The Integrin Receptor in Biologically Relevant Bilayers

DEFF Research Database (Denmark)

Kalli, Antreas C.; Róg, Tomasz; Vattulainen, Ilpo

2017-01-01

/talin complex was inserted in biologically relevant bilayers that resemble the cell plasma membrane containing zwitterionic and charged phospholipids, cholesterol and sphingolipids to study the dynamics of the integrin receptor and its effect on bilayer structure and dynamics. The results of this study...... demonstrate the dynamic nature of the integrin receptor and suggest that the presence of the integrin receptor alters the lipid organization between the two leaflets of the bilayer. In particular, our results suggest elevated density of cholesterol and of phosphatidylserine lipids around the integrin....../talin complex and a slowing down of lipids in an annulus of ~30 Å around the protein due to interactions between the lipids and the integrin/talin F2–F3 complex. This may in part regulate the interactions of integrins with other related proteins or integrin clustering thus facilitating signal transduction...

Developmental Testing of Liquid and Gaseous/Vaporous Decontamination on Bacterial Spores and Other Biological Warfare Agents on Military Relevant Surfaces

Science.gov (United States)

2016-02-11

Vaporous Decontamination on Bacterial Spores and Other Biological Warfare Agents on Military-Relevant Surfaces 5a. CONTRACT NUMBER 5b. GRANT... DECONTAMINATION ON BACTERIAL SPORES AND OTHER BIOLOGICAL WARFARE AGENTS ON MILITARY-RELEVANT SURFACES Page Paragraph 1. SCOPE...surfaces before and after decontamination . The protocol in this TOP is based on the developed test methodologies from Edgewood Chemical Biological

Beyond arousal and valence: the importance of the biological versus social relevance of emotional stimuli.

Science.gov (United States)

Sakaki, Michiko; Niki, Kazuhisa; Mather, Mara

2012-03-01

The present study addressed the hypothesis that emotional stimuli relevant to survival or reproduction (biologically emotional stimuli) automatically affect cognitive processing (e.g., attention, memory), while those relevant to social life (socially emotional stimuli) require elaborative processing to modulate attention and memory. Results of our behavioral studies showed that (1) biologically emotional images hold attention more strongly than do socially emotional images, (2) memory for biologically emotional images was enhanced even with limited cognitive resources, but (3) memory for socially emotional images was enhanced only when people had sufficient cognitive resources at encoding. Neither images' subjective arousal nor their valence modulated these patterns. A subsequent functional magnetic resonance imaging study revealed that biologically emotional images induced stronger activity in the visual cortex and greater functional connectivity between the amygdala and visual cortex than did socially emotional images. These results suggest that the interconnection between the amygdala and visual cortex supports enhanced attention allocation to biological stimuli. In contrast, socially emotional images evoked greater activity in the medial prefrontal cortex (MPFC) and yielded stronger functional connectivity between the amygdala and MPFC than did biological images. Thus, it appears that emotional processing of social stimuli involves elaborative processing requiring frontal lobe activity.

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.

The clinical implications and biologic relevance of neurofilament expression in gastroenteropancreatic neuroendocrine neoplasms.

Science.gov (United States)

Schimmack, Simon; Lawrence, Ben; Svejda, Bernhard; Alaimo, Daniele; Schmitz-Winnenthal, Hubertus; Fischer, Lars; Büchler, Markus W; Kidd, Mark; Modlin, Irvin

2012-05-15

Although gastroenteropancreatic neuroendocrine neoplasms (GEP-NENs) exhibit widely divergent behavior, limited biologic information (apart from Ki-67) is available to characterize malignancy. Therefore, the identification of alternative biomarkers is a key unmet need. Given the role of internexin alpha (INA) in neuronal development, the authors assessed its function in neuroendocrine cell systems and the clinical implications of its expression as a GEP-NEN biomarker. Functional assays were undertaken to investigate the mechanistic role of INA in the pancreatic BON cell line. Expression levels of INA were investigated in 50 pancreatic NENs (43 primaries, 7 metastases), 43 small intestinal NENs (25 primaries, 18 metastases), normal pancreas (n = 10), small intestinal mucosa (n = 16), normal enterochromaffin (EC) cells (n = 9), mouse xenografts (n = 4) and NEN cell lines (n = 6) using quantitative polymerase chain reaction, Western blot, and immunostaining analyses. In BON cells, decreased levels of INA messenger RNA and protein were associated with the inhibition of both proliferation and mitogen-activated protein kinase (MAPK) signaling. INA was not expressed in normal neuroendocrine cells but was overexpressed (from 2-fold to 42-fold) in NEN cell lines and murine xenografts. In pancreatic NENs, INA was overexpressed compared with pancreatic adenocarcinomas and normal pancreas (27-fold [P = .0001], and 9-fold [P = .02], respectively). INA transcripts were correlated positively with Ki-67 (correlation coefficient [r] = 0.5; P biologic information relevant to delineation of both pancreatic NEN tumor phenotypes and clinical behavior. Copyright © 2011 American Cancer Society.

Role of calibration, validation, and relevance in multi-level uncertainty integration

International Nuclear Information System (INIS)

Li, Chenzhao; Mahadevan, Sankaran

2016-01-01

Calibration of model parameters is an essential step in predicting the response of a complicated system, but the lack of data at the system level makes it impossible to conduct this quantification directly. In such a situation, system model parameters are estimated using tests at lower levels of complexity which share the same model parameters with the system. For such a multi-level problem, this paper proposes a methodology to quantify the uncertainty in the system level prediction by integrating calibration, validation and sensitivity analysis at different levels. The proposed approach considers the validity of the models used for parameter estimation at lower levels, as well as the relevance at the lower level to the prediction at the system level. The model validity is evaluated using a model reliability metric, and models with multivariate output are considered. The relevance is quantified by comparing Sobol indices at the lower level and system level, thus measuring the extent to which a lower level test represents the characteristics of the system so that the calibration results can be reliably used in the system level. Finally the results of calibration, validation and relevance analysis are integrated in a roll-up method to predict the system output. - Highlights: • Relevance analysis to quantify the closeness of two models. • Stochastic model reliability metric to integrate multiple validation experiments. • Extend the model reliability metric to deal with multivariate output. • Roll-up formula to integrate calibration, validation, and relevance.

Arbitrary protein−protein docking targets biologically relevant interfaces

International Nuclear Information System (INIS)

Martin, Juliette; Lavery, Richard

2012-01-01

Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking using PEBP (Phosphatidylethanolamine binding

Arbitrary protein−protein docking targets biologically relevant interfaces

Directory of Open Access Journals (Sweden)

Martin Juliette

2012-05-01

Full Text Available Abstract Background Protein-protein recognition is of fundamental importance in the vast majority of biological processes. However, it has already been demonstrated that it is very hard to distinguish true complexes from false complexes in so-called cross-docking experiments, where binary protein complexes are separated and the isolated proteins are all docked against each other and scored. Does this result, at least in part, reflect a physical reality? False complexes could reflect possible nonspecific or weak associations. Results In this paper, we investigate the twilight zone of protein-protein interactions, building on an interesting outcome of cross-docking experiments: false complexes seem to favor residues from the true interaction site, suggesting that randomly chosen partners dock in a non-random fashion on protein surfaces. Here, we carry out arbitrary docking of a non-redundant data set of 198 proteins, with more than 300 randomly chosen "probe" proteins. We investigate the tendency of arbitrary partners to aggregate at localized regions of the protein surfaces, the shape and compositional bias of the generated interfaces, and the potential of this property to predict biologically relevant binding sites. We show that the non-random localization of arbitrary partners after protein-protein docking is a generic feature of protein structures. The interfaces generated in this way are not systematically planar or curved, but tend to be closer than average to the center of the proteins. These results can be used to predict biological interfaces with an AUC value up to 0.69 alone, and 0.72 when used in combination with evolutionary information. An appropriate choice of random partners and number of docking models make this method computationally practical. It is also noted that nonspecific interfaces can point to alternate interaction sites in the case of proteins with multiple interfaces. We illustrate the usefulness of arbitrary docking

A biologically relevant method for considering patterns of oceanic retention in the Southern Ocean

Science.gov (United States)

Mori, Mao; Corney, Stuart P.; Melbourne-Thomas, Jessica; Klocker, Andreas; Sumner, Michael; Constable, Andrew

2017-12-01

Many marine species have planktonic forms - either during a larval stage or throughout their lifecycle - that move passively or are strongly influenced by ocean currents. Understanding these patterns of movement is important for informing marine ecosystem management and for understanding ecological processes generally. Retention of biological particles in a particular area due to ocean currents has received less attention than transport pathways, particularly for the Southern Ocean. We present a method for modelling retention time, based on the half-life for particles in a particular region, that is relevant for biological processes. This method uses geostrophic velocities at the ocean surface, derived from 23 years of satellite altimetry data (1993-2016), to simulate the advection of passive particles during the Southern Hemisphere summer season (from December to March). We assess spatial patterns in the retention time of passive particles and evaluate the processes affecting these patterns for the Indian sector of the Southern Ocean. Our results indicate that the distribution of retention time is related to bathymetric features and the resulting ocean dynamics. Our analysis also reveals a moderate level of consistency between spatial patterns of retention time and observations of Antarctic krill (Euphausia superba) distribution.

Analyzing the Biology on the System Level

OpenAIRE

Tong, Wei

2016-01-01

Although various genome projects have provided us enormous static sequence information, understanding of the sophisticated biology continues to require integrating the computational modeling, system analysis, technology development for experiments, and quantitative experiments all together to analyze the biology architecture on various levels, which is just the origin of systems biology subject. This review discusses the object, its characteristics, and research attentions in systems biology,...

CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources.

Science.gov (United States)

Bleda, Marta; Tarraga, Joaquin; de Maria, Alejandro; Salavert, Francisco; Garcia-Alonso, Luz; Celma, Matilde; Martin, Ainoha; Dopazo, Joaquin; Medina, Ignacio

2012-07-01

During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is far from being optimal. Some of the most common problems are that the information is spread out in many small databases; frequently there are different standards among repositories and some databases are no longer supported or they contain too specific and unconnected information. In addition, data size is increasingly becoming an obstacle when accessing or storing biological data. All these issues make very difficult to extract and integrate information from different sources, to analyze experiments or to access and query this information in a programmatic way. CellBase provides a solution to the growing necessity of integration by easing the access to biological data. CellBase implements a set of RESTful web services that query a centralized database containing the most relevant biological data sources. The database is hosted in our servers and is regularly updated. CellBase documentation can be found at http://docs.bioinfo.cipf.es/projects/cellbase.

Distinguishing Biologically Relevant Hexoses by Water Adduction to the Lithium-Cationized Molecule.

Science.gov (United States)

Campbell, Matthew T; Chen, Dazhe; Wallbillich, Nicholas J; Glish, Gary L

2017-10-03

A method to distinguish the four most common biologically relevant underivatized hexoses, d-glucose, d-galactose, d-mannose, and d-fructose, using only mass spectrometry with no prior separation/derivatization step has been developed. Electrospray of a solution containing hexose and a lithium salt generates [Hexose+Li] + . The lithium-cationized hexoses adduct water in a quadrupole ion trap. The rate of this water adduction reaction can be used to distinguish the four hexoses. Additionally, for each hexose, multiple lithiation sites are possible, allowing for multiple structures of [Hexose+Li] + . Electrospray produces at least one structure that reacts with water and at least one that does not. The ratio of unreactive lithium-cationized hexose to total lithium-cationized hexose is unique for the four hexoses studied, providing a second method for distinguishing the isomers. Use of the water adduction reaction rate or the unreactive ratio provides two separate methods for confidently (p ≤ 0.02) distinguishing the most common biologically relevant hexoses using only femtomoles of hexose. Additionally, binary mixtures of glucose and fructose were studied. A calibration curve was created by measuring the reaction rate of various samples with different ratios of fructose and glucose. The calibration curve was used to accurately measure the percentage of fructose in three samples of high fructose corn syrup (<4% error).

Radiation biology. Chapter 20

Energy Technology Data Exchange (ETDEWEB)

Wondergem, J. [International Atomic Energy Agency, Vienna (Austria)

2014-09-15

Radiation biology (radiobiology) is the study of the action of ionizing radiations on living matter. This chapter gives an overview of the biological effects of ionizing radiation and discusses the physical, chemical and biological variables that affect dose response at the cellular, tissue and whole body levels at doses and dose rates relevant to diagnostic radiology.

Biology relevant to space radiation

International Nuclear Information System (INIS)

Fry, R.J.M.

1996-01-01

The biological effects of the radiations to which mankind on earth are exposed are becoming known with an increasing degree of detail. This knowledge is the basis of the estimates of risk that, in turn, fosters a comprehensive and evolving radiation protection system. The substantial body of information has been, and is being, applied to questions about the biological effects of radiation is space and the associated risk estimates. The purpose of this paper is not to recount all the biological effect of radiation but to concentrate on those that may occur as a result from exposure to the radiations encountered in space. In general, the biological effects of radiation in space are the same as those on earth. However, the evidence that the effects on certain tissues by the heaviest-charged particles can be interpreted on the basis of our knowledge about other high-LET radiation is equivocal. This specific question will be discussed in greater detail later. It is important to point out the that there are only limited data about the effects on humans of two components of the radiations in space, namely protons and heavy ions. Thus predictions of effects on space crews are based on experimental systems exposed on earth at rates and fluences that are higher than those in space and one the effects of gamma or x rays with estimates of the equivalent doses using quality factors

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.

Relevance in the science classroom: A multidimensional analysis

Science.gov (United States)

Hartwell, Matthew F.

While perceived relevance is considered a fundamental component of adaptive learning, the experience of relevance and its conceptual definition have not been well described. The mixed-methods research presented in this dissertation aimed to clarify the conceptual meaning of relevance by focusing on its phenomenological experience from the students' perspective. Following a critical literature review, I propose an identity-based model of perceived relevance that includes three components: a contextual target, an identity target, and a connection type, or lens. An empirical investigation of this model that consisted of two general phases was implemented in four 9th grade-biology classrooms. Participants in Phase 1 (N = 118) completed a series of four open-ended writing activities focused on eliciting perceived personal connections to academic content. Exploratory qualitative content analysis of a 25% random sample of the student responses was used to identify the main meaning-units of the proposed model as well as different dimensions of student relevance perceptions. These meaning-units and dimensions provided the basis for the construction of a conceptual mapping sentence capturing students' perceived relevance, which was then applied in a confirmatory analysis to all other student responses. Participants in Phase 2 (N = 139) completed a closed survey designed based on the mapping sentence to assess their perceived relevance of a biology unit. The survey also included scales assessing other domain-level motivational processes. Exploratory factor analysis and non-metric multidimensional scaling indicated a coherent conceptual structure, which included a primary interpretive relevance dimension. Comparison of the conceptual structure across various groups (randomly-split sample, gender, academic level, domain-general motivational profiles) provided support for its ubiquity and insight into variation in the experience of perceived relevance among students of different

Cellular energy allocation in zebra mussels exposed along a pollution gradient: linking cellular effects to higher levels of biological organization

International Nuclear Information System (INIS)

Smolders, R.; Bervoets, L.; Coen, W. de; Blust, R.

2004-01-01

Organisms exposed to suboptimal environments incur a cost of dealing with stress in terms of metabolic resources. The total amount of energy available for maintenance, growth and reproduction, based on the biochemical analysis of the energy budget, may provide a sensitive measure of stress in an organism. While the concept is clear, linking cellular or biochemical responses to the individual and population or community level remains difficult. The aim of this study was to validate, under field conditions, using cellular energy budgets [i.e. changes in glycogen-, lipid- and protein-content and mitochondrial electron transport system (ETS)] as an ecologically relevant measurement of stress by comparing these responses to physiological and organismal endpoints. Therefore, a 28-day in situ bioassay with zebra mussels (Dreissena polymorpha) was performed in an effluent-dominated stream. Five locations were selected along the pollution gradient and compared with a nearby (reference) site. Cellular Energy Allocation (CEA) served as a biomarker of cellular energetics, while Scope for Growth (SFG) indicated effects on a physiological level and Tissue Condition Index and wet tissue weight/dry tissue weight ratio were used as endpoints of organismal effects. Results indicated that energy budgets at a cellular level of biological organization provided the fastest and most sensitive response and energy budgets are a relevant currency to extrapolate cellular effects to higher levels of biological organization within the exposed mussels. - Exposure of zebra mussels along a pollution gradient has adverse effects on the cellular energy allocation, and results can be linked with higher levels of biological organization

Cellular energy allocation in zebra mussels exposed along a pollution gradient: linking cellular effects to higher levels of biological organization

Energy Technology Data Exchange (ETDEWEB)

Smolders, R.; Bervoets, L.; Coen, W. de; Blust, R

2004-05-01

Organisms exposed to suboptimal environments incur a cost of dealing with stress in terms of metabolic resources. The total amount of energy available for maintenance, growth and reproduction, based on the biochemical analysis of the energy budget, may provide a sensitive measure of stress in an organism. While the concept is clear, linking cellular or biochemical responses to the individual and population or community level remains difficult. The aim of this study was to validate, under field conditions, using cellular energy budgets [i.e. changes in glycogen-, lipid- and protein-content and mitochondrial electron transport system (ETS)] as an ecologically relevant measurement of stress by comparing these responses to physiological and organismal endpoints. Therefore, a 28-day in situ bioassay with zebra mussels (Dreissena polymorpha) was performed in an effluent-dominated stream. Five locations were selected along the pollution gradient and compared with a nearby (reference) site. Cellular Energy Allocation (CEA) served as a biomarker of cellular energetics, while Scope for Growth (SFG) indicated effects on a physiological level and Tissue Condition Index and wet tissue weight/dry tissue weight ratio were used as endpoints of organismal effects. Results indicated that energy budgets at a cellular level of biological organization provided the fastest and most sensitive response and energy budgets are a relevant currency to extrapolate cellular effects to higher levels of biological organization within the exposed mussels. - Exposure of zebra mussels along a pollution gradient has adverse effects on the cellular energy allocation, and results can be linked with higher levels of biological organization.

Structural Biology for A-Level Students

Science.gov (United States)

Philip, Judith

2013-01-01

The relationship between the structure and function of proteins is an important area in biochemistry. Pupils studying A-level Biology are introduced to the four levels of protein structure (primary, secondary, tertiary and quaternary) and how these can be used to describe the progressive folding of a chain of amino acid residues to a final,…

A systems biology approach for pathway level analysis

OpenAIRE

Draghici, Sorin; Khatri, Purvesh; Tarca, Adi Laurentiu; Amin, Kashyap; Done, Arina; Voichita, Calin; Georgescu, Constantin; Romero, Roberto

2007-01-01

A common challenge in the analysis of genomics data is trying to understand the underlying phenomenon in the context of all complex interactions taking place on various signaling pathways. A statistical approach using various models is universally used to identify the most relevant pathways in a given experiment. Here, we show that the existing pathway analysis methods fail to take into consideration important biological aspects and may provide incorrect results in certain situations. By usin...

Physical, chemical, and biological properties of radiocerium relevant to radiation protection guidelines

International Nuclear Information System (INIS)

Anon.

1978-01-01

Present knowledge of the relevant physical, chemical, and biological properties of radiocerium as a basis for establishing radiation protection guidelines is summarized. The first section of the report reviews the chemical and physical properties of radiocerium relative to the biological behavior of internally-deposited cerium and other lanthanides. The second section of the report gives the sources of radiocerium in the environment and the pathways to man. The third section of the report describes the metabolic fate of cerium in several mammalian species as a basis for predicting its metabolic fate in man. The fourth section of the report considers the biomedical effects of radiocerium in light of extensive animal experimentation. The last two sections of the report describe the history of radiation protection guidelines for radiocerium and summarize data required for evaluating the adequacy of current radiation protection guidelines. Each section begins with a summary of the most important findings that follow

Making developmental biology relevant to undergraduates in an era of economic rationalism in Australia.

Science.gov (United States)

Key, Brian; Nurcombe, Victor

2003-01-01

This report describes the road map we followed at our university to accommodate three main factors: financial pressure within the university system; desire to enhance the learning experience of undergraduates; and motivation to increase the prominence of the discipline of developmental biology in our university. We engineered a novel, multi-year undergraduate developmental biology program which was "student-oriented," ensuring that students were continually exposed to the underlying principles and philosophy of this discipline throughout their undergraduate career. Among its key features are introductory lectures in core courses in the first year, which emphasize the relevance of developmental biology to tissue engineering, reproductive medicine, therapeutic approaches in medicine, agriculture and aquaculture. State-of-the-art animated computer graphics and images of high visual impact are also used. In addition, students are streamed into the developmental biology track in the second year, using courses like human embryology and courses shared with cell biology, which include practicals based on modern experimental approaches. Finally, fully dedicated third-year courses in developmental biology are undertaken in conjunction with stand-alone practical courses where students experiencefirst-hand work in a research laboratory. Our philosophy is a "cradle-to-grave" approach to the education of undergraduates so as to prepare highly motivated, enthusiastic and well-educated developmental biologists for entry into graduate programs and ultimately post-doctoral research.

SNAB: A New Advanced Level Biology Course

Science.gov (United States)

Reiss, Michael J.

2005-01-01

Of all the sciences, biology has probably made the most rapid progress in recent years and the need for this to be reflected in a new Advanced Level biology course has long been recognised in the UK. After wide-ranging consultation and successful piloting in over 50 schools and colleges in England and Wales, the new Salters-Nuffield Advanced…

Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS.

Science.gov (United States)

Yu, Hwanjo; Kim, Taehoon; Oh, Jinoh; Ko, Ilhwan; Kim, Sungchul; Han, Wook-Shin

2010-04-16

Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results. Researchers have applied machine learning techniques to find relevant articles by ranking the articles according to the learned relevance function. However, the process of learning and ranking is usually done offline without integrated with the keyword queries, and the users have to provide a large amount of training documents to get a reasonable learning accuracy. This paper proposes a novel multi-level relevance feedback system for PubMed, called RefMed, which supports both ad-hoc keyword queries and a multi-level relevance feedback in real time on PubMed. RefMed supports a multi-level relevance feedback by using the RankSVM as the learning method, and thus it achieves higher accuracy with less feedback. RefMed "tightly" integrates the RankSVM into RDBMS to support both keyword queries and the multi-level relevance feedback in real time; the tight coupling of the RankSVM and DBMS substantially improves the processing time. An efficient parameter selection method for the RankSVM is also proposed, which tunes the RankSVM parameter without performing validation. Thereby, RefMed achieves a high learning accuracy in real time without performing a validation process. RefMed is accessible at http://dm.postech.ac.kr/refmed. RefMed is the first multi-level relevance feedback system for PubMed, which achieves a high accuracy with less feedback. It effectively learns an accurate relevance function from the user's feedback and efficiently processes the function to return relevant articles in real time.

The asymmetric hetero-Diels-Alder reaction in the syntheses of biologically relevant compounds.

Science.gov (United States)

Eschenbrenner-Lux, Vincent; Kumar, Kamal; Waldmann, Herbert

2014-10-13

The hetero-Diels-Alder reaction is one of the most powerful transformations in the chemistry toolbox for the synthesis of aza- and oxa-heterocycles embodying multiple stereogenic centers. However, as compared to other cycloadditions, in particular the dipolar cycloadditions and the Diels-Alder reaction, the hetero-Diels-Alder reaction has been much less explored and exploited in organic synthesis. Nevertheless, this powerful transformation has opened up efficient and creative routes to biologically relevant small molecules and different natural products which contain six-membered oxygen or nitrogen ring systems. Recent developments in this field, in particular in the establishment of enantioselectively catalyzed hetero-Diels-Alder cycloadditions steered by a plethora of different catalysts and the application of the resulting small molecules in chemical biology and medicinal chemistry research, are highlighted in this Minireview. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

'Fish matters': the relevance of fish skin biology to investigative dermatology.

Science.gov (United States)

Rakers, Sebastian; Gebert, Marina; Uppalapati, Sai; Meyer, Wilfried; Maderson, Paul; Sell, Anne F; Kruse, Charli; Paus, Ralf

2010-04-01

Fish skin is a multi-purpose tissue that serves numerous vital functions including chemical and physical protection, sensory activity, behavioural purposes or hormone metabolism. Further, it is an important first-line defense system against pathogens, as fish are continuously exposed to multiple microbial challenges in their aquatic habitat. Fish skin excels in highly developed antimicrobial features, many of which have been preserved throughout evolution, and infection defense principles employed by piscine skin are still operative in human skin. This review argues that it is both rewarding and important for investigative dermatologists to revive their interest in fish skin biology, as it provides insights into numerous fundamental issues that are of major relevance to mammalian skin. The basic molecular insights provided by zebrafish in vivo-genomics for genetic, regeneration and melanoma research, the complex antimicrobial defense systems of fish skin and the molecular controls of melanocyte stem cells are just some of the fascinating examples that illustrate the multiple potential uses of fish skin models in investigative dermatology. We synthesize the essentials of fish skin biology and highlight selected aspects that are of particular comparative interest to basic and clinically applied human skin research.

Key Issues Concerning Biolog Use for Aerobic and Anaerobic Freshwater Bacterial Community-Level Physiological Profiling

Science.gov (United States)

Christian, Bradley W.; Lind, Owen T.

2006-06-01

Bacterial heterotrophy in aquatic ecosystems is important in the overall carbon cycle. Biolog MicroPlates provide information into the metabolic potential of bacteria involved in carbon cycling. Specifically, Biolog EcoPlatesTM were developed with ecologically relevant carbon substrates to allow investigators to measure carbon substrate utilization patterns and develop community-level physiological profiles from natural bacterial assemblages. However, understanding of the functionality of these plates in freshwater research is limited. We explored several issues of EcoPlate use for freshwater bacterial assemblages including inoculum density, incubation temperature, non-bacterial color development, and substrate selectivity. Each of these has various effects on plate interpretation. We offer suggestions and techniques to resolve these interpretation issues. Lastly we propose a technique to allow EcoPlate use in anaerobic freshwater bacterial studies.

Exposure to environmentally-relevant levels of ozone negatively influence pollen and fruit development.

Science.gov (United States)

Gillespie, Colin; Stabler, Daniel; Tallentire, Eva; Goumenaki, Eleni; Barnes, Jeremy

2015-11-01

A combination of in vitro and in vivo studies on tomato (Lycopersicon esculentum Mill. cv. Triton) revealed that environmentally-relevant levels of ozone (O3) pollution adversely affected pollen germination, germ tube growth and pollen-stigma interactions - pollen originating from plants raised in charcoal-Purafil(®) filtered air (CFA) exhibited reduced germ tube development on the stigma of plants exposed to environmentally-relevant levels of O3. The O3-induced decline in in vivo pollen viability was reflected in increased numbers of non-fertilized and fertilized non-viable ovules in immature fruit. Negative effects of O3 on fertilization occurred regardless of the timing of exposure, with reductions in ovule viability evident in O3 × CFA and CFA × O3 crossed plants. This suggests O3-induced reductions in fertilization were associated with reduced pollen viability and/or ovule development. Fruit born on trusses independently exposed to 100 nmol mol(-1) O3 (10 h d(-1)) from flowering exhibited a decline in seed number and this was reflected in a marked decline in the weight and size of individual fruit - a clear demonstration of the direct consequence of the effects of the pollutant on reproductive processes. Ozone exposure also resulted in shifts in the starch and ascorbic acid (Vitamin C) content of fruit that were consistent with accelerated ripening. The findings of this study draw attention to the need for greater consideration of, and possibly the adoption of weightings for the direct impacts of O3, and potentially other gaseous pollutants, on reproductive biology during 'risk assessment' exercises. Copyright © 2015 Elsevier Ltd. All rights reserved.

A theory of biological relativity: no privileged level of causation.

Science.gov (United States)

Noble, Denis

2012-02-06

Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.

Biological effects of environmentally relevant concentrations of the pharmaceutical Triclosan in the marine mussel Perna perna (Linnaeus, 1758)

Energy Technology Data Exchange (ETDEWEB)

Sanzi Cortez, Fernando, E-mail: lecotox@unisanta.br [Instituto de Pesquisas Energeticas e Nucleares IPEN-CNEN/SP, 05508-000 Sao Paulo, SP (Brazil); Laboratorio de Ecotoxicologia, Universidade Santa Cecilia, 11045-907 Santos, SP (Brazil); Dias Seabra Pereira, Camilo [Laboratorio de Ecotoxicologia, Universidade Santa Cecilia, 11045-907 Santos, SP (Brazil); Instituto do Mar, Universidade Federal de Sao Paulo, 11030-400 Santos, SP (Brazil); Ramos Santos, Aldo Ramos [Laboratorio de Ecotoxicologia, Universidade Santa Cecilia, 11045-907 Santos, SP (Brazil); Cesar, Augusto; Choueri, Rodrigo Brasil [Laboratorio de Ecotoxicologia, Universidade Santa Cecilia, 11045-907 Santos, SP (Brazil); Instituto do Mar, Universidade Federal de Sao Paulo, 11030-400 Santos, SP (Brazil); Martini, Gisela de Assis [Laboratorio de Ecotoxicologia, Universidade Santa Cecilia, 11045-907 Santos, SP (Brazil); Bohrer-Morel, Maria Beatriz [Instituto de Pesquisas Energeticas e Nucleares IPEN-CNEN/SP, 05508-000 Sao Paulo, SP (Brazil)

2012-09-15

Triclosan (5-Chloro-2-(2,4-dichlorophenoxy) phenol) is an antibacterial compound widely employed in pharmaceuticals and personal care products. Although this emerging compound has been detected in aquatic environments, scarce information is found on the effects of Triclosan to marine organisms. The aim of this study was to evaluate the toxicity of a concentration range of Triclosan through fertilization assay (reproductive success), embryo-larval development assay (early life stage) and physiological stress (Neutral Red Retention Time assay - NRRT) (adult stage) in the marine sentinel organism Perna perna. The mean inhibition concentrations for fertilization (IC{sub 50} = 0.490 mg L{sup -1}) and embryo-larval development (IC{sub 50} = 0.135 mg L{sup -1}) tests were above environmental relevant concentrations (ng L{sup -1}) given by previous studies. Differently, significant reduction on NRRT results was found at 12 ng L{sup -1}, demonstrating the current risk of the continuous introduction of Triclosan into aquatic environments, and the need of ecotoxicological studies oriented by the mechanism of action of the compound. - Highlights: Black-Right-Pointing-Pointer Triclosan causes biological adverse effects at environmental relevant concentrations. Black-Right-Pointing-Pointer Mechanisms of action oriented assays were more sensitive to detect biological damages. Black-Right-Pointing-Pointer Currently there is environmental risks concerned Triclosan in aquatic ecosystems. - Triclosan causes biological adverse effects at environmentally relevant concentrations.

Biological effects of environmentally relevant concentrations of the pharmaceutical Triclosan in the marine mussel Perna perna (Linnaeus, 1758)

International Nuclear Information System (INIS)

Sanzi Cortez, Fernando; Dias Seabra Pereira, Camilo; Ramos Santos, Aldo Ramos; Cesar, Augusto; Choueri, Rodrigo Brasil; Martini, Gisela de Assis; Bohrer-Morel, Maria Beatriz

2012-01-01

Triclosan (5-Chloro-2-(2,4-dichlorophenoxy) phenol) is an antibacterial compound widely employed in pharmaceuticals and personal care products. Although this emerging compound has been detected in aquatic environments, scarce information is found on the effects of Triclosan to marine organisms. The aim of this study was to evaluate the toxicity of a concentration range of Triclosan through fertilization assay (reproductive success), embryo-larval development assay (early life stage) and physiological stress (Neutral Red Retention Time assay - NRRT) (adult stage) in the marine sentinel organism Perna perna. The mean inhibition concentrations for fertilization (IC 50 = 0.490 mg L −1 ) and embryo-larval development (IC 50 = 0.135 mg L −1 ) tests were above environmental relevant concentrations (ng L −1 ) given by previous studies. Differently, significant reduction on NRRT results was found at 12 ng L −1 , demonstrating the current risk of the continuous introduction of Triclosan into aquatic environments, and the need of ecotoxicological studies oriented by the mechanism of action of the compound. - Highlights: ► Triclosan causes biological adverse effects at environmental relevant concentrations. ► Mechanisms of action oriented assays were more sensitive to detect biological damages. ► Currently there is environmental risks concerned Triclosan in aquatic ecosystems. - Triclosan causes biological adverse effects at environmentally relevant concentrations.

Quantum Biology at the Cellular Level - elements of the research program

OpenAIRE

Bordonaro, Michael; Ogryzko, Vasily

2013-01-01

Quantum Biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (Quantum Biology at Cellular Level), a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. Key words. decoherence, macroscopic superpositions, basis-dependence, formal superposition, non-classical correlations,...

Multi-level and hybrid modelling approaches for systems biology.

Science.gov (United States)

Bardini, R; Politano, G; Benso, A; Di Carlo, S

2017-01-01

During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity. Biological systems encompass a wide range of space and time scales, functioning according to flexible hierarchies of mechanisms making an intertwined and dynamic interplay of regulations. This becomes particularly evident in processes such as ontogenesis, where regulative assets change according to process context and timing, making structural phenotype and architectural complexities emerge from a single cell, through local interactions. The information collected from biological systems are naturally organized according to the functional levels composing the system itself. In systems biology, biological information often comes from overlapping but different scientific domains, each one having its own way of representing phenomena under study. That is, the different parts of the system to be modelled may be described with different formalisms. For a model to have improved accuracy and capability for making a good knowledge base, it is good to comprise different system levels, suitably handling the relative formalisms. Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology. This paper reviews some of the main contributions in this field.

Plant Systems Biology at the Single-Cell Level.

Science.gov (United States)

Libault, Marc; Pingault, Lise; Zogli, Prince; Schiefelbein, John

2017-11-01

Our understanding of plant biology is increasingly being built upon studies using 'omics and system biology approaches performed at the level of the entire plant, organ, or tissue. Although these approaches open new avenues to better understand plant biology, they suffer from the cellular complexity of the analyzed sample. Recent methodological advances now allow plant scientists to overcome this limitation and enable biological analyses of single-cells or single-cell-types. Coupled with the development of bioinformatics and functional genomics resources, these studies provide opportunities for high-resolution systems analyses of plant phenomena. In this review, we describe the recent advances, current challenges, and future directions in exploring the biology of single-cells and single-cell-types to enhance our understanding of plant biology as a system. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cellular energy allocation in zebra mussels exposed along a pollution gradient: linking cellular effects to higher levels of biological organization.

Science.gov (United States)

Smolders, R; Bervoets, L; De Coen, W; Blust, R

2004-05-01

Organisms exposed to suboptimal environments incur a cost of dealing with stress in terms of metabolic resources. The total amount of energy available for maintenance, growth and reproduction, based on the biochemical analysis of the energy budget, may provide a sensitive measure of stress in an organism. While the concept is clear, linking cellular or biochemical responses to the individual and population or community level remains difficult. The aim of this study was to validate, under field conditions, using cellular energy budgets [i.e. changes in glycogen-, lipid- and protein-content and mitochondrial electron transport system (ETS)] as an ecologically relevant measurement of stress by comparing these responses to physiological and organismal endpoints. Therefore, a 28-day in situ bioassay with zebra mussels (Dreissena polymorpha) was performed in an effluent-dominated stream. Five locations were selected along the pollution gradient and compared with a nearby (reference) site. Cellular Energy Allocation (CEA) served as a biomarker of cellular energetics, while Scope for Growth (SFG) indicated effects on a physiological level and Tissue Condition Index and wet tissue weight/dry tissue weight ratio were used as endpoints of organismal effects. Results indicated that energy budgets at a cellular level of biological organization provided the fastest and most sensitive response and energy budgets are a relevant currency to extrapolate cellular effects to higher levels of biological organization within the exposed mussels.

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…

Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students†

OpenAIRE

Beach, Dale L.; Alvarez, Consuelo J.

2015-01-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniq...

Physical interactions among plant MADS-box transcription factors and their biological relevance

NARCIS (Netherlands)

Nougalli Tonaco, I.A.

2008-01-01

The biological interpretation of the genome starts from transcription, and many different signaling pathways are integrated at this level. Transcription factors play a central role in the transcription process, because they select the down-stream genes and determine their spatial and temporal

Seven-day human biological rhythms: An expedition in search of their origin, synchronization, functional advantage, adaptive value and clinical relevance.

Science.gov (United States)

Reinberg, Alain E; Dejardin, Laurence; Smolensky, Michael H; Touitou, Yvan

2017-01-01

This fact-finding expedition explores the perspectives and knowledge of the origin and functional relevance of the 7 d domain of the biological time structure, with special reference to human beings. These biological rhythms are displayed at various levels of organization in diverse species - from the unicellular sea algae of Acetabularia and Goniaulax to plants, insects, fish, birds and mammals, including man - under natural as well as artificial, i.e. constant, environmental conditions. Nonetheless, very little is known about their derivation, functional advantage, adaptive value, synchronization and potential clinical relevance. About 7 d cosmic cycles are seemingly too weak, and the 6 d work/1 d rest week commanded from G-d through the Laws of Mosses to the Hebrews is too recent an event to be the origin in humans. Moreover, human and insect studies conducted under controlled constant conditions devoid of environmental, social and other time cues report the persistence of 7 d rhythms, but with a slightly different (free-running) period (τ), indicating their source is endogenous. Yet, a series of human and laboratory rodent studies reveal certain mainly non-cyclic exogenous events can trigger 7 d rhythm-like phenomena. However, it is unknown whether such triggers unmask, amplify and/or synchronize previous non-overtly expressed oscillations. Circadian (~24 h), circa-monthly (~30 d) and circannual (~1 y) rhythms are viewed as genetically based features of life forms that during evolution conferred significant functional advantage to individual organisms and survival value to species. No such advantages are apparent for endogenous 7 d rhythms, raising several questions: What is the significance of the 7 d activity/rest cycle, i.e. week, storied in the Book of Genesis and adopted by the Hebrews and thereafter the residents of nearby Mediterranean countries and ultimately the world? Why do humans require 1 d off per 7 d span? Do 7 d rhythms bestow functional

6,7-dimethoxy-coumarin as a probe of hydration dynamics in biologically relevant systems

Science.gov (United States)

Ghose, Avisek; Amaro, Mariana; Kovaricek, Petr; Hof, Martin; Sykora, Jan

2018-04-01

Coumarin derivatives are well known fluorescence reporters for investigating biological systems due to their strong micro-environment sensitivity. Despite having wide range of environment sensitive fluorescence probes, the potential of 6,7-dimethoxy-coumarin has not been studied extensively so far. With a perspective of its use in protein studies, namely using the unnatural amino acid technology or as a substrate for hydrolase enzymes, we study acetyloxymethyl-6,7-dimethoxycoumarin (Ac-DMC). We investigate the photophysics and hydration dynamics of this dye in aerosol-OT (AOT) reverse micelles at various water contents using the time dependent fluorescence shift (TDFS) method. The TDFS response in AOT reverse micelles from water/surfactant ratio of 0 to 20 confirms its sensitivity towards the hydration and mobility of its microenvironment. Moreover, we show that the fluorophore can be efficiently quenched by halide ions. Hence, we conclude that the 6,7-dimethoxy-methylcoumarin fluorophore is useful for studying hydration parameters in biologically relevant systems.

Biological intrusion of low-level-waste trench covers

International Nuclear Information System (INIS)

Hakonson, T.E.; Gladney, E.S.

1981-01-01

The long-term integrity of low-level waste shallow land burial sites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. Past research on low-level waste shallow land burial methods has emphasized physical (i.e., water infiltration, soil erosion) and chemical (radionuclide leaching) processes that can cause waste site failure and subsequent radionuclide transport. The purpose of this paper is to demonstrate the need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatments. Plants and animals not only can transport radionuclides to the ground surface via root systems and soil excavated from the cover profile by animal burrowing activities, but they modify physical and chemical processes within the cover profile by changing the water infiltration rates, soil erosion rates and chemical composition of the soil. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and soil overburden depth. The rate of biological intrusion through the various barrier materials is being evaluated through the use of activatable stable tracers

Biological intrusion of low-level-waste trench covers

Science.gov (United States)

Hakonson, T. E.; Gladney, E. S.

The long-term integrity of low-level waste shallow land burialsites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. The need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatment is demonstrated. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and sil overburden depth.

Inactivation of the antibacterial and cytotoxic properties of silver ions by biologically relevant compounds.

Directory of Open Access Journals (Sweden)

Geraldine Mulley

Full Text Available There has been a recent surge in the use of silver as an antimicrobial agent in a wide range of domestic and clinical products, intended to prevent or treat bacterial infections and reduce bacterial colonization of surfaces. It has been reported that the antibacterial and cytotoxic properties of silver are affected by the assay conditions, particularly the type of growth media used in vitro. The toxicity of Ag+ to bacterial cells is comparable to that of human cells. We demonstrate that biologically relevant compounds such as glutathione, cysteine and human blood components significantly reduce the toxicity of silver ions to clinically relevant pathogenic bacteria and primary human dermal fibroblasts (skin cells. Bacteria are able to grow normally in the presence of silver nitrate at >20-fold the minimum inhibitory concentration (MIC if Ag+ and thiols are added in a 1:1 ratio because the reaction of Ag+ with extracellular thiols prevents silver ions from interacting with cells. Extracellular thiols and human serum also significantly reduce the antimicrobial activity of silver wound dressings Aquacel-Ag (Convatec and Acticoat (Smith & Nephew to Staphylococcus aureus, Pseudomonas aeruginosa and Escherichia coli in vitro. These results have important implications for the deployment of silver as an antimicrobial agent in environments exposed to biological tissue or secretions. Significant amounts of money and effort have been directed at the development of silver-coated medical devices (e.g. dressings, catheters, implants. We believe our findings are essential for the effective design and testing of antimicrobial silver coatings.

Streptococcus pyogenes biofilms – formation, biology,and clinical relevance

Directory of Open Access Journals (Sweden)

Tomas eFiedler

2015-02-01

Full Text Available Streptococcus pyogenes (group A streptococci, GAS is an exclusive human bacterial pathogen. The virulence potential of this species is tremendous. Interactions with humans range from asymptomatic carriage over mild and superficial infections of skin and mucosal membranes up to systemic purulent toxic-invasive disease manifestations. Particularly the latter are a severe threat for predisposed patients and lead to significant death tolls worldwide. This places GAS among the most important Gram-positive bacterial pathogens. Many recent reviews have highlighted the GAS repertoire of virulence factors, regulators and regulatory circuits/networks that enable GAS to colonize the host and to deal with all levels of the host immune defense. This covers in vitro and in vivo studies, including animal infection studies based on mice and more relevant, macaque monkeys. It is now appreciated that GAS, like many other bacterial species, do not necessarily exclusively live in a planktonic lifestyle. GAS is capable of microcolony and biofilm formation on host cells and tissues. We are now beginning to understand that this feature significantly contributes to GAS pathogenesis. In this review we will discuss the current knowledge on GAS biofilm formation, the biofilm-phenotype associated virulence factors, regulatory aspects of biofilm formation, the clinical relevance, and finally contemporary treatment regimens and future treatment options.

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...

Low level radiation: biological effects

International Nuclear Information System (INIS)

Loken, M.K.

1983-01-01

It is imperative that physicians and scientists using radiations in health care delivery continue to assess the benefits derived, vs. potential risk, to patients and radiation workers being exposed to radiation in its various forms as part of our health delivery system. Insofar as possible we should assure our patients and ourselves that the benefits outweigh the potential hazards involved. Inferences as to the possible biological effects of low level radiation are generally based on extrapolations from those effects observed and measured following acute exposures to considerably higher doses of radiation. Thus, in order to shed light on the question of the possible biological effects of low level radiation, a wide variety of studies have been carried out using cells in culture and various species of plant and animal life. This manuscript makes reference to some of those studies with indications as to how and why the studies were done and the conclusions that might be drawn there from. In addition reference is made to the handling of this information by scientists, by environmentalists, and by the news media. Unfortunately, in many instances the public has been misled by what has been said and/or written. It is hoped that this presentation will provide an understandable and reasonable perspective on the various appropriate uses of radiation in our lives and how such uses do provide significant improvement in our health and in our quality of life

THE LEVEL OF KNOWLEDGE IN THE VALUE RELEVANCE LITERATURE

Directory of Open Access Journals (Sweden)

Mihaela Alina ROBU

2014-12-01

Full Text Available In the last decades, numerous studies have covered the relationship between stock price or stock return and financial information. These studies represent the "value-relevance" literature. Knowledge of this area of interest, through literature and the main ideas, yields scientific progress. The aim of the study is to achieve a qualitative and a quantitative analysis regarding the level of knowledge in the value relevance literature, in an international context. To achieve this aim, a number of 53 scientific articles published between 2001 and 2013 were selected, from the first two journals related to the number of citations in the rankings compiled by Google Scholar, Accounting and Taxation category. Qualitative analysis and quantitative analysis (factorial analysis of multiple correspondences as statistical method were used. The results reflect the importance of existing problems in the financial markets. The studies are focused on solving these problems, to support the investors.

Gregory Bateson's relevance to current molecular biology

DEFF Research Database (Denmark)

Bruni, Luis Emilio

2008-01-01

in a developmental pathway. Being a central figure in the development of cybernetic theory he collaborated with a range of researchers from the life sciences who were innovating their own disciplines by introducing cybernetic concepts in their particular fields and disciplines. In the light of this, it should...... not come as a surprise today to realize how the general ideas that he was postulating for the study of communication systems in biology fit so well with the astonishing findings of current molecular biology, for example in the field of cellular signal transduction networks. I guess this is the case due...

Inter-level relations in computer science, biology, and psychology

NARCIS (Netherlands)

Boogerd, Fred; Bruggeman, Frank; Jonker, Catholijn; Looren de Jong, Huib; Tamminga, Allard; Treur, Jan; Westerhoff, Hans; Wijngaards, Wouter

2002-01-01

Investigations into inter-level relations in computer science, biology and psychology call for an *empirical* turn in the philosophy of mind. Rather than concentrate on *a priori* discussions of inter-level relations between “completed” sciences, a case is made for the actual study of the way

Inter-level relations in computer science, biology, and psychology

NARCIS (Netherlands)

Boogerd, F.; Bruggeman, F.; Jonker, C.M.; Looren de Jong, H.; Tamminga, A.; Treur, J.; Westerhoff, H.V.; Wijngaards, W.C.A.

2002-01-01

Investigations into inter-level relations in computer science, biology and psychology call for an empirical turn in the philosophy of mind. Rather than concentrate on a priori discussions of inter-level relations between 'completed' sciences, a case is made for the actual study of the way

Inter-level relations in computer science, biology and psychology

NARCIS (Netherlands)

Boogerd, F.C.; Bruggeman, F.J.; Jonker, C.M.; Looren De Jong, H.; Tamminga, A.M.; Treur, J.; Westerhoff, H.V.; Wijngaards, W.C.A.

2002-01-01

Investigations into inter-level relations in computer science, biology and psychology call for an empirical turn in the philosophy of mind. Rather than concentrate on a priori discussions of inter-level relations between "completed" sciences, a case is made for the actual study of the way

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Directory of Open Access Journals (Sweden)

Sorokin Anatoly

2015-06-01

Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

A rapid Q-PCR titration protocol for adenovirus and helper-dependent adenovirus vectors that produces biologically relevant results

Science.gov (United States)

Gallaher, Sean D.; Berk, Arnold J.

2013-01-01

Adenoviruses are employed in the study of cellular processes and as expression vectors used in gene therapy. The success and reproducibility of these studies is dependent in part on having accurate and meaningful titers of replication competent and helper-dependent adenovirus stocks, which is problematic due to the use of varied and divergent titration protocols. Physical titration methods, which quantify the total number of viral particles, are used by many, but are poor at estimating activity. Biological titration methods, such as plaque assays, are more biologically relevant, but are time consuming and not applicable to helper-dependent gene therapy vectors. To address this, a protocol was developed called “infectious genome titration” in which viral DNA is isolated from the nuclei of cells ~3 h post-infection, and then quantified by Q-PCR. This approach ensures that only biologically active virions are counted as part of the titer determination. This approach is rapid, robust, sensitive, reproducible, and applicable to all forms of adenovirus. Unlike other Q-PCR-based methods, titers determined by this protocol are well correlated with biological activity. PMID:23624118

Stability of silver nanoparticles: agglomeration and oxidation in biological relevant conditions

Science.gov (United States)

Valenti, Laura E.; Giacomelli, Carla E.

2017-05-01

Silver nanoparticles (Ag-NP) are the most used nanomaterial in consumer products due to the intrinsic antimicrobial capacity of silver. However, Ag-NP may be also harmful to algae, aquatic species, mammalian cells, and higher plants because both Ag+ and nanoparticles are responsible of cell damages. The oxidative dissolution of Ag-NP would proceed to completion under oxic conditions, but the rate and extent of the dissolution depend on several factors. This work correlates the effect of the capping agent (albumin and citrate) with the stability of Ag-NP towards agglomeration in simulated body fluid (SBF) and oxidation in the presence of ROS species (H2O2). Capping provides colloidal stability only through electrostatic means, whereas albumin acts as bulky ligands giving steric and electrostatic repulsion, inhibiting the agglomeration in SBF. However, citrate capping protects Ag-NP from dissolution to a major extent than albumin does because of its reducing power. Moreover, citrate in solution minimizes the oxidation of albumin-coated Ag-NP even after long incubation times. H2O2-induced dissolution proceeds to completion with Ag-NP incubated in SBF, while incubation in citrate leads to an incomplete oxidation. In short, albumin is an excellent capping agent to minimize Ag-NP agglomeration whereas citrate provides a mild-reductive medium that prevents dissolution in biological relevant media as well as in the presence of ROS species. These results provide insight into how the surface properties and media composition affect the release of Ag+ from Ag-NP, related to the cell toxicity and relevant to the storage and lifetime of silver-containing nanomaterials.

Stability of silver nanoparticles: agglomeration and oxidation in biological relevant conditions

Energy Technology Data Exchange (ETDEWEB)

Valenti, Laura E.; Giacomelli, Carla E., E-mail: giacomel@fcq.unc.edu.ar [Universidad Nacional de Córdoba, Ciudad Universitaria, Instituto de Investigaciones en Físico Química de Córdoba (INFIQC) CONICET-UNC, Departamento de Fisicoquímica, Facultad de Ciencias Químicas (Argentina)

2017-05-15

Silver nanoparticles (Ag-NP) are the most used nanomaterial in consumer products due to the intrinsic antimicrobial capacity of silver. However, Ag-NP may be also harmful to algae, aquatic species, mammalian cells, and higher plants because both Ag{sup +} and nanoparticles are responsible of cell damages. The oxidative dissolution of Ag-NP would proceed to completion under oxic conditions, but the rate and extent of the dissolution depend on several factors. This work correlates the effect of the capping agent (albumin and citrate) with the stability of Ag-NP towards agglomeration in simulated body fluid (SBF) and oxidation in the presence of ROS species (H{sub 2}O{sub 2}). Capping provides colloidal stability only through electrostatic means, whereas albumin acts as bulky ligands giving steric and electrostatic repulsion, inhibiting the agglomeration in SBF. However, citrate capping protects Ag-NP from dissolution to a major extent than albumin does because of its reducing power. Moreover, citrate in solution minimizes the oxidation of albumin-coated Ag-NP even after long incubation times. H{sub 2}O{sub 2}-induced dissolution proceeds to completion with Ag-NP incubated in SBF, while incubation in citrate leads to an incomplete oxidation. In short, albumin is an excellent capping agent to minimize Ag-NP agglomeration whereas citrate provides a mild-reductive medium that prevents dissolution in biological relevant media as well as in the presence of ROS species. These results provide insight into how the surface properties and media composition affect the release of Ag{sup +} from Ag-NP, related to the cell toxicity and relevant to the storage and lifetime of silver-containing nanomaterials.

Next-generation mammalian genetics toward organism-level systems biology.

Science.gov (United States)

Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

2017-01-01

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

Entry to medical schools with 'A' level in mathematics rather than biology.

Science.gov (United States)

Spurgin, C B

1975-09-01

The majority of British medical schools now accept for their shortest courses students who have mathematics at A level in place of the former requirement of biology A level. Only a small fraction of the entry, less than one-fifth, enters this way, in spite of statements by most medical schools that they make no distinction between those with mathematics and those with biology when making conditional offers of places. There is no evidence that those without biology are at a disadvantage in the courses. If the prospects of entry without A level biology were better publicized medical schools would have a wider field of possibly abler entrants, and pupils entering sixth forms could defer for a year a choice between a medical (or dental) career and one involving physical science, engineering, or other mathematics-based university education.

Quantum biology at the cellular level--elements of the research program.

Science.gov (United States)

Bordonaro, Michael; Ogryzko, Vasily

2013-04-01

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Interaction of dermatologically relevant nanoparticles with skin cells and skin

Directory of Open Access Journals (Sweden)

Annika Vogt

2014-12-01

Full Text Available The investigation of nanoparticle interactions with tissues is complex. High levels of standardization, ideally testing of different material types in the same biological model, and combinations of sensitive imaging and detection methods are required. Here, we present our studies on nanoparticle interactions with skin, skin cells, and biological media. Silica, titanium dioxide and silver particles were chosen as representative examples for different types of skin exposure to nanomaterials, e.g., unintended environmental exposure (silica versus intended exposure through application of sunscreen (titanium dioxide or antiseptics (silver. Because each particle type exhibits specific physicochemical properties, we were able to apply different combinations of methods to examine skin penetration and cellular uptake, including optical microscopy, electron microscopy, X-ray microscopy on cells and tissue sections, flow cytometry of isolated skin cells as well as Raman microscopy on whole tissue blocks. In order to assess the biological relevance of such findings, cell viability and free radical production were monitored on cells and in whole tissue samples. The combination of technologies and the joint discussion of results enabled us to look at nanoparticle–skin interactions and the biological relevance of our findings from different angles.

Teaching information literacy skills to sophomore-level biology majors.

Science.gov (United States)

Thompson, Leigh; Blankinship, Lisa Ann

2015-05-01

Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university's databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner.

Functionally relevant microorganisms to enhanced biological phosphorus removal performance at full-scale wastewater treatment plants in the United States.

Science.gov (United States)

Gu, April Z; Saunders, A; Neethling, J B; Stensel, H D; Blackall, L L

2008-08-01

The abundance and relevance ofAccumulibacter phosphatis (presumed to be polyphosphate-accumulating organisms [PAOs]), Competibacter phosphatis (presumed to be glycogen-accumulating organisms [GAOs]), and tetrad-forming organisms (TFOs) to phosphorus removal performance at six full-scale enhanced biological phosphorus removal (EBPR) wastewater treatment plants were investigated. Coexistence of various levels of candidate PAOs and GAOs were found at these facilities. Accumulibacter were found to be 5 to 20% of the total bacterial population, and Competibacter were 0 to 20% of the total bacteria population. The TFO abundance varied from nondetectable to dominant. Anaerobic phosphorus (P) release to acetate uptake ratios (P(rel)/HAc(up)) obtained from bench tests were correlated positively with the abundance ratio of Accumulibacter/(Competibacter +TFOs) and negatively with the abundance of (Competibacter +TFOs) for all plants except one, suggesting the relevance of these candidate organisms to EBPR processes. However, effluent phosphorus concentration, amount of phosphorus removed, and process stability in an EBPR system were not directly related to high PAO abundance or mutually exclusive with a high GAO fraction. The plant that had the lowest average effluent phosphorus and highest stability rating had the lowest P(rel)/HAc(up) and the most TFOs. Evaluation of full-scale EBPR performance data indicated that low effluent phosphorus concentration and high process stability are positively correlated with the influent readily biodegradable chemical oxygen demand-to-phosphorus ratio. A system-level carbon-distribution-based conceptual model is proposed for capturing the dynamic competition between PAOs and GAOs and their effect on an EBPR process, and the results from this study seem to support the model hypothesis.

Towards Integration of Biological and Physiological Functions at Multiple Levels

Directory of Open Access Journals (Sweden)

Taishin eNomura

2010-12-01

Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

Levels of biological organization and the origin of novelty.

Science.gov (United States)

Hall, Brian K; Kerney, Ryan

2012-09-01

The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and assess the basis upon which they are regarded as novel. The six are: origin of the turtle shell, transition from fish fins to tetrapod limbs, origination of the neural crest and neural crest cells, cement glands in frogs and casquettes in fish, whale bone-eating tubeworms, and the digestion of plant proteins by nematodes. The article concludes with a discussion of means of acquiring novel genetic information that can account for novelty recognized at higher levels. These are co-options of existing genetic circuitry, gene duplication followed by neofunctionalization, gene rearrangements through mobile genetic elements, and lateral gene transfer. We conclude that on the molecular level only the latter category provides novel genetic information, in that there is no homologous precursor. However, novel phenotypes can be generated through both neofunctionalization and gene rearrangements. Therefore, assigning phenotypic or genotypic "novelty" is contingent on the level of biological organization addressed. Copyright © 2011 Wiley Periodicals, Inc.

Elements determination of clinical relevance in biological tissues Dmdmdx/J dystrophic mice strains investigated by NAA

International Nuclear Information System (INIS)

Metairon, Sabrina

2012-01-01

In this work the determination of chemistry elements in biological tissues (whole blood, bones and organs) of dystrophic mice, used as animal model of Duchenne Muscular Dystrophy (DMD), was performed using analytical nuclear technique. The aim of this work was to determine reference values of elements of clinical (Ca, Cl, K, Mg, Na) and nutritional (Br and S) relevance in whole blood, tibia, quadriceps and hearts from Dmdmdx/J (10 males and 10 females) dystrophic mice and C57BL/6J (10 males) control group mice, using Neutron Activation Analysis technique (NAA). To show in more details the alterations that this disease may cause in these biological tissues, correlations matrixes of the DMD mdx /J mouse strain were generated and compared with C57BL/6J control group. For this study 119 samples of biological tissue were irradiated in the IEA-R1 nuclear reactor at IPEN (Sao Paulo, Brazil). The concentrations of these elements in biological tissues of Dmd mdx /J and C57B/6J mice are the first indicative interval for reference values. Moreover, the alteration in some correlation coefficients data among the elements in the health status and in the diseased status indicates a connection between these elements in whole blood, tibia, quadriceps and heart. These results may help the researchers to evaluate the efficiency of new treatments and to compare the advantages of different treatment approaches before performing tests in patients with muscular dystrophy. (author)

Just the facts? Introductory undergraduate biology courses focus on low-level cognitive skills.

Science.gov (United States)

Momsen, Jennifer L; Long, Tammy M; Wyse, Sara A; Ebert-May, Diane

2010-01-01

Introductory biology courses are widely criticized for overemphasizing details and rote memorization of facts. Data to support such claims, however, are surprisingly scarce. We sought to determine whether this claim was evidence-based. To do so we quantified the cognitive level of learning targeted by faculty in introductory-level biology courses. We used Bloom's Taxonomy of Educational Objectives to assign cognitive learning levels to course goals as articulated on syllabi and individual items on high-stakes assessments (i.e., exams and quizzes). Our investigation revealed the following: 1) assessment items overwhelmingly targeted lower cognitive levels, 2) the cognitive level of articulated course goals was not predictive of the cognitive level of assessment items, and 3) there was no influence of course size or institution type on the cognitive levels of assessments. These results support the claim that introductory biology courses emphasize facts more than higher-order thinking.

Low-level radiation: biological interactions, risks, and benefits. A bibliography

International Nuclear Information System (INIS)

1978-09-01

The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem

Examining portfolio-based assessment in an upper-level biology course

Science.gov (United States)

Ziegler, Brittany Ann

Historically, students have been viewed as empty vessels and passive participants in the learning process but students actually are active forming their own conceptions. One way student learning is impacted is through assessment. Alternative assessment, which contrasts traditional assessment methods, takes into account how students learn by promoting engagement and construction of knowledge This dissertation explores portfolio-based assessment, a method of alternative assessment, which requires students to compose a purposeful collection of work demonstrating their knowledge in an upper-level biology course. The research objectives include characterizing and contributing to the understanding of portfolio-based assessment in higher education, examining reflection and inquiry portfolio components, determining student knowledge of biological concepts, and investigating student integrative thinking through the transformation of reflections into concept webs One main finding includes the majority of reflections categorized as naive or novice in quality. There was no difference in quality of reflections among biological topic. There was a relatively equal amount of high and low cognitive level questions. Students' knowledge of biological concepts significantly increased from the beginning to end of the course. Student written reflections were transformed into concept webs to allow for examination of student integrative thinking. Concepts, relationships, and interconnections in concept webs showed variation but declined by the end of the semester This study is one of the first examining portfolio-based assessment in an upper-level biology course We do not contend that this method of assessment is the only way to promote student learning but portfolio-based assessment may be a tool that can transform science education but currently the role of portfolio-based assessment in science education remains unclear. Additional research needs to be conducted before we will fully

Mathematical Biology Modules Based on Modern Molecular Biology and Modern Discrete Mathematics

Science.gov (United States)

Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network. PMID:20810955

Mathematical biology modules based on modern molecular biology and modern discrete mathematics.

Science.gov (United States)

Robeva, Raina; Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

We describe an ongoing collaborative curriculum materials development project between Sweet Briar College and Western Michigan University, with support from the National Science Foundation. We present a collection of modules under development that can be used in existing mathematics and biology courses, and we address a critical national need to introduce students to mathematical methods beyond the interface of biology with calculus. Based on ongoing research, and designed to use the project-based-learning approach, the modules highlight applications of modern discrete mathematics and algebraic statistics to pressing problems in molecular biology. For the majority of projects, calculus is not a required prerequisite and, due to the modest amount of mathematical background needed for some of the modules, the materials can be used for an early introduction to mathematical modeling. At the same time, most modules are connected with topics in linear and abstract algebra, algebraic geometry, and probability, and they can be used as meaningful applied introductions into the relevant advanced-level mathematics courses. Open-source software is used to facilitate the relevant computations. As a detailed example, we outline a module that focuses on Boolean models of the lac operon network.

Low-level radiation: biological interactions, risks, and benefits. A bibliography

Energy Technology Data Exchange (ETDEWEB)

None

1978-09-01

The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem.

Extracellular membrane vesicles in blood products-biology and clinical relevance

Directory of Open Access Journals (Sweden)

Emilija Krstova Krajnc

2016-01-01

Full Text Available Extracellular membrane vesicles are fragments shed from plasma membranes off all cell types that are undergoing apoptosis or are being subjected to various types of stimulation or stress.  Even in the process of programmed cell death (apoptosis, cell fall apart of varying size vesicles. They expose phosphatidylserine (PS on the outer leaflet of their membrane, and bear surface membrane antigens reflecting their cellular origin. Extracellular membrane vesicles have been isolated from many types of biological fluids, including serum, cerebrospinal fluid, urine, saliva, tears and conditioned culture medium. Flow cytometry is one of the many different methodological approaches that have been used to analyze EMVs. The method attempts to characterize the EMVs cellular origin, size, population, number, and structure. EMVs are present and accumulate in blood products (erythrocytes, platelets as well as in fresh frozen plasma during storage. The aim of this review is to highlight the importance of extracellular vesicles as a cell-to-cell communication system and the role in the pathogenesis of different diseases. Special emphasis will be given to the implication of extracellular membrane vesicles in blood products and their clinical relevance. Although our understanding of the role of  EMVs in disease is far from comprehensive, they display promise as biomarkers for different diseases in the future and also as a marker of quality and safety in the quality control of blood products.

Biological monitors for low levels of ionising radiation

International Nuclear Information System (INIS)

Mohankumar, M.N.; Jeevanram, R.K.

1995-01-01

The biological effects of high doses of ionising radiation are well understood and the methods of measurement of these doses well established. However the effects due to extremely low doses remain by and large uncertain. This is because of the fact that at such low doses no gross symptoms are seen. In fact, at these levels the occurrence of double strand breaks leading to the formation of chromosomal aberrations like dicentrics is rare and chances of mutation due to base damage are negligible. Hence neither chromosomal aberration studies nor mutational assays are useful for detecting doses of the order of a few milligray. Results of exhaustive work done by various laboratories indicate that below 20 mGy the chromosomal aberration technique based on scoring of dicentrics cannot distinguish between a linear or a threshold model. However indirect methods like unscheduled DNA synthesis (UDS) and sister chromatid exchanges (SCEs) appear to be promising for the detection of radiation exposures due to low levels of radiation. This report reviews the available literature on the biological effects of low levels of ionising radiation and highlights the merits and demerits of the various methods employed in the measurement of UDS and SCE. The phenomenon of radio-adaptive response (RAR) and its relation to DNA repair is also discussed. (author)

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Directory of Open Access Journals (Sweden)

Mi Huaiyu

2015-06-01

Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Science.gov (United States)

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

Science.gov (United States)

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest…

Just the Facts? Introductory Undergraduate Biology Courses Focus on Low-Level Cognitive Skills

Science.gov (United States)

Momsen, Jennifer L.; Long, Tammy M.; Wyse, Sara A.; Ebert-May, Diane

2010-01-01

Introductory biology courses are widely criticized for overemphasizing details and rote memorization of facts. Data to support such claims, however, are surprisingly scarce. We sought to determine whether this claim was evidence-based. To do so we quantified the cognitive level of learning targeted by faculty in introductory-level biology courses.…

Dose inhomogeneities at various levels of biological organization

International Nuclear Information System (INIS)

Bond, V.P.

1988-01-01

Dose inhomogeneities in both tumor and normal tissue, inherent to the application of boron neutron capture therapy (BNCT), can be the result not only of ununiform distribution of 10 B at various levels of biological organization, but also of the distribution of the thermal neutrons and of the energy depositions from more energetic neutrons and other radiations comprising the externally-applied beams. The severity of the problems resulting from such inhomogeneities, and approaches to evaluating them, are illustrated by three examples, at the macro, micro and intermediate levels

Biological monitors for low levels of ionising radiation

Energy Technology Data Exchange (ETDEWEB)

Mohankumar, M N; Jeevanram, R K [Safety Research and Health Physics Group, Indira Gandhi Centre for Atomic Research, Kalpakkam (India)

1996-12-31

The biological effects of high doses of ionising radiation are well understood and the methods of measurement of these doses well established. However the effects due to extremely low doses remain by and large uncertain. This is because of the fact that at such low doses no gross symptoms are seen. In fact, at these levels the occurrence of double strand breaks leading to the formation of chromosomal aberrations like dicentrics is rare and chances of mutation due to base damage are negligible. Hence neither chromosomal aberration studies nor mutational assays are useful for detecting doses of the order of a few milligray. Results of exhaustive work done by various laboratories indicate that below 20 mGy the chromosomal aberration technique based on scoring of dicentrics cannot distinguish between a linear or a threshold model. However indirect methods like unscheduled DNA synthesis (UDS) and sister chromatid exchanges (SCEs) appear to be promising for the detection of radiation exposures due to low levels of radiation. This report reviews the available literature on the biological effects of low levels of ionising radiation and highlights the merits and demerits of the various methods employed in the measurement of UDS and SCE. The phenomenon of radio-adaptive response (RAR) and its relation to DNA repair is also discussed. (author). 98 refs., 11 figs., 4 tabs.

Dose addition models based on biologically-relevant reductions in fetal testosterone accurately predict postnatal reproductive tract alterations by a phthalate mixture in rats

Science.gov (United States)

Challenges in cumulative risk assessment of anti-androgenic phthalate mixtures include a lack of data on all the individual phthalates and difficulty determining the biological relevance of reduction in fetal testosterone (T) on postnatal development. The objectives of the curren...

A meta-analysis of the abscopal effect in preclinical models: Is the biologically effective dose a relevant physical trigger?

Directory of Open Access Journals (Sweden)

Raffaella Marconi

Full Text Available Preclinical in vivo studies using small animals are considered crucial in translational cancer research and clinical implementation of novel treatments. This is of paramount relevance in radiobiology, especially for any technological developments permitted to deliver high doses in single or oligo-fractionated regimens, such as stereotactic ablative radiotherapy (SABR. In this context, clinical success in cancer treatment needs to be guaranteed, sparing normal tissue and preventing the potential spread of disease or local recurrence. In this work we introduce a new dose-response relationship based on relevant publications concerning preclinical models with regard to delivered dose, fractionation schedule and occurrence of biological effects on non-irradiated tissue, abscopal effects.We reviewed relevant publications on murine models and the abscopal effect in radiation cancer research following PRISMA methodology. In particular, through a log-likelihood method, we evaluated whether the occurrence of abscopal effects may be related to the biologically effective dose (BED. To this aim, studies accomplished with different tumor histotypes were considered in our analysis including breast, colon, lung, fibrosarcoma, pancreas, melanoma and head and neck cancer. For all the tumors, the α / β ratio was assumed to be 10 Gy, as generally adopted for neoplastic cells.Our results support the hypothesis that the occurrence rate of abscopal effects in preclinical models increases with BED. In particular, the probability of revealing abscopal effects is 50% when a BED of 60 Gy is generated.Our study provides evidence that SABR treatments associated with high BEDs could be considered an effective strategy in triggering the abscopal effect, thus shedding light on the promising outcomes revealed in clinical practice.

Biological/Genetic Regulation of Physical Activity Level: Consensus from GenBioPAC.

Science.gov (United States)

Lightfoot, J Timothy; DE Geus, Eco J C; Booth, Frank W; Bray, Molly S; DEN Hoed, Marcel; Kaprio, Jaakko; Kelly, Scott A; Pomp, Daniel; Saul, Michael C; Thomis, Martine A; Garland, Theodore; Bouchard, Claude

2018-04-01

Physical activity unquestionably maintains and improves health; however, physical activity levels globally are low and not rising despite all the resources devoted to this goal. Attention in both the research literature and the public policy domain has focused on social-behavioral factors; however, a growing body of literature suggests that biological determinants play a significant role in regulating physical activity levels. For instance, physical activity level, measured in various manners, has a genetic component in both humans and nonhuman animal models. This consensus article, developed as a result of an American College of Sports Medicine-sponsored round table, provides a brief review of the theoretical concepts and existing literature that supports a significant role of genetic and other biological factors in the regulation of physical activity. Future research on physical activity regulation should incorporate genetics and other biological determinants of physical activity instead of a sole reliance on social and other environmental determinants.

Computational Modeling of Biological Systems From Molecules to Pathways

CERN Document Server

2012-01-01

Computational modeling is emerging as a powerful new approach for studying and manipulating biological systems. Many diverse methods have been developed to model, visualize, and rationally alter these systems at various length scales, from atomic resolution to the level of cellular pathways. Processes taking place at larger time and length scales, such as molecular evolution, have also greatly benefited from new breeds of computational approaches. Computational Modeling of Biological Systems: From Molecules to Pathways provides an overview of established computational methods for the modeling of biologically and medically relevant systems. It is suitable for researchers and professionals working in the fields of biophysics, computational biology, systems biology, and molecular medicine.

Messina: a novel analysis tool to identify biologically relevant molecules in disease.

Directory of Open Access Journals (Sweden)

Mark Pinese

Full Text Available BACKGROUND: Morphologically similar cancers display heterogeneous patterns of molecular aberrations and follow substantially different clinical courses. This diversity has become the basis for the definition of molecular phenotypes, with significant implications for therapy. Microarray or proteomic expression profiling is conventionally employed to identify disease-associated genes, however, traditional approaches for the analysis of profiling experiments may miss molecular aberrations which define biologically relevant subtypes. METHODOLOGY/PRINCIPAL FINDINGS: Here we present Messina, a method that can identify those genes that only sometimes show aberrant expression in cancer. We demonstrate with simulated data that Messina is highly sensitive and specific when used to identify genes which are aberrantly expressed in only a proportion of cancers, and compare Messina to contemporary analysis techniques. We illustrate Messina by using it to detect the aberrant expression of a gene that may play an important role in pancreatic cancer. CONCLUSIONS/SIGNIFICANCE: Messina allows the detection of genes with profiles typical of markers of molecular subtype, and complements existing methods to assist the identification of such markers. Messina is applicable to any global expression profiling data, and to allow its easy application has been packaged into a freely-available stand-alone software package.

TaBoo SeArch Algorithm with a Modified Inverse Histogram for Reproducing Biologically Relevant Rare Events of Proteins.

Science.gov (United States)

Harada, Ryuhei; Takano, Yu; Shigeta, Yasuteru

2016-05-10

The TaBoo SeArch (TBSA) algorithm [ Harada et al. J. Comput. Chem. 2015 , 36 , 763 - 772 and Harada et al. Chem. Phys. Lett. 2015 , 630 , 68 - 75 ] was recently proposed as an enhanced conformational sampling method for reproducing biologically relevant rare events of a given protein. In TBSA, an inverse histogram of the original distribution, mapped onto a set of reaction coordinates, is constructed from trajectories obtained by multiple short-time molecular dynamics (MD) simulations. Rarely occurring states of a given protein are statistically selected as new initial states based on the inverse histogram, and resampling is performed by restarting the MD simulations from the new initial states to promote the conformational transition. In this process, the definition of the inverse histogram, which characterizes the rarely occurring states, is crucial for the efficiency of TBSA. In this study, we propose a simple modification of the inverse histogram to further accelerate the convergence of TBSA. As demonstrations of the modified TBSA, we applied it to (a) hydrogen bonding rearrangements of Met-enkephalin, (b) large-amplitude domain motions of Glutamine-Binding Protein, and (c) folding processes of the B domain of Staphylococcus aureus Protein A. All demonstrations numerically proved that the modified TBSA reproduced these biologically relevant rare events with nanosecond-order simulation times, although a set of microsecond-order, canonical MD simulations failed to reproduce the rare events, indicating the high efficiency of the modified TBSA.

The pros and cons of ecological risk assessment based on data from different levels of biological organization

Science.gov (United States)

Rohr, Jason R.; Salice, Christopher J.; Nisbet, Roger M.

2016-01-01

Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g. biomarkers), individual, population, community, ecosystem, and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study, and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, we also review mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, we provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing

The pros and cons of ecological risk assessment based on data from different levels of biological organization.

Science.gov (United States)

Rohr, Jason R; Salice, Christopher J; Nisbet, Roger M

2016-10-01

Ecological risk assessment (ERA) is the process used to evaluate the safety of manufactured chemicals to the environment. Here we review the pros and cons of ERA across levels of biological organization, including suborganismal (e.g., biomarkers), individual, population, community, ecosystem and landscapes levels. Our review revealed that level of biological organization is often related negatively with ease at assessing cause-effect relationships, ease of high-throughput screening of large numbers of chemicals (it is especially easier for suborganismal endpoints), and uncertainty of the ERA because low levels of biological organization tend to have a large distance between their measurement (what is quantified) and assessment endpoints (what is to be protected). In contrast, level of biological organization is often related positively with sensitivity to important negative and positive feedbacks and context dependencies within biological systems, and ease at capturing recovery from adverse contaminant effects. Some endpoints did not show obvious trends across levels of biological organization, such as the use of vertebrate animals in chemical testing and ease at screening large numbers of species, and other factors lacked sufficient data across levels of biological organization, such as repeatability, variability, cost per study and cost per species of effects assessment, the latter of which might be a more defensible way to compare costs of ERAs than cost per study. To compensate for weaknesses of ERA at any particular level of biological organization, we also review mathematical modeling approaches commonly used to extrapolate effects across levels of organization. Finally, we provide recommendations for next generation ERA, submitting that if there is an ideal level of biological organization to conduct ERA, it will only emerge if ERA is approached simultaneously from the bottom of biological organization up as well as from the top down, all while employing

The Relevance of Chromosome Aberration Yields for Biological Dosimetry After Low-Level Occupational Irradiation

Energy Technology Data Exchange (ETDEWEB)

Bauchinger, M.; Schmid, E.; Hug, O. [Gesellschaft fuer Strahlenforschung, Institut fuer Biologie, Neuherberg, Federal Republic of Germany (Germany); Strahlenbiologisches Institut der Universitaet Muenchen, Federal Republic of Germany (Germany)

1971-06-15

The usefulness of chromosome analysis for biological dosimetry has been tested in two groups of persons occupationally exposed to radiation: (I) in nurses employed in gynaecological radiology, exposed especially when handling radium inserts; and (II) in nuclear industry workers, all of which were exposed to external gamma irradiation and some of them also to internal radiation after incorporation of various radionuclides. The total dose registered with personal dosimeters ranged in Group 1 from 0.1 to 91.1 rem accumulated over working periods of 0.1 to 13 years, and in Group II from 1.0 to 18.2 rem accumulated over 1 to 9 years. Compared with unexposed controls, both groups exhibit a significant increase of cells with chromosome aberrations as well as larger numbers of breaks per cell. Dicentrics and rings could be observed in some cells, providing good evidence for previous radiation exposure, since these types of aberrations are extremely rare events in unexposed individuals. No correlation between the aberration yields and the film badge values could be demonstrated in Group II. Also, in Group I the fluctuations from individual to individual are rather high. Nevertheless, a positive correlation to the ''dose'' was obtained. Even a sub-group of the nurses that had only been exposed to 20 rem showed significantly more aberrations than control persons. From the results obtained, type and frequency of chromosome aberrations may be considered an indicator of radiation exposure even at the low doses. The reasons for lack of correspondence of chromosome aberration yields and the results of personal monitoring procedures are discussed in detail. (author)

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.

Hologenomics: Systems-Level Host Biology.

Science.gov (United States)

Theis, Kevin R

2018-01-01

The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

Altitude training causes haematological fluctuations with relevance for the Athlete Biological Passport

DEFF Research Database (Denmark)

Bonne, Thomas Christian; Lundby, Carsten; Lundby, Anne Kristine

2015-01-01

The impact of altitude training on haematological parameters and the Athlete Biological Passport (ABP) was evaluated in international-level elite athletes. One group of swimmers lived high and trained high (LHTH, n = 10) for three to four weeks at 2130 m or higher whereas a control group (n = 10......) completed a three-week training camp at sea-level. Haematological parameters were determined weekly three times before and four times after the training camps. ABP thresholds for haemoglobin concentration ([Hb]), reticulocyte percentage (RET%), OFF score and the abnormal blood profile score (ABPS) were...... calculated using the Bayesian model. After altitude training, six swimmers exceeded the 99% ABP thresholds: two swimmers exceeded the OFF score thresholds at day +7; one swimmer exceeded the OFF score threshold at day +28; one swimmer exceeded the threshold for RET% at day +14; and one swimmer surpassed...

Insights into Monascus biology at the genetic level.

Science.gov (United States)

Shao, Yanchun; Lei, Ming; Mao, Zejing; Zhou, Youxiang; Chen, Fusheng

2014-05-01

The genus of Monascus was nominated by van Tieghem in 1884, but its fermented product-red mold rice (RMR), namely red yeast rice, has been used as folk medicines, food colorants, and fermentation starters for more than thousands of years in oriental countries. Nowadays, RMR is widely developed as food supplements around the world due to its functional compounds such as monacolin K (MK, also called lovastatin) and γ-aminobutyric acid. But the usage of RMR also incurs controversy resulting from contamination of citrinin (a kind of mycotoxin) produced by some Monascus strains. In the past decade, it has made great progress to Monascus spp. at the genetic level with the application of molecular biology techniques to restrain the citrinin production and increase the yields of MK and pigment in RMR, as well as aid Monascus classification and phylogenesis. Up to now, hundreds of papers about Monascus molecular biology (MMB) have been published in the international primary journals. However, to our knowledge, there is no MMB review issued until now. In this review, current understanding of Monascus spp. from the view of molecular biology will be covered and insights into research areas that need to be further investigated will also be discussed.

Beta-defensin-2 protein is a serum biomarker for disease activity in psoriasis and reaches biologically relevant concentrations in lesional skin.

Directory of Open Access Journals (Sweden)

Patrick A M Jansen

Full Text Available BACKGROUND: Previous studies have extensively documented antimicrobial and chemotactic activities of beta-defensins. Human beta-defensin-2 (hBD-2 is strongly expressed in lesional psoriatic epidermis, and recently we have shown that high beta-defensin genomic copy number is associated with psoriasis susceptibility. It is not known, however, if biologically and pathophysiologically relevant concentrations of hBD-2 protein are present in vivo, which could support an antimicrobial and proinflammatory role of beta-defensins in lesional psoriatic epidermis. METHODOLOGY/PRINCIPAL FINDINGS: We found that systemic levels of hBD-2 showed a weak but significant correlation with beta defensin copy number in healthy controls but not in psoriasis patients with active disease. In psoriasis patients but not in atopic dermatitis patients, we found high systemic hBD-2 levels that strongly correlated with disease activity as assessed by the PASI score. Our findings suggest that systemic levels in psoriasis are largely determined by secretion from involved skin and not by genomic copy number. Modelling of the in vivo epidermal hBD-2 concentration based on the secretion rate in a reconstructed skin model for psoriatic epidermis provides evidence that epidermal hBD-2 levels in vivo are probably well above the concentrations required for in vitro antimicrobial and chemokine-like effects. CONCLUSIONS/SIGNIFICANCE: Serum hBD-2 appears to be a useful surrogate marker for disease activity in psoriasis. The discrepancy between hBD-2 levels in psoriasis and atopic dermatitis could explain the well known differences in infection rate between these two diseases.

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

Science.gov (United States)

Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

OpenAIRE

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (postte...

Biological ramifications of the subseabed disposal of high-level nuclear waste

International Nuclear Information System (INIS)

Gomez, L.S.; Hessler, R.R.; Jackson, D.W.; Marietta, M.G.; Smith, K.L. Jr.; Talbert, D.M.; Yayanos, A.A.

1980-01-01

The primary goal of the US Subseabed Disposal Program (SDP) is to assess the technical and environmental feasibility of disposing of high-level nuclear waste in deep-sea sediments. The subseabed biology program is charged with assessing possible ecosystem effects of radionuclides as well as possible health effects to man from radionuclides which may be released in the deep sea and transported to the ocean surface. Current biological investigations are attempting to determine benthic community structure; benthic community metabolism; the biology of deep-sea mobile scavengers; the faunal composition of midwater nekton; rates of microbial processes, and the radiation sensitivity of deep-sea organisms. Existing models of the dispersal of radionuclides in the deep sea have not considered many of the possible biological mechanisms which may influence the movement of radionuclides. Therefore, a multi-compartment foodweb model is being developed which considers both biological and physical influences on radionuclide transport. This model will allow parametric studies to be made of the impact on the ocean environment and on man of potential releases of radionuclides

Biological ramifications of the subseabed disposal of high-level nuclear waste

International Nuclear Information System (INIS)

Gomez, L.S.; Hessler, R.R.; Jackson, D.W.; Marietta, M.G.; Smith, K.L. Jr.; Talbert, D.M.; Yayanos, A.A.

1980-05-01

The primary goal of the US Subseabed Disposal Program (SDP) is to assess the technical and environmental feasibility of disposing of high-level nuclear waste in deep-sea sediments. The subseabed biology program is charged with assessing possible ecosystem effects of radionuclides as well as possible health effects to man from radionuclides which may be released in the deep sea and transported to the ocean surface. Current biological investigations are attempting to determine benthic community structure; benthic community metabolism; the biology of deep-sea mobile scavengers; the faunal composition of midwater nekton; rates of microbial processes; and the radiation sensitivity of deep-sea organisms. Existing models of the dispersal of radionuclides in the deep sea have not considered many of the possible biological mechanisms which may influence the movement of radionuclides. Therefore, a multi-compartment foodweb model is being developed which considers both biological and physical influences on radionuclide transport. This model will allow parametric studies to be made of the impact on the ocean environment and on man of potential releases of radionuclides

Monochloramine Cometabolism by Nitrifying Biofilm Relevant ...

Science.gov (United States)

Recently, biological monochloramine removal (i.e., cometabolism) by a pure culture ammonia–oxidizing bacteria, Nitrosomonas europaea, and a nitrifying mixed–culture have been shown to increase monochloramine demand. Although important, these previous suspended culture batch kinetic experiments were not representative of drinking water distribution systems where bacteria grow predominantly as biofilm attached to pipe walls or sediments and physiological differences may exist between suspension and biofilm growth. Therefore, the current research was an important next step in extending the previous results to investigate monochloramine cometabolism by biofilm grown in annular reactors under drinking water relevant conditions. Estimated monochloramine cometabolism kinetics were similar to those of ammonia metabolism, and monochloramine cometabolism was a significant loss mechanism (25–40% of the observed monochloramine loss). These results demonstrated that monochloramine cometabolism occurred in drinking water relevant nitrifying biofilm; thus, cometabolism may be a significant contribution to monochloramine loss during nitrification episodes in distribution systems. Investigate whether or not nitrifying biofilm can biologically transform monochloramine under drinking water relevant conditions.

The impact of an introductory college-level biology class on biology self-efficacy and attitude towards science

Science.gov (United States)

Thomas, Megan Elizabeth

Self-efficacy theory was first introduced in a seminal article by Albert Bandura in 1977 entitled "Self-efficacy: Toward a unifying theory of behavioral change". Since its original introduction, self-efficacy has been a major focus of academic performance, anxiety, career development, and teacher retention research. Self-efficacy can be defined as the belief an individual possesses about their ability to perform a given task. Bandura proposed that self-efficacy should be measured at the highest level of specificity due to the fact that different people are efficacious in different areas. Interested in students' efficacy toward biology, Ebert-May, Baldwin, & Allred (1997) created and validated a survey to measure students' biology self-efficacy. Their survey was modeled after the guidelines for science literacy, and loaded to three sub-factors; methods of biology, generalization to other science courses, and application of the concepts. As self-efficacy theory has been related to effort expenditure and persistence (Bandura, 1977; 1997), one might think it would have some effect on students' attitudes toward the topic at hand. The current research investigated what changes in biology self-efficacy occurred after an introductory biology course with an inquiry based laboratory learning environment. In addition, changes in students' attitudes towards science were explored and how self-efficacy might affect them.

Relevance of plasma malondialdehyde level and severity of portal hypertension in cirrhotic patients.

Science.gov (United States)

Wang, Sheng-Lan; Zhu, Xin-Yan; Zhang, Dong-Wei; Zhang, Zhao-Jie; Gao, Heng-Jun; Yang, Chang-Qing

2015-01-01

Portal hypertension is one of the death reasons for the liver cirrhosis patients. The oxidative stress is related to the occurrence and development of portal hypertension in cirrhosis. Malondialdehyde (MDA), one of the lipid peroxides, increases substantially in cirrhotic patients. To evaluate the relevance between the MDA level and portal hypertension in cirrhotic patients. 60 liver cirrhotic patients and 30 healthy controls were enrolled. The plasma MDA level and general blood tests including ALT, AST, ALB, total bilirubin, and platelet were measured. All people enrolled accepted endoscopic examination and B-Ultrasound check to evaluate the severity of portal hypertension. The MDA plasma level of cirrhotic patients was significantly higher than the controls (Pportal hypertension (Pportal vein (r=0.652, Pportal hypertension. Plasma MDA level may correlate with the severity of portal hypertension in cirrhotic patients.

A dedicated database system for handling multi-level data in systems biology

OpenAIRE

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Background Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging...

Self-Relevance Constructions of Biology Concepts: Meaning-Making and Identity-Formation

Science.gov (United States)

Davidson, Yonaton Sahar

2018-01-01

Recent research supports the benefit of students' construction of relevance through writing about the connection of content to their life. However, most such research defines relevance narrowly as utility value--perceived instrumentality of the content to the student's career goals. Furthermore, the scope of phenomenological and conceptual…

Role of accelerator mass spectrometry in biological dosimetry

International Nuclear Information System (INIS)

Felton, J.S.; Turteltaub, K.W.; Frantz, C.; Vogel, J.S.; Gledhill, B.L.

1992-01-01

Understanding risks from exposures to carcinogens and other chemicals depends upon measurement of their dose to target tissues and their reactivity with critical macromolecules. The authors have used AMS detection of radio-isotopes to assess doses and reactivities at low, environmentally relevant doses. Several biomedical investigations show the effectiveness of quantification of biologically important events at extremely high sensitivity with AMS. Specifically, they have measured the addition of environmental carcinogens such as 2-amino-3,8-dimethylimidazo[4,5-f]-quinoaxaline (MelQx), a chemical found in cooked food, to DNA at concentrations relevant to human exposure. Other low level detection problems in biology, such as immunoassay assessment of small environmental chemicals, is being developed with attomole sensitivity. AMS also aids the assessment of genotoxic risks from chemicals by quantifying the binding of labeled chemicals to DNA. The very toxic and potent carcinogen, tetrachlorodibenzo-p-dioxin (TCDD) was assessed for DNA binding, but no detectable radiocarbon-labeled TCDD was found associated with mouse liver DNA at less than systematically toxic levels. The data indicate that a mutation mechanism does not mediate TCDD carcinogenesis

Computational biology

DEFF Research Database (Denmark)

Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue

2011-01-01

Computation via biological devices has been the subject of close scrutiny since von Neumann’s early work some 60 years ago. In spite of the many relevant works in this field, the notion of programming biological devices seems to be, at best, ill-defined. While many devices are claimed or proved t...

Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology.

Energy Technology Data Exchange (ETDEWEB)

Davidson, George S.; Brown, William Michael

2007-09-01

Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

Continuum analysis of biological systems conserved quantities, fluxes and forces

CERN Document Server

Suraishkumar, G K

2014-01-01

This book addresses the analysis, in the continuum regime, of biological systems at various scales, from the cellular level to the industrial one. It presents both fundamental conservation principles (mass, charge, momentum and energy) and relevant fluxes resulting from appropriate driving forces, which are important for the analysis, design and operation of biological systems. It includes the concept of charge conservation, an important principle for biological systems that is not explicitly covered in any other book of this kind. The book is organized in five parts: mass conservation; charge conservation; momentum conservation; energy conservation; and multiple conservations simultaneously applied. All mathematical aspects are presented step by step, allowing any reader with a basic mathematical background (calculus, differential equations, linear algebra, etc.) to follow the text with ease. The book promotes an intuitive understanding of all the relevant principles and in so doing facilitates their applica...

Assessing therapeutic relevance of biologically interesting, ampholytic substances based on their physicochemical and spectral characteristics with chemometric tools

Science.gov (United States)

Judycka, U.; Jagiello, K.; Bober, L.; Błażejowski, J.; Puzyn, T.

2018-06-01

Chemometric tools were applied to investigate the biological behaviour of ampholytic substances in relation to their physicochemical and spectral properties. Results of the Principal Component Analysis suggest that size of molecules and their electronic and spectral characteristics are the key properties required to predict therapeutic relevance of the compounds examined. These properties were used for developing the structure-activity classification model. The classification model allows assessing the therapeutic behaviour of ampholytic substances on the basis of solely values of descriptors that can be obtained computationally. Thus, the prediction is possible without necessity of carrying out time-consuming and expensive laboratory tests, which is its main advantage.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

Science.gov (United States)

Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Dealing with immunogenicity of biologicals: assessment and clinical relevance

NARCIS (Netherlands)

Wolbink, Gerrit J.; Aarden, Lucien A.; Dijkmans, B. A. C.

2009-01-01

PURPOSE OF REVIEW: In the last decade, biologicals revolutionized rheumatology. An increasing number of patients benefit from biotherapeuticals. However, some patients do not respond to treatment and others lose their response after a certain time. Immunogenicity is one of the factors linked to

Chemical and biological attributes of a lowland soil affected by land leveling

Directory of Open Access Journals (Sweden)

José Maria Barbat Parfitt

2013-11-01

Full Text Available The objective of this work was to evaluate the relationship between soil chemical and biological attributes and the magnitude of cuts and fills after the land leveling process of a lowland soil. Soil samples were collected from the 0 - 0.20 m layer, before and after leveling, on a 100 point grid established in the experimental area, to evaluate chemical attributes and soil microbial biomass carbon (MBC. Leveling operations altered the magnitude of soil chemical and biological attributes. Values of Ca, Mg, S, cation exchange capacity, Mn, P, Zn, and soil organic matter (SOM decreased in the soil profile, whereas Al, K, and MBC increased after leveling. Land leveling decreased in 20% SOM average content in the 0 - 0.20 m layer. The great majority of the chemical attributes did not show relations between their values and the magnitude of cuts and fills. The relation was quadratic for SOM, P, and total N, and was linear for K, showing a positive slope and indicating increase in the magnitude of these attributes in cut areas and stability in fill areas. The relationships between these chemical attributes and the magnitude of cuts and fills indicate that the land leveling map may be a useful tool for degraded soil recuperation through amendments and organic fertilizers.

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks.

Science.gov (United States)

Muetze, Tanja; Goenawan, Ivan H; Wiencko, Heather L; Bernal-Llinares, Manuel; Bryan, Kenneth; Lynn, David J

2016-01-01

Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT), which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed) than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest. CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store ( http://apps.cytoscape.org/apps/chat).

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.

Correlation between γ-ray-induced DNA double-strand breakage and cell killing after biologically relevant doses: analysis by pulsed-field gel electrophoresis

International Nuclear Information System (INIS)

Murray, D.

1994-01-01

We examined the degree of correlation between γ-ray-induced lethality and DNA double-strand breaks (dsbs) after biologically relevant doses of radiation. Radiation lethality was modified by treating 14 C-labelled Chinese hamster ovary cells with either of two aminothiols (WR-1065 or WR-255591) and the associated effect on dsb induction was determined by pulsed-field gel electrophoresis (PFGE). The use of phosphorimaging to analyse the distribution of 14 C-activity in the gel greatly improved the low-dose resolution of the PFGE assay. Both WR-1065 and WR-255591 protected against dsb induction and lethality to a similar extent after low doses of radiation. although this correlation broke down when supralethal doses were used to induce dsbs. Thus, the level of dsbs induced in these cells as measured by PFGE after survival-curve doses of γ-radiation is consistently predictive of the degree of lethality obtained, implying a cause-effect relationship between these two parameters and confirming previous results obtained using the neutral filter elution assay for dsbs. (author)

Altitude training causes haematological fluctuations with relevance for the Athlete Biological Passport.

Science.gov (United States)

Bonne, Thomas Christian; Lundby, Carsten; Lundby, Anne Kristine; Sander, Mikael; Bejder, Jacob; Nordsborg, Nikolai Baastrup

2015-08-01

The impact of altitude training on haematological parameters and the Athlete Biological Passport (ABP) was evaluated in international-level elite athletes. One group of swimmers lived high and trained high (LHTH, n = 10) for three to four weeks at 2130 m or higher whereas a control group (n = 10) completed a three-week training camp at sea-level. Haematological parameters were determined weekly three times before and four times after the training camps. ABP thresholds for haemoglobin concentration ([Hb]), reticulocyte percentage (RET%), OFF score and the abnormal blood profile score (ABPS) were calculated using the Bayesian model. After altitude training, six swimmers exceeded the 99% ABP thresholds: two swimmers exceeded the OFF score thresholds at day +7; one swimmer exceeded the OFF score threshold at day +28; one swimmer exceeded the threshold for RET% at day +14; and one swimmer surpassed the ABPS threshold at day +14. In the control group, no values exceeded the individual ABP reference range. In conclusion, LHTH induces haematological changes in Olympic-level elite athletes which can exceed the individually generated references in the ABP. Training at altitude should be considered a confounding factor for ABP interpretation for up to four weeks after altitude exposure but does not consistently cause abnormal values in the ABP. Copyright © 2014 John Wiley & Sons, Ltd.

Student selection: are the school-leaving A-level grades in biology and chemistry important?

Science.gov (United States)

Green, A; Peters, T J; Webster, D J

1993-01-01

This study determined the relationships of grades in A-level biology and chemistry with examination success or failure during the medical course. By inspection of medical student records, A-level grades at entry to medical school and examination performance were obtained for 128 (91%) of the students who sat their final MBBCh examination at the University of Wales College of Medicine in June 1988. The majority, 92 (72%), completed their medical school careers with no professional examination failures; 15 failed examinations just in the period up to 2nd MB; 11 failed examinations in the clinical period only and 10 failed examinations in both periods. Whereas grade achieved in A-level chemistry was not associated with undergraduate examination performance, students with a grade A or B in A-level biology were less likely to have problems than the others (21% compared with 47%; the difference of 26% has a 95% confidence interval of 7% to 44%). Specifically, there appears to be a strong relationship between a low grade in biology and difficulties in the preclinical examinations. Moreover, for those who have difficulties at this stage, this association continues later in the course.

Relevance of PLUREL's results to policies at EU, national, regional and local level

DEFF Research Database (Denmark)

Fertner, Christian; Nielsen, Thomas Alexander Sick

and results to policies and policy development at the EU-level, as well as the national and regional level. PLUREL has peri-urban land use relationships as its main focus. This includes analysis of drivers, consequences, policies and scenarios for the future. Even though PLUREL aims for pan-European coverage...... of natural resources as well as an attractive development in general. Besides these spatial relevant sector policies, the EU enforces legislation which is translated into spatial explicit instruments on sub-regional level. E.g. the Habitat and Birds Directive caused the development of Natura 2000 areas......, an EU-wide network of nature protection areas. The implementation of Trans-European Networks through funding programmes is another sector policy having an impact on land-use change and rural-urban relations. On the sub-regional scale the perception on overall goals like sustainability can be very...

SysBioCube: A Data Warehouse and Integrative Data Analysis Platform Facilitating Systems Biology Studies of Disorders of Military Relevance.

Science.gov (United States)

Chowbina, Sudhir; Hammamieh, Rasha; Kumar, Raina; Chakraborty, Nabarun; Yang, Ruoting; Mudunuri, Uma; Jett, Marti; Palma, Joseph M; Stephens, Robert

2013-01-01

SysBioCube is an integrated data warehouse and analysis platform for experimental data relating to diseases of military relevance developed for the US Army Medical Research and Materiel Command Systems Biology Enterprise (SBE). It brings together, under a single database environment, pathophysio-, psychological, molecular and biochemical data from mouse models of post-traumatic stress disorder and (pre-) clinical data from human PTSD patients.. SysBioCube will organize, centralize and normalize this data and provide an access portal for subsequent analysis to the SBE. It provides new or expanded browsing, querying and visualization to provide better understanding of the systems biology of PTSD, all brought about through the integrated environment. We employ Oracle database technology to store the data using an integrated hierarchical database schema design. The web interface provides researchers with systematic information and option to interrogate the profiles of pan-omics component across different data types, experimental designs and other covariates.

Perspectives on the relevance of the circadian time structure to workplace threshold limit values and employee biological monitoring.

Science.gov (United States)

Smolensky, Michael H; Reinberg, Alain E; Sackett-Lundeen, Linda

2017-01-01

The circadian time structure (CTS) and its disruption by rotating and nightshift schedules relative to work performance, accident risk, and health/wellbeing have long been areas of occupational medicine research. Yet, there has been little exploration of the relevance of the CTS to setting short-term, time-weighted, and ceiling threshold limit values (TLVs); conducting employee biological monitoring (BM); and establishing normative reference biological exposure indices (BEIs). Numerous publications during the past six decades document the CTS substantially affects the disposition - absorption, distribution, metabolism, and elimination - and effects of medications. Additionally, laboratory animal and human studies verify the tolerance to chemical, biological (contagious), and physical agents can differ extensively according to the circadian time of exposure. Because of slow and usually incomplete CTS adjustment by rotating and permanent nightshift workers, occupational chemical and other contaminant encounters occur during a different circadian stage than for dayshift workers. Thus, the intended protection of some TLVs when working the nightshift compared to dayshift might be insufficient, especially in high-risk settings. The CTS is germane to employee BM in that large-amplitude predictable-in-time 24h variation can occur in the concentration of urine, blood, and saliva of monitored chemical contaminants and their metabolites plus biomarkers indicative of adverse xenobiotic exposure. The concept of biological time-qualified (for rhythms) reference values, currently of interest to clinical laboratory pathology practice, is seemingly applicable to industrial medicine as circadian time and workshift-specific BEIs to improve surveillance of night workers, in particular. Furthermore, BM as serial assessments performed frequently both during and off work, exemplified by employee self-measurement of lung function using a small portable peak expiratory flow meter, can

Detection of base damage in DNA in human blood exposed to ionizing radiation at biologically relevant doses

International Nuclear Information System (INIS)

Loon, A.A.W.M. van; Lohman, P.H.M.; Groenendijk, R.H.; Schans, G.P. van der; Baan, R.A.

1991-01-01

The alkaline elution technique for the detection of DNA damage has been adapted to allow application on unlabelled blood cells. Both the induction and subsequent repair have been studied of two classes of DNA damage, viz. single-strand breaks and base damage recognized by the γ-endonuclease activity in a cell-free extract of Micrococcus luteus bacteria. The high sensitivity of the assay permitted the measurement of induction and repair of base damage after in vitro exposure of full blood under aerobic conditions to biologically relevant doses of γ-rays (1.5-4.5 Gy). After a radiation dose of 3 Gy about 50% of the base damage was removed within 1.5 h of repair. Base damage could still be detected at 24h after exposure to 15 Gy. (author)

Action video game players' visual search advantage extends to biologically relevant stimuli.

Science.gov (United States)

Chisholm, Joseph D; Kingstone, Alan

2015-07-01

Research investigating the effects of action video game experience on cognition has demonstrated a host of performance improvements on a variety of basic tasks. Given the prevailing evidence that these benefits result from efficient control of attentional processes, there has been growing interest in using action video games as a general tool to enhance everyday attentional control. However, to date, there is little evidence indicating that the benefits of action video game playing scale up to complex settings with socially meaningful stimuli - one of the fundamental components of our natural environment. The present experiment compared action video game player (AVGP) and non-video game player (NVGP) performance on an oculomotor capture task that presented participants with face stimuli. In addition, the expression of a distractor face was manipulated to assess if action video game experience modulated the effect of emotion. Results indicate that AVGPs experience less oculomotor capture than NVGPs; an effect that was not influenced by the emotional content depicted by distractor faces. It is noteworthy that this AVGP advantage emerged despite participants being unaware that the investigation had to do with video game playing, and participants being equivalent in their motivation and treatment of the task as a game. The results align with the notion that action video game experience is associated with superior attentional and oculomotor control, and provides evidence that these benefits can generalize to more complex and biologically relevant stimuli. Copyright © 2015 Elsevier B.V. All rights reserved.

Synthetic biology, inspired by synthetic chemistry.

Science.gov (United States)

Malinova, V; Nallani, M; Meier, W P; Sinner, E K

2012-07-16

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Omics/systems biology and cancer cachexia.

Science.gov (United States)

Gallagher, Iain J; Jacobi, Carsten; Tardif, Nicolas; Rooyackers, Olav; Fearon, Kenneth

2016-06-01

Cancer cachexia is a complex syndrome generated by interaction between the host and tumour cells with a background of treatment effects and toxicity. The complexity of the physiological pathways likely involved in cancer cachexia necessitates a holistic view of the relevant biology. Emergent properties are characteristic of complex systems with the result that the end result is more than the sum of its parts. Recognition of the importance of emergent properties in biology led to the concept of systems biology wherein a holistic approach is taken to the biology at hand. Systems biology approaches will therefore play an important role in work to uncover key mechanisms with therapeutic potential in cancer cachexia. The 'omics' technologies provide a global view of biological systems. Genomics, transcriptomics, proteomics, lipidomics and metabolomics approaches all have application in the study of cancer cachexia to generate systems level models of the behaviour of this syndrome. The current work reviews recent applications of these technologies to muscle atrophy in general and cancer cachexia in particular with a view to progress towards integration of these approaches to better understand the pathology and potential treatment pathways in cancer cachexia. Copyright © 2016. Published by Elsevier Ltd.

Invited Review Article: Advanced light microscopy for biological space research

Science.gov (United States)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; van Loon, Jack J. W. A.; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Invited Review Article: Advanced light microscopy for biological space research

International Nuclear Information System (INIS)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; Loon, Jack J. W. A. van; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-01-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy

Invited Review Article: Advanced light microscopy for biological space research

Energy Technology Data Exchange (ETDEWEB)

De Vos, Winnok H., E-mail: winnok.devos@uantwerpen.be [Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp (Belgium); Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, Ghent (Belgium); Beghuin, Didier [Lambda-X, Nivelles (Belgium); Schwarz, Christian J. [European Space Agency (ESA), ESTEC, TEC-MMG, Noordwijk (Netherlands); Jones, David B. [Institute for Experimental Orthopaedics and Biomechanics, Philipps University, Marburg (Germany); Loon, Jack J. W. A. van [Department of Oral and Maxillofacial Surgery/Oral Pathology, VU University Medical Center and Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, Amsterdam (Netherlands); Bereiter-Hahn, Juergen; Stelzer, Ernst H. K. [Physical Biology, BMLS (FB15, IZN), Goethe University, Frankfurt am Main (Germany)

2014-10-15

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

The Androgen-Regulated Calcium-Activated Nucleotidase 1 (CANT1) Is Commonly Overexpressed in Prostate Cancer and Is Tumor-Biologically Relevant in Vitro

Science.gov (United States)

Gerhardt, Josefine; Steinbrech, Corinna; Büchi, Oralea; Behnke, Silvia; Bohnert, Annette; Fritzsche, Florian; Liewen, Heike; Stenner, Frank; Wild, Peter; Hermanns, Thomas; Müntener, Michael; Dietel, Manfred; Jung, Klaus; Stephan, Carsten; Kristiansen, Glen

2011-01-01

Previously, we identified the calcium-activated nucleotidase 1 (CANT1) transcript as up-regulated in prostate cancer. Now, we studied CANT1 protein expression in a large cohort of nearly 1000 prostatic tissue samples including normal tissue, prostatic intraepithelial neoplasia (PIN), primary carcinomas, metastases, and castrate-resistant carcinomas, and further investigated its functional relevance. CANT1 displayed predominantly a Golgi-type immunoreactivity with additional and variable cytoplasmic staining. In comparison to normal tissues, the staining intensity was significantly increased in PIN lesions and cancer. In cancer, high CANT1 levels were associated with a better prognosis, and castrate-resistant carcinomas commonly showed lower CANT1 levels than primary carcinomas. The functional role of CANT1 was investigated using RNA interference in two prostate cancer cell lines with abundant endogenous CANT1 protein. On CANT1 knockdown, a significantly diminished cell number and DNA synthesis rate, a cell cycle arrest in G1 phase, and a strong decrease of cell transmigration rate and wound healing capacity of CANT1 knockdown cells was found. However, on forced CANT1 overexpression, cell proliferation and migration remained unchanged. In summary, CANT1 is commonly overexpressed in the vast majority of primary prostate carcinomas and in the precursor lesion PIN and may represent a novel prognostic biomarker. Moreover, this is the first study to demonstrate a functional involvement of CANT1 in tumor biology. PMID:21435463

Clinicopathological variables of sporadic schwannomas of peripheral nerve in 291 patients and expression of biologically relevant markers.

Science.gov (United States)

Young, Eric D; Ingram, Davis; Metcalf-Doetsch, William; Khan, Dilshad; Al Sannaa, Ghadah; Le Loarer, Francois; Lazar, Alexander J F; Slopis, John; Torres, Keila E; Lev, Dina; Pollock, Raphael E; McCutcheon, Ian E

2017-09-08

OBJECTIVE While sporadic peripheral schwannomas (SPSs) are generally well treated with surgery, their biology is not well understood. Consequently, treatment options are limited. The aim of this study was to provide a comprehensive description of SPS. The authors describe clinicopathological features and treatment outcomes of patients harboring these tumors, and they assess expression of biomarkers using a clinically annotated tissue microarray. Together, these data give new insight into the biology and management of SPS. METHODS Patients presenting with a primary SPS between 1993 and 2011 (n = 291) were selected from an institutional registry to construct a clinical database. All patients underwent follow-up, and short- and long-term outcomes were assessed. Expression of relevant biomarkers was assessed using a new tissue microarray (n = 121). RESULTS SPSs were generally large (mean 5.5 cm) and frequently painful at presentation (55%). Most patients were treated with surgery (80%), the majority of whom experienced complete resolution (52%) or improvement (18%) of their symptoms. Tumors that were completely resected (85%) did not recur. Some patients experienced short-term (16%) and long-term (4%) complications postoperatively. Schwannomas expressed higher levels of platelet-derived growth factor receptor-β (2.1) than malignant peripheral nerve sheath tumors (MPNSTs) (1.5, p = 0.004) and neurofibromas (1.33, p = 0.007). Expression of human epidermal growth factor receptor-2 was greater in SPSs (0.91) than in MPNSTs (0.33, p = 0.002) and neurofibromas (0.33, p = 0.026). Epidermal growth factor receptor was expressed in far fewer SPS cells (10%) than in MPNSTs (58%, p SPSs more frequently expressed cytoplasmic survivin (66% of tumor cells) than normal nerve (46% of cells), but SPS expressed nuclear survivin in fewer tumor cells than in MPNSTs (24% and 50%, respectively; p = 0.018). CONCLUSIONS Complete resection is curative for SPS. Left untreated, however, these

Multiweek Cell Culture Project for Use in Upper-Level Biology Laboratories

Science.gov (United States)

Marion, Rebecca E.; Gardner, Grant E.; Parks, Lisa D.

2012-01-01

This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF,…

The Main Biological Hazards in Animal Biosafety Level 2 Facilities and Strategies for Control.

Science.gov (United States)

Li, Xiao Yan; Xue, Kang Ning; Jiang, Jin Sheng; Lu, Xuan Cheng

2016-04-01

Concern about the biological hazards involved in microbiological research, especially research involving laboratory animals, has increased in recent years. Working in an animal biosafety level 2 facility (ABSL-2), commonly used for research on infectious diseases, poses various biological hazards. Here, the regulations and standards related to laboratory biosafety in China are introduced, the potential biological hazards present in ABSL-2 facilities are analyzed, and a series of strategies to control the hazards are presented. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Sex as a Biological Variable: Who, What, When, Why, and How.

Science.gov (United States)

Bale, Tracy L; Epperson, C Neill

2017-01-01

The inclusion of sex as a biological variable in research is absolutely essential for improving our understanding of disease mechanisms contributing to risk and resilience. Studies focusing on examining sex differences have demonstrated across many levels of analyses and stages of brain development and maturation that males and females can differ significantly. This review will discuss examples of animal models and clinical studies to provide guidance and reference for the inclusion of sex as an important biological variable relevant to a Neuropsychopharmacology audience.

Evolutionary medicine: update on the relevance to family practice.

Science.gov (United States)

Naugler, Christopher T

2008-09-01

To review the relevance of evolutionary medicine to family practice and family physician training. Articles were located through a MEDLINE search, using the key words evolution, Darwin, and adaptation. Most references presented level III evidence (expert opinion), while a minority provided level II evidence (epidemiologic studies). Evolutionary medicine deals with the interplay of biology and the environment in the understanding of human disease. Yet medical schools have virtually ignored the need for family physicians to have more than a cursory knowledge of this topic. A review of the main trends in this field most relevant to family practice revealed that a basic knowledge of evolutionary medicine might help in explaining the causation of diseases to patients. Evolutionary medicine has also proven key to explaining the reasons for the development of antibiotic resistance and has the potential to explain cancer pathogenesis. As an organizing principle, this field also has potential in the teaching of family medicine. Evolutionary medicine should be studied further and incorporated into medical training and practice. Its practical utility will be proven through the generation of testable hypotheses and their application in relation to disease causation and possible prevention.

High-temperature Ionization-induced Synthesis of Biologically Relevant Molecules in the Protosolar Nebula

Science.gov (United States)

Bekaert, David V.; Derenne, Sylvie; Tissandier, Laurent; Marrocchi, Yves; Charnoz, Sebastien; Anquetil, Christelle; Marty, Bernard

2018-06-01

Biologically relevant molecules (hereafter biomolecules) have been commonly observed in extraterrestrial samples, but the mechanisms accounting for their synthesis in space are not well understood. While electron-driven production of organic solids from gas mixtures reminiscent of the photosphere of the protosolar nebula (PSN; i.e., dominated by CO–N2–H2) successfully reproduced key specific features of the chondritic insoluble organic matter (e.g., elementary and isotopic signatures of chondritic noble gases), the molecular diversity of organic materials has never been investigated. Here, we report that a large range of biomolecules detected in meteorites and comets can be synthesized under conditions typical of the irradiated gas phase of the PSN at temperatures = 800 K. Our results suggest that organic materials—including biomolecules—produced within the photosphere would have been widely dispersed in the protoplanetary disk through turbulent diffusion, providing a mechanism for the distribution of organic meteoritic precursors prior to any thermal/photoprocessing and subsequent modification by secondary parent body processes. Using a numerical model of dust transport in a turbulent disk, we propose that organic materials produced in the photosphere of the disk would likely be associated with small dust particles, which are coupled to the motion of gas within the disk and therefore preferentially lofted into the upper layers of the disk where organosynthesis occurs.

Biologics in pediatric psoriasis - efficacy and safety.

Science.gov (United States)

Dogra, Sunil; Mahajan, Rahul

2018-01-01

Childhood psoriasis is a special situation that is a management challenge for the treating dermatologist. As is the situation with traditional systemic agents, which are commonly used in managing severe psoriasis in children, the biologics are being increasingly used in the recalcitrant disease despite limited data on long term safety. Areas covered: We performed an extensive literature search to collect evidence-based data on the use of biologics in pediatric psoriasis. The relevant literature published from 2000 to September 2017 was obtained from PubMed, using the MeSH words 'biologics', 'biologic response modifiers' and 'treatment of pediatric/childhood psoriasis'. All clinical trials, randomized double-blind or single-blind controlled trials, open-label studies, retrospective studies, reviews, case reports and letters concerning the use of biologics in pediatric psoriasis were screened. Articles covering the use of biologics in pediatric psoriasis were screened and reference lists in the selected articles were scrutinized to identify other relevant articles that had not been found in the initial search. Articles without relevant information about biologics in general (e.g. its mechanism of action, pharmacokinetics and adverse effects) and its use in psoriasis in particular were excluded. We screened 427 articles and finally selected 41 relevant articles. Expert opinion: The available literature on the use of biologics such as anti-tumor necrosis factor (TNF)-α agents, and anti-IL-12/23 agents like ustekinumab suggests that these are effective and safe in managing severe pediatric psoriasis although there is an urgent need to generate more safety data. Dermatologists must be careful about the potential adverse effects of the biologics before administering them to children with psoriasis. It is likely that with rapidly evolving scenario of biologics in psoriasis, these will prove to be very useful molecules particularly in managing severe and recalcitrant

Biological variability in biomechanical engineering research: Significance and meta-analysis of current modeling practices.

Science.gov (United States)

Cook, Douglas; Julias, Margaret; Nauman, Eric

2014-04-11

Biological systems are characterized by high levels of variability, which can affect the results of biomechanical analyses. As a review of this topic, we first surveyed levels of variation in materials relevant to biomechanics, and compared these values to standard engineered materials. As expected, we found significantly higher levels of variation in biological materials. A meta-analysis was then performed based on thorough reviews of 60 research studies from the field of biomechanics to assess the methods and manner in which biological variation is currently handled in our field. The results of our meta-analysis revealed interesting trends in modeling practices, and suggest a need for more biomechanical studies that fully incorporate biological variation in biomechanical models and analyses. Finally, we provide some case study example of how biological variability may provide valuable insights or lead to surprising results. The purpose of this study is to promote the advancement of biomechanics research by encouraging broader treatment of biological variability in biomechanical modeling. Copyright © 2014 Elsevier Ltd. All rights reserved.

Disclosure Level of CPC 29 Biological Assets: Analysis of Determining Factors in Brazilian companies

Directory of Open Access Journals (Sweden)

Daniel Ramos Nogueira

2017-04-01

Full Text Available The research question guiding this research is "What are the Determining Factors of CPC 29 Disclosure in Brazilian Companies?". In this aspect, the research objective was to evaluate the main factors that affect the disclosure of information related to biological assets. For this, 5 variables highlighted in the literature were selected as evidence influencers. The sample was composed of Brazilian companies with biological assets in the Balance Sheet. From this list, financial statements, explanatory notes, corporate management level and independent auditing company for the 6 years (2010 to 2015 were collected. With the collected information, the dependent variable (Disclosure level of CPC 29 and the independent variables of each year were verified. At the end (after exclusions, 100 observations were analyzed. The results indicated that the variables Size, Representativeness of Biological Assets and Effectiveness of OCPC 07 positively impacted the level of Disclosure. The first two confirmed the predicted hypothesis and OCPC 07 presented a relation that was different from what was expected, showing an increase and not a reduction in the number of disclosures in the years 2014 and 2015.

Statistical approach for selection of biologically informative genes.

Science.gov (United States)

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

2018-05-20

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

Biological relevance of human papillomaviruses in vulvar cancer.

Science.gov (United States)

Halec, Gordana; Alemany, Laia; Quiros, Beatriz; Clavero, Omar; Höfler, Daniela; Alejo, Maria; Quint, Wim; Pawlita, Michael; Bosch, Francesc X; de Sanjose, Silvia

2017-04-01

The carcinogenic role of high-risk human papillomavirus (HR-HPV) types in the increasing subset of vulvar intraepithelial neoplasia and vulvar cancer in young women has been established. However, the actual number of vulvar cancer cases attributed to HPV is still imprecisely defined. In an attempt to provide a more precise definition of HPV-driven vulvar cancer, we performed HPV-type-specific E6*I mRNA analyses available for 20 HR-/possible HR (pHR)-HPV types, on tissue samples from 447 cases of vulvar cancer. HPV DNA genotyping was performed using SPF10-LiPA 25 assay due to its high sensitivity in formalin-fixed paraffin-embedded tissues. Data on p16 INK4a expression was available for comparative analysis via kappa statistics. The use of highly sensitive assays covering the detection of HPV mRNA in a broad spectrum of mucosal HPV types resulted in the detection of viral transcripts in 87% of HPV DNA+ vulvar cancers. Overall concordance between HPV mRNA+ and p16 INK4a upregulation (strong, diffuse immunostaining in >25% of tumor cells) was 92% (K=0.625, 95% confidence interval (CI)=0.531-0.719). Among these cases, 83% were concordant pairs of HPV mRNA+ and p16 INK4a + and 9% were concordant pairs of HPV mRNA- and p16 INK4a -. Our data confirm the biological role of HR-/pHR-HPV types in the great majority of HPV DNA+ vulvar cancers, resulting in an HPV-attributable fraction of at least 21% worldwide. Most HPV DNA+ vulvar cancers were associated with HPV16 (85%), but a causative role for other, less frequently occurring mucosal HPV types (HPV26, 66, 67, 68, 70 and 73) was also confirmed at the mRNA level for the first time. These findings should be taken into consideration for future screening options as HPV-associated vulvar preneoplastic lesions have increased in incidence in younger women and require different treatment than vulvar lesions that develop from rare autoimmune-related mechanisms in older women.

Spatial Modeling Tools for Cell Biology

National Research Council Canada - National Science Library

Przekwas, Andrzej; Friend, Tom; Teixeira, Rodrigo; Chen, Z. J; Wilkerson, Patrick

2006-01-01

.... Scientific potentials and military relevance of computational biology and bioinformatics have inspired DARPA/IPTO's visionary BioSPICE project to develop computational framework and modeling tools for cell biology...

Attempts to develop a new nuclear measurement technique of β-glucuronidase levels in biological samples

International Nuclear Information System (INIS)

Unak, T.; Avcibasi, U.; Yildirim, Y.; Cetinkaya, B.

2003-01-01

β-Glucuronidase is one of the most important hydrolytic enzymes in living systems and plays an essential role in the detoxification pathway of toxic materials incorporated into the metabolism. Some organs, especially liver and some tumour tissues, have high level of β-glucuronidase activity. As a result the enzymatic activity of some kind of tumour cells, the radiolabelled glucuronide conjugates of cytotoxic, as well as radiotoxic compounds have potentially very valuable diagnostic and therapeutic applications in cancer research. For this reason, a sensitive measurement of β-glucuronidase levels in normal and tumour tissues is a very important step for these kinds of applications. According to the classical measurement method of β-glucuronidase activity, in general, the quantity of phenolphthalein liberated from its glucuronide conjugate, i.e. phenolphthalein-glucuronide, by β-glucuronidase has been measured by use of the spectrophotometric technique. The lower detection limit of phenolphthalein by the spectrophotometric technique is about 1-3 mg. This means that the β-glucuronidase levels could not be detected in biological samples having lower levels of β-glucuronidase activity and therefore the applications of the spectrophotometric technique in cancer research are very seriously limited. Starting from this consideration, we recently attempted to develop a new nuclear technique to measure much lower concentrations of β-glucuronidase in biological samples. To improve the detection limit, phenolphthalein-glucuronide and also phenyl-N-glucuronide were radioiodinated with 131 I and their radioactivity was measured by use of the counting technique. Therefore, the quantity of phenolphthalein or aniline radioiodinated with 131 I and liberated by the deglucuronidation reactivity of β-glucuronidase was used in an attempt to measure levels lower than the spectrophotometric measurement technique. The results obtained clearly verified that 0.01 pg level of

Biotechnology by Design: An Introductory Level, Project-Based, Synthetic Biology Laboratory Program for Undergraduate Students.

Science.gov (United States)

Beach, Dale L; Alvarez, Consuelo J

2015-12-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic "parts," students construct a "reporter plasmid" expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a "sensor plasmid," the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses.

Biological, environmental, and social influences on childhood obesity.

Science.gov (United States)

Campbell, M Karen

2016-01-01

The prevalence of childhood obesity has increased globally over the past three decades, with evidence of recent leveling off in developed countries. Reduction in the, currently high, prevalence of obesity will require a full understanding of the biological and social pathways to obesity in order to develop appropriately targeted prevention strategies in early life. Determinants of childhood obesity include individual level factors, including biological, social, and behavioral risks, acting within the influence of the child's family environment, which is, in turn, imbedded in the context of the community environment. These influences act across childhood, with suggestions of early critical periods of biological and behavioral plasticity. There is evidence of sex and gender differences in the responses of boys and girls to their environments. The evidence that determinants of childhood obesity act at many levels and at different stages of childhood is of policy relevance to those planning early health promotion and primary prevention programs as it suggests the need to address the individual, the family, the physical environment, the social environment, and social policy. The purpose of this narrative review is to summarize current, and emerging, literature in a multilevel, life course framework.

Single Molecule Fluorescence: from Physical Fascination to Biological Relevance

OpenAIRE

Segers-Nolten, Gezina M.J.

2003-01-01

Confocal fluorescence microscopy is particularly well-known from the beautiful images that have been obtained with this technique from cells. Several cellular components could be nicely visualized simultaneously by staining them with different fluorophores. Not only for ensemble applications but also in single molecule research confocal fluorescence microscopy became a popular technique. In this thesis the possibilities are shown to study a complicated biological process, which is Nucleotide ...

The Use of Textbooks for Advanced-Level GCE Courses in Physics, Chemistry and Biology by Sixth-Form Students.

Science.gov (United States)

Newton, D. P.

1984-01-01

A survey of sixth-form students to determine the level of A-level textbook use in physics, chemistry, and biology in English schools found that texts are used primarily after the lesson, at the student's discretion, and with great variations between students. Biology texts were used most, and physics texts used least. (MBR)

Growing trend of CE at the omics level: the frontier of systems biology.

Science.gov (United States)

Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

2010-01-01

In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

A dedicated database system for handling multi-level data in systems biology.

Science.gov (United States)

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Clinical relevance of β₂-glycoprotein-I plasma levels in antiphospholipid syndrome (APS).

Science.gov (United States)

Banzato, Alessandra; Pengo, Vittorio

2014-06-01

Antiphospholipid syndrome (APS) is characterized by the presence of antiphospholipid (aPL) antibodies associated with thrombosis or pregnancy morbidity. The antibodies mainly involved in this disorder are directed against β2-glycoprotein I (β2-GPI). β2-GPI plasma level is usually not reported in studies on APS, because it is not regarded as relevant to the diagnosis and prognosis of APS. Nevertheless its measurement may be important for understanding the pathophysiology of the syndrome. This review summarizes available data from the literature on plasma concentrations of β2-GPI in patients with different antibody profiles.

Serum tree IGF-I, total IGF-I, IGFBP-1 and IGFBP-3 levels in an elderly population : relation to age and sex steroid levels

NARCIS (Netherlands)

Janssen, JAMJL; Stolk, RP; Pols, HAP; Grobbee, DE; de Jong, FH; Lamberts, SWJ

BACKGROUND Most previous studies concerning the relationship between IGF-I and age used assays measuring total IGF-I, Although free IGF-I is considered of greater biological relevance, little is known about its relationship with sex steroids levels in elderly healthy subjects, MEASUREMENTS In a

The Generalizability of Students' Interests in Biology Across Gender, Country and Religion

Science.gov (United States)

Hagay, G.; Baram-Tsabari, A.; Ametller, J.; Cakmakci, G.; Lopes, B.; Moreira, A.; Pedrosa-de-Jesus, H.

2013-06-01

In order to bridge the existing gap between biology curricula and students' interests in biology, a strategy for identifying students' interest based on their questions and integrating them into the curriculum was developed. To characterize the level of generalizability of students' science interests over 600 high school students from Portugal, Turkey, England and Israel, who chose biology as an advanced subject, their interest level was ranked in 36 questions that were originally raised by Israeli students. Results indicate that students from four different countries show interest in similar science questions. The most intriguing questions were the ones that dealt with human health and new developments in reproduction and genetics. Religious affiliation had the strongest effect on students' interest level, followed by national affiliation and gender. The findings suggest that students' interest in one context is relevant to the development of interest-based learning materials in a different context. However, despite these similarities, cultural and sociological differences need to be taken into account.

Parabolic equations in biology growth, reaction, movement and diffusion

CERN Document Server

Perthame, Benoît

2015-01-01

This book presents several fundamental questions in mathematical biology such as Turing instability, pattern formation, reaction-diffusion systems, invasion waves and Fokker-Planck equations. These are classical modeling tools for mathematical biology with applications to ecology and population dynamics, the neurosciences, enzymatic reactions, chemotaxis, invasion waves etc. The book presents these aspects from a mathematical perspective, with the aim of identifying those qualitative properties of the models that are relevant for biological applications. To do so, it uncovers the mechanisms at work behind Turing instability, pattern formation and invasion waves. This involves several mathematical tools, such as stability and instability analysis, blow-up in finite time, asymptotic methods and relative entropy properties. Given the content presented, the book is well suited as a textbook for master-level coursework.

Antibiotic resistance shaping multi-level population biology of bacteria.

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Baquero, Fernando; Tedim, Ana P; Coque, Teresa M

2013-01-01

Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level

The Biology of Cancer Health Disparities

Science.gov (United States)

These examples show how biology contributes to health disparities (differences in disease incidence and outcomes among distinct racial and ethnic groups, ), and how biological factors interact with other relevant factors, such as diet and the environment.

Lead levels in some biological samples of auto-mechanics in Abeokuta, Nigeria.

Science.gov (United States)

Babalola, O O; Ojo, L O; Aderemi, M O

2005-12-01

Lead levels were determined in the blood, scalp hair and fingernails of 38, all male auto-mechanics (aged 18-45 years) from Abeokuta, South-western Nigeria. The subjects were classified into four sub-groups based on the period of exposure namely: 1-5, 6-10, 11-15, and >16 years. Thirty-two occupationally unexposed subjects (mainly office workers) served as the control. The weight, height and body mass indexes of all subjects were noted, in addition to other information obtained through structured questionnaire. The mean values of blood lead (BPb), hair lead (HPb) and fingernail lead (NPb) of the occupationally exposed subjects (n=38) were 48.50 +/- 9.08 microg/dL, 17.75 +/- 5.16 microg/g, and 5.92 +/- 3.30 microg/g respectively, while the corresponding mean values for these parameters in the control subjects (n = 32) were 33.(,5 +/- 10.09 microg/dL, 14.30 +/- 5.90 microg/g and 5.31 +/- 2.77 microg/g respectively. The differences in BPb and HPb levels of the two groups were statistically significant (P <0.05 and P <0.01 respectively), while that of NPb was not significant. The levels of lead in the biological samples appeared to have no relationship with the number of years on the job. From these results, it was obvious that the higher levels of lead in the biological samples of test subjects, compared with those of the controls were from environmental sources.

Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks.

Directory of Open Access Journals (Sweden)

Parameswaran Ramachandran

Full Text Available Co-expression networks have long been used as a tool for investigating the molecular circuitry governing biological systems. However, most algorithms for constructing co-expression networks were developed in the microarray era, before high-throughput sequencing-with its unique statistical properties-became the norm for expression measurement. Here we develop Bayesian Relevance Networks, an algorithm that uses Bayesian reasoning about expression levels to account for the differing levels of uncertainty in expression measurements between highly- and lowly-expressed entities, and between samples with different sequencing depths. It combines data from groups of samples (e.g., replicates to estimate group expression levels and confidence ranges. It then computes uncertainty-moderated estimates of cross-group correlations between entities, and uses permutation testing to assess their statistical significance. Using large scale miRNA data from The Cancer Genome Atlas, we show that our Bayesian update of the classical Relevance Networks algorithm provides improved reproducibility in co-expression estimates and lower false discovery rates in the resulting co-expression networks. Software is available at www.perkinslab.ca.

Redox-capacitor to connect electrochemistry to redox-biology.

Science.gov (United States)

Kim, Eunkyoung; Leverage, W Taylor; Liu, Yi; White, Ian M; Bentley, William E; Payne, Gregory F

2014-01-07

It is well-established that redox-reactions are integral to biology for energy harvesting (oxidative phosphorylation), immune defense (oxidative burst) and drug metabolism (phase I reactions), yet there is emerging evidence that redox may play broader roles in biology (e.g., redox signaling). A critical challenge is the need for tools that can probe biologically-relevant redox interactions simply, rapidly and without the need for a comprehensive suite of analytical methods. We propose that electrochemistry may provide such a tool. In this tutorial review, we describe recent studies with a redox-capacitor film that can serve as a bio-electrode interface that can accept, store and donate electrons from mediators commonly used in electrochemistry and also in biology. Specifically, we (i) describe the fabrication of this redox-capacitor from catechols and the polysaccharide chitosan, (ii) discuss the mechanistic basis for electron exchange, (iii) illustrate the properties of this redox-capacitor and its capabilities for promoting redox-communication between biology and electrodes, and (iv) suggest the potential for enlisting signal processing strategies to "extract" redox information. We believe these initial studies indicate broad possibilities for enlisting electrochemistry and signal processing to acquire "systems level" redox information from biology.

Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface.

Science.gov (United States)

Sarkar, Rupa; Ghosh, Manoranjan; Pal, Samir Kumar

2005-02-01

We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.

Long-time data storage: relevant time scales

NARCIS (Netherlands)

Elwenspoek, Michael Curt

2011-01-01

Dynamic processes relevant for long-time storage of information about human kind are discussed, ranging from biological and geological processes to the lifecycle of stars and the expansion of the universe. Major results are that life will end ultimately and the remaining time that the earth is

[THE INCONSISTENCIES OF REGULATION OF METABOLISM IN PHYLOGENESIS AT THREE LEVELS OF "RELATIVE BIOLOGICAL PERFECTION": ETIOLOGY OF METABOLIC PANDEMICS].

Science.gov (United States)

Titov, V N

2015-11-01

The regulation of metabolism in vivo can be comprehended by considering stages of becoming inphylogenesis of humoral, hormonal, vegetative regulators separately: at the level of cells; in paracrin-regulated cenosises of cells; organs and systems under open blood circulation and closed system of blood flow. The levels of regulations formed at different stages of phylogenesis. Their completion occurred at achievement of "relative biological perfection". Only this way need of cells in functional, structural interaction and forming of multicellular developed. The development of organs and systems of organs also completed at the level of "relative biological perfection". From the same level the third stage of becoming of regulation of metabolism at the level of organism started. When three conditions of "relative biological perfection" achieved consequently at level in vivo are considered in species Homo sapiens using system approach it is detected that "relative biological perfection" in vivo is accompanied by different inconsistencies of regulation of metabolism. They are etiologic factors of "metabolic pandemics ". The inconsistencies (etiological factors) are consider as exemplified by local (at the level of paracrin-regulated cenosises of cells) and system (at the level of organism) regulation of biological reaction metabolism-microcirculation that results in dysfunction of target organs and development of pathogenesis of essential metabolic arterial hypertension. The article describes phylogenetic difference between visceral fatty cells and adpocytes, regulation of metabolism by phylogenetically late insulin, reaction of albumin at increasing of content of unesterified fatty acids in blood plasma, difference of function of resident macrophage and monocytes-macrophages in pathogenesis of atherosclerosis, metabolic syndrome, insulin resistance, obesity, under diabetes mellitus and essential metabolic arterial hypertension.

Atypical biological motion kinematics are represented by complementary lower-level and top-down processes during imitation learning.

Science.gov (United States)

Hayes, Spencer J; Dutoy, Chris A; Elliott, Digby; Gowen, Emma; Bennett, Simon J

2016-01-01

Learning a novel movement requires a new set of kinematics to be represented by the sensorimotor system. This is often accomplished through imitation learning where lower-level sensorimotor processes are suggested to represent the biological motion kinematics associated with an observed movement. Top-down factors have the potential to influence this process based on the social context, attention and salience, and the goal of the movement. In order to further examine the potential interaction between lower-level and top-down processes in imitation learning, the aim of this study was to systematically control the mediating effects during an imitation of biological motion protocol. In this protocol, we used non-human agent models that displayed different novel atypical biological motion kinematics, as well as a control model that displayed constant velocity. Importantly the three models had the same movement amplitude and movement time. Also, the motion kinematics were displayed in the presence, or absence, of end-state-targets. Kinematic analyses showed atypical biological motion kinematics were imitated, and that this performance was different from the constant velocity control condition. Although the imitation of atypical biological motion kinematics was not modulated by the end-state-targets, movement time was more accurate in the absence, compared to the presence, of an end-state-target. The fact that end-state targets modulated movement time accuracy, but not biological motion kinematics, indicates imitation learning involves top-down attentional, and lower-level sensorimotor systems, which operate as complementary processes mediated by the environmental context. Copyright © 2015 Elsevier B.V. All rights reserved.

Consistent robustness analysis (CRA) identifies biologically relevant properties of regulatory network models.

Science.gov (United States)

Saithong, Treenut; Painter, Kevin J; Millar, Andrew J

2010-12-16

A number of studies have previously demonstrated that "goodness of fit" is insufficient in reliably classifying the credibility of a biological model. Robustness and/or sensitivity analysis is commonly employed as a secondary method for evaluating the suitability of a particular model. The results of such analyses invariably depend on the particular parameter set tested, yet many parameter values for biological models are uncertain. Here, we propose a novel robustness analysis that aims to determine the "common robustness" of the model with multiple, biologically plausible parameter sets, rather than the local robustness for a particular parameter set. Our method is applied to two published models of the Arabidopsis circadian clock (the one-loop [1] and two-loop [2] models). The results reinforce current findings suggesting the greater reliability of the two-loop model and pinpoint the crucial role of TOC1 in the circadian network. Consistent Robustness Analysis can indicate both the relative plausibility of different models and also the critical components and processes controlling each model.

Possible domestication of uranium oxides using biological assistance reduction

Directory of Open Access Journals (Sweden)

Slah Hidouri

2017-01-01

Full Text Available Uranium has been defined in material research engineering field as one of the most energetic radioactive elements in the entire Mendeleev periodic table. The manipulation of uranium needs higher theories and sophisticated apparatus even in nuclear energy extraction or in many other chemical applications. Above the nuclear exploitation level, the chemical conventional approaches used, require a higher temperature and pressure to control the destination of ionic form. However, it has been discovered later that at biological scale, the manipulation of this actinide is possible under friendly conditions. The review summarizes the relevant properties of uranium element and a brief characterization of nanoparticles, based on some structural techniques. These techniques reveal the common link between chemical approaches and biological assistance in nanoparticles. Also, those biological entities have been able to get it after reduction. Uranium is known for its ability to destroy ductile materials. So, if biological cell can really reduce uranium, then how does it work?

Molecular biology - Part I: Techniques, terminology, and concepts

International Nuclear Information System (INIS)

Brown, J. Martin

1996-01-01

Purpose/Objective: One of the barriers to understanding modern molecular biology is the lack of a clear understanding of the relevant terminology, techniques, and concepts. This refresher course is intended to address these deficiencies starting from a basic level. The lecture will cover many of the common uses of recombinant DNA, including gene cloning and manipulation. The goal is to enable the nonspecialist to increase his or her understanding of molecular biology in order to more fully enjoy reading current publications and/or listening seminars. Radiation biologists trying to understand a little more molecular biology should also benefit. The following concepts will be among those explained and illustrated: restriction endonucleases, gel electrophoresis, gene cloning, use of vectors such as plasmids, bacteriophage, cosmids and viruses, cDNA and genomic libraries, Southern, Northern, and Western blotting, fluorescent in situ hybridization, polymerase chain reaction (PCR), gel retardation, and reporter gene assays

Investigation of some biologically relevant redox reactions using electrochemical mass spectrometry interfaced by desorption electrospray ionization.

Science.gov (United States)

Lu, Mei; Wolff, Chloe; Cui, Weidong; Chen, Hao

2012-04-01

Recently we have shown that, as a versatile ionization technique, desorption electrospray ionization (DESI) can serve as a useful interface to combine electrochemistry (EC) with mass spectrometry (MS). In this study, the EC/DESI-MS method has been further applied to investigate some aqueous phase redox reactions of biological significance, including the reduction of peptide disulfide bonds and nitroaromatics as well as the oxidation of phenothiazines. It was found that knotted/enclosed disulfide bonds in the peptides apamin and endothelin could be electrochemically cleaved. Subsequent tandem MS analysis of the resulting reduced peptide ions using collision-induced dissociation (CID) and electron-capture dissociation (ECD) gave rise to extensive fragment ions, providing a fast protocol for sequencing peptides with complicated disulfide bond linkages. Flunitrazepam and clonazepam, a class of nitroaromatic drugs, are known to undergo reduction into amines which was proposed to involve nitroso and N-hydroxyl intermediates. Now in this study, these corresponding intermediate ions were successfully intercepted and their structures were confirmed by CID. This provides mass spectrometric evidence for the mechanism of the nitro to amine conversion process during nitroreduction, an important redox reaction involved in carcinogenesis. In addition, the well-known oxidation reaction of chlorpromazine was also examined. The putative transient one-electron transfer product, the chlorpromazine radical cation (m/z 318), was captured by MS, for the first time, and its structure was also verified by CID. In addition to these observations, some features of the DESI-interfaced electrochemical mass spectrometry were discussed, such as simple instrumentation and the lack of background signal. These results further demonstrate the feasibility of EC/DESI-MS for the study of the biology-relevant redox chemistry and would find applications in proteomics and drug development research.

Distribution and Biological Effects of Nanoparticles in the Reproductive System.

Science.gov (United States)

Liu, Ying; Li, Hongxia; Xiao, Kai

2016-01-01

Nanoparticles have shown great potential in biomedical applications such as imaging probes and drug delivery. However, the increasing use of nanoparticles has raised concerns about their adverse effects on human health and environment. Reproductive tissues and gametes represent highly delicate biological systems with the essential function of transmitting genetic information to the offspring, which is highly sensitive to environmental toxicants. This review aims to summarzie the penetration of physiological barriers (blood-testis barrier and placental barrier), distribution and biological effects of nanoparticles in the reproductive system, which is essential to control the beneficial effects of nanoparticles applications and to avoid their adverse effects on the reproductive system. We referred to a large number of relevant peer-reviewed research articles about the reproductive toxicity of nanoparticles. The comprehensive information was summarized into two parts: physiological barrier penetration and biological effects of nanoparticles in male or female reproductive system; distribution and metabolism of nanoparticles in the reproductive system. The representative examples were also presented in four tables. The in vitro and in vivo studies imply that some nanoparticles are able to cross the blood-testis barrier or placental barrier, and their penetration depends on the physicochemical characteristics of nanoparticles (e.g., composition, shape, particle size and surface coating). The toxicity assays indicate that nanoparticles might induce adverse physiological effects and impede fertility or embryogenesis. The barrier penetration, adverse physiological effects, distribution and metabolism are closely related to physicochemical characteristics of nanoparticles. Further systematic and mechanistic studies using well-characterized nanoparticles, relevant administration routes, and doses relevant to the expected exposure level are required to improve our

Predicting in vivo effect levels for repeat-dose systemic toxicity using chemical, biological, kinetic and study covariates.

Science.gov (United States)

Truong, Lisa; Ouedraogo, Gladys; Pham, LyLy; Clouzeau, Jacques; Loisel-Joubert, Sophie; Blanchet, Delphine; Noçairi, Hicham; Setzer, Woodrow; Judson, Richard; Grulke, Chris; Mansouri, Kamel; Martin, Matthew

2018-02-01

In an effort to address a major challenge in chemical safety assessment, alternative approaches for characterizing systemic effect levels, a predictive model was developed. Systemic effect levels were curated from ToxRefDB, HESS-DB and COSMOS-DB from numerous study types totaling 4379 in vivo studies for 1247 chemicals. Observed systemic effects in mammalian models are a complex function of chemical dynamics, kinetics, and inter- and intra-individual variability. To address this complex problem, systemic effect levels were modeled at the study-level by leveraging study covariates (e.g., study type, strain, administration route) in addition to multiple descriptor sets, including chemical (ToxPrint, PaDEL, and Physchem), biological (ToxCast), and kinetic descriptors. Using random forest modeling with cross-validation and external validation procedures, study-level covariates alone accounted for approximately 15% of the variance reducing the root mean squared error (RMSE) from 0.96 log 10 to 0.85 log 10  mg/kg/day, providing a baseline performance metric (lower expectation of model performance). A consensus model developed using a combination of study-level covariates, chemical, biological, and kinetic descriptors explained a total of 43% of the variance with an RMSE of 0.69 log 10  mg/kg/day. A benchmark model (upper expectation of model performance) was also developed with an RMSE of 0.5 log 10  mg/kg/day by incorporating study-level covariates and the mean effect level per chemical. To achieve a representative chemical-level prediction, the minimum study-level predicted and observed effect level per chemical were compared reducing the RMSE from 1.0 to 0.73 log 10  mg/kg/day, equivalent to 87% of predictions falling within an order-of-magnitude of the observed value. Although biological descriptors did not improve model performance, the final model was enriched for biological descriptors that indicated xenobiotic metabolism gene expression, oxidative stress, and

Effects of low-level radiation on biologic systems: a literature review

International Nuclear Information System (INIS)

Best, T.L.; Hoditschek, B.

1980-12-01

This review presents an organized survey of scientific literature dealing with the biologic effects of low-level radiation. It includes brief discussions of topics of particular interest, a listing of useful review articles, an extensive bibliography, and listings of sources that can be used to update this document in the future. The topics discussed include experimental studies, the linear hypothesis, medical effects, occupational effects, effects of exposure to naturally occurring radiation, consumer products, and laws and regulations

Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...

Bibliographical review on the teaching of Biology and research

Directory of Open Access Journals (Sweden)

Mª Luz Rodríguez Palmero

2000-09-01

Full Text Available This review complements another one done by the same author, in 1997, regarding the role of comprehending the concept of cell in the learning of Biology. In addition, some general papers on science education that provide a better understanding of research approaches used in the investigation of this topic have been included. The reviewed papers have been organized into categories according to the object of study, the relevance assigned to the cell concept, and the framework of analysis. The review shows that the concept of cell is very important in the biological conceptualization, however, it also shows the need of additional research on this matter, from theoretical frameworks that pay more attention to the psychological level, in order to provide some guidance to improve the teaching and learning processes of the biological content that presupose the comprehension of living beings.

On making nursing undergraduate human reproductive physiology content meaningful and relevant: discussion of human pleasure in its biological context.

Science.gov (United States)

McClusky, Leon Mendel

2012-01-01

The traditional presentation of the Reproductive Physiology component in an Anatomy and Physiology course to nursing undergraduates focuses on the broad aspects of hormonal regulation of reproduction and gonadal anatomy, with the role of the higher centres of the brain omitted. An introductory discussion is proposed which could precede the lectures on the reproductive organs. The discussion gives an overview of the biological significance of human pleasure, the involvement of the neurotransmitter dopamine, and the role of pleasure in the survival of the individual and even species. Pleasure stimuli (positive and negative) and the biological significance of naturally-induced pleasurable experiences are briefly discussed in the context of reproduction and the preservation of genetic material with an aim to foster relevancy between subject material and human behaviour in any type of society. The tenderness of this aspect of the human existence is well-understood because of its invariable association with soul-revealing human expressions such as love, infatuation, sexual flirtations, all of which are underpinned by arousal, desire and/or pleasure. Assuming that increased knowledge correlates with increased confidence, the proposed approach may provide the nurse with an adequate knowledge base to overcome well-known barriers in communicating with their patients about matters of sexual health and intimacy. Copyright © 2011 Elsevier Ltd. All rights reserved.

The common extremalities in biology and physics maximum energy dissipation principle in chemistry, biology, physics and evolution

CERN Document Server

Moroz, Adam

2011-01-01

This book is the first unified systemic description of dissipative phenomena, taking place in biology, and non-dissipative (conservative) phenomena, which is more relevant to physics. Fully updated and revised, this new edition extends our understanding of nonlinear phenomena in biology and physics from the extreme / optimal perspective. The first book to provide understanding of physical phenomena from a biological perspective and biological phenomena from a physical perspective Discusses emerging fields and analysis Provides examples.

Stress and adaptation : Toward ecologically relevant animal models

NARCIS (Netherlands)

Koolhaas, Jaap M.; Boer, Sietse F. de; Buwalda, Bauke

Animal models have contributed considerably to the current understanding of mechanisms underlying the role of stress in health and disease. Despite the progress made already, much more can be made by more carefully exploiting animals' and humans' shared biology, using ecologically relevant models.

LANGUAGE EXPERIENCE SHAPES PROCESSING OF PITCH RELEVANT INFORMATION IN THE HUMAN BRAINSTEM AND AUDITORY CORTEX: ELECTROPHYSIOLOGICAL EVIDENCE.

Science.gov (United States)

Krishnan, Ananthanarayan; Gandour, Jackson T

2014-12-01

Pitch is a robust perceptual attribute that plays an important role in speech, language, and music. As such, it provides an analytic window to evaluate how neural activity relevant to pitch undergo transformation from early sensory to later cognitive stages of processing in a well coordinated hierarchical network that is subject to experience-dependent plasticity. We review recent evidence of language experience-dependent effects in pitch processing based on comparisons of native vs. nonnative speakers of a tonal language from electrophysiological recordings in the auditory brainstem and auditory cortex. We present evidence that shows enhanced representation of linguistically-relevant pitch dimensions or features at both the brainstem and cortical levels with a stimulus-dependent preferential activation of the right hemisphere in native speakers of a tone language. We argue that neural representation of pitch-relevant information in the brainstem and early sensory level processing in the auditory cortex is shaped by the perceptual salience of domain-specific features. While both stages of processing are shaped by language experience, neural representations are transformed and fundamentally different at each biological level of abstraction. The representation of pitch relevant information in the brainstem is more fine-grained spectrotemporally as it reflects sustained neural phase-locking to pitch relevant periodicities contained in the stimulus. In contrast, the cortical pitch relevant neural activity reflects primarily a series of transient temporal neural events synchronized to certain temporal attributes of the pitch contour. We argue that experience-dependent enhancement of pitch representation for Chinese listeners most likely reflects an interaction between higher-level cognitive processes and early sensory-level processing to improve representations of behaviorally-relevant features that contribute optimally to perception. It is our view that long

Cerebral oxygen transport failure?: decreasing hemoglobin and hematocrit levels after ischemic stroke predict poor outcome and mortality: STroke: RelevAnt Impact of hemoGlobin, Hematocrit and Transfusion (STRAIGHT)--an observational study.

Science.gov (United States)

Kellert, Lars; Martin, Evgenia; Sykora, Marek; Bauer, Harald; Gussmann, Philipp; Diedler, Jennifer; Herweh, Christian; Ringleb, Peter A; Hacke, Werner; Steiner, Thorsten; Bösel, Julian

2011-10-01

Although conceivably relevant for penumbra oxygenation, the optimal levels of hemoglobin (Hb) and hematocrit (Hct) in patients with acute ischemic stroke are unknown. We identified patients from our prospective local stroke database who received intravenous thrombolysis based on multimodal magnet resonance imaging during the years 1998 to 2009. A favorable outcome at 3 months was defined as a modified Rankin Scale score≤2 and a poor outcome as a modified Rankin Scale score≥3. The dynamics of Hemoglobin (Hb), Hematocrit (Hct), and other relevant laboratory parameters as well as cardiovascular risk factors were retrospectively assessed and analyzed between these 2 groups. Of 217 patients, 114 had a favorable and 103 a poor outcome. In a multivariable regression model, anemia until day 5 after admission (odds ratio [OR]=2.61; 95% CI, 1.33 to 5.11; P=0.005), Hb nadir (OR=0.81; 95% CI, 0.67 to 0.99; P=0.038), and Hct nadir (OR=0.93; 95% CI, 0.87 to 0.99; P=0.038) remained independent predictors for poor outcome at 3 months. Mortality after 3 months was independently associated with Hb nadir (OR=0.80; 95% CI, 0.65 to 0.98; P=0.028) and Hb decrease (OR=1.34; 95% CI, 1.01 to 1.76; P=0.04) as well as Hct decrease (OR=1.12; 95% CI, 1.01 to 1.23; P=0.027). Poor outcome and mortality after ischemic stroke are strongly associated with low and further decreasing Hb and Hct levels. This decrease of Hb and Hct levels after admission might be more relevant and accessible to treatment than are baseline levels.

Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits.

Science.gov (United States)

van Boxtel, Jeroen J A; Lu, Hongjing

2013-01-01

People with Autism Spectrum Disorder (ASD) are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

Impaired global, and compensatory local, biological motion processing in people with high levels of autistic traits

Directory of Open Access Journals (Sweden)

Jeroen J A Van Boxtel

2013-04-01

Full Text Available People with Autism Spectrum Disorder (ASD are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD.

High School and College Biology: A Multi-Level Model of the Effects of High School Courses on Introductory Course Performance

Science.gov (United States)

Loehr, John F.; Almarode, John T.; Tai, Robert H.; Sadler, Philip M.

2012-01-01

In a climate where increasing numbers of students are encouraged to pursue post-secondary education, the level of preparedness students have for college-level coursework is not far from the minds of all educators, especially high school teachers. Specifically within the biological sciences, introductory biology classes often serve as the…

Exemplary Programs in Secondary School Biology.

Science.gov (United States)

McComas, William F.; Penick, John E.

1989-01-01

Summarizes 10 exemplary programs which address topics on individualized biology, a modified team approach, limnology, physical anthropology, the relevance of biology to society, ecology, and health. Provides names and addresses of contact persons for further information. Units cover a broad range of abilities and activities. (RT)

Bidimensional microdosimetry as a tool for evaluating biological response and target structure

International Nuclear Information System (INIS)

Booz, J.; Schmitz, Th.; Feinendegen, L.E.; Olko, P.

1992-01-01

The paper addresses the issue of the relevance of microdosimetric spectra for quantifying the effects of low-level exposures to radiation. Biological response functions derived to date from numerical analyses of radiobiological and microdosimetric observations refer to uniform targets of a preassumed size. The characteristic two-modal shape of functions obtained for several endpoints reflects the importance of two different pathways of damage formation, each of them related in fact to different target sizes. The correlated energy deposition distributions in such a bidimensional system are suggested as a more appropriate physical input for analysing biological response and target structure. (author)

Asymmetric positive feedback loops reliably control biological responses.

Science.gov (United States)

Ratushny, Alexander V; Saleem, Ramsey A; Sitko, Katherine; Ramsey, Stephen A; Aitchison, John D

2012-04-24

Positive feedback is a common mechanism enabling biological systems to respond to stimuli in a switch-like manner. Such systems are often characterized by the requisite formation of a heterodimer where only one of the pair is subject to feedback. This ASymmetric Self-UpREgulation (ASSURE) motif is central to many biological systems, including cholesterol homeostasis (LXRα/RXRα), adipocyte differentiation (PPARγ/RXRα), development and differentiation (RAR/RXR), myogenesis (MyoD/E12) and cellular antiviral defense (IRF3/IRF7). To understand why this motif is so prevalent, we examined its properties in an evolutionarily conserved transcriptional regulatory network in yeast (Oaf1p/Pip2p). We demonstrate that the asymmetry in positive feedback confers a competitive advantage and allows the system to robustly increase its responsiveness while precisely tuning the response to a consistent level in the presence of varying stimuli. This study reveals evolutionary advantages for the ASSURE motif, and mechanisms for control, that are relevant to pharmacologic intervention and synthetic biology applications.

The relevance of nanoscale biological fragments for ice nucleation in clouds

Science.gov (United States)

O‧Sullivan, D.; Murray, B. J.; Ross, J. F.; Whale, T. F.; Price, H. C.; Atkinson, J. D.; Umo, N. S.; Webb, M. E.

2015-01-01

Most studies of the role of biological entities as atmospheric ice-nucleating particles have focused on relatively rare supermicron particles such as bacterial cells, fungal spores and pollen grains. However, it is not clear that there are sufficient numbers of these particles in the atmosphere to strongly influence clouds. Here we show that the ice-nucleating activity of a fungus from the ubiquitous genus Fusarium is related to the presence of nanometre-scale particles which are far more numerous, and therefore potentially far more important for cloud glaciation than whole intact spores or hyphae. In addition, we quantify the ice-nucleating activity of nano-ice nucleating particles (nano-INPs) washed off pollen and also show that nano-INPs are present in a soil sample. Based on these results, we suggest that there is a reservoir of biological nano-INPs present in the environment which may, for example, become aerosolised in association with fertile soil dust particles.

Synthetic biology analysed tools for discussion and evaluation

CERN Document Server

2016-01-01

Synthetic biology is a dynamic, young, ambitious, attractive, and heterogeneous scientific discipline. It is constantly developing and changing, which makes societal evaluation of this emerging new science a challenging task, prone to misunderstandings. Synthetic biology is difficult to capture, and confusion arises not only regarding which part of synthetic biology the discussion is about, but also with respect to the underlying concepts in use. This book offers a useful toolbox to approach this complex and fragmented field. It provides a biological access to the discussion using a 'layer' model that describes the connectivity of synthetic or semisynthetic organisms and cells to the realm of natural organisms derived by evolution. Instead of directly reviewing the field as a whole, firstly our book addresses the characteristic features of synthetic biology that are relevant to the societal discussion. Some of these features apply only to parts of synthetic biology, whereas others are relevant to synthetic bi...

A metabolomic study of fipronil for the anxiety-like behavior in zebrafish larvae at environmentally relevant levels

International Nuclear Information System (INIS)

Wang, Cui; Qian, Yi; Zhang, Xiaofeng; Chen, Fang; Zhang, Quan; Li, Zhuoyu; Zhao, Meirong

2016-01-01

Field residue of fipronil can interfere with the physiological characters of the domesticated fish; thus, lethal dose test and the general biomarker cannot delineate the low-level situation. Manipulating by video track, we observed an anxiety-like behavior including high speed and abnormal photoperiod accommodation after exposure to fipronil at environmental typical dose in zebrafish larvae. Examining the unbiased metabolomic profiles, we found perturbation in several metabolic pathways, including the increased contents of fatty acids and glycerol and the decreased levels of the glycine, serine, and branched amino acid. We presumed that observed enhanced fatty acid utility was in response to increase energy demands caused by anxiety like behavior. Additionally, the body burden of neurotransmitter such as glycine and L-glutamate may concurrently stimulate the swimming behavior. The insight of this study showed that integral perturbation such as metabolism helps us to further understand the risk to aquatic fish at the environmentally relevant levels. - Highlights: • Fipronil increased the swimming speed at 10 μg/L to zebrafish larvae. • Accommodation to light–dark photoperiod switch was disturbed by fipronil. • Metabolomics indicated an increase energy availability for anxiety-like behavior. • Anxiety-like behavior induced by fipronil may attribute to neurotransmitter changes. - Zebrafish larvae exposed to environmentally relevant concentrations of fipronil display anxiety like behavior that may attribute to observed changes in energy utilization and neurotransmitter disturbances.

Impact of Thermodynamic Principles in Systems Biology

NARCIS (Netherlands)

Heijnen, J.J.

2010-01-01

It is shown that properties of biological systems which are relevant for systems biology motivated mathematical modelling are strongly shaped by general thermodynamic principles such as osmotic limit, Gibbs energy dissipation, near equilibria and thermodynamic driving force. Each of these aspects

Biologically effective dose distribution based on the linear quadratic model and its clinical relevance

International Nuclear Information System (INIS)

Lee, Steve P.; Leu, Min Y.; Smathers, James B.; McBride, William H.; Parker, Robert G.; Withers, H. Rodney

1995-01-01

Purpose: Radiotherapy plans based on physical dose distributions do not necessarily entirely reflect the biological effects under various fractionation schemes. Over the past decade, the linear-quadratic (LQ) model has emerged as a convenient tool to quantify biological effects for radiotherapy. In this work, we set out to construct a mechanism to display biologically oriented dose distribution based on the LQ model. Methods and Materials: A computer program that converts a physical dose distribution calculated by a commercially available treatment planning system to a biologically effective dose (BED) distribution has been developed and verified against theoretical calculations. This software accepts a user's input of biological parameters for each structure of interest (linear and quadratic dose-response and repopulation kinetic parameters), as well as treatment scheme factors (number of fractions, fractional dose, and treatment time). It then presents a two-dimensional BED display in conjunction with anatomical structures. Furthermore, to facilitate clinicians' intuitive comparison with conventional fractionation regimen, a conversion of BED to normalized isoeffective dose (NID) is also allowed. Results: Two sample cases serve to illustrate the application of our tool in clinical practice. (a) For an orthogonal wedged pair of x-ray beams treating a maxillary sinus tumor, the biological effect at the ipsilateral mandible can be quantified, thus illustrates the so-called 'double-trouble' effects very well. (b) For a typical four-field, evenly weighted prostate treatment using 10 MV x-rays, physical dosimetry predicts a comparable dose at the femoral necks between an alternate two-fields/day and four-fields/day schups. However, our BED display reveals an approximate 21% higher BED for the two-fields/day scheme. This excessive dose to the femoral necks can be eliminated if the treatment is delivered with a 3:2 (anterio-posterior/posterio-anterior (AP

The Relevance of Biological Sciences in the 21st Century | Onyeka ...

African Journals Online (AJOL)

Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives ... Biological Sciences, as the name implies, is a group of sciences, rather than a ... knowledge is better assessed by the various problems of modern civilization ... in the improvement of food supply and elimination of hereditary diseases.

Top-down models in biology: explanation and control of complex living systems above the molecular level.

Science.gov (United States)

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

Some nonlinear challenges in biology

International Nuclear Information System (INIS)

Mosconi, Francesco; Julou, Thomas; Desprat, Nicolas; Sinha, Deepak Kumar; Allemand, Jean-François; Croquette, Vincent; Bensimon, David

2008-01-01

Driven by a deluge of data, biology is undergoing a transition to a more quantitative science. Making sense of the data, building new models, asking the right questions and designing smart experiments to answer them are becoming ever more relevant. In this endeavour, nonlinear approaches can play a fundamental role. The biochemical reactions that underlie life are very often nonlinear. The functional features exhibited by biological systems at all levels (from the activity of an enzyme to the organization of a colony of ants, via the development of an organism or a functional module like the one responsible for chemotaxis in bacteria) are dynamically robust. They are often unaffected by order of magnitude variations in the dynamical parameters, in the number or concentrations of actors (molecules, cells, organisms) or external inputs (food, temperature, pH, etc). This type of structural robustness is also a common feature of nonlinear systems, exemplified by the fundamental role played by dynamical fixed points and attractors and by the use of generic equations (logistic map, Fisher–Kolmogorov equation, the Stefan problem, etc.) in the study of a plethora of nonlinear phenomena. However, biological systems differ from these examples in two important ways: the intrinsic stochasticity arising from the often very small number of actors and the role played by evolution. On an evolutionary time scale, nothing in biology is frozen. The systems observed today have evolved from solutions adopted in the past and they will have to adapt in response to future conditions. The evolvability of biological system uniquely characterizes them and is central to biology. As the great biologist T Dobzhansky once wrote: 'nothing in biology makes sense except in the light of evolution'. (open problem)

Crossing Boundaries in Undergraduate Biology Education

Science.gov (United States)

Vanderklein, Dirk; Munakata, Mika; McManus, Jason

2016-01-01

In an effort to make mathematics relevant to biology students, the authors developed two modules that sought to integrate mathematics and ecology instruction to differing degrees. The modules were developed by a team of biology and mathematics educators and were implemented in an ecology course using three different instructional methods for three…

Integrative assessment of Evolutionary theory acceptance and knowledge levels of Biology undergraduate students from a Brazilian university

Science.gov (United States)

Tavares, Gustavo Medina; Bobrowski, Vera Lucia

2018-03-01

The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students' perceptions towards evolution, and studies can help to reveal those factors. We used a conceptual questionnaire, the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and a Knowledge test to assess (1) the level of acceptance and understanding of 23 undergraduate Biology students nearing the end of their course, (2) other factors that could affect these levels, including course structure, and (3) the most difficult topics regarding evolutionary biology. The results of this study showed that the students, on average, had a 'Very High Acceptance' (89.91) and a 'Very Low Knowledge' (59.42%) of Evolutionary theory, and also indicated a moderate positive correlation between the two (r = 0.66, p = .001). The most difficult topics were related to the definition of evolution and dating techniques. We believe that the present study provides evidence for policymakers to reformulate current school and university curricula in order to improve the teachers' acceptance and understanding of evolution and other biological concepts, consequently, helping students reduce their misconceptions related to evolutionary biology.

Advanced Level Biology Teachers' Attitudes towards Assessment and Their Engagement in Assessment for Learning

Science.gov (United States)

Bramwell-Lalor, Sharon; Rainford, Marcia

2015-01-01

This paper reports on a Mixed Methods study involving an investigation into the attitudes of advanced level biology teachers towards assessment and describes the teachers' experiences while being engaged in Assessment for Learning (AfL) practices such as sharing of learning objectives and peer- and self-assessment. Quantitative data were collected…

International safeguards relevant to geologic disposal of high-level wastes and spent fuels

International Nuclear Information System (INIS)

Pillay, K.K.S.; Picard, R.R.

1989-01-01

Spent fuels from once-through fuel cycles placed in underground repositories have the potential to become attractive targets for diversion and/or theft because of their valuable material content and decreasing radioactivity. The first geologic repository in the US, as currently designed, will contain approximately 500 Mt of plutonium, 60,000 Mt of uranium and a host of other fissile and strategically important elements. This paper identifies some of the international safeguards issues relevant to the various proposed scenarios for disposing of the spent fuel. In the context of the US program for geologic disposal of spent fuels, this paper highlights several issues that should be addressed in the near term by US industries, the Department of Energy, and the Nuclear Regulatory Commission before the geologic repositories for spent fuels become a reality. Based on US spent fuel discharges, an example is presented to illustrate the enormity of the problem of verifying spent fuel inventories. The geologic disposal scenario for high-level wastes originating from defense facilities produced a ''practicably irrecoverable'' waste form. Therefore, safeguards issues for geologic disposal of high-level waste now in the US are less pressing. 56 refs. , 2 figs

Spatial transcriptomics: paving the way for tissue-level systems biology.

Science.gov (United States)

Moor, Andreas E; Itzkovitz, Shalev

2017-08-01

The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates. In this review we describe how recent advances in spatial transcriptomics open the way for tissue-level systems biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Effects of Using Concept Mapping for Improving Advanced Level Biology Students' Lower- and Higher-Order Cognitive Skills

Science.gov (United States)

Bramwell-Lalor, Sharon; Rainford, Marcia

2014-01-01

This paper reports on teachers' use of concept mapping as an alternative assessment strategy in advanced level biology classes and its effects on students' cognitive skills on selected biology concepts. Using a mixed methods approach, the study employed a pre-test/post-test quasi-experimental design involving 156 students and 8 teachers from…

Assessing the relevance of ecotoxicological studies for regulatory decision making.

Science.gov (United States)

Rudén, Christina; Adams, Julie; Ågerstrand, Marlene; Brock, Theo Cm; Poulsen, Veronique; Schlekat, Christian E; Wheeler, James R; Henry, Tala R

2017-07-01

Regulatory policies in many parts of the world recognize either the utility of or the mandate that all available studies be considered in environmental or ecological hazard and risk assessment (ERA) of chemicals, including studies from the peer-reviewed literature. Consequently, a vast array of different studies and data types need to be considered. The first steps in the evaluation process involve determining whether the study is relevant to the ERA and sufficiently reliable. Relevance evaluation is typically performed using existing guidance but involves application of "expert judgment" by risk assessors. In the present paper, we review published guidance for relevance evaluation and, on the basis of the practical experience within the group of authors, we identify additional aspects and further develop already proposed aspects that should be considered when conducting a relevance assessment for ecotoxicological studies. From a regulatory point of view, the overarching key aspect of relevance concerns the ability to directly or indirectly use the study in ERA with the purpose of addressing specific protection goals and ultimately regulatory decision making. Because ERA schemes are based on the appropriate linking of exposure and effect estimates, important features of ecotoxicological studies relate to exposure relevance and biological relevance. Exposure relevance addresses the representativeness of the test substance, environmental exposure media, and exposure regime. Biological relevance deals with the environmental significance of the test organism and the endpoints selected, the ecological realism of the test conditions simulated in the study, as well as a mechanistic link of treatment-related effects for endpoints to the protection goal identified in the ERA. In addition, uncertainties associated with relevance should be considered in the assessment. A systematic and transparent assessment of relevance is needed for regulatory decision making. The relevance

Physiological relevance of plant 2-Cys peroxiredoxin overoxidation level and oligomerization status.

Science.gov (United States)

Cerveau, Delphine; Ouahrani, Djelloul; Marok, Mohamed Amine; Blanchard, Laurence; Rey, Pascal

2016-01-01

Peroxiredoxins are ubiquitous thioredoxin-dependent peroxidases presumed to display, upon environmental constraints, a chaperone function resulting from a redox-dependent conformational switch. In this work, using biochemical and genetic approaches, we aimed to unravel the factors regulating the redox status and the conformation of the plastidial 2-Cys peroxiredoxin (2-Cys PRX) in plants. In Arabidopsis, we show that in optimal growth conditions, the overoxidation level mainly depends on the availability of thioredoxin-related electron donors, but not on sulfiredoxin, the enzyme reducing the 2-Cys PRX overoxidized form. We also observed that upon various physiological temperature, osmotic and light stress conditions, the overoxidation level and oligomerization status of 2-Cys PRX can moderately vary depending on the constraint type. Further, no major change was noticed regarding protein conformation in water-stressed Arabidopsis, barley and potato plants, whereas species-dependent up- and down-variations in overoxidation were observed. In contrast, both 2-Cys PRX overoxidation and oligomerization were strongly induced during a severe oxidative stress generated by methyl viologen. From these data, revealing that the oligomerization status of plant 2-Cys PRX does not exhibit important variation and is not tightly linked to the protein redox status upon physiologically relevant environmental constraints, the possible in planta functions of 2-Cys PRX are discussed. © 2015 John Wiley & Sons Ltd.

Industrial systems biology and its impact on synthetic biology of yeast cell factories.

Science.gov (United States)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Human Capital and Economic Growth: The Quest for the Most Relevant Level of Education in Pakistan

OpenAIRE

Sultan, Faisal; Tehseen, Syed; Arif, Imtiaz

2009-01-01

The study examines the role of human capital in the economic growth of Pakistan by using primary, secondary and higher education enrolments as proxies for human capital in three different specifications. The idea behind these models is to find out the most relevant level of education in terms of its contribution in economic growth. The order of integration of the variables is checked through Augmented Dickey Fuller and Phillips Perron test. In order to find out the evidences of the long run r...

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.

Mesoscopic models of biological membranes

DEFF Research Database (Denmark)

Venturoli, M.; Sperotto, Maria Maddalena; Kranenburg, M.

2006-01-01

Phospholipids are the main components of biological membranes and dissolved in water these molecules self-assemble into closed structures, of which bilayers are the most relevant from a biological point of view. Lipid bilayers are often used, both in experimental and by theoretical investigations...... to coarse grain a biological membrane. The conclusion of this comparison is that there can be many valid different strategies, but that the results obtained by the various mesoscopic models are surprisingly consistent. A second objective of this review is to illustrate how mesoscopic models can be used...

Turkish students' perceptions of their biology learning environments: the effects of gender and grade level

NARCIS (Netherlands)

Telli, S.; Brok, den P.J.; Tekkaya, C.; Cakiroglu, J.

2009-01-01

This study investigates the effects of gender and grade level on Turkish secondary school students’ perceptions of their biology learning environment. A total of 1474 high school students completed the What is Happening in This Classroom (WIHIC) questionnaire. The WIHIC maps several important

Bridging Physics and Biology Using Resistance and Axons

Science.gov (United States)

Dyer, Joshua M.

2014-01-01

When teaching physics, it is often difficult to get biology-oriented students to see the relevance of physics. A complaint often heard is that biology students are required to take physics for the Medical College Admission Test (MCAT) as part of a "weeding out" process, but that they don't feel like they need physics for biology. Despite…

Exploring the Alignment of the Intended and Implemented Curriculum through Teachers' Interpretation: A Case Study of A-Level Biology Practical Work

Science.gov (United States)

Phaeton, Mukaro Joe; Stears, Michèle

2017-01-01

The research reported on here is part of a larger study exploring the alignment of the intended, implemented and attained curriculum with regard to practical work in the Zimbabwean A-level Biology curriculum. In this paper we focus on the alignment between the intended and implemented A-Level Biology curriculum through the lens of teachers'…

Environmental biodosimetry: a biologically relevant tool for ecological risk assessment and biomonitoring

Energy Technology Data Exchange (ETDEWEB)

Ulsh, B. E-mail: ulshb@mcmaster.ca; Hinton, T.G.; Congdon, J.D.; Dugan, L.C.; Whicker, F.W.; Bedford, J.S

2003-07-01

Biodosimetry, the estimation of received doses by determining the frequency of radiation-induced chromosome aberrations, is widely applied in humans acutely exposed as a result of accidents or for clinical purposes, but biodosimetric techniques have not been utilized in organisms chronically exposed to radionuclides in contaminated environments. The application of biodosimetry to environmental exposure scenarios could greatly improve the accuracy, and reduce the uncertainties, of ecological risk assessments and biomonitoring studies, because no assumptions are required regarding external exposure rates and the movement of organisms into and out of contaminated areas. Furthermore, unlike residue analyses of environmental media environmental biodosimetry provides a genetically relevant biomarker of cumulative lifetime exposure. Symmetrical chromosome translocations can impact reproductive success, and could therefore prove to be ecologically relevant as well. We describe our experience in studying aberrations in the yellow-bellied slider turtle as an example of environmental biodosimetry.

Repository environmental parameters and models/methodologies relevant to assessing the performance of high-level waste packages in basalt, tuff, and salt

Energy Technology Data Exchange (ETDEWEB)

Claiborne, H.C.; Croff, A.G.; Griess, J.C.; Smith, F.J.

1987-09-01

This document provides specifications for models/methodologies that could be employed in determining postclosure repository environmental parameters relevant to the performance of high-level waste packages for the Basalt Waste Isolation Project (BWIP) at Richland, Washington, the tuff at Yucca Mountain by the Nevada Test Site, and the bedded salt in Deaf Smith County, Texas. Guidance is provided on the identify of the relevant repository environmental parameters; the models/methodologies employed to determine the parameters, and the input data base for the models/methodologies. Supporting studies included are an analysis of potential waste package failure modes leading to identification of the relevant repository environmental parameters, an evaluation of the credible range of the repository environmental parameters, and a summary of the review of existing models/methodologies currently employed in determining repository environmental parameters relevant to waste package performance. 327 refs., 26 figs., 19 tabs.

Repository environmental parameters and models/methodologies relevant to assessing the performance of high-level waste packages in basalt, tuff, and salt

International Nuclear Information System (INIS)

Claiborne, H.C.; Croff, A.G.; Griess, J.C.; Smith, F.J.

1987-09-01

This document provides specifications for models/methodologies that could be employed in determining postclosure repository environmental parameters relevant to the performance of high-level waste packages for the Basalt Waste Isolation Project (BWIP) at Richland, Washington, the tuff at Yucca Mountain by the Nevada Test Site, and the bedded salt in Deaf Smith County, Texas. Guidance is provided on the identify of the relevant repository environmental parameters; the models/methodologies employed to determine the parameters, and the input data base for the models/methodologies. Supporting studies included are an analysis of potential waste package failure modes leading to identification of the relevant repository environmental parameters, an evaluation of the credible range of the repository environmental parameters, and a summary of the review of existing models/methodologies currently employed in determining repository environmental parameters relevant to waste package performance. 327 refs., 26 figs., 19 tabs

Relevance Feedback in Content Based Image Retrieval: A Review

Directory of Open Access Journals (Sweden)

Manesh B. Kokare

2011-01-01

Full Text Available This paper provides an overview of the technical achievements in the research area of relevance feedback (RF in content-based image retrieval (CBIR. Relevance feedback is a powerful technique in CBIR systems, in order to improve the performance of CBIR effectively. It is an open research area to the researcher to reduce the semantic gap between low-level features and high level concepts. The paper covers the current state of art of the research in relevance feedback in CBIR, various relevance feedback techniques and issues in relevance feedback are discussed in detail.

An Improved Optimization Method for the Relevance Voxel Machine

DEFF Research Database (Denmark)

Ganz, Melanie; Sabuncu, M. R.; Van Leemput, Koen

2013-01-01

In this paper, we will re-visit the Relevance Voxel Machine (RVoxM), a recently developed sparse Bayesian framework used for predicting biological markers, e.g., presence of disease, from high-dimensional image data, e.g., brain MRI volumes. The proposed improvement, called IRVoxM, mitigates the ...

World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia. Part 3

DEFF Research Database (Denmark)

Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas

2015-01-01

These updated guidelines are based on the first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in the years 2005 and 2006. For this 2015 revision, all available publications pertaining to the biological...... treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations which are clinically and scientifically relevant. They are intended to be used by all physicians diagnosing and treating patients with schizophrenia...

Electron Transfer in Chemistry and Biology - The Primary Events in ...

Indian Academy of Sciences (India)

transfers, occurs in a cascade in many biological processes, including photosynthesis. ... the model reactions of photosynthetic ... biological relevance. GENERAL I ARTICLE of electrons, respectively. This has entirely changed the earlier framework of interpreting reactions in chemistry and biology. This shift in emphasis ...

IQ Predicts Biological Motion Perception in Autism Spectrum Disorders

Science.gov (United States)

Rutherford, M. D.; Troje, Nikolaus F.

2012-01-01

Biological motion is easily perceived by neurotypical observers when encoded in point-light displays. Some but not all relevant research shows significant deficits in biological motion perception among those with ASD, especially with respect to emotional displays. We tested adults with and without ASD on the perception of masked biological motion…

Basics and principles of particle image velocimetry (PIV) for mapping biogenic and biologically relevant flows

NARCIS (Netherlands)

Stamhuis, Eize J.

2006-01-01

Particle image velocimetry (PIV) has proven to be a very useful technique in mapping animal-generated flows or flow patterns relevant to biota. Here, theoretical background is provided and experimental details of 2-dimensional digital PIV are explained for mapping flow produced by or relevant to

Ecological principles relevant to nuclear war

International Nuclear Information System (INIS)

Hutchinson, T.C.; Cropper, W.P. Jr.; Grover, H.D.

1985-01-01

The ecological principles outlined are very basic ones; the authors anticipate a readership trained in a broad range of disciplines, including those unfamiliar with the academic discipline of ecology. The authors include substantial discussion on ecophysiology (i.e., the responses of organisms to their environment) because this is relevant to the new understanding of the potential climatic consequences of nuclear war. In particular, the physiological sensitivity of organisms to reduced levels of light and temperature are a key part of the analysis of the potential ecological effects and agricultural effects of nuclear war. Much of the ecological analysis has been organized around major biological units called biomes. The authors describe the biome concept and discuss some of the environmental-climatic factors that are believed to control biome distribution. Emphasis is given to plants because of their controlling influence on ecosystem functions through their role as primary producers. Future reports are needed to address more fully the potential effects on animals. Much more research needs to be done on both plant and animal responses to the types of perturbations possible for the aftermath of a nuclear war. Another important element for analysis of the potential ecological consequences of nuclear war concerns recovery processes. As the post-nuclear war environmental extremes ameliorate, ecological communities in devastated regions would begin to reorganize. It is not possible to predict the course of such a succession precisely, but some principles concerning post-perturbation replacement (such as seed banks and germination), relevant successional patterns, and organism strategies are discussed

Conservation biology in Asia: the major policy challenges.

Science.gov (United States)

McNeely, Jeffrey A; Kapoor-Vijay, Promila; Zhi, Lu; Olsvig-Whittaker, Linda; Sheikh, Kashif M; Smith, Andrew T

2009-08-01

With about half the world's human population and booming economies, Asia faces numerous challenges to its biodiversity. The Asia Section of the Society for Conservation Biology has identified some key policy issues in which significant progress can be made. These include developing new sources of funding for forest conservation; identifying potential impacts of energy alternatives on the conservation of biodiversity; curbing the trade in endangered species of plants and animals; a special focus on the conservation of mountain biodiversity; enhancing relevant research; ensuring that conservation biology contributes to major international conventions and funding mechanisms; using conservation biology to build a better understanding of zoonotic diseases; more effectively addressing human-animal conflicts; enhancing community-based conservation; and using conservation biology to help address the pervasive water-deficit problems in much of Asia. These challenges can be met through improved regional cooperation among the relevant stakeholders.

Methods of small parameter in mathematical biology

CERN Document Server

Banasiak, Jacek

2014-01-01

This monograph presents new tools for modeling multiscale biological processes. Natural processes are usually driven by mechanisms widely differing from each other in the time or space scale at which they operate and thus should be described by appropriate multiscale models. However, looking at all such scales simultaneously is often infeasible, costly, and provides information that is redundant for a particular application. Hence, there has been a growing interest in providing a more focused description of multiscale processes by aggregating variables in a way that is relevant and preserves the salient features of the dynamics. The aim of this book is to present a systematic way of deriving the so-called limit equations for such aggregated variables and ensuring that the coefficients of these equations encapsulate the relevant information from the discarded levels of description. Since any approximation is only valid if an estimate of the incurred error is available, the tools described allow for proving tha...

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

Science.gov (United States)

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; 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 1 of SBML Level 3 Core. 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/.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

OpenAIRE

Matthew P. Adams; Catherine J. Collier; Sven Uthicke; Yan X. Ow; Lucas Langlois; Katherine R. O’Brien

2017-01-01

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluat...

Biological treatment of Crohn's disease

DEFF Research Database (Denmark)

Nielsen, Ole Haagen; Bjerrum, Jacob Tveiten; Seidelin, Jakob Benedict

2012-01-01

Introduction of biological agents for the treatment of Crohn's disease (CD) has led to a transformation of the treatment paradigm. Several biological compounds have been approved for patients with CD refractory to conventional treatment: infliximab, adalimumab and certolizumab pegol (and...... natalizumab in several countries outside the European Union). However, despite the use of biologics for more than a decade, questions still remain about the true efficacy and the best treatment regimens - especially about when to discontinue treatment. Furthermore, a need for optimizing treatment...... with biologics still exists, as 20-40% of patients with CD (depending on selection criteria) do not have any relevant response to the current biological agents (i.e. primary failures). A better patient selection might maximize the clinical outcome while minimizing the complications associated with this type...

Systems Biology-an interdisciplinary approach.

Science.gov (United States)

Friboulet, Alain; Thomas, Daniel

2005-06-15

System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

Contextual Hub Analysis Tool (CHAT: A Cytoscape app for identifying contextually relevant hubs in biological networks [version 2; referees: 2 approved

Directory of Open Access Journals (Sweden)

Tanja Muetze

2016-08-01

Full Text Available Highly connected nodes (hubs in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest. The relative importance of a hub node, however, can change depending on the biological context. Here, we report a Cytoscape app, the Contextual Hub Analysis Tool (CHAT, which enables users to easily construct and visualize a network of interactions from a gene or protein list of interest, integrate contextual information, such as gene expression or mass spectrometry data, and identify hub nodes that are more highly connected to contextual nodes (e.g. genes or proteins that are differentially expressed than expected by chance. In a case study, we use CHAT to construct a network of genes that are differentially expressed in Dengue fever, a viral infection. CHAT was used to identify and compare contextual and degree-based hubs in this network. The top 20 degree-based hubs were enriched in pathways related to the cell cycle and cancer, which is likely due to the fact that proteins involved in these processes tend to be highly connected in general. In comparison, the top 20 contextual hubs were enriched in pathways commonly observed in a viral infection including pathways related to the immune response to viral infection. This analysis shows that such contextual hubs are considerably more biologically relevant than degree-based hubs and that analyses which rely on the identification of hubs solely based on their connectivity may be biased towards nodes that are highly connected in general rather than in the specific context of interest.   Availability: CHAT is available for Cytoscape 3.0+ and can be installed via the Cytoscape App Store (http://apps.cytoscape.org/apps/chat.

EURASIP journal on bioinformatics & systems biology

National Research Council Canada - National Science Library

2006-01-01

"The overall aim of "EURASIP Journal on Bioinformatics and Systems Biology" is to publish research results related to signal processing and bioinformatics theories and techniques relevant to a wide...

Self-assembled structures and pKa value of oleic acid in systems of biological relevance.

Science.gov (United States)

Salentinig, Stefan; Sagalowicz, Laurent; Glatter, Otto

2010-07-20

In the human digestion process, triglycerides are hydrolyzed by lipases to monoglycerides and the corresponding fatty acids. Here we report the self-assembly of structures in biologically relevant, emulsified oleic acid-monoolein mixtures at various pH values and oleic acid concentrations. Small-angle X-ray scattering, cryogenic transmission electron microscopy, and dynamic light scattering were used to investigate the structures formed, and to follow their transitions while these factors were varied. The addition of oleic acid to monoolein-based cubosomes was found to increase the critical packing parameter in the system. Structural transitions from bicontinuous cubosomes through hexosomes and micellar cubosomes (Fd3m symmetry) to emulsified microemulsions occur with increasing oleic acid concentration. At sufficiently high oleic acid concentration, the internal particle structure was also found to strongly depend on the pH of the aqueous phase: transformations from emulsified microemulsion through micellar cubosomes, hexosomes, and bicontinuous cubosomes to vesicles can be observed as a function of increasing pH. The reversible transition from liquid crystals to vesicles occurs at intestinal pH values (between pH 7 and 8). The hydrodynamic radius of the particles decreases from around 120 nm for internally structured particles to around 60 nm for vesicles. All transitions with pH are reversible. Finally, the apparent pK(a) for oleic acid in monoolein could be determined from the change of structure with pH. This value is within the physiological pH range of the intestine and depends somewhat on composition.

Daily sea level prediction at Chiayi coast, Taiwan using extreme learning machine and relevance vector machine

Science.gov (United States)

Imani, Moslem; Kao, Huan-Chin; Lan, Wen-Hau; Kuo, Chung-Yen

2018-02-01

The analysis and the prediction of sea level fluctuations are core requirements of marine meteorology and operational oceanography. Estimates of sea level with hours-to-days warning times are especially important for low-lying regions and coastal zone management. The primary purpose of this study is to examine the applicability and capability of extreme learning machine (ELM) and relevance vector machine (RVM) models for predicting sea level variations and compare their performances with powerful machine learning methods, namely, support vector machine (SVM) and radial basis function (RBF) models. The input dataset from the period of January 2004 to May 2011 used in the study was obtained from the Dongshi tide gauge station in Chiayi, Taiwan. Results showed that the ELM and RVM models outperformed the other methods. The performance of the RVM approach was superior in predicting the daily sea level time series given the minimum root mean square error of 34.73 mm and the maximum determination coefficient of 0.93 (R2) during the testing periods. Furthermore, the obtained results were in close agreement with the original tide-gauge data, which indicates that RVM approach is a promising alternative method for time series prediction and could be successfully used for daily sea level forecasts.

Students' Personal Connection with Science: Investigating the Multidimensional Phenomenological Structure of Self-Relevance

Science.gov (United States)

Hartwell, Matthew; Kaplan, Avi

2018-01-01

This paper presents findings from a two-phase mixed methods study investigating the phenomenological structure of self-relevance among ninth-grade junior high school biology students (Phase 1: N = 118; Phase 2: N = 139). We begin with a phenomenological multidimensional definition of self-relevance as comprising three dimensions: the academic…

Bacteriophage lambda: early pioneer and still relevant

Science.gov (United States)

Casjens, Sherwood R.; Hendrix, Roger W.

2015-01-01

Molecular genetic research on bacteriophage lambda carried out during its golden age from the mid 1950's to mid 1980's was critically important in the attainment of our current understanding of the sophisticated and complex mechanisms by which the expression of genes is controlled, of DNA virus assembly and of the molecular nature of lysogeny. The development of molecular cloning techniques, ironically instigated largely by phage lambda researchers, allowed many phage workers to switch their efforts to other biological systems. Nonetheless, since that time the ongoing study of lambda and its relatives have continued to give important new insights. In this review we give some relevant early history and describe recent developments in understanding the molecular biology of lambda's life cycle. PMID:25742714

Alkali Metal Ion Complexes with Phosphates, Nucleotides, Amino Acids, and Related Ligands of Biological Relevance. Their Properties in Solution.

Science.gov (United States)

Crea, Francesco; De Stefano, Concetta; Foti, Claudia; Lando, Gabriele; Milea, Demetrio; Sammartano, Silvio

2016-01-01

Alkali metal ions play very important roles in all biological systems, some of them are essential for life. Their concentration depends on several physiological factors and is very variable. For example, sodium concentrations in human fluids vary from quite low (e.g., 8.2 mmol dm(-3) in mature maternal milk) to high values (0.14 mol dm(-3) in blood plasma). While many data on the concentration of Na(+) and K(+) in various fluids are available, the information on other alkali metal cations is scarce. Since many vital functions depend on the network of interactions occurring in various biofluids, this chapter reviews their complex formation with phosphates, nucleotides, amino acids, and related ligands of biological relevance. Literature data on this topic are quite rare if compared to other cations. Generally, the stability of alkali metal ion complexes of organic and inorganic ligands is rather low (usually log K  Na(+) > K(+) > Rb(+) > Cs(+). For example, for citrate it is: log K ML = 0.88, 0.80, 0.48, 0.38, and 0.13 at 25 °C and infinite dilution. Some considerations are made on the main aspects related to the difficulties in the determination of weak complexes. The importance of the alkali metal ion complexes was also studied in the light of modelling natural fluids and in the use of these cations as probes for different processes. Some empirical relationships are proposed for the dependence of the stability constants of Na(+) complexes on the ligand charge, as well as for correlations among log K values of NaL, KL or LiL species (L = generic ligand).

Reflections on rural people's knowledge and skill and relevance in ...

African Journals Online (AJOL)

UNLICENSED

objective is to assess the relevance of indigenous knowledge in agriculture. ... transmit the knowledge to the youths and researchers to document it and government to protect it. ... mechanisms to protect the earth's biological diversity. ... and other development agencies to embrace Agenda 21 as .... ecological characteristics.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species.

Science.gov (United States)

Adams, Matthew P; Collier, Catherine J; Uthicke, Sven; Ow, Yan X; Langlois, Lucas; O'Brien, Katherine R

2017-01-04

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (T opt ) for maximum photosynthetic rate (P max ). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.

Model fit versus biological relevance: Evaluating photosynthesis-temperature models for three tropical seagrass species

Science.gov (United States)

Adams, Matthew P.; Collier, Catherine J.; Uthicke, Sven; Ow, Yan X.; Langlois, Lucas; O'Brien, Katherine R.

2017-01-01

When several models can describe a biological process, the equation that best fits the data is typically considered the best. However, models are most useful when they also possess biologically-meaningful parameters. In particular, model parameters should be stable, physically interpretable, and transferable to other contexts, e.g. for direct indication of system state, or usage in other model types. As an example of implementing these recommended requirements for model parameters, we evaluated twelve published empirical models for temperature-dependent tropical seagrass photosynthesis, based on two criteria: (1) goodness of fit, and (2) how easily biologically-meaningful parameters can be obtained. All models were formulated in terms of parameters characterising the thermal optimum (Topt) for maximum photosynthetic rate (Pmax). These parameters indicate the upper thermal limits of seagrass photosynthetic capacity, and hence can be used to assess the vulnerability of seagrass to temperature change. Our study exemplifies an approach to model selection which optimises the usefulness of empirical models for both modellers and ecologists alike.

An integrative approach to inferring biologically meaningful gene modules

Directory of Open Access Journals (Sweden)

Wang Kai

2011-07-01

Full Text Available Abstract Background The ability to construct biologically meaningful gene networks and modules is critical for contemporary systems biology. Though recent studies have demonstrated the power of using gene modules to shed light on the functioning of complex biological systems, most modules in these networks have shown little association with meaningful biological function. We have devised a method which directly incorporates gene ontology (GO annotation in construction of gene modules in order to gain better functional association. Results We have devised a method, Semantic Similarity-Integrated approach for Modularization (SSIM that integrates various gene-gene pairwise similarity values, including information obtained from gene expression, protein-protein interactions and GO annotations, in the construction of modules using affinity propagation clustering. We demonstrated the performance of the proposed method using data from two complex biological responses: 1. the osmotic shock response in Saccharomyces cerevisiae, and 2. the prion-induced pathogenic mouse model. In comparison with two previously reported algorithms, modules identified by SSIM showed significantly stronger association with biological functions. Conclusions The incorporation of semantic similarity based on GO annotation with gene expression and protein-protein interaction data can greatly enhance the functional relevance of inferred gene modules. In addition, the SSIM approach can also reveal the hierarchical structure of gene modules to gain a broader functional view of the biological system. Hence, the proposed method can facilitate comprehensive and in-depth analysis of high throughput experimental data at the gene network level.

Increasing the biological value of dietary cutlets

OpenAIRE

SYZDYKOVA L.S.; DIKHANBAYEVA F.T.; BAZYLHANOVA E.CH

2015-01-01

Relevance of work: meat products are the main source of the proteins, necessary for activity of the person. In this article is determined the biological value of the cutlets with dietary properties. The purpose of this work is development of the production technology of dietary cutlets in branches of public catering and determination of their biological value. As a result of work dietary cutlets with the increased biological value due to addition of oatmeal are received.

Biologics in dermatology: An integrated review

Directory of Open Access Journals (Sweden)

Virendra N Sehgal

2014-01-01

Full Text Available The advent of biologics in dermatologic treatment armentarium has added refreshing dimensions, for it is a major breakthrough. Several agents are now available for use. It is therefore imperative to succinctly comprehend their pharmacokinetics for their apt use. A concerted endeavor has been made to delve on this subject. The major groups of biologics have been covered and include: Drugs acting against TNF-α, Alefacept, Ustekinumab, Rituximab, IVIG and Omalizumab. The relevant pharmacokinetic characteristics have been detailed. Their respective label (approved and off-label (unapproved indications have been defined, highlighting their dosage protocol, availability and mode of administration. The evidence level of each indication has also been discussed to apprise the clinician of their current and prospective uses. Individual anti-TNF drugs are not identical in their actions and often one is superior to the other in a particular disease. Hence, the section on anti-TNF agents mentions the literature on each drug separately, and not as a group. The limitations for their use have also been clearly brought out.

Perceptions of patients with rheumatic diseases treated with subcutaneous biologicals on their level of information: RHEU-LIFE Survey.

Science.gov (United States)

de Toro, Javier; Cea-Calvo, Luis; Battle, Enrique; Carmona, Loreto; Arteaga, María J; Fernández, Sabela; González, Carlos M

2017-12-22

To investigate, in Spanish patients with rheumatic diseases treated with subcutaneous biological drugs, their sources of information, which sources they consider most relevant, and their satisfaction with the information received in the hospital. Rheumatologists from 50 hospitals handed out an anonymous survey to 20 consecutive patients with rheumatoid arthritis, axial spondyloarthritis or psoriatic arthritis treated with subcutaneous biologicals. The survey was developed ad hoc by 4 rheumatologists and 3 patients, and included questions with closed-ended responses on sources of information and satisfaction. The survey was handed-out to 1,000 patients, 592 of whom completed it (response rate: 59.2%). The rheumatologist was mentioned as the most important source of information (75%), followed by the primary care physician, nurses, and electronic resources; 45.2% received oral and written information about the biological, 46.1% oral only, and 6.0% written only; 8.7% stated that they had not been taught to inject the biological. The percentage of patients satisfied with the information received was high (87.2%), although the satisfaction was lower in relation to safety. If the information came from the rheumatologist, the satisfaction was higher (89.6%) than when coming from other sources (59.6%; P<.001). Satisfaction was also higher if the information was provided orally and written (92.8%) than if provided only orally (86.1%; P=.013); 45.2% reported having sought information from sources outside the hospital. The rheumatologist is key in transmitting satisfactory information on biological treatment to patients. He or she must also act as a guide, since a high percentage of patients seeks information in other different sources. Copyright © 2017. Publicado por Elsevier España, S.L.U.

Biological effectiveness of neutrons: Research needs

International Nuclear Information System (INIS)

Casarett, G.W.; Braby, L.A.; Broerse, J.J.; Elkind, M.M.; Goodhead, D.T.; Oleinick, N.L.

1994-02-01

The goal of this report was to provide a conceptual plan for a research program that would provide a basis for determining more precisely the biological effectiveness of neutron radiation with emphasis on endpoints relevant to the protection of human health. This report presents the findings of the experts for seven particular categories of scientific information on neutron biological effectiveness. Chapter 2 examines the radiobiological mechanisms underlying the assumptions used to estimate human risk from neutrons and other radiations. Chapter 3 discusses the qualitative and quantitative models used to organize and evaluate experimental observations and to provide extrapolations where direct observations cannot be made. Chapter 4 discusses the physical principles governing the interaction of radiation with biological systems and the importance of accurate dosimetry in evaluating radiation risk and reducing the uncertainty in the biological data. Chapter 5 deals with the chemical and molecular changes underlying cellular responses and the LET dependence of these changes. Chapter 6, in turn, discusses those cellular and genetic changes which lead to mutation or neoplastic transformation. Chapters 7 and 8 examine deterministic and stochastic effects, respectively, and the data required for the prediction of such effects at different organizational levels and for the extrapolation from experimental results in animals to risks for man. Gaps and uncertainties in this data are examined relative to data required for establishing radiation protection standards for neutrons and procedures for the effective and safe use of neutron and other high-LET radiation therapy

Biological effectiveness of neutrons: Research needs

Energy Technology Data Exchange (ETDEWEB)

Casarett, G.W.; Braby, L.A.; Broerse, J.J.; Elkind, M.M.; Goodhead, D.T.; Oleinick, N.L.

1994-02-01

The goal of this report was to provide a conceptual plan for a research program that would provide a basis for determining more precisely the biological effectiveness of neutron radiation with emphasis on endpoints relevant to the protection of human health. This report presents the findings of the experts for seven particular categories of scientific information on neutron biological effectiveness. Chapter 2 examines the radiobiological mechanisms underlying the assumptions used to estimate human risk from neutrons and other radiations. Chapter 3 discusses the qualitative and quantitative models used to organize and evaluate experimental observations and to provide extrapolations where direct observations cannot be made. Chapter 4 discusses the physical principles governing the interaction of radiation with biological systems and the importance of accurate dosimetry in evaluating radiation risk and reducing the uncertainty in the biological data. Chapter 5 deals with the chemical and molecular changes underlying cellular responses and the LET dependence of these changes. Chapter 6, in turn, discusses those cellular and genetic changes which lead to mutation or neoplastic transformation. Chapters 7 and 8 examine deterministic and stochastic effects, respectively, and the data required for the prediction of such effects at different organizational levels and for the extrapolation from experimental results in animals to risks for man. Gaps and uncertainties in this data are examined relative to data required for establishing radiation protection standards for neutrons and procedures for the effective and safe use of neutron and other high-LET radiation therapy.

Approaches to chemical synthetic biology.

Science.gov (United States)

Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

2012-07-16

Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Prognostic relevance of motor talent predictors in early adolescence: A group- and individual-based evaluation considering different levels of achievement in youth football.

Science.gov (United States)

Höner, Oliver; Votteler, Andreas

2016-12-01

In the debate about the usefulness of motor diagnostics in the talent identification process, the prognostic validity for tests conducted in early adolescence is of critical interest. Using a group- and individual-based statistical approach, this prospective cohort study evaluated a nationwide assessment of speed abilities and technical skills regarding its relevance for future achievement levels. The sample consisted of 22,843 U12-players belonging to the top 4% in German football. The U12-results in five tests served as predictors for players' selection levels in U16-U19 (youth national team, regional association, youth academy, not selected). Group-mean differences proved the prognostic relevance for all predictors. Low individual selection probabilities demonstrated limited predictive values, while excellent test results proved their particular prognostic relevance. Players scoring percentile ranks (PRs) ≥ 99 had a 12 times higher chance to become youth national team players than players scoring PR talents) but also led to lower sensitivity (loss of talents). Extending the current research, these different approaches revealed the ambiguity of the diagnostics' prognostic relevance, representing both the usefulness and several pitfalls of nationwide diagnostics. Therefore, the present diagnostics can support but not substitute for coaches' subjective decisions for talent identification, and multidisciplinary designs are required.

Selected factors associated with achievement of biology preparatory students and their follow-up to higher level biology courses

Science.gov (United States)

Biermann, Carol A.; Sarinsky, Gary B.

This study was undertaken to determine whether a biology preparatory course given at an urban community college was helping students to develop the proper skills and background necessary for them to successfully complete follow-up courses in biology. A group of students who enrolled in a biology preparatory course, and subsequently, a follow-up anatomy and physiology or general biology course (experimental group) was compared to a group of students who should have registered for the preparatory course, but who enrolled directly into the anatomy and physiology or general biology course (control group). It was shown that there was no significant difference in their anatomy and physiology or general biology grades. Furthermore, only 16% of the initial group of preparatory students enrolled in and passed a follow-up biology course. Examination of the preparatory group using discriminant analysis ascertained that mathematics score was the principle discriminator between pass/fail groups. A stepwise multiple regression analysis of the variables explaining the preparatory grade showed that mathematics score, reading score, and type of high school degree explained 33% of the variance. Of the students who did pass the preparatory course and enrolled in a follow-up biology class, their preparatory grade was a good predictor of their achievement (measured by follow-up course grade), as determined by multiple regression.

Identifying novel glioma associated pathways based on systems biology level meta-analysis.

Science.gov (United States)

Hu, Yangfan; Li, Jinquan; Yan, Wenying; Chen, Jiajia; Li, Yin; Hu, Guang; Shen, Bairong

2013-01-01

With recent advances in microarray technology, including genomics, proteomics, and metabolomics, it brings a great challenge for integrating this "-omics" data to analysis complex disease. Glioma is an extremely aggressive and lethal form of brain tumor, and thus the study of the molecule mechanism underlying glioma remains very important. To date, most studies focus on detecting the differentially expressed genes in glioma. However, the meta-analysis for pathway analysis based on multiple microarray datasets has not been systematically pursued. In this study, we therefore developed a systems biology based approach by integrating three types of omics data to identify common pathways in glioma. Firstly, the meta-analysis has been performed to study the overlapping of signatures at different levels based on the microarray gene expression data of glioma. Among these gene expression datasets, 12 pathways were found in GeneGO database that shared by four stages. Then, microRNA expression profiles and ChIP-seq data were integrated for the further pathway enrichment analysis. As a result, we suggest 5 of these pathways could be served as putative pathways in glioma. Among them, the pathway of TGF-beta-dependent induction of EMT via SMAD is of particular importance. Our results demonstrate that the meta-analysis based on systems biology level provide a more useful approach to study the molecule mechanism of complex disease. The integration of different types of omics data, including gene expression microarrays, microRNA and ChIP-seq data, suggest some common pathways correlated with glioma. These findings will offer useful potential candidates for targeted therapeutic intervention of glioma.

Modern Biology

OpenAIRE

ALEKSIC, Branko

2014-01-01

The purpose of this course is to learn the philosophy, principles, and techniques of modern biology. The course is particularly designed for those who have not learned biology previously or whose major is other than biology, and who may think that they do not need to know any biology at all. The topics are covered in a rather general, overview manner, but certain level of diligence in grasping concepts and memorizing the terminology is expected.

Perceptual and categorical decision making: goal-relevant representation of two domains at different levels of abstraction.

Science.gov (United States)

Shankar, Swetha; Kayser, Andrew S

2017-06-01

decision information varies in multiple domains at different levels of abstraction. Behavioral and modeling results suggest that categorical (more abstract) information is weighted more strongly than perceptual (more concrete) information but that perceptual and categorical domains interact to influence decisions. Frontoparietal brain activity during categorization flexibly represents decision-relevant features and highlights significant dissociations in frontal and parietal activity during decision making. Copyright © 2017 the American Physiological Society.

Rethinking the central dogma: noncoding RNAs are biologically relevant.

Science.gov (United States)

Robinson, Victoria L

2009-01-01

Non-coding RNAs (ncRNAs) are a large class of functional molecules with over 100 unique classes described to date. ncRNAs are diverse in terms of their function and size. A relatively new class of small ncRNA, called microRNAs (miRNA), have received a great deal of attention in the literature in recent years. miRNAs are endogenously encoded gene families that demonstrate striking evolutionary conservation. miRNAs serve essential and diverse physiological functions such as differentiation and development, proliferation, maintaining cell type phenotypes, and many others. The discovery and ongoing investigation of miRNAs is part of a revolution in biology that is changing the basic concepts of gene expression and RNA functionality. A single miRNA can participate in controlling the expression of up to several hundred protein-coding genes by interacting with mRNAs, generally in 3' untranslated regions. Our new and developing understanding of miRNAs, and other ncRNAs, promises to lead to significant contributions to medicine. Specifically, miRNAs are likely to serve as the basis for novel therapies and diagnostic tools.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

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

2018-03-09

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. 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 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

Science.gov (United States)

Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

International Nuclear Information System (INIS)

2016-01-01

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

WE-DE-202-00: Connecting Radiation Physics with Computational Biology

Energy Technology Data Exchange (ETDEWEB)

NONE

2016-06-15

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

Multiple levels of epigenetic control for bone biology and pathology.

Science.gov (United States)

Montecino, Martin; Stein, Gary; Stein, Janet; Zaidi, Kaleem; Aguilar, Rodrigo

2015-12-01

Multiple dimensions of epigenetic control contribute to regulation of gene expression that governs bone biology and pathology. Once confined to DNA methylation and a limited number of post-translational modifications of histone proteins, the definition of epigenetic mechanisms is expanding to include contributions of non-coding RNAs and mitotic bookmarking, a mechanism for retaining phenotype identity during cell proliferation. Together these different levels of epigenetic control of physiological processes and their perturbations that are associated with compromised gene expression during the onset and progression of disease, have contributed to an unprecedented understanding of the activities (operation) of the genomic landscape. Here, we address general concepts that explain the contribution of epigenetic control to the dynamic regulation of gene expression during eukaryotic transcription. This article is part of a Special Issue entitled Epigenetics and Bone. Copyright © 2015 Elsevier Inc. All rights reserved.

MEASUREMENT OF TRACE LEVELS OF DEUTERIUM OXIDE IN BIOLOGIC FLUIDS USING INFRARED SPECTROPHOTOMETRY.

Science.gov (United States)

Experimental data relevant to the assay of D2O in human serum, urine, and parotid fluid are presented. For serum, with triplicate scans, values of precision...and of accuracy of plus or minus 3% at the 250 p.p.m. D2O level are obtained. By use of parotid fluid the values are narrowed to plus or minus 2% at...aqueous compartments using values for serum water content. Parotid fluid appears to be particularly suitable for biomedical applications due to its ease

Interactive Effects of Working Memory Self-Regulatory Ability and Relevance Instructions on Text Processing

Science.gov (United States)

Hamilton, Nancy Jo

2012-01-01

Reading is a process that requires the enactment of many cognitive processes. Each of these processes uses a certain amount of working memory resources, which are severely constrained by biology. More efficiency in the function of working memory may mediate the biological limits of same. Reading relevancy instructions may be one such method to…

Neutron Scattering in Biology Techniques and Applications

CERN Document Server

Fitter, Jörg; Katsaras, John

2006-01-01

The advent of new neutron facilities and the improvement of existing sources and instruments world wide supply the biological community with many new opportunities in the areas of structural biology and biological physics. The present volume offers a clear description of the various neutron-scattering techniques currently being used to answer biologically relevant questions. Their utility is illustrated through examples by some of the leading researchers in the field of neutron scattering. This volume will be a reference for researchers and a step-by-step guide for young scientists entering the field and the advanced graduate student.

Astrophysical relevance of γ transition energies

International Nuclear Information System (INIS)

Rauscher, Thomas

2008-01-01

The relevant γ energy range is explicitly identified where additional γ strength must be located to have an impact on astrophysically relevant reactions. It is shown that folding the energy dependences of the transmission coefficients and the level density leads to maximal contributions for γ energies of 2≤E γ ≤4 unless quantum selection rules allow isolated states to contribute. Under this condition, electric dipole transitions dominate. These findings allow us to more accurately judge the relevance of modifications of the γ strength for astrophysics

The effects on populations of exposure to low levels of ionizing radiation. Report of the Advisory Committee on the Biological Effects of Ionizing Radiations

Energy Technology Data Exchange (ETDEWEB)

NONE

1972-11-01

In the summer of 1970, the Federal Radiation Council (whose activities have since been transferred to the Radiation Office of the EPA) asked the National Academy of Sciences for information relevant to an evaluation of present radiation protection guides. This report is in response to that request. It presents a summary and analysis, by members of the Advisory Committee on the Biological Effects of Ionizing Radiations and its subcommittees, of current knowledge relating to risks from exposure to ionizing radiation. In many respects, the report is a sequel to the reports of the Committee on the Biological Effects of Atomic Radiation, published by the NAS-NRC from 1956 to 1961.

The effects on populations of exposure to low levels of ionizing radiation. Report of the Advisory Committee on the Biological Effects of Ionizing Radiations

International Nuclear Information System (INIS)

1972-11-01

In the summer of 1970, the Federal Radiation Council (whose activities have since been transferred to the Radiation Office of the EPA) asked the National Academy of Sciences for information relevant to an evaluation of present radiation protection guides. This report is in response to that request. It presents a summary and analysis, by members of the Advisory Committee on the Biological Effects of Ionizing Radiations and its subcommittees, of current knowledge relating to risks from exposure to ionizing radiation. In many respects, the report is a sequel to the reports of the Committee on the Biological Effects of Atomic Radiation, published by the NAS-NRC from 1956 to 1961

Establishing the Biological Relevance of Dipentyl Phthalate Reductions in Fetal Rat Testosterone Production and Plasma and Testis Testosterone Levels

Science.gov (United States)

Phthalate esters (PEs) constitute a large class of compounds that are used for many consumer product applications. Many of the C2-C7 di-ortho PEs reduce fetal testicular hormone and gene expression levels in rats resulting in adverse effects seen later in life but it appears that...

Using Mathematics and Engineering to Solve Problems in Secondary Level Biology

Science.gov (United States)

Cox, Charles; Reynolds, Birdy; Schunn, Christian; Schuchardt, Anita

2016-01-01

There are strong classroom ties between mathematics and the sciences of physics and chemistry, but those ties seem weaker between mathematics and biology. Practicing biologists realize both that there are interesting mathematics problems in biology, and that viewing classroom biology in the context of another discipline could support students'…

Intertwining personal and reward relevance: evidence from the drift-diffusion model.

Science.gov (United States)

Yankouskaya, A; Bührle, R; Lugt, E; Stolte, M; Sui, J

2018-01-24

In their seminal paper 'Is our self nothing but reward', Northoff and Hayes (Biol Psychiatry 69(11):1019-1025, Northoff, Hayes, Biological Psychiatry 69(11):1019-1025, 2011) proposed three models of the relationship between self and reward and opened a continuing debate about how these different fields can be linked. To date, none of the proposed models received strong empirical support. The present study tested common and distinct effects of personal relevance and reward values by de-componenting different stages of perceptual decision making using a drift-diffusion approach. We employed a recently developed associative matching paradigm where participants (N = 40) formed mental associations between five geometric shapes and five labels referring personal relevance in the personal task, or five shape-label pairings with different reward values in the reward task and then performed a matching task by indicating whether a displayed shape-label pairing was correct or incorrect. We found that common effects of personal relevance and monetary reward were manifested in the facilitation of behavioural performance for high personal relevance and high reward value as socially important signals. The differential effects between personal and monetary relevance reflected non-decisional time in a perceptual decision process, and task-specific prioritization of stimuli. Our findings support the parallel processing model (Northoff & Hayes, Biol Psychiatry 69(11):1019-1025, Northoff, Hayes, Biological Psychiatry 69(11):1019-1025, 2011) and suggest that self-specific processing occurs in parallel with high reward processing. Limitations and further directions are discussed.

Data on environmentally relevant level of aflatoxin B1-induced human dendritic cells' functional alteration

Directory of Open Access Journals (Sweden)

Jalil Mehrzad

2018-06-01

Full Text Available We assessed the effects of naturally occurring levels of AFB1 on the expression of key immune molecules and function of human monocyte-derived dendritic cells (MDDCs by cell culture, RT-qPCR, and flow cytometry. Data here revealed that an environmentally relevant level of AFB1 led to remarkably weakened key functional capacity of DCs, up-regulation of key transcripts and DCs apoptosis, down-regulation of key phagocytic element, CD64, and creation of pseudolicensing direction of DCs. Flow cytometry data confirmed a damage towards DCs, i.e., increased apoptosis. The detailed data and their mechanistic effects and the outcome are available in this research article (Mehrzad et al., 2018 [1]. The impaired phagocytosis capacity with triggered pseudolicensing direction of MDDCs caused by AFB1 and dysregulation of the key functional genes could provide a mechanistic explanation for the observed in vivo immunotoxicity associated with this mycotoxin. Keywords: AFB1, Apoptosis, AFB1-detoxifying genes, Dendritic cells, Flow cytometry, Functional genes, Immunnoderegulation, Phagocytosis, RT-qPCR

Evaluating biological transport of radionuclides at low-level waste burial sites

International Nuclear Information System (INIS)

Cadwell, L.L.; Kennedy, W.E.; McKenzie, D.H.

1983-08-01

The purpose of the work reported here is to develop and demonstrate methods for evaluating the long-term impact of biological processes at low-level waste (LLW) disposal sites. As part of this effort, we developed order-of-magnitude estimates of dose-to-man resulting from animal burrowing activity and plant translocation of radionuclides. Reference low-level waste sites in both arid and humid areas of the United States were examined. The results of our evaluation for generalized arid LLW burial site are presented here. Dose-to-man estimates resulting from biotic transport are compared with doses calculated from human intrusion exposure scenarios. Dose-to-man estimates, as a result of biotic transport, are of the same order of magnitude as those resulting from a more commonly evaluated human intrusion scenario. The reported lack of potential importance of biotic transport at LLW sites in earlier assessment studies is not confirmed by our findings. These results indicate that biotic transport has the long-term potential to mobilize radionuclides. Therefore, biotic transport should be carefully evaluated during burial site assessment

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

Transforming Big Data into cancer-relevant insight: An initial, multi-tier approach to assess reproducibility and relevance* | Office of Cancer Genomics

Science.gov (United States)

The Cancer Target Discovery and Development (CTD^2) Network was established to accelerate the transformation of "Big Data" into novel pharmacological targets, lead compounds, and biomarkers for rapid translation into improved patient outcomes. It rapidly became clear in this collaborative network that a key central issue was to define what constitutes sufficient computational or experimental evidence to support a biologically or clinically relevant finding.

Inorganic concepts relevant to metal binding, activity, and toxicity in a biological system

Energy Technology Data Exchange (ETDEWEB)

Hoeschele, J.D. (Warner-Lambert Co., Ann Arbor, MI (USA). Parke-Davis Pharmaceutical Research Div.); Turner, J.E.; England, M.W. (Oak Ridge National Lab., TN (USA))

1990-01-01

The purpose of this paper is to review selected physical and inorganic concepts and factors which might be important in assessing and/or understanding the fact and disposition of a metal system in a biological environment. Hopefully, such inquiries will ultimately permit us to understand, rationalize, and predict differences and trends in biological effects as a function of the basic nature of a metal system and, in optimal cases, serve as input to a system of guidelines for the notion of Chemical Dosimetry.'' The plan of this paper is to first review, in general terms, the basic principles of the Crystal Field Theory (CFT), a unifying theory of bonding in metal complexes. This will provide the necessary theoretical background for the subsequent discussion of selected concepts and factors. 21 refs., 7 figs., 6 tabs.

Evaluation of geologic materials to limit biological intrusion of low-level waste site covers

International Nuclear Information System (INIS)

Hakonson, T.E.; White, G.C.; Karlen, E.M.

1982-01-01

The long-term integrity of low-level waste shallow land burial sites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. This paper reports the preliminary results of a screening study to-determine the effectiveness of four biobarrier materials to stop plant root and animal penetration into simulated low-level wastes. Experiments employed 288 lysimeters consisting of 25-cm-diam PVC pipe, with four factors tested: plant species (alfalfa, barley, and sweet clover); top soil thickness (30 and 60 cm); biobarrier material (crushed tuff, bentonite clay, cobble, and cobble-gravel); and biobarrier thickness (clay-15, 30, and 45 cm, others 30, 60, and 90 cm). The crushed tuff, a sandy backfill material, offers little resistance to root and animal intrusion through the cover profile, while bentonite clay, cobble, and cobble-gravel combinations do reduce plant root and animal intrusion thorugh cover profiles. However, dessication of the clay barrier by invading plant roots may limit the usefulness of this material as a moisture and/or biological barrier. The cobble-gravel combination appears to be the best candidate for further testing on a larger scale because the gravel helps impede the imgration of soil into the cobble layer - the probable cause of failure of cobble-only biobarriers

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/.

Food words distract the hungry: Evidence of involuntary semantic processing of task-irrelevant but biologically-relevant unexpected auditory words.

Science.gov (United States)

Parmentier, Fabrice B R; Pacheco-Unguetti, Antonia P; Valero, Sara

2018-01-01

Rare changes in a stream of otherwise repeated task-irrelevant sounds break through selective attention and disrupt performance in an unrelated visual task by triggering shifts of attention to and from the deviant sound (deviance distraction). Evidence indicates that the involuntary orientation of attention to unexpected sounds is followed by their semantic processing. However, past demonstrations relied on tasks in which the meaning of the deviant sounds overlapped with features of the primary task. Here we examine whether such processing is observed when no such overlap is present but sounds carry some relevance to the participants' biological need to eat when hungry. We report the results of an experiment in which hungry and satiated participants partook in a cross-modal oddball task in which they categorized visual digits (odd/even) while ignoring task-irrelevant sounds. On most trials the irrelevant sound was a sinewave tone (standard sound). On the remaining trials, deviant sounds consisted of spoken words related to food (food deviants) or control words (control deviants). Questionnaire data confirmed state (but not trait) differences between the two groups with respect to food craving, as well as a greater desire to eat the food corresponding to the food-related words in the hungry relative to the satiated participants. The results of the oddball task revealed that food deviants produced greater distraction (longer response times) than control deviants in hungry participants while the reverse effect was observed in satiated participants. This effect was observed in the first block of trials but disappeared thereafter, reflecting semantic saturation. Our results suggest that (1) the semantic content of deviant sounds is involuntarily processed even when sharing no feature with the primary task; and that (2) distraction by deviant sounds can be modulated by the participants' biological needs.

Biology, Bionomics and Molecular Biology of Anopheles sinensis Wiedemann 1828 (Diptera: Culicidae), Main Malaria Vector in China.

Science.gov (United States)

Feng, Xinyu; Zhang, Shaosen; Huang, Fang; Zhang, Li; Feng, Jun; Xia, Zhigui; Zhou, Hejun; Hu, Wei; Zhou, Shuisen

2017-01-01

China has set a goal to eliminate all malaria in the country by 2020, but it is unclear if current understanding of malaria vectors and transmission is sufficient to achieve this objective. Anopheles sinensis is the most widespread malaria vector specie in China, which is also responsible for vivax malaria outbreak in central China. We reviewed literature from 1954 to 2016 on An. sinensis with emphasis on biology, bionomics, and molecular biology. A total of 538 references were relevant and included. An. sienesis occurs in 29 Chinese provinces. Temperature can affect most life-history parameters. Most An. sinensis are zoophilic, but sometimes they are facultatively anthropophilic. Sporozoite analysis demonstrated An. sinensis efficacy on Plasmodium vivax transmission. An. sinensis was not stringently refractory to P. falciparum under experimental conditions, however, sporozoite was not found in salivary glands of field collected An. sinensis . The literature on An. sienesis biology and bionomics was abundant, but molecular studies, such as gene functions and mechanisms, were limited. Only 12 molecules (genes, proteins or enzymes) have been studied. In addition, there were considerable untapped omics resources for potential vector control tools. Existing information on An. sienesis could serve as a baseline for advanced research on biology, bionomics and genetics relevant to vector control strategies.

Classical and spatial stochastic processes with applications to biology

CERN Document Server

Schinazi, Rinaldo B

2014-01-01

The revised and expanded edition of this textbook presents the concepts and applications of random processes with the same illuminating simplicity as its first edition, but with the notable addition of substantial modern material on biological modeling. While still treating many important problems in fields such as engineering and mathematical physics, the book also focuses on the highly relevant topics of cancerous mutations, influenza evolution, drug resistance, and immune response. The models used elegantly apply various classical stochastic models presented earlier in the text, and exercises are included throughout to reinforce essential concepts. The second edition of Classical and Spatial Stochastic Processes is suitable as a textbook for courses in stochastic processes at the advanced-undergraduate and graduate levels, or as a self-study resource for researchers and practitioners in mathematics, engineering, physics, and mathematical biology. Reviews of the first edition: An appetizing textbook for a f...

Biological radiolesions and repair

International Nuclear Information System (INIS)

Laskowski, W.

1981-01-01

In 7 chapters, the book answers the following questions: 1) What reactions are induced in biological matter by absorption of radiation energy. 2) In what parts of the cell do the radiation-induced reactions with detectable biological effects occur. 3) In which way are these cell components changed by different qualities of radiation. 4) What are the cell mechanisms by which radiation-induced changes can be repaired. 5) What is the importance of these repair processes for man, his life and evolution. At the end of each chapter, there is a bibliography of relevant publications in this field. (orig./MG) [de

[How to be prudent with synthetic biology. Synthetic Biology and the precautionary principle].

Science.gov (United States)

Rodríguez López, Blanca

2014-01-01

Synthetic biology is a new discipline that is twofold: firstly it offers the promise to pay benefits that can alleviate some of the ills that plague mankind; On the other hand, like all technologies, holds risks. Given these, the most critical and concerned about the risks, invoke the application of the precautionary principle, common in cases where an activity or new technology creates risks to the environment and/or human health, but far from universally accepted happens to be currently one of the most controversial principles. In this paper the question of the risks and benefits of synthetic biology and the relevance of applying the precautionary principle are analyzed. To do this we proceed as follows. The first part focuses on synthetic biology. At first, this discipline is characterized, with special attention to what is novel compared to the known as "genetic engineering". In the second stage both the benefits and the risks associated with it are discussed. The first part concludes with a review of the efforts currently being made to control or minimize the risks. The second part aims to analyze the precautionary principle and its possible relevance to the case of Synthetic Biology. At first, the different versions and interpretations of the principle and the various criticisms of which has been the subject are reviewed. Finally, after discarding the Precautionary Principle as an useful tool, it is seen as more appropriate some recent proposals to treat technologies that take into account not only risks but also their benefits.

Comparison of the biological effects of {sup 18}F at different intracellular levels

Energy Technology Data Exchange (ETDEWEB)

Kashino, Genro, E-mail: kashino@oita-u.ac.jp [Advanced Molecular Imaging Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita 879-5593 (Japan); Hayashi, Kazutaka; Douhara, Kazumasa [Advanced Molecular Imaging Center, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita 879-5593 (Japan); Kobashigawa, Shinko; Mori, Hiromu [Department of Radiology, Faculty of Medicine, Oita University, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita 879-5593 (Japan)

2014-11-07

Highlights: • We estimated the inductions of DNA DSB in cell treated with {sup 18}F-FDG. • We found that inductions of DNA DSB are dependent on accumulation of {sup 18}F in cell. • Accumulation of {sup 18}F in cell may be indispensable for risk estimation of PET. - Abstract: We herein examined the biological effects of cells treated with {sup 18}F labeled drugs for positron emission tomography (PET). The relationship between the intracellular distribution of {sup 18}F and levels of damaged DNA has yet to be clarified in detail. We used culture cells (Chinese Hamster Ovary cells) treated with two types of {sup 18}F labeled drugs, fluorodeoxyglucose (FDG) and fluorine ion (HF). FDG efficiently accumulated in cells, whereas HF did not. To examine the induction of DNA double strand breaks (DSB), we measured the number of foci for 53BP1 that formed at the site of DNA DSB. The results revealed that although radioactivity levels were the same, the induction of 53BP1 foci was stronger in cells treated with {sup 18}F-FDG than in those treated with {sup 18}F-HF. The clonogenic survival of cells was significantly lower with {sup 18}F-FDG than with {sup 18}F-HF. We concluded that the efficient accumulation of {sup 18}F in cells led to stronger biological effects due to more severe cellular lethality via the induction of DNA DSB.

3S - Systematic, systemic, and systems biology and toxicology.

Science.gov (United States)

Smirnova, Lena; Kleinstreuer, Nicole; Corvi, Raffaella; Levchenko, Andre; Fitzpatrick, Suzanne C; Hartung, Thomas

2018-01-01

A biological system is more than the sum of its parts - it accomplishes many functions via synergy. Deconstructing the system down to the molecular mechanism level necessitates the complement of reconstructing functions on all levels, i.e., in our conceptualization of biology and its perturbations, our experimental models and computer modelling. Toxicology contains the somewhat arbitrary subclass "systemic toxicities"; however, there is no relevant toxic insult or general disease that is not systemic. At least inflammation and repair are involved that require coordinated signaling mechanisms across the organism. However, the more body components involved, the greater the challenge to reca-pitulate such toxicities using non-animal models. Here, the shortcomings of current systemic testing and the development of alternative approaches are summarized. We argue that we need a systematic approach to integrating existing knowledge as exemplified by systematic reviews and other evidence-based approaches. Such knowledge can guide us in modelling these systems using bioengineering and virtual computer models, i.e., via systems biology or systems toxicology approaches. Experimental multi-organ-on-chip and microphysiological systems (MPS) provide a more physiological view of the organism, facilitating more comprehensive coverage of systemic toxicities, i.e., the perturbation on organism level, without using substitute organisms (animals). The next challenge is to establish disease models, i.e., micropathophysiological systems (MPPS), to expand their utility to encompass biomedicine. Combining computational and experimental systems approaches and the chal-lenges of validating them are discussed. The suggested 3S approach promises to leverage 21st century technology and systematic thinking to achieve a paradigm change in studying systemic effects.

Student-oriented learning: an inquiry-based developmental biology lecture course.

Science.gov (United States)

Malacinski, George M

2003-01-01

In this junior-level undergraduate course, developmental life cycles exhibited by various organisms are reviewed, with special attention--where relevant--to the human embryo. Morphological features and processes are described and recent insights into the molecular biology of gene expression are discussed. Ways are studied in which model systems, including marine invertebrates, amphibia, fruit flies and other laboratory species are employed to elucidate general principles which apply to fertilization, cleavage, gastrulation and organogenesis. Special attention is given to insights into those topics which will soon be researched with data from the Human Genome Project. The learning experience is divided into three parts: Part I is a in which the Socratic (inquiry) method is employed by the instructor (GMM) to organize a review of classical developmental phenomena; Part II represents an in which students study the details related to the surveys included in Part I as they have been reported in research journals; Part III focuses on a class project--the preparation of a spiral bound on a topic of relevance to human developmental biology (e.g.,Textbook of Embryonal Stem Cells). Student response to the use of the Socratic method increases as the course progresses and represents the most successful aspect of the course.

Optical sensors and their applications for probing biological systems

DEFF Research Database (Denmark)

Palanco, Marta Espina

There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant and mammal......There is a great interest in exploring and developing new optical sensitive methodologies for probing complex biological systems. In this project we developed non-invasive and sensitive biosensor strategies for studying physiologically relevant chemical and physical properties of plant...... of a trapped cell. The project could provide new insights into the desired biosensor for future membrane-protein cell studies....

Why relevance theory is relevant for lexicography

DEFF Research Database (Denmark)

Bothma, Theo; Tarp, Sven

2014-01-01

This article starts by providing a brief summary of relevance theory in information science in relation to the function theory of lexicography, explaining the different types of relevance, viz. objective system relevance and the subjective types of relevance, i.e. topical, cognitive, situational...... that is very important for lexicography as well as for information science, viz. functional relevance. Since all lexicographic work is ultimately aimed at satisfying users’ information needs, the article then discusses why the lexicographer should take note of all these types of relevance when planning a new...... dictionary project, identifying new tasks and responsibilities of the modern lexicographer. The article furthermore discusses how relevance theory impacts on teaching dictionary culture and reference skills. By integrating insights from lexicography and information science, the article contributes to new...

The Systems Biology Markup Language (SBML: Language Specification for Level 3 Version 2 Core

Directory of Open Access Journals (Sweden)

Hucka Michael

2018-03-01

Full Text Available Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that different software systems can exchange. 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 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language, validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

The Systems Biology Markup Language (SBML: Language Specification for Level 3 Version 1 Core

Directory of Open Access Journals (Sweden)

Hucka Michael

2018-04-01

Full Text Available Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML is a file format for representing computational models in a declarative form that different software systems can exchange. 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 Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language, validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

Science.gov (United States)

Olivier, Brett G; Bergmann, Frank T

2015-09-04

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

Predicting Subtype Selectivity for Adenosine Receptor Ligands with Three-Dimensional Biologically Relevant Spectrum (BRS-3D)

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He, Song-Bing; Ben Hu; Kuang, Zheng-Kun; Wang, Dong; Kong, De-Xin

2016-11-01

Adenosine receptors (ARs) are potential therapeutic targets for Parkinson’s disease, diabetes, pain, stroke and cancers. Prediction of subtype selectivity is therefore important from both therapeutic and mechanistic perspectives. In this paper, we introduced a shape similarity profile as molecular descriptor, namely three-dimensional biologically relevant spectrum (BRS-3D), for AR selectivity prediction. Pairwise regression and discrimination models were built with the support vector machine methods. The average determination coefficient (r2) of the regression models was 0.664 (for test sets). The 2B-3 (A2B vs A3) model performed best with q2 = 0.769 for training sets (10-fold cross-validation), and r2 = 0.766, RMSE = 0.828 for test sets. The models’ robustness and stability were validated with 100 times resampling and 500 times Y-randomization. We compared the performance of BRS-3D with 3D descriptors calculated by MOE. BRS-3D performed as good as, or better than, MOE 3D descriptors. The performances of the discrimination models were also encouraging, with average accuracy (ACC) 0.912 and MCC 0.792 (test set). The 2A-3 (A2A vs A3) selectivity discrimination model (ACC = 0.882 and MCC = 0.715 for test set) outperformed an earlier reported one (ACC = 0.784). These results demonstrated that, through multiple conformation encoding, BRS-3D can be used as an effective molecular descriptor for AR subtype selectivity prediction.

Pollen Contaminated With Field-Relevant Levels of Cyhalothrin Affects Honey Bee Survival, Nutritional Physiology, and Pollen Consumption Behavior.

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Dolezal, Adam G; Carrillo-Tripp, Jimena; Miller, W Allen; Bonning, Bryony C; Toth, Amy L

2016-02-01

Honey bees are exposed to a variety of environmental factors that impact their health, including nutritional stress, pathogens, and pesticides. In particular, there has been increasing evidence that sublethal exposure to pesticides can cause subtle, yet important effects on honey bee health and behavior. Here, we add to this body of knowledge by presenting data on bee-collected pollen containing sublethal levels of cyhalothrin, a pyrethroid insecticide, which, when fed to young honey bees, resulted in significant changes in lifespan, nutritional physiology,and behavior. For the first time, we show that when young, nest-aged bees are presented with pollen containing field-relevant levels of cyhalothrin, they reduce their consumption of contaminated pollen. This indicates that, at least for some chemicals, young bees are able to detect contamination in pollen and change their behavioral response, even if the contamination levels do not prevent foraging honey bees from collecting the contaminated pollen.

Epidemiologic studies of occupational pesticide exposure and cancer: regulatory risk assessments and biologic plausibility.

Science.gov (United States)

Acquavella, John; Doe, John; Tomenson, John; Chester, Graham; Cowell, John; Bloemen, Louis

2003-01-01

Epidemiologic studies frequently show associations between self-reported use of specific pesticides and human cancers. These findings have engendered debate largely on methodologic grounds. However, biologic plausibility is a more fundamental issue that has received only superficial attention. The purpose of this commentary is to review briefly the toxicology and exposure data that are developed as part of the pesticide regulatory process and to discuss the applicability of this data to epidemiologic research. The authors also provide a generic example of how worker pesticide exposures might be estimated and compared to relevant toxicologic dose levels. This example provides guidance for better characterization of exposure and for consideration of biologic plausibility in epidemiologic studies of pesticides.

Realistic biological approaches for improving thermoradiotherapy

DEFF Research Database (Denmark)

Horsman, Michael R

2016-01-01

There is now definitive clinical evidence that hyperthermia can successfully improve the response of certain human tumour types to radiation therapy, but, there is still the need for improvement. From a biological standpoint this can be achieved by either targeting the cellular or vascular...... or radiation in preclinical models and clear benefits in tumour response observed. But few of these methods have actually been combined with thermoradiotherapy. Furthermore, very few combinations have been tested in relevant normal tissue studies, despite the fact that it is the normal tissue response...... that controls the maximal heat or radiation treatment that can be applied. Here we review the most clinically relevant biological approaches that have been shown to enhance thermoradiotherapy, or have the potential to be applied in this context, and suggest how these should be moved forward into the clinic....

Applications of Microfluidics in Quantitative Biology.

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Bai, Yang; Gao, Meng; Wen, Lingling; He, Caiyun; Chen, Yuan; Liu, Chenli; Fu, Xiongfei; Huang, Shuqiang

2018-05-01

Quantitative biology is dedicated to taking advantage of quantitative reasoning and advanced engineering technologies to make biology more predictable. Microfluidics, as an emerging technique, provides new approaches to precisely control fluidic conditions on small scales and collect data in high-throughput and quantitative manners. In this review, the authors present the relevant applications of microfluidics to quantitative biology based on two major categories (channel-based microfluidics and droplet-based microfluidics), and their typical features. We also envision some other microfluidic techniques that may not be employed in quantitative biology right now, but have great potential in the near future. © 2017 Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

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

Cold Spring Harbor symposia on quantitative biology: Volume 49, Recombination at the DNA level

International Nuclear Information System (INIS)

1984-01-01

This volume contains full papers prepared by the participants to the 1984 Cold Springs Harbor Symposia on Quantitative Biology. This year's theme is entitled Recombination at the DNA level. The volume consists of 93 articles grouped into subject areas entitled chromosome mechanics, yeast systems, mammalian homologous recombination, transposons, mu, plant transposons/T4 recombination, topoisomerase, resolvase and gyrase, Escherichia coli general recombination, RecA, repair, leukaryotic enzymes, integration and excision of bacteriophage, site-specific recombination, and recombination in vitro

Increasing URM Undergraduate Student Success through Assessment-Driven Interventions: A Multiyear Study Using Freshman-Level General Biology as a Model System

Science.gov (United States)

Carmichael, Mary C.; St. Clair, Candace; Edwards, Andrea M.; Barrett, Peter; McFerrin, Harris; Davenport, Ian; Awad, Mohamed; Kundu, Anup; Ireland, Shubha Kale

2016-01-01

Xavier University of Louisiana leads the nation in awarding BS degrees in the biological sciences to African-American students. In this multiyear study with ~5500 participants, data-driven interventions were adopted to improve student academic performance in a freshman-level general biology course. The three hour-long exams were common and…

Solid-supported synthesis: From pharmacologically relevant heterocycles to biologically active surfaces

DEFF Research Database (Denmark)

Komnatnyy, Vitaly V.

for solid-phase synthesis, methods for on - and off-bead screening of combinatorial libraries and their applic ation to various biological targets. The first part of the thesis is dedicated to the development of methodology for the synthesis of structurally diverse heterocyclic scaffolds via N...... methods for the controlled organo-functionalization of titanium, one of the most prominent materials in medicinal device industry, have been suggested . Initial acidic and oxidative treatment s of the metal surface genera te reactive hydroxyl moieties , which are subsequently modified with synthetically...... versatile amine -containing reagents. Subsequent applications in antimicrobial peptide synthesis, metal -catalysis, release from the surface, and polymer grafti ng, are also presented....

Bone biology and physiology: Part I. The fundamentals.

Science.gov (United States)

Buck, Donald W; Dumanian, Gregory A

2012-06-01

The principles of bone biology and physiology permeate all subspecialty practices in plastic and reconstructive surgery from hand surgery to aesthetic surgery. Despite its importance in our practices, the biology of bone healing and bone physiology rarely surfaces within textbooks, literature reviews, or residency curricula. In this article, the authors present the first of a two-part series reviewing the important concepts of bone biology and bone physiology relevant to plastic surgery in an effort to ameliorate this educational gap.

Biological Evidence Management for DNA Analysis in Cases of Sexual Assault

Science.gov (United States)

Magalhães, Teresa; Dinis-Oliveira, Ricardo Jorge; Silva, Benedita; Corte-Real, Francisco; Nuno Vieira, Duarte

2015-01-01

Biological evidence with forensic interest may be found in several cases of assault, being particularly relevant if sexually related. Sexual assault cases are characterized by low rates of disclosure, reporting, prosecution, and conviction. Biological evidence is sometimes the only way to prove the occurrence of sexual contact and to identify the perpetrator. The major focus of this review is to propose practical approaches and guidelines to help health, forensic, and law enforcement professionals to deal with biological evidence for DNA analysis. Attention should be devoted to avoiding contamination, degradation, and loss of biological evidence, as well as respecting specific measures to properly handle evidence (i.e., selection, collection, packing, sealing, labeling, storage, preservation, transport, and guarantee of the chain custody). Biological evidence must be carefully managed since the relevance of any finding in Forensic Genetics is determined, in the first instance, by the integrity and quantity of the samples submitted for analysis. PMID:26587562

Biological Evidence Management for DNA Analysis in Cases of Sexual Assault

Directory of Open Access Journals (Sweden)

Teresa Magalhães

2015-01-01

Full Text Available Biological evidence with forensic interest may be found in several cases of assault, being particularly relevant if sexually related. Sexual assault cases are characterized by low rates of disclosure, reporting, prosecution, and conviction. Biological evidence is sometimes the only way to prove the occurrence of sexual contact and to identify the perpetrator. The major focus of this review is to propose practical approaches and guidelines to help health, forensic, and law enforcement professionals to deal with biological evidence for DNA analysis. Attention should be devoted to avoiding contamination, degradation, and loss of biological evidence, as well as respecting specific measures to properly handle evidence (i.e., selection, collection, packing, sealing, labeling, storage, preservation, transport, and guarantee of the chain custody. Biological evidence must be carefully managed since the relevance of any finding in Forensic Genetics is determined, in the first instance, by the integrity and quantity of the samples submitted for analysis.

The Effects of Urban Sprawl on Birds at Multiple Levels of Biological Organization

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Robert Blair

2004-12-01

Full Text Available Urban sprawl affects the environment in myriad ways and at multiple levels of biological organization. In this paper I explore the effects of sprawl on native bird communities by comparing the occurrence of birds along gradients of urban land use in southwestern Ohio and northern California and by examining patterns at the individual, species, community, landscape, and continental levels. I do this by assessing the distribution and abundance of all bird species occupying sites of differing land-use intensity in Ohio and California. Additionally, I conducted predation experiments using artificial nests, tracked the nest fate of American Robins and Northern Cardinals, and assessed land cover in these sites. At the individual level, predation on artificial nests decreased with urbanization; however, this trend was not reflected in the nesting success of robins and cardinals, which did not increase with urbanization. At the species level, sprawl affected local patterns of extinction and invasion; the density of different species peaked at different levels of urbanization. At the community level, species richness and diversity peaked at moderate levels of urbanization, and the number of low-nesting species and of species with multiple broods increased with urbanization. The community-level results may reflect both the species-level patterns of local extinction and invasion as well as broader landscape-level patterns. At the landscape level, a linear combination of spatial heterogeneity and density of woody patches accurately predicted both species richness and Shannon Diversity. At the continental level, local extinction of endemic species, followed by the invasion of ubiquitous weedy species, leads to faunal homogenization between ecoregions.

S-Nitrosothiol measurements in biological systems⋄

Science.gov (United States)

Gow, Andrew; Doctor, Allan; Mannick, Joan; Gaston, Benjamin

2007-01-01

S-Nitrosothiol (SNO) cysteine modifications are regulated signaling reactions that dramatically affect, and are affected by, protein conformation. The lability of the S-NO bond can make SNO-modified proteins cumbersome to measure accurately. Here, we review methodologies for detecting SNO modifications in biology. There are three caveats. 1) Many assays for biological SNOs are used near the limit of detection: standard curves must be in the biologically relevant concentration range. 2) The assays that are most reliable are those that modify SNO protein or peptide chemistry the least. 3) Each result should be quantitatively validated using more than one assay. Improved assays are needed and are in development. PMID:17379583

Multiweek cell culture project for use in upper-level biology laboratories.

Science.gov (United States)

Marion, Rebecca E; Gardner, Grant E; Parks, Lisa D

2012-06-01

This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF, caffeine, epinephrine, heavy metals, and FBS. Students researched primary literature to determine their experimental variables, made their own solutions, and treated their cells over a period of 2 wk. Before this, a sterile technique laboratory was developed to teach students how to work with the cells and minimize contamination. Students designed their experiments, mixed their solutions, seeded their cells, and treated them with their control and experimental media. Students had the choice of manipulating a number of variables, including incubation times, exposure to treatment media, and temperature. At the end of the experiment, students observed the effects of their treatment, harvested and dyed their cells, counted relative cell numbers in control and treatment flasks, and determined the ratio of living to dead cells using a hemocytometer. At the conclusion of the experiment, students presented their findings in a poster presentation. This laboratory can be expanded or adapted to include additional cell lines and treatments. The ability to design and implement their own experiments has been shown to increase student engagement in the biology-related laboratory activities as well as develop the critical thinking skills needed for independent research.

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.

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

Pareto Optimal Design for Synthetic Biology.

Science.gov (United States)

Patanè, Andrea; Santoro, Andrea; Costanza, Jole; Carapezza, Giovanni; Nicosia, Giuseppe

2015-08-01

Recent advances in synthetic biology call for robust, flexible and efficient in silico optimization methodologies. We present a Pareto design approach for the bi-level optimization problem associated to the overproduction of specific metabolites in Escherichia coli. Our method efficiently explores the high dimensional genetic manipulation space, finding a number of trade-offs between synthetic and biological objectives, hence furnishing a deeper biological insight to the addressed problem and important results for industrial purposes. We demonstrate the computational capabilities of our Pareto-oriented approach comparing it with state-of-the-art heuristics in the overproduction problems of i) 1,4-butanediol, ii) myristoyl-CoA, i ii) malonyl-CoA , iv) acetate and v) succinate. We show that our algorithms are able to gracefully adapt and scale to more complex models and more biologically-relevant simulations of the genetic manipulations allowed. The Results obtained for 1,4-butanediol overproduction significantly outperform results previously obtained, in terms of 1,4-butanediol to biomass formation ratio and knock-out costs. In particular overproduction percentage is of +662.7%, from 1.425 mmolh⁻¹gDW⁻¹ (wild type) to 10.869 mmolh⁻¹gDW⁻¹, with a knockout cost of 6. Whereas, Pareto-optimal designs we have found in fatty acid optimizations strictly dominate the ones obtained by the other methodologies, e.g., biomass and myristoyl-CoA exportation improvement of +21.43% (0.17 h⁻¹) and +5.19% (1.62 mmolh⁻¹gDW⁻¹), respectively. Furthermore CPU time required by our heuristic approach is more than halved. Finally we implement pathway oriented sensitivity analysis, epsilon-dominance analysis and robustness analysis to enhance our biological understanding of the problem and to improve the optimization algorithm capabilities.

Global Ozone Distribution relevant to Human Health: Metrics and present day levels from the Tropospheric Ozone Assessment Report (TOAR)

Science.gov (United States)

Fleming, Z. L.; Doherty, R. M.; von Schneidemesser, E.; Cooper, O. R.; Malley, C.; Colette, A.; Xu, X.; Pinto, J. P.; Simpson, D.; Schultz, M. G.; Hamad, S.; Moola, R.; Solberg, S.; Feng, Z.

2017-12-01

Using stations from the TOAR surface ozone database, this study quantifies present-day global and regional distributions of five ozone metrics relevant for both short-term and long-term human exposure. These metrics were explored at ozone monitoring sites globally, and re-classified for this project as urban or non-urban using population densities and night-time lights. National surface ozone limit values are usually related to an annual number of exceedances of daily maximum 8-hour running mean (MDA8), with many countries not even having any ozone limit values. A discussion and comparison of exceedances in the different ozone metrics, their locations and the seasonality of exceedances provides clues as to the regions that potentially have more serious ozone health implications. Present day ozone levels (2010-2014) have been compared globally and show definite geographical differences (see Figure showing the annual 4th highest MDA8 for present day ozone for all non-urban stations). Higher ozone levels are seen in western compared to eastern US, and between southern and northern Europe, and generally higher levels in east Asia. The metrics reflective of peak concentrations show highest values in western North America, southern Europe and East Asia. A number of the metrics show similar distributions of North-South gradients, most prominent across Europe and Japan. The interquartile range of the regional ozone metrics was largest in East Asia, higher for urban stations in Asia but higher for non-urban stations in Europe and North America. With over 3000 monitoring stations included in this analysis and despite the higher densities of monitoring stations in Europe, north America and East Asia, this study provides the most comprehensive global picture to date of surface ozone levels in terms of health-relevant metrics.

The rebirth of the morphogenetic field as an explanatory tool in biology

Directory of Open Access Journals (Sweden)

Perović Slobodan

2013-01-01

Full Text Available I discuss two uses of the concept of the morphogenetic field, a tool of the 19th century biology motivated by particular ontological views of the time, which has been re-emerging and increasingly relevant in explaining microbiological phenomena. I also consider the relation of these uses to the Central Dogma of modern biology as well as Modern Synthesis of Darwinism and genetics. An induced morphogenetic field is determined by a physical (e.g., gravitational field, or it acquires a physical (e.g., visco-elastic field’s characteristics. Such a morphogenetic field presents only a weak challenge to the Central Dogma of Modern Synthesis by indirectly, albeit severely, constraining variability at the molecular level. I discuss explanations that introduce structural inheritance in ciliate protozoa, as well as the experimental evidence on which these arguments are based. The global cellular morphogenetic field is a unit of such inheritance. I discuss relevant cases of structural inheritance in ciliates that bring about internal cellular as well as functional changes and point out that DNA is absent in the cortex and that RNA controls neither intermediary nor the global level of the field. I go on to argue that utilizing knowledge of known physical fields may advance explanations and understanding of the morphogenetic field in ciliates as the unit of both development and inheritance. [Projekat Ministarstva nauke Republike Srbije, br. 179041: Dynamic Systems in nature and society: Philosophical and empirical aspects

Teleology then and now: the question of Kant's relevance for contemporary controversies over function in biology.

Science.gov (United States)

Zammito, John

2006-12-01

'Naturalism' is the aspiration of contemporary philosophy of biology, and Kant simply cannot be refashioned into a naturalist. Instead, epistemological 'deflation' was the decisive feature of Kant's treatment of the 'biomedical' science in his day, so it is not surprising that this might attract some philosophers of science to him today. A certain sense of impasse in the contemporary 'function talk' seems to motivate renewed interest in Kant. Kant--drawing on his eighteenth-century predecessors-provided a discerning and powerful characterization of what biologists had to explain in organic form. His difference from the rest is that he opined that it was impossible to explain it. Its 'inscrutability' was intrinsic. The third Critique essentially proposed the reduction of biology to a kind of pre-scientific descriptivism, doomed never to attain authentic scientificity, to have its 'Newton of the blade of grass'. By contrast, for Locke, and a fortiori for Buffon and his followers, 'intrinsic purposiveness' was a fact of the matter about concrete biological phenomena; the features of internal self-regulation were hypotheses arising out of actual research practice. The difference comes most vividly to light once we recognize Kant's distinction of the concept of organism from the concept of life. If biology must conceptualize self-organization as actual in the world, Kant's regulative/constitutive distinction is pointless in practice and the (naturalist) philosophy of biology has urgent work to undertake for which Kant turns out not to be very helpful.

Biological aspects of chondrosarcoma: Leaps and hurdles.

Science.gov (United States)

Mery, Benoîte; Espenel, Sophie; Guy, Jean-Baptiste; Rancoule, Chloé; Vallard, Alexis; Aloy, Marie-Thérèse; Rodriguez-Lafrasse, Claire; Magné, Nicolas

2018-06-01

Chondrosarcomas are characterized by their chemo- and radioresistance leading to a therapeutic surgical approach which remains the only available treatment with a 10-year survival between 30% and 80% depending on the grade. Non-surgical treatments are under investigation and rely on an accurate biological understanding of drug resistance mechanisms. Novel targeted therapy which represents a new relevant therapeutic approach will open new treatment options by targeting several pathways responsible for processes of proliferation and invasion. Survival pathways such as PI3K, AKT, mTOR and VEGF have been shown to be involved in proliferation of chondrosarcoma cells and antiapoptotic proteins may also play a relevant role. Other proteins such as p53 or COX2 have been identified as potential new targets. This review provides an insight into the biological substantial treatment challenges of CHS and focuses on improving our understanding of CH biology through an overview of major signaling pathways that could represent targets for new therapeutic approaches. Copyright © 2018 Elsevier B.V. All rights reserved.

Biology and relevance of human acute myeloid leukemia stem cells.

Science.gov (United States)

Thomas, Daniel; Majeti, Ravindra

2017-03-23

Evidence of human acute myeloid leukemia stem cells (AML LSCs) was first reported nearly 2 decades ago through the identification of rare subpopulations of engrafting cells in xenotransplantation assays. These AML LSCs were shown to reside at the apex of a cellular hierarchy that initiates and maintains the disease, exhibiting properties of self-renewal, cell cycle quiescence, and chemoresistance. This cancer stem cell model offers an explanation for chemotherapy resistance and disease relapse and implies that approaches to treatment must eradicate LSCs for cure. More recently, a number of studies have both refined and expanded our understanding of LSCs and intrapatient heterogeneity in AML using improved xenotransplant models, genome-scale analyses, and experimental manipulation of primary patient cells. Here, we review these studies with a focus on the immunophenotype, biological properties, epigenetics, genetics, and clinical associations of human AML LSCs and discuss critical questions that need to be addressed in future research. © 2017 by The American Society of Hematology.

Systematic reconstruction of autism biology from massive genetic mutation profiles.

Science.gov (United States)

Luo, Weijun; Zhang, Chaolin; Jiang, Yong-Hui; Brouwer, Cory R

2018-04-01

Autism spectrum disorder (ASD) affects 1% of world population and has become a pressing medical and social problem worldwide. As a paradigmatic complex genetic disease, ASD has been intensively studied and thousands of gene mutations have been reported. Because these mutations rarely recur, it is difficult to (i) pinpoint the fewer disease-causing versus majority random events and (ii) replicate or verify independent studies. A coherent and systematic understanding of autism biology has not been achieved. We analyzed 3392 and 4792 autism-related mutations from two large-scale whole-exome studies across multiple resolution levels, that is, variants (single-nucleotide), genes (protein-coding unit), and pathways (molecular module). These mutations do not recur or replicate at the variant level, but significantly and increasingly do so at gene and pathway levels. Genetic association reveals a novel gene + pathway dual-hit model, where the mutation burden becomes less relevant. In multiple independent analyses, hundreds of variants or genes repeatedly converge to several canonical pathways, either novel or literature-supported. These pathways define recurrent and systematic ASD biology, distinct from previously reported gene groups or networks. They also present a catalog of novel ASD risk factors including 118 variants and 72 genes. At a subpathway level, most variants disrupt the pathway-related gene functions, and in the same gene, they tend to hit residues extremely close to each other and in the same domain. Multiple interacting variants spotlight key modules, including the cAMP (adenosine 3',5'-monophosphate) second-messenger system and mGluR (metabotropic glutamate receptor) signaling regulation by GRKs (G protein-coupled receptor kinases). At a superpathway level, distinct pathways further interconnect and converge to three biology themes: synaptic function, morphology, and plasticity.

Reconstruction of biological networks based on life science data integration.

Science.gov (United States)

Kormeier, Benjamin; Hippe, Klaus; Arrigo, Patrizio; Töpel, Thoralf; Janowski, Sebastian; Hofestädt, Ralf

2010-10-27

For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH--an integration toolkit for building life science data warehouses, CardioVINEdb--a information system for biological data in cardiovascular-disease and VANESA--a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

Mandatory and Voluntary Disclosures of Serbian Listed Companies - Achieved Level and Some Recommendation for Improving their Relevance

Directory of Open Access Journals (Sweden)

Ksenija Denčić-Mihajlov

2016-04-01

Full Text Available Purpose – This paper investigates mandatory and voluntary disclosure practices of non-financial listed companies on the Belgrade Stock Exchange. The results help in determining the level of transparency of Serbian s listed companies and in formulating recommendations for improving the quality and relevance of disclosed information. Design/methodology/approach – We focus on modeling both mandatory and voluntary disclosure indices for financial and non-financial information in order to evaluate the level of disclosure of 63 Serbian companies for reporting period 2012. Findings – We found the low level of both mandatory and voluntary disclosures. Concerning mandatary disclosure, the information that is least frequently disclosed by the sample companies are those related to the material content of the financial statements (information on changes in accounting estimates and corrections of fundamental errors in the previous period, as well as related companies. Serbian companies usually disclose information that contributes to their greater visibility. Similar to the mandatory disclosure, usually published voluntary information are mostly "neutral" from the point of impact on the values reported in the financial statements, which do not contribute to a better understanding of the financial position, profitability and cash flows of the company. Research limitations/implications – There is a limitation concerning the sample size (which is generally intrinsic to Serbian capital market size and the sample structure (research is limited to listed non-financial companies. The study covers the annual reports for 2012 which in Serbia coincides with a crisis period. The same research methodology could be applied on a larger and comprehensive database (non-listed companies and include period after 2012, which will allow the analysis of evolution of disclosure practices by companies within new accounting framework. Originality/value – The authors give

Genetic damage from low-level and natural background radiation

International Nuclear Information System (INIS)

Oftedal, P.

1988-01-01

Relevant predictions that have been made of possible low level biological effects on man are reviewed, and the estimate of genetic damage is discussed. It is concluded that in spite of a number of attempts, no clear-cut case of effects in human populations of radiation at natural levels has been demonstrated. The stability of genetic material is dynamic, with damage, repair and selection running as continuous processes. Genetic materials are well protected and are conservative in the extreme, not least because evolution by genetic adaptation is an expensive process: Substitution of one allele A 1 by another A 2 means the death of the whole A 1 population

Perception analysis of undergraduate students in the health field about the topic Cell Biology

Directory of Open Access Journals (Sweden)

Carlos Alberto Andrade Monerat

2015-06-01

Full Text Available The Brazilian education has been changing over time, especially with the increased offer on the various levels of education. In undergraduate courses, in the health area, the cell biology becomes an essential discipline, because various sectors are directly influenced by their recent discoveries and research. This work aimed to analyze, with undergraduate students, perceptions about the themes at Cell Biology, revealing, with its results, pertinent aspects, as insufficient knowledge about the proposed theme. The definition of a concept of cell, considered a basic aspect, however relevant in this context, exemplifies this situation, because it showed a considerable rate of unsatisfactory answers. On the other hand, was verified the recognition of Cell Biology as an area that presents important contents in the training of these students, due the numerous scientific researches that show its constant evolution in association with themes of medicine and public health.

Clinical and Biological Predictors of Plasma Levels of Soluble RAGE in Critically Ill Patients: Secondary Analysis of a Prospective Multicenter Observational Study

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Thibaut Pranal

2018-01-01

Full Text Available Rationale. Although soluble forms of the receptor for advanced glycation end products (RAGE have been recently proposed as biomarkers in multiple acute or chronic diseases, few studies evaluated the influence of usual clinical and biological parameters, or of patient characteristics and comorbidities, on circulating levels of soluble RAGE in the intensive care unit (ICU setting. Objectives. To determine, among clinical and biological parameters that are usually recorded upon ICU admission, which variables, if any, could be associated with plasma levels of soluble RAGE. Methods. Data for this ancillary study were prospectively obtained from adult patients with at least one ARDS risk factor upon ICU admission enrolled in a large multicenter observational study. At ICU admission, plasma levels of total soluble RAGE (sRAGE and endogenous secretory (esRAGE were measured by duplicate ELISA and baseline patient characteristics, comorbidities, and usual clinical and biological indices were recorded. After univariate analyses, significant variables were used in multivariate, multidimensional analyses. Measurements and Main Results. 294 patients were included in this ancillary study, among whom 62% were admitted for medical reasons, including septic shock (11%, coma (11%, and pneumonia (6%. Although some variables were associated with plasma levels of RAGE soluble forms in univariate analysis, multidimensional analyses showed no significant association between admission parameters and baseline plasma sRAGE or esRAGE. Conclusions. We found no obvious association between circulating levels of soluble RAGE and clinical and biological indices that are usually recorded upon ICU admission. This trial is registered with NCT02070536.

Do women on management board increase fair value relevance?

OpenAIRE

Velte, Patrick

2017-01-01

The purpose of this paper is the link between women on management board and the value relevance of fair value accounting according to IFRS 13. The empirical quantitative study covers a sample of German companies listed at the Prime Standard of the Frankfurt Stock Exchange for the business years 2013-2015 (411 firm-year observations). Value relevance is measured by the modified Ohlson (1995) model and we separate fair value accounting in level 1, level 2 and level 3 fair values. Multiple regre...

Mathematical biology

CERN Document Server

Murray, James D

1993-01-01

The book is a textbook (with many exercises) giving an in-depth account of the practical use of mathematical modelling in the biomedical sciences. The mathematical level required is generally not high and the emphasis is on what is required to solve the real biological problem. The subject matter is drawn, e.g. from population biology, reaction kinetics, biological oscillators and switches, Belousov-Zhabotinskii reaction, reaction-diffusion theory, biological wave phenomena, central pattern generators, neural models, spread of epidemics, mechanochemical theory of biological pattern formation and importance in evolution. Most of the models are based on real biological problems and the predictions and explanations offered as a direct result of mathematical analysis of the models are important aspects of the book. The aim is to provide a thorough training in practical mathematical biology and to show how exciting and novel mathematical challenges arise from a genuine interdisciplinary involvement with the biosci...

Quantification of biologically effective environmental UV irradiance

Science.gov (United States)

Horneck, G.

To determine the impact of environmental UV radiation on human health and ecosystems demands monitoring systems that weight the spectral irradiance according to the biological responses under consideration. In general, there are three different approaches to quantify a biologically effective solar irradiance: (i) weighted spectroradiometry where the biologically weighted radiometric quantities are derived from spectral data by multiplication with an action spectrum of a relevant photobiological reaction, e.g. erythema, DNA damage, skin cancer, reduced productivity of terrestrial plants and aquatic foodweb; (ii) wavelength integrating chemical-based or physical dosimetric systems with spectral sensitivities similar to a biological response curve; and (iii) biological dosimeters that directly weight the incident UV components of sunlight in relation to the effectiveness of the different wavelengths and to interactions between them. Most biological dosimeters, such as bacteria, bacteriophages, or biomolecules, are based on the UV sensitivity of DNA. If precisely characterized, biological dosimeters are applicable as field and personal dosimeters.

A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Directory of Open Access Journals (Sweden)

Mosca Ettore

2007-08-01

it aims to become a useful resource for collecting all the information related to actual and future models of this network. The flexibility of the database allows the addition of mathematical data which are used for simulating the behavior of the cell cycle components in the different models. The resource deals with two relevant problems in systems biology: data integration and mathematical simulation of a crucial biological process related to cancer, such as the cell cycle. In this way the resource is useful both to retrieve information about cell cycle model components and to analyze their dynamical properties. The Cell Cycle Database can be used to find system-level properties, such as stable steady states and oscillations, by coupling structure and dynamical information about models.

Mesoscopic biology

Indian Academy of Sciences (India)

In this paper we present a qualitative outlook of mesoscopic biology where the typical length scale is of the order of nanometers and the energy scales comparable to thermal energy. Novel biomolecular machines, governed by coded information at the level of DNA and proteins, operate at these length scales in biological ...

Answering biological questions: Querying a systems biology database for nutrigenomics

NARCIS (Netherlands)

Evelo, C.T.; Bochove, K. van; Saito, J.T.

2011-01-01

The requirement of systems biology for connecting different levels of biological research leads directly to a need for integrating vast amounts of diverse information in general and of omics data in particular. The nutritional phenotype database addresses this challenge for nutrigenomics. A

Feasibility of disposal of high-level radioactive waste into the seabed. Volume 6: Deep-sea biology, biological processes and radiobiology

International Nuclear Information System (INIS)

Pentreath, R.J.; Hargrave, B.T.; Roe, H.S.J.; Sibuet, M.

1988-01-01

One of the options suggested for disposal of high-level radioactive waste resulting from the generation of nuclear power is burial beneath the deep ocean floor in geologically stable sediment formations which have no economic value. The 8-volume series provides an assessment of the technical feasibility and radiological safety of this disposal concept based on the results obtained by ten years of co-operation and information exchange among the Member countries participating in the NEA Seabed Working Group. This report summarizes the biological description of selected sites, the means by which radionuclides could result in human exposure via seafood pathways, and the doses likely to be received by, and effects on, the deep-sea fauna

Complex mixtures: Relevance of combined exposure to substances at low dose levels

NARCIS (Netherlands)

Leeman, W.R.; Krul, L.; Houben, G.F.

2013-01-01

Upon analysis of chemically complex food matrices a forest of peaks is likely to be found. Identification of these peaks and concurrent determination of the toxicological relevance upon exposure is very time consuming, expensive and often requires animal studies. Recently, a safety assessment

Occurrence of 210Po and Biological Effects of Low-Level Exposure: The Need for Research

Science.gov (United States)

Wiemels, Joseph L.

2012-01-01

Background: Polonium-210 (210Po) concentrations that exceed 1 Bq/L in drinking-water supplies have been reported from four widely separated U.S. states where exposure to it went unnoticed for decades. The radionuclide grandparents of 210Po are common in sediments, and segments of the public may be chronically exposed to low levels of 210Po in drinking water or in food products from animals raised in contaminated areas. Objectives: We summarized information on the environmental behavior, biokinetics, and toxicology of 210Po and identified the need for future research. Methods: Potential linkages between environmental exposure to 210Po and human health effects were identified in a literature review. Discussion: 210Po accumulates in the ovaries where it kills primary oocytes at low doses. Because of its radiosensitivity and tendency to concentrate 210Po, the ovary may be the critical organ in determining the lowest injurious dose for 210Po. 210Po also accumulates in the yolk sac of the embryo and in the fetal and placental tissues. Low-level exposure to 210Po may have subtle, long-term biological effects because of its tropism towards reproductive and embryonic and fetal tissues where exposure to a single alpha particle may kill or damage critical cells. 210Po is present in cigarettes and maternal smoking has several effects that appear consistent with the toxicology of 210Po. Conclusions: Much of the important biological and toxicological research on 210Po is more than four decades old. New research is needed to evaluate environmental exposure to 210Po and the biological effects of low-dose exposure to it so that public health officials can develop appropriate mitigation measures where necessary. PMID:22538346

Electro-induced reactions of biologically important molecules

International Nuclear Information System (INIS)

Kocisek, J.

2010-01-01

The thesis presents the results of research activities in the field of electron interactions with biologically relevant molecules which was carried out during my PhD studies at the Department of Experimental Physics, Comenius University in Bratislava. Electron induced interactions with biologically relevant molecules were experimentally studied using crossed electron-molecule beams experiment. The obtained results, were presented in four publications in international scientific journals. First study of deals with electron impact ionisation of furanose alcohols [see 1. in list of author publications on page 22]. It has been motivated by most important works in the field of electron induced damages of DNA bases [4]. Studied 3-hydroxytetrahydrofuran and tetrahydrofurfuryl alcohol, are important model molecules for more complex biological systems (e.g. deoxyribose).The influence of hydroxyl group on stabilisation of the positive ions of the molecules, together with the stability of furan ring in ionized form are main themes of the study. The studies of small amides and aminoacids are connected to scientific studies in the field of formation of the aminoacids and other biologically relevant molecules in space and works trying to explain electron induced processes in more complex molecules[12, 13, 24]. The most important results were obtained for aminoacid Serine [see 2. in list of author publications on page 22]. We have showed that additional OH group of Serine considerably lower the reaction enthalpy limit of reactions resulting to formation of neutral water molecules, in comparison to other amino acids. Also the study of (M-H)- reaction channel using the electron beam with FWHM under 100 meV is of high importance in the field. The last part of the thesis is focused on the electron interactions with organosilane compounds. Materials prepared from organosilane molecules in plasmas have wide range of applications in both biology and medicine. We have studied electron

Set membership experimental design for biological systems

Directory of Open Access Journals (Sweden)

Marvel Skylar W

2012-03-01

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

Assimilable organic carbon (AOC) variation in reclaimed water: Insight on biological stability evaluation and control for sustainable water reuse.

Science.gov (United States)

Chen, Zhuo; Yu, Tong; Ngo, Huu Hao; Lu, Yun; Li, Guoqiang; Wu, Qianyuan; Li, Kuixiao; Bai, Yu; Liu, Shuming; Hu, Hong-Ying

2018-04-01

This review highlights the importance of conducting biological stability evaluation due to water reuse progression. Specifically, assimilable organic carbon (AOC) has been identified as a practical indicator for microbial occurrence and regrowth which ultimately influence biological stability. Newly modified AOC bioassays aimed for reclaimed water are introduced. Since elevated AOC levels are often detected after tertiary treatment, the review emphasizes that actions can be taken to either limit AOC levels prior to disinfection or conduct post-treatment (e.g. biological filtration) as a supplement to chemical oxidation based approaches (e.g. ozonation and chlorine disinfection). During subsequent distribution and storage, microbial community and possible microbial regrowth caused by complex interactions are discussed. It is suggested that microbial surveillance, AOC threshold values, real-time field applications and surrogate parameters could provide additional information. This review can be used to formulate regulatory plans and strategies, and to aid in deriving relevant control, management and operational guidance. Copyright © 2018 Elsevier Ltd. All rights reserved.

Alteration of serum thymus and activation-regulated chemokine level during biologic therapy for psoriasis: Possibility as a marker reflecting favorable response to anti-interleukin-17A agents.

Science.gov (United States)

Shibuya, Takashi; Honma, Masaru; Iinuma, Shin; Iwasaki, Takeshi; Takahashi, Hidetoshi; Ishida-Yamamoto, Akemi

2018-06-01

Biologics show great efficacy in treating psoriasis, a chronic inflammatory skin disease. The high cost and side-effects of biologics, dose-reduction, elongation of administration interval and suspension are possible options. However, there has been no reliable biomarker we can use when we consider these moderations in therapy. This study was conducted to test the possibility of using serum thymus and activation-regulated chemokine (TARC) level as an indicator for step down of biologic therapy. Serum TARC level was measured in 70 psoriatic patients at Asahikawa Medical University, and a correlation of TARC and severity of skin lesions was analyzed. Referring to serum TARC level, psoriatic patients can be divided into two groups. One is a population in which serum TARC level is positively correlated with severity of skin lesions, and the other is a population with low psoriatic severity and high TARC level. Serum TARC level was higher in the group that achieved PASI-clear with biologics than in the group which did not achieve PASI-clear. Among biologics, the group treated with secukinumab, an anti-interleukin (IL)-17A agent, showed significantly higher TARC level compared with the group treated with anti-tumor necrosis factor agents. In certain populations achieving PASI-clear, serum TARC level may be a potent marker reflecting better response to IL-17A inhibitors, and in this case step down of treatment for psoriasis is possible. © 2018 Japanese Dermatological Association.

Biology and Mechanics of Blood Flows Part I: Biology

CERN Document Server

Thiriet, Marc

2008-01-01

Biology and Mechanics of Blood Flows presents the basic knowledge and state-of-the-art techniques necessary to carry out investigations of the cardiovascular system using modeling and simulation. Part I of this two-volume sequence, Biology, addresses the nanoscopic and microscopic scales. The nanoscale corresponds to the scale of biochemical reaction cascades involved in cell adaptation to mechanical stresses among other stimuli. The microscale is the scale of stress-induced tissue remodeling associated with acute or chronic loadings. The cardiovascular system, like any physiological system, has a complicated three-dimensional structure and composition. Its time dependent behavior is regulated, and this complex system has many components. In this authoritative work, the author provides a survey of relevant cell components and processes, with detailed coverage of the electrical and mechanical behaviors of vascular cells, tissues, and organs. Because the behaviors of vascular cells and tissues are tightly coupl...

Teaching Biology through Statistics: Application of Statistical Methods in Genetics and Zoology Courses

Science.gov (United States)

Colon-Berlingeri, Migdalisel; Burrowes, Patricia A.

2011-01-01

Incorporation of mathematics into biology curricula is critical to underscore for undergraduate students the relevance of mathematics to most fields of biology and the usefulness of developing quantitative process skills demanded in modern biology. At our institution, we have made significant changes to better integrate mathematics into the…

Web-Based Learning Enhancements: Video Lectures through Voice-Over PowerPoint in a Majors-Level Biology Course

Science.gov (United States)

Lents, Nathan H.; Cifuentes, Oscar E.

2009-01-01

This study is an experimental introduction of web-based lecture delivery into a majors-level introductory biology course. Web-based delivery, achieved through the use of prerecorded Voice-Over PowerPoint video lectures, was introduced on a limited basis to an experimental section while a control group, with the same instructor, received standard…

Reconstruction of biological networks based on life science data integration

Directory of Open Access Journals (Sweden)

Kormeier Benjamin

2010-06-01

Full Text Available For the implementation of the virtual cell, the fundamental question is how to model and simulate complex biological networks. Therefore, based on relevant molecular database and information systems, biological data integration is an essential step in constructing biological networks. In this paper, we will motivate the applications BioDWH - an integration toolkit for building life science data warehouses, CardioVINEdb - a information system for biological data in cardiovascular-disease and VANESA- a network editor for modeling and simulation of biological networks. Based on this integration process, the system supports the generation of biological network models. A case study of a cardiovascular-disease related gene-regulated biological network is also presented.

Computational Systems Chemical Biology

OpenAIRE

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander

2011-01-01

There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

Integrated pathway clusters with coherent biological themes for target prioritisation.

Directory of Open Access Journals (Sweden)

Yi-An Chen

Full Text Available Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied repositories often differs in scope and content, preventing a more effective and comprehensive characterisation of gene sets. Here we describe a new approach to constructing biologically coherent gene sets from pathway data in major public repositories and employing them for functional analysis of large gene sets. We first revealed significant overlaps in gene content between different pathways and then defined a clustering method based on the shared gene content and the similarity of gene overlap patterns. We established the biological relevance of the constructed pathway clusters using independent quantitative measures and we finally demonstrated the effectiveness of the constructed pathway clusters in comparative functional enrichment analysis of gene sets associated with diverse human diseases gathered from the literature. The pathway clusters and gene mappings have been integrated into the TargetMine data warehouse and are likely to provide a concise, manageable and biologically relevant means of functional analysis of gene sets and to facilitate candidate gene prioritisation.

Is 'class effect' relevant when assessing the benefit/risk profile of a biologic agent?

NARCIS (Netherlands)

Sterry, W.; Kerkhof, P.C.M. van de

2012-01-01

Psoriasis is a chronic, genetically predisposed skin disorder, characterised by thickened scaly plaques. Although no therapy is recognised as curative, therapies aimed at symptom control include biologic agents that are generally designed to block molecular activation of cellular pathways of a

Biologically-inspired approaches for self-organization, adaptation, and collaboration of heterogeneous autonomous systems

Science.gov (United States)

Steinberg, Marc

2011-06-01

This paper presents a selective survey of theoretical and experimental progress in the development of biologicallyinspired approaches for complex surveillance and reconnaissance problems with multiple, heterogeneous autonomous systems. The focus is on approaches that may address ISR problems that can quickly become mathematically intractable or otherwise impractical to implement using traditional optimization techniques as the size and complexity of the problem is increased. These problems require dealing with complex spatiotemporal objectives and constraints at a variety of levels from motion planning to task allocation. There is also a need to ensure solutions are reliable and robust to uncertainty and communications limitations. First, the paper will provide a short introduction to the current state of relevant biological research as relates to collective animal behavior. Second, the paper will describe research on largely decentralized, reactive, or swarm approaches that have been inspired by biological phenomena such as schools of fish, flocks of birds, ant colonies, and insect swarms. Next, the paper will discuss approaches towards more complex organizational and cooperative mechanisms in team and coalition behaviors in order to provide mission coverage of large, complex areas. Relevant team behavior may be derived from recent advances in understanding of the social and cooperative behaviors used for collaboration by tens of animals with higher-level cognitive abilities such as mammals and birds. Finally, the paper will briefly discuss challenges involved in user interaction with these types of systems.

How does undergraduate college biology students' level of understanding, in regard to the role of the seed plant root system, relate to their level of understanding of photosynthesis?

Science.gov (United States)

Njeng'ere, James Gicheha

This research study investigated how undergraduate college biology students' level of understanding of the role of the seed plant root system relates to their level of understanding of photosynthesis. This research was conducted with 65 undergraduate non-majors biology who had completed 1 year of biology at Louisiana State University in Baton Rouge and Southeastern Louisiana University in Hammond. A root probe instrument was developed from some scientifically acceptable propositional statements about the root system, the process of photosynthesis, as well as the holistic nature of the tree. These were derived from research reviews of the science education and the arboriculture literature. This was administered to 65 students selected randomly from class lists of the two institutions. Most of the root probe's items were based on the Live Oak tree. An in-depth, clinical interview-based analysis was conducted with 12 of those tested students. A team of root experts participated by designing, validating and answering the same questions that the students were asked. A "systems" lens as defined by a team of college instructors, root experts (Shigo, 1991), and this researcher was used to interpret the results. A correlational coefficient determining students' level of understanding of the root system and their level of understanding of the process of photosynthesis was established by means of Pearson's r correlation (r = 0.328) using the SAS statistical analysis (SAS, 1987). From this a coefficient of determination (r2 = 0.104) was determined. Students' level of understanding of the Live Oak root system (mean score 5.94) was not statistically different from their level of understanding of the process of photosynthesis (mean score 5.54) as assessed by the root probe, t (129) = 0.137, p > 0.05 one tailed-test. This suggests that, to some degree, level of the root system limits level of understanding of photosynthesis and vice versa. Analysis of quantitative and qualitative

A biologia na violência Biology in the violence

Directory of Open Access Journals (Sweden)

Renato Zamora Flores

2002-01-01

Full Text Available As contribuições da biologia, em especial da genética do comportamento e da psicologia evolucionista, para o entendimento da violência nas sociedades contemporâneas não têm sido bem entendidas por outras áreas do conhecimento que estudam o mesmo fenômeno em níveis de maior complexidade, como as ciências sociais. Estudos recentes mostram que, no nível teórico, o descaso em relação à importância de abordagens genéticas e darwinianas da violência deixam lacunas nos modelos causais utilizados. No exercício prático da resolução de problemas sociais, a exclusão dos aspectos biológicos, como a relevância de certos estados mentais nas condutas violentas, leva à ausência de recursos de saúde e assistência social, na sociedade, para auxiliar indivíduos predispostos a comportamentos violentos a lidarem com suas circunstâncias.The contributions of biology, especially behavior genetics and evolutionary psychology, to understanding violence in the contemporarys societies have not been understood by other areas of the knowledge that study the same phenomenon at levels of bigher complexity, as the social sciences. Recent studies show that, at the theoretical level, the indifference about the importance of genetics and Darwinians approaches to violence leaves gaps in the causal models used. In the practical exercise of the resolution of social problems, the exclusion of the biological aspects, as the relevance of certain mental states in violent behaviors, generate the absence of health and social resources to assist persons predisposed to violent behavior to deal with it.

Comparing human peritoneal fluid and phosphate-buffered saline for drug delivery: do we need bio-relevant media?

Science.gov (United States)

Bhusal, Prabhat; Rahiri, Jamie Lee; Sua, Bruce; McDonald, Jessica E; Bansal, Mahima; Hanning, Sara; Sharma, Manisha; Chandramouli, Kaushik; Harrison, Jeff; Procter, Georgina; Andrews, Gavin; Jones, David S; Hill, Andrew G; Svirskis, Darren

2018-06-01

An understanding of biological fluids at the site of administration is important to predict the fate of drug delivery systems in vivo. Little is known about peritoneal fluid; therefore, we have investigated this biological fluid and compared it to phosphate-buffered saline, a synthetic media commonly used for in vitro evaluation of intraperitoneal drug delivery systems. Human peritoneal fluid samples were analysed for electrolyte, protein and lipid levels. In addition, physicochemical properties were measured alongside rheological parameters. Significant inter-patient variations were observed with regard to pH (p < 0.001), buffer capacity (p < 0.05), osmolality (p < 0.001) and surface tension (p < 0.05). All the investigated physicochemical properties of peritoneal fluid differed from phosphate-buffered saline (p < 0.001). Rheological examination of peritoneal fluid demonstrated non-Newtonian shear thinning behaviour and predominantly exhibited the characteristics of an entangled network. Inter-patient and inter-day variability in the viscosity of peritoneal fluid was observed. The solubility of the local anaesthetic lidocaine in peritoneal fluid was significantly higher (p < 0.05) when compared to phosphate-buffered saline. Interestingly, the dissolution rate of lidocaine was not significantly different between the synthetic and biological media. Importantly, and with relevance to intraperitoneal drug delivery systems, the sustained release of lidocaine from a thermosensitive gel formulation occurred at a significantly faster rate into peritoneal fluid. Collectively, these data demonstrate the variation between commonly used synthetic media and human peritoneal fluid. The differences in drug release rates observed illustrate the need for bio-relevant media, which ultimately would improve in vitro-in vivo correlation.

Biological challenges of true space settlement

Science.gov (United States)

Mankins, John C.; Mankins, Willa M.; Walter, Helen

2018-05-01

"Space Settlements" - i.e., permanent human communities beyond Earth's biosphere - have been discussed within the space advocacy community since the 1970s. Now, with the end of the International Space Station (ISS) program fast approaching (planned for 2024-2025) and the advent of low cost Earth-to-orbit (ETO) transportation in the near future, the concept is coming once more into mainstream. Considerable attention has been focused on various issues associated with the engineering and human health considerations of space settlement such as artificial gravity and radiation shielding. However, relatively little attention has been given to the biological implications of a self-sufficient space settlement. Three fundamental questions are explored in this paper: (1) what are the biological "foundations" of truly self-sufficient space settlements in the foreseeable future, (2) what is the minimum scale for such self-sustaining human settlements, and (3) what are the integrated biologically-driven system requirements for such settlements? The paper examines briefly the implications of the answers to these questions in relevant potential settings (including free space, the Moon and Mars). Finally, this paper suggests relevant directions for future research and development in order for such space settlements to become viable in the future.

Neutron interactions with biological tissue. Final report

International Nuclear Information System (INIS)

1998-01-01

This program was aimed at creating a quantitative physical description, at the micrometer and nanometer levels, of the physical interactions of neutrons with tissue through the ejected secondary charged particles. The authors used theoretical calculations whose input includes neutron cross section data; range, stopping power, ion yield, and straggling information; and geometrical properties. Outputs are initial and slowing-down spectra of charged particles, kerma factors, average values of quality factors, microdosimetric spectra, and integral microdosimetric parameters such as bar y F , bar y D , y * . Since it has become apparent that nanometer site sizes are also relevant to radiobiological effects, the calculations of event size spectra and their parameters were extended to these smaller diameters. This information is basic to radiological physics, radiation biology, radiation protection of workers, and standards for neutron dose measurement

Preliminary assessment of geologic materials to minimize biological intrusion of low-level waste trench covers and plans for the future

International Nuclear Information System (INIS)

Hakonson, T.E.; White, G.C.; Gladney, E.S.; Muller, M.

1981-01-01

The long-term integrity of low-level waste shallow land burial sites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. Past research on low-level waste shallow land burial methods has emphasized physical (i.e., water infiltration, soil erosion) and chemical (radionuclide leaching) processes that can cause radionuclide transport from a waste site. Preliminary results demonstrate that a sandy backfill material offers little resistance to root and animal intrusion through the cover profile. However, bentonite clay, cobble, and cobble-gravel combinations do reduce plant root and animal intrusion through cover profiles compared with sandy backfill soil. However, bentonite clay barrier systems appear to be degraded by plant roots through time. Desiccation of the clay barrier by invading plant roots may limit the usefulness of bentonite clay as a moisture and/or biological carrier unless due consideration is given to this interaction. Future experiments are described that further examine the effect of plant roots on clay barrier systems and that determine the effectiveness of proposed biological barriers on larger scales and under various stress conditions

Hearing Tests on Mobile Devices: Evaluation of the Reference Sound Level by Means of Biological Calibration.

Science.gov (United States)

Masalski, Marcin; Kipiński, Lech; Grysiński, Tomasz; Kręcicki, Tomasz

2016-05-30

Hearing tests carried out in home setting by means of mobile devices require previous calibration of the reference sound level. Mobile devices with bundled headphones create a possibility of applying the predefined level for a particular model as an alternative to calibrating each device separately. The objective of this study was to determine the reference sound level for sets composed of a mobile device and bundled headphones. Reference sound levels for Android-based mobile devices were determined using an open access mobile phone app by means of biological calibration, that is, in relation to the normal-hearing threshold. The examinations were conducted in 2 groups: an uncontrolled and a controlled one. In the uncontrolled group, the fully automated self-measurements were carried out in home conditions by 18- to 35-year-old subjects, without prior hearing problems, recruited online. Calibration was conducted as a preliminary step in preparation for further examination. In the controlled group, audiologist-assisted examinations were performed in a sound booth, on normal-hearing subjects verified through pure-tone audiometry, recruited offline from among the workers and patients of the clinic. In both the groups, the reference sound levels were determined on a subject's mobile device using the Bekesy audiometry. The reference sound levels were compared between the groups. Intramodel and intermodel analyses were carried out as well. In the uncontrolled group, 8988 calibrations were conducted on 8620 different devices representing 2040 models. In the controlled group, 158 calibrations (test and retest) were conducted on 79 devices representing 50 models. Result analysis was performed for 10 most frequently used models in both the groups. The difference in reference sound levels between uncontrolled and controlled groups was 1.50 dB (SD 4.42). The mean SD of the reference sound level determined for devices within the same model was 4.03 dB (95% CI 3

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

Two bridges between biology and learning

Directory of Open Access Journals (Sweden)

Jorun Nyléhn

2016-04-01

Full Text Available Human biology, in terms of organization of our brains and our evolutionary past, constrains and enables learning. Two examples where neurobiology and evolution influences learning are given and discussed in relation to education: mirror neurons and adaptive memory. Mirror neurons serves imitation and understanding of other peoples intentions. Adaptive memory implies that our memory is an adaptation influenced by our evolutionary past, enabling us to solve problems in the present and in the future. Additionally, the aim is to contribute to bridges between natural and social sciences in an attempt to achieve an improved understanding of learning. The relevance of perspectives on learning founded in biology are discussed, and the article argues for including biological perspectives in discussions of education and learning processes.

Carcinogenesis-relevant biological events in the pathophysiology of the efferocytosis phenomenon

Directory of Open Access Journals (Sweden)

Gargi Sachin Sarode

2017-12-01

Full Text Available The effective removal of cells undergoing programmed cell death, which is referred to as efferocytosis, prevents the leakage of intracellular contents into the surrounding tissue, which could lead to tissue damage and inflammation. Efferocytosis involves a coordinated orchestration of multiple steps that lead to a swift, coherent and immunologically silent removal of dying cells. The release of wound healing cytokines, which resolve inflammation and enhance tissue repair, is an important feature of efferocytosis. However, in addition to the healing cytokines released during efferocytosis, the immunosuppressive action of cytokines promotes the tumor microenvironment, enhances the motility of cancer cells and promotes the evasion of antitumor immunity. The aim of the present review was to comprehensively discuss the efferocytosis phenomenon, the important players associated with this process and their role in cancer-related biological events.

Positive affect and markers of inflammation: discrete positive emotions predict lower levels of inflammatory cytokines.

Science.gov (United States)

Stellar, Jennifer E; John-Henderson, Neha; Anderson, Craig L; Gordon, Amie M; McNeil, Galen D; Keltner, Dacher

2015-04-01

Negative emotions are reliably associated with poorer health (e.g., Kiecolt-Glaser, McGuire, Robles, & Glaser, 2002), but only recently has research begun to acknowledge the important role of positive emotions for our physical health (Fredrickson, 2003). We examine the link between dispositional positive affect and one potential biological pathway between positive emotions and health-proinflammatory cytokines, specifically levels of interleukin-6 (IL-6). We hypothesized that greater trait positive affect would be associated with lower levels of IL-6 in a healthy sample. We found support for this hypothesis across two studies. We also explored the relationship between discrete positive emotions and IL-6 levels, finding that awe, measured in two different ways, was the strongest predictor of lower levels of proinflammatory cytokines. These effects held when controlling for relevant personality and health variables. This work suggests a potential biological pathway between positive emotions and health through proinflammatory cytokines. (c) 2015 APA, all rights reserved).

Chemistry and the worm: Caenorhabditis elegans as a platform for integrating chemical and biological research.

Science.gov (United States)

Hulme, S Elizabeth; Whitesides, George M

2011-05-16

This Review discusses the potential usefulness of the worm Caenorhabditis elegans as a model organism for chemists interested in studying living systems. C. elegans, a 1 mm long roundworm, is a popular model organism in almost all areas of modern biology. The worm has several features that make it attractive for biology: it is small (1000 cells), transparent, and genetically tractable. Despite its simplicity, the worm exhibits complex phenotypes associated with multicellularity: the worm has differentiated cells and organs, it ages and has a well-defined lifespan, and it is capable of learning and remembering. This Review argues that the balance between simplicity and complexity in the worm will make it a useful tool in determining the relationship between molecular-scale phenomena and organism-level phenomena, such as aging, behavior, cognition, and disease. Following an introduction to worm biology, the Review provides examples of current research with C. elegans that is chemically relevant. It also describes tools-biological, chemical, and physical-that are available to researchers studying the worm. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Co-culture systems and technologies: taking synthetic biology to the next level.

Science.gov (United States)

Goers, Lisa; Freemont, Paul; Polizzi, Karen M

2014-07-06

Co-culture techniques find myriad applications in biology for studying natural or synthetic interactions between cell populations. Such techniques are of great importance in synthetic biology, as multi-species cell consortia and other natural or synthetic ecology systems are widely seen to hold enormous potential for foundational research as well as novel industrial, medical and environmental applications with many proof-of-principle studies in recent years. What is needed for co-cultures to fulfil their potential? Cell-cell interactions in co-cultures are strongly influenced by the extracellular environment, which is determined by the experimental set-up, which therefore needs to be given careful consideration. An overview of existing experimental and theoretical co-culture set-ups in synthetic biology and adjacent fields is given here, and challenges and opportunities involved in such experiments are discussed. Greater focus on foundational technology developments for co-cultures is needed for many synthetic biology systems to realize their potential in both applications and answering biological questions. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Biological condition gradient: Applying a framework for determining the biological integrity of coral reefs

Science.gov (United States)

The goals of the U.S. Clean Water Act (CWA) are to restore and maintain the chemical, physical and biological integrity of water resources. Although clean water is a goal, another is to safeguard biological communities by defining levels of biological integrity to protect aquatic...

Tributyltin induces premature hatching and reduces locomotor activity in zebrafish (Danio rerio) embryos/larvae at environmentally relevant levels.

Science.gov (United States)

Liang, Xuefang; Souders, Christopher L; Zhang, Jiliang; Martyniuk, Christopher J

2017-12-01

Tributyltin (TBT) is an organotin compound that is the active ingredient of many biocides and antifouling agents. In addition to its well established role as an endocrine disruptor, TBT is also associated with adverse effects on the nervous system and behavior. In this study, zebrafish (Danio rerio) embryos were exposed to environmentally relevant concentrations of TBT (0.01, 0.1, 1 nM) to determine how low levels affected development and behavior. Fish exposed to 1 nM TBT hatched earlier when compared to controls. Following a 96-h exposure, total swimming distance, velocity, and activity of zebrafish larvae were reduced compared to controls. To identify putative mechanisms for these altered endpoints, we assessed embryo bioenergetics and gene expression. We reasoned that the accelerated hatch time could be related to ATP production and energy, thus embryos were exposed to TBT for 24 and 48-h exposure prior to hatch. There were no differences among groups for endpoints related to bioenergetics (i.e. basal, ATP-dependent, and maximal respiration). To address mechanisms related to changes in behavioral activity, we measured transcripts associated with muscle function (myf6, myoD, and myoG) and dopamine signaling (th, dat, dopamine receptors) as dopamine regulates behavior. No transcript was altered in expression by TBT in larvae, suggesting that other mechanisms exist that may explain changes in higher level endpoints. These results suggest that endpoints related to the whole animal (i.e. timing of hatch and locomotor behavior) are more sensitive to environmentally-relevant concentrations of TBT compared to the molecular and metabolic endpoints examined here. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ranked retrieval of Computational Biology models.

Science.gov (United States)

Henkel, Ron; Endler, Lukas; Peters, Andre; Le Novère, Nicolas; Waltemath, Dagmar

2010-08-11

The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, however, becomes more challenging with the increasing number of computational models available, and even more when considering the models' growing complexity. Firstly, among a set of potential model candidates it is difficult to decide for the model that best suits ones needs. Secondly, it is hard to grasp the nature of an unknown model listed in a search result set, and to judge how well it fits for the particular problem one has in mind. Here we present an improved search approach for computational models of biological processes. It is based on existing retrieval and ranking methods from Information Retrieval. The approach incorporates annotations suggested by MIRIAM, and additional meta-information. It is now part of the search engine of BioModels Database, a standard repository for computational models. The introduced concept and implementation are, to our knowledge, the first application of Information Retrieval techniques on model search in Computational Systems Biology. Using the example of BioModels Database, it was shown that the approach is feasible and extends the current possibilities to search for relevant models. The advantages of our system over existing solutions are that we incorporate a rich set of meta-information, and that we provide the user with a relevance ranking of the models found for a query. Better search capabilities in model databases are expected to have a positive effect on the reuse of existing models.

PathText: a text mining integrator for biological pathway visualizations

Science.gov (United States)

Kemper, Brian; Matsuzaki, Takuya; Matsuoka, Yukiko; Tsuruoka, Yoshimasa; Kitano, Hiroaki; Ananiadou, Sophia; Tsujii, Jun'ichi

2010-01-01

Motivation: Metabolic and signaling pathways are an increasingly important part of organizing knowledge in systems biology. They serve to integrate collective interpretations of facts scattered throughout literature. Biologists construct a pathway by reading a large number of articles and interpreting them as a consistent network, but most of the models constructed currently lack direct links to those articles. Biologists who want to check the original articles have to spend substantial amounts of time to collect relevant articles and identify the sections relevant to the pathway. Furthermore, with the scientific literature expanding by several thousand papers per week, keeping a model relevant requires a continuous curation effort. In this article, we present a system designed to integrate a pathway visualizer, text mining systems and annotation tools into a seamless environment. This will enable biologists to freely move between parts of a pathway and relevant sections of articles, as well as identify relevant papers from large text bases. The system, PathText, is developed by Systems Biology Institute, Okinawa Institute of Science and Technology, National Centre for Text Mining (University of Manchester) and the University of Tokyo, and is being used by groups of biologists from these locations. Contact: brian@monrovian.com. PMID:20529930

Non-Linear Relationships between Aflatoxin B1 Levels and the Biological Response of Monkey Kidney Vero Cells

Directory of Open Access Journals (Sweden)

Mendel Friedman

2013-08-01

Full Text Available Aflatoxin-producing fungi contaminate food and feed during pre-harvest, storage and processing periods. Once consumed, aflatoxins (AFs accumulate in tissues, causing illnesses in animals and humans. Most human exposure to AF seems to be a result of consumption of contaminated plant and animal products. The policy of blending and dilution of grain containing higher levels of aflatoxins with uncontaminated grains for use in animal feed implicitly assumes that the deleterious effects of low levels of the toxins are linearly correlated to concentration. This assumption may not be justified, since it involves extrapolation of these nontoxic levels in feed, which are not of further concern. To develop a better understanding of the significance of low dose effects, in the present study, we developed quantitative methods for the detection of biologically active aflatoxin B1 (AFB1 in Vero cells by two independent assays: the green fluorescent protein (GFP assay, as a measure of protein synthesis by the cells, and the microculture tetrazolium (MTT assay, as a measure of cell viability. The results demonstrate a non-linear dose-response relationship at the cellular level. AFB1 at low concentrations has an opposite biological effect to higher doses that inhibit protein synthesis. Additional studies showed that heat does not affect the stability of AFB1 in milk and that the Vero cell model can be used to determine the presence of bioactive AFB1 in spiked beef, lamb and turkey meat. The implication of the results for the cumulative effects of low amounts of AFB1 in numerous foods is discussed.

The Effect of Knowledge Linking Levels in Biology Lessons upon Students' Knowledge Structure

Science.gov (United States)

Wadouh, Julia; Liu, Ning; Sandmann, Angela; Neuhaus, Birgit J.

2014-01-01

Knowledge structure is an important aspect for defining students' competency in biology learning, but how knowledge structure is influenced by the teaching process in naturalistic biology classroom settings has scarcely been empirically investigated. In this study, 49 biology lessons in the teaching unit "blood and circulatory system" in…

Intraoperative validation of CT-based lymph nodal levels, sublevels IIa and IIb: Is it of clinical relevance in selective radiation therapy?

International Nuclear Information System (INIS)

Levendag, Peter; Gregoire, Vincent; Hamoir, Marc; Voet, Peter; Est, Henrie van der; Heijmen, Ben; Kerrebijn, Jeroen

2005-01-01

Purpose: The objectives of this study are to discuss the intraoperative validation of CT-based boundaries of lymph nodal levels in the neck, and in particular the clinical relevance of the delineation of sublevels IIa and IIb in case of selective radiation therapy (RT). Methods and Materials: To validate the radiologically defined level contours, clips were positioned intraoperatively at the level boundaries defined by surgical anatomy. In 10 consecutive patients, clips were placed, at the time of a neck dissection being performed, at the most cranial border of the neck. Anterior-posterior and lateral X-ray films were obtained intraoperatively. Next, in 3 patients, neck levels were contoured on preoperative contrast-enhanced CT scans according to the international consensus guidelines. From each of these 3 patients, an intraoperative CT scan was also obtained, with clips placed at the surgical-anatomy-based level boundaries. The preoperative (CT-based) and intraoperative (surgery-defined) CT scans were matched. Results: Clips placed at the most cranial part of the neck lined up at the caudal part of the transverse process of the cervical vertebra C-I. The posterior border of surgical level IIa (spinal accessory nerve [SAN]) did not match with the posterior border of CT-based level IIa (internal jugular vein [IJV]). Other surgical boundaries and CT-based contours were in good agreement. Conclusions: The cranial border of the neck, i.e., the cranial border of level IIa/IIb, corresponds to the caudal edge of the lateral process of C-I. Except for the posterior border between level IIa and level IIb, a perfect match was observed between the other surgical-clip-identified levels II-V boundaries (surgical-anatomy) and the CT-based delineation contours. It is argued that (1) because of the parotid gland overlapping part of level II, and (2) the frequent infestation of occult metastatic cells in the lymph channels around the IJV, the division of level II into radiologic

Identifying novel genes and biological processes relevant to the development of cancer therapy-induced mucositis: An informative gene network analysis.

Directory of Open Access Journals (Sweden)

Cielito C Reyes-Gibby

biological processes, including pathways related to inflammation and oxidative stress, that are relevant to mucositis development, thus providing the basis for future studies to improve the management and treatment of mucositis in patients with cancer.

Identifying novel genes and biological processes relevant to the development of cancer therapy-induced mucositis: An informative gene network analysis.

Science.gov (United States)

Reyes-Gibby, Cielito C; Melkonian, Stephanie C; Wang, Jian; Yu, Robert K; Shelburne, Samuel A; Lu, Charles; Gunn, Gary Brandon; Chambers, Mark S; Hanna, Ehab Y; Yeung, Sai-Ching J; Shete, Sanjay

2017-01-01

Mucositis is a complex, dose-limiting toxicity of chemotherapy or radiotherapy that leads to painful mouth ulcers, difficulty eating or swallowing, gastrointestinal distress, and reduced quality of life for patients with cancer. Mucositis is most common for those undergoing high-dose chemotherapy and hematopoietic stem cell transplantation and for those being treated for malignancies of the head and neck. Treatment and management of mucositis remain challenging. It is expected that multiple genes are involved in the formation, severity, and persistence of mucositis. We used Ingenuity Pathway Analysis (IPA), a novel network-based approach that integrates complex intracellular and intercellular interactions involved in diseases, to systematically explore the molecular complexity of mucositis. As a first step, we searched the literature to identify genes that harbor or are close to the genetic variants significantly associated with mucositis. Our literature review identified 27 candidate genes, of which ERCC1, XRCC1, and MTHFR were the most frequently studied for mucositis. On the basis of this 27-gene list, we used IPA to generate gene networks for mucositis. The most biologically significant novel molecules identified through IPA analyses included TP53, CTNNB1, MYC, RB1, P38 MAPK, and EP300. Additionally, uracil degradation II (reductive) and thymine degradation pathways (p = 1.06-08) were most significant. Finally, utilizing 66 SNPs within the 8 most connected IPA-derived candidate molecules, we conducted a genetic association study for oral mucositis in the head and neck cancer patients who were treated using chemotherapy and/or radiation therapy (186 head and neck cancer patients with oral mucositis vs. 699 head and neck cancer patients without oral mucositis). The top ranked gene identified through this association analysis was RB1 (rs2227311, p-value = 0.034, odds ratio = 0.67). In conclusion, gene network analysis identified novel molecules and biological

Observations on the biological cold fusion or the biological transmutation of elements

International Nuclear Information System (INIS)

Komaki, Hisatoki

1993-01-01

In previous paper, the author, with Prof. Dr. C. Louis KERVRAN, suggested the probable occurrence of the biological cold fusion or the biological transmutation of elements. In order to confirm the phenomena, under the more controlled condition, potassium, magnesium, iron and calcium were determined in cells of Aspergillus niger IFO 4066, Penicillium chrysogenum IFO 4689, Rhizopus nigricans IFO 5781, Mucor rouxii IFO 0396, Saccharomyces cerevisiae IFO 0308, Torulopsis utilis IFO 0396, Saccharomyces ellipsoideus IFO 0213 and Hansenula anomala IFO 0118 cultured in normal medium and media deficient in one of potassium, magnesium iron or calcium. Values of potassium 1890-2650 μg, magnesium 380-510 μg, iron 95-120 μg, and calcium 60-95 μg were obtained per g dried cells cultured in each deficient medium, while potassium 8650-11050 μg, magnesium 1920-2160 μg, iron 510-680 μg, and calcium 380-450 μg were found per g dried cells obtained by cultivation in the normal medium. The author would like to suggest the probable occurrence of the phenomena relevant to biological cold fusion. (author)

WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

International Nuclear Information System (INIS)

McMahon, S.

2016-01-01

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

WE-DE-202-03: Modeling of Biological Processes - What Happens After Early Molecular Damage?

Energy Technology Data Exchange (ETDEWEB)

McMahon, S. [Massachusetts General Hospital and Harvard Medical School (United States)

2016-06-15

Radiation therapy for the treatment of cancer has been established as a highly precise and effective way to eradicate a localized region of diseased tissue. To achieve further significant gains in the therapeutic ratio, we need to move towards biologically optimized treatment planning. To achieve this goal, we need to understand how the radiation-type dependent patterns of induced energy depositions within the cell (physics) connect via molecular, cellular and tissue reactions to treatment outcome such as tumor control and undesirable effects on normal tissue. Several computational biology approaches have been developed connecting physics to biology. Monte Carlo simulations are the most accurate method to calculate physical dose distributions at the nanometer scale, however simulations at the DNA scale are slow and repair processes are generally not simulated. Alternative models that rely on the random formation of individual DNA lesions within one or two turns of the DNA have been shown to reproduce the clusters of DNA lesions, including single strand breaks (SSBs), double strand breaks (DSBs) without the need for detailed track structure simulations. Efficient computational simulations of initial DNA damage induction facilitate computational modeling of DNA repair and other molecular and cellular processes. Mechanistic, multiscale models provide a useful conceptual framework to test biological hypotheses and help connect fundamental information about track structure and dosimetry at the sub-cellular level to dose-response effects on larger scales. In this symposium we will learn about the current state of the art of computational approaches estimating radiation damage at the cellular and sub-cellular scale. How can understanding the physics interactions at the DNA level be used to predict biological outcome? We will discuss if and how such calculations are relevant to advance our understanding of radiation damage and its repair, or, if the underlying biological

A computational systems biology software platform for multiscale modeling and simulation: Integrating whole-body physiology, disease biology, and molecular reaction networks

Directory of Open Access Journals (Sweden)

Thomas eEissing

2011-02-01

Full Text Available Today, in silico studies and trial simulations already complement experimental approaches in pharmaceutical R&D and have become indispensable tools for decision making and communication with regulatory agencies. While biology is multi-scale by nature, project work and software tools usually focus on isolated aspects of drug action, such as pharmacokinetics at the organism scale or pharmacodynamic interaction on the molecular level. We present a modeling and simulation software platform consisting of PK-Sim® and MoBi® capable of building and simulating models that integrate across biological scales. A prototypical multiscale model for the progression of a pancreatic tumor and its response to pharmacotherapy is constructed and virtual patients are treated with a prodrug activated by hepatic metabolization. Tumor growth is driven by signal transduction leading to cell cycle transition and proliferation. Free tumor concentrations of the active metabolite inhibit Raf kinase in the signaling cascade and thereby cell cycle progression. In a virtual clinical study, the individual therapeutic outcome of the chemotherapeutic intervention is simulated for a large population with heterogeneous genomic background. Thereby, the platform allows efficient model building and integration of biological knowledge and prior data from all biological scales. Experimental in vitro model systems can be linked with observations in animal experiments and clinical trials. The interplay between patients, diseases, and drugs and topics with high clinical relevance such as the role of pharmacogenomics, drug-drug or drug-metabolite interactions can be addressed using this mechanistic, insight driven multiscale modeling approach.

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.

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

NARCIS (Netherlands)

Mason, P.G.; Cock, M.J.W.; Barratt, B.I.P.; Klapwijk, J.N.; Lenteren, van J.C.; Brodeur, J.; Hoelmer, K.A.; Heimpel, G.E.

2018-01-01

The Nagoya Protocol is a supplementary agreement to the Convention on Biological Diversity that provides a framework for the effective implementation of the fair and equitable sharing of benefits arising out of the utilization of genetic resources, including invertebrate biological control agents.

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

Science.gov (United States)

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

Carbon-13 NMR spectroscopy of biological systems

CERN Document Server

Beckmann, Nicolau

1995-01-01

This book is intended to provide an in-depth understanding of 13C NMR as a tool in biological research. 13C NMR has provided unique information concerning complex biological systems, from proteins and nucleic acids to animals and humans. The subjects addressed include multidimensional heteronuclear techniques for structural studies of molecules in the liquid and solid states, the investigation of interactions in model membranes, the elucidation of metabolic pathwaysin vitro and in vivo on animals, and noninvasive metabolic studies performed on humans. The book is a unique mix of NMR methods and biological applications which makes it a convenient reference for those interested in research in this interdisciplinary area of physics, chemistry, biology, and medicine.Key Features* An interdisciplinary text with emphasis on both 13C NMR methodology and the relevant biological and biomedical issues* State-of-the-art 13C NMR techniques are described; Whenever possible, their advantages over other approaches are empha...

Making Research Fly in Schools: "Drosophila" as a Powerful Modern Tool for Teaching Biology

Science.gov (United States)

Harbottle, Jennifer; Strangward, Patrick; Alnuamaani, Catherine; Lawes, Surita; Patel, Sanjai; Prokop, Andreas

2016-01-01

The "droso4schools" project aims to introduce the fruit fly "Drosophila" as a powerful modern teaching tool to convey curriculum-relevant specifications in biology lessons. Flies are easy and cheap to breed and have been at the forefront of biology research for a century, providing unique conceptual understanding of biology and…

Biological responses of two marine organisms of ecological relevance to on-going ocean acidification and global warming.

Science.gov (United States)

Gomiero, A; Bellerby, R G J; Manca Zeichen, M; Babbini, L; Viarengo, A

2018-05-01

Recently, there has been a growing concern that climate change may rapidly and extensively alter global ecosystems with unknown consequences for terrestrial and aquatic life. While considerable emphasis has been placed on terrestrial ecology consequences, aquatic environments have received relatively little attention. Limited knowledge is available on the biological effects of increments of seawater temperature and pH decrements on key ecological species, i.e., primary producers and/or organisms representative of the basis of the trophic web. In the present study, we addressed the biological effects of global warming and ocean acidification on two model organisms, the microbenthic marine ciliate Euplotes crassus and the green alga Dunaliella tertiocleta using a suite of high level ecological endpoint tests and sub-lethal stress measures. Organisms were exposed to combinations of pH and temperature (TR1: 7.9 [pH], 25.5 °C and TR2: 7.8 [pH], 27,0 °C) simulating two possible environmental scenarios predicted to occur in the habitats of the selected species before the end of this century. The outcomes of the present study showed that the tested scenarios did not induce a significant increment of mortality on protozoa. Under the most severe exposure conditions, sub-lethal stress indices show that pH homeostatic mechanisms have energetic costs that divert energy from essential cellular processes and functions. The marine protozoan exhibited significant impairment of the lysosomal compartment and early signs of oxidative stress under these conditions. Similarly, significant impairment of photosynthetic efficiency and an increment in lipid peroxidation were observed in the autotroph model organism held under the most extreme exposure condition tested. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biological Soil Crust Web Site

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www.soilcrust.org Crust 101 Advanced Gallery References CCERS site Links Biological Soil Crusts Textbook Corrections Level of Development Index Biological soil crusts are the community of organisms , mosses, liverworts and lichens. A Field Guide to Biological Soil Crusts of Western U.S. Drylands: Common

German National Proficiency Scales in Biology: Internal Structure, Relations to General Cognitive Abilities and Verbal Skills

Science.gov (United States)

KÖLLER, OLAF

2016-01-01

ABSTRACT National and international large‐scale assessments (LSA) have a major impact on educational systems, which raises fundamental questions about the validity of the measures regarding their internal structure and their relations to relevant covariates. Given its importance, research on the validity of instruments specifically developed for LSA is still sparse, especially in science and its subdomains biology, chemistry, and physics. However, policy decisions for the improvement of educational quality based on LSA can only be helpful if valid information on students’ achievement levels is provided. In the present study, the nature of the measurement instruments based on the German Educational Standards in Biology is examined. On the basis of data from 3,165 students in Grade 10, we present dimensional analyses and report the relationship between different subdimensions of biology literacy and cognitive covariates such as general cognitive abilities and verbal skills. A theory‐driven two‐dimensional model fitted the data best. Content knowledge and scientific inquiry, two subdimensions of biology literacy, are highly correlated and show differential correlational patterns to the covariates. We argue that the underlying structure of biology should be incorporated into curricula, teacher training and future assessments. PMID:27818532

Genomics and systems biology - How relevant are the developments to veterinary pharmacology, toxicology and therapeutics?

NARCIS (Netherlands)

Witkamp, R.F.

2005-01-01

This review discusses some of the recent developments in genomics and its current and future relevance for veterinary pharmacology and toxicology. With the rapid progress made in this field several new approaches in pharmacological and toxicological research have developed and drug discovery and

Bringing the Real World into the Biology Curriculum

Science.gov (United States)

Lewis, Jenny

2006-01-01

This study followed a small but diverse group of biology teachers through the first two years of the pilot for a new Advanced Level Biology course--Salters-Nuffield Advanced Biology. SNAB aims to modernise A-level Biology using real world contexts and examples as the starting point, promoting conceptual understanding rather than factual recall,…

Explaining citizens’ perceptions of international climate-policy relevance

International Nuclear Information System (INIS)

Schleich, Joachim; Faure, Corinne

2017-01-01

This paper empirically analyses the antecedents of citizens’ perceptions of the relevance of international climate policy. Its use of representative surveys in the USA, China and Germany controls for different environmental attitudes and socio-economic factors between countries. The findings of the micro-econometric analysis suggest that the perceived relevance of international climate policy is positively affected by its perceived effectiveness, approval of the key topics discussed at international climate conferences, and environmental attitudes, but is not affected by perceived procedural justice. A higher level of perceived trust in international climate policy was positively related to perceived relevance in the USA and in China, but not in Germany. Citizens who felt that they were well informed and that their position was represented at climate summits were more likely to perceive international climate policy as relevant in China in particular. Generally, the results show only weak evidence of socio-demographic effects. - Highlights: • Perceptions of climate-policy relevance increase with perceptions of effectiveness. • In China and the USA, trust increases perceptions of climate-policy relevance. • Environmental attitudes are related to perceptions of climate-policy relevance. • In China, well-informed citizens perceive climate policy as more relevant. • Socio-demographics only weakly affect perceptions of climate-policy relevance.

High-level specification of a proposed information architecture for support of a bioterrorism early-warning system.

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Berkowitz, Murray R

2013-01-01

Current information systems for use in detecting bioterrorist attacks lack a consistent, overarching information architecture. An overview of the use of biological agents as weapons during a bioterrorist attack is presented. Proposed are the design, development, and implementation of a medical informatics system to mine pertinent databases, retrieve relevant data, invoke appropriate biostatistical and epidemiological software packages, and automatically analyze these data. The top-level information architecture is presented. Systems requirements and functional specifications for this level are presented. Finally, future studies are identified.

Extracting physics of life at the molecular level: A review of single-molecule data analyses.

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Colomb, Warren; Sarkar, Susanta K

2015-06-01

Studying individual biomolecules at the single-molecule level has proved very insightful recently. Single-molecule experiments allow us to probe both the equilibrium and nonequilibrium properties as well as make quantitative connections with ensemble experiments and equilibrium thermodynamics. However, it is important to be careful about the analysis of single-molecule data because of the noise present and the lack of theoretical framework for processes far away from equilibrium. Biomolecular motion, whether it is free in solution, on a substrate, or under force, involves thermal fluctuations in varying degrees, which makes the motion noisy. In addition, the noise from the experimental setup makes it even more complex. The details of biologically relevant interactions, conformational dynamics, and activities are hidden in the noisy single-molecule data. As such, extracting biological insights from noisy data is still an active area of research. In this review, we will focus on analyzing both fluorescence-based and force-based single-molecule experiments and gaining biological insights at the single-molecule level. Inherently nonequilibrium nature of biological processes will be highlighted. Simulated trajectories of biomolecular diffusion will be used to compare and validate various analysis techniques. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Inferring individual-level processes from population-level patterns in cultural evolution

Science.gov (United States)

Wilder, Bryan

2017-01-01

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution. PMID:28989786

Inferring individual-level processes from population-level patterns in cultural evolution.

Science.gov (United States)

Kandler, Anne; Wilder, Bryan; Fortunato, Laura

2017-09-01

Our species is characterized by a great degree of cultural variation, both within and between populations. Understanding how group-level patterns of culture emerge from individual-level behaviour is a long-standing question in the biological and social sciences. We develop a simulation model capturing demographic and cultural dynamics relevant to human cultural evolution, focusing on the interface between population-level patterns and individual-level processes. The model tracks the distribution of variants of cultural traits across individuals in a population over time, conditioned on different pathways for the transmission of information between individuals. From these data, we obtain theoretical expectations for a range of statistics commonly used to capture population-level characteristics (e.g. the degree of cultural diversity). Consistent with previous theoretical work, our results show that the patterns observed at the level of groups are rooted in the interplay between the transmission pathways and the age structure of the population. We also explore whether, and under what conditions, the different pathways can be distinguished based on their group-level signatures, in an effort to establish theoretical limits to inference. Our results show that the temporal dynamic of cultural change over time retains a stronger signature than the cultural composition of the population at a specific point in time. Overall, the results suggest a shift in focus from identifying the one individual-level process that likely produced the observed data to excluding those that likely did not. We conclude by discussing the implications for empirical studies of human cultural evolution.

Mining biological networks from full-text articles.

Science.gov (United States)

Czarnecki, Jan; Shepherd, Adrian J

2014-01-01

The study of biological networks is playing an increasingly important role in the life sciences. Many different kinds of biological system can be modelled as networks; perhaps the most important examples are protein-protein interaction (PPI) networks, metabolic pathways, gene regulatory networks, and signalling networks. Although much useful information is easily accessible in publicly databases, a lot of extra relevant data lies scattered in numerous published papers. Hence there is a pressing need for automated text-mining methods capable of extracting such information from full-text articles. Here we present practical guidelines for constructing a text-mining pipeline from existing code and software components capable of extracting PPI networks from full-text articles. This approach can be adapted to tackle other types of biological network.

Electrochemical Behavior of Biologically Important Indole Derivatives

Directory of Open Access Journals (Sweden)

Cigdem Karaaslan

2011-01-01

Full Text Available Voltammetric techniques are most suitable to investigate the redox properties of a new drug. Use of electrochemistry is an important approach in drug discovery and research as well as quality control, drug stability, and determination of physiological activity. The indole nucleus is an essential element of a number of natural and synthetic products with significant biological activity. Indole derivatives are the well-known electroactive compounds that are readily oxidized at carbon-based electrodes, and thus analytical procedures, such as electrochemical detection and voltammetry, have been developed for the determination of biologically important indoles. This paper explains some of the relevant and recent achievements in the electrochemistry processes and parameters mainly related to biologically important indole derivatives in view of drug discovery and analysis.

Biologic interventions for fatigue in rheumatoid arthritis

DEFF Research Database (Denmark)

Almeida, Celia; Choy, Ernest H S; Hewlett, Sarah

2016-01-01

BACKGROUND: Fatigue is a common and potentially distressing symptom for patients with rheumatoid arthritis (RA), with no accepted evidence-based management guidelines. Evidence suggests that biologic interventions improve symptoms and signs in RA as well as reducing joint damage. OBJECTIVES......: To evaluate the effect of biologic interventions on fatigue in rheumatoid arthritis. SEARCH METHODS: We searched the following electronic databases up to 1 April 2014: Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE, Cochrane Database of Systematic Reviews, Current Controlled Trials...... and contacted key authors. SELECTION CRITERIA: We included randomised controlled trials if they evaluated a biologic intervention in people with rheumatoid arthritis and had self reported fatigue as an outcome measure. DATA COLLECTION AND ANALYSIS: Two reviewers selected relevant trials, assessed methodological...

Mathematical simulation of biologically equivalent doses for LDR-HDR

International Nuclear Information System (INIS)

Slosarek, K.; Zajusz, A.

1996-01-01

Based on the LQ model examples of biologically equivalent doses LDR, HDR and external beams were calculated. The biologically equivalent doses for LDR were calculated by appending to the LQ model the corrector for the time of repair of radiation sublethal damages. For radiation continuously delivered at a low dose rate the influence of sublethal damage repair time changes on biologically equivalent doses were analysed. For fractionated treatment with high dose rate the biologically equivalent doses were calculated by adding to the LQ model the formula of accelerated repopulation. For total biologically equivalent dose calculation for combine LDR-HDR-Tele irradiation examples are presented with the use of different parameters of the time of repair of sublethal damages and accelerated repopulation. The calculations performed show, that the same biologically equivalent doses can be obtained for different parameters of cell kinetics changes during radiation treatment. It also shows, that during biologically equivalent dose calculations for different radiotherapy schedules, ignorance of cell kinetics parameters can lead to relevant errors

Toward computational cumulative biology by combining models of biological datasets.

Science.gov (United States)

Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

2014-01-01

A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

Methodological challenges of optical tweezers-based X-ray fluorescence imaging of biological model organisms at synchrotron facilities.

Science.gov (United States)

Vergucht, Eva; Brans, Toon; Beunis, Filip; Garrevoet, Jan; Bauters, Stephen; De Rijcke, Maarten; Deruytter, David; Janssen, Colin; Riekel, Christian; Burghammer, Manfred; Vincze, Laszlo

2015-07-01

Recently, a radically new synchrotron radiation-based elemental imaging approach for the analysis of biological model organisms and single cells in their natural in vivo state was introduced. The methodology combines optical tweezers (OT) technology for non-contact laser-based sample manipulation with synchrotron radiation confocal X-ray fluorescence (XRF) microimaging for the first time at ESRF-ID13. The optical manipulation possibilities and limitations of biological model organisms, the OT setup developments for XRF imaging and the confocal XRF-related challenges are reported. In general, the applicability of the OT-based setup is extended with the aim of introducing the OT XRF methodology in all research fields where highly sensitive in vivo multi-elemental analysis is of relevance at the (sub)micrometre spatial resolution level.

Using Conjugate Gradient Network to Classify Stress Level of Patients.

Directory of Open Access Journals (Sweden)

Er. S. Pawar

2013-02-01

Full Text Available Diagnosis of stress is important because it can cause many diseases e.g., heart disease, headache, migraine, sleep problems, irritability etc. Diagnosis of stress in patients often involves acquisition of biological signals for example heart rate, electrocardiogram (ECG, electromyography signals (EMG etc. Stress diagnosis using biomedical signals is difficult and since the biomedical signals are too complex to generate any rule an experienced person or expert is needed to determine stress levels. Also, it is not feasible to use all the features that are available or possible to extract from the signal. So, relevant features should be chosen from the extracted features that are capable to diagnose stress. Electronics devices are increasingly being seen in the field of medicine for diagnosis, therapy, checking of stress levels etc. The research and development work of medical electronics engineers leads to the manufacturing of sophisticated diagnostic medical equipment needed to ensure good health care. Biomedical engineering combines the design and problem solving skills of engineering with medical and biological sciences to improve health care diagnosis and treatment.

Loosening the shackles of scientific disciplines with network science. Reply to comments on "Network science of biological systems at different scales: A review"

Science.gov (United States)

Gosak, Marko; Markovič, Rene; Dolenšek, Jurij; Rupnik, Marjan Slak; Marhl, Marko; Stožer, Andraž; Perc, Matjaž

2018-03-01

We would like to thank all the experts for their insightful and very interesting comments that have been submitted in response to our review "Network science of biological systems at different scales" [1]. We are delighted with the number of comments that have been written, and even more so with the positive opinions that these comments communicate to the wider audience [2-9]. Although methods of network science have long proven their value in relevantly addressing various challenges in the biological sciences, such interdisciplinary research often still struggles for funding and recognition at many academic levels.

Charge migration induced by attosecond pulses in bio-relevant molecules

International Nuclear Information System (INIS)

Calegari, Francesca; Castrovilli, Mattea C; Nisoli, Mauro; Trabattoni, Andrea; Palacios, Alicia; Ayuso, David; Martín, Fernando; Greenwood, Jason B; Decleva, Piero

2016-01-01

After sudden ionization of a large molecule, the positive charge can migrate throughout the system on a sub-femtosecond time scale, purely guided by electronic coherences. The possibility to actively explore the role of the electron dynamics in the photo-chemistry of bio-relevant molecules is of fundamental interest for understanding, and perhaps ultimately controlling, the processes leading to damage, mutation and, more generally, to the alteration of the biological functions of the macromolecule. Attosecond laser sources can provide the extreme time resolution required to follow this ultrafast charge flow. In this review we will present recent advances in attosecond molecular science: after a brief description of the results obtained for small molecules, recent experimental and theoretical findings on charge migration in bio-relevant molecules will be discussed. (topical review)

Testing aggressive behaviour in a feeding context: Importance of ethologically relevant stimuli.

Science.gov (United States)

González, Daniel; Szenczi, Péter; Bánszegi, Oxána; Hudson, Robyn

2018-05-01

The choice of stimuli used in tests of animal behaviour can have a critical effect on the outcome. Here we report two experiments showing how different foods influenced aggressive behaviour in competition tests at weaning among littermates of the domestic cat. Whereas in Experiment 1 canned food elicited almost no overt competition, a piece of raw beef rib elicited clearly aggressive behaviour among littermates. In Experiment 2 the food stimuli were chosen to differ from raw beef rib in various combinations of taste/smell, texture and monopolizability. Kittens showed different levels of aggression in response to the five stimuli tested, which suggests that the strong effect of beef rib in eliciting aggressive behaviour was due to a complex combination of features. We suggest that using stimuli approximating the evolved, functional significance to the species concerned is more likely to result in robust, biologically relevant behaviours than more artificial stimuli. Copyright © 2018 Elsevier B.V. All rights reserved.

Geomicrobiology and its relevance to nuclear waste disposal - a further annotated bibliography

International Nuclear Information System (INIS)

West, J.M.; Arme, S.C.

1984-07-01

Scientific investigations into the disposal of high/intermediate level radioactive waste into deep geological formations includes work in the field of geomicrobiology. It has been shown that microbes exist in deep and shallow geological formations and that they could alter the geochemical environment of a waste repository and influence radionuclide migration. A preliminary literature survey indicated a lack of annotated material and an initial report (West, McKinley and Christofi, 1982) provided the first bibliography. This report is an updated annotated bibliography of relevant geomicrobiological research published since 1982 and should be used in conjunction with the previous report. Those without specific biological experience may find the glossary of common terms in the initial report of use. A major area of work which has not been referenced widely here is near surface disposal of both radioactive and conventional industrial waste. This vast topic can be accessed via some of the general reviews in this report. (author)

A Personalized Approach to Biological Therapy Using Prediction of Clinical Response Based on MRP8/14 Serum Complex Levels in Rheumatoid Arthritis Patients.

Directory of Open Access Journals (Sweden)

S C Nair

Full Text Available Measurement of MRP8/14 serum levels has shown potential in predicting clinical response to different biological agents in rheumatoid arthritis (RA. We aimed to develop a treatment algorithm based on a prediction score using MRP8/14 measurements and clinical parameters predictive for response to different biological agents.Baseline serum levels of MRP8/14 were measured in 170 patients starting treatment with infliximab, adalimumab or rituximab. We used logistic regression analysis to develop a predictive score for clinical response at 16 weeks. MRP8/14 levels along with clinical variables at baseline were investigated. We also investigated how the predictive effect of MRP8/14 was modified by drug type. A treatment algorithm was developed based on categorizing the expected response per drug type as high, intermediate or low for each patient and optimal treatment was defined. Finally, we present the utility of using this treatment algorithm in clinical practice.The probability of response increased with higher baseline MRP8/14 complex levels (OR = 1.39, differentially between the TNF-blockers and rituximab (OR of interaction term = 0.78, and also increased with higher DAS28 at baseline (OR = 1.28. Rheumatoid factor positivity, functional disability (a higher HAQ, and previous use of a TNF-inhibitor decreased the probability of response. Based on the treatment algorithm 80 patients would have been recommended for anti-TNF treatment, 8 for rituximab, 13 for another biological treatment (other than TNFi or rituximab and for 69 no recommendation was made. The predicted response rates matched the observed response in the cohort well. On group level the predicted response based on the algorithm resulted in a modest 10% higher response rate in our cohort with much higher differences in response probability in individual patients treated contrary to treatment recommendation.Prediction of response using MRP8/14 levels along with clinical predictors has

ICBEN review of research on the biological effects of noise 2011-2014

Science.gov (United States)

Basner, Mathias; Brink, Mark; Bristow, Abigail; de Kluizenaar, Yvonne; Finegold, Lawrence; Hong, Jiyoung; Janssen, Sabine A; Klaeboe, Ronny; Leroux, Tony; Liebl, Andreas; Matsui, Toshihito; Schwela, Dieter; Sliwinska-Kowalska, Mariola; Sörqvist, Patrik

2015-01-01

The mandate of the International Commission on Biological Effects of Noise (ICBEN) is to promote a high level of scientific research concerning all aspects of noise-induced effects on human beings and animals. In this review, ICBEN team chairs and co-chairs summarize relevant findings, publications, developments, and policies related to the biological effects of noise, with a focus on the period 2011-2014 and for the following topics: Noise-induced hearing loss; nonauditory effects of noise; effects of noise on performance and behavior; effects of noise on sleep; community response to noise; and interactions with other agents and contextual factors. Occupational settings and transport have been identified as the most prominent sources of noise that affect health. These reviews demonstrate that noise is a prevalent and often underestimated threat for both auditory and nonauditory health and that strategies for the prevention of noise and its associated negative health consequences are needed to promote public health. PMID:25774609

"Life-bearing molecules" versus "life-embodying systems": Two contrasting views on the what-is-life (WIL) problem persisting from the early days of molecular biology to the post-genomic cell- and organism-level biology.

Science.gov (United States)

Sato, Naoki

2018-05-01

"What is life?" is an ultimate biological quest for the principle that makes organisms alive. This 'WIL problem' is not, however, a simple one that we have a straightforward strategy to attack. From the beginning, molecular biology tried to identify molecules that bear the essence of life: the double helical DNA represented replication, and enzymes were micro-actuators of biological activities. A dominating idea behind these mainstream biological studies relies on the identification of life-bearing molecules, which themselves are models of life. Another, prevalent idea emphasizes that life resides in the whole system of an organism, but not in some particular molecules. The behavior of a complex system may be considered to embody the essence of life. The thermodynamic view of life system in the early 20th century was remodeled as physics of complex systems and systems biology. The two views contrast with each other, but they are no longer heritage of the historical dualism in biology, such as mechanism/materialism versus vitalism, or reductionism versus holism. These two views are both materialistic and mechanistic, and act as driving forces of modern biology. In reality, molecules function in a context of systems, whereas systems presuppose functional molecules. A key notion to reconcile this conflict is that subjects of biological studies are given before we start to study them. Cell- or organism-level biology is destined to the dialectic of molecules and systems, but this antagonism can be resolved by dynamic thinking involving biological evolution. Copyright © 2018 Elsevier B.V. All rights reserved.

Adapting to Biology: Maintaining Container-Closure System Compatibility with the Therapeutic Biologic Revolution.

Science.gov (United States)

Degrazio, Dominick

Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to the dimension of evolving therapeutic biologics. Important concerns associated with this changeover are becoming forefront, as challenges develop of varying complexity uncommon with the synthesis and production of traditional drugs. Therefore, alternative measures must be established that aim to preserve the efficacy and functionality of a biologic that might not be implemented for small molecules. Conserving protein stability is relative to perpetuating a net equilibrium of both intrinsic and extrinsic factors. Key to sustaining this balance is the ability of container-closure systems to maintain their compatibility with the ever-changing dynamics of therapeutic biologics. Failure to recognize and adjust the material properties of packaging components to support compatibility with therapeutic biologics can compromise patient safety, drug productivity, and biological stability. This review will examine the differences between small-molecule drugs and therapeutic biologics, lay a basic foundation for understanding the stability of therapeutic biologics, and demonstrate potential sources of container-closure systems' incompatibilities with therapeutic biologics at a mechanistic level. Many pharmaceutical companies are transitioning their research and development drug product pipeline from traditional small-molecule injectables to recombinantly derived therapeutic biologics. Concerns associated with this transformation are becoming prominent, as therapeutic biologics are uncharacteristic to small-molecule drugs. Maintaining the stability of a therapeutic biologic is a combination of balancing intrinsic factors and external elements within the biologic's microenvironment. An important aspect of this balance is relegated to the overall compatibility of primary, parenteral container-closure systems with therapeutic biologics

Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

Science.gov (United States)

Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

2017-04-01

The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O 2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H 2 O 2 ) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

A Western Blot-based Investigation of the Yeast Secretory Pathway Designed for an Intermediate-Level Undergraduate Cell Biology Laboratory

Science.gov (United States)

Hood-DeGrenier, Jennifer K.

2008-01-01

The movement of newly synthesized proteins through the endomembrane system of eukaryotic cells, often referred to generally as the secretory pathway, is a topic covered in most intermediate-level undergraduate cell biology courses. An article previously published in this journal described a laboratory exercise in which yeast mutants defective in…

Molecular profiles to biology and pathways: a systems biology approach.

Science.gov (United States)

Van Laere, Steven; Dirix, Luc; Vermeulen, Peter

2016-06-16

Interpreting molecular profiles in a biological context requires specialized analysis strategies. Initially, lists of relevant genes were screened to identify enriched concepts associated with pathways or specific molecular processes. However, the shortcoming of interpreting gene lists by using predefined sets of genes has resulted in the development of novel methods that heavily rely on network-based concepts. These algorithms have the advantage that they allow a more holistic view of the signaling properties of the condition under study as well as that they are suitable for integrating different data types like gene expression, gene mutation, and even histological parameters.

Biological Aspects of Anorexia Nervosa and Bulimia Nervosa.

Science.gov (United States)

Kaplan, Allan S.; Woodside, D. Blake

1987-01-01

Reviews biological factors relevant to the understanding of anorexia nervosa and bulimia nervosa. Considers the physical presentation of these disorders; the medical complications of starvation, binging, and purging; and the cognitive and behavioral effects of starvation. Reviews neurophysiological and neurochemical aspects of these illnesses and…

Sex and gonadal hormones in mouse models of Alzheimer’s disease: what is relevant to the human condition?

Directory of Open Access Journals (Sweden)

Dubal Dena B

2012-11-01

Full Text Available Abstract Biologic sex and gonadal hormones matter in human aging and diseases of aging such as Alzheimer’s – and the importance of studying their influences relates directly to human health. The goal of this article is to review the literature to date on sex and hormones in mouse models of Alzheimer’s disease (AD with an exclusive focus on interpreting the relevance of findings to the human condition. To this end, we highlight advances in AD and in sex and hormone biology, discuss what these advances mean for merging the two fields, review the current mouse model literature, raise major unresolved questions, and offer a research framework that incorporates human reproductive aging for future studies aimed at translational discoveries in this important area. Unraveling human relevant pathways in sex and hormone-based biology may ultimately pave the way to novel and urgently needed treatments for AD and other neurodegenerative diseases.

The temporal-relevance temporal-uncertainty model of prospective duration judgment.

Science.gov (United States)

Zakay, Dan

2015-12-15

A model aimed at explaining prospective duration judgments in real life settings (as well as in the laboratory) is presented. The model is based on the assumption that situational meaning is continuously being extracted by humans' perceptual and cognitive information processing systems. Time is one of the important dimensions of situational meaning. Based on the situational meaning, a value for Temporal Relevance is set. Temporal Relevance reflects the importance of temporal aspects for enabling adaptive behavior in a specific moment in time. When Temporal Relevance is above a certain threshold a prospective duration judgment process is evoked automatically. In addition, a search for relevant temporal information is taking place and its outcomes determine the level of Temporal Uncertainty which reflects the degree of knowledge one has regarding temporal aspects of the task to be performed. The levels of Temporal Relevance and Temporal Uncertainty determine the amount of attentional resources allocated for timing by the executive system. The merit of the model is in connecting timing processes with the ongoing general information processing stream. The model rests on findings in various domains which indicate that cognitive-relevance and self-relevance are powerful determinants of resource allocation policy. The feasibility of the model is demonstrated by analyzing various temporal phenomena. Suggestions for further empirical validation of the model are presented. Copyright © 2015 Elsevier Inc. All rights reserved.

Deep learning relevance

DEFF Research Database (Denmark)

Lioma, Christina; Larsen, Birger; Petersen, Casper

2016-01-01

train a Recurrent Neural Network (RNN) on existing relevant information to that query. We then use the RNN to "deep learn" a single, synthetic, and we assume, relevant document for that query. We design a crowdsourcing experiment to assess how relevant the "deep learned" document is, compared...... to existing relevant documents. Users are shown a query and four wordclouds (of three existing relevant documents and our deep learned synthetic document). The synthetic document is ranked on average most relevant of all....

Hyperpolarized NMR Probes for Biological Assays

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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.

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

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.

Safety, security, and serving the public interest in synthetic biology.

Science.gov (United States)

Gronvall, Gigi Kwik

2018-03-21

This article describes what may be done by scientists and by the biotechnology industry, generally, to address the safety and security challenges in synthetic biology. Given the technical expertise requirements for developing sound policy options, as well as the importance of these issues to the future of the industry, scientists who work in synthetic biology should be informed about these challenges and get involved in shaping policies relevant to the field.

The Systems Biology Markup Language (SBML Level 3 Package: Layout, Version 1 Core

Directory of Open Access Journals (Sweden)

Gauges Ralph

2015-06-01

Full Text Available Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on. For software tools that also read and write models in SBML (Systems Biology Markup Language format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded.

Evolutionary cell biology: two origins, one objective.

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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.

Towards physical principles of biological evolution

Science.gov (United States)

Katsnelson, Mikhail I.; Wolf, Yuri I.; Koonin, Eugene V.

2018-03-01

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in ‘emergent phenomena’. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice

Workshop Introduction: Systems Biology and Biological Models

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As we consider the future of toxicity testing, the importance of applying biological models to this problem is clear. Modeling efforts exist along a continuum with respect to the level of organization (e.g. cell, tissue, organism) linked to the resolution of the model. Generally,...

Systems Biology and Health Systems Complexity in;

NARCIS (Netherlands)

Donald Combs, C.; Barham, S.R.; Sloot, P.M.A.

2016-01-01

Systems biology addresses interactions in biological systems at different scales of biological organization, from the molecular to the cellular, organ, organism, societal, and ecosystem levels. This chapter expands on the concept of systems biology, explores its implications for individual patients

Creatine level and lipide analysis in radiosensitive organs of mice after total body irradiation - a contribution to further development of biologic radiodosimetry

Energy Technology Data Exchange (ETDEWEB)

Breiter, N; Ungemach, F R; Hegner, D; Beck, G; Mayr, A

1986-02-01

The authors intended to test the suitability of creatine level and/or certain criteria of lipide analysis in radiosensitive organs for an individual (i.e. considering biologic variations of radiosensitivity), qualitative and quantitative demonstration of an irradiation damage. It was found that creatine determination and several criteria of lipide peroxydation are not suitable for a biologic radiation dosimetry due to the absence of organ dependent, radiation dose dependent, and time dependent changes. The reasons are discussed.

Creatine level and lipide analysis in radiosensitive organs of mice after total body irradiation - a contribution to further development of biologic radiodosimetry

International Nuclear Information System (INIS)

Breiter, N.; Ungemach, F.R.; Hegner, D.; Beck, G.; Mayr, A.

1986-01-01

The authors intended to test the suitability of creatine level and/or certain criteria of lipide analysis in radiosensitive organs for an individual (i.e. considering biologic variations of radiosensitivity), qualitative and quantitative demonstration of an irradiation damage. It was found that creatine determination and several criteria of lipide peroxydation are not suitable for a biologic radiation dosimetry due to the absence of organ dependent, radiation dose dependent, and time dependent changes. The reasons are discussed. (orig.) [de

Impact of biology knowledge on the conservation and management of large pelagic sharks

OpenAIRE

Yokoi, Hiroki; Ijima, Hirotaka; Ohshimo, Seiji; Yokawa, Kotaro

2017-01-01

Population growth rate, which depends on several biological parameters, is valuable information for the conservation and management of pelagic sharks, such as blue and shortfin mako sharks. However, reported biological parameters for estimating the population growth rates of these sharks differ by sex and display large variability. To estimate the appropriate population growth rate and clarify relationships between growth rate and relevant biological parameters, we developed a two-sex age-str...

Bridging Physics and Biology Using Resistance and Axons

Science.gov (United States)

Dyer, Joshua M.

2014-11-01

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

Occurrence of ²¹⁰Po and biological effects of low-level exposure: the need for research.

Science.gov (United States)

Seiler, Ralph L; Wiemels, Joseph L

2012-09-01

Polonium-210 (²¹⁰Po) concentrations that exceed 1 Bq/L in drinking-water supplies have been reported from four widely separated U.S. states where exposure to it went unnoticed for decades. The radionuclide grandparents of ²¹⁰Po are common in sediments, and segments of the public may be chronically exposed to low levels of ²¹⁰Po in drinking water or in food products from animals raised in contaminated areas. We summarized information on the environmental behavior, biokinetics, and toxicology of ²¹⁰Po and identified the need for future research. Potential linkages between environmental exposure to ²¹⁰Po and human health effects were identified in a literature review. ²¹⁰Po accumulates in the ovaries where it kills primary oocytes at low doses. Because of its radiosensitivity and tendency to concentrate ²¹⁰Po, the ovary may be the critical organ in determining the lowest injurious dose for ²¹⁰Po. ²¹⁰Po also accumulates in the yolk sac of the embryo and in the fetal and placental tissues. Low-level exposure to ²¹⁰Po may have subtle, long-term biological effects because of its tropism towards reproductive and embryonic and fetal tissues where exposure to a single alpha particle may kill or damage critical cells. ²¹⁰Po is present in cigarettes and maternal smoking has several effects that appear consistent with the toxicology of ²¹⁰Po. Much of the important biological and toxicological research on ²¹⁰Po is more than four decades old. New research is needed to evaluate environmental exposure to ²¹⁰Po and the biological effects of low-dose exposure to it so that public health officials can develop appropriate mitigation measures where necessary.

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...

Protein and mRNA levels support the notion that a genetic regulatory circuit controls growth phases in E. coli populations

Directory of Open Access Journals (Sweden)

Agustino Martinez-Antonio

2015-09-01

Full Text Available Bacterial populations transition between growing and non-growing phases, based on nutrient availability and stresses conditions. The hallmark of a growing state is anabolism, including DNA replication and cell division. In contrast, bacteria in a growth-arrested state acquire a resistant physiology and diminished metabolism. However, there is little knowledge on how this transition occurs at the molecular level. Here, we provide new evidence that a multi-element genetic regulatory circuit might work to maintain genetic control among growth-phase transitions in Escherichia coli. This work contributes to the discovering of design principles behind the performance of biological functions, which could be of relevance on the new disciplines of biological engineering and synthetic biology.

SYMBIOSIS: development, implementation, and assessment of a model curriculum across biology and mathematics at the introductory level.

Science.gov (United States)

Depelteau, Audrey M; Joplin, Karl H; Govett, Aimee; Miller, Hugh A; Seier, Edith

2010-01-01

"It takes a lot of courage to release the familiar and seemingly secure, to embrace the new. But there is no real security in what is no longer meaningful. There is more security in the adventurous and exciting, for in movement there is life, and in change there is power." Alan Cohen (Used by permission. All rights reserved. For more information on Alan Cohen's books and programs, see (www.alancohen.com.) With the support of the East Tennessee State University (ETSU) administration and a grant from Howard Hughes Medical Institute, the departments of Biological Sciences, Mathematics and Statistics, and Curriculum and Instruction have developed a biology-math integrated curriculum. An interdisciplinary faculty team, charged with teaching the 18 curriculum modules, designed this three-semester curriculum, known as SYMBIOSIS. This curriculum was piloted to two student cohorts during the developmental stage. The positive feedback and assessment results of this project have given us the foundation to implement the SYMBIOSIS curriculum as a replacement for the standard biology majors curriculum at the introductory level. This article addresses the history and development of the curriculum, previous assessment results and current assessment protocol, and the future of ETSU's approach to implementing the SYMBIOSIS curriculum.

Integration of cardiac proteome biology and medicine by a specialized knowledgebase.

Science.gov (United States)

Zong, Nobel C; Li, Haomin; Li, Hua; Lam, Maggie P Y; Jimenez, Rafael C; Kim, Christina S; Deng, Ning; Kim, Allen K; Choi, Jeong Ho; Zelaya, Ivette; Liem, David; Meyer, David; Odeberg, Jacob; Fang, Caiyun; Lu, Hao-Jie; Xu, Tao; Weiss, James; Duan, Huilong; Uhlen, Mathias; Yates, John R; Apweiler, Rolf; Ge, Junbo; Hermjakob, Henning; Ping, Peipei

2013-10-12

Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10,924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

Biological markers for kidney injury and renal function in the intensive care unit

NARCIS (Netherlands)

Royakkers, A.A.N.M.

2014-01-01

The purpose of the investigations described in this thesis was to seek for answers to two relevant questions in ICUs in resource-rich settings, i.e., can new biological markers play a role in early recognition of AKI, and can new biological markers predict recovery of renal function in patients who

Australian Biology Test Item Bank, Years 11 and 12. Volume II: Year 12.

Science.gov (United States)

Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

Australian Biology Test Item Bank, Years 11 and 12. Volume I: Year 11.

Science.gov (United States)

Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

Clinically Relevant Levels of 4-Aminopyridine Strengthen Physiological Responses in Intact Motor Circuits in Rats, Especially After Pyramidal Tract Injury.

Science.gov (United States)

Sindhurakar, Anil; Mishra, Asht M; Gupta, Disha; Iaci, Jennifer F; Parry, Tom J; Carmel, Jason B

2017-04-01

4-Aminopyridine (4-AP) is a Food and Drug Administration-approved drug to improve motor function in people with multiple sclerosis. Preliminary results suggest the drug may act on intact neural circuits and not just on demyelinated ones. To determine if 4-AP at clinically relevant levels alters the excitability of intact motor circuits. In anesthetized rats, electrodes were placed over motor cortex and the dorsal cervical spinal cord for electrical stimulation, and electromyogram electrodes were inserted into biceps muscle to measure responses. The motor responses to brain and spinal cord stimulation were measured before and for 5 hours after 4-AP administration both in uninjured rats and rats with a cut lesion of the pyramidal tract. Blood was collected at the same time as electrophysiology to determine drug plasma concentration with a goal of 20 to 100 ng/mL. We first determined that a bolus infusion of 0.32 mg/kg 4-AP was optimal: it produced on average 61.5 ± 1.8 ng/mL over the 5 hours after infusion. This dose of 4-AP increased responses to spinal cord stimulation by 1.3-fold in uninjured rats and 3-fold in rats with pyramidal tract lesion. Responses to cortical stimulation also increased by 2-fold in uninjured rats and up to 4-fold in the injured. Clinically relevant levels of 4-AP strongly augment physiological responses in intact circuits, an effect that was more robust after partial injury, demonstrating its broad potential in treating central nervous system injuries.

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.

The Fortymile caribou herd: novel proposed management and relevant biology, 1992-1997

Directory of Open Access Journals (Sweden)

Rodney D. Boertje

2000-04-01

Full Text Available A diverse, international Fortymile Planning Team wrote a novel Fortymile caribou herd {Rangifer tarandus granti Management Plan in 1995 (Boertje & Gardner, 1996: 56-77. The primary goal of this plan is to begin restoring the Fortymile herd to its former range; >70% of the herd's former range was abandoned as herd size declined. Specific objectives call for increasing the Fortymile herd by at least 5-10% annually from 1998-2002. We describe demographics of the herd, factors limiting the herd, and condition of the herd and range during 1992-1997. These data were useful in proposing management actions for the herd and should be instrumental in future evaluations of the plan's actions. The following points summarize herd biology relevant to management proposed by the Fortymile Planning Team: 1. Herd numbers remained relatively stable during 1990-1995 (about 22 000-23 000 caribou. On 21 June 1996 we counted about 900 additional caribou in the herd, probably a result of increased pregnancy rates in 1996. On 26 June 1997 we counted about 2500 additional caribou in the herd, probably a result of recruitment of the abundant 1996 calves and excellent early survival of the 1997 calves. The Team deemed that implementing management actions during a period of natural growth would be opportune. 2. Wolf (Canis lupus and grizzly bear (Ursus arctos predation were the most important sources of mortality, despite over a decade of the most liberal regulations in the state for harvesting of wolves and grizzly bears. Wolves were the most important predator. Wolves killed between 2000 and 3000 caribou calves annually during this study and between 1000 and 2300 older caribou; 1200-1900 calves were killed from May through September. No significant differences in annual wolf predation rates on calves or adults were observed between 1994 and early winter 1997. Reducing wolf predation was judged by the Team to be the most manageable way to help hasten or stimulate

Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection.

Science.gov (United States)

Labots, Mariette; van der Mijn, Johannes C; Beekhof, Robin; Piersma, Sander R; de Goeij-de Haas, Richard R; Pham, Thang V; Knol, Jaco C; Dekker, Henk; van Grieken, Nicole C T; Verheul, Henk M W; Jiménez, Connie R

2017-06-06

Mass spectrometry-based phosphoproteomics of cancer cell and tissue lysates provides insight in aberrantly activated signaling pathways and potential drug targets. For improved understanding of individual patient's tumor biology and to allow selection of tyrosine kinase inhibitors in individual patients, phosphoproteomics of small clinical samples should be feasible and reproducible. We aimed to scale down a pTyr-phosphopeptide enrichment protocol to biopsy-level protein input and assess reproducibility and applicability to tumor needle biopsies. To this end, phosphopeptide immunoprecipitation using anti-phosphotyrosine beads was performed using 10, 5 and 1mg protein input from lysates of colorectal cancer (CRC) cell line HCT116. Multiple needle biopsies from 7 human CRC resection specimens were analyzed at the 1mg-level. The total number of phosphopeptides captured and detected by LC-MS/MS ranged from 681 at 10mg input to 471 at 1mg HCT116 protein. ID-reproducibility ranged from 60.5% at 10mg to 43.9% at 1mg. Per 1mg-level biopsy sample, >200 phosphopeptides were identified with 57% ID-reproducibility between paired tumor biopsies. Unsupervised analysis clustered biopsies from individual patients together and revealed known and potential therapeutic targets. This study demonstrates the feasibility of label-free pTyr-phosphoproteomics at the tumor biopsy level based on reproducible analyses using 1mg of protein input. The considerable number of identified phosphopeptides at this level is attributed to an effective down-scaled immuno-affinity protocol as well as to the application of ID propagation in the data processing and analysis steps. Unsupervised cluster analysis reveals patient-specific profiles. Together, these findings pave the way for clinical trials in which pTyr-phosphoproteomics will be performed on pre- and on-treatment biopsies. Such studies will improve our understanding of individual tumor biology and may enable future p

Telomere biology in aging and cancer: early history and perspectives.

Science.gov (United States)

Hayashi, Makoto T

2018-01-20

The ends of eukaryotic linear chromosomes are protected from undesired enzymatic activities by a nucleoprotein complex called the telomere. Expanding evidence indicates that telomeres have central functions in human aging and tumorigenesis. While it is undoubtedly important to follow current advances in telomere biology, it is also fruitful to be well informed in seminal historical studies for a comprehensive understanding of telomere biology, and for the anticipation of future directions. With this in mind, I here summarize the early history of telomere biology and current advances in the field, mostly focusing on mammalian studies relevant to aging and cancer.

Effects of balneotherapy and spa therapy on levels of cortisol as a stress biomarker: a systematic review

Science.gov (United States)

Antonelli, Michele; Donelli, Davide

2018-02-01

Balneotherapy and spa therapy are well-known practices, even though limited evidence has been produced about their biological effects. This systematic review primarily aims at assessing if balneotherapy, mud/peloid therapy, and spa therapy may influence cortisol levels. Secondarily, it aims at understanding if these interventions may improve stress resilience. PubMed/Medline, Embase, and Cochrane Library were searched for relevant articles in English or Italian about studies involving healthy and sub-healthy subjects or patients with a diagnosed disease about effects of balneotherapy, mud/peloid therapy, and spa therapy on serum and salivary cortisol levels. Fifteen studies involving 684 subjects were included. Five studies investigated biological effects of balneotherapy alone. Two of them reported significant changes of cortisol levels in healthy participants. The other three studies reported no significant variations in patients with rheumatic conditions. No studies investigated biological effects of mud/peloid therapy alone. Ten studies investigated biological effects of spa therapy with or without included mud/peloid therapy, and in all but two studies, significant variations of cortisol levels were reported. Our main findings suggest that balneotherapy may have the potential to influence cortisol levels in healthy subjects, in such a way as to improve stress resilience. Spa therapy with or without included mud/peloid therapy demonstrated the same potential to influence cortisol levels also in sub-healthy subjects and in patients with a diagnosed disease. Therefore, balneotherapy and spa therapy may be considered as useful interventions for the management of stress conditions. Further investigation is needed because of limited available data.

The case for policy-relevant conservation science.

Science.gov (United States)

Rose, David C

2015-06-01

Drawing on the "evidence-based" (Sutherland et al. 2013) versus "evidence-informed" debate (Adams & Sandbrook 2013), which has become prominent in conservation science, I argue that science can be influential if it holds a dual reference (Lentsch & Weingart 2011) that contributes to the needs of policy makers whilst maintaining technical rigor. In line with such a strategy, conservation scientists are increasingly recognizing the usefulness of constructing narratives through which to enhance the influence of their evidence (Leslie et al. 2013; Lawton & Rudd 2014). Yet telling stories alone is rarely enough to influence policy; instead, these narratives must be policy relevant. To ensure that evidence is persuasive alongside other factors in a complex policy-making process, conservation scientists could follow 2 steps: reframe within salient political contexts and engage more productively in boundary work, which is defined as the ways in which scientists "construct, negotiate, and defend the boundary between science and policy" (Owens et al. 2006:640). These will both improve the chances of evidence-informed conservation policy. © 2015 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of Society for Conservation Biology.

Geochemical and biological research at the NEA dumpsite for low-level radioactive waste

International Nuclear Information System (INIS)

Rutgers van der Loeff, M.M.; Lavaleye, M.S.S.

1984-01-01

A geochemical and biological study of the sea floor at the NEA dumpsite for low-level radioactive waste is reported. The sea bottom has rather steep hillsides. Slumps are usual phenomena and could be triggered by the dumping operations. The sediment is described in terms of its mineralogical and elemental composition. The variation in CaCO 3 content accounts for most of the variation in the elemental composition and cation exchange capacity. The present depth of the lysocline is shown to be about 4700 m. A description is given of the early diagenetic processes: (1) Mineralization of organic material, (2) Cation exchange, (3) Change in redox conditions and (4) Carbonate dissolution and recrystallization; and discussed in terms of their effects on the redistribution and transport of trace elements and radionuclides within the sediment and between sediment and overlying water. (orig.)

Experiences performed at the C:R: Saluggia of ENEA in low-level determination of plutonium in biological and environmental samples

International Nuclear Information System (INIS)

Spezzano, Pasquale

1997-10-01

This report describes some experiences performed at the Research Center Saluggia of ENEA concerning low-level determination of plutonium in biological and environmental samples, with discussions of practical analytical problems. The main characteristics and properties of plutonium with emphasis to aqueous solutions chemistry and environmental behaviour are also reported

Trends in Surface Level Ozone Observations from Human-health Relevant Metrics: Results from the Tropospheric Ozone Assessment Report (TOAR)

Science.gov (United States)

Fleming, Z. L.; von Schneidemesser, E.; Doherty, R. M.; Malley, C.; Cooper, O. R.; Pinto, J. P.; Colette, A.; Xu, X.; Simpson, D.; Schultz, M.; Hamad, S.; Moola, R.; Solberg, S.; Feng, Z.

2017-12-01

Ozone is an air pollutant formed in the atmosphere from precursor species (NOx, VOCs, CH4, CO) that is detrimental to human health and ecosystems. The global Tropospheric Ozone Assessment Report (TOAR) initiative has assembled a global database of surface ozone observations and generated ozone exposure metrics at thousands of measurement sites around the world. This talk will present results from the assessment focused on those indicators most relevant to human health. Specifically, the trends in ozone, comparing different time periods and patterns across regions and among metrics will be addressed. In addition, the fraction of population exposed to high ozone levels and how this has changed between 2000 and 2014 will also be discussed. The core time period analyzed for trends was 2000-2014, selected to include a greater number of sites in East Asia. Negative trends were most commonly observed at many US and some European sites, whereas many sites in East Asia showed positive trends, while sites in Japan showed more of a mix of positive and negative trends. More than half of the sites showed a common direction and significance in the trends for all five human-health relevant metrics. The peak ozone metrics indicate a reduction in exposure to peak levels of ozone related to photochemical episodes in Europe and the US. A considerable number of European countries and states within the US have shown a decrease in population-weighted ozone over time. The 2000-2014 results will be augmented and compared to the trend analysis for additional time periods that cover a greater number of years, but by necessity are based on fewer sites. Trends are found to be statistically significant at a larger fraction of sites with longer time series, compared to the shorter (2000-2014) time series.

Automated force volume image processing for biological samples.

Directory of Open Access Journals (Sweden)

Pavel Polyakov

2011-04-01

Full Text Available Atomic force microscopy (AFM has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image.

Nanotechnology for biology and medicine at the building block level

CERN Document Server

Silva, Gabriel A

2011-01-01

This text book will bring together a mix of both internationally known and established senior scientists along side up and coming (but already accomplished) junior scientists that have varying expertise in fundamental and applied nanotechnology to biology and medicine.

Is there a Biological Basis for Therapeutic Applications of Millimetre Waves and THz Waves?

Science.gov (United States)

Mattsson, Mats-Olof; Zeni, Olga; Simkó, Myrtill

2018-03-01

Millimetre wave (MMW) and THz wave (THz) applications are already employed in certain industrial and medical environments for non-destructive quality control, and medical imaging, diagnosis, and therapy, respectively. The aim of the present study is to investigate if published experimental studies (in vivo and in vitro) provide evidence for "non-thermal" biological effects of MMW and THz. Such effects would occur in absence of tissue heating and associated damage and are the ones that can be exploited for therapeutic medical use. The investigated studies provide some evidence for both MMW and THz that can influence biological systems in a manner that is not obviously driven by tissue heating. However, the number of relevant studies is very limited which severely limits the drawing of any far-reaching conclusions. Furthermore, the studies have not addressed specific interaction mechanisms and do not provide hints for future mechanistic studies. Also, the studies do not indicate any specific importance regarding power density levels, frequencies, or exposure duration. It is also unclear if any specific biological endpoints are especially sensitive. Any therapeutic potential of MMW or THz has to be evaluated based on future high-quality studies dealing with physical, bio-physical, and biological aspects that have specific health-related perspectives in mind.

Probabilistic biological network alignment.

Science.gov (United States)

Todor, Andrei; Dobra, Alin; Kahveci, Tamer

2013-01-01

Interactions between molecules are probabilistic events. An interaction may or may not happen with some probability, depending on a variety of factors such as the size, abundance, or proximity of the interacting molecules. In this paper, we consider the problem of aligning two biological networks. Unlike existing methods, we allow one of the two networks to contain probabilistic interactions. Allowing interaction probabilities makes the alignment more biologically relevant at the expense of explosive growth in the number of alternative topologies that may arise from different subsets of interactions that take place. We develop a novel method that efficiently and precisely characterizes this massive search space. We represent the topological similarity between pairs of aligned molecules (i.e., proteins) with the help of random variables and compute their expected values. We validate our method showing that, without sacrificing the running time performance, it can produce novel alignments. Our results also demonstrate that our method identifies biologically meaningful mappings under a comprehensive set of criteria used in the literature as well as the statistical coherence measure that we developed to analyze the statistical significance of the similarity of the functions of the aligned protein pairs.

Dietary antioxidant synergy in chemical and biological systems.

Science.gov (United States)