Risk communication starts during clinical trials and continues after product approval. A combination of hazard identification, risk assessment and risk management allows for drug development to proceed

Extended automated separation techniques in destructive neutron activation analysis; application to various biological materials, including human tissues and blood

International Nuclear Information System (INIS)

Tjioe, P.S.; Goeij, J.J.M. de; Houtman, J.P.W.

1976-09-01

Neutron activation analysis may be performed as a multi-element and low-level technique for many important trace elements in biological materials, provided that post-irradiation chemical separations are applied. This paper describes a chemical separation consisting of automated procedures for destruction, distillation, and anion-chromatography. The system developed enables the determination of 14 trace elements in biological materials, viz. antimony, arsenic, bromine, cadmium, chromium, cobalt, copper, gold, iron, mercury, molybdenum, nickel, selenium, and zinc. The aspects of sample preparation, neutron irradiation, gamma-spectrum evaluation, and blank-value contribution are also discussed

Review of Biological Network Data and Its Applications

Directory of Open Access Journals (Sweden)

Donghyeon Yu

2013-12-01

Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

The mathematics behind biological invasions

CERN Document Server

Lewis, Mark A; Potts, Jonathan R

2016-01-01

This book investigates the mathematical analysis of biological invasions. Unlike purely qualitative treatments of ecology, it draws on mathematical theory and methods, equipping the reader with sharp tools and rigorous methodology. Subjects include invasion dynamics, species interactions, population spread, long-distance dispersal, stochastic effects, risk analysis, and optimal responses to invaders. While based on the theory of dynamical systems, including partial differential equations and integrodifference equations, the book also draws on information theory, machine learning, Monte Carlo methods, optimal control, statistics, and stochastic processes. Applications to real biological invasions are included throughout. Ultimately, the book imparts a powerful principle: that by bringing ecology and mathematics together, researchers can uncover new understanding of, and effective response strategies to, biological invasions. It is suitable for graduate students and established researchers in mathematical ecolo...

Role of biologics in intractable urticaria

Directory of Open Access Journals (Sweden)

Cooke A

2015-04-01

Full Text Available Andrew Cooke,1 Adeeb Bulkhi,1,2 Thomas B Casale1 1Department of Internal Medicine, Division of Allergy and Immunology, University of South Florida, Tampa, FL, USA; 2Department of Internal Medicine, College of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia Abstract: Chronic urticaria (CU is a common condition faced by many clinicians. CU has been estimated to affect approximately 0.5%–1% of the population, with nearly 20% of sufferers remaining symptomatic 20 years after onset. Antihistamines are the first-line therapy for CU. Unfortunately, nearly half of these patients will fail this first-line therapy and require other medication, including immune response modifiers or biologics. Recent advances in our understanding of urticarial disorders have led to more targeted therapeutic options for CU and other urticarial diseases. The specific biologic agents most investigated for antihistamine-refractory CU are omalizumab, rituximab, and intravenous immunoglobulin (IVIG. Of these, the anti-IgE monoclonal antibody omalizumab is the best studied, and has recently been approved for the management of CU. Other agents, such as interleukin-1 inhibitors, have proved beneficial for Schnitzler syndrome and cryopyrin-associated periodic syndromes (CAPS, diseases associated with urticaria. This review summarizes the relevant data regarding the efficacy of biologics in antihistamine-refractory CU. Keywords: chronic urticaria, omalizumab, intravenous immunoglobulin, anakinra, canakinumab

An organelle-specific protein landscape identifies novel diseases and molecular mechanisms.

Science.gov (United States)

Boldt, Karsten; van Reeuwijk, Jeroen; Lu, Qianhao; Koutroumpas, Konstantinos; Nguyen, Thanh-Minh T; Texier, Yves; van Beersum, Sylvia E C; Horn, Nicola; Willer, Jason R; Mans, Dorus A; Dougherty, Gerard; Lamers, Ideke J C; Coene, Karlien L M; Arts, Heleen H; Betts, Matthew J; Beyer, Tina; Bolat, Emine; Gloeckner, Christian Johannes; Haidari, Khatera; Hetterschijt, Lisette; Iaconis, Daniela; Jenkins, Dagan; Klose, Franziska; Knapp, Barbara; Latour, Brooke; Letteboer, Stef J F; Marcelis, Carlo L; Mitic, Dragana; Morleo, Manuela; Oud, Machteld M; Riemersma, Moniek; Rix, Susan; Terhal, Paulien A; Toedt, Grischa; van Dam, Teunis J P; de Vrieze, Erik; Wissinger, Yasmin; Wu, Ka Man; Apic, Gordana; Beales, Philip L; Blacque, Oliver E; Gibson, Toby J; Huynen, Martijn A; Katsanis, Nicholas; Kremer, Hannie; Omran, Heymut; van Wijk, Erwin; Wolfrum, Uwe; Kepes, François; Davis, Erica E; Franco, Brunella; Giles, Rachel H; Ueffing, Marius; Russell, Robert B; Roepman, Ronald

2016-05-13

Cellular organelles provide opportunities to relate biological mechanisms to disease. Here we use affinity proteomics, genetics and cell biology to interrogate cilia: poorly understood organelles, where defects cause genetic diseases. Two hundred and seventeen tagged human ciliary proteins create a final landscape of 1,319 proteins, 4,905 interactions and 52 complexes. Reverse tagging, repetition of purifications and statistical analyses, produce a high-resolution network that reveals organelle-specific interactions and complexes not apparent in larger studies, and links vesicle transport, the cytoskeleton, signalling and ubiquitination to ciliary signalling and proteostasis. We observe sub-complexes in exocyst and intraflagellar transport complexes, which we validate biochemically, and by probing structurally predicted, disruptive, genetic variants from ciliary disease patients. The landscape suggests other genetic diseases could be ciliary including 3M syndrome. We show that 3M genes are involved in ciliogenesis, and that patient fibroblasts lack cilia. Overall, this organelle-specific targeting strategy shows considerable promise for Systems Medicine.

The relativity of biological function.

Science.gov (United States)

Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja

2015-12-01

Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

A Drosophila LexA Enhancer-Trap Resource for Developmental Biology and Neuroendocrine Research

Directory of Open Access Journals (Sweden)

Lutz Kockel

2016-10-01

Full Text Available Novel binary gene expression tools like the LexA-LexAop system could powerfully enhance studies of metabolism, development, and neurobiology in Drosophila. However, specific LexA drivers for neuroendocrine cells and many other developmentally relevant systems remain limited. In a unique high school biology course, we generated a LexA-based enhancer trap collection by transposon mobilization. The initial collection provides a source of novel LexA-based elements that permit targeted gene expression in the corpora cardiaca, cells central for metabolic homeostasis, and other neuroendocrine cell types. The collection further contains specific LexA drivers for stem cells and other enteric cells in the gut, and other developmentally relevant tissue types. We provide detailed analysis of nearly 100 new LexA lines, including molecular mapping of insertions, description of enhancer-driven reporter expression in larval tissues, and adult neuroendocrine cells, comparison with established enhancer trap collections and tissue specific RNAseq. Generation of this open-resource LexA collection facilitates neuroendocrine and developmental biology investigations, and shows how empowering secondary school science can achieve research and educational goals.

Advances in Structural Biology and the Application to Biological Filament Systems.

Science.gov (United States)

Popp, David; Koh, Fujiet; Scipion, Clement P M; Ghoshdastider, Umesh; Narita, Akihiro; Holmes, Kenneth C; Robinson, Robert C

2018-04-01

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. © 2018 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Synthetic biology between technoscience and thing knowledge.

Science.gov (United States)

Gelfert, Axel

2013-06-01

Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called 'thing knowledge'. As such, they should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world-knowledge that, in turn, can be accessed via continuous experimental interrogation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dicentric chromosome aberration analysis using giemsa and centromere specific fluorescence in-situ hybridization for biological dosimetry: An inter- and intra-laboratory comparison in Indian laboratories

International Nuclear Information System (INIS)

Bhavani, M.; Tamizh Selvan, G.; Kaur, Harpreet; Adhikari, J.S.; Vijayalakshmi, J.; Venkatachalam, P.; Chaudhury, N.K.

2014-01-01

To facilitate efficient handling of large samples, an attempt towards networking of laboratories in India for biological dosimetry was carried out. Human peripheral blood samples were exposed to 60 Co γ-radiation for ten different doses (0–5 Gy) at a dose rate of 0.7 and 2 Gy/min. The chromosomal aberrations (CA) were scored in Giemsa-stained and fluorescence in-situ hybridization with centromere-specific probes. No significant difference (p>0.05) was observed in the CA yield for given doses except 4 and 5 Gy, between the laboratories, among the scorers and also staining methods adapted suggest the reliability and validates the inter-lab comparisons exercise for triage applications. - Highlights: • This is the first report from India on Networking for Biological Dosimetry preparedness using dicentric chromosomal (DC) aberration assay. • There is no significant difference in the in vitro dose response curve (Slope, Intercept, Curvature) constructed among the two labs. • No significant variation in the scoring of DC aberrations between the scorers irrespective of labs. • The DC results obtained by the labs from the Giemsa stained metaphase preparations were confirmed with centromere specific-FISH for further reliability and validity

MAK and BAT values list 2015. Maximum permissible concentrations at the place of work and biological tolerance values for working materials

International Nuclear Information System (INIS)

2015-01-01

The book on the MAK (maximum permissible concentrations at the place of work) and BAT (biological tolerance values for working materials) value list 2015 includes the following chapters: (a) Maximum permissible concentrations at the place of work: definition, application and determination of MAT values, list of materials; carcinogenic working materials, sensibilizing working materials, aerosols, limiting the exposition peaks, skin resorption, MAK values during pregnancy, germ cell mutagens, specific working materials; (b) Biological tolerance values for working materials: definition and application of BAT values, list of materials, carcinogenic working materials, biological guide values, biological working material reference values.

MAK and BAT values list 2014. Maximum permissible concentrations at the place of work and biological tolerance values for working materials

International Nuclear Information System (INIS)

2014-01-01

The book on the MAK (maximum permissible concentrations at the place of work) and BAT (biological tolerance values for working materials) value list 2014 includes the following chapters: (a) Maximum permissible concentrations at the place of work: definition, application and determination of MAT values, list of materials; carcinogenic working materials, sensibilizing working materials, aerosols, limiting the exposition peaks, skin resorption, MAK values during pregnancy, germ cell mutagens, specific working materials; (b) Biological tolerance values for working materials: definition and application of BAT values, list of materials, carcinogenic working materials, biological guide values, biological working material reference values.

Meeting the specifications for mechanical-biological waste treament and dumping; Umsetzung der Ablagerungsanforderungen im MBA- und Deponiebetrieb

Energy Technology Data Exchange (ETDEWEB)

Ketelsen, K. [IBA Ingenieurbuero fuer Abfallwirtschaft und Entsorgung GmbH, Hannover (Germany)

2001-07-01

The new German ordinances will have a dramatic influence on the waste treatment processes and air/exhaust management in mechanical-biological waste treatment plants. The potentials of process control and optimization should be fully utilized. The extensive in-service inspections and specifications will change the requirements on the process and staff qualification. The additional cost must be balanced by technically and economically feasible projecting and solutions. The need to keep up with thermal processes will lead to the construction of plants with a size of 50,000 Mg/a and more as these have higher economic efficiency, i.e. small regional utilities will have to co-operate. In mechanical-biological waste treatment plants, about 40-50% of the total cost is accounted for by the waste treatment process, i.e. economic efficiency will depend on the cost of dumping of the stabilized fine-grained fraction(about 20%) and the cost of utilization of the high-calorific waste (about 30%). In view of the high fixed cost, mechanical-biological waste treatment concepts will be economically efficient only if the plant capacity is fully utilized. [German] Mit Verabschiedung der Verordnungen ist die MBA 'gesellschaftsfaehiger' geworden. Die Verordnungen werden einen nachhaltigen Einfluss auf die Verfahrenstechnik und das gesamte Luft-/Abgasmanagement haben. Die Entwicklungspotentiale in der Prozesssteuerung und -optimierung muessen verstaerkt ausgeschoepft werden. Durch die geforderten umfangreichen Untersuchungs- und Nachweispflichten werden sich die Anforderungen an die Betriebsfuehrung und Personalqualifikation veraendern. Die aus den hoeheren Anforderungen resultierenden Mehrkosten muessen durch technisch und wirtschftlich sinnvolle Planungen und Loesungen in vertretbaren Grenzen gehalten werden. Die Notwendigkeit zur Wirtschaftlichkeit im Wettbewerb mit rein thermischen Verfahren wird auch bei den MBA zur Realisierung wirtschaftlicher Anlagengroessen von groesser

Designing and Implementing a New Advanced Level Biology Course

Science.gov (United States)

Hall, Angela; Reiss, Michael J.; Rowell, Cathy; Scott, Anne

2003-01-01

Salters-Nuffield Advanced Biology is a new advanced level biology course, piloted from September 2002 in England with around 1200 students. This paper discusses the reasons for developing a new advanced biology course at this time, the philosophy of the project and how the materials are being written and the specification devised. The aim of the…

Biological and medical sensor technologies

CERN Document Server

Iniewski, Krzysztof

2012-01-01

Biological and Medical Sensor Technologies presents contributions from top experts who explore the development and implementation of sensors for various applications used in medicine and biology. Edited by a pioneer in the area of advanced semiconductor materials, the book is divided into two sections. The first part covers sensors for biological applications. Topics include: Advanced sensing and communication in the biological world DNA-derivative architectures for long-wavelength bio-sensing Label-free silicon photonics Quartz crystal microbalance-based biosensors Lab-on-chip technologies fo

The emerging molecular biology toolbox for the study of long noncoding RNA biology.

Science.gov (United States)

Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

2017-10-01

Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

Development of biology student worksheets to facilitate science process skills of student

Science.gov (United States)

Rahayu, Y. S.; Pratiwi, R.; Indana, S.

2018-01-01

This research aims to describe development of Biology student worksheets to facilitate science process skills of student, at the same time to facilitate thinking skills of students in senior high school are equipped with Assesment Sheets. The worksheets development refers to cycle which includes phase analysis (analysis), planning (planning), design (design), development (development), implementation (implementation), evaluation and revision (evaluation and revision). Phase evaluation and revision is an ongoing activity conducted in each phase of the development cycle. That is, after the evaluation of the results of these activities and make revisions at any phase, then continue to the next phase. Based on the test results for grade X, XI, and XII in St. Agnes Surabaya high school, obtained some important findings. The findings are as follows. (1) Developed biology student worksheets could be used to facilitate thinking ability of students in particular skills integrated process that includes components to formulate the problem, formulate hypotheses, determine the study variables, formulate an operational definition of variables, determine the steps in the research, planning data tables, organizing Data in the form of tables/charts, drawing conclusions, (2) Developed biology student worksheets could also facilitate the development of social interaction of students such as working together, listening/respect the opinions of others, assembling equipment and materials, discuss and share information and facilitate the upgrading of skills hands-on student activity. (3) Developed biology worksheets basically could be implemented with the guidance of the teacher step by step, especially for students who have never used a similar worksheet. Guidance at the beginning of this need, especially for worksheets that require special skills or understanding of specific concepts as a prerequisite, such as using a microscope, determine the heart rate, understand the mechanism of

Travel and biologic therapy: travel-related infection risk, vaccine response and recommendations.

Science.gov (United States)

Hall, Victoria; Johnson, Douglas; Torresi, Joseph

2018-01-01

Biologic therapy has revolutionized the management of refractory chronic autoimmune and auto-inflammatory disease, as well as several malignancies, providing rapid symptomatic relief and/or disease remission. Patients receiving biologic therapies have an improved quality of life, facilitating travel to exotic destinations and potentially placing them at risk of a range of infections. For each biologic agent, we review associated travel-related infection risk and expected travel vaccine response and effectiveness. A PUBMED search [vaccination OR vaccine] AND/OR ['specific vaccine'] AND/OR [immunology OR immune response OR response] AND [biologic OR biological OR biologic agent] was performed. A review of the literature was performed in order to develop recommendations on vaccination for patients in receipt of biologic therapy travelling to high-risk travel destinations. There is a paucity of literature in this area, however, it is apparent that travel-related infection risk is increased in patients on biologic therapy and when illness occurs they are at a higher risk of complication and hospitalization. Patients in receipt of biologic agents are deemed as having a high level of immunosuppression-live vaccines, including the yellow fever vaccine, are contraindicated. Inactivated vaccines are considered safe; however, vaccine response can be attenuated by the patient's biologic therapy, thereby resulting in reduced vaccine effectiveness and protection. Best practice requires a collaborative approach between the patient's primary healthcare physician, relevant specialist and travel medicine expert, who should all be familiar with the immunosuppressive and immunomodulatory effects resulting from the biologic therapies. Timing of vaccines should be carefully planned, and if possible, vaccination provided well before established immunosuppression.

The Latin American Biological Dosimetry Network (LBDNet)

International Nuclear Information System (INIS)

Garcia, O.; Lamadrid, A.I.; Gonzalez, J.E.; Romero, I.; Mandina, T.; Di Giorgio, M.; Radl, A.; Taja, M.R.; Sapienza, C.E.; Deminge, M.M.; Fernandez Rearte, J.; Stuck Oliveira, M.; Valdivia, P.; Guerrero-Carbajal, C.; Arceo Maldonado, C.; Cortina Ramirez, G.E.; Espinoza, M.; Martinez-Lopez, W.; Di Tomasso, M.

2016-01-01

Biological Dosimetry is a necessary support for national radiation protection programmes and emergency response schemes. The Latin American Biological Dosimetry Network (LBDNet) was formally founded in 2007 to provide early biological dosimetry assistance in case of radiation emergencies in the Latin American Region. Here are presented the main topics considered in the foundational document of the network, which comprise: mission, partners, concept of operation, including the mechanism to request support for biological dosimetry assistance in the region, and the network capabilities. The process for network activation and the role of the coordinating laboratory during biological dosimetry emergency response is also presented. This information is preceded by historical remarks on biological dosimetry cooperation in Latin America. A summary of the main experimental and practical results already obtained by the LBDNet is also included. (authors)

BIOLOGICAL CONTROL OF WEEDS BY MEANS OF PLANT PATHOGENS

OpenAIRE

Marija Ravlić; Renata Baličević

2014-01-01

Biological control is the use of live beneficial organisms and products of their metabolism in the pests control. Plant pathogens can be used for weed control in three different ways: as classical, conservation and augmentative (inoculative and inundated) biological control. Inundated biological control involves the use of bioherbicides (mycoherbicides) or artificial breeding of pathogens and application in specific stages of crops and weeds. Biological control of weeds can be used where chem...

Modulation of mutagen-induced biological effects by inhibitors of DNA repair

International Nuclear Information System (INIS)

Natarajan, A.T.; Mullenders, L.F.H.; Zwanenburg, T.S.B.

1986-01-01

When lesions are induced in the DNA by mutagenic agents, they are subjected to cellular repair. Unrepaired and misrepaired lesions lead to biological effects, such as cell killing, point mutations and chromosomal alterations (aberrations and sister chromatid exchanges - SCEs). It is very difficult to directly correlate any particular type of lesion to a specific biological effect. However, in specific cases, this has been done. For example, short wave UV induced biological effects (cell killing, chromosomal alterations) result predominantly from induced cyclobutane dimers and by photoreactivation experiments, one can demonstrate that with the removal of dimers all types biological effects are diminished. In cases where many types of lesions are considered responsible for the observed biological effects other strategies have been employed to identify the possible lesion. The frequencies of induced chromosomal alterations and point mutations increase with the dose of the mutagen employed and an inhibition of DNA repair following treatment with the mutagen. Prevention of the cells from dividing following mutagen treatment allows them to repair premutational damage, thus reducing the biological effects induced. By comprehensive studies involving quantification of primary DNA lesions, their repair and biological effects will enable us to understand to some extent the complex processes involved in the manifestation of specific biological effects that follow the treatment of cells with mutagenic carcinogens

Anthropic principle in biology and radiation biology

International Nuclear Information System (INIS)

Akif'ev, A. P.; Degtyarev, S.V.

1999-01-01

It was suggested to add the anthropic principle of the Universe according to which the physical constants of fundamental particles of matter and the laws of their counteraction are those that an appearance of man and mind becomes possible and necessary, with some biological constants to the set of fundamental constants. With reparation of DNA as an example it was shown how a cell ran some parameters of Watson-Crick double helix. It was pointed that the concept of the anthropic principle of the Universe in its full body including biological constants was a key to developing of a unified theory of evolution of the Universe within the limits of scientific creationism [ru

Novel Method To Identify Source-Associated Phylogenetic Clustering Shows that Listeria monocytogenes Includes Niche-Adapted Clonal Groups with Distinct Ecological Preferences

DEFF Research Database (Denmark)

Nightingale, K. K.; Lyles, K.; Ayodele, M.

2006-01-01

population are identified (TreeStats test). Analysis of sequence data for 120 L. monocytogenes isolates revealed evidence of clustering between isolates from the same source, based on the phylogenies inferred from actA and inlA (P = 0.02 and P = 0.07, respectively; SourceCluster test). Overall, the Tree...... are biologically valid. Overall, our data show that (i) the SourceCluster and TreeStats tests can identify biologically meaningful source-associated phylogenetic clusters and (ii) L. monocytogenes includes clonal groups that have adapted to infect specific host species or colonize nonhost environments......., including humans, animals, and food. If the null hypothesis that the genetic distances for isolates within and between source populations are identical can be rejected (SourceCluster test), then particular clades in the phylogenetic tree with significant overrepresentation of sequences from a given source...

Information on biological health effects of ionizing radiation and radionuclides: the rule of a web site

International Nuclear Information System (INIS)

Comte, A.; Gaillard-Lecanu, E.; Flury-Herard, A.; Ourly, F.; Hemidy, P.; Lallemand, J.

2006-01-01

The purpose of this project is to provide a source of information on biological and health effects of radionuclides and ionizing radiation in an easy to use format. Reported work is made up of two distinct parts: data sheets for selected radionuclides and a web file. Data sheets: Specific radiation data sheets provide an overview of the properties, the environmental behaviour, the different pathways of human exposure and the biological and health consequences of selected radionuclides. Radionuclides that have been selected are those commonly dealt with in nuclear industry (and in other areas such as medicine) and released to the environment or naturally occurring (plutonium, tritium, carbon 14). Data sheets corresponding to the different radionuclides are based on the main sources of scientific information in dosimetry, epidemiology, radiobiology and radiation protection. These data sheets are intended for radiation protection specialists and physicians. They include: main physical and chemical characteristics, main radiation protection data: dose coefficients (public, workers), dose limits sources, total released estimate (nuclear industry, atmospheric tests, main pathway of human exposure and biological behaviour, biological and health effects, medical supervision, treatment a list of the main references, appendix providing accurate information. Web file: http://www-dsv.cea.fr/doc/carmin_ext/fond.php This web file provides a source of information on biological and health effects of ionizing radiation and biological basic knowledge of radiation protection. Available for consultation via Internet, compiled information provides, in a same file, subjects as varied as biological mechanisms, ionizing radiations action, biological and health effects, risk assessment This file is mainly intended to assist in informing and training of non-specialist readership (students, teaching on radiation protection basic knowledge. This electronic document is divided in three

Delivery of Biologics Across the Blood-Brain Barrier with Molecular Trojan Horse Technology.

Science.gov (United States)

Pardridge, William M

2017-12-01

Biologics are potential new therapeutics for many diseases of the central nervous system. Biologics include recombinant lysosomal enzymes, neurotrophins, decoy receptors, and therapeutic antibodies. These are large molecule drugs that do not cross the blood-brain barrier (BBB). All classes of biologics have been tested, without success, in clinical trials of brain disease over the last 25 years. In none of these past clinical trials was the biologic re-engineered to enable transport across the BBB. If the biologic does not cross the BBB, the drug cannot reach the target site in brain, and success in a clinical trial is not expected. Biologics can be re-engineered for BBB transport with the use of molecular Trojan horse technology. A BBB molecular Trojan horse is a monoclonal antibody (MAb) against an endogenous BBB receptor transporter, such as the insulin receptor or transferrin receptor. The receptor-specific MAb penetrates the brain via transport on the endogenous BBB receptor. The MAb acts as a molecular Trojan horse to deliver across the BBB the biologic pharmaceutical that is genetically fused to the MAb. The lead Trojan horse is a MAb against the human insulin receptor (HIR), and HIRMAb-derived fusion proteins have entered clinical trials for the treatment of brain disease.

Systems biology of personalized nutrition

NARCIS (Netherlands)

Ommen, B. van; Broek, T. van den; Hoogh, I. de; Erk, M. van; Someren, E. van; Rouhani-Rankouhi, T.; Anthony, J.C.; Hogenelst, K.; Pasman, W.; Boorsma, A.; Wopereis, S.

2017-01-01

Personalized nutrition is fast becoming a reality due to a number of technological, scientific, and societal developments that complement and extend current public health nutrition recommendations. Personalized nutrition tailors dietary recommendations to specific biological requirements on the

Organic chemistry and biology: chemical biology through the eyes of collaboration.

Science.gov (United States)

Hruby, Victor J

2009-12-18

From a scientific perspective, efforts to understand biology including what constitutes health and disease has become a chemical problem. However, chemists and biologists "see" the problems of understanding biology from different perspectives, and this has retarded progress in solving the problems especially as they relate to health and disease. This suggests that close collaboration between chemists and biologists is not only necessary but essential for progress in both the biology and chemistry that will provide solutions to the global questions of biology. This perspective has directed my scientific efforts for the past 45 years, and in this overview I provide my perspective of how the applications of synthetic chemistry, structural design, and numerous other chemical principles have intersected in my collaborations with biologists to provide new tools, new science, and new insights that were only made possible and fruitful by these collaborations.

Topics in mathematical biology

CERN Document Server

Hadeler, Karl Peter

2017-01-01

This book analyzes the impact of quiescent phases on biological models. Quiescence arises, for example, when moving individuals stop moving, hunting predators take a rest, infected individuals are isolated, or cells enter the quiescent compartment of the cell cycle. In the first chapter of Topics in Mathematical Biology general principles about coupled and quiescent systems are derived, including results on shrinking periodic orbits and stabilization of oscillations via quiescence. In subsequent chapters classical biological models are presented in detail and challenged by the introduction of quiescence. These models include delay equations, demographic models, age structured models, Lotka-Volterra systems, replicator systems, genetic models, game theory, Nash equilibria, evolutionary stable strategies, ecological models, epidemiological models, random walks and reaction-diffusion models. In each case we find new and interesting results such as stability of fixed points and/or periodic orbits, excitability...

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

Science.gov (United States)

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.

Mammalian Synthetic Biology: Engineering Biological Systems.

Science.gov (United States)

Black, Joshua B; Perez-Pinera, Pablo; Gersbach, Charles A

2017-06-21

The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.

Doctoral Conceptual Thresholds in Cellular and Molecular Biology

Science.gov (United States)

Feldon, David F.; Rates, Christopher; Sun, Chongning

2017-01-01

In the biological sciences, very little is known about the mechanisms by which doctoral students acquire the skills they need to become independent scientists. In the postsecondary biology education literature, identification of specific skills and effective methods for helping students to acquire them are limited to undergraduate education. To…

Tramesan, a novel polysaccharide from Trametes versicolor. Structural characterization and biological effects.

Directory of Open Access Journals (Sweden)

Marzia Scarpari

Full Text Available Mushrooms represent a formidable source of bioactive compounds. Some of these may be considered as biological response modifiers; these include compounds with a specific biological function: antibiotics (e.g. plectasin, immune system stimulator (e,g, lentinan, antitumor agents (e.g. krestin, PSK and hypolipidemic agents (e.g. lovastatin inter alia. In this study, we focused on the Chinese medicinal mushroom "yun zhi", Trametes versicolor, traditionally used for (cit. "replenish essence and qi (vital energy". Previous studies indicated the potential activity of extracts from culture filtrate of asexual mycelia of T. versicolor in controlling the growth and secondary metabolism (e.g. mycotoxins of plant pathogenic fungi. The quest of active principles produced by T. versicolor, allowed us characterising an exo-polysaccharide released in its culture filtrate and naming it Tramesan. Herein we evaluate the biological activity of Tramesan in different organisms: plants, mammals and plant pathogenic fungi. We suggest that the bioactivity of Tramesan relies mostly on its ability to act as pro antioxidant molecule regardless the biological system on which it was applied.

Analysis of the biological spectrum of vascular flora of Ravni Srem flood forests

Directory of Open Access Journals (Sweden)

Jurišić Branislav

2011-01-01

Full Text Available One of the essential analyses performed during the floristic study of a region is the analysis of the biological spectrum. The analysis of the biological spectrum of the flora includes the determination of the type of life form for each taxon described in the flora of the study region. If it is considered that life form is a specific structural-functional response to the environmental effects and the result of the adaptation during the species evolution, it is clear that the basic characteristics of the site are more or less reflected in any life form. This fact is confirmed by the analysis of the biological spectrum of the flora of Ravni Srem. The analysis of the Ravni Srem flora shows the domination of the hemicryptophytes and the subdomination of the phanerophytes with a considerable participation of the therophytes.

Aging in a Relativistic Biological Space-Time

Directory of Open Access Journals (Sweden)

Davide Maestrini

2018-05-01

Full Text Available Here we present a theoretical and mathematical perspective on the process of aging. We extend the concepts of physical space and time to an abstract, mathematically-defined space, which we associate with a concept of “biological space-time” in which biological dynamics may be represented. We hypothesize that biological dynamics, represented as trajectories in biological space-time, may be used to model and study different rates of biological aging. As a consequence of this hypothesis, we show how dilation or contraction of time analogous to relativistic corrections of physical time resulting from accelerated or decelerated biological dynamics may be used to study precipitous or protracted aging. We show specific examples of how these principles may be used to model different rates of aging, with an emphasis on cancer in aging. We discuss how this theory may be tested or falsified, as well as novel concepts and implications of this theory that may improve our interpretation of biological aging.

Biological control agents elevate hantavirus by subsidizing deer mouse populations

Science.gov (United States)

Dean E. Pearson; Ragan M. Callaway

2006-01-01

Biological control of exotic invasive plants using exotic insects is practiced under the assumption that biological control agents are safe if they do not directly attack non-target species. We tested this assumption by evaluating the potential for two host-specific biological control agents (Urophora spp.), widely established in North America for spotted...

Associations between functional polymorphisms and response to biological treatment in Danish patients with psoriasis

DEFF Research Database (Denmark)

Loft, N D; Skov, L; Iversen, L.

2018-01-01

Biological agents including anti-tumor necrosis factor (anti-TNF; adalimumab, infliximab, etanercept) and anti-interleukin-12/13 (IL12/23; ustekinumab) are essential for treatment of patients with severe psoriasis. However, a significant proportion of the patients do not respond to a specific tre...... with ustekinumab.The Pharmacogenomics Journal advance online publication, 11 July 2017; doi:10.1038/tpj.2017.31....

INNOVATION IN ACCOUNTING BIOLOGIC ASSETS

OpenAIRE

Stolуarova M. A.; Shcherbina I. D.

2016-01-01

The article describes the innovations in the classification and measurement of biological assets according to IFRS (IAS) 41 "Agriculture". The difficulties faced by agricultural producers using standard, set out in article. The classification based on the adopted amendments, according to which the fruit-bearing plants, previously accounted for as biological assets are measured at fair value are included in the category of fixed assets. The structure of biological assets and main means has bee...

Opportunities in Biological Sciences; [VGM Career Horizons Series].

Science.gov (United States)

Winter, Charles A.

This book provides job descriptions and discusses career opportunities in various fields of the biological sciences. These fields include: (1) biotechnology, genetics, biomedical engineering, microbiology, mycology, systematic biology, marine and aquatic biology, botany, plant physiology, plant pathology, ecology, and wildlife biology; (2) the…

Organic Chemistry and Biology: Chemical Biology Through the Eyes of Collaboration

Science.gov (United States)

Hruby, Victor J.

2011-01-01

From a scientific perspective, efforts to understand biology including what constitutes health and disease has become a chemical problem. However, chemists and biologists “see” the problems of understanding biology from different perspectives, and this has retarded progress in solving the problems especially as they relate to health and disease. This suggests that close collaboration between chemists and biologists is not only necessary but essential for progress in both the biology and chemistry that will provide solutions to the global questions of biology. This perspective has directed my scientific efforts for the past 45 years, and in this overview I provide my perspective of how the applications of synthetic chemistry, structural design, and numerous other chemical principles have intersected in my collaborations with biologists to provide new tools, new science, and new insights that were only made possible and fruitful by these collaborations. PMID:20000552

Review of Pasteuria penetrans: Biology, Ecology, and Biological Control Potential.

Science.gov (United States)

Chen, Z X; Dickson, D W

1998-09-01

Pasteuria penetrans is a mycelial, endospore-forming, bacterial parasite that has shown great potential as a biological control agent of root-knot nematodes. Considerable progress has been made during the last 10 years in understanding its biology and importance as an agent capable of effectively suppressing root-knot nematodes in field soil. The objective of this review is to summarize the current knowledge of the biology, ecology, and biological control potential of P. penetrans and other Pasteuria members. Pasteuria spp. are distributed worldwide and have been reported from 323 nematode species belonging to 116 genera of free-living, predatory, plant-parasitic, and entomopathogenic nematodes. Artificial cultivation of P. penetrans has met with limited success; large-scale production of endospores depends on in vivo cultivation. Temperature affects endospore attachment, germination, pathogenesis, and completion of the life cycle in the nematode pseudocoelom. The biological control potential of Pasteuria spp. have been demonstrated on 20 crops; host nematodes include Belonolaimus longicaudatus, Heterodera spp., Meloidogyne spp., and Xiphinema diversicaudatum. Pasteuria penetrans plays an important role in some suppressive soils. The efficacy of the bacterium as a biological control agent has been examined. Approximately 100,000 endospores/g of soil provided immediate control of the peanut root-knot nematode, whereas 1,000 and 5,000 endospores/g of soil each amplified in the host nematode and became suppressive after 3 years.

Review on biological degradation of mycotoxins

Directory of Open Access Journals (Sweden)

Cheng Ji

2016-09-01

Full Text Available The worldwide contamination of feeds and foods with mycotoxins is a significant problem. Mycotoxins pose huge health threat to animals and humans. As well, mycotoxins bring enormous economic losses in food industry and animal husbandry annually. Thus, strategies to eliminate or inactivate mycotoxins in food and feed are urgently needed. Traditional physical and chemical methods have some limitations such as limited efficacy, safety issues, losses in the nutritional value and the palatability of feeds, as well as the expensive equipment required to implement these techniques. Biological degradation of mycotoxins has shown promise because it works under mild, environmentally friendly conditions. Aflatoxin (AF, zearalenone (ZEA and deoxynivalenol (DON are considered the most economically important mycotoxins in terms of their high prevalence and significant negative effects on animal performance. Therefore, this review will comprehensively describe the biological degradation of AF, ZEA and DON by microorganisms (including fungi and bacteria and specific enzymes isolated from microbial systems that can convert mycotoxins with varied efficiency to non- or less toxic products. Finally, some strategies and advices on existing difficulties of biodegradation research are also briefly proposed in this paper.

Marine Biology and Human Affairs

Science.gov (United States)

Russell, F. S.

1976-01-01

Marine biology has become an important area for study throughout the world. The author of this article discusses some of the important discoveries and fields of research in marine biology that are useful for mankind. Topics include food from the sea, fish farming, pesticides, pollution, and conservation. (MA)

Sub-terahertz resonance spectroscopy of biological macromolecules and cells

Science.gov (United States)

Globus, Tatiana; Moyer, Aaron; Gelmont, Boris; Khromova, Tatyana; Sizov, Igor; Ferrance, Jerome

2013-05-01

Recently we introduced a Sub-THz spectroscopic system for characterizing vibrational resonance features from biological materials. This new, continuous-wave, frequency-domain spectroscopic sensor operates at room temperature between 315 and 480 GHz with spectral resolution of at least 1 GHz and utilizes the source and detector components from Virginia Diode, Inc. In this work we present experimental results and interpretation of spectroscopic signatures from bacterial cells and their biological macromolecule structural components. Transmission and absorption spectra of the bacterial protein thioredoxin, DNA and lyophilized cells of Escherichia coli (E. coli), as well as spores of Bacillus subtillis and B. atrophaeus have been characterized. Experimental results for biomolecules are compared with absorption spectra calculated using molecular dynamics simulation, and confirm the underlying physics for resonance spectroscopy based on interactions between THz radiation and vibrational modes or groups of modes of atomic motions. Such interactions result in multiple intense and narrow specific resonances in transmission/absorption spectra from nano-gram samples with spectral line widths as small as 3 GHz. The results of this study indicate diverse relaxation dynamic mechanisms relevant to sub-THz vibrational spectroscopy, including long-lasting processes. We demonstrate that high sensitivity in resolved specific absorption fingerprints provides conditions for reliable detection, identification and discrimination capability, to the level of strains of the same bacteria, and for monitoring interactions between biomaterials and reagents in near real-time. Additionally, it creates the basis for the development of new types of advanced biological sensors through integrating the developed system with a microfluidic platform for biomaterial samples.

Creating biological nanomaterials using synthetic biology

International Nuclear Information System (INIS)

Rice, MaryJoe K; Ruder, Warren C

2014-01-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

Creating biological nanomaterials using synthetic biology.

Science.gov (United States)

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

Practical approaches to biological inorganic chemistry

CERN Document Server

Louro, Ricardo O

2012-01-01

The book reviews the use of spectroscopic and related methods to investigate the complex structures and mechanisms of biological inorganic systems that contain metals. Each chapter presents an overview of the technique including relevant theory, clearly explains what it is and how it works and then presents how the technique is actually used to evaluate biological structures. Practical examples and problems are included to illustrate each technique and to aid understanding. Designed for students and researchers who want to learn both the basics, and more advanced aspects of bioinorganic chemistry. It includes many colour illustrations enable easier visualization of molecular mechanisms and structures. It provides worked examples and problems that are included to illustrate and test the reader's understanding of each technique. It is written by a multi-author team who use and teach the most important techniques used today to analyse complex biological structures.

Synthetic Biology: Engineering Living Systems from Biophysical Principles.

Science.gov (United States)

Bartley, Bryan A; Kim, Kyung; Medley, J Kyle; Sauro, Herbert M

2017-03-28

Synthetic biology was founded as a biophysical discipline that sought explanations for the origins of life from chemical and physical first principles. Modern synthetic biology has been reinvented as an engineering discipline to design new organisms as well as to better understand fundamental biological mechanisms. However, success is still largely limited to the laboratory and transformative applications of synthetic biology are still in their infancy. Here, we review six principles of living systems and how they compare and contrast with engineered systems. We cite specific examples from the synthetic biology literature that illustrate these principles and speculate on their implications for further study. To fully realize the promise of synthetic biology, we must be aware of life's unique properties. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A comparison of fisheries biological reference points estimated from temperature-specific multi-species and single-species climate-enhanced stock assessment models

Science.gov (United States)

Holsman, Kirstin K.; Ianelli, James; Aydin, Kerim; Punt, André E.; Moffitt, Elizabeth A.

2016-12-01

Multi-species statistical catch at age models (MSCAA) can quantify interacting effects of climate and fisheries harvest on species populations, and evaluate management trade-offs for fisheries that target several species in a food web. We modified an existing MSCAA model to include temperature-specific growth and predation rates and applied the modified model to three fish species, walleye pollock (Gadus chalcogrammus), Pacific cod (Gadus macrocephalus) and arrowtooth flounder (Atheresthes stomias), from the eastern Bering Sea (USA). We fit the model to data from 1979 through 2012, with and without trophic interactions and temperature effects, and use projections to derive single- and multi-species biological reference points (BRP and MBRP, respectively) for fisheries management. The multi-species model achieved a higher over-all goodness of fit to the data (i.e. lower negative log-likelihood) for pollock and Pacific cod. Variability from water temperature typically resulted in 5-15% changes in spawning, survey, and total biomasses, but did not strongly impact recruitment estimates or mortality. Despite this, inclusion of temperature in projections did have a strong effect on BRPs, including recommended yield, which were higher in single-species models for Pacific cod and arrowtooth flounder that included temperature compared to the same models without temperature effects. While the temperature-driven multi-species model resulted in higher yield MBPRs for arrowtooth flounder than the same model without temperature, we did not observe the same patterns in multi-species models for pollock and Pacific cod, where variability between harvest scenarios and predation greatly exceeded temperature-driven variability in yield MBRPs. Annual predation on juvenile pollock (primarily cannibalism) in the multi-species model was 2-5 times the annual harvest of adult fish in the system, thus predation represents a strong control on population dynamics that exceeds temperature

Advances in radiation biology

International Nuclear Information System (INIS)

Lett, J.T.; Ehmann, U.K.; Cox, A.B.

1987-01-01

The classical period of radiation biology is coming to a close. Such change always occurs at a time when the ideas and concepts that promoted the burgeoning of an infant science are no longer adequate. This volume covers a number of areas in which new ideas and research are playing a vital role, including cellular radiation sensitivity, radioactive waste disposal, and space radiation biology

Mechanical–biological treatment: Performance and potentials. An LCA of 8 MBT plants including waste characterization

DEFF Research Database (Denmark)

Montejo, Cristina; Tonini, Davide; Márquez, María del Carmen

2013-01-01

recovery through increased automation of the selection and to prioritize biogas-electricity production from the organic fraction over direct composting. The optimal strategy for refuse derived fuel (RDF) management depends upon the environmental compartment to be prioritized and the type of marginal...... of the MBT plants. These widely differed in type of biological treatment and recovery efficiencies. The results indicated that the performance is strongly connected with energy and materials recovery efficiency. The recommendation for upgrading and/or commissioning of future plants is to optimize materials...... electricity source in the system. It was estimated that, overall, up to ca. 180—190 kt CO2-eq. y−1 may be saved by optimizing the MBT plants under assessment....

Cardiovascular toxicities of biological therapies

DEFF Research Database (Denmark)

Ryberg, Marianne

2013-01-01

The development of biological therapy is based on growing knowledge regarding the molecular changes required in cells for the development and progression of cancer to occur. Molecular targeted therapy is designed to inhibit the major molecular pathways identified as essential for a specific...

Biological background of dermal substitutes

NARCIS (Netherlands)

van der Veen, V. C.; van der Wal, M.B.; van Leeuwen, M.C.; Ulrich, M.; Middelkoop, E.

2010-01-01

Dermal substitutes are of major importance in treating full thickness skin defects, both in acute and chronic wounds. In this review we will outline specific requirements of three classes of dermal substitutes:-natural biological materials, with a more or less intact extracellular matrix

Radiochemical and biological studies, including in non-human primates, towards indigenous development of 153Sm-EDTMP for metastatic bone pain palliation

International Nuclear Information System (INIS)

Saraswathy, P.; Mehra, K.S.; Ranganatha, D.K.; Das, M.K.; Balasubramanian, P.S.; Ananthakrishnan, M.; Ramamoorthy, N.; Gunasekaran, S.; Shanthly, N.; Retna Ponmalar, J.; Narasimhan, S.

2001-01-01

The combination of ease of formulation and superior biological features of 153 Sm-EDTMP in terms of safety and efficacy for metastatic bone pain palliation, together with the prospect of better logistics of production, has prompted extensive efforts by many groups world over for its preparation and evaluation. Our efforts have been directed towards exploring the feasibility for formulation of 153 Sm-EDTMP suitable for human use by neutron activation in medium flux reactors of the freely available and inexpensive natural samarium oxide target. The emphasis in biological studies was placed on tests in larger animals (monkeys) as a prelude to clinical evaluation. Feasibility to achieve reasonably high specific activity of 300-700 mCi/mg Sm at EOB with natural samarium has been adequately demonstrated. The radioeuropium contamination, estimated by γ-spectrometry to be 153 Sm-EDTMP from natural samarium at high radioactive concentrations of 40-50 mCi 153 Sm/mL, acceptable biolocalization, as revealed by both biodistribution studies in rats (femur uptake of 2-3% injected dose at 1h p.i. and retention up to 120 h p.i.) and gamma camera images in monkeys and adequate stability have been feasible. Excellent quality bone images of monkeys were recorded showing rapid clearance from blood, visualization of skeleton, clearance from kidneys within 2 hours and retention in skeleton up to 116 hours p.i. No significant activity in other soft tissues was noted. Comparative evaluation of the product prepared from enriched samarium as well as using in-house synthesized EDTMP has, likewise, revealed identical biolocalization features. EDTMP dose tolerance test in mice showed a safety factor of about 100 for a product made from natural samarium at an adult human dose of 50 mCi 153 Sm. Feasibility for production, reasonable safety and satisfactory biolocalisation of the indigenous product has been adequately established so as to warrant clinical trials in patients. (author)

Use of artificial neural networks to predict biological outcomes for patients receiving radical radiotherapy of the prostate

International Nuclear Information System (INIS)

Gulliford, Sarah L.; Webb, Steve; Rowbottom, Carl G.; Corne, David W.; Dearnaley, David P.

2004-01-01

Background and purpose: This paper discusses the application of artificial neural networks (ANN) in predicting biological outcomes following prostate radiotherapy. A number of model-based methods have been developed to correlate the dose distributions calculated for a patient receiving radiotherapy and the radiobiological effect this will produce. Most widely used are the normal tissue complication probability and tumour control probability models. An alternative method for predicting specific examples of tumour control and normal tissue complications is to use an ANN. One of the advantages of this method is that there is no need for a priori information regarding the relationship between the data being correlated. Patients and methods: A set of retrospective clinical data from patients who received radical prostate radiotherapy was used to train ANNs to predict specific biological outcomes by learning the relationship between the treatment plan prescription, dose distribution and the corresponding biological effect. The dose and volume were included as a differential dose-volume histogram in order to provide a holistic description of the available data. Results: It was shown that the ANNs were able to predict biochemical control and specific bladder and rectum complications with sensitivity and specificity of above 55% when the outcomes were dichotomised. It was also possible to analyse information from the ANNs to investigate the effect of individual treatment parameters on the outcome. Conclusion: ANNs have been shown to learn something of the complex relationship between treatment parameters and outcome which, if developed further, may prove to be a useful tool in predicting biological outcomes

The Latin American Biological Dosimetry Network (LBDNet).

Science.gov (United States)

García, O; Di Giorgio, M; Radl, A; Taja, M R; Sapienza, C E; Deminge, M M; Fernández Rearte, J; Stuck Oliveira, M; Valdivia, P; Lamadrid, A I; González, J E; Romero, I; Mandina, T; Guerrero-Carbajal, C; ArceoMaldonado, C; Cortina Ramírez, G E; Espinoza, M; Martínez-López, W; Di Tomasso, M

2016-09-01

Biological Dosimetry is a necessary support for national radiation protection programmes and emergency response schemes. The Latin American Biological Dosimetry Network (LBDNet) was formally founded in 2007 to provide early biological dosimetry assistance in case of radiation emergencies in the Latin American Region. Here are presented the main topics considered in the foundational document of the network, which comprise: mission, partners, concept of operation, including the mechanism to request support for biological dosimetry assistance in the region, and the network capabilities. The process for network activation and the role of the coordinating laboratory during biological dosimetry emergency response is also presented. This information is preceded by historical remarks on biological dosimetry cooperation in Latin America. A summary of the main experimental and practical results already obtained by the LBDNet is also included. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Tissue-specific tagging of endogenous loci in Drosophila melanogaster

Directory of Open Access Journals (Sweden)

Kate Koles

2016-01-01

Full Text Available Fluorescent protein tags have revolutionized cell and developmental biology, and in combination with binary expression systems they enable diverse tissue-specific studies of protein function. However these binary expression systems often do not recapitulate endogenous protein expression levels, localization, binding partners and/or developmental windows of gene expression. To address these limitations, we have developed a method called T-STEP (tissue-specific tagging of endogenous proteins that allows endogenous loci to be tagged in a tissue specific manner. T-STEP uses a combination of efficient CRISPR/Cas9-enhanced gene targeting and tissue-specific recombinase-mediated tag swapping to temporally and spatially label endogenous proteins. We have employed this method to GFP tag OCRL (a phosphoinositide-5-phosphatase in the endocytic pathway and Vps35 (a Parkinson's disease-implicated component of the endosomal retromer complex in diverse Drosophila tissues including neurons, glia, muscles and hemocytes. Selective tagging of endogenous proteins allows, for the first time, cell type-specific live imaging and proteomics in complex tissues.

BiologicalNetworks 2.0 - an integrative view of genome biology data

Directory of Open Access Journals (Sweden)

Ponomarenko Julia

2010-12-01

Full Text Available Abstract Background A significant problem in the study of mechanisms of an organism's development is the elucidation of interrelated factors which are making an impact on the different levels of the organism, such as genes, biological molecules, cells, and cell systems. Numerous sources of heterogeneous data which exist for these subsystems are still not integrated sufficiently enough to give researchers a straightforward opportunity to analyze them together in the same frame of study. Systematic application of data integration methods is also hampered by a multitude of such factors as the orthogonal nature of the integrated data and naming problems. Results Here we report on a new version of BiologicalNetworks, a research environment for the integral visualization and analysis of heterogeneous biological data. BiologicalNetworks can be queried for properties of thousands of different types of biological entities (genes/proteins, promoters, COGs, pathways, binding sites, and other and their relations (interactions, co-expression, co-citations, and other. The system includes the build-pathways infrastructure for molecular interactions/relations and module discovery in high-throughput experiments. Also implemented in BiologicalNetworks are the Integrated Genome Viewer and Comparative Genomics Browser applications, which allow for the search and analysis of gene regulatory regions and their conservation in multiple species in conjunction with molecular pathways/networks, experimental data and functional annotations. Conclusions The new release of BiologicalNetworks together with its back-end database introduces extensive functionality for a more efficient integrated multi-level analysis of microarray, sequence, regulatory, and other data. BiologicalNetworks is freely available at http://www.biologicalnetworks.org.

Systems Biology and Stem Cell Pluripotency

DEFF Research Database (Denmark)

Mashayekhi, Kaveh; Hall, Vanessa Jane; Freude, Kristine

2016-01-01

Recent breakthroughs in stem cell biology have accelerated research in the area of regenerative medicine. Over the past years, it has become possible to derive patient-specific stem cells which can be used to generate different cell populations for potential cell therapy. Systems biological...... modeling of stem cell pluripotency and differentiation have largely been based on prior knowledge of signaling pathways, gene regulatory networks, and epigenetic factors. However, there is a great need to extend the complexity of the modeling and to integrate different types of data, which would further...... improve systems biology and its uses in the field. In this chapter, we first give a general background on stem cell biology and regenerative medicine. Stem cell potency is introduced together with the hierarchy of stem cells ranging from pluripotent embryonic stem cells (ESCs) and induced pluripotent stem...

[Biologics and mycobacterial diseases].

Science.gov (United States)

Tsuyuguchi, Kazunari; Matsumoto, Tomoshige

2013-03-01

Various biologics such as TNF-alpha inhibitor or IL-6 inhibitor are now widely used for treatment of rheumatoid arthritis. Many reports suggested that one of the major issues is high risk of developing tuberculosis (TB) associated with using these agents, which is especially important in Japan where tuberculosis still remains endemic. Another concern is the risk of development of nontuberculous mycobacterial (NTM) diseases and we have only scanty information about it. The purpose of this symposium is to elucidate the role of biologics in the development of mycobacterial diseases and to establish the strategy to control them. First, Dr. Tohma showed the epidemiologic data of TB risks associated with using biologics calculated from the clinical database on National Database of Rheumatic Diseases by iR-net in Japan. He estimated TB risks in rheumatoid arthritis (RA) patients to be about four times higher compared with general populations and to become even higher by using biologics. He also pointed out a low rate of implementation of QuantiFERON test (QFT) as screening test for TB infection. Next, Dr. Tokuda discussed the issue of NTM disease associated with using biologics. He suggested the airway disease in RA patients might play some role in the development of NTM disease, which may conversely lead to overdiagnosis of NTM disease in RA patients. He suggested that NTM disease should not be uniformly considered a contraindication to treatment with biologics, considering from the results of recent multicenter study showing relatively favorable outcome of NTM patients receiving biologics. Patients with latent tuberculosis infection (LTBI) should receive LTBI treatment before starting biologics. Dr. Kato, a chairperson of the Prevention Committee of the Japanese Society for Tuberculosis, proposed a new LTBI guideline including active implementation of LTBI treatment, introducing interferon gamma release assay, and appropriate selection of persons at high risk for

Detection and differentiation of coxiella burnetii in biological fluids

Energy Technology Data Exchange (ETDEWEB)

Frazier, Marvin E. (Richland, WA); Mallavia, Louis P. (Moscow, ID); Samuel, James E. (Pullman, WA); Baca, Oswald G. (Albuquerque, NM)

1990-01-01

Methods for detecting the presence of Coxiella burenetii in biological samples, as well as a method for differentiating strains of C. burnetii that are capable of causing acute disease from those strains capable of causing chronic disease are disclosed. The methods generally comprise treating cells contained within the biological sample to expose cellular DNA, and hybridizing the cellular DNA (specifically rickettsial DNA) with a C. burnetii-specific labeled DNA probe. Radioisotope and biotin labels are preferred, allowing detection through autoradiography and colorimetric assays, respectively.

Detection and differentiation of coxiella burnetii in biological fluids

Energy Technology Data Exchange (ETDEWEB)

Frazier, Marvin E. (Richland, WA); Mallavia, Louis P. (Moscow, ID); Baca, Oswald G. (Albuquerque, NM); Samuel, James E. (Pullman, WA)

1989-01-01

Methods for detecting the presence of Coxiella burnetii in biological samples, as well as a method for differentiating strains of C. burnetii that are capable of causing acute disease from those strains capable of causing chronic disease are disclosed. The methods generally comprise treating cells contained within the biological sample to expose cellular DNA, and hybridizing the cellular DNA (specifically rickettsial DNA) with a C. burnetii-specific labeled DNA probe. Radioisotope and biotin labels are preferred, allowing detection through autoradiography and colorimetric assays, respectively.

Radioimmunoassay of the myelin basic protein in biological fluids, conditions improving sensitivity and specificity

International Nuclear Information System (INIS)

Delassalle, A.; Jacque, C.; Raoul, M.; Legrand, J.C.; Cesselin, F.; Drouet, J.

1980-01-01

The radioimmunoassay (RIA) for myelin basic protein (MBP) in biological fluids was reassessed in order to improve its sensitivity and eliminate some interferences. By using the pre-incubation technique and the charcoal-dextram-horse serum mixture for the separation step, the detection limit could be lowered to 200 pg/ml for cerebrospinal fluids (CSF), amniotic fluids (AF) and nervous tissue extracts and 600 pg/ml for sera. The RIA could be used directly on CSF, AF and nervous tissue extracts. Sera, however, had to be heated in citrate buffer at 100 0 C in order to discard interfering material. The present method is 10 to 20 times more sensitive than others previously published. Moreover, it can be applied to amniotic fluid. The biological fluids had to be promptly frozen to avoid degradation of MBP

Space biology research development

Science.gov (United States)

Bonting, Sjoerd L.

1993-01-01

The purpose of the Search for Extraterrestrial Intelligence (SETI) Institute is to conduct and promote research related activities regarding the search for extraterrestrial life, particularly intelligent life. Such research encompasses the broad discipline of 'Life in the Universe', including all scientific and technological aspects of astronomy and the planetary sciences, chemical evolution, the origin of life, biological evolution, and cultural evolution. The primary purpose was to provide funding for the Principal Investigator to collaborate with the personnel of the SETI Institute and the NASA-Ames Research center in order to plan and develop space biology research on and in connection with Space Station Freedom; to promote cooperation with the international partners in the space station; to conduct a study on the use of biosensors in space biology research and life support system operation; and to promote space biology research through the initiation of an annual publication 'Advances in Space Biology and Medicine'.

Synergistic Synthetic Biology: Units in Concert

Science.gov (United States)

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

International Nuclear Information System (INIS)

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.

Multidisciplinaire richtlijn "Verantwoord gebruik van biologicals"

NARCIS (Netherlands)

Bijlsma, J. W. J. Hans; Hagemeijer, J. W. Annemarie; Bijl, Marc; Jansen, Tim L. Th A.; van de Laar, Mart A. F. J.; Landewé, Robert B. M.; Nurmohamed, Mike T.

2011-01-01

A multidisciplinary working group has developed a practice guideline containing various recommendations on the responsible and efficient use of biologicals. These biologicals include both soluble immune-receptor proteins and monoclonal antibodies that are aimed at immune mediators, receptors or

Effects of substrate concentration, specific surface area and hydraulic loading on the treatment efficiency in a submerged biological filter. Sesshoku bakkiho no shori koritsu ni taisuru kishitsu nodo, hihyo menseki oyobi suiryo fuka no eikyo

Energy Technology Data Exchange (ETDEWEB)

Iyo, T; Ono, S; Yoshino, T [Kitasato University, Kanagawa (Japan). School of Hygienic Science

1991-06-10

Effects of substrate concentration, specific surface area, and hydraulic loading, which are major factors influencing treatment efficiency in a submerged biological filter, were analyzed through the test with a special apparatus. In the test, the wall of the submerged biological filter was regarded as the contact material, and the specific surface area was changed by adjusting the sectional form of the filter. Using specimens from actual plant reservoirs, treatment efficiency for each case of three kinds of substrate concentration and hydraulic loading was measured. BOD removal rate was lower with smaller specific surface area. It was conspicuous particularly with higher BOD concentration in influent water. After the multiple regression analysis of the test results, the multiple regression equation to estimate BOD residual rate from three variates such as BOD concentration, specific surface area, and hydraulic loading was obtained. When 200mg l as BOD concentration and 50m{sup 2} m{sup {minus}3} as specific surface area were applied in this equation, the result almost agreed with the tendency obtained from data of actual plants. 6 refs., 4 figs., 1 tab.

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

Directory of Open Access Journals (Sweden)

Martin Florian

2012-05-01

Full Text Available Abstract Background High-throughput measurement technologies produce data sets that have the potential to elucidate the biological impact of disease, drug treatment, and environmental agents on humans. The scientific community faces an ongoing challenge in the analysis of these rich data sources to more accurately characterize biological processes that have been perturbed at the mechanistic level. Here, a new approach is built on previous methodologies in which high-throughput data was interpreted using prior biological knowledge of cause and effect relationships. These relationships are structured into network models that describe specific biological processes, such as inflammatory signaling or cell cycle progression. This enables quantitative assessment of network perturbation in response to a given stimulus. Results Four complementary methods were devised to quantify treatment-induced activity changes in processes described by network models. In addition, companion statistics were developed to qualify significance and specificity of the results. This approach is called Network Perturbation Amplitude (NPA scoring because the amplitudes of treatment-induced perturbations are computed for biological network models. The NPA methods were tested on two transcriptomic data sets: normal human bronchial epithelial (NHBE cells treated with the pro-inflammatory signaling mediator TNFα, and HCT116 colon cancer cells treated with the CDK cell cycle inhibitor R547. Each data set was scored against network models representing different aspects of inflammatory signaling and cell cycle progression, and these scores were compared with independent measures of pathway activity in NHBE cells to verify the approach. The NPA scoring method successfully quantified the amplitude of TNFα-induced perturbation for each network model when compared against NF-κB nuclear localization and cell number. In addition, the degree and specificity to which CDK

Fostering Students' Conceptual Knowledge in Biology in the Context of German National Education Standards

Science.gov (United States)

Förtsch, Christian; Dorfner, Tobias; Baumgartner, Julia; Werner, Sonja; von Kotzebue, Lena; Neuhaus, Birgit J.

2018-04-01

The German National Education Standards (NES) for biology were introduced in 2005. The content part of the NES emphasizes fostering conceptual knowledge. However, there are hardly any indications of what such an instructional implementation could look like. We introduce a theoretical framework of an instructional approach to foster students' conceptual knowledge as demanded in the NES (Fostering Conceptual Knowledge) including instructional practices derived from research on single core ideas, general psychological theories, and biology-specific features of instructional quality. First, we aimed to develop a rating manual, which is based on this theoretical framework. Second, we wanted to describe current German biology instruction according to this approach and to quantitatively analyze its effectiveness. And third, we aimed to provide qualitative examples of this approach to triangulate our findings. In a first step, we developed a theoretically devised rating manual to measure Fostering Conceptual Knowledge in videotaped lessons. Data for quantitative analysis included 81 videotaped biology lessons of 28 biology teachers from different German secondary schools. Six hundred forty students completed a questionnaire on their situational interest after each lesson and an achievement test. Results from multilevel modeling showed significant positive effects of Fostering Conceptual Knowledge on students' achievement and situational interest. For qualitative analysis, we contrasted instruction of four teachers, two with high and two with low student achievement and situational interest using the qualitative method of thematic analysis. Qualitative analysis revealed five main characteristics describing Fostering Conceptual Knowledge. Therefore, implementing Fostering Conceptual Knowledge in biology instruction seems promising. Examples of how to implement Fostering Conceptual Knowledge in instruction are shown and discussed.

Circulating VEGF as a biological marker in patients with rheumatoid arthritis? Preanalytical and biological variability in healthy persons and in patients

DEFF Research Database (Denmark)

Hetland, Merete Lund; Christensen, Ib Jarle; Lottenburger, Tine

2008-01-01

/ml (range: non-detectable to 352); serum: 328 pg/ml (53-1791)) were independent of gender and age. Short- and long-term biologic variability included diurnal variation (sampling should take place after 7 AM) and impact of exercise (increased VEGF immediately after bicycling normalised within 1 hour......BACKGROUND: Soluble vascular endothelial growth factor (VEGF) is a promising biomarker in monitoring rheumatoid arthritis (RA), but studies of pre-analytical and biologic variability are few. METHODS: VEGF was measured by ELISA methods in serum and plasma from healthy persons and RA patients. Pre......). CONCLUSIONS: Pre-analytical factors and biologic variability including diurnal variation and impact of exercise should be accounted for in future studies that include circulating VEGF as a biological marker....

US Competitiveness in Synthetic Biology.

Science.gov (United States)

Gronvall, Gigi Kwik

2015-01-01

Synthetic biology is an emerging technical field that aims to make biology easier to engineer; the field has applications in strategically important sectors for the US economy. While the United States currently leads in synthetic biology R&D, other nations are heavily investing in order to boost their economies, which will inevitably diminish the US leadership position. This outcome is not entirely negative--additional investments will expand markets--but it is critical that the US government take steps to remain competitive: There are applications from which the US population and economy may benefit; there are specific applications with importance for national defense; and US technical leadership will ensure that US experts have a leading role in synthetic biology governance, regulation, and oversight. Measures to increase competitiveness in S&T generally are broadly applicable for synthetic biology and should be pursued. However, the US government will also need to take action on fundamental issues that will affect the field's development, such as countering anti-GMO (genetically modified organism) sentiments and anti-GMO legislation. The United States should maintain its regulatory approach so that it is the product that is regulated, not the method used to create a product. At the same time, the United States needs to ensure that the regulatory framework is updated so that synthetic biology products do not fall into regulatory gaps. Finally, the United States needs to pay close attention to how synthetic biology applications may be governed internationally, such as through the Nagoya Protocol of the Convention on Biological Diversity, so that beneficial applications may be realized.

A Brief Review of the Biology of Anorexia Nervosa

DEFF Research Database (Denmark)

Sjögren, Magnus

2015-01-01

PUBMED and the following search terms: “Anorexia Nervosa” and “biomarker” revealed 180 articles (8th of May 2015). Additional searches included the search terms “gene”, “genetic”, “epigenetic”, “appetite”, “hormone”, and a specific search on “biology” and “review”. Furthermore, articles of interest were...... retrieved from the reference lists of the identified articles of the first PUBMED search. Results: In general, there is a shortage of studies on biomarkers and the biology of AN, at least when you compare to similar fields of research in Affective disorders and Schizophrenia. The studies performed reveals...

Aspergilli: Systems biology and industrial applications

DEFF Research Database (Denmark)

Knuf, Christoph; Nielsen, Jens

2012-01-01

possible to implement systems biology tools to advance metabolic engineering. These tools include genome-wide transcription analysis and genome-scale metabolic models. Herein, we review achievements in the field and highlight the impact of Aspergillus systems biology on industrial biotechnology....

From darwin to the census of marine life: marine biology as big science.

Science.gov (United States)

Vermeulen, Niki

2013-01-01

With the development of the Human Genome Project, a heated debate emerged on biology becoming 'big science'. However, biology already has a long tradition of collaboration, as natural historians were part of the first collective scientific efforts: exploring the variety of life on earth. Such mappings of life still continue today, and if field biology is gradually becoming an important subject of studies into big science, research into life in the world's oceans is not taken into account yet. This paper therefore explores marine biology as big science, presenting the historical development of marine research towards the international 'Census of Marine Life' (CoML) making an inventory of life in the world's oceans. Discussing various aspects of collaboration--including size, internationalisation, research practice, technological developments, application, and public communication--I will ask if CoML still resembles traditional collaborations to collect life. While showing both continuity and change, I will argue that marine biology is a form of natural history: a specific way of working together in biology that has transformed substantially in interaction with recent developments in the life sciences and society. As a result, the paper does not only give an overview of transformations towards large scale research in marine biology, but also shines a new light on big biology, suggesting new ways to deepen the understanding of collaboration in the life sciences by distinguishing between different 'collective ways of knowing'.

From darwin to the census of marine life: marine biology as big science.

Directory of Open Access Journals (Sweden)

Niki Vermeulen

Full Text Available With the development of the Human Genome Project, a heated debate emerged on biology becoming 'big science'. However, biology already has a long tradition of collaboration, as natural historians were part of the first collective scientific efforts: exploring the variety of life on earth. Such mappings of life still continue today, and if field biology is gradually becoming an important subject of studies into big science, research into life in the world's oceans is not taken into account yet. This paper therefore explores marine biology as big science, presenting the historical development of marine research towards the international 'Census of Marine Life' (CoML making an inventory of life in the world's oceans. Discussing various aspects of collaboration--including size, internationalisation, research practice, technological developments, application, and public communication--I will ask if CoML still resembles traditional collaborations to collect life. While showing both continuity and change, I will argue that marine biology is a form of natural history: a specific way of working together in biology that has transformed substantially in interaction with recent developments in the life sciences and society. As a result, the paper does not only give an overview of transformations towards large scale research in marine biology, but also shines a new light on big biology, suggesting new ways to deepen the understanding of collaboration in the life sciences by distinguishing between different 'collective ways of knowing'.

X-ray absorption spectroscopy in biological systems. Opportunities and limitations

Energy Technology Data Exchange (ETDEWEB)

Bovenkamp, Gudrun Lisa

2013-05-15

X-ray absorption spectroscopy has become more important for applications in the material sciences, geology, environmental science and biology, specifically in the field of molecular biology. The scope of this thesis is to add more experimental evidence in order to show how applicable X-ray absorption near edge structure (XANES) is to biology. Two biological systems were investigated, at the molecular level, lead uptake in plants and the effect of silver on bacteria. This investigation also included an analysis of the sensitivity of Pb L{sub 3}- and Ag L{sub 3}-XANES spectra with regard to their chemical environment. It was shown that Pb L{sub 3}- and Ag L{sub 3}-XANES spectra are sensitive to an environment with at least differences in the second coordination shell. The non-destructive and element specific properties of XANES are the key advantages that were very important for this investigation. However, in both projects the adequate selection of reference compounds, which required in some cases a chemical synthesis, was the critical factor to determine the chemical speciation and, finally, possible uptake and storage mechanisms for plants and antibacterial mechanisms of silver. The chemical environment of Pb in roots and leaves of plants from four different plant families and a lichen from a former lead mining site in the Eifel mountains in Germany was determined using both solid compounds and aqueous solutions of different ionic strength, which simulate the plant environment. The results can be interpreted in such a way that lead is sorbed on the surface of cell walls. Silver bonding as reaction with Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli bacteria was determined using inorganic silver compounds and synthesized silver amino acids. Silver binds to sulfur, amine and carboxyl groups in amino acids.

X-ray absorption spectroscopy in biological systems. Opportunities and limitations

International Nuclear Information System (INIS)

Bovenkamp, Gudrun Lisa

2013-05-01

X-ray absorption spectroscopy has become more important for applications in the material sciences, geology, environmental science and biology, specifically in the field of molecular biology. The scope of this thesis is to add more experimental evidence in order to show how applicable X-ray absorption near edge structure (XANES) is to biology. Two biological systems were investigated, at the molecular level, lead uptake in plants and the effect of silver on bacteria. This investigation also included an analysis of the sensitivity of Pb L 3 - and Ag L 3 -XANES spectra with regard to their chemical environment. It was shown that Pb L 3 - and Ag L 3 -XANES spectra are sensitive to an environment with at least differences in the second coordination shell. The non-destructive and element specific properties of XANES are the key advantages that were very important for this investigation. However, in both projects the adequate selection of reference compounds, which required in some cases a chemical synthesis, was the critical factor to determine the chemical speciation and, finally, possible uptake and storage mechanisms for plants and antibacterial mechanisms of silver. The chemical environment of Pb in roots and leaves of plants from four different plant families and a lichen from a former lead mining site in the Eifel mountains in Germany was determined using both solid compounds and aqueous solutions of different ionic strength, which simulate the plant environment. The results can be interpreted in such a way that lead is sorbed on the surface of cell walls. Silver bonding as reaction with Staphylococcus aureus, Listeria monocytogenes, and Escherichia coli bacteria was determined using inorganic silver compounds and synthesized silver amino acids. Silver binds to sulfur, amine and carboxyl groups in amino acids.

Low penetrance breast cancer susceptibility loci are associated with specific breast tumor subtypes

DEFF Research Database (Denmark)

Broeks, Annegien; Schmidt, Marjanka K; Sherman, Mark E

2011-01-01

Breast cancers demonstrate substantial biological, clinical and etiological heterogeneity. We investigated breast cancer risk associations of eight susceptibility loci identified in GWAS and two putative susceptibility loci in candidate genes in relation to specific breast tumor subtypes. Subtype...... stratification might help in the identification and characterization of novel risk factors for breast cancer subtypes. This may eventually result in further improvements in prevention, early detection and treatment.......Breast cancers demonstrate substantial biological, clinical and etiological heterogeneity. We investigated breast cancer risk associations of eight susceptibility loci identified in GWAS and two putative susceptibility loci in candidate genes in relation to specific breast tumor subtypes. Subtypes...... were defined by five markers (ER, PR, HER2, CK5/6, EGFR) and other pathological and clinical features. Analyses included up to 30 040 invasive breast cancer cases and 53 692 controls from 31 studies within the Breast Cancer Association Consortium. We confirmed previous reports of stronger associations...

Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of /ital Homo sapiens/

International Nuclear Information System (INIS)

1986-01-01

This volume is the second part of a collection of papers submitted by the participants to the 1986 Cold Spring Harbor Symposium on Quantitative Biology entitled Molecular Biology of /ital Homo sapiens/. The 49 papers included in this volume are grouped by subject into receptors, human cancer genes, and gene therapy. (DT)

Analysis of specific absorption rate and internal electric field in human biological tissues surrounding an air-core coil-type transcutaneous energy transmission transformer.

Science.gov (United States)

Shiba, Kenji; Zulkifli, Nur Elina Binti; Ishioka, Yuji

2017-06-01

In this study, we analyzed the internal electric field E and specific absorption rate (SAR) of human biological tissues surrounding an air-core coil transcutaneous energy transmission transformer. Using an electromagnetic simulator, we created a model of human biological tissues consisting of a dry skin, wet skin, fat, muscle, and cortical bone. A primary coil was placed on the surface of the skin, and a secondary coil was located subcutaneously inside the body. The E and SAR values for the model representing a 34-year-old male subject were analyzed using electrical frequencies of 0.3-1.5 MHz. The transmitting power was 15 W, and the load resistance was 38.4 Ω. The results showed that the E values were below the International Commission on Non-ionizing Radiation Protection (ICNIRP) limit for the general public exposure between the frequencies of 0.9 and 1.5 MHz, and SAR values were well below the limit prescribed by the ICNIRP for the general public exposure between the frequencies of 0.3 and 1.2 MHz.

Biological Motion Perception in Autism

Directory of Open Access Journals (Sweden)

J Cusack

2011-04-01

Full Text Available Typically developing adults can readily recognize human actions, even when conveyed to them via point-like markers placed on the body of the actor (Johansson, 1973. Previous research has suggested that children affected by autism spectrum disorder (ASD are not equally sensitive to this type of visual information (Blake et al, 2003, but it remains unknown why ASD would impact the ability to perceive biological motion. We present evidence which looks at how adolescents and adults with autism are affected by specific factors which are important in biological motion perception, such as (eg, inter-agent synchronicity, upright/inverted, etc.

Network Biology (http://www.iaees.org/publications/journals/nb/online-version.asp

Directory of Open Access Journals (Sweden)

networkbiology@iaees.org

Full Text Available Network Biology ISSN 2220-8879 URL: http://www.iaees.org/publications/journals/nb/online-version.asp RSS: http://www.iaees.org/publications/journals/nb/rss.xml E-mail: networkbiology@iaees.org Editor-in-Chief: WenJun Zhang Aims and Scope NETWORK BIOLOGY (ISSN 2220-8879; CODEN NBEICS is an open access, peer-reviewed international journal that considers scientific articles in all different areas of network biology. It is the transactions of the International Society of Network Biology. It dedicates to the latest advances in network biology. The goal of this journal is to keep a record of the state-of-the-art research and promote the research work in these fast moving areas. The topics to be covered by Network Biology include, but are not limited to: •Theories, algorithms and programs of network analysis •Innovations and applications of biological networks •Ecological networks, food webs and natural equilibrium •Co-evolution, co-extinction, biodiversity conservation •Metabolic networks, protein-protein interaction networks, biochemical reaction networks, gene networks, transcriptional regulatory networks, cell cycle networks, phylogenetic networks, network motifs •Physiological networks •Network regulation of metabolic processes, human diseases and ecological systems •Social networks, epidemiological networks •System complexity, self-organized systems, emergence of biological systems, agent-based modeling, individual-based modeling, neural network modeling, and other network-based modeling, etc. We are also interested in short communications that clearly address a specific issue or completely present a new ecological network, food web, or metabolic or gene network, etc. Authors can submit their works to the email box of this journal, networkbiology@iaees.org. All manuscripts submitted to this journal must be previously unpublished and may not be considered for publication elsewhere at any time during review period of this journal

New Approaches in Cancer Biology Can Inform the Biology Curriculum.

Science.gov (United States)

Jones, Lynda; Gordon, Diana; Zelinski, Mary

2018-03-01

Students tend to be very interested in medical issues that affect them and their friends and family. Using cancer as a hook, the ART of Reproductive Medicine: Oncofertility curriculum (free, online, and NIH sponsored) has been developed to supplement the teaching of basic biological concepts and to connect biology and biomedical research. This approach allows integration of up-to-date information on cancer and cancer treatment, cell division, male and female reproductive anatomy and physiology, cryopreservation, fertility preservation, stem cells, ethics, and epigenetics into an existing biology curriculum. Many of the topics covered in the curriculum relate to other scientific disciplines, such as the latest developments in stem cell research including tissue bioengineering and gene therapy for inherited mitochondrial disease, how epigenetics occurs chemically to affect gene expression or suppression and how it can be passed down through the generations, and the variety of biomedical careers students could pursue. The labs are designed to be open-ended and inquiry-based, and extensions to the experiments are provided so that students can explore questions further. Case studies and ethical dilemmas are provided to encourage thoughtful discussion. In addition, each chapter of the curriculum includes links to scientific papers, additional resources on each topic, and NGSS alignment.

Modification degrees at specific sites on heparan sulphate: an approach to measure chemical modifications on biological molecules with stable isotope labelling

Science.gov (United States)

Wu, Zhengliang L.; Lech, Miroslaw

2005-01-01

Chemical modification of biological molecules is a general mechanism for cellular regulation. A quantitative approach has been developed to measure the extent of modification on HS (heparan sulphates). Sulphation on HS by sulphotransferases leads to variable sulphation levels, which allows cells to tune their affinities to various extracellular proteins, including growth factors. With stable isotope labelling and HPLC-coupled MS, modification degrees at various O-sulphation sites could be determined. A bovine kidney HS sample was first saturated in vitro with 34S by an OST (O-sulphotransferase), then digested with nitrous acid and analysed with HPLC-coupled MS. The 34S-labelled oligosaccharides were identified based on their unique isotope clusters. The modification degrees at the sulphotransferase recognition sites were obtained by calculating the intensities of isotopic peaks in the isotope clusters. The modification degrees at 3-OST-1 and 6-OST-1 sites were examined in detail. This approach can also be used to study other types of chemical modifications on biological molecules. PMID:15743272

Disease specific protein corona

Science.gov (United States)

Rahman, M.; Mahmoudi, M.

2015-03-01

It is now well accepted that upon their entrance into the biological environments, the surface of nanomaterials would be covered by various biomacromolecules (e.g., proteins and lipids). The absorption of these biomolecules, so called `protein corona', onto the surface of (nano)biomaterials confers them a new `biological identity'. Although the formation of protein coronas on the surface of nanoparticles has been widely investigated, there are few reports on the effect of various diseases on the biological identity of nanoparticles. As the type of diseases may tremendously changes the composition of the protein source (e.g., human plasma/serum), one can expect that amount and composition of associated proteins in the corona composition may be varied, in disease type manner. Here, we show that corona coated silica and polystyrene nanoparticles (after interaction with in the plasma of the healthy individuals) could induce unfolding of fibrinogen, which promotes release of the inflammatory cytokines. However, no considerable releases of inflammatory cytokines were observed for corona coated graphene sheets. In contrast, the obtained corona coated silica and polystyrene nanoparticles from the hypofibrinogenemia patients could not induce inflammatory cytokine release where graphene sheets do. Therefore, one can expect that disease-specific protein coronas can provide a novel approach for applying nanomedicine to personalized medicine, improving diagnosis and treatment of different diseases tailored to the specific conditions and circumstances.

Hierarchy, determinism, and specificity in theories of development and evolution.

Science.gov (United States)

Deichmann, Ute

2017-10-16

The concepts of hierarchical organization, genetic determinism and biological specificity (for example of species, biologically relevant macromolecules, or genes) have played a crucial role in biology as a modern experimental science since its beginnings in the nineteenth century. The idea of genetic information (specificity) and genetic determination was at the basis of molecular biology that developed in the 1940s with macromolecules, viruses and prokaryotes as major objects of research often labelled "reductionist". However, the concepts have been marginalized or rejected in some of the research that in the late 1960s began to focus additionally on the molecularization of complex biological structures and functions using systems approaches. This paper challenges the view that 'molecular reductionism' has been successfully replaced by holism and a focus on the collective behaviour of cellular entities. It argues instead that there are more fertile replacements for molecular 'reductionism', in which genomics, embryology, biochemistry, and computer science intertwine and result in research that is as exact and causally predictive as earlier molecular biology.

Ten good reasons to consider biological processes in prevention and intervention research.

Science.gov (United States)

Beauchaine, Theodore P; Neuhaus, Emily; Brenner, Sharon L; Gatzke-Kopp, Lisa

2008-01-01

Most contemporary accounts of psychopathology acknowledge the importance of both biological and environmental influences on behavior. In developmental psychopathology, multiple etiological mechanisms for psychiatric disturbance are well recognized, including those operating at genetic, neurobiological, and environmental levels of analysis. However, neuroscientific principles are rarely considered in current approaches to prevention or intervention. In this article, we explain why a deeper understanding of the genetic and neural substrates of behavior is essential for the next generation of preventive interventions, and we outline 10 specific reasons why considering biological processes can improve treatment efficacy. Among these, we discuss (a) the role of biomarkers and endophenotypes in identifying those most in need of prevention; (b) implications for treatment of genetic and neural mechanisms of homotypic comorbidity, heterotypic comorbidity, and heterotypic continuity; (c) ways in which biological vulnerabilities moderate the effects of environmental experience; (d) situations in which Biology x Environment interactions account for more variance in key outcomes than main effects; and (e) sensitivity of neural systems, via epigenesis, programming, and neural plasticity, to environmental moderation across the life span. For each of the 10 reasons outlined we present an example from current literature and discuss critical implications for prevention.

Ten good reasons to consider biological processes in prevention and intervention research

Science.gov (United States)

BEAUCHAINE, THEODORE P.; NEUHAUS, EMILY; BRENNER, SHARON L.; GATZKE-KOPP, LISA

2009-01-01

Most contemporary accounts of psychopathology acknowledge the importance of both biological and environmental influences on behavior. In developmental psychopathology, multiple etiological mechanisms for psychiatric disturbance are well recognized, including those operating at genetic, neurobiological, and environmental levels of analysis. However, neuroscientific principles are rarely considered in current approaches to prevention or intervention. In this article, we explain why a deeper understanding of the genetic and neural substrates of behavior is essential for the next generation of preventive interventions, and we outline 10 specific reasons why considering biological processes can improve treatment efficacy. Among these, we discuss (a) the role of biomarkers and endophenotypes in identifying those most in need of prevention; (b) implications for treatment of genetic and neural mechanisms of homotypic comorbidity, heterotypic comorbidity, and heterotypic continuity; (c) ways in which biological vulnerabilities moderate the effects of environmental experience; (d) situations in which Biology×Environment interactions account for more variance in key outcomes than main effects; and (e) sensitivity of neural systems, via epigenesis, programming, and neural plasticity, to environmental moderation across the life span. For each of the 10 reasons outlined we present an example from current literature and discuss critical implications for prevention. PMID:18606030

Visualization in simulation tools: requirements and a tool specification to support the teaching of dynamic biological processes.

Science.gov (United States)

Jørgensen, Katarina M; Haddow, Pauline C

2011-08-01

Simulation tools are playing an increasingly important role behind advances in the field of systems biology. However, the current generation of biological science students has either little or no experience with such tools. As such, this educational glitch is limiting both the potential use of such tools as well as the potential for tighter cooperation between the designers and users. Although some simulation tool producers encourage their use in teaching, little attempt has hitherto been made to analyze and discuss their suitability as an educational tool for noncomputing science students. In general, today's simulation tools assume that the user has a stronger mathematical and computing background than that which is found in most biological science curricula, thus making the introduction of such tools a considerable pedagogical challenge. This paper provides an evaluation of the pedagogical attributes of existing simulation tools for cell signal transduction based on Cognitive Load theory. Further, design recommendations for an improved educational simulation tool are provided. The study is based on simulation tools for cell signal transduction. However, the discussions are relevant to a broader biological simulation tool set.

A critical analysis of the new biology and the biological revolution: their impact - from medicine to evolution.

Science.gov (United States)

Dev, Sukhendu B

2010-01-01

In this article, I critically analyze the impact of the new biology and the biological revolution. I argue that indiscriminate use of the words such as 'interdisciplinary,' 'integrative,' and 'revolution' has caused only confusion when applied to biology. The recent debate, especially after the exploding field of systems biology, has brought back the controversy whether molecular biology is reductionist or holistic. I look at the issues involved critically. I discuss the problem of defining the word 'gene' and argue that recent attempts to redefine the central dogma of molecular biology about the information flow from DNA to RNA to protein are not justified. I support my view with comments from the scientist who discovered RNA splicing. Several aspects of evo-devo, a new branch of biology, are discussed. I give examples from this evolution-developmental biology to show how some of Darwin's inspired guesses have had resounding victory when it was found that specific genes during embryonic development of the Galapagos finches decided the size and shape of their beaks. I discuss the recent publications which show that the conditions in the island, such as wet to dry to wet season, can bring about evolutionary changes from year to year. Thus it is essential to monitor both short and long-term evolutionary changes to get the full picture of evolution.

Vignettes from the field of mathematical biology: the application of mathematics to biology and medicine.

Science.gov (United States)

Murray, J D

2012-08-06

The application of mathematical models in biology and medicine has a long history. From the sparse number of papers in the first half of the twentieth century with a few scientists working in the field it has become vast with thousands of active researchers. We give a brief, and far from definitive history, of how some parts of the field have developed and how the type of research has changed. We describe in more detail just two examples of specific models which are directly related to real biological problems, namely animal coat patterns and the growth and image enhancement of glioblastoma brain tumours.

Review of biological monitoring programs at nuclear facilities

International Nuclear Information System (INIS)

Quintana, L.R.; Oakes, T.W.; Shank, K.E.

Biological monitoring programs, as well as relevant radioecological research studies, are reviewed at specific Department of Energy facilities; the program at Oak Ridge National Laboratory is discussed in detail. The biological measurements that are being used for interpreting the impact of a facility on its surrounding environment and nearby population are given. Suggestions which could facilitate interlaboratory comparison studies are presented

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

Science.gov (United States)

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016

Directory of Open Access Journals (Sweden)

Schreiber Falk

2016-09-01

Full Text Available Standards are essential to the advancement of science and technology. In systems and synthetic biology, numerous standards and associated tools have been developed over the last 16 years. This special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards, as well as to provide centralised and easily citable access to them.

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

Science.gov (United States)

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.

MAK and BAT values list 2017. Maximum permissible concentrations at the place of work and biological tolerance values for working materials; MAK- und BAT-Werte-Liste 2017. Maximale Arbeitsplatzkonzentrationen und Biologische Arbeitsstofftoleranzwerte

Energy Technology Data Exchange (ETDEWEB)

NONE

2017-08-01

The MAK and BAT values list 2017 includes the maximum permissible concentrations at the place of work and biological tolerance values for working materials. The following working materials are covered: carcinogenic working materials, sensitizing materials and aerosols. The report discusses the restriction of exposure peaks, skin resorption, MAK (maximum working place concentration) values during pregnancy, germ cell mutagens and specific working materials. Importance and application of BAT (biological working material tolerance) values, list of materials, carcinogens, biological guide values and reference values are also included.

Molecular biology of the cell

CERN Document Server

Alberts, Bruce; Lewis, Julian

2000-01-01

Molecular Biology of the Cell is the classic in-dept text reference in cell biology. By extracting the fundamental concepts from this enormous and ever-growing field, the authors tell the story of cell biology, and create a coherent framework through which non-expert readers may approach the subject. Written in clear and concise language, and beautifully illustrated, the book is enjoyable to read, and it provides a clear sense of the excitement of modern biology. Molecular Biology of the Cell sets forth the current understanding of cell biology (completely updated as of Autumn 2001), and it explores the intriguing implications and possibilities of the great deal that remains unknown. The hallmark features of previous editions continue in the Fourth Edition. The book is designed with a clean and open, single-column layout. The art program maintains a completely consistent format and style, and includes over 1,600 photographs, electron micrographs, and original drawings by the authors. Clear and concise concept...

Visual event-related potentials to biological motion stimuli in autism spectrum disorders

Science.gov (United States)

Bletsch, Anke; Krick, Christoph; Siniatchkin, Michael; Jarczok, Tomasz A.; Freitag, Christine M.; Bender, Stephan

2014-01-01

Atypical visual processing of biological motion contributes to social impairments in autism spectrum disorders (ASD). However, the exact temporal sequence of deficits of cortical biological motion processing in ASD has not been studied to date. We used 64-channel electroencephalography to study event-related potentials associated with human motion perception in 17 children and adolescents with ASD and 21 typical controls. A spatio-temporal source analysis was performed to assess the brain structures involved in these processes. We expected altered activity already during early stimulus processing and reduced activity during subsequent biological motion specific processes in ASD. In response to both, random and biological motion, the P100 amplitude was decreased suggesting unspecific deficits in visual processing, and the occipito-temporal N200 showed atypical lateralization in ASD suggesting altered hemispheric specialization. A slow positive deflection after 400 ms, reflecting top-down processes, and human motion-specific dipole activation differed slightly between groups, with reduced and more diffuse activation in the ASD-group. The latter could be an indicator of a disrupted neuronal network for biological motion processing in ADS. Furthermore, early visual processing (P100) seems to be correlated to biological motion-specific activation. This emphasizes the relevance of early sensory processing for higher order processing deficits in ASD. PMID:23887808

Biological Water Quality Criteria

Science.gov (United States)

Page contains links to Technical Documents pertaining to Biological Water Quality Criteria, including, technical assistance documents for states, tribes and territories, program overviews, and case studies.

Basic radiotherapy physics and biology

CERN Document Server

Chang, David S; Das, Indra J; Mendonca, Marc S; Dynlacht, Joseph R

2014-01-01

This book is a concise and well-illustrated review of the physics and biology of radiation therapy intended for radiation oncology residents, radiation therapists, dosimetrists, and physicists. It presents topics that are included on the Radiation Therapy Physics and Biology examinations and is designed with the intent of presenting information in an easily digestible format with maximum retention in mind. The inclusion of mnemonics, rules of thumb, and reader-friendly illustrations throughout the book help to make difficult concepts easier to grasp. Basic Radiotherapy Physics and Biology is a

Precision control of recombinant gene transcription for CHO cell synthetic biology.

Science.gov (United States)

Brown, Adam J; James, David C

2016-01-01

The next generation of mammalian cell factories for biopharmaceutical production will be genetically engineered to possess both generic and product-specific manufacturing capabilities that may not exist naturally. Introduction of entirely new combinations of synthetic functions (e.g. novel metabolic or stress-response pathways), and retro-engineering of existing functional cell modules will drive disruptive change in cellular manufacturing performance. However, before we can apply the core concepts underpinning synthetic biology (design, build, test) to CHO cell engineering we must first develop practical and robust enabling technologies. Fundamentally, we will require the ability to precisely control the relative stoichiometry of numerous functional components we simultaneously introduce into the host cell factory. In this review we discuss how this can be achieved by design of engineered promoters that enable concerted control of recombinant gene transcription. We describe the specific mechanisms of transcriptional regulation that affect promoter function during bioproduction processes, and detail the highly-specific promoter design criteria that are required in the context of CHO cell engineering. The relative applicability of diverse promoter development strategies are discussed, including re-engineering of natural sequences, design of synthetic transcription factor-based systems, and construction of synthetic promoters. This review highlights the potential of promoter engineering to achieve precision transcriptional control for CHO cell synthetic biology. Copyright © 2015. Published by Elsevier Inc.

Order-Specific Fertility Rates for Germany
Estimates from Perinatal Statistics for the Period 2001-2008

OpenAIRE

Michaela Kreyenfeld; Rembrandt Scholz; Frederik Peters; Ines Wlosnewski

2011-01-01

Until 2008, Germany’s vital statistics did not include information on the biological order of each birth. This resulted in a dearth of important demographic indicators, such as the mean age at first birth and the level of childlessness. Researchers have tried to fill this gap by generating order-specific birth rates from survey data, and by combining survey data with vital statistics. This paper takes a different approach by using Perinatal Statistics to generate birth order-specific fertilit...

Grades and Withdrawal Rates in Cell Biology and Genetics Based upon Institution Type for General Biology and Implications for Transfer Articulation Agreements

Science.gov (United States)

Regier, Kimberly Fayette

2016-01-01

General biology courses (for majors) are often transferred from one institution to another. These courses must prepare students for upper division courses in biology. In Colorado, a Biology Transfer Articulation Agreement that includes general biology has been created across the state. An evaluation was conducted of course grades in two upper…

Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily

Science.gov (United States)

Lukk, Tiit; Sakai, Ayano; Kalyanaraman, Chakrapani; Brown, Shoshana D.; Imker, Heidi J.; Song, Ling; Fedorov, Alexander A.; Fedorov, Elena V.; Toro, Rafael; Hillerich, Brandan; Seidel, Ronald; Patskovsky, Yury; Vetting, Matthew W.; Nair, Satish K.; Babbitt, Patricia C.; Almo, Steven C.; Gerlt, John A.; Jacobson, Matthew P.

2012-01-01

The rapid advance in genome sequencing presents substantial challenges for protein functional assignment, with half or more of new protein sequences inferred from these genomes having uncertain assignments. The assignment of enzyme function in functionally diverse superfamilies represents a particular challenge, which we address through a combination of computational predictions, enzymology, and structural biology. Here we describe the results of a focused investigation of a group of enzymes in the enolase superfamily that are involved in epimerizing dipeptides. The first members of this group to be functionally characterized were Ala-Glu epimerases in Eschericiha coli and Bacillus subtilis, based on the operon context and enzymological studies; these enzymes are presumed to be involved in peptidoglycan recycling. We have subsequently studied more than 65 related enzymes by computational methods, including homology modeling and metabolite docking, which suggested that many would have divergent specificities;, i.e., they are likely to have different (unknown) biological roles. In addition to the Ala-Phe epimerase specificity reported previously, we describe the prediction and experimental verification of: (i) a new group of presumed Ala-Glu epimerases; (ii) several enzymes with specificity for hydrophobic dipeptides, including one from Cytophaga hutchinsonii that epimerizes D-Ala-D-Ala; and (iii) a small group of enzymes that epimerize cationic dipeptides. Crystal structures for certain of these enzymes further elucidate the structural basis of the specificities. The results highlight the potential of computational methods to guide experimental characterization of enzymes in an automated, large-scale fashion. PMID:22392983

Simultaneous multi-species determination of trimethyllead, monomethylmercury and three butyltin compounds by species-specific isotope dilution GC-ICP-MS in biological samples

Energy Technology Data Exchange (ETDEWEB)

Poperechna, Nataliya; Heumann, Klaus G. [Johannes Gutenberg-University Mainz (Germany). Institute of Inorganic Chemistry and Analytical Chemistry

2005-09-01

An accurate and sensitive multi-species species-specific isotope dilution GC-ICP-MS method was developed for the simultaneous determination of trimethyllead (Me{sub 3}Pb{sup +}), monomethylmercury (MeHg{sup +}) and the three butyltin species Bu{sub 3}Sn{sup +}, Bu{sub 2}Sn{sup 2+}, and BuSn{sup 3+} in biological samples. The method was validated by three biological reference materials (CRM 477, mussel tissue certified for butyltins; CRM 463, tuna fish certified for MeHg{sup +}; DORM 2, dogfish muscle certified for MeHg{sup +}). Under certain conditions, and with minor modifications of the sample pretreatment procedure, this method could also be transferred to environmental samples such as sediments, as demonstrated by analyzing sediment reference material BCR 646 (freshwater sediment, certified for butyltins). The detection limits of the multi-species GC-ICP-IDMS method for biological samples were 1.4 ng g{sup -1} for MeHg{sup +}, 0.06 ng g{sup -1} for Me{sub 3}Pb{sup +}, 0.3 ng g{sup -1} for BuSn{sup 3+} and Bu{sub 3}Sn{sup +}, and 1.2 ng g{sup -1} for Bu{sub 2}Sn{sup 2+}. Because of the high relevance of these heavy metal alkyl species to the quality assurance of seafood, the method was also applied to corresponding samples purchased from a supermarket. The methylated lead fraction in these samples, correlated to total lead, varied over a broad range (from 0.01% to 7.6%). On the other hand, the MeHg{sup +} fraction was much higher, normally in the range of 80-100%. Considering that we may expect tighter legislative limitations on MeHg{sup +} levels in seafood in the future, we found the highest methylmercury contents (up to 10.6 {mu}g g{sup -1}) in two shark samples, an animal which is at the end of the marine food chain, whereas MeHg{sup +} contents of less than 0.2 {mu}g g{sup -1} were found in most other seafood samples; these results correlate with the idea that MeHg{sup +} is usually of biological origin in the marine environment. The concentration of

Perspective: Reaches of chemical physics in biology

Science.gov (United States)

Gruebele, Martin; Thirumalai, D.

2013-01-01

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry. PMID:24089712

Perspective: Reaches of chemical physics in biology.

Science.gov (United States)

Gruebele, Martin; Thirumalai, D

2013-09-28

Chemical physics as a discipline contributes many experimental tools, algorithms, and fundamental theoretical models that can be applied to biological problems. This is especially true now as the molecular level and the systems level descriptions begin to connect, and multi-scale approaches are being developed to solve cutting edge problems in biology. In some cases, the concepts and tools got their start in non-biological fields, and migrated over, such as the idea of glassy landscapes, fluorescence spectroscopy, or master equation approaches. In other cases, the tools were specifically developed with biological physics applications in mind, such as modeling of single molecule trajectories or super-resolution laser techniques. In this introduction to the special topic section on chemical physics of biological systems, we consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry.

Toward University Modeling Instruction—Biology: Adapting Curricular Frameworks from Physics to Biology

Science.gov (United States)

Manthey, Seth; Brewe, Eric

2013-01-01

University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence. PMID:23737628

Toward university modeling instruction--biology: adapting curricular frameworks from physics to biology.

Science.gov (United States)

Manthey, Seth; Brewe, Eric

2013-06-01

University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence.

Applications of dynamical systems in biology and medicine

CERN Document Server

Radunskaya, Ami

2015-01-01

This volume highlights problems from a range of biological and medical applications that can be interpreted as questions about system behavior or control.  Topics include drug resistance in cancer and malaria, biological fluid dynamics, auto-regulation in the kidney, anti-coagulation therapy, evolutionary diversification and photo-transduction.  Mathematical techniques used to describe and investigate these biological and medical problems include ordinary, partial and stochastic differentiation equations, hybrid discrete-continuous approaches, as well as 2 and 3D numerical simulation. .

Molecular Imaging in Synthetic Biology, and Synthetic Biology in Molecular Imaging.

Science.gov (United States)

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

Biomedical synthetic biology is an emerging field in which cells are engineered at the genetic level to carry out novel functions with relevance to biomedical and industrial applications. This approach promises new treatments, imaging tools, and diagnostics for diseases ranging from gastrointestinal inflammatory syndromes to cancer, diabetes, and neurodegeneration. As these cellular technologies undergo pre-clinical and clinical development, it is becoming essential to monitor their location and function in vivo, necessitating appropriate molecular imaging strategies, and therefore, we have created an interest group within the World Molecular Imaging Society focusing on synthetic biology and reporter gene technologies. Here, we highlight recent advances in biomedical synthetic biology, including bacterial therapy, immunotherapy, and regenerative medicine. We then discuss emerging molecular imaging approaches to facilitate in vivo applications, focusing on reporter genes for noninvasive modalities such as magnetic resonance, ultrasound, photoacoustic imaging, bioluminescence, and radionuclear imaging. Because reporter genes can be incorporated directly into engineered genetic circuits, they are particularly well suited to imaging synthetic biological constructs, and developing them provides opportunities for creative molecular and genetic engineering.

Practising Conservation Biology in a Virtual Rainforest World

Science.gov (United States)

Schedlbauer, Jessica L.; Nadolny, Larysa; Woolfrey, Joan

2016-01-01

The interdisciplinary science of conservation biology provides undergraduate biology students with the opportunity to connect the biological sciences with disciplines including economics, social science and philosophy to address challenging conservation issues. Because of its complexity, students do not often have the opportunity to practise…

Increased biological activity of deglycosylated recombinant human granulocyte/macrophage colony-stimulating factor produced by yeast or animal cells

International Nuclear Information System (INIS)

Moonen, P.; Mermod, J.J.; Ernst, J.F.; Hirschi, M.; DeLamarter, J.F.

1987-01-01

Human granulocyte/macrophage colony-stimulating factor (hGM-CSF) produced by several recombinant sources including Escherichia coli, yeast, and animal cells was studied. Recombinant animal cells produced hGM-CSF in low quantities and in multiple forms of varying size. Mammalian hGM-CSF was purified 200,000-fold using immunoaffinity and lectin chromatography. Partially purified proteins produced in yeast and mammalian cells were assayed for the effects of deglycosylation. Following enzymatic deglycosylation, immunoreactivity was measured by radioimmunoassay and biological activity was measured in vitro on responsive human primary cells. Removal of N-linked oligosaccharides from both proteins increased their immunoreactivities by 4- to 8-fold. Removal of these oligosaccharides also increased their specific biological activities about 20-fold, to reach approximately the specific activity of recombinant hGM-CSF from E. coli. The E. coli produced-protein-lacking any carbohydrate- had by far the highest specific activity observed for the recombinant hGM-CSFs

Human papillomavirus molecular biology.

Science.gov (United States)

Harden, Mallory E; Munger, Karl

Human papillomaviruses are small DNA viruses with a tropism for squamous epithelia. A unique aspect of human papillomavirus molecular biology involves dependence on the differentiation status of the host epithelial cell to complete the viral lifecycle. A small group of these viruses are the etiologic agents of several types of human cancers, including oral and anogenital tract carcinomas. This review focuses on the basic molecular biology of human papillomaviruses. Copyright © 2016 Elsevier B.V. All rights reserved.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

KAUST Repository

Perozziello, G.; Giugni, Andrea; Allione, Marco; Torre, Bruno; Das, Gobind; Coluccio, M. L.; Marini, Monica; Tirinato, Luca; Moretti, Manola; Limongi, Tania; Candeloro, P.; Di Fabrizio, Enzo M.

2017-01-01

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Nanoplasmonic and Microfluidic Devices for Biological Sensing

KAUST Repository

Perozziello, G.

2017-02-16

In this chapter we report about recent advances on the development and application of 2D and 3D plasmonic nanostructures used for sensing of biological samples by Raman spectroscopy at unprecedented resolution of analysis. Besides, we explain how the integration of these nanodevices in a microfluidic apparatus can simplify the analysis of biological samples. In the first part we introduce and motivate the convenience of using nanoplasmonic enhancers and Raman spectroscopy for biological sensing, describing the phenomena and the current approaches to fabricate nanoplasmonic structures. In the second part, we explain how specific multi-element devices produce the optimal enhancement of the Raman scattering. We report cases where biological sensing of DNA was performed at few molecules level with nanometer spatial resolutions. Finally, we show an example of microfluidic device integrating plasmonic nanodevices to sort and drive biological samples, like living cells, towards the optical probe in order to obtain optimal conditions of analysis.

Next-generation biology

DEFF Research Database (Denmark)

Rodrigues da Fonseca, Rute Andreia; Albrechtsen, Anders; Themudo, Goncalo Espregueira Cruz

2016-01-01

we present an overview of the current sequencing technologies and the methods used in typical high-throughput data analysis pipelines. Subsequently, we contextualize high-throughput DNA sequencing technologies within their applications in non-model organism biology. We include tips regarding managing...

Synchrotron Radiation in Biology and Medicine

International Nuclear Information System (INIS)

Pelka, J.B.

2008-01-01

This work is focused on a present status of synchrotron radiation X-ray applications in medicine and biology to imaging, diagnostics, and radio- therapy. Properties of X-ray beams generated by synchrotron sources are compared with radiation produced by classical laboratory X-ray tubes. A list of operating and planned synchrotron facilities applicable to biomedical purposes is given, together with their basic characteristics. A concise overview of typical X-ray synchrotron techniques in biology and medicine is carried out with discussion of their specific properties and examples of typical results. (author)

Radioreceptor assay for benzodiazepines in biological fluids using a new dry and stable receptor preparation

International Nuclear Information System (INIS)

Lund, J.

1981-01-01

A method for determination of benzodiazepines in human blood, plasma, saliva and urine has been developed. The method is based upon the competition between 3 H-flunitrazepam and biologically active benzodiazepines in biological fluids for brain specific receptors, prepared in a stable, dry form and easy to handle. The pharmacological specificity for benzodiazepines of the dry stable receptor preparation is closely similar to that of fresh membrane-bound rat brain receptors. The method is specific for biologically active benzodiazepines; it is relatively rapid, sensitive and reproducible, and can be performed at room temperature. (author)

Biologic Therapy and Asthma.

Science.gov (United States)

Viswanathan, Ravi K; Busse, William W

2018-02-01

Although airway inflammation is an intrinsic and key feature of asthma, this response varies in its intensity and translation to clinical characteristics and responsiveness to treatment. The observations that clinical heterogeneity is an important aspect of asthma and a feature that likely dictates and determines responses to treatment in severe asthma, patient responsiveness to medication is incomplete, and risks for exacerbation are increased. The development of biologics, which target selected and specific components of inflammation, has been a promising advance to achieve asthma control in patients with severe disease. This article reviews the current biologics available and under development and how their use has affected asthma and which subpopulations appear to benefit the greatest. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

The Dominance Behavioral System and Psychopathology: Evidence from Self-Report, Observational, and Biological Studies

Science.gov (United States)

Johnson, Sheri L.; Leedom, Liane J.; Muhtadie, Luma

2012-01-01

The dominance behavioral system (DBS) can be conceptualized as a biologically-based system which guides dominance motivation, dominant and subordinate behavior, and responsivity to perceptions of power and subordination. A growing body of research suggests that problems with the DBS are evident across a broad range of psychopathologies. We begin by describing psychological, social, and biological correlates of the dominance behavioral system (DBS). Extensive research suggests that externalizing disorders, mania-proneness, and narcissistic traits are related to heightened dominance motivation and behaviors. Mania and narcissistic traits also appear related to inflated self-perceptions of power. Anxiety and depression are related to subordination and submissiveness, as well as a desire to avoid subordination. Models of the DBS have received support from research with humans and animals; from self-report, observational, and biological methods; and using naturalistic and experimental paradigms. Limitations of available research include the relative lack of longitudinal studies using multiple measures of the DBS and the absence of relevant studies using diagnosed samples to study narcissistic personality disorder and bipolar disorder. We provide suggestions for future research on the DBS and psychopathology, including investigations of whether the DBS can be used to differentiate specific disorder outcomes; the need for more sophisticated biological research; and the value of longitudinal dynamical research. Implications of using the DBS as a tool in clinical assessment and treatment are discussed. PMID:22506751

Designing and implementing a new advanced level biology course.

OpenAIRE

Hall, Angela; Reiss, Michael; Rowell, Cathy; Scott, C.; Scott, Anne

2003-01-01

Salters-Nuffield Advanced Biology is a new advanced level biology course currently being piloted from September 2002 in England with around 1200 students. This paper discusses the reasons for developing a new advanced biology course at this time, the philosophy of the project and how the materials are being written and the specification devised. The aim of the project is to provide an up-to-date course that interests students, is considered appropriate by teachers and other professionals in b...

Proceedings of the 4th workshop on ion-beam-applied biology

International Nuclear Information System (INIS)

Kobayashi, Yasuhiko; Funayama, Tomoo; Wada, Seiichi; Hamada, Nobuyuki

2005-09-01

In order to promote research on biological application using ion beam at TIARA, we have annually hold the Workshop on Ion-beam-applied Biology at JAERI Takasaki since 2002. The 4th workshop entitled 'New Frontiers of Biological Research using microbeam - Application to Radio-microsurgery and Cellular Response to Radiations -' was held on June 22nd, 2005, aimed to overview the recent progress in microbeam-applied researches, and discuss the future direction of application of microbeam not to researches in life science and biotechnology, but also to clinical medicine. This workshop was hosted by JAERI Takasaki, with the cooperation of The Ion Beam Breeding Society, The Japan Radiation Research Society, The Japanese Society for Biological Sciences in Space, The Kanto-Kohetsu Branch of The Atomic Energy Society of Japan, and The Japan Radioisotope Association. There were 104 participants including clinicians attended from universities, public research institutions, and private companies. The papers presented in the workshop were about the ion-beam-applied biological researches at JAERI, the present status of microbeam facilities in Japan and foreign countries, and the microbeam-based analyses of damage repair machinery in insects and radiation-induced bystander effects. It was realized again that microbeam is quite useful for functional analyses by targeted disruption of specific tissues in bio-organisms, and is of critical importance in investigating biological influences of low-dose radiations as well as in its radiological application. These researches using microbeam are expected to further march on. The 13 of the presented papers are indexed individually. (J.P.N.)

Physicochemical Mechanisms of Synergistic Biological Action of Combinations of Aromatic Heterocyclic Compounds

OpenAIRE

Evstigneev, Maxim P.

2013-01-01

The mechanisms of synergistic biological effects observed in the simultaneous use of aromatic heterocyclic compounds in combination are reviewed, and the specific biological role of heteroassociation of aromatic molecules is discussed.

Porous silicon structures with high surface area/specific pore size

Science.gov (United States)

Northrup, M.A.; Yu, C.M.; Raley, N.F.

1999-03-16

Fabrication and use of porous silicon structures to increase surface area of heated reaction chambers, electrophoresis devices, and thermopneumatic sensor-actuators, chemical preconcentrates, and filtering or control flow devices. In particular, such high surface area or specific pore size porous silicon structures will be useful in significantly augmenting the adsorption, vaporization, desorption, condensation and flow of liquids and gases in applications that use such processes on a miniature scale. Examples that will benefit from a high surface area, porous silicon structure include sample preconcentrators that are designed to adsorb and subsequently desorb specific chemical species from a sample background; chemical reaction chambers with enhanced surface reaction rates; and sensor-actuator chamber devices with increased pressure for thermopneumatic actuation of integrated membranes. Examples that benefit from specific pore sized porous silicon are chemical/biological filters and thermally-activated flow devices with active or adjacent surfaces such as electrodes or heaters. 9 figs.

Biological variability of glycated hemoglobin.

Science.gov (United States)

Braga, Federica; Dolci, Alberto; Mosca, Andrea; Panteghini, Mauro

2010-11-11

The measurement of glycated hemoglobin (HbA(1c)) has a pivotal role in monitoring glycemic state in diabetic patients. Furthermore, the American Diabetes Association has recently recommended the use of HbA(1c) for diabetes diagnosis, but a clear definition of the clinically allowable measurement error is still lacking. Information on biological variability of the analyte can be used to achieve this goal. We systematically reviewed the published studies on the biological variation of HbA(1c) to check consistency of available data in order to accurately define analytical goals. The nine recruited studies were limited by choice of analytic methodology, population selection, protocol application and statistical analyses. There is an urgent need to determine biological variability of HbA(1c) using a specific and traceable assay, appropriate protocol and appropriate statistical evaluation of data. 2010 Elsevier B.V. All rights reserved.

Understanding specificity in metabolic pathways-Structural biology of human nucleotide metabolism

International Nuclear Information System (INIS)

Welin, Martin; Nordlund, Paer

2010-01-01

Interactions are the foundation of life at the molecular level. In the plethora of activities in the cell, the evolution of enzyme specificity requires the balancing of appropriate substrate affinity with a negative selection, in order to minimize interactions with other potential substrates in the cell. To understand the structural basis for enzyme specificity, the comparison of structural and biochemical data between enzymes within pathways using similar substrates and effectors is valuable. Nucleotide metabolism is one of the largest metabolic pathways in the human cell and is of outstanding therapeutic importance since it activates and catabolises nucleoside based anti-proliferative drugs and serves as a direct target for anti-proliferative drugs. In recent years the structural coverage of the enzymes involved in human nucleotide metabolism has been dramatically improved and is approaching completion. An important factor has been the contribution from the Structural Genomics Consortium (SGC) at Karolinska Institutet, which recently has solved 33 novel structures of enzymes and enzyme domains in human nucleotide metabolism pathways and homologs thereof. In this review we will discuss some of the principles for substrate specificity of enzymes in human nucleotide metabolism illustrated by a selected set of enzyme families where a detailed understanding of the structural determinants for specificity is now emerging.

Blood miRNAs as sensitive and specific biological indicators of environmental and occupational exposure to volatile organic compound (VOC).

Science.gov (United States)

Song, Mi-Kyung; Ryu, Jae-Chun

2015-10-01

To date, there is still shortage of highly sensitive and specific minimally invasive biomarkers for assessment of environmental toxicants exposure. Because of the significance of microRNA (miRNA) in various diseases, circulating miRNAs in blood may be unique biomarkers for minimally invasive prediction of toxicants exposure. We identified and validated characteristic miRNA expression profiles of human whole blood in workers exposed to volatile organic compounds (VOCs) and compared the usefulness of miRNA indicator of VOCs with the effectiveness of the already used urinary biomarkers of occupational exposure. Using a microarray based approach we screened and detected deregulated miRNAs in their expression in workers exposed to VOCs (toluene [TOL], xylene [XYL] and ethylbenzene [EBZ]). Total 169 workers from four dockyards were enrolled in current study, and 50 subjects of them were used for miRNA microarray analysis. We identified 467 miRNAs for TOL, 211 miRNAs for XYL, and 695 miRNAs for XYL as characteristic discernible exposure indicator, which could discerned each VOC from the control group with higher accuracy, sensitivity, and specificity than urinary biomarkers. Current observations from this study point out that the altered levels of circulating miRNAs can be a reliable novel, minimally invasive biological indicator of occupational exposure to VOCs. Copyright © 2015 Elsevier GmbH. All rights reserved.

Biological optimization systems for enhancing photosynthetic efficiency and methods of use

Science.gov (United States)

Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

2012-11-06

Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

The biology of plant metabolomics

NARCIS (Netherlands)

Hall, R.D.

2011-01-01

Following a general introduction, this book includes details of metabolomics of model species including Arabidopsis and tomato. Further chapters provide in-depth coverage of abiotic stress, data integration, systems biology, genetics, genomics, chemometrics and biostatisitcs. Applications of plant

TiGER: a database for tissue-specific gene expression and regulation.

Science.gov (United States)

Liu, Xiong; Yu, Xueping; Zack, Donald J; Zhu, Heng; Qian, Jiang

2008-06-09

Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation). The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM) detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

TiGER: A database for tissue-specific gene expression and regulation

Directory of Open Access Journals (Sweden)

Zack Donald J

2008-06-01

Full Text Available Abstract Background Understanding how genes are expressed and regulated in different tissues is a fundamental and challenging question. However, most of currently available biological databases do not focus on tissue-specific gene regulation. Results The recent development of computational methods for tissue-specific combinational gene regulation, based on transcription factor binding sites, enables us to perform a large-scale analysis of tissue-specific gene regulation in human tissues. The results are stored in a web database called TiGER (Tissue-specific Gene Expression and Regulation. The database contains three types of data including tissue-specific gene expression profiles, combinatorial gene regulations, and cis-regulatory module (CRM detections. At present the database contains expression profiles for 19,526 UniGene genes, combinatorial regulations for 7,341 transcription factor pairs and 6,232 putative CRMs for 2,130 RefSeq genes. Conclusion We have developed and made publicly available a database, TiGER, which summarizes and provides large scale data sets for tissue-specific gene expression and regulation in a variety of human tissues. This resource is available at 1.

Biological indicators of radiation quality

International Nuclear Information System (INIS)

Bender, M.A.; Wong, R.M.A.

1982-01-01

The induction of many biological effects by high linear energy transfer (LET) radiation is strikingly different in one or two respects from the induction by acute low-LET radiation. If the acute low-LET dose-effect curve is of the usual quadratic form, it becomes linear as LET increases. In any case the linear slope increases as LET increases; that is, the relative biological effectiveness (RBE) increases. Both changes might be exploited as biological indicators of whether or not the recent recalculations of dose and of neutron contribution to dose at Hiroshima and Nagasaki seem consistent with the epidemiological observations. The biological end points that have been extensively studied in survivors include acute effects, growth and development after in utero or childhood exposure, genetic and cytogenetic effects in offspring, somatic chromosomal aberrations in survivors, and, of course, cancers, including leukemia. No significant indication among offspring of genetic or cytogenetic effects attributable to parental exposure has been found. Among the remaining end points, only the data on somatic chromosomal aberrations and on cancers appear robust enough to allow one to draw definite inferences by comparing experiences at the two cities

Radiations at the physics-biology interface. Utilization of radiations for research

International Nuclear Information System (INIS)

Douzou, P.

1997-01-01

Structural biology, which study the relation between the structure of biomolecules and their function, is at the interface between physics and biology. With the help of large radiation instruments such as X ray diffraction and neutron scattering, important advancements have been accomplished in the understanding of specific biological functions and led to the development of protein engineering (such as directed mutagenesis)

Preferred SH3 domain partners of ADAM metalloproteases include shared and ADAM-specific SH3 interactions.

Directory of Open Access Journals (Sweden)

Iivari Kleino

Full Text Available A disintegrin and metalloproteinases (ADAMs constitute a protein family essential for extracellular signaling and regulation of cell adhesion. Catalytic activity of ADAMs and their predicted potential for Src-homology 3 (SH3 domain binding show a strong correlation. Here we present a comprehensive characterization of SH3 binding capacity and preferences of the catalytically active ADAMs 8, 9, 10, 12, 15, 17, and 19. Our results revealed several novel interactions, and also confirmed many previously reported ones. Many of the identified SH3 interaction partners were shared by several ADAMs, whereas some were ADAM-specific. Most of the ADAM-interacting SH3 proteins were adapter proteins or kinases, typically associated with sorting and endocytosis. Novel SH3 interactions revealed in this study include TOCA1 and CIP4 as preferred partners of ADAM8, and RIMBP1 as a partner of ADAM19. Our results suggest that common as well as distinct mechanisms are involved in regulation and execution of ADAM signaling, and provide a useful framework for addressing the pathways that connect ADAMs to normal and aberrant cell behavior.

The effect of network biology on drug toxicology

DEFF Research Database (Denmark)

Gautier, Laurent; Taboureau, Olivier; Audouze, Karine Marie Laure

2013-01-01

Introduction: The high failure rate of drug candidates due to toxicity, during clinical trials, is a critical issue in drug discovery. Network biology has become a promising approach, in this regard, using the increasingly large amount of biological and chemical data available and combining...... it with bioinformatics. With this approach, the assessment of chemical safety can be done across multiple scales of complexity from molecular to cellular and system levels in human health. Network biology can be used at several levels of complexity. Areas covered: This review describes the strengths and limitations...... of network biology. The authors specifically assess this approach across different biological scales when it is applied to toxicity. Expert opinion: There has been much progress made with the amount of data that is generated by various omics technologies. With this large amount of useful data, network...

Generative mechanistic explanation building in undergraduate molecular and cellular biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-09-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among scientists, we created and applied a theoretical framework to explore the strategies students use to construct explanations for 'novel' biological phenomena. Specifically, we explored how students navigated the multi-level nature of complex biological systems using generative mechanistic reasoning. Interviews were conducted with introductory and upper-division biology students at a large public university in the United States. Results of qualitative coding revealed key features of students' explanation building. Students used modular thinking to consider the functional subdivisions of the system, which they 'filled in' to varying degrees with mechanistic elements. They also hypothesised the involvement of mechanistic entities and instantiated abstract schema to adapt their explanations to unfamiliar biological contexts. Finally, we explored the flexible thinking that students used to hypothesise the impact of mutations on multi-leveled biological systems. Results revealed a number of ways that students drew mechanistic connections between molecules, functional modules (sets of molecules with an emergent function), cells, tissues, organisms and populations.

Application of proteomics to ecology and population biology.

Science.gov (United States)

Karr, T L

2008-02-01

Proteomics is a relatively new scientific discipline that merges protein biochemistry, genome biology and bioinformatics to determine the spatial and temporal expression of proteins in cells, tissues and whole organisms. There has been very little application of proteomics to the fields of behavioral genetics, evolution, ecology and population dynamics, and has only recently been effectively applied to the closely allied fields of molecular evolution and genetics. However, there exists considerable potential for proteomics to impact in areas related to functional ecology; this review will introduce the general concepts and methodologies that define the field of proteomics and compare and contrast the advantages and disadvantages with other methods. Examples of how proteomics can aid, complement and indeed extend the study of functional ecology will be discussed including the main tool of ecological studies, population genetics with an emphasis on metapopulation structure analysis. Because proteomic analyses provide a direct measure of gene expression, it obviates some of the limitations associated with other genomic approaches, such as microarray and EST analyses. Likewise, in conjunction with associated bioinformatics and molecular evolutionary tools, proteomics can provide the foundation of a systems-level integration approach that can enhance ecological studies. It can be envisioned that proteomics will provide important new information on issues specific to metapopulation biology and adaptive processes in nature. A specific example of the application of proteomics to sperm ageing is provided to illustrate the potential utility of the approach.

Research Collaboration Workshop for Women in Mathematical Biology

CERN Document Server

Miller, Laura

2017-01-01

Inspired by the Research Collaboration Workshop for Women in Mathematical Biology, this volume contains research and review articles that cover topics ranging from models of animal movement to the flow of blood cells in the embryonic heart. Hosted by the National Institute for Mathematics and Biological Synthesis (NIMBioS), the workshop brought together women working in biology and mathematics to form four research groups that encouraged multidisciplinary collaboration and lifetime connections in the STEM field. This volume introduces many of the topics from the workshop, including the aerodynamics of spider ballooning; sleep, circadian rhythms, and pain; blood flow regulation in the kidney; and the effects of antimicrobial therapy on gut microbiota and microbiota and Clostridium difficile. Perfect for students and researchers in mathematics and biology, the papers included in this volume offer an introductory glimpse at recent research in mathematical biology. .

Genome annotation in a community college cell biology lab.

Science.gov (United States)

Beagley, C Timothy

2013-01-01

The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

Biomaterials for mediation of chemical and biological warfare agents.

Science.gov (United States)

Russell, Alan J; Berberich, Jason A; Drevon, Geraldine F; Koepsel, Richard R

2003-01-01

Recent events have emphasized the threat from chemical and biological warfare agents. Within the efforts to counter this threat, the biocatalytic destruction and sensing of chemical and biological weapons has become an important area of focus. The specificity and high catalytic rates of biological catalysts make them appropriate for decommissioning nerve agent stockpiles, counteracting nerve agent attacks, and remediation of organophosphate spills. A number of materials have been prepared containing enzymes for the destruction of and protection against organophosphate nerve agents and biological warfare agents. This review discusses the major chemical and biological warfare agents, decontamination methods, and biomaterials that have potential for the preparation of decontamination wipes, gas filters, column packings, protective wear, and self-decontaminating paints and coatings.

Specific RNP capture with antisense LNA/DNA mixmers.

Science.gov (United States)

Rogell, Birgit; Fischer, Bernd; Rettel, Mandy; Krijgsveld, Jeroen; Castello, Alfredo; Hentze, Matthias W

2017-08-01

RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins. © 2017 Rogell et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Accumulating Data to Optimally Predict Obesity Treatment (ADOPT): Recommendations from the Biological Domain.

Science.gov (United States)

Rosenbaum, Michael; Agurs-Collins, Tanya; Bray, Molly S; Hall, Kevin D; Hopkins, Mark; Laughlin, Maren; MacLean, Paul S; Maruvada, Padma; Savage, Cary R; Small, Dana M; Stoeckel, Luke

2018-04-01

The responses to behavioral, pharmacological, or surgical obesity treatments are highly individualized. The Accumulating Data to Optimally Predict obesity Treatment (ADOPT) project provides a framework for how obesity researchers, working collectively, can generate the evidence base needed to guide the development of tailored, and potentially more effective, strategies for obesity treatment. The objective of the ADOPT biological domain subgroup is to create a list of high-priority biological measures for weight-loss studies that will advance the understanding of individual variability in response to adult obesity treatments. This list includes measures of body composition, energy homeostasis (energy intake and output), brain structure and function, and biomarkers, as well as biobanking procedures, which could feasibly be included in most, if not all, studies of obesity treatment. The recommended high-priority measures are selected to balance needs for sensitivity, specificity, and/or comprehensiveness with feasibility to achieve a commonality of usage and increase the breadth and impact of obesity research. The accumulation of data on key biological factors, along with behavioral, psychosocial, and environmental factors, can generate a more precise description of the interplay and synergy among them and their impact on treatment responses, which can ultimately inform the design and delivery of effective, tailored obesity treatments. © 2018 The Obesity Society.

Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules.

Science.gov (United States)

Seghal Kiran, G; Ramasamy, Pasiyappazham; Sekar, Sivasankari; Ramu, Meenatchi; Hassan, Saqib; Ninawe, A S; Selvin, Joseph

2018-06-01

The discovery of genes responsible for the production of bioactive metabolites via metabolic pathways combined with the advances in synthetic biology tools, has allowed the establishment of numerous microbial cell factories, for instance the yeast cell factories, for the manufacture of highly useful metabolites from renewable biomass. Genome mining and metagenomics are two platforms provide base-line data for reconstruction of genomes and metabolomes which is based in the development of synthetic/semi-synthetic genomes for marine natural products discovery. Engineered biofilms are being innovated on synthetic biology platform using genetic circuits and cell signalling systems as represillators controlling biofilm formation. Recombineering is a process of homologous recombination mediated genetic engineering, includes insertion, deletion or modification of any sequence specifically. Although this discipline considered new to the scientific domain, this field has now developed as promising endeavor on the accomplishment of sustainable exploitation of marine natural products. Copyright © 2018 Elsevier B.V. All rights reserved.

BIOLOGICAL CONTROL OF WEEDS BY MEANS OF PLANT PATHOGENS

Directory of Open Access Journals (Sweden)

Marija Ravlić

2014-06-01

Full Text Available Biological control is the use of live beneficial organisms and products of their metabolism in the pests control. Plant pathogens can be used for weed control in three different ways: as classical, conservation and augmentative (inoculative and inundated biological control. Inundated biological control involves the use of bioherbicides (mycoherbicides or artificial breeding of pathogens and application in specific stages of crops and weeds. Biological control of weeds can be used where chemical herbicides are not allowed, if resistant weed species are present or in the integrated pest management against weeds with reduced herbicides doses and other non-chemical measures, but it has certain limitations and disadvantages.

Biological Soft Robotics.

Science.gov (United States)

Feinberg, Adam W

2015-01-01

In nature, nanometer-scale molecular motors are used to generate force within cells for diverse processes from transcription and transport to muscle contraction. This adaptability and scalability across wide temporal, spatial, and force regimes have spurred the development of biological soft robotic systems that seek to mimic and extend these capabilities. This review describes how molecular motors are hierarchically organized into larger-scale structures in order to provide a basic understanding of how these systems work in nature and the complexity and functionality we hope to replicate in biological soft robotics. These span the subcellular scale to macroscale, and this article focuses on the integration of biological components with synthetic materials, coupled with bioinspired robotic design. Key examples include nanoscale molecular motor-powered actuators, microscale bacteria-controlled devices, and macroscale muscle-powered robots that grasp, walk, and swim. Finally, the current challenges and future opportunities in the field are addressed.

Synthetic Biology with Cytochromes P450 Using Photosynthetic Chassis

DEFF Research Database (Denmark)

Gnanasekaran, Thiyagarajan

, this modern field of synthetic biology is completely dependent on the nature of the chassis - the host organisms - for its endeavor. Of all the chassis, photosynthetic organisms such as cyanobacteria and plants gains special attention due to the remarkable amount of sunlight that is striking the Earth...... in cyanobacteria and plant chloroplasts for the purpose of light driven synthesis of bioactive compounds by using synthetic biology approaches. As model pathways, in this thesis, the pathway involved in the synthesis of the cyanogenic glucoside dhurrin from Sorghum bicolor, and the pathway involved......Synthetic biology is a rapidly growing engineering discipline in biology. It aims at building novel biological systems that do not exist in nature by selecting the interchangeable standardized biological parts that are already available in the nature, and assembling them in a specific order. Today...

Magnetic Nanotweezers for Interrogating Biological Processes in Space and Time.

Science.gov (United States)

Kim, Ji-Wook; Jeong, Hee-Kyung; Southard, Kaden M; Jun, Young-Wook; Cheon, Jinwoo

2018-04-17

The ability to sense and manipulate the state of biological systems has been extensively advanced during the past decade with the help of recent developments in physical tools. Unlike standard genetic and pharmacological perturbation techniques-knockdown, overexpression, small molecule inhibition-that provide a basic on/off switching capability, these physical tools provide the capacity to control the spatial, temporal, and mechanical properties of the biological targets. Among the various physical cues, magnetism offers distinct advantages over light or electricity. Magnetic fields freely penetrate biological tissues and are already used for clinical applications. As one of the unique features, magnetic fields can be transformed into mechanical stimuli which can serve as a cue in regulating biological processes. However, their biological applications have been limited due to a lack of high-performance magnetism-to-mechanical force transducers with advanced spatiotemporal capabilities. In this Account, we present recent developments in magnetic nanotweezers (MNTs) as a useful tool for interrogating the spatiotemporal control of cells in living tissue. MNTs are composed of force-generating magnetic nanoparticles and field generators. Through proper design and the integration of individual components, MNTs deliver controlled mechanical stimulation to targeted biomolecules at any desired space and time. We first discuss about MNT configuration with different force-stimulation modes. By modulating geometry of the magnetic field generator, MNTs exert pulling, dipole-dipole attraction, and rotational forces to the target specifically and quantitatively. We discuss the key physical parameters determining force magnitude, which include magnetic field strength, magnetic field gradient, magnetic moment of the magnetic particle, as well as distance between the field generator and the particle. MNTs also can be used over a wide range of biological time scales. By simply

Prion potency in stem cells biology.

Science.gov (United States)

Lopes, Marilene H; Santos, Tiago G

2012-01-01

Prion protein (PrP) can be considered a pivotal molecule because it interacts with several partners to perform a diverse range of critical biological functions that might differ in embryonic and adult cells. In recent years, there have been major advances in elucidating the putative role of PrP in the basic biology of stem cells in many different systems. Here, we review the evidence indicating that PrP is a key molecule involved in driving different aspects of the potency of embryonic and tissue-specific stem cells in self-perpetuation and differentiation in many cell types. It has been shown that PrP is involved in stem cell self-renewal, controlling pluripotency gene expression, proliferation, and neural and cardiomyocyte differentiation. PrP also has essential roles in distinct processes that regulate tissue-specific stem cell biology in nervous and hematopoietic systems and during muscle regeneration. Results from our own investigations have shown that PrP is able to modulate self-renewal and proliferation in neural stem cells, processes that are enhanced by PrP interactions with stress inducible protein 1 (STI1). Thus, the available data reveal the influence of PrP in acting upon the maintenance of pluripotent status or the differentiation of stem cells from the early embryogenesis through adulthood.

Influence of prosthetic radioiodination on the chemical and biological behavior of chemotactic peptides labeled at high specific activity

International Nuclear Information System (INIS)

Pozzi, Oscar R.; Sajaroff, Elisa O.; Edreira, Martin M.

2006-01-01

The influence of radioiodination made through prosthetic group N-succinimidyl-3-[ 131 I]iodo-benzoate ([ 131 I]SIB) on the behavior of small peptides was investigated using as model the chemotactic hexapeptide Nα-for-Nle-Leu-Phe-Nle-Tyr-Lys. No carrier added labeled peptide was isolated by reverse-phase HPLC (RP-HPLC) with coupling efficiencies up to 59-75%. Biodistribution in normal and infected C57 mice showed mainly a hepatobiliary clearance, a very low thyroid uptake and the highest uptake at the infection site was within 1h of injection. Superoxide production and competitive binding assays studies in human polymorphonuclear leukocytes showed a preserved biological activity and high-affinity specific binding. However, the results indicated that the changes observed in the receptor-binding properties with an IC 50 almost twice than the unlabeled peptide and the increasing in the hepatobiliary excretion could be the consequence of the increased lipophicity observed due to the presence of the prosthetic group together with a strong influence of the radioisotope per se

Influence of prosthetic radioiodination on the chemical and biological behavior of chemotactic peptides labeled at high specific activity

Energy Technology Data Exchange (ETDEWEB)

Pozzi, Oscar R. [National Atomic Energy Commission, Ezeiza Atomic Centre, Buenos Aires (Argentina)]. E-mail: oscar.pozzi@duke.edu; Sajaroff, Elisa O. [National Atomic Energy Commission, Ezeiza Atomic Centre, Buenos Aires (Argentina); Edreira, Martin M. [National Atomic Energy Commission, Ezeiza Atomic Centre, Buenos Aires (Argentina)

2006-06-15

The influence of radioiodination made through prosthetic group N-succinimidyl-3-[{sup 131}I]iodo-benzoate ([{sup 131}I]SIB) on the behavior of small peptides was investigated using as model the chemotactic hexapeptide N{alpha}-for-Nle-Leu-Phe-Nle-Tyr-Lys. No carrier added labeled peptide was isolated by reverse-phase HPLC (RP-HPLC) with coupling efficiencies up to 59-75%. Biodistribution in normal and infected C57 mice showed mainly a hepatobiliary clearance, a very low thyroid uptake and the highest uptake at the infection site was within 1h of injection. Superoxide production and competitive binding assays studies in human polymorphonuclear leukocytes showed a preserved biological activity and high-affinity specific binding. However, the results indicated that the changes observed in the receptor-binding properties with an IC{sub 50} almost twice than the unlabeled peptide and the increasing in the hepatobiliary excretion could be the consequence of the increased lipophicity observed due to the presence of the prosthetic group together with a strong influence of the radioisotope per se.

An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B.

Science.gov (United States)

Winter, Georg E; Rix, Uwe; Lissat, Andrej; Stukalov, Alexey; Müllner, Markus K; Bennett, Keiryn L; Colinge, Jacques; Nijman, Sebastian M; Kubicek, Stefan; Kovar, Heinrich; Kontny, Udo; Superti-Furga, Giulio

2011-10-01

Ewing's sarcoma is a pediatric cancer of the bone that is characterized by the expression of the chimeric transcription factor EWS-FLI1 that confers a highly malignant phenotype and results from the chromosomal translocation t(11;22)(q24;q12). Poor overall survival and pronounced long-term side effects associated with traditional chemotherapy necessitate the development of novel, targeted, therapeutic strategies. We therefore conducted a focused viability screen with 200 small molecule kinase inhibitors in 2 different Ewing's sarcoma cell lines. This resulted in the identification of several potential molecular intervention points. Most notably, tozasertib (VX-680, MK-0457) displayed unique nanomolar efficacy, which extended to other cell lines, but was specific for Ewing's sarcoma. Furthermore, tozasertib showed strong synergies with the chemotherapeutic drugs etoposide and doxorubicin, the current standard agents for Ewing's sarcoma. To identify the relevant targets underlying the specific vulnerability toward tozasertib, we determined its cellular target profile by chemical proteomics. We identified 20 known and unknown serine/threonine and tyrosine protein kinase targets. Additional target deconvolution and functional validation by RNAi showed simultaneous inhibition of Aurora kinases A and B to be responsible for the observed tozasertib sensitivity, thereby revealing a new mechanism for targeting Ewing's sarcoma. We further corroborated our cellular observations with xenograft mouse models. In summary, the multilayered chemical biology approach presented here identified a specific vulnerability of Ewing's sarcoma to concomitant inhibition of Aurora kinases A and B by tozasertib and danusertib, which has the potential to become a new therapeutic option.

Profil Kompetensi Profesional Guru Mapel Biologi Pasca Sertifikasi di Karesidenan Surakarta

Directory of Open Access Journals (Sweden)

Sofyan Anif

2015-07-01

Full Text Available As stated in UU No. 14, 2005 and PP No. 74, 2008 that teachers as proffessional educator have to possess four competences, namely: pedagogic, proffessional, character, and social. However the condition in Indonesia is not like that. In general, they are in low category, specifically in pedagogic and proffessional. Those conditions happen in biology teachers and other teacher subjects. Then the aim of this study is to observe the profile of biology teachers especially their proffessional competence pasca sertification in Surakarta residance. The population of this study is all biology teachers (332 persons that have rechieved sertification through direct, portofolio, and PLPG program. Purposive random sampling is used to get 116 teachers. Data are collected by depth interview, documentation, and test, then the collected data are analysed by descriptive qualitative. The result shows that the profile of proffessional competence of biology teachers can be grouped into three: low, middle, and high. The teachers are low in: concept implementation, using tool of measurements, biology experiment planning, using the result of reflection, self reflection, understanding the principles and theories of savety work, doing action research, and understanding the steps of biology experiement correctly. The teachers are middle in: understanding the objective of the study, creative and innovative in implementing and developing science of biology nad correlated sciences, undesrtanding thinking process of biology, using symbolic language, undesrtanding standard competence, and understanding the scoupe of biology. They are high in: understanding the structure biology science and its correlation, selecting the material, cooking the material creatively, understanding the concepts, laws, and biology theories, undesrtanding the history of the natural science, specifically biology, understanding the basic competence of the subject or topic, updating their knowledge from

ERLN Biological Focus Area

Science.gov (United States)

The Environmental Response Laboratory Network supports the goal to increase national capacity for biological analysis of environmental samples. This includes methods development and verification, technology transfer, and collaboration with USDA, FERN, CDC.

Enantiomer-specific ketorolac pharmacokinetics in young women, including pregnancy and postpartum period

Directory of Open Access Journals (Sweden)

Aida Kulo

2017-02-01

Full Text Available Racemic ketorolac clearance (CL is significantly higher at delivery, but S-ketorolac disposition determines the analgesic effects. The aim of this study was to investigate the effect of pregnancy and postpartum period on enantiomer-specific (S and R intravenous (IV ketorolac pharmacokinetics (PKs. Data in women shortly following cesarean delivery (n=39 were pooled with data in a subgroup of these women that was reevaluated in the later postpartum period (postpartum group, n=8/39 and with eight healthy female volunteers. All women received single IV bolus of 30 mg ketorolac tromethamine. Five plasma samples were collected at 1, 2, 4, 6, and 8 hours and plasma concentrations were determined using high performance liquid chromatography. Enantiomer-specific PKs were calculated using PKSolver. Unpaired analysis showed that distribution volume at steady state (Vss, L/kg for S- and R-ketorolac was significantly higher in women shortly following cesarean delivery (n=31 compared to postpartum group (n=8 or to healthy female volunteers (n=8. CL, CL to body weight, and CL to body surface area (CL/BSA for S- and R-ketorolac were also significantly higher in women following delivery. In addition, S/R-ketorolac CL/BSA ratio was significantly higher at delivery. Paired PK analysis in eight women shortly following delivery and in postpartum group showed the same pattern. Finally, the simultaneous increase in CL and Vss resulted in similar estimates for elimination half-life in both unpaired and paired analysis. In conclusion, pregnancy affects S-, R-, and S/R-ketorolac disposition. This is of clinical relevance since S-ketorolac (analgesia CL is even more increased compared to R-ketorolac CL, and S/R-ketorolac CL ratio is higher following delivery compared to postpartum period or to healthy female volunteers.

Education science and biological anthropology.

Science.gov (United States)

Krebs, Uwe

2014-01-01

This contribution states deficits and makes proposals in order to overcome them. First there is the question as to why the Biological Anthropology--despite all its diversifications--hardly ever deals with educational aspects of its subject. Second it is the question as to why Educational Science neglects or even ignores data of Biological Anthropology which are recognizably important for its subject. It is postulated that the stated deficits are caused by several adverse influences such as, the individual identity of each of the involved single sciences; aspects of the recent history of the German Anthropology; a lack of conceptual understanding of each other; methodological differences and, last but not least, the structure of the universities. The necessity to remedy this situation was deduced from two groups of facts. First, more recent data of the Biological Anthropology (e.g. brain functions and learning, sex specificity and education) are of substantial relevance for the Educational Science. Second, the epistemological requirements of complex subjects like education need interdisciplinary approaches. Finally, a few suggestions of concrete topics are given which are related to both, Educational Science and Biological Anthropology.

The normal limits, subclinical significance, related metabolic derangements and distinct biological effects of body site-specific adiposity in relatively healthy population.

Directory of Open Access Journals (Sweden)

Chun-Ho Yun

Full Text Available BACKGROUND: The accumulation of visceral adipose tissue that occurs with normal aging is associated with increased cardiovascular risks. However, the clinical significance, biological effects, and related cardiometabolic derangements of body-site specific adiposity in a relatively healthy population have not been well characterized. MATERIALS AND METHODS: In this cross-sectional study, we consecutively enrolled 608 asymptomatic subjects (mean age: 47.3 years, 27% female from 2050 subjects undergoing an annual health survey in Taiwan. We measured pericardial (PCF and thoracic peri-aortic (TAT adipose tissue volumes by 16-slice multi-detector computed tomography (MDCT (Aquarius 3D Workstation, TeraRecon, San Mateo, CA, USA and related these to clinical characteristics, body fat composition (Tanita 305 Corporation, Tokyo, Japan, coronary calcium score (CCS, serum insulin, high-sensitivity C-reactive protein (Hs-CRP level and circulating leukocytes count. Metabolic risk was scored by Adult Treatment Panel III guidelines. RESULTS: TAT, PCF, and total body fat composition all increased with aging and higher metabolic scores (all p<0.05. Only TAT, however, was associated with higher circulating leukocyte counts (ß-coef.:0.24, p<0.05, serum insulin (ß-coef.:0.17, p<0.05 and high sensitivity C-reactive protein (ß-coef.:0.24, p<0.05. These relationships persisted after adjustment in multivariable models (all p<0.05. A TAT volume of 8.29 ml yielded the largest area under the receiver operating characteristic curve (AUROC: 0.79, 95%CI: 0.74-0.83 to identify metabolic syndrome. TAT but not PCF correlated with higher coronary calcium score after adjustment for clinical variables (all p<0.05. CONCLUSION: In our study, we observe that age-related body-site specific accumulation of adipose tissue may have distinct biological effects. Compared to other adiposity measures, peri-aortic adiposity is more tightly associated with cardiometabolic risk profiles and

The Biological and Chemical Oceanography Data Management Office

Science.gov (United States)

Allison, M. D.; Chandler, C. L.; Groman, R. C.; Wiebe, P. H.; Glover, D. M.; Gegg, S. R.

2011-12-01

Oceanography and marine ecosystem research are inherently interdisciplinary fields of study that generate and require access to a wide variety of measurements. In late 2006 the Biological and Chemical Oceanography Sections of the National Science Foundation (NSF) Geosciences Directorate Division of Ocean Sciences (OCE) funded the Biological and Chemical Oceanography Data Management Office (BCO-DMO). In late 2010 additional funding was contributed to support management of research data from the NSF Office of Polar Programs Antarctic Organisms & Ecosystems Program. The BCO-DMO is recognized in the 2011 Division of Ocean Sciences Sample and Data Policy as one of several program specific data offices that support NSF OCE funded researchers. BCO-DMO staff members offer data management support throughout the project life cycle to investigators from large national programs and medium-sized collaborative research projects, as well as researchers from single investigator awards. The office manages and serves all types of oceanographic data and information generated during the research process and contributed by the originating investigators. BCO-DMO has built a data system that includes the legacy data from several large ocean research programs (e.g. United States Joint Global Ocean Flux Study and United States GLOBal Ocean ECosystems Dynamics), to which data have been contributed from recently granted NSF OCE and OPP awards. The BCO-DMO data system can accommodate many different types of data including: in situ and experimental biological, chemical, and physical measurements; modeling results and synthesis data products. The system enables reuse of oceanographic data for new research endeavors, supports synthesis and modeling activities, provides availability of "real data" for K-12 and college level use, and provides decision-support field data for policy-relevant investigations. We will present an overview of the data management system capabilities including: map

Is synthetic biology mechanical biology?

Science.gov (United States)

Holm, Sune

2015-12-01

A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms does not necessarily imply a commitment to mechanical biology. The ideal of applying engineering principles to biology is best understood as expressing recognition of the machine-unlikeness of natural organisms and the limits of human cognition. The paper suggests an interpretation of the identification of organisms with machines in synthetic biology according to which it expresses a strategy for representing, understanding, and constructing living systems that are more machine-like than natural organisms.

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

Directory of Open Access Journals (Sweden)

Ivo D Dinov

2008-05-01

Full Text Available 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

Ecological aspects od electromagnetic irradiation effects of biological objects

International Nuclear Information System (INIS)

Volobuev, A.P.; Donnik, I.M.; Alekseenko, N.N.

2005-01-01

General description of electromagnetic field effects on biological objects depending on its frequency properties is stated in the paper. Basic principles of low frequency field effect (10 -1 -0 2 Hz) are detailed. General and specific regularities of biological objects response to a low frequency field on subcell, cell, and system levels were considered taking into account their functional state. (author)

On the history of biological theories of homosexuality.

Science.gov (United States)

Herrn, R

1995-01-01

Biological theories of homosexuality fit into the discourse on reproduction and sexuality that began in the nineteenth century. They arose in the context of the early homosexual rights movement, with its claim for natural rights, and the psychiatric discussions about sexual perversions. With the classification of homosexuality as a distinct category, homosexuals were excluded from the "normal". Biological theories of homosexuality were attempts not only to explain its causes, but also to maintain the exclusion of homosexuals as the "other". Biological explanations can be categorized as genetic, constitutional, endocrinological, and ethological. On the one hand, biological theories were used in the struggle for homosexual rights. On the other hand, they were used to "cure"e homosexuals. Every theory led to a specific therapy. This paper points out the roots of this thinking, traces the development of various theories, and shows the utilization of biological theories in treating homosexuality.

Biological Control Strategies for Mosquito Vectors of Arboviruses.

Science.gov (United States)

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.

Single cell biology beyond the era of antibodies: relevance, challenges, and promises in biomedical research.

Science.gov (United States)

Abraham, Parvin; Maliekal, Tessy Thomas

2017-04-01

Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems. Even though microfluidics and microraft array are newer techniques exploited for single cell biology, fluorescence-activated cell sorting (FACS) remains the gold standard technique for isolation of cells for many biomedical applications, like stem cell therapy. Here, we present a comprehensive and comparative account of some of the probes that are useful in FACS. Further, we illustrate how these techniques could be applied in biomedical research. It is postulated that intracellular molecular markers like nucleostemin (GNL3), alkaline phosphatase (ALPL) and HIRA can be used for improving the outcome of cardiac as well as bone regeneration. Another field that could utilize intracellular markers is diagnostics, and we propose the use of specific peptide nucleic acid probes (PNPs) against certain miRNAs for cancer surgical margin prediction. The newer techniques for single cell biology, based on intracellular molecules, will immensely enhance the repertoire of possible markers for the isolation of cell types useful in biomedical research.

Open-field host specificity test of Gratiana boliviana (Coleoptera: Chrysomelidae), a biological control agent of tropical soda apple (Solanaceae) in the United States

International Nuclear Information System (INIS)

Gandolfo, D.; McKay, F.; Medal, J.C.; Cuda, J.P.

2007-01-01

An open-field experiment was conducted to assess the suitability of the South American leaf feeding beetle Gratiana boliviana Spaeth for biological control of Solanum viarum Dunal in the USA. An open-field test with eggplant, Solanum melongena L., was conducted on the campus of the University of Buenos Aires, Argentina, and a S. viarum control plot was established 40 km from the campus. One hundred adult beetles were released in each plot at the beginning of the experiment during the vegetative stage of the plants, and forty additional beetles were released in the S. melongena plot at the flowering stage. All the plants in each plot were checked twice a week and the number of adults, immatures, and eggs recorded. Results showed almost a complete rejection of eggplant by G. boliviana. No noticeable feeding damage was ever recorded on eggplant. The experiment was ended when the eggplants started to senesce or were severely damaged by whiteflies and spider mites. The results of this open-field experiment corroborate previous quarantine/laboratory host-specificity tests indicating that a host range expansion of G. boliviana to include eggplant is highly unlikely. Gratiana boliviana was approved for field release in May 2003 in the USA. To date, no non-target effects have been observed either on eggplant or native species of Solanum. (author) [es

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017

Directory of Open Access Journals (Sweden)

Schreiber Falk

2018-03-01

Full Text Available Standards are essential to the advancement of Systems and Synthetic Biology. COMBINE provides a formal body and a centralised platform to help develop and disseminate relevant standards and related resources. The regular special issue of the Journal of Integrative Bioinformatics aims to support the exchange, distribution and archiving of these standards by providing unified, easily citable access. This paper provides an overview of existing COMBINE standards and presents developments of the last year.

Biological mechanisms discriminating growth rate and adult body weight phenotypes in two Chinese indigenous chicken breeds.

Science.gov (United States)

Dou, Tengfei; Zhao, Sumei; Rong, Hua; Gu, Dahai; Li, Qihua; Huang, Ying; Xu, Zhiqiang; Chu, Xiaohui; Tao, Linli; Liu, Lixian; Ge, Changrong; Te Pas, Marinus F W; Jia, Junjing

2017-06-20

Intensive selection has resulted in increased growth rates and muscularity in broiler chickens, in addition to adverse effects, including delayed organ development, sudden death syndrome, and altered metabolic rates. The biological mechanisms underlying selection responses remain largely unknown. Non-artificially-selected indigenous Chinese chicken breeds display a wide variety of phenotypes, including differential growth rate, body weight, and muscularity. The Wuding chicken breed is a fast growing large chicken breed, and the Daweishan mini chicken breed is a slow growing small chicken breed. Together they form an ideal model system to study the biological mechanisms underlying broiler chicken selection responses in a natural system. The objective of this study was to study the biological mechanisms underlying differential phenotypes between the two breeds in muscle and liver tissues, and relate these to the growth rate and body development phenotypes of the two breeds. The muscle tissue in the Wuding breed showed higher expression of muscle development genes than muscle tissue in the Daweishan chicken breed. This expression was accompanied by higher expression of acute inflammatory response genes in Wuding chicken than in Daweishan chicken. The muscle tissue of the Daweishan mini chicken breed showed higher expression of genes involved in several metabolic mechanisms including endoplasmic reticulum, protein and lipid metabolism, energy metabolism, as well as specific immune traits than in the Wuding chicken. The liver tissue showed fewer differences between the two breeds. Genes displaying higher expression in the Wuding breed than in the Daweishan breed were not associated with a specific gene network or biological mechanism. Genes highly expressed in the Daweishan mini chicken breed compared to the Wuding breed were enriched for protein metabolism, ABC receptors, signal transduction, and IL6-related mechanisms. We conclude that faster growth rates and larger

The Biology of Behaviour.

Science.gov (United States)

Broom, D. M.

1981-01-01

Discusses topics to aid in understanding animal behavior, including the value of the biological approach to psychology, functional systems, optimality and fitness, universality of environmental effects on behavior, and evolution of social behavior. (DS)

Including a Service Learning Educational Research Project in a Biology Course-I: Assessing Community Awareness of Childhood Lead Poisoning

Science.gov (United States)

Abu-Shakra, Amal; Saliim, Eric

2012-01-01

A university course project was developed and implemented in a biology course, focusing on environmental problems, to assess community awareness of childhood lead poisoning. A set of 385 questionnaires was generated and distributed in an urban community in North Carolina, USA. The completed questionnaires were sorted first into yes and no sets…

Robustness: confronting lessons from physics and biology.

Science.gov (United States)

Lesne, Annick

2008-11-01

The term robustness is encountered in very different scientific fields, from engineering and control theory to dynamical systems to biology. The main question addressed herein is whether the notion of robustness and its correlates (stability, resilience, self-organisation) developed in physics are relevant to biology, or whether specific extensions and novel frameworks are required to account for the robustness properties of living systems. To clarify this issue, the different meanings covered by this unique term are discussed; it is argued that they crucially depend on the kind of perturbations that a robust system should by definition withstand. Possible mechanisms underlying robust behaviours are examined, either encountered in all natural systems (symmetries, conservation laws, dynamic stability) or specific to biological systems (feedbacks and regulatory networks). Special attention is devoted to the (sometimes counterintuitive) interrelations between robustness and noise. A distinction between dynamic selection and natural selection in the establishment of a robust behaviour is underlined. It is finally argued that nested notions of robustness, relevant to different time scales and different levels of organisation, allow one to reconcile the seemingly contradictory requirements for robustness and adaptability in living systems.

Stable States of Biological Organisms

Science.gov (United States)

Yukalov, V. I.; Sornette, D.; Yukalova, E. P.; Henry, J.-Y.; Cobb, J. P.

2009-04-01

A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole. The organism is modeled by a five-dimensional dynamical system. The organism homeostasis is described by the evolution equations for five interacting components: healthy cells, ill cells, innate immune cells, specific immune cells, and pathogens. The stability analysis demonstrates that, in a wide domain of the parameter space, the system exhibits robust structural stability. There always exist four stable stationary solutions characterizing four qualitatively differing states of the organism: alive state, boundary state, critical state, and dead state.

Piezoelectric microelectromechanical resonant sensors for chemical and biological detection.

Science.gov (United States)

Pang, Wei; Zhao, Hongyuan; Kim, Eun Sok; Zhang, Hao; Yu, Hongyu; Hu, Xiaotang

2012-01-07

Piezoelectric microelectromechanical systems (MEMS) resonant sensors, known for their excellent mass resolution, have been studied for many applications, including DNA hybridization, protein-ligand interactions, and immunosensor development. They have also been explored for detecting antigens, organic gas, toxic ions, and explosives. Most piezoelectric MEMS resonant sensors are acoustic sensors (with specific coating layers) that enable selective and label-free detection of biological events in real time. These label-free technologies have recently garnered significant attention for their sensitive and quantitative multi-parameter analysis of biological systems. Since piezoelectric MEMS resonant sensors do more than transform analyte mass or thickness into an electrical signal (e.g., frequency and impedance), special attention must be paid to their potential beyond microweighing, such as measuring elastic and viscous properties, and several types of sensors currently under development operate at different resonant modes (i.e., thickness extensional mode, thickness shear mode, lateral extensional mode, flexural mode, etc.). In this review, we provide an overview of recent developments in micromachined resonant sensors and activities relating to biochemical interfaces for acoustic sensors.

"Known Unknowns": Current Questions in Muscle Satellite Cell Biology.

Science.gov (United States)

Cornelison, Ddw

2018-01-01

Our understanding of satellite cells, now known to be the obligate stem cells of skeletal muscle, has increased dramatically in recent years due to the introduction of new molecular, genetic, and technical resources. In addition to their role in acute repair of damaged muscle, satellite cells are of interest in the fields of aging, exercise, neuromuscular disease, and stem cell therapy, and all of these applications have driven a dramatic increase in our understanding of the activity and potential of satellite cells. However, many fundamental questions of satellite cell biology remain to be answered, including their emergence as a specific lineage, the degree and significance of heterogeneity within the satellite cell population, the roles of their interactions with other resident and infiltrating cell types during homeostasis and regeneration, and the relative roles of intrinsic vs extrinsic factors that may contribute to satellite cell dysfunction in the context of aging or disease. This review will address the current state of these open questions in satellite cell biology. © 2018 Elsevier Inc. All rights reserved.

Fundamentals of bioinformatics and computational biology methods and exercises in matlab

CERN Document Server

Singh, Gautam B

2015-01-01

This book offers comprehensive coverage of all the core topics of bioinformatics, and includes practical examples completed using the MATLAB bioinformatics toolbox™. It is primarily intended as a textbook for engineering and computer science students attending advanced undergraduate and graduate courses in bioinformatics and computational biology. The book develops bioinformatics concepts from the ground up, starting with an introductory chapter on molecular biology and genetics. This chapter will enable physical science students to fully understand and appreciate the ultimate goals of applying the principles of information technology to challenges in biological data management, sequence analysis, and systems biology. The first part of the book also includes a survey of existing biological databases, tools that have become essential in today’s biotechnology research. The second part of the book covers methodologies for retrieving biological information, including fundamental algorithms for sequence compar...

[Synthetic biology and rearrangements of microbial genetic material].

Science.gov (United States)

Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

2011-10-01

As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.

Fraxinus: A Plant with Versatile Pharmacological and Biological Activities.

Science.gov (United States)

Sarfraz, Iqra; Rasul, Azhar; Jabeen, Farhat; Younis, Tahira; Zahoor, Muhammad Kashif; Arshad, Muhammad; Ali, Muhammad

2017-01-01

Fraxinus , a member of the Oleaceae family, commonly known as ash tree is found in northeast Asia, north America, east and western France, China, northern areas of Pakistan, India, and Afghanistan. Chemical constituents of Fraxinus plant include various secoiridoids, phenylethanoids, flavonoids, coumarins, and lignans; therefore, it is considered as a plant with versatile biological and pharmacological activities. Its tremendous range of pharmacotherapeutic properties has been well documented including anticancer, anti-inflammatory, antioxidant, antimicrobial, and neuroprotective. In addition, its bioactive phytochemicals and secondary metabolites can be effectively used in cosmetic industry and as a competent antiaging agent. Fraxinus presents pharmacological effectiveness by targeting the novel targets in several pathological conditions, which provide a spacious therapeutic time window. Our aim is to update the scientific research community with recent endeavors with specifically highlighting the mechanism of action in different diseases. This potentially efficacious pharmacological drug candidate should be used for new drug discovery in future. This review suggests that this plant has extremely important medicinal utilization but further supporting studies and scientific experimentations are mandatory to determine its specific intracellular targets and site of action to completely figure out its pharmacological applications.