Automatic Screening for Perturbations in Boolean Networks.

PubMed

Schwab, Julian D; Kestler, Hans A

2018-01-01

A common approach to address biological questions in systems biology is to simulate regulatory mechanisms using dynamic models. Among others, Boolean networks can be used to model the dynamics of regulatory processes in biology. Boolean network models allow simulating the qualitative behavior of the modeled processes. A central objective in the simulation of Boolean networks is the computation of their long-term behavior-so-called attractors. These attractors are of special interest as they can often be linked to biologically relevant behaviors. Changing internal and external conditions can influence the long-term behavior of the Boolean network model. Perturbation of a Boolean network by stripping a component of the system or simulating a surplus of another element can lead to different attractors. Apparently, the number of possible perturbations and combinations of perturbations increases exponentially with the size of the network. Manually screening a set of possible components for combinations that have a desired effect on the long-term behavior can be very time consuming if not impossible. We developed a method to automatically screen for perturbations that lead to a user-specified change in the network's functioning. This method is implemented in the visual simulation framework ViSiBool utilizing satisfiability (SAT) solvers for fast exhaustive attractor search.

Photostable fluorescent organic dots with aggregation-induced emission (AIE dots) for noninvasive long-term cell tracing

NASA Astrophysics Data System (ADS)

Li, Kai; Qin, Wei; Ding, Dan; Tomczak, Nikodem; Geng, Junlong; Liu, Rongrong; Liu, Jianzhao; Zhang, Xinhai; Liu, Hongwei; Liu, Bin; Tang, Ben Zhong

2013-01-01

Long-term noninvasive cell tracing by fluorescent probes is of great importance to life science and biomedical engineering. For example, understanding genesis, development, invasion and metastasis of cancerous cells and monitoring tissue regeneration after stem cell transplantation require continual tracing of the biological processes by cytocompatible fluorescent probes over a long period of time. In this work, we successfully developed organic far-red/near-infrared dots with aggregation-induced emission (AIE dots) and demonstrated their utilities as long-term cell trackers. The high emission efficiency, large absorptivity, excellent biocompatibility, and strong photobleaching resistance of the AIE dots functionalized by cell penetrating peptides derived from transactivator of transcription proteins ensured outstanding long-term noninvasive in vitro and in vivo cell tracing. The organic AIE dots outperform their counterparts of inorganic quantum dots, opening a new avenue in the development of fluorescent probes for following biological processes such as carcinogenesis.

Local and global aspects of biological motion perception in children born at very low birth weight

PubMed Central

Williamson, K. E.; Jakobson, L. S.; Saunders, D. R.; Troje, N. F.

2015-01-01

Biological motion perception can be assessed using a variety of tasks. In the present study, 8- to 11-year-old children born prematurely at very low birth weight (<1500 g) and matched, full-term controls completed tasks that required the extraction of local motion cues, the ability to perceptually group these cues to extract information about body structure, and the ability to carry out higher order processes required for action recognition and person identification. Preterm children exhibited difficulties in all 4 aspects of biological motion perception. However, intercorrelations between test scores were weak in both full-term and preterm children—a finding that supports the view that these processes are relatively independent. Preterm children also displayed more autistic-like traits than full-term peers. In preterm (but not full-term) children, these traits were negatively correlated with performance in the task requiring structure-from-motion processing, r(30) = −.36, p < .05), but positively correlated with the ability to extract identity, r(30) = .45, p < .05). These findings extend previous reports of vulnerability in systems involved in processing dynamic cues in preterm children and suggest that a core deficit in social perception/cognition may contribute to the development of the social and behavioral difficulties even in members of this population who are functioning within the normal range intellectually. The results could inform the development of screening, diagnostic, and intervention tools. PMID:25103588

How Do Preservice Biology Teachers Explain the Origin of Biological Traits?: A Philosophical Analysis

ERIC Educational Resources Information Center

Kampourakis, Kostas; Silveira, Patricia; Strasser, Bruno J.

2016-01-01

Research suggests that students tend to explain the origin of biological traits in terms of needs or purposes and/or as the direct product of genes, rather than as the outcome of evolutionary and developmental processes. We suggest that in order for students to be able to construct scientific explanations, it is important to clearly and explicitly…

Comparison of Modules of Wild Type and Mutant Huntingtin and TP53 Protein Interaction Networks: Implications in Biological Processes and Functions

PubMed Central

Basu, Mahashweta; Bhattacharyya, Nitai P.; Mohanty, Pradeep K.

2013-01-01

Disease-causing mutations usually change the interacting partners of mutant proteins. In this article, we propose that the biological consequences of mutation are directly related to the alteration of corresponding protein protein interaction networks (PPIN). Mutation of Huntingtin (HTT) which causes Huntington's disease (HD) and mutations to TP53 which is associated with different cancers are studied as two example cases. We construct the PPIN of wild type and mutant proteins separately and identify the structural modules of each of the networks. The functional role of these modules are then assessed by Gene Ontology (GO) enrichment analysis for biological processes (BPs). We find that a large number of significantly enriched () GO terms in mutant PPIN were absent in the wild type PPIN indicating the gain of BPs due to mutation. Similarly some of the GO terms enriched in wild type PPIN cease to exist in the modules of mutant PPIN, representing the loss. GO terms common in modules of mutant and wild type networks indicate both loss and gain of BPs. We further assign relevant biological function(s) to each module by classifying the enriched GO terms associated with it. It turns out that most of these biological functions in HTT networks are already known to be altered in HD and those of TP53 networks are altered in cancers. We argue that gain of BPs, and the corresponding biological functions, are due to new interacting partners acquired by mutant proteins. The methodology we adopt here could be applied to genetic diseases where mutations alter the ability of the protein to interact with other proteins. PMID:23741403

Invasive Species Biology, Control, and Research. Part 2. Multiflora Rose (Rosa multiflora)

DTIC Science & Technology

2008-11-01

species and alter long-term successional processes (Vidra et al. 2007), although they could also enhance the biodiversity of the plant community...3. Biological control ( fungi or insects) 4. Fire management 5. Prescribed grazing. Because the plant grows in large, dense thickets, possesses

Towards a semantic lexicon for biological language processing

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

Verspoor, K.

It is well understood that natural language processing (NLP) applications require sophisticated lexical resources to support their processing goals. In the biomedical domain, we are privileged to have access to extensive terminological resources in the form of controlled vocabularies and ontologies, which have been integrated into the framework of the National Library of Medicine's Unified Medical Language System's (UMLS) Metathesaurus. However, the existence of such terminological resources does not guarantee their utility for NLP. In particular, we have two core requirements for lexical resources for NLP in addition to the basic enumeration of important domain terms: representation of morphosyntactic informationmore » about those terms, specifically part of speech information and inflectional patterns to support parsing and lemma assignment, and representation of semantic information indicating general categorical information about terms, and significant relations between terms to support text understanding and inference (Hahn et at, 1999). Biomedical vocabularies by and large commonly leave out morphosyntactic information, and where they address semantic considerations, they often do so in an unprincipled manner, for instance by indicating a relation between two concepts without indicating the type of that relation. But all is not lost. The UMLS knowledge sources include two additional resources which are relevant - the SPECIALIST lexicon, a lexicon addressing our morphosyntactic requirements, and the Semantic Network, a representation of core conceptual categories in the biomedical domain. The coverage of these two knowledge sources with respect to the full coverage of the Metathesaurus is, however, not entirely clear. Furthermore, when our goals are specifically to process biological text - and often more specifically, text in the molecular biology domain - it is difficult to say whether the coverage of these resources is meaningful. The utility of the UMLS knowledge sources for medical language processing (MLP) has been explored (Johnson, 1999; Friedman et al 2001); the time has now come to repeat these experiments with respect to biological language processing (BLP). To that end, this paper presents an analysis of ihe UMLS resources, specifically with an eye towards constructing lexical resources suitable for BLP. We follow the paradigm presented in Johnson (1999) for medical language, exploring overlap between the UMLS Metathesaurus and SPECIALIST lexicon to construct a morphosyntactic and semantically-specified lexicon, and then further explore the overlap with a relevant domain corpus for molecular biology.« less

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

PubMed

Zheng, Jie; Harris, Marcelline R; Masci, Anna Maria; Lin, Yu; Hero, Alfred; Smith, Barry; He, Yongqun

2016-09-14

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. The terms in OBCS including 'data collection', 'data transformation in statistics', 'data visualization', 'statistical data analysis', and 'drawing a conclusion based on data', cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. Currently, OBCS comprehends 878 terms, representing 20 BFO classes, 403 OBI classes, 229 OBCS specific classes, and 122 classes imported from ten other OBO ontologies. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. Other ongoing projects using OBCS for statistical data processing are also discussed. The OBCS source code and documentation are available at: https://github.com/obcs/obcs . The Ontology of Biological and Clinical Statistics (OBCS) is a community-based open source ontology in the domain of biological and clinical statistics. OBCS is a timely ontology that represents statistics-related terms and their relations in a rigorous fashion, facilitates standard data analysis and integration, and supports reproducible biological and clinical research.

Vitalism, purpose and superstition.

PubMed

Lindeman, Marjaana; Saher, Marieke

2007-02-01

Developmental studies have shown that children assign purpose to objects more liberally than adults, and that they explain biological processes in terms of vitalistic causality. This study tested the hypothesis that similar misconceptions can be found among superstitious adults. The results from 116 superstitious and 123 sceptical individuals showed that more than sceptics, superstitious individuals attributed purpose to objects, and explained biological processes in terms of organ intentionality and energy transmission. In addition, they thought of energy as a vital force, attributing life and mental properties to it. These conceptual confusions were positively associated to all types of superstitions as well as belief in alternative medicine. The results support the argument that category mistakes and ontological confusions underlie superstitious and vitalistic thinking.

Evaluating the feasibility of biological waste processing for long term space missions.

PubMed

Garland, J L; Alazraki, M P; Atkinson, C F; Finger, B W

1998-01-01

Recycling waste products during orbital (e.g., International Space Station) and planetary missions (e.g., lunar base, Mars transit mission, Martian base) will reduce storage and resupply costs. Wastes streams on the space station will include human hygiene water, urine, faeces, and trash. Longer term missions will contain human waste and inedible plant material from plant growth systems used for atmospheric regeneration, food production, and water recycling. The feasibility of biological and physical-chemical waste recycling is being investigated as part of National Aeronautics and Space Administration's (NASA) Advanced Life Support (ALS) Program. In-vessel composting has lower manpower requirements, lower water and volume requirements, and greater potential for sanitization of human waste compared to alternative bioreactor designs such as continuously stirred tank reactors (CSTR). Residual solids from the process (i.e. compost) could be used a biological air filter, a plant nutrient source, and a carbon sink. Potential in-vessel composting designs for both near- and long-term space missions are presented and discussed with respect to the unique aspects of space-based systems.

Evaluating the feasibility of biological waste processing for long term space missions

NASA Technical Reports Server (NTRS)

Garland, J. L.; Alazraki, M. P.; Atkinson, C. F.; Finger, B. W.; Sager, J. C. (Principal Investigator)

1998-01-01

Recycling waste products during orbital (e.g., International Space Station) and planetary missions (e.g., lunar base, Mars transit mission, Martian base) will reduce storage and resupply costs. Wastes streams on the space station will include human hygiene water, urine, faeces, and trash. Longer term missions will contain human waste and inedible plant material from plant growth systems used for atmospheric regeneration, food production, and water recycling. The feasibility of biological and physical-chemical waste recycling is being investigated as part of National Aeronautics and Space Administration's (NASA) Advanced Life Support (ALS) Program. In-vessel composting has lower manpower requirements, lower water and volume requirements, and greater potential for sanitization of human waste compared to alternative bioreactor designs such as continuously stirred tank reactors (CSTR). Residual solids from the process (i.e. compost) could be used a biological air filter, a plant nutrient source, and a carbon sink. Potential in-vessel composting designs for both near- and long-term space missions are presented and discussed with respect to the unique aspects of space-based systems.

RuleGO: a logical rules-based tool for description of gene groups by means of Gene Ontology

PubMed Central

Gruca, Aleksandra; Sikora, Marek; Polanski, Andrzej

2011-01-01

Genome-wide expression profiles obtained with the use of DNA microarray technology provide abundance of experimental data on biological and molecular processes. Such amount of data need to be further analyzed and interpreted in order to obtain biological conclusions on the basis of experimental results. The analysis requires a lot of experience and is usually time-consuming process. Thus, frequently various annotation databases are used to improve the whole process of analysis. Here, we present RuleGO—the web-based application that allows the user to describe gene groups on the basis of logical rules that include Gene Ontology (GO) terms in their premises. Presented application allows obtaining rules that reflect coappearance of GO-terms describing genes supported by the rules. The ontology level and number of coappearing GO-terms is adjusted in automatic manner. The user limits the space of possible solutions only. The RuleGO application is freely available at http://rulego.polsl.pl/. PMID:21715384

Muscle Research and Gene Ontology: New standards for improved data integration.

PubMed

Feltrin, Erika; Campanaro, Stefano; Diehl, Alexander D; Ehler, Elisabeth; Faulkner, Georgine; Fordham, Jennifer; Gardin, Chiara; Harris, Midori; Hill, David; Knoell, Ralph; Laveder, Paolo; Mittempergher, Lorenza; Nori, Alessandra; Reggiani, Carlo; Sorrentino, Vincenzo; Volpe, Pompeo; Zara, Ivano; Valle, Giorgio; Deegan, Jennifer

2009-01-29

The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO) Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology.

Positioning Genomics in Biology Education: Content Mapping of Undergraduate Biology Textbooks†

PubMed Central

Wernick, Naomi L. B.; Ndung’u, Eric; Haughton, Dominique; Ledley, Fred D.

2014-01-01

Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science. PMID:25574293

Positioning genomics in biology education: content mapping of undergraduate biology textbooks.

PubMed

Wernick, Naomi L B; Ndung'u, Eric; Haughton, Dominique; Ledley, Fred D

2014-12-01

Biological thought increasingly recognizes the centrality of the genome in constituting and regulating processes ranging from cellular systems to ecology and evolution. In this paper, we ask whether genomics is similarly positioned as a core concept in the instructional sequence for undergraduate biology. Using quantitative methods, we analyzed the order in which core biological concepts were introduced in textbooks for first-year general and human biology. Statistical analysis was performed using self-organizing map algorithms and conventional methods to identify clusters of terms and their relative position in the books. General biology textbooks for both majors and nonmajors introduced genome-related content after text related to cell biology and biological chemistry, but before content describing higher-order biological processes. However, human biology textbooks most often introduced genomic content near the end of the books. These results suggest that genomics is not yet positioned as a core concept in commonly used textbooks for first-year biology and raises questions about whether such textbooks, or courses based on the outline of these textbooks, provide an appropriate foundation for understanding contemporary biological science.

Extending gene ontology with gene association networks.

PubMed

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

2016-04-15

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

Tissue regeneration with photobiomodulation

NASA Astrophysics Data System (ADS)

Tang, Elieza G.; Arany, Praveen R.

2013-03-01

Low level light therapy (LLLT) has been widely reported to reduce pain and inflammation and enhance wound healing and tissue regeneration in various settings. LLLT has been noted to have both stimulatory and inhibitory biological effects and these effects have been termed Photobiomodulation (PBM). Several elegant studies have shown the key role of Cytochrome C oxidase and ROS in initiating this process. The downstream biological responses remain to be clearly elucidated. Our work has demonstrated activation of an endogenous latent growth factor complex, TGF-β1, as one of the major biological events in PBM. TGF-β1 has critical roles in various biological processes especially in inflammation, immune responses, wound healing and stem cell biology. This paper overviews some of the studies demonstrating the efficacy of PBM in promoting tissue regeneration.

Quantifying electron transfer reactions in biological systems: what interactions play the major role?

NASA Astrophysics Data System (ADS)

Sjulstok, Emil; Olsen, Jógvan Magnus Haugaard; Solov'Yov, Ilia A.

2015-12-01

Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.

Long-Term Alterations in Neural and Endocrine Processes Induced by Motherhood

PubMed Central

Bridges, Robert S.

2015-01-01

The reproductive experience of pregnancy, lactation and motherhood can significantly remodel the female’s biological state, affecting endocrine, neuroendocrine, neural, and immunological processes. The brain, pituitary gland, liver, thymus, and mammary tissue are among the structures that are modified by reproductive experience. The present review that focuses on rodent research, but also includes pertinent studies in sheep and other species, identifies specific changes in these processes brought about by the biological states of pregnancy, parturition, and lactation and how the components of reproductive experience contribute to the remodeling of the maternal brain and organ systems. Findings indicate that prior parity alters key circulating hormone levels and neural receptor gene expression. Moreover, reproductive experience results in modifications in neural processes and glial support. The possible role of pregnancy-induced neurogenesis is considered in the context of neuroplasticity and behavior, and the effects of reproductive experience on maternal memory, i.e. the retention of maternal behavior, together with anxiety and learning are presented. Together, these sets of findings support the concept that the neural and biological state of the adult female is significantly and dramatically altered on a long-term basis by the experiences of parity and motherhood. Remodeling of the maternal brain and other biological systems is posited to help facilitate adaptations to environmental/ecological challenges as the female raises young and ages. PMID:26388065

The Value of Animations in Biology Teaching: A Study of Long-Term Memory Retention

PubMed Central

2007-01-01

Previous work has established that a narrated animation is more effective at communicating a complex biological process (signal transduction) than the equivalent graphic with figure legend. To my knowledge, no study has been done in any subject area on the effectiveness of animations versus graphics in the long-term retention of information, a primary and critical issue in studies of teaching and learning. In this study, involving 393 student responses, three different animations and two graphics—one with and one lacking a legend—were used to determine the long-term retention of information. The results show that students retain more information 21 d after viewing an animation without narration compared with an equivalent graphic whether or not that graphic had a legend. Students' comments provide additional insight into the value of animations in the pedagogical process, and suggestions for future work are proposed. PMID:17785404

The value of animations in biology teaching: a study of long-term memory retention.

PubMed

O'Day, Danton H

2007-01-01

Previous work has established that a narrated animation is more effective at communicating a complex biological process (signal transduction) than the equivalent graphic with figure legend. To my knowledge, no study has been done in any subject area on the effectiveness of animations versus graphics in the long-term retention of information, a primary and critical issue in studies of teaching and learning. In this study, involving 393 student responses, three different animations and two graphics-one with and one lacking a legend-were used to determine the long-term retention of information. The results show that students retain more information 21 d after viewing an animation without narration compared with an equivalent graphic whether or not that graphic had a legend. Students' comments provide additional insight into the value of animations in the pedagogical process, and suggestions for future work are proposed.

Exploring autophagy with Gene Ontology

PubMed Central

2018-01-01

ABSTRACT Autophagy is a fundamental cellular process that is well conserved among eukaryotes. It is one of the strategies that cells use to catabolize substances in a controlled way. Autophagy is used for recycling cellular components, responding to cellular stresses and ridding cells of foreign material. Perturbations in autophagy have been implicated in a number of pathological conditions such as neurodegeneration, cardiac disease and cancer. The growing knowledge about autophagic mechanisms needs to be collected in a computable and shareable format to allow its use in data representation and interpretation. The Gene Ontology (GO) is a freely available resource that describes how and where gene products function in biological systems. It consists of 3 interrelated structured vocabularies that outline what gene products do at the biochemical level, where they act in a cell and the overall biological objectives to which their actions contribute. It also consists of ‘annotations’ that associate gene products with the terms. Here we describe how we represent autophagy in GO, how we create and define terms relevant to autophagy researchers and how we interrelate those terms to generate a coherent view of the process, therefore allowing an interoperable description of its biological aspects. We also describe how annotation of gene products with GO terms improves data analysis and interpretation, hence bringing a significant benefit to this field of study. PMID:29455577

Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

PubMed

Louridas, George E; Lourida, Katerina G

2017-02-21

Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

Criteria for High Quality Biology Teaching: An Analysis

ERIC Educational Resources Information Center

Tasci, Guntay

2015-01-01

This study aims to analyze the process under which biology lessons are taught in terms of teaching quality criteria (TQC). Teaching quality is defined as the properties of efficient teaching and is considered to be the criteria used to measure teaching quality both in general and specific to a field. The data were collected through classroom…

Quantum effects in the understanding of consciousness.

PubMed

Hameroff, Stuart R; Craddock, Travis J A; Tuszynski, Jack A

2014-06-01

This paper presents a historical perspective on the development and application of quantum physics methodology beyond physics, especially in biology and in the area of consciousness studies. Quantum physics provides a conceptual framework for the structural aspects of biological systems and processes via quantum chemistry. In recent years individual biological phenomena such as photosynthesis and bird navigation have been experimentally and theoretically analyzed using quantum methods building conceptual foundations for quantum biology. Since consciousness is attributed to human (and possibly animal) mind, quantum underpinnings of cognitive processes are a logical extension. Several proposals, especially the Orch OR hypothesis, have been put forth in an effort to introduce a scientific basis to the theory of consciousness. At the center of these approaches are microtubules as the substrate on which conscious processes in terms of quantum coherence and entanglement can be built. Additionally, Quantum Metabolism, quantum processes in ion channels and quantum effects in sensory stimulation are discussed in this connection. We discuss the challenges and merits related to quantum consciousness approaches as well as their potential extensions.

Muscle Research and Gene Ontology: New standards for improved data integration

PubMed Central

Feltrin, Erika; Campanaro, Stefano; Diehl, Alexander D; Ehler, Elisabeth; Faulkner, Georgine; Fordham, Jennifer; Gardin, Chiara; Harris, Midori; Hill, David; Knoell, Ralph; Laveder, Paolo; Mittempergher, Lorenza; Nori, Alessandra; Reggiani, Carlo; Sorrentino, Vincenzo; Volpe, Pompeo; Zara, Ivano; Valle, Giorgio; Deegan née Clark, Jennifer

2009-01-01

Background The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO) Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. Results The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. Conclusion The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki . PMID:19178689

Phenol wastewater remediation: advanced oxidation processes coupled to a biological treatment.

PubMed

Rubalcaba, A; Suárez-Ojeda, M E; Stüber, F; Fortuny, A; Bengoa, C; Metcalfe, I; Font, J; Carrera, J; Fabregat, A

2007-01-01

Nowadays, there are increasingly stringent regulations requiring more and more treatment of industrial effluents to generate product waters which could be easily reused or disposed of to the environment without any harmful effects. Therefore, different advanced oxidation processes were investigated as suitable precursors for the biological treatment of industrial effluents containing phenol. Wet air oxidation and Fenton process were tested batch wise, while catalytic wet air oxidation and H2O2-promoted catalytic wet air oxidation processes were studied in a trickle bed reactor, the last two using over activated carbon as catalyst. Effluent characterisation was made by means of substrate conversion (using high liquid performance chromatography), chemical oxygen demand and total organic carbon. Biodegradation parameters (i.e. maximum oxygen uptake rate and oxygen consumption) were obtained from respirometric tests using activated sludge from an urban biological wastewater treatment plant (WWTP). The main goal was to find the proper conditions in terms of biodegradability enhancement, so that these phenolic effluents could be successfully treated in an urban biological WWTP. Results show promising research ways for the development of efficient coupled processes for the treatment of wastewater containing toxic or biologically non-degradable compounds.

Invited review liquid crystal models of biological materials and silk spinning.

PubMed

Rey, Alejandro D; Herrera-Valencia, Edtson E

2012-06-01

A review of thermodynamic, materials science, and rheological liquid crystal models is presented and applied to a wide range of biological liquid crystals, including helicoidal plywoods, biopolymer solutions, and in vivo liquid crystals. The distinguishing characteristics of liquid crystals (self-assembly, packing, defects, functionalities, processability) are discussed in relation to biological materials and the strong correspondence between different synthetic and biological materials is established. Biological polymer processing based on liquid crystalline precursors includes viscoelastic flow to form and shape fibers. Viscoelastic models for nematic and chiral nematics are reviewed and discussed in terms of key parameters that facilitate understanding and quantitative information from optical textures and rheometers. It is shown that viscoelastic modeling the silk spinning process using liquid crystal theories sheds light on textural transitions in the duct of spiders and silk worms as well as on tactoidal drops and interfacial structures. The range and consistency of the predictions demonstrates that the use of mesoscopic liquid crystal models is another tool to develop the science and biomimetic applications of mesogenic biological soft matter. Copyright © 2011 Wiley Periodicals, Inc.

Short-term bioassay of complex organic mixtures. Part II. Mutagenicity testing

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

Epler, J.L.; Clark, B.R.; Ho, C.

1978-01-01

The feasibility of using short-term mutagenicity assays to predict the potential biohazard of various crude and complex test materials has been examined in a coupled chemical and biological approach. The principal focus of the research has involved the preliminary chemical characterizatiion and preparation for bioassay, followed by testing in the Salmonella histidine reversion assay system. The mutagenicity tests are intended to act as predictors of profound long-range health effects such as mutagenesis and/or carcinogenesis; act as a mechanism to rapidly isolate and identify a hazardous agent in a complex mixture; and function as a measure of biological activity correlating baselinemore » data with changes in process conditions. Since complex mixtures can be fractionated and approached in these short-term assays, information reflecting on the actual compounds responsible for the biological effect may be accumulated.« less

From biology to mathematical models and back: teaching modeling to biology students, and biology to math and engineering students.

PubMed

Chiel, Hillel J; McManus, Jeffrey M; Shaw, Kendrick M

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a "live" textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology.

Fast gene ontology based clustering for microarray experiments.

PubMed

Ovaska, Kristian; Laakso, Marko; Hautaniemi, Sampsa

2008-11-21

Analysis of a microarray experiment often results in a list of hundreds of disease-associated genes. In order to suggest common biological processes and functions for these genes, Gene Ontology annotations with statistical testing are widely used. However, these analyses can produce a very large number of significantly altered biological processes. Thus, it is often challenging to interpret GO results and identify novel testable biological hypotheses. We present fast software for advanced gene annotation using semantic similarity for Gene Ontology terms combined with clustering and heat map visualisation. The methodology allows rapid identification of genes sharing the same Gene Ontology cluster. Our R based semantic similarity open-source package has a speed advantage of over 2000-fold compared to existing implementations. From the resulting hierarchical clustering dendrogram genes sharing a GO term can be identified, and their differences in the gene expression patterns can be seen from the heat map. These methods facilitate advanced annotation of genes resulting from data analysis.

When mothering goes awry: Challenges and opportunities for utilizing evidence across rodent, nonhuman primate and human studies to better define the biological consequences of negative early caregiving☆

PubMed Central

Sánchez, Mar M.; Gonzalez, Andrea

2016-01-01

Across mammalian species, mothers shape socio-emotional development and serve as essential external regulators of infant physiology, brain development, behavior patterns, and emotional regulation. Caregiving quality, consistency and predictability shape the infant's underlying neurobiological processes. Although the requirements for “optimal” caregiving differ across species, the negative long-term consequences of the absence of needed caregiving (e.g. neglect) or the presence of harmful/aversive caregiving (e.g. physical abuse), are translatable across species. Recognizing the significant potential of cross species comparisons in terms of defining underlying mechanisms, effective translation requires consideration of the evolutionary, ecological, and fundamental biological and developmental differences between and among species. This review provides both an overview of several success stories of cross-species translations in relation to negative caregiving and a template for future studies seeking to most effectively define the underlying biological processes and advance research dedicated to mitigating the lasting negative health consequences of child maltreatment. PMID:26506032

Scaffolded biology.

PubMed

Minelli, Alessandro

2016-09-01

Descriptions and interpretations of the natural world are dominated by dichotomies such as organism vs. environment, nature vs. nurture, genetic vs. epigenetic, but in the last couple of decades strong dissatisfaction with those partitions has been repeatedly voiced and a number of alternative perspectives have been suggested, from perspectives such as Dawkins' extended phenotype, Turner's extended organism, Oyama's Developmental Systems Theory and Odling-Smee's niche construction theory. Last in time is the description of biological phenomena in terms of hybrids between an organism (scaffolded system) and a living or non-living scaffold, forming unit systems to study processes such as reproduction and development. As scaffold, eventually, we can define any resource used by the biological system, especially in development and reproduction, without incorporating it as happens in the case of resources fueling metabolism. Addressing biological systems as functionally scaffolded systems may help pointing to functional relationships that can impart temporal marking to the developmental process and thus explain its irreversibility; revisiting the boundary between development and metabolism and also regeneration phenomena, by suggesting a conceptual framework within which to investigate phenomena of regular hypermorphic regeneration such as characteristic of deer antlers; fixing a periodization of development in terms of the times at which a scaffolding relationship begins or is terminated; and promoting plant galls to legitimate study objects of developmental biology.

Analysis of cancer-related lncRNAs using gene ontology and KEGG pathways.

PubMed

Chen, Lei; Zhang, Yu-Hang; Lu, Guohui; Huang, Tao; Cai, Yu-Dong

2017-02-01

Cancer is a disease that involves abnormal cell growth and can invade or metastasize to other tissues. It is known that several factors are related to its initiation, proliferation, and invasiveness. Recently, it has been reported that long non-coding RNAs (lncRNAs) can participate in specific functional pathways and further regulate the biological function of cancer cells. Studies on lncRNAs are therefore helpful for uncovering the underlying mechanisms of cancer biological processes. We investigated cancer-related lncRNAs using gene ontology (GO) terms and KEGG pathway enrichment scores of neighboring genes that are co-expressed with the lncRNAs by extracting important GO terms and KEGG pathways that can help us identify cancer-related lncRNAs. The enrichment theory of GO terms and KEGG pathways was adopted to encode each lncRNA. Then, feature selection methods were employed to analyze these features and obtain the key GO terms and KEGG pathways. The analysis indicated that the extracted GO terms and KEGG pathways are closely related to several cancer associated processes, such as hormone associated pathways, energy associated pathways, and ribosome associated pathways. And they can accurately predict cancer-related lncRNAs. This study provided novel insight of how lncRNAs may affect tumorigenesis and which pathways may play important roles during it. These results could help understanding the biological mechanisms of lncRNAs and treating cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

Strategies for Stabilizing Nitrogenous Compounds in ECLSS Wastewater: Top-Down System Design and Unit Operation Selection with Focus on Bio-Regenerative Processes for Short and Long Term Scenarios

NASA Technical Reports Server (NTRS)

Lunn, Griffin M.

2011-01-01

Water recycling and eventual nutrient recovery is crucial for surviving in or past low earth orbit. New approaches and syste.m architecture considerations need to be addressed to meet current and future system requirements. This paper proposes a flexible system architecture that breaks down pretreatment , steps into discrete areas where multiple unit operations can be considered. An overview focusing on the urea and ammonia conversion steps allows an analysis on each process's strengths and weaknesses and synergy with upstream and downstream processing. Process technologies to be covered include chemical pretreatment, biological urea hydrolysis, chemical urea hydrolysis, combined nitrification-denitrification, nitrate nitrification, anammox denitrification, and regenerative ammonia absorption through struvite formation. Biological processes are considered mainly for their ability to both maximize water recovery and to produce nutrients for future plant systems. Unit operations can be considered for traditional equivalent system mass requirements in the near term or what they can provide downstream in the form of usable chemicals or nutrients for the long term closed-loop ecological control and life support system. Optimally this would allow a system to meet the former but to support the latter without major modification.

Nanoparticle interface to biology: applications in probing and modulating biological processes.

PubMed

Kah, James Chen Yong; Yeo, Eugenia Li Ling; Koh, Wee Ling; Poinard, Barbara Elodie Ariane; Neo, Dawn Jing Hui

2013-01-01

Nanomaterials can be considered as "pseudo" subcellular entities that are similar to endogenous biomolecules because of their size and ability to interact with other biomolecules. The interaction between nanoparticles and biomolecules gives rise to the nano-bio interface between a nanoparticle and its biological environment. This is often defined in terms of the biomolecules that are present on the surface of the nanoparticles. The nano-bio interface alters the surface characteristics and is what the biological system sees and interacts with. The nanoparticle can thus be viewed as a "scaffold" to which molecules are attached. Intelligent design of this nano-bio interface is therefore crucial to the functionality of nanoscale systems in biology. In this review, we discuss the most common nano-bio interfaces formed from molecules including DNA, polymers, proteins, and antibodies, and discuss their applications in probing and modulating biological processes. We focus our discussion on the nano-bio interface formed on gold nanoparticles as our nanoparticle "scaffold" of interest in part because of our research interest as well as their unique physicochemical properties. While not exhaustive, this review provides a good overview of the latest advances in the use of gold nanomaterial interface to probe and modulate biological processes.

Long-term alterations in neural and endocrine processes induced by motherhood in mammals.

PubMed

Bridges, Robert S

2016-01-01

This article is part of a Special Issue "Parental Care". The reproductive experience of pregnancy, lactation and motherhood can significantly remodel the female's biological state, affecting endocrine, neuroendocrine, neural, and immunological processes. The brain, pituitary gland, liver, thymus, and mammary tissue are among the structures that are modified by reproductive experience. The present review that focuses on rodent research, but also includes pertinent studies in sheep and other species, identifies specific changes in these processes brought about by the biological states of pregnancy, parturition, and lactation and how the components of reproductive experience contribute to the remodeling of the maternal brain and organ systems. Findings indicate that prior parity alters key circulating hormone levels and neural receptor gene expression. Moreover, reproductive experience results in modifications in neural processes and glial support. The possible role of pregnancy-induced neurogenesis is considered in the context of neuroplasticity and behavior, and the effects of reproductive experience on maternal memory, i.e. the retention of maternal behavior, together with anxiety and learning are presented. Together, these sets of findings support the concept that the neural and biological state of the adult female is significantly and dramatically altered on a long-term basis by the experiences of parity and motherhood. Remodeling of the maternal brain and other biological systems is posited to help facilitate adaptations to environmental/ecological challenges as the female raises young and ages. Copyright © 2015 Elsevier Inc. All rights reserved.

Conceptual Modeling in Systems Biology Fosters Empirical Findings: The mRNA Lifecycle

PubMed Central

Dori, Dov; Choder, Mordechai

2007-01-01

One of the main obstacles to understanding complex biological systems is the extent and rapid evolution of information, way beyond the capacity individuals to manage and comprehend. Current modeling approaches and tools lack adequate capacity to model concurrently structure and behavior of biological systems. Here we propose Object-Process Methodology (OPM), a holistic conceptual modeling paradigm, as a means to model both diagrammatically and textually biological systems formally and intuitively at any desired number of levels of detail. OPM combines objects, e.g., proteins, and processes, e.g., transcription, in a way that is simple and easily comprehensible to researchers and scholars. As a case in point, we modeled the yeast mRNA lifecycle. The mRNA lifecycle involves mRNA synthesis in the nucleus, mRNA transport to the cytoplasm, and its subsequent translation and degradation therein. Recent studies have identified specific cytoplasmic foci, termed processing bodies that contain large complexes of mRNAs and decay factors. Our OPM model of this cellular subsystem, presented here, led to the discovery of a new constituent of these complexes, the translation termination factor eRF3. Association of eRF3 with processing bodies is observed after a long-term starvation period. We suggest that OPM can eventually serve as a comprehensive evolvable model of the entire living cell system. The model would serve as a research and communication platform, highlighting unknown and uncertain aspects that can be addressed empirically and updated consequently while maintaining consistency. PMID:17849002

Modeling ecohydrologic processes at Hubbard Brook: Initial results for Watershed 6 stream discharge and chemistry

EPA Science Inventory

The Hubbard Brook Long Term Ecological Research site has produced some of the most extensive and long-running databases on the hydrology, biology and chemistry of forest ecosystem responses to climate and forest harvest. We used these long-term databases to calibrate and apply G...

A social ecology approach to understanding urban ecosystems and landscapes

Treesearch

J. Morgan Grove; Karen E. Hinson; Robert J. Northrop

2003-01-01

The shape and dynamics of cities are the result of physical, biological, and social forces. We include the term dynamic to emphasize that cities change over time and are the result of both idiosyncratic events and dominant trends. To begin to understand the patterns and processes of cities, we approach the idiosyncratic and dominant - whether it is physical, biological...

Determination of Ammonia Oxidizing Bacteria and Nitrate Oxidizing Bacteria in Wastewater and Bioreactors

NASA Technical Reports Server (NTRS)

Francis, Somilez Asya

2014-01-01

The process of water purification has many different physical, chemical, and biological processes. One part of the biological process is the task of ammonia oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB). Both play critical roles in the treatment of wastewater by oxidizing toxic compounds. The broad term is nitrification, a naturally occurring process that is carried out by AOB and NOB by using oxidation to convert ammonia to nitrite and nitrite to nitrate. To monitor this biological activity, bacterial staining was performed on wastewater contained in inoculum tanks and biofilm samples from bioreactors. Using microscopy and qPCR, the purpose of this experiment was to determine if the population of AOB and NOB in wastewater and membrane bioreactors changed depending on temperature and hibernation conditions to determine the optimal parameters for AOB/NOB culture to effectively clean wastewater.

Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations.

PubMed

Farzadfard, Fahim; Lu, Timothy K

2014-11-14

Cellular memory is crucial to many natural biological processes and sophisticated synthetic biology applications. Existing cellular memories rely on epigenetic switches or recombinases, which are limited in scalability and recording capacity. In this work, we use the DNA of living cell populations as genomic "tape recorders" for the analog and distributed recording of long-term event histories. We describe a platform for generating single-stranded DNA (ssDNA) in vivo in response to arbitrary transcriptional signals. When coexpressed with a recombinase, these intracellularly expressed ssDNAs target specific genomic DNA addresses, resulting in precise mutations that accumulate in cell populations as a function of the magnitude and duration of the inputs. This platform could enable long-term cellular recorders for environmental and biomedical applications, biological state machines, and enhanced genome engineering strategies. Copyright © 2014, American Association for the Advancement of Science.

Biological stress response terminology: Integrating the concepts of adaptive response and preconditioning stress within a hormetic dose-response framework.

PubMed

Calabrese, Edward J; Bachmann, Kenneth A; Bailer, A John; Bolger, P Michael; Borak, Jonathan; Cai, Lu; Cedergreen, Nina; Cherian, M George; Chiueh, Chuang C; Clarkson, Thomas W; Cook, Ralph R; Diamond, David M; Doolittle, David J; Dorato, Michael A; Duke, Stephen O; Feinendegen, Ludwig; Gardner, Donald E; Hart, Ronald W; Hastings, Kenneth L; Hayes, A Wallace; Hoffmann, George R; Ives, John A; Jaworowski, Zbigniew; Johnson, Thomas E; Jonas, Wayne B; Kaminski, Norbert E; Keller, John G; Klaunig, James E; Knudsen, Thomas B; Kozumbo, Walter J; Lettieri, Teresa; Liu, Shu-Zheng; Maisseu, Andre; Maynard, Kenneth I; Masoro, Edward J; McClellan, Roger O; Mehendale, Harihara M; Mothersill, Carmel; Newlin, David B; Nigg, Herbert N; Oehme, Frederick W; Phalen, Robert F; Philbert, Martin A; Rattan, Suresh I S; Riviere, Jim E; Rodricks, Joseph; Sapolsky, Robert M; Scott, Bobby R; Seymour, Colin; Sinclair, David A; Smith-Sonneborn, Joan; Snow, Elizabeth T; Spear, Linda; Stevenson, Donald E; Thomas, Yolene; Tubiana, Maurice; Williams, Gary M; Mattson, Mark P

2007-07-01

Many biological subdisciplines that regularly assess dose-response relationships have identified an evolutionarily conserved process in which a low dose of a stressful stimulus activates an adaptive response that increases the resistance of the cell or organism to a moderate to severe level of stress. Due to a lack of frequent interaction among scientists in these many areas, there has emerged a broad range of terms that describe such dose-response relationships. This situation has become problematic because the different terms describe a family of similar biological responses (e.g., adaptive response, preconditioning, hormesis), adversely affecting interdisciplinary communication, and possibly even obscuring generalizable features and central biological concepts. With support from scientists in a broad range of disciplines, this article offers a set of recommendations we believe can achieve greater conceptual harmony in dose-response terminology, as well as better understanding and communication across the broad spectrum of biological disciplines.

Sex that moves mountains: The influence of spawning fish on river profiles over geologic timescales

NASA Astrophysics Data System (ADS)

Fremier, Alexander K.; Yanites, Brian J.; Yager, Elowyn M.

2018-03-01

A key component of resilience is to understand feedbacks among components of biophysical systems, such as physical drivers, ecological responses and the subsequent feedbacks onto physical process. While physically based explanations of biological speciation are common (e.g., mountains separating a species can lead to speciation), less common is the inverse process examined: can a speciation event have significant influence on physical processes and patterns in a landscape? When such processes are considered, such as with 'ecosystem engineers', many studies have focused on the short-term physical and biological effects rather than the long-term impacts. Here, we formalized the physical influence of salmon spawning on stream beds into a model of channel profile evolution by altering the critical shear stress required to move stream bed particles. We then asked if spawning and an adaptive radiation event (similar to the one that occurred in Pacific salmon species) could have an effect on channel erosion processes and stream profiles over geological timescales. We found that spawning can profoundly influence the longitudinal profiles of stream beds and thereby the evolution of entire watersheds. The radiation of five Pacific salmon from a common ancestor, additionally, could also cause significant geomorphic change by altering a wider section of the profile for a given distribution of grain sizes. This modeling study suggests that biological evolution can impact landscape evolution by increasing the sediment transport and erosion efficiency of mountain streams. Moreover, the physical effects of a species on its environment might be a complementary explanation for rapid radiation events in species through the creation of new habitat types. This example provides an illustrative case for thinking about the long- and short-term coupling of biotic and abiotic systems.

Temperature: Human Regulating, Ants Conforming

ERIC Educational Resources Information Center

Clopton, Joe R.

2007-01-01

Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

Biology-Culture Co-evolution in Finite Populations.

PubMed

de Boer, Bart; Thompson, Bill

2018-01-19

Language is the result of two concurrent evolutionary processes: biological and cultural inheritance. An influential evolutionary hypothesis known as the moving target problem implies inherent limitations on the interactions between our two inheritance streams that result from a difference in pace: the speed of cultural evolution is thought to rule out cognitive adaptation to culturally evolving aspects of language. We examine this hypothesis formally by casting it as as a problem of adaptation in time-varying environments. We present a mathematical model of biology-culture co-evolution in finite populations: a generalisation of the Moran process, treating co-evolution as coupled non-independent Markov processes, providing a general formulation of the moving target hypothesis in precise probabilistic terms. Rapidly varying culture decreases the probability of biological adaptation. However, we show that this effect declines with population size and with stronger links between biology and culture: in realistically sized finite populations, stochastic effects can carry cognitive specialisations to fixation in the face of variable culture, especially if the effects of those specialisations are amplified through cultural evolution. These results support the view that language arises from interactions between our two major inheritance streams, rather than from one primary evolutionary process that dominates another.

Foundations of anticipatory logic in biology and physics.

PubMed

Bettinger, Jesse S; Eastman, Timothy E

2017-12-01

Recent advances in modern physics and biology reveal several scenarios in which top-down effects (Ellis, 2016) and anticipatory systems (Rosen, 1980) indicate processes at work enabling active modeling and inference such that anticipated effects project onto potential causes. We extrapolate a broad landscape of anticipatory systems in the natural sciences extending to computational neuroscience of perception in the capacity of Bayesian inferential models of predictive processing. This line of reasoning also comes with philosophical foundations, which we develop in terms of counterfactual reasoning and possibility space, Whitehead's process thought, and correlations with Eastern wisdom traditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

A neuromorphic circuit mimicking biological short-term memory.

PubMed

Barzegarjalali, Saeid; Parker, Alice C

2016-08-01

Research shows that the way we remember things for a few seconds is a different mechanism from the way we remember things for a longer time. Short-term memory is based on persistently firing neurons, whereas storing information for a longer time is based on strengthening the synapses or even forming new neural connections. Information about location and appearance of an object is segregated and processed by separate neurons. Furthermore neurons can continue firing using different mechanisms. Here, we have designed a biomimetic neuromorphic circuit that mimics short-term memory by firing neurons, using biological mechanisms to remember location and shape of an object. Our neuromorphic circuit has a hybrid architecture. Neurons are designed with CMOS 45nm technology and synapses are designed with carbon nanotubes (CNT).

Simplified pulse reactor for real-time long-term in vitro testing of biological heart valves.

PubMed

Schleicher, Martina; Sammler, Günther; Schmauder, Michael; Fritze, Olaf; Huber, Agnes J; Schenke-Layland, Katja; Ditze, Günter; Stock, Ulrich A

2010-05-01

Long-term function of biological heart valve prostheses (BHV) is limited by structural deterioration leading to failure with associated arterial hypertension. The objective of this work was development of an easy to handle real-time pulse reactor for evaluation of biological and tissue engineered heart valves under different pressures and long-term conditions. The pulse reactor was made of medical grade materials for placement in a 37 degrees C incubator. Heart valves were mounted in a housing disc moving horizontally in culture medium within a cylindrical culture reservoir. The microprocessor-controlled system was driven by pressure resulting in a cardiac-like cycle enabling competent opening and closing of the leaflets with adjustable pulse rates and pressures between 0.25 to 2 Hz and up to 180/80 mmHg, respectively. A custom-made imaging system with an integrated high-speed camera and image processing software allow calculation of effective orifice areas during cardiac cycle. This simple pulse reactor design allows reproducible generation of patient-like pressure conditions and data collection during long-term experiments.

Herpesviruses that infect fish.

PubMed

Hanson, Larry; Dishon, Arnon; Kotler, Moshe

2011-11-01

Herpesviruses are host specific pathogens that are widespread among vertebrates. Genome sequence data demonstrate that most herpesviruses of fish and amphibians are grouped together (family Alloherpesviridae) and are distantly related to herpesviruses of reptiles, birds and mammals (family Herpesviridae). Yet, many of the biological processes of members of the order Herpesvirales are similar. Among the conserved characteristics are the virion structure, replication process, the ability to establish long term latency and the manipulation of the host immune response. Many of the similar processes may be due to convergent evolution. This overview of identified herpesviruses of fish discusses the diseases that alloherpesviruses cause, the biology of these viruses and the host-pathogen interactions. Much of our knowledge on the biology of Alloherpesvirdae is derived from research with two species: Ictalurid herpesvirus 1 (channel catfish virus) and Cyprinid herpesvirus 3 (koi herpesvirus).

Herpesviruses that Infect Fish

PubMed Central

Hanson, Larry; Dishon, Arnon; Kotler, Moshe

2011-01-01

Herpesviruses are host specific pathogens that are widespread among vertebrates. Genome sequence data demonstrate that most herpesviruses of fish and amphibians are grouped together (family Alloherpesviridae) and are distantly related to herpesviruses of reptiles, birds and mammals (family Herpesviridae). Yet, many of the biological processes of members of the order Herpesvirales are similar. Among the conserved characteristics are the virion structure, replication process, the ability to establish long term latency and the manipulation of the host immune response. Many of the similar processes may be due to convergent evolution. This overview of identified herpesviruses of fish discusses the diseases that alloherpesviruses cause, the biology of these viruses and the host-pathogen interactions. Much of our knowledge on the biology of Alloherpesvirdae is derived from research with two species: Ictalurid herpesvirus 1 (channel catfish virus) and Cyprinid herpesvirus 3 (koi herpesvirus). PMID:22163339

From Biology to Mathematical Models and Back: Teaching Modeling to Biology Students, and Biology to Math and Engineering Students

PubMed Central

McManus, Jeffrey M.; Shaw, Kendrick M.

2010-01-01

We describe the development of a course to teach modeling and mathematical analysis skills to students of biology and to teach biology to students with strong backgrounds in mathematics, physics, or engineering. The two groups of students have different ways of learning material and often have strong negative feelings toward the area of knowledge that they find difficult. To give students a sense of mastery in each area, several complementary approaches are used in the course: 1) a “live” textbook that allows students to explore models and mathematical processes interactively; 2) benchmark problems providing key skills on which students make continuous progress; 3) assignment of students to teams of two throughout the semester; 4) regular one-on-one interactions with instructors throughout the semester; and 5) a term project in which students reconstruct, analyze, extend, and then write in detail about a recently published biological model. Based on student evaluations and comments, an attitude survey, and the quality of the students' term papers, the course has significantly increased the ability and willingness of biology students to use mathematical concepts and modeling tools to understand biological systems, and it has significantly enhanced engineering students' appreciation of biology. PMID:20810957

Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems

PubMed Central

Ruiz-Mirazo, Kepa; Briones, Carlos

2017-01-01

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. PMID:28446711

Chemical roots of biological evolution: the origins of life as a process of development of autonomous functional systems.

PubMed

Ruiz-Mirazo, Kepa; Briones, Carlos; de la Escosura, Andrés

2017-04-01

In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals. On these lines, a concrete proposal for the set of molecular control mechanisms that must be coupled to bring about autonomous functional systems, at the interface between chemistry and biology, is provided. © 2017 The Authors.

Importance of Data Management in a Long-Term Biological Monitoring Program

NASA Astrophysics Data System (ADS)

Christensen, Sigurd W.; Brandt, Craig C.; McCracken, Mary K.

2011-06-01

The long-term Biological Monitoring and Abatement Program (BMAP) has always needed to collect and retain high-quality data on which to base its assessments of ecological status of streams and their recovery after remediation. Its formal quality assurance, data processing, and data management components all contribute to meeting this need. The Quality Assurance Program comprehensively addresses requirements from various institutions, funders, and regulators, and includes a data management component. Centralized data management began a few years into the program when an existing relational database was adapted and extended to handle biological data. The database's main data tables and several key reference tables are described. One of the most important related activities supporting long-term analyses was the establishing of standards for sampling site names, taxonomic identification, flagging, and other components. The implemented relational database supports the transmittal of data to the Oak Ridge Environmental Information System (OREIS) as the permanent repository. We also discuss some limitations to our implementation. Some types of program data were not easily accommodated in the central systems, and many possible data-sharing and integration options are not easily accessible to investigators. From our experience we offer data management advice to other biologically oriented long-term environmental sampling and analysis programs.

Linking MedDRA®-coded Clinical Phenotypes to Biological Mechanisms by The Ontology of Adverse Events: A pilot study on Tyrosine Kinase Inhibitors (TKIs)

PubMed Central

Sarntivijai, Sirarat; Zhang, Shelley; Jagannathan, Desikan G.; Zaman, Shadia; Burkhart, Keith K.; Omenn, Gilbert S.; He, Yongqun; Athey, Brian D.; Abernethy, Darrell R.

2016-01-01

Introduction A translational bioinformatics challenge lies in connecting population and individual’s clinical phenotypes in various formats to biological mechanisms. The Medical Dictionary for Regulatory Activities (MedDRA®) is the default dictionary for Adverse Event (AE) reporting in the FDA Adverse Event Reporting System (FAERS). The Ontology of Adverse Events (OAE) represents AEs as pathological processes occurring after drug exposures. Objectives The aim is to establish a semantic framework to link biological mechanisms to phenotypes of AEs by combining OAE with MedDRA® in FAERS data analysis. We investigated the AEs associated with Tyrosine Kinase Inhibitors (TKIs) and monoclonal antibodies (mAbs) targeting tyrosine kinases. The selected 5 TKIs/mAbs (i.e., dasatinib, imatinib, lapatinib, cetuximab, and trastuzumab) are known to induce impaired ventricular function (non-QT) cardiotoxicity. Results Statistical analysis of FAERS data identified 1,053 distinct MedDRA® terms significantly associated with TKIs/mAbs, where 884 did not have corresponding OAE terms. We manually annotated these terms, added them to OAE by the standard OAE development strategy, and mapped them to MedDRA®. The data integration to provide insights into molecular mechanisms for drug-associated AEs is performed by including linkages in OAE for all related AE terms to MedDRA® and existing ontologies including Human Phenotype Ontology (HP), Uber Anatomy Ontology (UBERON), and Gene Ontology (GO). Sixteen AEs are shared by all 5 TKIs/mAbs, and each of 17 cardiotoxicity AEs was associated with at least one TKI/mAb. As an example, we analyzed ‘cardiac failure’ using the relations established in OAE with other ontologies, and demonstrated that one of the biological processes associated with cardiac failure maps to the genes associated with heart contraction. Conclusion By expanding existing OAE ontological design, our TKI use case demonstrates that the combination of OAE and MedDRA® provides a semantic framework to link clinical phenotypes of adverse drug events to biological mechanisms. PMID:27003817

Processes of carbonate precipitation in modern microbial mats

NASA Astrophysics Data System (ADS)

Dupraz, Christophe; Reid, R. Pamela; Braissant, Olivier; Decho, Alan W.; Norman, R. Sean; Visscher, Pieter T.

2009-10-01

Microbial mats are ecosystems that arguably greatly affected the conditions of the biosphere on Earth through geological time. These laminated organosedimentary systems, which date back to > 3.4 Ga bp, are characterized by high metabolic rates, and coupled to this, rapid cycling of major elements on very small (mm-µm) scales. The activity of the mat communities has changed Earth's redox conditions (i.e. oxidation state) through oxygen and hydrogen production. Interpretation of fossil microbial mats and their potential role in alteration of the Earth's geochemical environment is challenging because these mats are generally not well preserved. Preservation of microbial mats in the fossil record can be enhanced through carbonate precipitation, resulting in the formation of lithified mats, or microbialites. Several types of microbially-mediated mineralization can be distinguished, including biologically-induced and biologically influenced mineralization. Biologically-induced mineralization results from the interaction between biological activity and the environment. Biologically-influenced mineralization is defined as passive mineralization of organic matter (biogenic or abiogenic in origin), whose properties influence crystal morphology and composition. We propose to use the term organomineralization sensu lato as an umbrella term encompassing biologically influenced and biologically induced mineralization. Key components of organomineralization sensu lato are the "alkalinity" engine (microbial metabolism and environmental conditions impacting the calcium carbonate saturation index) and an organic matrix comprised of extracellular polymeric substances (EPS), which may provide a template for carbonate nucleation. Here we review the specific role of microbes and the EPS matrix in various mineralization processes and discuss examples of modern aquatic (freshwater, marine and hypersaline) and terrestrial microbialites.

Lesson plan profile of senior high school biology teachers in Subang

NASA Astrophysics Data System (ADS)

Rohayati, E.; Diana, S. W.; Priyandoko, D.

2018-05-01

Lesson plan have important role for biology teachers in teaching and learning process. The aim of this study was intended to gain an overview of lesson plan of biology teachers’ at Senior High Schools in Subang which were the members of biology teachers association in Subang. The research method was descriptive method. Data was collected from 30 biology teachers. The result of study showed that lesson plan profile in terms of subject’s identity had good category with 83.33 % of average score. Analysis on basic competence in fair category with 74.45 % of average score. The compatibility of method/strategy was in fair category with average score 72.22 %. The compatibility of instrument, media, and learning resources in fair category with 71.11 % of average score. Learning scenario was in good category with 77.00 % of average score. The compatibility of evaluation was in low category with 56.39 % of average score. It can be concluded that biology teachers in Subang were good enough in making lesson plan, however in terms of the compatibility of evaluation needed to be fixed. Furthermore, teachers’ training for biology teachers’ association was recommended to increasing teachers’ skill to be professional teachers.

When mothering goes awry: Challenges and opportunities for utilizing evidence across rodent, nonhuman primate and human studies to better define the biological consequences of negative early caregiving.

PubMed

Drury, Stacy S; Sánchez, Mar M; Gonzalez, Andrea

2016-01-01

This article is part of a Special Issue "Parental Care".Across mammalian species, mothers shape socio-emotional development and serve as essential external regulators of infant physiology, brain development, behavior patterns, and emotional regulation. Caregiving quality, consistency and predictability shape the infant's underlying neurobiological processes. Although the requirements for "optimal" caregiving differ across species, the negative long-term consequences of the absence of needed caregiving (e.g. neglect) or the presence of harmful/aversive caregiving (e.g. physical abuse), are translatable across species. Recognizing the significant potential of cross species comparisons in terms of defining underlying mechanisms, effective translation requires consideration of the evolutionary, ecological, and fundamental biological and developmental differences between and among species. This review provides both an overview of several success stories of cross-species translations in relation to negative caregiving and a template for future studies seeking to most effectively define the underlying biological processes and advance research dedicated to mitigating the lasting negative health consequences of child maltreatment. Copyright © 2015 Elsevier Inc. All rights reserved.

Biological determinants of spontaneous late preterm and early term birth: a retrospective cohort study.

PubMed

Brown, H K; Speechley, K N; Macnab, J; Natale, R; Campbell, M K

2015-03-01

Our aim was to examine the association between biological determinants of preterm birth (infection and inflammation, placental ischaemia and other hypoxia, diabetes mellitus, other) and spontaneous late preterm (34-36 weeks) and early term (37-38 weeks) birth. Retrospective cohort study. City of London and Middlesex County, Canada. Singleton live births, delivered at 34-41 weeks to London-Middlesex mothers following spontaneous labour. Data were obtained from a city-wide perinatal database on births between 2002 and 2011 (n = 17,678). Multivariable analyses used multinomial logistic regression. The outcome of interest was the occurrence of late preterm (34-36 weeks) and early term (37-38 weeks) birth, compared with full term birth (39-41 weeks). After controlling for covariates, there were associations between infection and inflammation and late preterm birth (aOR = 2.07, 95% CI 1.65, 2.60); between placental ischaemia and other hypoxia and late preterm (aOR = 2.21, 95% CI 1.88, 2.61) and early term (aOR = 1.25, 95% CI 1.13, 1.39) birth; between diabetes mellitus and late preterm (aOR = 3.89, 95% CI 2.90, 5.21) and early term (aOR = 2.66, 95% CI 2.19, 3.23) birth; and between other biological determinants (polyhydramnios, oligohydramnios) and late preterm (aOR = 2.81, 95% CI 1.70, 4.64) and early term (aOR = 1.89, 95% CI 1.32, 2.70) birth. Our findings show that delivery following spontaneous labour even close to full term may be a result of pathological processes. Because these biological determinants of preterm birth contribute to an adverse intrauterine environment, they have important implications for fetal and neonatal health. © 2014 Royal College of Obstetricians and Gynaecologists.

Characterizing local biological hotspots in the Gulf of Maine using remote sensing data

NASA Astrophysics Data System (ADS)

Ribera, Marta M.

Researchers increasingly advocate the use of ecosystem-based management (EBM) for managing complex marine ecosystems. This approach requires managers to focus on processes and cross-scale interactions, rather than individual components. However, they often lack appropriate tools and data sources to pursue this change in management approach. One method that has been proposed to understand the ecological complexity inherent in marine ecosystems is the study of biological hotspots. Biological hotspots are locations where organisms from different trophic levels aggregate to feed on abundant supplies, and they are considered a first step toward understanding the processes driving spatial and temporal heterogeneity in marine systems. Biological hotspots are supported by phytoplankton aggregations, which are characterized by high spatial and temporal variability. As a result, methods developed to locate biological hotspots in relatively stable terrestrial systems are not well suited for more dynamic marine ecosystems. The main objective of this thesis is thus to identify and characterize local-scale biological hotspots in the western side of the Gulf of Maine. The first chapter describes a new methodological framework with the steps needed to locate these types of hotspots in marine ecosystems using remote sensing datasets. Then, in the second chapter these hotspots are characterized using a novel metric that uses time series information and spatial statistics to account for both the temporal variability and spatial structure of these marine aggregations. This metric redefines biological hotspots as areas with a high probability of exhibiting positive anomalies of productivity compared to the expected regional seasonal pattern. Finally, the third chapter compares the resulting biological hotspots to fishery-dependent abundance indices of surface and benthic predators to determine the effect of the location and magnitude of phytoplankton aggregations on the rest of the ecosystem. Analyses indicate that the spatial scale and magnitude of biological hotspots in the Gulf of Maine depend on the location and time of the year. Results also show that these hotspots change over time in response to both short-term oceanographic processes and long-term climatic cycles. Finally, the new metric presented here facilitates the spatial comparison between different trophic levels, thus allowing interdisciplinary ecosystem-wide studies.

The Design of a Molecular Assembly Line Based on Biological Molecules

DTIC Science & Technology

2003-06-01

and will demonstrate how one can construct a purely synthetic analogue of a polyketide synthase . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF...scaffold in programmed assembly and molecular electronics. It is based on the principles of the biological molecules polyketide synthase and kinesin, and in...stereoselective centers) with any reasonable yield, not including the R&D and process development time. Figure 1.6 shows how a polyketide synthase

FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences

PubMed Central

Minneci, Federico; Piovesan, Damiano; Cozzetto, Domenico; Jones, David T.

2013-01-01

To understand fully cell behaviour, biologists are making progress towards cataloguing the functional elements in the human genome and characterising their roles across a variety of tissues and conditions. Yet, functional information – either experimentally validated or computationally inferred by similarity – remains completely missing for approximately 30% of human proteins. FFPred was initially developed to bridge this gap by targeting sequences with distant or no homologues of known function and by exploiting clear patterns of intrinsic disorder associated with particular molecular activities and biological processes. Here, we present an updated and improved version, which builds on larger datasets of protein sequences and annotations, and uses updated component feature predictors as well as revised training procedures. FFPred 2.0 includes support vector regression models for the prediction of 442 Gene Ontology (GO) terms, which largely expand the coverage of the ontology and of the biological process category in particular. The GO term list mainly revolves around macromolecular interactions and their role in regulatory, signalling, developmental and metabolic processes. Benchmarking experiments on newly annotated proteins show that FFPred 2.0 provides more accurate functional assignments than its predecessor and the ProtFun server do; also, its assignments can complement information obtained using BLAST-based transfer of annotations, improving especially prediction in the biological process category. Furthermore, FFPred 2.0 can be used to annotate proteins belonging to several eukaryotic organisms with a limited decrease in prediction quality. We illustrate all these points through the use of both precision-recall plots and of the COGIC scores, which we recently proposed as an alternative numerical evaluation measure of function prediction accuracy. PMID:23717476

Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

PubMed Central

Xu, Qiongqiong; Luo, Juntao; Shi, Yingdi; Li, Xiaoxia; Yan, Xiaonan; Zhang, Junfang

2016-01-01

DNA methylation is an essential epigenetic mechanism involved in multiple biological processes. However, the relationship between DNA methylation and cold acclimation remains poorly understood. In this study, Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) was performed to reveal a genome-wide methylation profile of zebrafish (Danio rerio) embryonic fibroblast cells (ZF4) and its variation under cold pressure. MeDIP-seq assay was conducted with ZF4 cells cultured at appropriate temperature of 28°C and at low temperature of 18°C for 5 (short-term) and 30 (long-term) days, respectively. Our data showed that DNA methylation level of whole genome increased after a short-term cold exposure and decreased after a long-term cold exposure. It is interesting that metabolism of folate pathway is significantly hypomethylated after short-term cold exposure, which is consistent with the increased DNA methylation level. 21% of methylation peaks were significantly altered after cold treatment. About 8% of altered DNA methylation peaks are located in promoter regions, while the majority of them are located in non-coding regions. Methylation of genes involved in multiple cold responsive biological processes were significantly affected, such as anti-oxidant system, apoptosis, development, chromatin modifying and immune system suggesting that those processes are responsive to cold stress through regulation of DNA methylation. Our data indicate the involvement of DNA methylation in cellular response to cold pressure, and put a new insight into the genome-wide epigenetic regulation under cold pressure. PMID:27494266

Twelve testable hypotheses on the geobiology of weathering.

PubMed

Brantley, S L; Megonigal, J P; Scatena, F N; Balogh-Brunstad, Z; Barnes, R T; Bruns, M A; Van Cappellen, P; Dontsova, K; Hartnett, H E; Hartshorn, A S; Heimsath, A; Herndon, E; Jin, L; Keller, C K; Leake, J R; McDowell, W H; Meinzer, F C; Mozdzer, T J; Petsch, S; Pett-Ridge, J; Pregitzer, K S; Raymond, P A; Riebe, C S; Shumaker, K; Sutton-Grier, A; Walter, R; Yoo, K

2011-03-01

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earth's surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby controlling the location and extent of biological weathering. (2) Biological stoichiometry drives changes in mineral stoichiometry and distribution through weathering. (3) On landscapes experiencing little erosion, biology drives weathering during initial succession, whereas weathering drives biology over the long term. (4) In eroding landscapes, weathering-front advance at depth is coupled to surface denudation via biotic processes. (5) Biology shapes the topography of the Critical Zone. (6) The impact of climate forcing on denudation rates in natural systems can be predicted from models incorporating biogeochemical reaction rates and geomorphological transport laws. (7) Rising global temperatures will increase carbon losses from the Critical Zone. (8) Rising atmospheric P(CO2) will increase rates and extents of mineral weathering in soils. (9) Riverine solute fluxes will respond to changes in climate primarily due to changes in water fluxes and secondarily through changes in biologically mediated weathering. (10) Land use change will impact Critical Zone processes and exports more than climate change. (11) In many severely altered settings, restoration of hydrological processes is possible in decades or less, whereas restoration of biodiversity and biogeochemical processes requires longer timescales. (12) Biogeochemical properties impart thresholds or tipping points beyond which rapid and irreversible losses of ecosystem health, function, and services can occur. © 2011 Blackwell Publishing Ltd.

SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs

PubMed Central

Shaikh, Tanvir R; Gao, Haixiao; Baxter, William T; Asturias, Francisco J; Boisset, Nicolas; Leith, Ardean; Frank, Joachim

2009-01-01

This protocol describes the reconstruction of biological molecules from the electron micrographs of single particles. Computation here is performed using the image-processing software SPIDER and can be managed using a graphical user interface, termed the SPIDER Reconstruction Engine. Two approaches are described to obtain an initial reconstruction: random-conical tilt and common lines. Once an existing model is available, reference-based alignment can be used, a procedure that can be iterated. Also described is supervised classification, a method to look for homogeneous subsets when multiple known conformations of the molecule may coexist. PMID:19180078

Memory and learning behaviors mimicked in nanogranular SiO2-based proton conductor gated oxide-based synaptic transistors

NASA Astrophysics Data System (ADS)

Wan, Chang Jin; Zhu, Li Qiang; Zhou, Ju Mei; Shi, Yi; Wan, Qing

2013-10-01

In neuroscience, signal processing, memory and learning function are established in the brain by modifying ionic fluxes in neurons and synapses. Emulation of memory and learning behaviors of biological systems by nanoscale ionic/electronic devices is highly desirable for building neuromorphic systems or even artificial neural networks. Here, novel artificial synapses based on junctionless oxide-based protonic/electronic hybrid transistors gated by nanogranular phosphorus-doped SiO2-based proton-conducting films are fabricated on glass substrates by a room-temperature process. Short-term memory (STM) and long-term memory (LTM) are mimicked by tuning the pulse gate voltage amplitude. The LTM process in such an artificial synapse is due to the proton-related interfacial electrochemical reaction. Our results are highly desirable for building future neuromorphic systems or even artificial networks via electronic elements.In neuroscience, signal processing, memory and learning function are established in the brain by modifying ionic fluxes in neurons and synapses. Emulation of memory and learning behaviors of biological systems by nanoscale ionic/electronic devices is highly desirable for building neuromorphic systems or even artificial neural networks. Here, novel artificial synapses based on junctionless oxide-based protonic/electronic hybrid transistors gated by nanogranular phosphorus-doped SiO2-based proton-conducting films are fabricated on glass substrates by a room-temperature process. Short-term memory (STM) and long-term memory (LTM) are mimicked by tuning the pulse gate voltage amplitude. The LTM process in such an artificial synapse is due to the proton-related interfacial electrochemical reaction. Our results are highly desirable for building future neuromorphic systems or even artificial networks via electronic elements. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr02987e

Artificial Synaptic Devices Based on Natural Chicken Albumen Coupled Electric-Double-Layer Transistors

NASA Astrophysics Data System (ADS)

Wu, Guodong; Feng, Ping; Wan, Xiang; Zhu, Liqiang; Shi, Yi; Wan, Qing

2016-03-01

Recent progress in using biomaterials to fabricate functional electronics has got growing attention for the new generation of environmentally friendly and biocompatible electronic devices. As a kind of biological material with rich source, proteins are essential natural component of all organisms. At the same time, artificial synaptic devices are of great significance for neuromorphic systems because they can emulate the signal process and memory behaviors of biological synapses. In this report, natural chicken albumen with high proton conductivity was used as the coupling electrolyte film for organic/inorganic hybrid synaptic devices fabrication. Some important synaptic functions including paired-pulse facilitation, dynamic filtering, short-term to long-term memory transition and spatial summation and shunting inhibition were successfully mimicked. Our results are very interesting for biological friendly artificial neuron networks and neuromorphic systems.

Genomically Encoded Analog Memory with Precise In vivo DNA Writing in Living Cell Populations

PubMed Central

Farzadfard, Fahim; Lu, Timothy K.

2014-01-01

Cellular memory is crucial to many natural biological processes and for sophisticated synthetic-biology applications. Existing cellular memories rely on epigenetic switches or recombinases, which are limited in scalability and recording capacity. Here, we use the DNA of living cell populations as genomic ‘tape recorders’ for the analog and distributed recording of long-term event histories. We describe a platform for generating single-stranded DNA (ssDNA) in vivo in response to arbitrary transcriptional signals. When co-expressed with a recombinase, these intracellularly expressed ssDNAs target specific genomic DNA addresses, resulting in precise mutations that accumulate in cell populations as a function of the magnitude and duration of the inputs. This platform could enable long-term cellular recorders for environmental and biomedical applications, biological state machines, and enhanced genome engineering strategies. PMID:25395541

Encapsulation of biomaterials in porous glass-like matrices prepared via an aqueous colloidal sol-gel process

DOEpatents

Liu, Dean-Mo; Chen, I-Wei

2001-01-01

The present invention provides a process for the encapsulation of biologically important proteins into transparent, porous silica matrices by an alcohol-free, aqueous, colloidal sol-gel process, and to the biological materials encapsulated thereby. The process is exemplified by studies involving encapsulated cytochrome c, catalase, myoglobin, and hemoglobin, although non-proteinaceous biomaterials, such as active DNA or RNA fragments, cells or even tissues, may also be encapsulated in accordance with the present methods. Conformation, and hence activity of the biomaterial, is successfully retained after encapsulation as demonstrated by optical characterization of the molecules, even after long-term storage. The retained conformation of the biomaterial is strongly correlated to both the rate of gelation and the subsequent drying speed of the encapsulatng matrix. Moreover, in accordance with this process, gelation is accelerated by the use of a higher colloidal solid concentration and a lower synthesis pH than conventional methods, thereby enhancing structural stability and retained conformation of the biomaterials. Thus, the invention also provides a remarkable improvement in retaining the biological activity of the encapsulated biomaterial, as compared with those involved in conventional alkoxide-based processes. It further provides new methods for the quantitative and qualitative detection of test substances that are reactive to, or catalyzed by, the active, encapsulated biological materials.

Reversible and long-term immobilization in a hydrogel-microbead matrix for high-resolution imaging of Caenorhabditis elegans and other small organisms

PubMed Central

Cornaglia, Matteo; Krishnamani, Gopalan; Zhang, Jingwei; Mouchiroud, Laurent; Lehnert, Thomas; Auwerx, Johan; Gijs, Martin A. M.

2018-01-01

The nematode Caenorhabditis elegans is an important model organism for biomedical research and genetic studies relevant to human biology and disease. Such studies are often based on high-resolution imaging of dynamic biological processes in the worm body tissues, requiring well-immobilized and physiologically active animals in order to avoid movement-related artifacts and to obtain meaningful biological information. However, existing immobilization methods employ the application of either anesthetics or servere physical constraints, by using glue or specific microfluidic on-chip mechanical structures, which in some cases may strongly affect physiological processes of the animals. Here, we immobilize C. elegans nematodes by taking advantage of a biocompatible and temperature-responsive hydrogel-microbead matrix. Our gel-based immobilization technique does not require a specific chip design and enables fast and reversible immobilization, thereby allowing successive imaging of the same single worm or of small worm populations at all development stages for several days. We successfully demonstrated the applicability of this method in challenging worm imaging contexts, in particular by applying it for high-resolution confocal imaging of the mitochondrial morphology in worm body wall muscle cells and for the long-term quantification of number and size of specific protein aggregates in different C. elegans neurodegenerative disease models. Our approach was also suitable for immobilizing other small organisms, such as the larvae of the fruit fly Drosophila melanogaster and the unicellular parasite Trypanosoma brucei. We anticipate that this versatile technique will significantly simplify biological assay-based longitudinal studies and long-term observation of small model organisms. PMID:29509812

Integrating Grant-Funded Research into the Undergraduate Biology Curriculum Using IMG-ACT

ERIC Educational Resources Information Center

Ditty, Jayna L.; Williams, Kayla M.; Keller, Megan M.; Chen, Grischa Y.; Liu, Xianxian; Parales, Rebecca E.

2013-01-01

It has become clear in current scientific pedagogy that the emersion of students in the scientific process in terms of designing, implementing, and analyzing experiments is imperative for their education; as such, it has been our goal to model this active learning process in the classroom and laboratory in the context of a genuine scientific…

Of drug administration, war and oïkos: mediating cancer with nanomedicines.

PubMed

Loeve, Sacha

2015-01-01

This paper focuses on nano-enabled drug delivery systems (NDDS) in the context of cancer medicine. It regards NDDS as relational objects whose modes of existence are defined by their relationships with a complex biocultural environment that includes both the biological processes of our bodies and the values representations and metaphors our societies associate with cancer and cancer therapy. Within this framework the abundant use of war metaphors in NDDS --from 'smart bombs' to 'magic nano-bullets'--is discussed from various angles: in terms of therapeutic efficacy, it limits the potential of the technique by preventing the inclusion of the (patho)biological environment in the nanomedicine's mode of action. In terms of development opportunities, the military strategy of active specific targeting faces cost and complexity bottlenecks. In terms of ethical values, it favors the questionable image of cancer patients as 'fighters'. On the basis of these criticisms different metaphorical frameworks are suggested, in particular that of oïkos, whereby nanomedicine is reframed as a kind of domestic economy addressing the system-environment relationships of embodied processes with further imagination and care.

Tunable Low Energy, Compact and High Performance Neuromorphic Circuit for Spike-Based Synaptic Plasticity

PubMed Central

Rahimi Azghadi, Mostafa; Iannella, Nicolangelo; Al-Sarawi, Said; Abbott, Derek

2014-01-01

Cortical circuits in the brain have long been recognised for their information processing capabilities and have been studied both experimentally and theoretically via spiking neural networks. Neuromorphic engineers are primarily concerned with translating the computational capabilities of biological cortical circuits, using the Spiking Neural Network (SNN) paradigm, into in silico applications that can mimic the behaviour and capabilities of real biological circuits/systems. These capabilities include low power consumption, compactness, and relevant dynamics. In this paper, we propose a new accelerated-time circuit that has several advantages over its previous neuromorphic counterparts in terms of compactness, power consumption, and capability to mimic the outcomes of biological experiments. The presented circuit simulation results demonstrate that, in comparing the new circuit to previous published synaptic plasticity circuits, reduced silicon area and lower energy consumption for processing each spike is achieved. In addition, it can be tuned in order to closely mimic the outcomes of various spike timing- and rate-based synaptic plasticity experiments. The proposed circuit is also investigated and compared to other designs in terms of tolerance to mismatch and process variation. Monte Carlo simulation results show that the proposed design is much more stable than its previous counterparts in terms of vulnerability to transistor mismatch, which is a significant challenge in analog neuromorphic design. All these features make the proposed design an ideal circuit for use in large scale SNNs, which aim at implementing neuromorphic systems with an inherent capability that can adapt to a continuously changing environment, thus leading to systems with significant learning and computational abilities. PMID:24551089

Tunable low energy, compact and high performance neuromorphic circuit for spike-based synaptic plasticity.

PubMed

Rahimi Azghadi, Mostafa; Iannella, Nicolangelo; Al-Sarawi, Said; Abbott, Derek

2014-01-01

Cortical circuits in the brain have long been recognised for their information processing capabilities and have been studied both experimentally and theoretically via spiking neural networks. Neuromorphic engineers are primarily concerned with translating the computational capabilities of biological cortical circuits, using the Spiking Neural Network (SNN) paradigm, into in silico applications that can mimic the behaviour and capabilities of real biological circuits/systems. These capabilities include low power consumption, compactness, and relevant dynamics. In this paper, we propose a new accelerated-time circuit that has several advantages over its previous neuromorphic counterparts in terms of compactness, power consumption, and capability to mimic the outcomes of biological experiments. The presented circuit simulation results demonstrate that, in comparing the new circuit to previous published synaptic plasticity circuits, reduced silicon area and lower energy consumption for processing each spike is achieved. In addition, it can be tuned in order to closely mimic the outcomes of various spike timing- and rate-based synaptic plasticity experiments. The proposed circuit is also investigated and compared to other designs in terms of tolerance to mismatch and process variation. Monte Carlo simulation results show that the proposed design is much more stable than its previous counterparts in terms of vulnerability to transistor mismatch, which is a significant challenge in analog neuromorphic design. All these features make the proposed design an ideal circuit for use in large scale SNNs, which aim at implementing neuromorphic systems with an inherent capability that can adapt to a continuously changing environment, thus leading to systems with significant learning and computational abilities.

From noise to synthetic nucleoli: can synthetic biology achieve new insights?

PubMed

Ciechonska, Marta; Grob, Alice; Isalan, Mark

2016-04-18

Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."

“Gestaltomics”: Systems Biology Schemes for the Study of Neuropsychiatric Diseases

PubMed Central

Gutierrez Najera, Nora A.; Resendis-Antonio, Osbaldo; Nicolini, Humberto

2017-01-01

The integration of different sources of biological information about what defines a behavioral phenotype is difficult to unify in an entity that reflects the arithmetic sum of its individual parts. In this sense, the challenge of Systems Biology for understanding the “psychiatric phenotype” is to provide an improved vision of the shape of the phenotype as it is visualized by “Gestalt” psychology, whose fundamental axiom is that the observed phenotype (behavior or mental disorder) will be the result of the integrative composition of every part. Therefore, we propose the term “Gestaltomics” as a term from Systems Biology to integrate data coming from different sources of information (such as the genome, transcriptome, proteome, epigenome, metabolome, phenome, and microbiome). In addition to this biological complexity, the mind is integrated through multiple brain functions that receive and process complex information through channels and perception networks (i.e., sight, ear, smell, memory, and attention) that in turn are programmed by genes and influenced by environmental processes (epigenetic). Today, the approach of medical research in human diseases is to isolate one disease for study; however, the presence of an additional disease (co-morbidity) or more than one disease (multimorbidity) adds complexity to the study of these conditions. This review will present the challenge of integrating psychiatric disorders at different levels of information (Gestaltomics). The implications of increasing the level of complexity, for example, studying the co-morbidity with another disease such as cancer, will also be discussed. PMID:28536537

Development of an Ontology for Periodontitis.

PubMed

Suzuki, Asami; Takai-Igarashi, Takako; Nakaya, Jun; Tanaka, Hiroshi

2015-01-01

In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will give periodontal researchers opportunities to elucidate pathways and mechanisms of periodontitis. An ontology for periodontitis can be a model for integration of large variety of factors relating to a complex disease such as chronic inflammation in different organs accompanied by bone remodeling and immune system disorders, which has recently been referred to as osteoimmunology. Terms characteristic of descriptions related to the onset and progression of periodontitis were manually extracted from 194 review articles and PubMed abstracts by experts in periodontology. We specified all the relations between the extracted terms and constructed them into an ontology for periodontitis. We also investigated matching between classes of our ontology and that of Gene Ontology Biological Process. We developed an ontology for periodontitis called Periodontitis-Ontology (PeriO). The pathological progression of periodontitis is caused by complex, multi-factor interrelationships. PeriO consists of all the required concepts to represent the pathological progression and clinical treatment of periodontitis. The pathological processes were formalized with reference to Basic Formal Ontology and Relation Ontology, which accounts for participants in the processes realized by biological objects such as molecules and cells. We investigated the peculiarity of biological processes observed in pathological progression and medical treatments for the disease in comparison with Gene Ontology Biological Process (GO-BP) annotations. The results indicated that peculiarities of Perio existed in 1) granularity and context dependency of both the conceptualizations, and 2) causality intrinsic to the pathological processes. PeriO defines more specific concepts than GO-BP, and thus can be added as descendants of GO-BP leaf nodes. PeriO defines causal relationships between the process concepts, which are not shown in GO-BP. The difference can be explained by the goal of conceptualization: PeriO focuses on mechanisms of the pathogenic progress, while GO-BP focuses on cataloguing all of the biological processes observed in experiments. The goal of conceptualization in PeriO may reflect the domain knowledge where a consequence in the causal relationships is a primary interest. We believe the peculiarities can be shared among other diseases when comparing processes in disease against GO-BP. This is the first open biomedical ontology of periodontitis capable of providing a foundation for an ontology-based model of aspects of molecular biology and pathological processes related to periodontitis, as well as its relations with systemic diseases. PeriO is available at http://bio-omix.tmd.ac.jp/periodontitis/.

A craniometric analysis of early modern Romania and Hungary: The roles of migration and conversion in shaping European Ottoman population history.

PubMed

Allen, Kathryn Grow; von Cramon-Taubadel, Noreen

2017-11-01

Debate persists regarding the biological makeup of European Ottoman communities settled during the expansion of the Ottoman Empire during the 16th and 17th centuries, and the roles of conversion and migration in shaping demography and population history. The aim of this study was to perform an assessment of the biological affinities of three European Ottoman series based on craniometric data. Craniometric data collected from three Ottoman series from Hungary and Romania were compared to European and Anatolian comparative series, selected to represent biological affinity representative of historically recorded migration and conversion influences. Sex-separated samples were analyzed using D 2 -matrices, along with principal coordinates and PERMANOVA analyses to investigate biological affinities. Discriminant function analysis was employed to assign Ottoman individuals to two potential classes: European or Anatolian. Affinity analyses show larger than expected biological differences between males and females within each of the Ottoman communities. Discriminant function analyses show that the majority of Ottoman individuals could be classified as either European or Anatolian with a high probability. Moreover, location within Europe proved influential, as the Ottomans from a location of more geopolitical importance (Budapest) diverged from more hinterland communities in terms of biological affinity patterns. The results suggest that male and female Ottomans may possess distinct population histories, with males and females divergent from each other in terms of their biological affinities. The Ottoman communities appear diverse in terms of constituting a mix of peoples from different biological backgrounds. The greater distances between sexes from the same community, and the differences between communities, may be evidence that the processes of migration and conversion impacted individual people and groups diversely. © 2017 Wiley Periodicals, Inc.

Emulating short-term synaptic dynamics with memristive devices

NASA Astrophysics Data System (ADS)

Berdan, Radu; Vasilaki, Eleni; Khiat, Ali; Indiveri, Giacomo; Serb, Alexandru; Prodromakis, Themistoklis

2016-01-01

Neuromorphic architectures offer great promise for achieving computation capacities beyond conventional Von Neumann machines. The essential elements for achieving this vision are highly scalable synaptic mimics that do not undermine biological fidelity. Here we demonstrate that single solid-state TiO2 memristors can exhibit non-associative plasticity phenomena observed in biological synapses, supported by their metastable memory state transition properties. We show that, contrary to conventional uses of solid-state memory, the existence of rate-limiting volatility is a key feature for capturing short-term synaptic dynamics. We also show how the temporal dynamics of our prototypes can be exploited to implement spatio-temporal computation, demonstrating the memristors full potential for building biophysically realistic neural processing systems.

Comparative Study on Interaction of Form and Motion Processing Streams by Applying Two Different Classifiers in Mechanism for Recognition of Biological Movement

PubMed Central

2014-01-01

Research on psychophysics, neurophysiology, and functional imaging shows particular representation of biological movements which contains two pathways. The visual perception of biological movements formed through the visual system called dorsal and ventral processing streams. Ventral processing stream is associated with the form information extraction; on the other hand, dorsal processing stream provides motion information. Active basic model (ABM) as hierarchical representation of the human object had revealed novelty in form pathway due to applying Gabor based supervised object recognition method. It creates more biological plausibility along with similarity with original model. Fuzzy inference system is used for motion pattern information in motion pathway creating more robustness in recognition process. Besides, interaction of these paths is intriguing and many studies in various fields considered it. Here, the interaction of the pathways to get more appropriated results has been investigated. Extreme learning machine (ELM) has been implied for classification unit of this model, due to having the main properties of artificial neural networks, but crosses from the difficulty of training time substantially diminished in it. Here, there will be a comparison between two different configurations, interactions using synergetic neural network and ELM, in terms of accuracy and compatibility. PMID:25276860

Biological embedding: evaluation and analysis of an emerging concept for nursing scholarship.

PubMed

Nist, Marliese Dion

2017-02-01

The purpose of this paper was to report the analysis of the concept of biological embedding. Research that incorporates a life course perspective is becoming increasingly prominent in the health sciences. Biological embedding is a central concept in life course theory and may be important for nursing theories to enhance our understanding of health states in individuals and populations. Before the concept of biological embedding can be used in nursing theory and research, an analysis of the concept is required to advance it towards full maturity. Concept analysis. PubMed, CINAHL and PsycINFO were searched for publications using the term 'biological embedding' or 'biological programming' and published through 2015. An evaluation of the concept was first conducted to determine the concept's level of maturity and was followed by a concept comparison, using the methods for concept evaluation and comparison described by Morse. A consistent definition of biological embedding - the process by which early life experience alters biological processes to affect adult health outcomes - was found throughout the literature. The concept has been used in several theories that describe the mechanisms through which biological embedding might occur and highlight its role in the development of health trajectories. Biological embedding is a partially mature concept, requiring concept comparison with an overlapping concept - biological programming - to more clearly establish the boundaries of biological embedding. Biological embedding has significant potential for theory development and application in multiple academic disciplines, including nursing. © 2016 John Wiley & Sons Ltd.

Interacting Physical and Biological Processes Affecting Nutrient Transport Through Human Dominated Landscapes

NASA Astrophysics Data System (ADS)

Finlay, J. C.

2015-12-01

Human activities increasingly dominate biogeochemical cycles of limiting nutrients on Earth. Urban and agricultural landscapes represent the largest sources of excess nutrients that drive water quality degradation. The physical structure of both urban and agricultural watersheds has been extensively modified, and these changes have large impacts on water and nutrient transport. Despite strong physical controls over nutrient transport in human dominated landscapes, biological processes play important roles in determining the fates of both nitrogen and phosphorus. This talk uses examples from research in urban and agricultural watersheds in the Midwestern USA to illustrate interactions of physical and biological controls over nutrient cycles that have shifted nitrogen (N) and phosphorus (P) sources and cycling in unexpected ways in response to management changes. In urban watersheds, efforts to improve water quality have been hindered by legacy sources of phosphorus added to storm water through transport to drainage systems by vegetation. Similarly, reductions in field erosion in agricultural watersheds have not led to major reductions in phosphorus transport, because of continued release of biological sources of P. Where management of phosphorus has been most effective in reducing eutrophication of lakes, decreases in N removal processes have led to long term increases in N concentration and transport. Together, these examples show important roles for biological processes affecting nutrient movement in highly modified landscapes. Consideration of the downstream physical and biological responses of management changes are thus critical toward identification of actions that will most effectively reduce excess nutrients watersheds and coastal zones.

Long-term biological investigations in space.

PubMed

Lotz, R G; Fuchs, H; Bertsche, U

1975-01-01

Missions in space within the next two decades will be of longer duration than those carried out up to the present time, and the effects of such long-term flights on biological organisms are unknown. Results of biological experiments that have been performed to date cannot be extrapolated to results in future flights because of the unknown influence of adaptation over a long period of time. Prior experiments with Axolotl, fishes, and vertebrates by our research team (in part with sounding rockets) showed that these specimens did not appear to be suitable for long-term missions on which minimization of expense, technique, and energy is required. Subsequent investigations have shown the suitability of the leech (Hirudo medicinalis), which consumes blood of mammals up to ten times its own weight (1 g) and can live more than 2 years without further food supply. Emphasis in the experiments with Hirudo medicinalis is placed on metabolic rhythm and motility. Resorption and diffusion in tissue, development, and growth under long-term effects of cosmic proton radiation and zero-gravity are other focal points. The constancy of cellular life in the mature animals is a point in favor of these specimens. We have also taken into account the synergistic effects of the space environment on the problems just mentioned. The life-support system constructed for the leech has been tested successfully in four sounding rocket flights and, on that basis, has been prepared for a long-term mission. Long-term investigations out of the terrestrial biosphere will provide us with information concerning the degree of adaptation of certain physiological and biochemical functions and as to what extent biological readjustment or repair processes can occur under the specific stress conditions of space flight.

Degradation alternatives for a commercial fungicide in water: biological, photo-Fenton, and coupled biological photo-Fenton processes.

PubMed

López-Loveira, Elsa; Ariganello, Federico; Medina, María Sara; Centrón, Daniela; Candal, Roberto; Curutchet, Gustavo

2017-11-01

Imazalil (IMZ) is a widely used fungicide for the post-harvest treatment of citrus, classified as "likely to be carcinogenic in humans" for EPA, that can be only partially removed by conventional biological treatment. Consequently, specific or combined processes should be applied to prevent its release to the environment. Biological treatment with adapted microorganism consortium, photo-Fenton, and coupled biological photo-Fenton processes were tested as alternatives for the purification of water containing high concentration of the fungicide and the coadjutants present in the commercial formulation. IMZ-resistant consortium with the capacity to degrade IMZ in the presence of a C-rich co-substrate was isolated from sludge coming from a fruit packaging company wastewater treatment plant. This consortium was adapted to resist and degrade the organics present in photo-Fenton-oxidized IMZ water solution. Bacteria colonies from the consortia were isolated and identified. The effect of H 2 O 2 initial concentration and dosage on IMZ degradation rate, average oxidation state (AOS), organic acid concentration, oxidation, and mineralization percentage after photo-Fenton process was determined. The application of biological treatment to the oxidized solutions notably decreased the total organic carbon (TOC) in solution. The effect of the oxidation degree, limited by H 2 O 2 concentration and dosage, on the percentage of mineralization obtained after the biological treatment was determined and explained in terms of changes in AOS. The concentration of H 2 O 2 necessary to eliminate IMZ by photo-Fenton and to reduce TOC and chemical oxygen demand (COD) by biological treatment, in order to allow the release of the effluents to rivers with different flows, was estimated.

Quantitative imaging biomarker ontology (QIBO) for knowledge representation of biomedical imaging biomarkers.

PubMed

Buckler, Andrew J; Liu, Tiffany Ting; Savig, Erica; Suzek, Baris E; Ouellette, M; Danagoulian, J; Wernsing, G; Rubin, Daniel L; Paik, David

2013-08-01

A widening array of novel imaging biomarkers is being developed using ever more powerful clinical and preclinical imaging modalities. These biomarkers have demonstrated effectiveness in quantifying biological processes as they occur in vivo and in the early prediction of therapeutic outcomes. However, quantitative imaging biomarker data and knowledge are not standardized, representing a critical barrier to accumulating medical knowledge based on quantitative imaging data. We use an ontology to represent, integrate, and harmonize heterogeneous knowledge across the domain of imaging biomarkers. This advances the goal of developing applications to (1) improve precision and recall of storage and retrieval of quantitative imaging-related data using standardized terminology; (2) streamline the discovery and development of novel imaging biomarkers by normalizing knowledge across heterogeneous resources; (3) effectively annotate imaging experiments thus aiding comprehension, re-use, and reproducibility; and (4) provide validation frameworks through rigorous specification as a basis for testable hypotheses and compliance tests. We have developed the Quantitative Imaging Biomarker Ontology (QIBO), which currently consists of 488 terms spanning the following upper classes: experimental subject, biological intervention, imaging agent, imaging instrument, image post-processing algorithm, biological target, indicated biology, and biomarker application. We have demonstrated that QIBO can be used to annotate imaging experiments with standardized terms in the ontology and to generate hypotheses for novel imaging biomarker-disease associations. Our results established the utility of QIBO in enabling integrated analysis of quantitative imaging data.

The biobank of the Norwegian mother and child cohort Study: A resource for the next 100 years

PubMed Central

Rønningen, Kjersti S.; Paltiel, Liv; Meltzer, Helle M.; Nordhagen, Rannveig; Lie, Kari K.; Hovengen, Ragnhild; Haugen, Margaretha; Nystad, Wenche; Magnus, Per; Hoppin, Jane A.

2007-01-01

Introduction Long-term storage of biological materials is a critical component of any epidemiological study. In designing specimen repositories, efforts need to balance future needs for samples with logistical constraints necessary to process and store samples in a timely fashion. Objectives In the Norwegian Mother and Child Cohort Study (MoBa), the Biobank was charged with long-term storage of more than 380,000 biological samples from pregnant women, their partners and their children for up to 100 years. Methods Biological specimens include whole blood, plasma, DNA and urine; samples are collected at 50 hospitals in Norway. All samples are sent via ordinary mail to the Biobank in Oslo where the samples are registered, aliquoted and DNA extracted. DNA is stored at −20 °C while whole blood, urine and plasma are stored at − 80 °C. Results As of July 2006, over 227,000 sample sets have been collected, processed and stored at the Biobank. Currently 250–300 sets are received daily. An important part of the Biobank is the quality control program. Conclusion With the unique combination of biological specimens and questionnaire data, the MoBa Study will constitute a resource for many future investigations of the separate and combined effects of genetic, environmental factors on pregnancy outcome and on human morbidity, mortality and health in general. PMID:17031521

Using coordinate-based meta-analyses to explore structural imaging genetics.

PubMed

Janouschek, Hildegard; Eickhoff, Claudia R; Mühleisen, Thomas W; Eickhoff, Simon B; Nickl-Jockschat, Thomas

2018-05-05

Imaging genetics has become a highly popular approach in the field of schizophrenia research. A frequently reported finding is that effects from common genetic variation are associated with a schizophrenia-related structural endophenotype. Genetic contributions to a structural endophenotype may be easier to delineate, when referring to biological rather than diagnostic criteria. We used coordinate-based meta-analyses, namely the anatomical likelihood estimation (ALE) algorithm on 30 schizophrenia-related imaging genetics studies, representing 44 single-nucleotide polymorphisms at 26 gene loci investigated in 4682 subjects. To test whether analyses based on biological information would improve the convergence of results, gene ontology (GO) terms were used to group the findings from the published studies. We did not find any significant results for the main contrast. However, our analysis enrolling studies on genotype × diagnosis interaction yielded two clusters in the left temporal lobe and the medial orbitofrontal cortex. All other subanalyses did not yield any significant results. To gain insight into possible biological relationships between the genes implicated by these clusters, we mapped five of them to GO terms of the category "biological process" (AKT1, CNNM2, DISC1, DTNBP1, VAV3), then five to "cellular component" terms (AKT1, CNNM2, DISC1, DTNBP1, VAV3), and three to "molecular function" terms (AKT1, VAV3, ZNF804A). A subsequent cluster analysis identified representative, non-redundant subsets of semantically similar terms that aided a further interpretation. We regard this approach as a new option to systematically explore the richness of the literature in imaging genetics.

Thermochemical pretreatments of organic fraction of municipal solid waste from a mechanical-biological treatment plant.

PubMed

Álvarez-Gallego, Carlos José; Fdez-Güelfo, Luis Alberto; de los Ángeles Romero Aguilar, María; Romero García, Luis Isidoro

2015-02-09

The organic fraction of municipal solid waste (OFMSW) usually contains high lignocellulosic and fatty fractions. These fractions are well-known to be a hard biodegradable substrate for biological treatments and its presence involves limitations on the performance of anaerobic processes. To avoid this, thermochemical pretreatments have been applied on the OFMSW coming from a full-scale mechanical-biological treatment (MBT) plant, in order to pre-hydrolyze the waste and improve the organic matter solubilisation. To study the solubilisation yield, the increments of soluble organic matter have been measured in terms of dissolved organic carbon (DOC), soluble chemical oxygen demand (sCOD), total volatile fatty acids (TVFA) and acidogenic substrate as carbon (ASC). The process variables analyzed were temperature, pressure and NaOH dosage. The levels of work for each variable were three: 160-180-200 °C, 3.5-5.0-6.5 bar and 2-3-4 g NaOH/L. In addition, the pretreatment time was also modified among 15 and 120 min. The best conditions for organic matter solubilisation were 160 °C, 3 g NaOH/L, 6.5 bar and 30 min, with yields in terms of DOC, sCOD, TVFA and ASC of 176%, 123%, 119% and 178% respectively. Thus, predictably the application of this pretreatment in these optimum conditions could improve the H2 production during the subsequent Dark Fermentation process.

Short-term changes in soil C, N, and biota following harvesting and regeneration of loblolly pine (Pinus taeda L.)

Treesearch

Mason C. Carter; Thomas J. Dean; Minyi Zhou; Michael G. Messina; Ziyin Wang

2002-01-01

In affiliation with the USDA-FS long-term soil productivity program, a series of studies have been established in the US gulf coast region to monitor the effects of intensive silviculture on site productivity. This report presents early results of a study of the interactive effects of harvest intensity and cultural treatments on soil C, N, and biological processes...

The fairytale of the GSSG/GSH redox potential.

PubMed

Flohé, Leopold

2013-05-01

The term GSSG/GSH redox potential is frequently used to explain redox regulation and other biological processes. The relevance of the GSSG/GSH redox potential as driving force of biological processes is critically discussed. It is recalled that the concentration ratio of GSSG and GSH reflects little else than a steady state, which overwhelmingly results from fast enzymatic processes utilizing, degrading or regenerating GSH. A biological GSSG/GSH redox potential, as calculated by the Nernst equation, is a deduced electrochemical parameter based on direct measurements of GSH and GSSG that are often complicated by poorly substantiated assumptions. It is considered irrelevant to the steering of any biological process. GSH-utilizing enzymes depend on the concentration of GSH, not on [GSH](2), as is predicted by the Nernst equation, and are typically not affected by GSSG. Regulatory processes involving oxidants and GSH are considered to make use of mechanistic principles known for thiol peroxidases which catalyze the oxidation of hydroperoxides by GSH by means of an enzyme substitution mechanism involving only bimolecular reaction steps. The negligibly small rate constants of related spontaneous reactions as compared with enzyme-catalyzed ones underscore the superiority of kinetic parameters over electrochemical or thermodynamic ones for an in-depth understanding of GSH-dependent biological phenomena. At best, the GSSG/GSH potential might be useful as an analytical tool to disclose disturbances in redox metabolism. This article is part of a Special Issue entitled Cellular Functions of Glutathione. Copyright © 2012 Elsevier B.V. All rights reserved.

Biological intrusion of low-level-waste trench covers

NASA Astrophysics Data System (ADS)

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.

Kamikazes and cultural evolution.

PubMed

Allen-Hermanson, Sean

2017-02-01

Is cultural evolution needed to explain altruistic selfsacrifice? Some contend that cultural traits (e.g. beliefs, behaviors, and for some "memes") replicate according to selection processes that have "floated free" from biology. One test case is the example of suicide kamikaze attacks in wartime Japan. Standard biological mechanisms-such as reciprocal altruism and kin selection-might not seem to apply here: The suicide pilots did not act on the expectation that others would reciprocate, and they were supposedly sacrificing themselves for country and emperor, not close relatives. Yet an examination of both the historical record and the demands of evolutionary theory suggest the kamikaze phenomenon does not cry out for explanation in terms of a special non-biological selection process. This weakens the case for cultural evolution, and has interesting implications for our understanding of altruistic self-sacrifice. Copyright © 2016 Elsevier Ltd. All rights reserved.

Antiquity of the biological sulphur cycle: evidence from sulphur and carbon isotopes in 2700 million-year-old rocks of the Belingwe Belt, Zimbabwe.

PubMed Central

Grassineau, N V; Nisbet, E G; Bickle, M J; Fowler, C M; Lowry, D; Mattey, D P; Abell, P; Martin, A

2001-01-01

Sulphur and carbon isotopic analyses on small samples of kerogens and sulphide minerals from biogenic and non-biogenic sediments of the 2.7 x 10(9) years(Ga)-old Belingwe Greenstone Belt (Zimbabwe) imply that a complex biological sulphur cycle was in operation. Sulphur isotopic compositions display a wider range of biological fractionation than hitherto reported from the Archaean. Carbon isotopic values in kerogen record fractionations characteristic of rubisco activity methanogenesis and methylotrophy and possibly anoxygenic photosynthesis. Carbon and sulphur isotopic fractionations have been interpreted in terms of metabolic processes in 2.7 Ga prokaryote mat communities, and indicate the operation of a diverse array of metabolic processes. The results are consistent with models of early molecular evolution derived from ribosomal RNA. PMID:11209879

Development of a software tool to support chemical and biological terrorism intelligence analysis

NASA Astrophysics Data System (ADS)

Hunt, Allen R.; Foreman, William

1997-01-01

AKELA has developed a software tool which uses a systems analytic approach to model the critical processes which support the acquisition of biological and chemical weapons by terrorist organizations. This tool has four major components. The first is a procedural expert system which describes the weapon acquisition process. It shows the relationship between the stages a group goes through to acquire and use a weapon, and the activities in each stage required to be successful. It applies to both state sponsored and small group acquisition. An important part of this expert system is an analysis of the acquisition process which is embodied in a list of observables of weapon acquisition activity. These observables are cues for intelligence collection The second component is a detailed glossary of technical terms which helps analysts with a non- technical background understand the potential relevance of collected information. The third component is a linking capability which shows where technical terms apply to the parts of the acquisition process. The final component is a simple, intuitive user interface which shows a picture of the entire process at a glance and lets the user move quickly to get more detailed information. This paper explains e each of these five model components.

Nitrate removal from drinking water with a focus on biological methods: a review.

PubMed

Rezvani, Fariba; Sarrafzadeh, Mohammad-Hossein; Ebrahimi, Sirous; Oh, Hee-Mock

2017-05-31

This article summarizes several developed and industrial technologies for nitrate removal from drinking water, including physicochemical and biological techniques, with a focus on autotrophic nitrate removal. Approaches are primarily classified into separation-based and elimination-based methods according to the fate of the nitrate in water treatment. Biological denitrification as a cost-effective and promising method of biological nitrate elimination is reviewed in terms of its removal process, applicability, efficiency, and associated disadvantages. The various pathways during biological nitrate removal, including assimilatory and dissimilatory nitrate reduction, are also explained. A comparative study was carried out to provide a better understanding of the advantages and disadvantages of autotrophic and heterotrophic denitrification. Sulfur-based and hydrogen-based denitrifications, which are the most common autotrophic processes of nitrate removal, are reviewed with the aim of presenting the salient features of hydrogenotrophic denitrification along with some drawbacks of the technology and research areas in which it could be used but currently is not. The application of algae-based water treatment is also introduced as a nature-inspired approach that may broaden future horizons of nitrate removal technology.

Fast Quantum Algorithm for Predicting Descriptive Statistics of Stochastic Processes

NASA Technical Reports Server (NTRS)

Williams Colin P.

1999-01-01

Stochastic processes are used as a modeling tool in several sub-fields of physics, biology, and finance. Analytic understanding of the long term behavior of such processes is only tractable for very simple types of stochastic processes such as Markovian processes. However, in real world applications more complex stochastic processes often arise. In physics, the complicating factor might be nonlinearities; in biology it might be memory effects; and in finance is might be the non-random intentional behavior of participants in a market. In the absence of analytic insight, one is forced to understand these more complex stochastic processes via numerical simulation techniques. In this paper we present a quantum algorithm for performing such simulations. In particular, we show how a quantum algorithm can predict arbitrary descriptive statistics (moments) of N-step stochastic processes in just O(square root of N) time. That is, the quantum complexity is the square root of the classical complexity for performing such simulations. This is a significant speedup in comparison to the current state of the art.

[Characteristic of the removal of 2,4-dichlorophenol by biological activated carbon].

PubMed

Liu, Hong; Li, An-jie; Quan, Xiang-chun; Kong, Xiang-hui; Yun, Ying

2004-11-01

The adsorption characteristics and kinetics of 2,4-Dichlorophenol (2,4-DCP) by biological activated carbon (BAC) was studied through contrast experiments with conventional activated sludge alone or quartz as the carrier. The advantage and disadvantage of removing 2,4-DCP using BAC and the mechanism of this process were investigated. The results show that the method of removing 2,4-DCP by BAC is applicable in practices, and the process of BAC demonstrates high removal rate than the process of suspended activated sludge and biofilm with quartz as the carrier. In addition, the BAC process showed high resistance to shock loadings, therefore, it is suitable to be utilized at high organic loading and under long-term operation. In BAC-system, activated carbon could not only adsorb 2,4-DCP but also oxidized 2,4-DCP.

Scientific Process Flowchart Assessment (SPFA): A Method for Evaluating Changes in Understanding and Visualization of the Scientific Process in a Multidisciplinary Student Population.

PubMed

Wilson, Kristy J; Rigakos, Bessie

The scientific process is nonlinear, unpredictable, and ongoing. Assessing the nature of science is difficult with methods that rely on Likert-scale or multiple-choice questions. This study evaluated conceptions about the scientific process using student-created visual representations that we term "flowcharts." The methodology, Scientific Process Flowchart Assessment (SPFA), consisted of a prompt and rubric that was designed to assess students' understanding of the scientific process. Forty flowcharts representing a multidisciplinary group without intervention and 26 flowcharts representing pre- and postinstruction were evaluated over five dimensions: connections, experimental design, reasons for doing science, nature of science, and interconnectivity. Pre to post flowcharts showed a statistically significant improvement in the number of items and ratings for the dimensions. Comparison of the terms used and connections between terms on student flowcharts revealed an enhanced and more nuanced understanding of the scientific process, especially in the areas of application to society and communication within the scientific community. We propose that SPFA can be used in a variety of circumstances, including in the determination of what curricula or interventions would be useful in a course or program, in the assessment of curriculum, or in the evaluation of students performing research projects. © 2016 K. J. Wilson and B. Rigakos. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

BioTextQuest(+): a knowledge integration platform for literature mining and concept discovery.

PubMed

Papanikolaou, Nikolas; Pavlopoulos, Georgios A; Pafilis, Evangelos; Theodosiou, Theodosios; Schneider, Reinhard; Satagopam, Venkata P; Ouzounis, Christos A; Eliopoulos, Aristides G; Promponas, Vasilis J; Iliopoulos, Ioannis

2014-11-15

The iterative process of finding relevant information in biomedical literature and performing bioinformatics analyses might result in an endless loop for an inexperienced user, considering the exponential growth of scientific corpora and the plethora of tools designed to mine PubMed(®) and related biological databases. Herein, we describe BioTextQuest(+), a web-based interactive knowledge exploration platform with significant advances to its predecessor (BioTextQuest), aiming to bridge processes such as bioentity recognition, functional annotation, document clustering and data integration towards literature mining and concept discovery. BioTextQuest(+) enables PubMed and OMIM querying, retrieval of abstracts related to a targeted request and optimal detection of genes, proteins, molecular functions, pathways and biological processes within the retrieved documents. The front-end interface facilitates the browsing of document clustering per subject, the analysis of term co-occurrence, the generation of tag clouds containing highly represented terms per cluster and at-a-glance popup windows with information about relevant genes and proteins. Moreover, to support experimental research, BioTextQuest(+) addresses integration of its primary functionality with biological repositories and software tools able to deliver further bioinformatics services. The Google-like interface extends beyond simple use by offering a range of advanced parameterization for expert users. We demonstrate the functionality of BioTextQuest(+) through several exemplary research scenarios including author disambiguation, functional term enrichment, knowledge acquisition and concept discovery linking major human diseases, such as obesity and ageing. The service is accessible at http://bioinformatics.med.uoc.gr/biotextquest. g.pavlopoulos@gmail.com or georgios.pavlopoulos@esat.kuleuven.be Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Use of a business excellence model to improve conservation programs.

PubMed

Black, Simon; Groombridge, Jim

2010-12-01

The current shortfall in effectiveness within conservation biology is illustrated by increasing interest in "evidence-based conservation," whose proponents have identified the need to benchmark conservation initiatives against actions that lead to proven positive effects. The effectiveness of conservation policies, approaches, and evaluation is under increasing scrutiny, and in these areas models of excellence used in business could prove valuable. Typically, conservation programs require years of effort and involve rigorous long-term implementation processes. Successful balance of long-term efforts alongside the achievement of short-term goals is often compromised by management or budgetary constraints, a situation also common in commercial businesses. "Business excellence" is an approach many companies have used over the past 20 years to ensure continued success. Various business excellence evaluations have been promoted that include concepts that could be adapted and applied in conservation programs. We describe a conservation excellence model that shows how scientific processes and results can be aligned with financial and organizational measures of success. We applied the model to two well-documented species conservation programs. In the first, the Po'ouli program, several aspects of improvement were identified, such as more authority for decision making in the field and better integration of habitat management and population recovery processes. The second example, the black-footed ferret program, could have benefited from leadership effort to reduce bureaucracy and to encourage use of best-practice species recovery approaches. The conservation excellence model enables greater clarity in goal setting, more-effective identification of job roles within programs, better links between technical approaches and measures of biological success, and more-effective use of resources. The model could improve evaluation of a conservation program's effectiveness and may be used to compare different programs, for example during reviews of project performance by sponsoring organizations. © 2010 Society for Conservation Biology.

Cultural and biological factors modulate spatial biases over development.

PubMed

Girelli, Luisa; Marinelli, Chiara Valeria; Grossi, Giuseppe; Arduino, Lisa S

2017-11-01

Increasing evidence supports the contribution of both biological and cultural factors to visuospatial processing. The present study adds to the literature by exploring the interplay of perceptual and linguistic mechanisms in determining visuospatial asymmetries in adults (Experiment 1) and children (Experiment 2). In particular, pre-schoolers (3 and 5 year-olds), school-aged children (8 year-old), and adult participants were required to bisect different types of stimuli, that is, lines, words, and figure strings. In accordance with the literature, results yielded a leftward bias for lines and words and a rightward bias for figure strings, in adult participants. More critically, different biases were found for lines, words, and figure strings in children as a function of age, reflecting the impact of both cultural and biological factors on the processing of different visuospatial materials. Specifically, an adult-like pattern of results emerged only in the older group of children (8 year-old), but not in pre-schoolers. Results are discussed in terms of literacy, reading habits exposure, and biological maturation.

A Biobehavioral Model of Cancer Stress and Disease Course

PubMed Central

Andersen, Barbara L.; Kiecolt-Glaser, Janice K.; Glaser, Ronald

2009-01-01

Approximately 1 million Americans are diagnosed with cancer each year and must cope with the disease and treatments. Many studies have documented the deteriorations in quality of life that occur. These data suggest that the adjustment process is burdensome and lengthy. There is ample evidence showing that adults experiencing other long-term stressors experience not only high rates of adjustment difficulties (e.g., syndromal depression) but important biologic effects, such as persistent downregulation of elements of the immune system, and adverse health outcomes, such as higher rates of respiratory tract infections. Thus, deteriorations in quality of life with cancer are underscored if they have implications for biological processes, such as the immune system, relating to disease progression and spread. Considering these and other data, a biobehavioral model of adjustment to the stresses of cancer is offered, and mechanisms by which psychological and behavioral responses may influence biological processes and, perhaps, health outcomes are proposed. Finally, strategies for testing the model via experiments testing psychological interventions are offered. PMID:8024167

Synaptic plasticity functions in an organic electrochemical transistor

NASA Astrophysics Data System (ADS)

Gkoupidenis, Paschalis; Schaefer, Nathan; Strakosas, Xenofon; Fairfield, Jessamyn A.; Malliaras, George G.

2015-12-01

Synaptic plasticity functions play a crucial role in the transmission of neural signals in the brain. Short-term plasticity is required for the transmission, encoding, and filtering of the neural signal, whereas long-term plasticity establishes more permanent changes in neural microcircuitry and thus underlies memory and learning. The realization of bioinspired circuits that can actually mimic signal processing in the brain demands the reproduction of both short- and long-term aspects of synaptic plasticity in a single device. Here, we demonstrate the implementation of neuromorphic functions similar to biological memory, such as short- to long-term memory transition, in non-volatile organic electrochemical transistors (OECTs). Depending on the training of the OECT, the device displays either short- or long-term plasticity, therefore, exhibiting non von Neumann characteristics with merged processing and storing functionalities. These results are a first step towards the implementation of organic-based neuromorphic circuits.

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

PubMed

Kreyssig, Peter; Wozar, Christian; Peter, Stephan; Veloz, Tomás; Ibrahim, Bashar; Dittrich, Peter

2014-09-01

The functioning of many biological processes depends on the appearance of only a small number of a single molecular species. Additionally, the observation of molecular crowding leads to the insight that even a high number of copies of species do not guarantee their interaction. How single particles contribute to stabilizing biological systems is not well understood yet. Hence, we aim at determining the influence of single molecules on the long-term behaviour of biological systems, i.e. whether they can reach a steady state. We provide theoretical considerations and a tool to analyse Systems Biology Markup Language models for the possibility to stabilize because of the described effects. The theory is an extension of chemical organization theory, which we called discrete chemical organization theory. Furthermore we scanned the BioModels Database for the occurrence of discrete chemical organizations. To exemplify our method, we describe an application to the Template model of the mitotic spindle assembly checkpoint mechanism. http://www.biosys.uni-jena.de/Services.html. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Quantum formalism as an optimisation procedure of information flows for physical and biological systems.

PubMed

Baladrón, Carlos; Khrennikov, Andrei

2016-12-01

The similarities between biological and physical systems as respectively defined in quantum information biology (QIB) and in a Darwinian approach to quantum mechanics (DAQM) have been analysed. In both theories the processing of information is a central feature characterising the systems. The analysis highlights a mutual support on the thesis contended by each theory. On the one hand, DAQM provides a physical basis that might explain the key role played by quantum information at the macroscopic level for bio-systems in QIB. On the other hand, QIB offers the possibility, acting as a macroscopic testing ground, to analyse the emergence of quantumness from classicality in the terms held by DAQM. As an added result of the comparison, a tentative definition of quantum information in terms of classical information flows has been proposed. The quantum formalism would appear from this comparative analysis between QIB and DAQM as an optimal information scheme that would maximise the stability of biological and physical systems at any scale. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Deriving principles of microbiology by multiscaling laws of molecular physics.

PubMed

Ortoleva, Peter; Adhangale, P; Cheluvaraja, S; Fontus, Max; Shreif, Zeina

2009-01-01

It has long been an objective of the physical sciences to derive principles of biology from the laws of physics. At the angstrom scale for processes evolving on timescales of 10(-14) s, many systems can be characterized in terms of atomic vibrations and collisions. In contrast, biological systems display dramatic transformations including self-assembly and reorganization from one cell phenotype to another as the microenvironment changes. We have developed a framework for understanding the emergence of living systems from the underlying atomic chaos.

Biological and Dose Thresholds for an Early Genomic Biomarker of Liver Carcinogenesis in Mice.

EPA Science Inventory

Traditional data sources for cancer risk assessment are resource-intensive, retrospective, and not feasible for the vast majority of environmental chemicals. The use of quantitative short-term genomic biomarkers may streamline this process by providing protective limits for known...

Biological and Dose Thresholds for an Early Genomic Biomarker of Liver Carcinogenesis in Mice

EPA Science Inventory

Traditional data sources for cancer risk assessment are resource-intensive, retrospective, and not feasible for the vast majority of environmental chemicals. The use of quantitative short-term genomic biomarkers may streamline this process by providing protective limits for known...

77 FR 31387 - Remanded Biological Opinions on the Coordinated Long-Term Operation of the Central Valley Project...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-25

... process will be accepted on or before June 28, 2012. ADDRESSES: Send written comments to Janice Pi[ntilde... FURTHER INFORMATION CONTACT: Janice Pi[ntilde]ero at (916) 414- 2428; or email at [email protected

Are all intertidal wetlands naturally created equal? Bottlenecks, thresholds and knowledge gaps to mangrove and saltmarsh ecosystems

USGS Publications Warehouse

Friess, Daniel A.; Krauss, Ken W.; Horstman, Erik M.; Balke, Thorsten; Bouma, Tjeerd J.; Galli, Demis; Webb, Edward L.

2011-01-01

Intertidal wetlands such as saltmarshes and mangroves provide numerous important ecological functions, though they are in rapid and global decline. To better conserve and restore these wetland ecosystems, we need an understanding of the fundamental natural bottlenecks and thresholds to their establishment and long-term ecological maintenance. Despite inhabiting similar intertidal positions, the biological traits of these systems differ markedly in structure, phenology, life history, phylogeny and dispersal, suggesting large differences in biophysical interactions. By providing the first systematic comparison between saltmarshes and mangroves, we unravel how the interplay between species-specific life-history traits, biophysical interactions and biogeomorphological feedback processes determine where, when and what wetland can establish, the thresholds to long-term ecosystem stability, and constraints to genetic connectivity between intertidal wetland populations at the landscape level. To understand these process interactions, research into the constraints to wetland development, and biological adaptations to overcome these critical bottlenecks and thresholds requires a truly interdisciplinary approach.

The use of mineral crystals as bio-markers in the search for life on Mars

NASA Technical Reports Server (NTRS)

Schwartz, D. E.; Mancinelli, R. L.; Kaneshiro, E. S.

1992-01-01

It is proposed that minerals resulting from biologically controlled mineralization processes be utilized as biomarkers because of their favorable qualities. Universal signatures of life (biomarkers) are discussed in terms of their terrestrial forms and hypothetical Martian counterparts including organics, suites of specific inorganic and organic compounds, and isotopic ratios. It is emphasized that minerals produced under biologic control have morphological and isotopic compositions that are not found in their abiotic counterparts. Other biomarkers are not necessarily indicative of biological origin and are therefore unreliable resources for scientific study. Mineral crystals are also stable over long geological periods, and the minerals from Martian fluvial features can therefore be employed to search for fossils and biomarkers of early biological activity.

Physical constraints on biological integral control design for homeostasis and sensory adaptation.

PubMed

Ang, Jordan; McMillen, David R

2013-01-22

Synthetic biology includes an effort to use design-based approaches to create novel controllers, biological systems aimed at regulating the output of other biological processes. The design of such controllers can be guided by results from control theory, including the strategy of integral feedback control, which is central to regulation, sensory adaptation, and long-term robustness. Realization of integral control in a synthetic network is an attractive prospect, but the nature of biochemical networks can make the implementation of even basic control structures challenging. Here we present a study of the general challenges and important constraints that will arise in efforts to engineer biological integral feedback controllers or to analyze existing natural systems. Constraints arise from the need to identify target output values that the combined process-plus-controller system can reach, and to ensure that the controller implements a good approximation of integral feedback control. These constraints depend on mild assumptions about the shape of input-output relationships in the biological components, and thus will apply to a variety of biochemical systems. We summarize our results as a set of variable constraints intended to provide guidance for the design or analysis of a working biological integral feedback controller. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Ludwig von Bertalanffy's organismic view on the theory of evolution.

PubMed

Drack, Manfred

2015-03-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. © 2015 Wiley Periodicals, Inc.

Biological nitric oxide signalling: chemistry and terminology

PubMed Central

Heinrich, Tassiele A; da Silva, Roberto S; Miranda, Katrina M; Switzer, Christopher H; Wink, David A; Fukuto, Jon M

2013-01-01

Biological nitrogen oxide signalling and stress is an area of extreme clinical, pharmacological, toxicological, biochemical and chemical research interest. The utility of nitric oxide and derived species as signalling agents is due to their novel and vast chemical interactions with a variety of biological targets. Herein, the chemistry associated with the interaction of the biologically relevant nitrogen oxide species with fundamental biochemical targets is discussed. Specifically, the chemical interactions of nitrogen oxides with nucleophiles (e.g. thiols), metals (e.g. hemeproteins) and paramagnetic species (e.g. dioxygen and superoxide) are addressed. Importantly, the terms associated with the mechanisms by which NO (and derived species) react with their respective biological targets have been defined by numerous past chemical studies. Thus, in order to assist researchers in referring to chemical processes associated with nitrogen oxide biology, the vernacular associated with these chemical interactions is addressed. PMID:23617570

Contamination Mitigation Strategies for Long Duration Human Spaceflight Missions

NASA Technical Reports Server (NTRS)

Lewis, Ruthan; Lupisella, Mark; Bleacher, Jake; Farrell, William

2017-01-01

Contamination control issues are particularly challenging for long-term human spaceflight and are associated with the search for life, dynamic environmental conditions, human-robotic-environment interaction, sample collection and return, biological processes, waste management, long-term environmental disturbance, etc. These issues impact mission success, human health, planetary protection, and research and discovery. Mitigation and control techniques and strategies may include and integrate long-term environmental monitoring and reporting, contamination control and planetary protection protocols, habitation site design, habitat design, and surface exploration and traverse pathways and area access planning.

Water-quality and aquatic-community characteristics of selected reaches of the St. Croix River, Minnesota and Wisconsin, 2000

USGS Publications Warehouse

Payne, G.A.; Lee, K.E.; Montz, G.R.; Talmage, P.J.; Hirsch, J.K.; Larson, J.D.

2002-01-01

Resource monitoring, consisting of short-term diagnostic studies, may be needed in parts of the St. Croix River mainstem and tributaries where results from this study indicate constituent loading is greatest and where the aquatic community composition indicates disturbance. Longer-term trend monitoring may be needed to detect physical, chemical and biological responses to natural processes and human activities in the St. Croix River Basin.

Biological Embedding: Evaluation and Analysis of an Emerging Concept for Nursing Scholarship

PubMed Central

Nist, Marliese Dion

2016-01-01

Aim The purpose of this paper is to report the analysis of the concept of biological embedding. Background Research that incorporates a life course perspective is becoming increasingly prominent in the health sciences. Biological embedding is a central concept in life course theory and may be important for nursing theories to enhance our understanding of health states in individuals and populations. Before the concept of biological embedding can be used in nursing theory and research, an analysis of the concept is required to advance it toward full maturity. Design Concept analysis. Data Sources PubMed, CINAHL and PsycINFO were searched for publications using the term ‘biological embedding’ or ‘biological programming’ and published through 2015. Methods An evaluation of the concept was first conducted to determine the concept’s level of maturity and was followed by a concept comparison, using the methods for concept evaluation and comparison described by Morse. Results A consistent definition of biological embedding – the process by which early life experience alters biological processes to affect adult health outcomes – was found throughout the literature. The concept has been used in several theories that describe the mechanisms through which biological embedding might occur and highlight its role in the development of health trajectories. Biological embedding is a partially mature concept, requiring concept comparison with an overlapping concept – biological programming – to more clearly establish the boundaries of biological embedding. Conclusions Biological embedding has significant potential for theory development and application in multiple academic disciplines, including nursing. PMID:27682606

Antibodies and antimatter: the resurgence of immuno-PET.

PubMed

Wu, Anna M

2009-01-01

The completion of the human genome, coupled with parallel major research efforts in proteomics and systems biology, has led to a flood of information on the roles of individual genes and proteins in normal physiologic processes and their disruptions in disease. In practical terms, this information has opened the door to increasingly targeted therapies as specific molecular markers are identified and validated. The ongoing transition from empiric to molecular medicine has engendered a need for corresponding molecular diagnostics, including noninvasive molecular imaging. Convergence of knowledge regarding key biomarkers that define normal biologic processes and disease with protein and imaging technology makes this an opportune time to revisit the combination of antibodies and PET, or immuno-PET.

Modeling of Solid Waste Processing Options in BIO-Plex

NASA Technical Reports Server (NTRS)

Rodriguez, Luis F.; Finn, Cory; Kang, Sukwon; Hogan, John; Luna, Bernadette (Technical Monitor)

2000-01-01

BIO-Plex is a ground-based test bed currently under development by NASA for testing technologies and practices that may be utilized in future long-term life support missions. All aspects of such an Advanced Life Support (ALS) System must be considered to confidently construct a reliable system, which will not only allow the crew to survive in harsh environments, but allow the crew time to perform meaningful research. Effective handling of solid wastes is a critical aspect of the system, especially when recovery of resources contained in the waste is required. This is particularly important for ALS Systems configurations that include a Biomass Production Chamber. In these cases, significant amounts of inedible biomass waste may be produced, which can ultimately serve as a repository of necessary resources for sustaining life, notably carbon, water, and plant nutrients. Numerous biological and physicochemical solid waste processing options have been considered. Biological options include composting, aerobic digestion, and anaerobic digestion. Physicochemical options include pyrolysis, SCWO (supercritical water oxidation), various incineration configurations, microwave incineration, magnetically assisted gasification, and low temperature plasma reaction. Modeling of these options is a necessary step to assist in the design process. A previously developed top-level model of BIO-Plex implemented in MATLAB Simulink (r) for the use of systems analysis and design has been adopted for this analysis. Presently, this model only considered incineration for solid waste processing. Present work, reported here, includes the expansion of this model to include a wider array of solid waste processing options selected from the above options, bearing in mind potential, near term solid waste treatment systems. Furthermore, a trade study has also been performed among these solid waste processing technologies in an effort to determine the ideal technology for long-term life support missions.

The Mind and Brain of Short-Term Memory

PubMed Central

Jonides, John; Lewis, Richard L.; Nee, Derek Evan; Lustig, Cindy A.; Berman, Marc G.; Moore, Katherine Sledge

2014-01-01

The past 10 years have brought near-revolutionary changes in psychological theories about short-term memory, with similarly great advances in the neurosciences. Here, we critically examine the major psychological theories (the “mind”) of short-term memory and how they relate to evidence about underlying brain mechanisms. We focus on three features that must be addressed by any satisfactory theory of short-term memory. First, we examine the evidence for the architecture of short-term memory, with special attention to questions of capacity and how—or whether—short-term memory can be separated from long-term memory. Second, we ask how the components of that architecture enact processes of encoding, maintenance, and retrieval. Third, we describe the debate over the reason about forgetting from short-term memory, whether interference or decay is the cause. We close with a conceptual model tracing the representation of a single item through a short-term memory task, describing the biological mechanisms that might support psychological processes on a moment-by-moment basis as an item is encoded, maintained over a delay with some forgetting, and ultimately retrieved. PMID:17854286

ENVIRONMENTAL IMPACTS AND MONITORING: A HISTORICAL PERSPECTIVE ON THE USE OF NATURAL ATTENUATION FOR SUBSURFACE REMEDIATION

EPA Science Inventory

The collective processes that constitute the broadly used term Anatural attenuation,@ as it relates to subsurface remediation of contaminants, refer to the physical, chemical, and biological interactions that, without human intervention, reduce or contain contaminants in the sub...

Long-Term Prospects for Developments in Space (A Scenario Approach)

DTIC Science & Technology

1977-10-30

to operate and maintain the facility. Its first products were biological materials of great purity unavailable from earth-bound processes ( vaccines ...as autism , schizo- phrenia, and severe neuroses; these all came about by the year 2025 because of the computer. Within the dominant knowledge-oriented

Structure, Agency, Complexity Theory and Interdisciplinary Research in Education Studies

ERIC Educational Resources Information Center

Smith, John A.

2013-01-01

This article argues that Education Studies needs to develop its existing interdisciplinarity understanding of structures and agencies by giving greater attention to the modern process theories of self-organisation in the physical, biological, psychological and social sciences, sometimes given the umbrella term "complexity theory". The…

Developmental engineering: a new paradigm for the design and manufacturing of cell-based products. Part II: from genes to networks: tissue engineering from the viewpoint of systems biology and network science.

PubMed

Lenas, Petros; Moos, Malcolm; Luyten, Frank P

2009-12-01

The field of tissue engineering is moving toward a new concept of "in vitro biomimetics of in vivo tissue development." In Part I of this series, we proposed a theoretical framework integrating the concepts of developmental biology with those of process design to provide the rules for the design of biomimetic processes. We named this methodology "developmental engineering" to emphasize that it is not the tissue but the process of in vitro tissue development that has to be engineered. To formulate the process design rules in a rigorous way that will allow a computational design, we should refer to mathematical methods to model the biological process taking place in vitro. Tissue functions cannot be attributed to individual molecules but rather to complex interactions between the numerous components of a cell and interactions between cells in a tissue that form a network. For tissue engineering to advance to the level of a technologically driven discipline amenable to well-established principles of process engineering, a scientifically rigorous formulation is needed of the general design rules so that the behavior of networks of genes, proteins, or cells that govern the unfolding of developmental processes could be related to the design parameters. Now that sufficient experimental data exist to construct plausible mathematical models of many biological control circuits, explicit hypotheses can be evaluated using computational approaches to facilitate process design. Recent progress in systems biology has shown that the empirical concepts of developmental biology that we used in Part I to extract the rules of biomimetic process design can be expressed in rigorous mathematical terms. This allows the accurate characterization of manufacturing processes in tissue engineering as well as the properties of the artificial tissues themselves. In addition, network science has recently shown that the behavior of biological networks strongly depends on their topology and has developed the necessary concepts and methods to describe it, allowing therefore a deeper understanding of the behavior of networks during biomimetic processes. These advances thus open the door to a transition for tissue engineering from a substantially empirical endeavor to a technology-based discipline comparable to other branches of engineering.

A rigorous approach to investigating common assumptions about disease transmission: Process algebra as an emerging modelling methodology for epidemiology.

PubMed

McCaig, Chris; Begon, Mike; Norman, Rachel; Shankland, Carron

2011-03-01

Changing scale, for example, the ability to move seamlessly from an individual-based model to a population-based model, is an important problem in many fields. In this paper, we introduce process algebra as a novel solution to this problem in the context of models of infectious disease spread. Process algebra allows us to describe a system in terms of the stochastic behaviour of individuals, and is a technique from computer science. We review the use of process algebra in biological systems, and the variety of quantitative and qualitative analysis techniques available. The analysis illustrated here solves the changing scale problem: from the individual behaviour we can rigorously derive equations to describe the mean behaviour of the system at the level of the population. The biological problem investigated is the transmission of infection, and how this relates to individual interactions.

Physical/chemical closed-loop water-recycling

NASA Technical Reports Server (NTRS)

Herrmann, Cal C.; Wydeven, Theodore

1991-01-01

Water needs, water sources, and means for recycling water are examined in terms appropriate to the water quality requirements of a small crew and spacecraft intended for long duration exploration missions. Inorganic, organic, and biological hazards are estimated for waste water sources. Sensitivities to these hazards for human uses are estimated. The water recycling processes considered are humidity condensation, carbon dioxide reduction, waste oxidation, distillation, reverse osmosis, pervaporation, electrodialysis, ion exchange, carbon sorption, and electrochemical oxidation. Limitations and applications of these processes are evaluated in terms of water quality objectives. Computerized simulation of some of these chemical processes is examined. Recommendations are made for development of new water recycling technology and improvement of existing technology for near term application to life support systems for humans in space. The technological developments are equally applicable to water needs on Earth, in regions where extensive water recycling is needed or where advanced water treatment is essential to meet EPA health standards.

Self-transcending meditation is good for mental health: why this should be the case.

PubMed

Hankey, Alex; Shetkar, Rashmi

2016-06-01

A simple theory of health has recently been proposed: while poor quality regulation corresponds to poor quality health so that improving regulation should improve health, optimal regulation optimizes function and optimizes health. Examining the term 'optimal regulation' in biological systems leads to a straightforward definition in terms of 'criticality' in complexity biology, a concept that seems to apply universally throughout biology. Criticality maximizes information processing and sensitivity of response to external stimuli, and for these reasons may be held to optimize regulation. In this way a definition of health has been given in terms of regulation, a scientific concept, which ties into detailed properties of complex systems, including brain cortices, and mental health. Models of experience and meditation built on complexity also point to criticality: it represents the condition making self-awareness possible, and is strengthened by meditation practices leading to the state of pure consciousness-the content-free state of mind in deep meditation. From this it follows that healthy function of the brain cortex, its sensitivity,y and consistency of response to external challenges should improve by practicing techniques leading to content-free awareness-transcending the original focus introduced during practice. Evidence for this is reviewed.

Surface transport processes in charged porous media

DOE PAGES

Gabitto, Jorge; Tsouris, Costas

2017-03-03

Surface transport processes are important in chemistry, colloidal sciences, engineering, biology, and geophysics. Natural or externally produced charges on surfaces create electrical double layers (EDLs) at the solid-liquid interface. The existence of the EDLs produces several complex processes including bulk and surface transport of ions. In this work, a model is presented to simulate bulk and transport processes in homogeneous porous media comprising big pores. It is based on a theory for capacitive charging by ideally polarizable porous electrodes without Faradaic reactions or specific adsorption of ions. A volume averaging technique is used to derive the averaged transport equations inmore » the limit of thin electrical double layers. Description of the EDL between the electrolyte solution and the charged wall is accomplished using the Gouy-Chapman-Stern (GCS) model. The surface transport terms enter into the average equations due to the use of boundary conditions for diffuse interfaces. Two extra surface transports terms appear in the closed average equations. One is a surface diffusion term equivalent to the transport process in non-charged porous media. The second surface transport term is a migration term unique to charged porous media. The effective bulk and transport parameters for isotropic porous media are calculated solving the corresponding closure problems.« less

Surface transport processes in charged porous media

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

Gabitto, Jorge; Tsouris, Costas

Surface transport processes are important in chemistry, colloidal sciences, engineering, biology, and geophysics. Natural or externally produced charges on surfaces create electrical double layers (EDLs) at the solid-liquid interface. The existence of the EDLs produces several complex processes including bulk and surface transport of ions. In this work, a model is presented to simulate bulk and transport processes in homogeneous porous media comprising big pores. It is based on a theory for capacitive charging by ideally polarizable porous electrodes without Faradaic reactions or specific adsorption of ions. A volume averaging technique is used to derive the averaged transport equations inmore » the limit of thin electrical double layers. Description of the EDL between the electrolyte solution and the charged wall is accomplished using the Gouy-Chapman-Stern (GCS) model. The surface transport terms enter into the average equations due to the use of boundary conditions for diffuse interfaces. Two extra surface transports terms appear in the closed average equations. One is a surface diffusion term equivalent to the transport process in non-charged porous media. The second surface transport term is a migration term unique to charged porous media. The effective bulk and transport parameters for isotropic porous media are calculated solving the corresponding closure problems.« less

Nitrous Oxide Production at a Fully Covered Wastewater Treatment Plant: Results of a Long-Term Online Monitoring Campaign.

PubMed

Kosonen, Heta; Heinonen, Mari; Mikola, Anna; Haimi, Henri; Mulas, Michela; Corona, Francesco; Vahala, Riku

2016-06-07

The nitrous oxide emissions of the Viikinmäki wastewater treatment plant were measured in a 12 month online monitoring campaign. The measurements, which were conducted with a continuous gas analyzer, covered all of the unit operations of the advanced wastewater-treatment process. The relation between the nitrous oxide emissions and certain process parameters, such as the wastewater temperature, influent biological oxygen demand, and ammonium nitrogen load, was investigated by applying online data obtained from the process-control system at 1 min intervals. Although seasonal variations in the measured nitrous oxide emissions were remarkable, the measurement data indicated no clear relationship between these emissions and seasonal changes in the wastewater temperature. The diurnal variations of the nitrous oxide emissions did, however, strongly correlate with the alternation of the influent biological oxygen demand and ammonium nitrogen load to the aerated zones of the activated sludge process. Overall, the annual nitrous oxide emissions of 168 g/PE/year and the emission factor of 1.9% of the influent nitrogen load are in the high range of values reported in the literature but in very good agreement with the results of other long-term online monitoring campaigns implemented at full-scale wastewater-treatment plants.

Repair and tissue engineering techniques for articular cartilage

PubMed Central

Makris, Eleftherios A.; Gomoll, Andreas H.; Malizos, Konstantinos N.; Hu, Jerry C.; Athanasiou, Kyriacos A.

2015-01-01

Chondral and osteochondral lesions due to injury or other pathology commonly result in the development of osteoarthritis, eventually leading to progressive total joint destruction. Although current progress suggests that biologic agents can delay the advancement of deterioration, such drugs are incapable of promoting tissue restoration. The limited ability of articular cartilage to regenerate renders joint arthroplasty an unavoidable surgical intervention. This Review describes current, widely used clinical repair techniques for resurfacing articular cartilage defects; short-term and long-term clinical outcomes of these techniques are discussed. Also reviewed is a developmental pipeline of regenerative biological products that over the next decade could revolutionize joint care by functionally healing articular cartilage. These products include cell-based and cell-free materials such as autologous and allogeneic cell-based approaches and multipotent and pluripotent stem-cell-based techniques. Central to these efforts is the prominent role that tissue engineering has in translating biological technology into clinical products; therefore, concomitant regulatory processes are also discussed. PMID:25247412

Retardation and Sedimentation of Chernobyl-derived Radiocesium in the Photic Zone Sedimenttrap Deployment Studies in the Norwegian Sea

NASA Astrophysics Data System (ADS)

Baumann, Marion

One long-term and three short-term sedimenttrap-deployments have been installed in the Norwegian Sea shortly after the reactor-accident at Chernobyl in April 1986. Radiocesium investigations of the sedimenttrap material were combined with detailed biological investigations on sedimentation processes in the photic Zone. Lacking efficient export processes in the photic Zone, radiocesium first was retained in the photic Zone for several weeks. Then the break down and successive sedimentation of the heterotrophic community exported about 10 % of surface deposition of radiocesium to larger water depths and to the seafloor at 1450 m.

Influence of carbon source amendment on effectiveness of anaerobic soil disinfestation

USDA-ARS?s Scientific Manuscript database

Anaerobic soil disinfestation (ASD; also termed biological soil disinfestation or soil reductive sterilization) is a non-chemical soil disinfestation process which includes 1) soil incorporation of a labile carbon (C) source, 2) mulching with a polyethylene film to limit gas exchange, and 3) drip ir...

Apes have eyes to the future.

PubMed

Vonk, Jennifer

2016-09-01

Kano and Hirata (Current Biology, 25, 2513-2517, 2015) recently showed that apes process object and location information and anticipate the repeated presentation of such events in short film clips. Their methodology, using eyetracking, can provide a foundation for further explications of long-term prospective and episodic memory in nonverbal species.

Biological Components of Colour Preference in Infancy

ERIC Educational Resources Information Center

Franklin, Anna; Bevis, Laura; Ling, Yazhu; Hurlbert, Anya

2010-01-01

Adult colour preference has been summarized quantitatively in terms of weights on the two fundamental neural processes that underlie early colour encoding: the S-(L+M) ("blue-yellow") and L-M ("red-green") cone-opponent contrast channels ( Ling, Hurlbert & Robinson, 2006; Hurlbert & Ling, 2007). Here, we investigate whether colour preference in…

Aerobic Digestion. Student Manual. Biological Treatment Process Control.

ERIC Educational Resources Information Center

Klopping, Paul H.

This manual contains the textual material for a single-lesson unit on aerobic sludge digestion. Topic areas addressed include: (1) theory of aerobic digestion; (2) system components; (3) performance factors; (4) indicators of stable operation; and (5) operational problems and their solutions. A list of objectives, glossary of key terms, and…

Coupled Reactions "versus" Connected Reactions: Coupling Concepts with Terms

ERIC Educational Resources Information Center

Aledo, Juan Carlos

2007-01-01

A hallmark of living matter is its ability to extract and transform energy from the environment. Not surprisingly, biology students are required to take thermodynamics. The necessity of coupling exergonic reactions to endergonic processes is easily grasped by most undergraduate students. However, when addressing the thermodynamic concept of…

26 CFR 1.142(a)(6)-1 - Exempt facility bonds: solid waste disposal facilities.

Code of Federal Regulations, 2012 CFR

2012-04-01

... biological, engineering, industrial, or technological method. (1) Final disposal process. The term final... solid material derived from any agricultural, commercial, consumer, governmental, or industrial... industrial operation or activity, or a component of any such product or activity, and that has been used...

26 CFR 1.142(a)(6)-1 - Exempt facility bonds: solid waste disposal facilities.

Code of Federal Regulations, 2013 CFR

2013-04-01

... biological, engineering, industrial, or technological method. (1) Final disposal process. The term final... solid material derived from any agricultural, commercial, consumer, governmental, or industrial... industrial operation or activity, or a component of any such product or activity, and that has been used...

Nutritional impacts on gene expression in the surface mucosa of blue catfish (Ictalurus furcatus)

USDA-ARS?s Scientific Manuscript database

Short-term feed deprivation is a common occurrence in both wild and farmed fish species, due to reproductive processes, seasonal variations in temperature, or in response to a disease outbreak. Fasting can have dramatic physiological and biological onsequences for fish, including impacts on mucosal ...

A visual metaphor describing neural dynamics in schizophrenia.

PubMed

van Beveren, Nico J M; de Haan, Lieuwe

2008-07-09

In many scientific disciplines the use of a metaphor as an heuristic aid is not uncommon. A well known example in somatic medicine is the 'defense army metaphor' used to characterize the immune system. In fact, probably a large part of the everyday work of doctors consists of 'translating' scientific and clinical information (i.e. causes of disease, percentage of success versus risk of side-effects) into information tailored to the needs and capacities of the individual patient. The ability to do so in an effective way is at least partly what makes a clinician a good communicator. Schizophrenia is a severe psychiatric disorder which affects approximately 1% of the population. Over the last two decades a large amount of molecular-biological, imaging and genetic data have been accumulated regarding the biological underpinnings of schizophrenia. However, it remains difficult to understand how the characteristic symptoms of schizophrenia such as hallucinations and delusions are related to disturbances on the molecular-biological level. In general, psychiatry seems to lack a conceptual framework with sufficient explanatory power to link the mental- and molecular-biological domains. Here, we present an essay-like study in which we propose to use visualized concepts stemming from the theory on dynamical complex systems as a 'visual metaphor' to bridge the mental- and molecular-biological domains in schizophrenia. We first describe a computer model of neural information processing; we show how the information processing in this model can be visualized, using concepts from the theory on complex systems. We then describe two computer models which have been used to investigate the primary theory on schizophrenia, the neurodevelopmental model, and show how disturbed information processing in these two computer models can be presented in terms of the visual metaphor previously described. Finally, we describe the effects of dopamine neuromodulation, of which disturbances have been frequently described in schizophrenia, in terms of the same visualized metaphor. The conceptual framework and metaphor described offers a heuristic tool to understand the relationship between the mental- and molecular-biological domains in an intuitive way. The concepts we present may serve to facilitate communication between researchers, clinicians and patients.

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology

PubMed Central

Roncaglia, Paola; Howe, Douglas G.; Laulederkind, Stanley J.F.; Khodiyar, Varsha K.; Berardini, Tanya Z.; Tweedie, Susan; Foulger, Rebecca E.; Osumi-Sutherland, David; Campbell, Nancy H.; Huntley, Rachael P.; Talmud, Philippa J.; Blake, Judith A.; Breckenridge, Ross; Riley, Paul R.; Lambiase, Pier D.; Elliott, Perry M.; Clapp, Lucie; Tinker, Andrew; Hill, David P.

2018-01-01

Background: A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. Methods and Results: In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. Conclusions: We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects. PMID:29440116

Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology.

PubMed

Lovering, Ruth C; Roncaglia, Paola; Howe, Douglas G; Laulederkind, Stanley J F; Khodiyar, Varsha K; Berardini, Tanya Z; Tweedie, Susan; Foulger, Rebecca E; Osumi-Sutherland, David; Campbell, Nancy H; Huntley, Rachael P; Talmud, Philippa J; Blake, Judith A; Breckenridge, Ross; Riley, Paul R; Lambiase, Pier D; Elliott, Perry M; Clapp, Lucie; Tinker, Andrew; Hill, David P

2018-02-01

A systems biology approach to cardiac physiology requires a comprehensive representation of how coordinated processes operate in the heart, as well as the ability to interpret relevant transcriptomic and proteomic experiments. The Gene Ontology (GO) Consortium provides structured, controlled vocabularies of biological terms that can be used to summarize and analyze functional knowledge for gene products. In this study, we created a computational resource to facilitate genetic studies of cardiac physiology by integrating literature curation with attention to an improved and expanded ontological representation of heart processes in the Gene Ontology. As a result, the Gene Ontology now contains terms that comprehensively describe the roles of proteins in cardiac muscle cell action potential, electrical coupling, and the transmission of the electrical impulse from the sinoatrial node to the ventricles. Evaluating the effectiveness of this approach to inform data analysis demonstrated that Gene Ontology annotations, analyzed within an expanded ontological context of heart processes, can help to identify candidate genes associated with arrhythmic disease risk loci. We determined that a combination of curation and ontology development for heart-specific genes and processes supports the identification and downstream analysis of genes responsible for the spread of the cardiac action potential through the heart. Annotating these genes and processes in a structured format facilitates data analysis and supports effective retrieval of gene-centric information about cardiac defects. © 2018 The Authors.

Tissue Engineering and Regenerative Medicine 2017: A Year in Review.

PubMed

Park, Kyung Min; Shin, Young Min; Kim, Kyobum; Shin, Heungsoo

2018-04-26

In 2017, a new paradigm change caused by artificial intelligence and big data analysis resulted in innovation in each field of science and technology, and also significantly influenced progress in tissue engineering and regenerative medicine (TERM). TERM has continued to make technological advances based on interdisciplinary approaches and has contributed to the overall field of biomedical technology, including cancer biology, personalized medicine, development biology, and cell-based therapeutics. While researchers are aware that there is still a long way to go until TERM reaches the ultimate goal of patient treatment through clinical translation, the rapid progress in convergence studies led by technological improvements in TERM has been encouraging. In this review, we highlighted the significant advances made in TERM in 2017 (with an overlap of 5 months in 2016). We identified major progress in TERM in a manner similar to previous reviews published in the last few years. In addition, we carefully considered all four previous reviews during the selection process and chose main themes that minimize the duplication of the topics. Therefore, we have identified three areas that have been the focus of most journal publications in the TERM community in 2017: (i) advanced biomaterials and three-dimensional (3D) cell printing, (ii) exosomes as bioactive agents for regenerative medicine, and (iii) 3D culture in regenerative medicine.

Innovation: an emerging focus from cells to societies.

PubMed

Hochberg, Michael E; Marquet, Pablo A; Boyd, Robert; Wagner, Andreas

2017-12-05

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability.This article is part of the theme issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

Innovation: an emerging focus from cells to societies

PubMed Central

Boyd, Robert

2017-01-01

Innovations are generally unexpected, often spectacular changes in phenotypes and ecological functions. The contributions to this theme issue are the latest conceptual, theoretical and experimental developments, addressing how ecology, environment, ontogeny and evolution are central to understanding the complexity of the processes underlying innovations. Here, we set the stage by introducing and defining key terms relating to innovation and discuss their relevance to biological, cultural and technological change. Discovering how the generation and transmission of novel biological information, environmental interactions and selective evolutionary processes contribute to innovation as an ecosystem will shed light on how the dominant features across life come to be, generalize to social, cultural and technological evolution, and have applications in the health sciences and sustainability. This article is part of the theme issue ‘Process and pattern in innovations from cells to societies’. PMID:29061887

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

PubMed

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

2011-10-13

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

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

PubMed Central

2011-01-01

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

37 CFR 1.779 - Calculation of patent term extension for a veterinary biological product.

Code of Federal Regulations, 2011 CFR

2011-07-01

... extension for a veterinary biological product. 1.779 Section 1.779 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a veterinary biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a veterinary biological product is eligible for extension, the term...

37 CFR 1.779 - Calculation of patent term extension for a veterinary biological product.

Code of Federal Regulations, 2010 CFR

2010-07-01

... extension for a veterinary biological product. 1.779 Section 1.779 Patents, Trademarks, and Copyrights... Calculation of patent term extension for a veterinary biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a veterinary biological product is eligible for extension, the term...

An improved Pearson's correlation proximity-based hierarchical clustering for mining biological association between genes.

PubMed

Booma, P M; Prabhakaran, S; Dhanalakshmi, R

2014-01-01

Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality.

An Improved Pearson's Correlation Proximity-Based Hierarchical Clustering for Mining Biological Association between Genes

PubMed Central

Booma, P. M.; Prabhakaran, S.; Dhanalakshmi, R.

2014-01-01

Microarray gene expression datasets has concerned great awareness among molecular biologist, statisticians, and computer scientists. Data mining that extracts the hidden and usual information from datasets fails to identify the most significant biological associations between genes. A search made with heuristic for standard biological process measures only the gene expression level, threshold, and response time. Heuristic search identifies and mines the best biological solution, but the association process was not efficiently addressed. To monitor higher rate of expression levels between genes, a hierarchical clustering model was proposed, where the biological association between genes is measured simultaneously using proximity measure of improved Pearson's correlation (PCPHC). Additionally, the Seed Augment algorithm adopts average linkage methods on rows and columns in order to expand a seed PCPHC model into a maximal global PCPHC (GL-PCPHC) model and to identify association between the clusters. Moreover, a GL-PCPHC applies pattern growing method to mine the PCPHC patterns. Compared to existing gene expression analysis, the PCPHC model achieves better performance. Experimental evaluations are conducted for GL-PCPHC model with standard benchmark gene expression datasets extracted from UCI repository and GenBank database in terms of execution time, size of pattern, significance level, biological association efficiency, and pattern quality. PMID:25136661

Biologically-Oriented Processes in the Coastal Sea Ice Zone of the White Sea

NASA Astrophysics Data System (ADS)

Melnikov, I. A.

2002-12-01

The annual advance and retreat of sea ice is a major physical determinant of spatial and temporal changes in the structure and function of marine coastal biological communities. Sea ice biological data obtained in the tidal zone of Kandalaksha Gulf (White Sea) during 1996-2001 period will be presented. Previous observations in this area were mainly conducted during the ice-free summer season. However, there is little information on the ice-covered winter season (6-7 months duration), and, especially, on the sea-ice biology in the coastal zone within tidal regimes. During the January-May period time-series observations were conducted on transects along shorelines with coastal and fast ice. Trends in the annual extent of sea ice showed significant impacts on ice-associated biological communities. Three types of sea ice impact on kelps, balanoides, littorinas and amphipods are distinguished: (i) positive, when sea ice protects these populations from grinding (ii) negative, when ice grinds both fauna and flora, and (iii) a combined effect, when fast ice protects, but anchored ice grinds plant and animals. To understand the full spectrum of ecological problems caused by pollution on the coastal zone, as well as the problems of sea ice melting caused by global warming, an integrated, long-term study of the physical, chemical, and biological processes is needed.

Cytokines as endogenous pyrogens.

PubMed

Dinarello, C A

1999-03-01

Cytokines are pleiotropic molecules mediating several pathologic processes. Long before the discovery of cytokines as immune system growth factors or as bone marrow stimulants, investigators learned a great deal about cytokines when they studied them as the endogenous mediators of fever. The terms "granulocytic" or "endogenous pyrogen" were used to describe substances with the biologic property of fever induction. Today, we recognize that pyrogenicity is a fundamental biologic property of several cytokines and hence the clinically recognizeable property of fever links host perturbations during disease with fundamental perturbations in cell biology. In this review, the discoveries made on endogenous pyrogens are revisited, with insights into the importance of the earlier work to the present-day understanding of cytokines in health and in disease.

Systems biology approach to bioremediation

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

Chakraborty, Romy; Wu, Cindy H.; Hazen, Terry C.

2012-06-01

Bioremediation has historically been approached as a ‘black box’ in terms of our fundamental understanding. Thus it succeeds and fails, seldom without a complete understanding of why. Systems biology is an integrated research approach to study complex biological systems, by investigating interactions and networks at the molecular, cellular, community, and ecosystem level. The knowledge of these interactions within individual components is fundamental to understanding the dynamics of the ecosystem under investigation. Finally, understanding and modeling functional microbial community structure and stress responses in environments at all levels have tremendous implications for our fundamental understanding of hydrobiogeochemical processes and the potentialmore » for making bioremediation breakthroughs and illuminating the ‘black box’.« less

Synthetic biology: advancing the design of diverse genetic systems

PubMed Central

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

2013-01-01

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

Biological Relevance of Free Radicals and Nitroxides.

PubMed

Prescott, Christopher; Bottle, Steven E

2017-06-01

Nitroxides are stable, kinetically-persistent free radicals which have been successfully used in the study and intervention of oxidative stress, a critical issue pertaining to cellular health which results from an imbalance in the levels of damaging free radicals and redox-active species in the cellular environment. This review gives an overview of some of the biological processes that produce radicals and other reactive oxygen species with relevance to oxidative stress, and then discusses interactions of nitroxides with these species in terms of the use of nitroxides as redox-sensitive probes and redox-active therapeutic agents.

GPS for QSP: A Summary of the ACoP6 Symposium on Quantitative Systems Pharmacology and a Stage for Near‐Term Efforts in the Field

PubMed Central

Musante, CJ; Abernethy, DR; Allerheiligen, SR; Lauffenburger, DA

2016-01-01

Quantitative Systems Pharmacology (QSP) is experiencing increased application in the drug discovery and development process. Like its older sibling, systems biology, the QSP field is comprised of a mix of established disciplines and methods, from molecular biology to engineering to pharmacometrics.1 As a result, there exist critical segments of the discipline that differ dramatically in approach and a need to bring these groups together toward a common goal. PMID:27639191

Nanostructures Enabled by On-Wire Lithography (OWL)

PubMed Central

Braunschweig, Adam B.; Schmucker, Abrin L.; Wei, Wei David; Mirkin, Chad A.

2010-01-01

Nanostructures fabricated by a novel technique, termed On-Wire-Lithography (OWL), can be combined with organic and biological molecules to create systems with emergent and highly functional properties. OWL is a template-based, electrochemical process for forming gapped cylindrical structures on a solid support, with feature sizes (both gap and segment length) that can be controlled on the sub-100 nm length scale. Structures prepared by this method have provided valuable insight into the plasmonic properties of noble metal nanomaterials and have formed the basis for novel molecular electronic, encoding, and biological detection devices. PMID:20396668

Illuminating Cell Biology

NASA Technical Reports Server (NTRS)

2002-01-01

NASA's Ames Research Center awarded Ciencia, Inc., a Small Business Innovation Research contract to develop the Cell Fluorescence Analysis System (CFAS) to address the size, mass, and power constraints of using fluorescence spectroscopy in the International Space Station's Life Science Research Facility. The system will play an important role in studying biological specimen's long-term adaptation to microgravity. Commercial applications for the technology include diverse markets such as food safety, in situ environmental monitoring, online process analysis, genomics and DNA chips, and non-invasive diagnostics. Ciencia has already sold the system to the private sector for biosensor applications.

Gene Ontology Consortium: going forward

PubMed Central

2015-01-01

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. PMID:25428369

Biogeochemical Cycles of Carbon and Sulfur

NASA Technical Reports Server (NTRS)

DesMarais, David J.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The elements carbon (C) and sulfur (S) interact with each other across a network of elemental reservoirs that are interconnected by an array of physical, chemical and biological processes. These networks are termed the biogeochemical C and S cycles. The compounds of C are highly important, not only as organic matter, but also as atmospheric greenhouse gases, pH buffers in seawater, oxidation-reduction buffers virtually everywhere, and key magmatic constituents affecting plutonism and volcanism. The element S assumes important roles as an oxidation-reduction partner with C and Fe in biological systems, as a key constituent in magmas and volcanic gases, and as a major influence upon pH in certain environments. This presentation describes the modern biogeochemical C and S cycles. Measurements are described whereby stable isotopes can help to infer the nature and quantitative significance of biological and geological processes involved in the C and S cycles. This lecture also summarizes the geological and climatologic aspects of the ancient C and S cycles, as well as the planetary and extraterrestrial processes that influenced their evolution over millions to billions of years.

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

PubMed Central

Ibrahim, Bashar; Dittrich, Peter

2014-01-01

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

Comparative muscle transcriptome associated with carcass traits of Nellore cattle.

PubMed

Silva-Vignato, Bárbara; Coutinho, Luiz L; Cesar, Aline S M; Poleti, Mirele D; Regitano, Luciana C A; Balieiro, Júlio C C

2017-07-03

Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.

Biomolecular Materials. Report of the January 13-15, 2002 Workshop

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

Alper, M. D.; Stupp, S. I.

2002-01-15

Twenty-two scientists from around the nation and the world met to discuss the way that the molecules, structures, processes and concepts of the biological world could be used or mimicked in designing novel materials, processes or devices of potential practical significance. The emphasis was on basic research, although the long-term goal is, in addition to increased knowledge, the development of applications to further the mission of the Department of Energy.

Long-term simulation of vertical transport process and its impact on bottom DO in Chesapeake Bay

NASA Astrophysics Data System (ADS)

Du, J.; Shen, J.

2016-02-01

Hypoxia in coastal waters is a widespread phenomenon that appears to have been growing globally for at least 60 years. The fact that physical transport processes and biological processes are equally important in determining the bottom DO in Chesapeake Bay is commonly agreed. However, the quantitative impact of physical transport processes is rarely documented. In this study, we use a timescale, vertical exchange time (VET), to quantify the impact of all physical processes that might have on the bottom DO. Simulation of VET from 1985 to 2012 is conducted and the monthly observed DO data along the deep channel in the Bay's main stem is collected. A conceptual bottom DO budget model is applied, using the VET to quantify the physical condition and net oxygen consumption rate to quantify biological activities. The DO budget model results show that the interannual variations of physical conditions accounts for 88.8% of the interannual variations of observed DO. The high similarity between the VET spatial pattern and the observed DO suggests that physical processes play a key role in regulating the DO condition. Model results also show that long-term VET has a slight increase in summer, but no statistically significant trend is found. Correlations among southerly wind strength, North Atlantic Oscillation index, and VET demonstrate that the physical condition in the Chesapeake Bay is highly controlled by the large-scale climate variation. The relationship is most significant during the summer, when the southerly wind dominates throughout the Chesapeake Bay.

Food and water supply

NASA Technical Reports Server (NTRS)

Popov, I. G.

1975-01-01

Supplying astronauts with adequate food and water on short and long-term space flights is discussed based on experiences gained in space flight. Food consumption, energy requirements, and suitability of the foodstuffs for space flight are among the factors considered. Physicochemical and biological methods of food production and regeneration of water from astronaut metabolic wastes, as well as wastes produced in a closed ecological system, or as a result of technical processes taking place in various spacecraft systems are suggested for long-term space flights.

Inference, simulation, modeling, and analysis of complex networks, with special emphasis on complex networks in systems biology

NASA Astrophysics Data System (ADS)

Christensen, Claire Petra

Across diverse fields ranging from physics to biology, sociology, and economics, the technological advances of the past decade have engendered an unprecedented explosion of data on highly complex systems with thousands, if not millions of interacting components. These systems exist at many scales of size and complexity, and it is becoming ever-more apparent that they are, in fact, universal, arising in every field of study. Moreover, they share fundamental properties---chief among these, that the individual interactions of their constituent parts may be well-understood, but the characteristic behaviour produced by the confluence of these interactions---by these complex networks---is unpredictable; in a nutshell, the whole is more than the sum of its parts. There is, perhaps, no better illustration of this concept than the discoveries being made regarding complex networks in the biological sciences. In particular, though the sequencing of the human genome in 2003 was a remarkable feat, scientists understand that the "cellular-level blueprints" for the human being are cellular-level parts lists, but they say nothing (explicitly) about cellular-level processes. The challenge of modern molecular biology is to understand these processes in terms of the networks of parts---in terms of the interactions among proteins, enzymes, genes, and metabolites---as it is these processes that ultimately differentiate animate from inanimate, giving rise to life! It is the goal of systems biology---an umbrella field encapsulating everything from molecular biology to epidemiology in social systems---to understand processes in terms of fundamental networks of core biological parts, be they proteins or people. By virtue of the fact that there are literally countless complex systems, not to mention tools and techniques used to infer, simulate, analyze, and model these systems, it is impossible to give a truly comprehensive account of the history and study of complex systems. The author's own publications have contributed network inference, simulation, modeling, and analysis methods to the much larger body of work in systems biology, and indeed, in network science. The aim of this thesis is therefore twofold: to present this original work in the historical context of network science, but also to provide sufficient review and reference regarding complex systems (with an emphasis on complex networks in systems biology) and tools and techniques for their inference, simulation, analysis, and modeling, such that the reader will be comfortable in seeking out further information on the subject. The review-like Chapters 1, 2, and 4 are intended to convey the co-evolution of network science and the slow but noticeable breakdown of boundaries between disciplines in academia as research and comparison of diverse systems has brought to light the shared properties of these systems. It is the author's hope that theses chapters impart some sense of the remarkable and rapid progress in complex systems research that has led to this unprecedented academic synergy. Chapters 3 and 5 detail the author's original work in the context of complex systems research. Chapter 3 presents the methods and results of a two-stage modeling process that generates candidate gene-regulatory networks of the bacterium B.subtilis from experimentally obtained, yet mathematically underdetermined microchip array data. These networks are then analyzed from a graph theoretical perspective, and their biological viability is critiqued by comparing the networks' graph theoretical properties to those of other biological systems. The results of topological perturbation analyses revealing commonalities in behavior at multiple levels of complexity are also presented, and are shown to be an invaluable means by which to ascertain the level of complexity to which the network inference process is robust to noise. Chapter 5 outlines a learning algorithm for the development of a realistic, evolving social network (a city) into which a disease is introduced. The results of simulations in populations spanning two orders of magnitude are compared to prevaccine era measles data for England and Wales and demonstrate that the simulations are able to capture the quantitative and qualitative features of epidemics in populations as small as 10,000 people. The work presented in Chapter 5 validates the utility of network simulation in concurrently probing contact network dynamics and disease dynamics.

Structure-function relations in physiology education: Where's the mechanism?

PubMed

Lira, Matthew E; Gardner, Stephanie M

2017-06-01

Physiology demands systems thinking: reasoning within and between levels of biological organization and across different organ systems. Many physiological mechanisms explain how structures and their properties interact at one level of organization to produce emergent functions at a higher level of organization. Current physiology principles, such as structure-function relations, selectively neglect mechanisms by not mentioning this term explicitly. We explored how students characterized mechanisms and functions to shed light on how students make sense of these terms. Students characterized mechanisms as 1 ) processes that occur at levels of organization lower than that of functions; and 2 ) as detailed events with many steps involved. We also found that students produced more variability in how they characterized functions compared with mechanisms: students characterized functions in relation to multiple levels of organization and multiple definitions. We interpret these results as evidence that students see mechanisms as holding a more narrow definition than used in the biological sciences, and that students struggle to coordinate and distinguish mechanisms from functions due to cognitive processes germane to learning in many domains. We offer the instructional suggestion that we scaffold student learning by affording students opportunities to relate and also distinguish between these terms so central to understanding physiology. Copyright © 2017 the American Physiological Society.

Long-term biological hydrogen production by agar immobilized Rhodobacter capsulatus in a sequential batch photobioreactor.

PubMed

Elkahlout, Kamal; Alipour, Siamak; Eroglu, Inci; Gunduz, Ufuk; Yucel, Meral

2017-04-01

In this study, agar immobilization technique was employed for biological hydrogen production using Rhodobacter capsulatus DSM 1710 (wild type) and YO3 (hup-mutant) strains in sequential batch process. Different agar and glutamate concentrations were tested with defined nutrient medium. Agar concentration 4% (w/v) and 4 mM glutamate were selected for bacterial immobilization in terms of rate and longevity of hydrogen production. Acetate concentration was increased from 40 to 60-100 and 60 mM gave best results with both bacterial strains immobilized in 4% (w/v) agar. Cell concentration was increased from 2.5 to 5 mg dcw mL -1 agar and it was found that increasing cell concentration of wild-type strain caused decrease in yield and productivity while these parameters improved by increasing cell concentration of mutant strain. Also, the hydrogen production time has extended from 17 days up to 60 days according to the process conditions and parameters. Hydrogen production by immobilized photosynthetic bacteria is a convenient technology for hydrogen production as it enables to produce hydrogen with high organic acid concentrations comparing to suspended cultures. Besides, immobilization increases the stability of the system and allowed sequential batch operation for long-term application.

Imaging windows for long-term intravital imaging

PubMed Central

Alieva, Maria; Ritsma, Laila; Giedt, Randy J; Weissleder, Ralph; van Rheenen, Jacco

2014-01-01

Intravital microscopy is increasingly used to visualize and quantitate dynamic biological processes at the (sub)cellular level in live animals. By visualizing tissues through imaging windows, individual cells (e.g., cancer, host, or stem cells) can be tracked and studied over a time-span of days to months. Several imaging windows have been developed to access tissues including the brain, superficial fascia, mammary glands, liver, kidney, pancreas, and small intestine among others. Here, we review the development of imaging windows and compare the most commonly used long-term imaging windows for cancer biology: the cranial imaging window, the dorsal skin fold chamber, the mammary imaging window, and the abdominal imaging window. Moreover, we provide technical details, considerations, and trouble-shooting tips on the surgical procedures and microscopy setups for each imaging window and explain different strategies to assure imaging of the same area over multiple imaging sessions. This review aims to be a useful resource for establishing the long-term intravital imaging procedure. PMID:28243510

Imaging windows for long-term intravital imaging: General overview and technical insights.

PubMed

Alieva, Maria; Ritsma, Laila; Giedt, Randy J; Weissleder, Ralph; van Rheenen, Jacco

2014-01-01

Intravital microscopy is increasingly used to visualize and quantitate dynamic biological processes at the (sub)cellular level in live animals. By visualizing tissues through imaging windows, individual cells (e.g., cancer, host, or stem cells) can be tracked and studied over a time-span of days to months. Several imaging windows have been developed to access tissues including the brain, superficial fascia, mammary glands, liver, kidney, pancreas, and small intestine among others. Here, we review the development of imaging windows and compare the most commonly used long-term imaging windows for cancer biology: the cranial imaging window, the dorsal skin fold chamber, the mammary imaging window, and the abdominal imaging window. Moreover, we provide technical details, considerations, and trouble-shooting tips on the surgical procedures and microscopy setups for each imaging window and explain different strategies to assure imaging of the same area over multiple imaging sessions. This review aims to be a useful resource for establishing the long-term intravital imaging procedure.

Brain age and other bodily 'ages': implications for neuropsychiatry.

PubMed

Cole, James H; Marioni, Riccardo E; Harris, Sarah E; Deary, Ian J

2018-06-11

As our brains age, we tend to experience cognitive decline and are at greater risk of neurodegenerative disease and dementia. Symptoms of chronic neuropsychiatric diseases are also exacerbated during ageing. However, the ageing process does not affect people uniformly; nor, in fact, does the ageing process appear to be uniform even within an individual. Here, we outline recent neuroimaging research into brain ageing and the use of other bodily ageing biomarkers, including telomere length, the epigenetic clock, and grip strength. Some of these techniques, using statistical approaches, have the ability to predict chronological age in healthy people. Moreover, they are now being applied to neurological and psychiatric disease groups to provide insights into how these diseases interact with the ageing process and to deliver individualised predictions about future brain and body health. We discuss the importance of integrating different types of biological measurements, from both the brain and the rest of the body, to build more comprehensive models of the biological ageing process. Finally, we propose seven steps for the field of brain-ageing research to take in coming years. This will help us reach the long-term goal of developing clinically applicable statistical models of biological processes to measure, track and predict brain and body health in ageing and disease.

Microarray gene-expression study in fibroblast and lymphoblastoid cell lines from antipsychotic-naïve first-episode schizophrenia patients.

PubMed

Gassó, Patricia; Mas, Sergi; Rodríguez, Natalia; Boloc, Daniel; García-Cerro, Susana; Bernardo, Miquel; Lafuente, Amalia; Parellada, Eduard

2017-12-01

Schizophrenia (SZ) is a chronic psychiatric disorder whose onset of symptoms occurs in late adolescence and early adulthood. The etiology is complex and involves important gene-environment interactions. Microarray gene-expression studies on SZ have identified alterations in several biological processes. The heterogeneity in the results can be attributed to the use of different sample types and other important confounding factors including age, illness chronicity and antipsychotic exposure. The aim of the present microarray study was to analyze, for the first time to our knowledge, differences in gene expression profiles in 18 fibroblast (FCLs) and 14 lymphoblastoid cell lines (LCLs) from antipsychotic-naïve first-episode schizophrenia (FES) patients and healthy controls. We used an analytical approach based on protein-protein interaction network construction and functional annotation analysis to identify the biological processes that are altered in SZ. Significant differences in the expression of 32 genes were found when LCLs were assessed. The network and gene set enrichment approach revealed the involvement of similar biological processes in FCLs and LCLs, including apoptosis and related biological terms such as cell cycle, autophagy, cytoskeleton organization and response to stress and stimulus. Metabolism and other processes, including signal transduction, kinase activity and phosphorylation, were also identified. These results were replicated in two independent cohorts using the same analytical approach. This provides more evidence for altered apoptotic processes in antipsychotic-naïve FES patients and other important biological functions such as cytoskeleton organization and metabolism. The convergent results obtained in both peripheral cell models support their usefulness for transcriptome studies on SZ. Copyright © 2017 Elsevier Ltd. All rights reserved.

Networking Omic Data to Envisage Systems Biological Regulation.

PubMed

Kalapanulak, Saowalak; Saithong, Treenut; Thammarongtham, Chinae

To understand how biological processes work, it is necessary to explore the systematic regulation governing the behaviour of the processes. Not only driving the normal behavior of organisms, the systematic regulation evidently underlies the temporal responses to surrounding environments (dynamics) and long-term phenotypic adaptation (evolution). The systematic regulation is, in effect, formulated from the regulatory components which collaboratively work together as a network. In the drive to decipher such a code of lives, a spectrum of technologies has continuously been developed in the post-genomic era. With current advances, high-throughput sequencing technologies are tremendously powerful for facilitating genomics and systems biology studies in the attempt to understand system regulation inside the cells. The ability to explore relevant regulatory components which infer transcriptional and signaling regulation, driving core cellular processes, is thus enhanced. This chapter reviews high-throughput sequencing technologies, including second and third generation sequencing technologies, which support the investigation of genomics and transcriptomics data. Utilization of this high-throughput data to form the virtual network of systems regulation is explained, particularly transcriptional regulatory networks. Analysis of the resulting regulatory networks could lead to an understanding of cellular systems regulation at the mechanistic and dynamics levels. The great contribution of the biological networking approach to envisage systems regulation is finally demonstrated by a broad range of examples.

Estimating tree species richness from forest inventory plot data

Treesearch

Ronald E. McRoberts; Dacia M. Meneguzzo

2007-01-01

Montreal Process Criterion 1, Conservation of Biological Diversity, expresses species diversity in terms of number of forest dependent species. Species richness, defined as the total number of species present, is a common metric for analyzing species diversity. A crucial difficulty in estimating species richness from sample data obtained from sources such as inventory...

Science Teachers' Representations of Classroom Practice in the Process of Formative Assessment Design

ERIC Educational Resources Information Center

Heredia, Sara C.; Furtak, Erin Marie; Morrison, Deb; Renga, Ian Parker

2016-01-01

Formative assessment has been recognized as an essential element of effective classroom practice; as a result, teachers are increasingly required to create formative assessments for their classrooms. This study examines data drawn from a long-term, site-based professional development program that supported a department of biology teachers in the…

Circadian Modulation of Short-Term Memory in "Drosophila"

ERIC Educational Resources Information Center

Lyons, Lisa C.; Roman, Gregg

2009-01-01

Endogenous biological clocks are widespread regulators of behavior and physiology, allowing for a more efficient allocation of efforts and resources over the course of a day. The extent that different processes are regulated by circadian oscillators, however, is not fully understood. We investigated the role of the circadian clock on short-term…

A Microarray Tool Provides Pathway and GO Term Analysis.

PubMed

Koch, Martin; Royer, Hans-Dieter; Wiese, Michael

2011-12-01

Analysis of gene expression profiles is no longer exclusively a task for bioinformatic experts. However, gaining statistically significant results is challenging and requires both biological knowledge and computational know-how. Here we present a novel, user-friendly microarray reporting tool called maRt. The software provides access to bioinformatic resources, like gene ontology terms and biological pathways by use of the DAVID and the BioMart web-service. Results are summarized in structured HTML reports, each presenting a different layer of information. In these report, contents of diverse sources are integrated and interlinked. To speed up processing, maRt takes advantage of the multi-core technology of modern desktop computers by using parallel processing. Since the software is built upon a RCP infrastructure it might be an outset for developers aiming to integrate novel R based applications. Installer, documentation and various kinds of tutorials are available under LGPL license at the website of our institute http://www.pharma.uni-bonn.de/www/mart. This software is free for academic use. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

PubMed Central

Caetano-Anollés, Gustavo; Caetano-Anollés, Derek

2015-01-01

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules. PMID:27096056

The Ontology for Biomedical Investigations.

PubMed

Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

2016-01-01

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

The Ontology for Biomedical Investigations

PubMed Central

Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; Chibucos, Marcus C.; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A.; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L.; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A.; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H.; Schober, Daniel; Smith, Barry; Soldatova, Larisa N.; Stoeckert, Christian J.; Taylor, Chris F.; Torniai, Carlo; Turner, Jessica A.; Vita, Randi; Whetzel, Patricia L.; Zheng, Jie

2016-01-01

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl. PMID:27128319

Biological effects of the electrostatic field: red blood cell-related alterations of oxidative processes in blood

NASA Astrophysics Data System (ADS)

Harutyunyan, Hayk A.; Sahakyan, Gohar V.

2016-01-01

The aim of this study was to determine activities of pro-/antioxidant enzymes, reactive oxygen species (ROS) content, and oxidative modification of proteins and lipids in red blood cells (RBCs) and blood plasma of rats exposed to electrostatic field (200 kV/m) during the short (1 h) and the long periods (6 day, 6 h daily). Short-term exposure was characterized by the increase of oxidatively damaged proteins in blood of rats. This was strongly expressed in RBC membranes. After long-term action, RBC content in peripheral blood was higher than in control ( P < 0.01) and the attenuation of prooxidant processes was shown.

Limits on characteristics of invertebrate assemblages associated with streamflow patterns in the western United States

NASA Astrophysics Data System (ADS)

Konrad, C.; Brasher, A.; May, J.

2007-12-01

River restoration depends on re-establishment of the range of physical and biological processes that comprise the river ecosystem. Streamflow is the definitive physical processes for river ecosystems, so hydrologic alteration represents a potentially significant issue to be addressed by restoration efforts. Given adaptation of lotic species to naturally variable streamflow patterns over evolutionary time scales, however, lotic communities are resilient to at least some forms of hydrologic variability. As a result, river restoration may be successful despite limited but biologically insignificant hydrologic alteration. The responses of benthic invertebrate assemblages to variation in streamflow patterns across the western United States were investigated to identify biologically important forms and magnitudes of hydrologic variability. Biological responses to streamflow patterns were analyzed in terms of ceilings and floors on invertebrate assemblage diversity and structure using a non-parametric screening procedure and quantile regression. Variability at daily and monthly time scales was the most common streamflow pattern associated with broad metrics of invertebrate assemblages including abundance; richness and relative abundance of Ephemeroptera, Plecoptera, Trichoptera and non-insects; dominance; and diversity. Low flow magnitude and annual variability were associated with richness and trophic structure. The frequency, magnitude, and duration of high flows were associated with abundance and richness. Longer term streamflow metrics (calculated over at least 5 years) were more important than recent flows (30 and 100 days prior to invertebrate sampling). The results can be used as general guidance about when hydrologic alteration is likely to be an important factor and what streamflow patterns may need to be re-established for successful river restoration.

Evolutionary game theory for physical and biological scientists. II. Population dynamics equations can be associated with interpretations

PubMed Central

Liao, David; Tlsty, Thea D.

2014-01-01

The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely ‘empirical’ equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods for in vitro and in vivo experiments. PMID:25097752

Long-Term Phenological Shifts in Raptor Migration and Climate

PubMed Central

Jaffré, Mikaël; Beaugrand, Grégory; Goberville, Éric; Jiguet, Frédéric; Kjellén, Nils; Troost, Gerard; Dubois, Philippe J.; Leprêtre, Alain; Luczak, Christophe

2013-01-01

Climate change is having a discernible effect on many biological and ecological processes. Among observed changes, modifications in bird phenology have been widely documented. However, most studies have interpreted phenological shifts as gradual biological adjustments in response to the alteration of the thermal regime. Here we analysed a long-term dataset (1980-2010) of short-distance migratory raptors in five European regions. We revealed that the responses of these birds to climate-induced changes in autumn temperatures are abrupt and synchronous at a continental scale. We found that when the temperatures increased, birds delayed their mean passage date of autumn migration. Such delay, in addition to an earlier spring migration, suggests that a significant warming may induce an extension of the breeding-area residence time of migratory raptors, which may eventually lead to residency. PMID:24223888

Working and Learning in a Field Excursion.

PubMed

Hole, Torstein Nielsen

2018-06-01

This study aimed to discern sociocultural processes through which students learn in field excursions. To achieve this aim, short-term ethnographic techniques were employed to examine how undergraduate students work and enact knowledge (or knowing) during a specific field excursion in biology. The students participated in a working practice that employed research methods and came to engage with various biological phenomena over the course of their work. A three-level analysis of the students' experiences focused on three processes that emerged: participatory appropriation, guided participation, and apprenticeship. These processes derive from advances in practice-oriented theories of knowing. Through their work in the field, the students were able to enact science autonomously; they engaged with peers and teachers in specific ways and developed new understandings about research and epistemology founded on their experiences in the field. Further discussion about the use of "practice" and "work" as analytical concepts in science education is also included.

Dimension reduction for stochastic dynamical systems forced onto a manifold by large drift: a constructive approach with examples from theoretical biology

NASA Astrophysics Data System (ADS)

Parsons, Todd L.; Rogers, Tim

2017-10-01

Systems composed of large numbers of interacting agents often admit an effective coarse-grained description in terms of a multidimensional stochastic dynamical system, driven by small-amplitude intrinsic noise. In applications to biological, ecological, chemical and social dynamics it is common for these models to posses quantities that are approximately conserved on short timescales, in which case system trajectories are observed to remain close to some lower-dimensional subspace. Here, we derive explicit and general formulae for a reduced-dimension description of such processes that is exact in the limit of small noise and well-separated slow and fast dynamics. The Michaelis-Menten law of enzyme-catalysed reactions, and the link between the Lotka-Volterra and Wright-Fisher processes are explored as a simple worked examples. Extensions of the method are presented for infinite dimensional systems and processes coupled to non-Gaussian noise sources.

Integration of the Gene Ontology into an object-oriented architecture.

PubMed

Shegogue, Daniel; Zheng, W Jim

2005-05-10

To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes.

Integration of the Gene Ontology into an object-oriented architecture

PubMed Central

Shegogue, Daniel; Zheng, W Jim

2005-01-01

Background To standardize gene product descriptions, a formal vocabulary defined as the Gene Ontology (GO) has been developed. GO terms have been categorized into biological processes, molecular functions, and cellular components. However, there is no single representation that integrates all the terms into one cohesive model. Furthermore, GO definitions have little information explaining the underlying architecture that forms these terms, such as the dynamic and static events occurring in a process. In contrast, object-oriented models have been developed to show dynamic and static events. A portion of the TGF-beta signaling pathway, which is involved in numerous cellular events including cancer, differentiation and development, was used to demonstrate the feasibility of integrating the Gene Ontology into an object-oriented model. Results Using object-oriented models we have captured the static and dynamic events that occur during a representative GO process, "transforming growth factor-beta (TGF-beta) receptor complex assembly" (GO:0007181). Conclusion We demonstrate that the utility of GO terms can be enhanced by object-oriented technology, and that the GO terms can be integrated into an object-oriented model by serving as a basis for the generation of object functions and attributes. PMID:15885145

Wildfire Effects on In-stream Nutrient Processing and Hydrologic Transport

NASA Astrophysics Data System (ADS)

Rhea, A.; Covino, T. P.; Rhoades, C.; Fegel, T.

2017-12-01

In many forests throughout the Western U.S., drought, climate change, and growing fuel loads are contributing to increased fire frequency and severity. Wildfires can influence watershed nutrient retention as they fundamentally alter the biological composition and physical structure in upland landscapes, riparian corridors, and stream channels. While numerous studies have documented substantial short-term increases in stream nutrient concentrations and export (particularly reactive nitrogen, N) following forest fires, the long-term implications for watershed nutrient cycling remain unclear. For example, recent work indicates that nitrate concentrations and export can remain elevated for a decade or more following wildfire, yet the controls on these processes are unknown. In this research, we use empirical observations from nutrient tracer injections, nutrient diffusing substrates, and continuous water quality monitoring to isolate biological and physical controls on nutrient export across a burn-severity gradient. Tracer results demonstrate substantial stream-groundwater exchange, but little biological nutrient uptake in burned streams. This in part explains patterns of elevated nutrient export. Paired nutrient diffusing substrate experiments allow us to further investigate shifts in N, phosphorus, and carbon limitation that may suppress post-fire stream nutrient uptake. By isolating the mechanisms that reduce the capacity of fire-affected streams to retain and transform nutrient inputs, we can better predict dynamics in post-fire water quality and help prioritize upland and riparian restoration.

Silent cries, dancing tears: the metapsychology of art revisited/revised.

PubMed

Aragno, Anna

2011-04-01

Against the backdrop of a broad survey of the literature on applied psychoanalysis, a number of concepts underpinning the metapsychology of art are revisited and revised: sublimation; interrelationships between primary and secondary processes; symbolization; "fantasy"; and "cathexis." Concepts embedded in dichotomous or drive/energic contexts are examined and reformulated in terms of a continuum of semiotic processes. Freudian dream structure is viewed as a biological/natural template for nonrepressive artistic forms of sublimation. The synthesis presented proposes a model of continuous rather than discontinuous processes, in a nonenergic, biosemiotic metatheoretical framework.

A data science approach to candidate gene selection of pain regarded as a process of learning and neural plasticity.

PubMed

Ultsch, Alfred; Kringel, Dario; Kalso, Eija; Mogil, Jeffrey S; Lötsch, Jörn

2016-12-01

The increasing availability of "big data" enables novel research approaches to chronic pain while also requiring novel techniques for data mining and knowledge discovery. We used machine learning to combine the knowledge about n = 535 genes identified empirically as relevant to pain with the knowledge about the functions of thousands of genes. Starting from an accepted description of chronic pain as displaying systemic features described by the terms "learning" and "neuronal plasticity," a functional genomics analysis proposed that among the functions of the 535 "pain genes," the biological processes "learning or memory" (P = 8.6 × 10) and "nervous system development" (P = 2.4 × 10) are statistically significantly overrepresented as compared with the annotations to these processes expected by chance. After establishing that the hypothesized biological processes were among important functional genomics features of pain, a subset of n = 34 pain genes were found to be annotated with both Gene Ontology terms. Published empirical evidence supporting their involvement in chronic pain was identified for almost all these genes, including 1 gene identified in March 2016 as being involved in pain. By contrast, such evidence was virtually absent in a randomly selected set of 34 other human genes. Hence, the present computational functional genomics-based method can be used for candidate gene selection, providing an alternative to established methods.

[Side effects of biologic therapies in psoriasis].

PubMed

Altenburg, A; Augustin, M; Zouboulis, C C

2018-04-01

The introduction of biologics has revolutionized the treatment of moderate to severe plaque psoriasis. Due to the continuous expansion of biological therapies for psoriasis, it is particularly important to acknowledge efficacy and safety of the compounds not only in clinical trials but also in long-term registry-based observational studies. Typical side effects and significant risks of antipsoriatic biologic therapies considering psoriatic control groups are presented. A selective literature search was conducted in PubMed and long-term safety studies of the psoriasis registries PsoBest, PSOLAR and BADBIR were evaluated. To assess the long-term safety of biologics, the evaluation of the course of large patient cohorts in long-term registries is of particular medical importance. Newer biologic drugs seem to exhibit a better safety profile than older ones.

Pyramidal neurovision architecture for vision machines

NASA Astrophysics Data System (ADS)

Gupta, Madan M.; Knopf, George K.

1993-08-01

The vision system employed by an intelligent robot must be active; active in the sense that it must be capable of selectively acquiring the minimal amount of relevant information for a given task. An efficient active vision system architecture that is based loosely upon the parallel-hierarchical (pyramidal) structure of the biological visual pathway is presented in this paper. Although the computational architecture of the proposed pyramidal neuro-vision system is far less sophisticated than the architecture of the biological visual pathway, it does retain some essential features such as the converging multilayered structure of its biological counterpart. In terms of visual information processing, the neuro-vision system is constructed from a hierarchy of several interactive computational levels, whereupon each level contains one or more nonlinear parallel processors. Computationally efficient vision machines can be developed by utilizing both the parallel and serial information processing techniques within the pyramidal computing architecture. A computer simulation of a pyramidal vision system for active scene surveillance is presented.

[Hygiene and security management in medical biology laboratory].

PubMed

Vinner, E; Odou, M F; Fovet, B; Ghnassia, J C

2013-06-01

Risk management in Medical Biology Laboratory (MBL) which includes hygiene and waste management, is an integrated process to the whole MBL organisation. It is composed of three stages: risks factors identification, grading and prioritization, and their evaluation in the system. From the legislation and NF EN ISO 15189 standard's requirements viewpoint, prevention and protection actions to implement are described, at premises level, but also at work station environment's one (human resources and equipments) towards biological, chemical, linked to gas, to ionizing or non ionizing radiations and fire riks, in order not to compromise patients safety, employees safety, and quality results. Then, although NF EN 15189 standard only enacts requirements in terms of prevention, curative actions after established blood or chemical exposure accident are defined.

Stable-isotope fingerprints of biological agents as forensic tools.

PubMed

Horita, Juske; Vass, Arpad A

2003-01-01

Naturally occurring stable isotopes of light elements in chemical and biological agents may possess unique "stable-isotope fingerprints" depending on their sources and manufacturing processes. To test this hypothesis, two strains of bacteria (Bacillus globigii and Erwinia agglomerans) were grown under controlled laboratory conditions. We observed that cultured bacteria cells faithfully inherited the isotopic composition (hydrogen, carbon, and nitrogen) of media waters and substrates in predictable manners in terms of bacterial metabolism and that even bacterial cells of the same strain, which grew in media water and substrates of different isotopic compositions, have readily distinguishable isotopic signatures. These "stable-isotopic fingerprints" of chemical and biological agents can be used as forensic tools in the event of biochemical terrorist attacks.

Biologic agents for IBD: practical insights.

PubMed

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

2015-09-01

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

Synthetic biology and the technicity of biofuels.

PubMed

Mackenzie, Adrian

2013-06-01

The principal existing real-world application of synthetic biology is biofuels. Several 'next generation biofuel' companies-Synthetic Genomics, Amyris and Joule Unlimited Technologies-claim to be using synthetic biology to make biofuels. The irony of this is that highly advanced science and engineering serves the very mundane and familiar realm of transport. Despite their rather prosaic nature, biofuels could offer an interesting way to highlight the novelty of synthetic biology from several angles at once. Drawing on the French philosopher of technology and biology Gilbert Simondon, we can understand biofuels as technical objects whose genesis involves processes of concretisation that negotiate between heterogeneous geographical, biological, technical, scientific and commercial realities. Simondon's notion of technicity, the degree of concretisation of a technical object, usefully conceptualises this relationality. Viewed in terms of technicity, we might understand better how technical entities, elements, and ensembles are coming into being in the name of synthetic biology. The broader argument here is that when we seek to identify the newness of disciplines, their newness might be less epistemic and more logistic. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Synthetic Biology and Personalized Medicine

PubMed Central

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

Physical/chemical closed-loop water-recycling for long-duration missions

NASA Technical Reports Server (NTRS)

Herrmann, Cal C.; Wydeven, Ted

1990-01-01

Water needs, water sources, and means for recycling water are examined in terms appropriate to the water quality requirements of a small crew and spacecraft intended for long duration exploration missions. Inorganic, organic, and biological hazards are estimated for waste water sources. Sensitivities to these hazards for human uses are estimated. The water recycling processes considered are humidity condensation, carbon dioxide reduction, waste oxidation, distillation, reverse osmosis, pervaporation, electrodialysis, ion exchange, carbon sorption, and electrochemical oxidation. Limitations and applications of these processes are evaluated in terms of water quality objectives. Computerized simulation of some of these chemical processes is examined. Recommendations are made for development of new water recycling technology and improvement of existing technology for near term application to life support systems for humans in space. The technological developments are equally applicable to water needs on earth, in regions where extensive water ecycling is needed or where advanced water treatment is essential to meet EPA health standards.

Textpresso: An Ontology-Based Information Retrieval and Extraction System for Biological Literature

PubMed Central

Müller, Hans-Michael; Kenny, Eimear E

2004-01-01

We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org. PMID:15383839

Recent biological trends in management of fracture non-union

PubMed Central

Emara, Khaled M; Diab, Ramy Ahmed; Emara, Ahmed Khaled

2015-01-01

Bone regeneration is a complex, well-orchestrated physiological process of bone formation, which can be seen during normal fracture healing, and is involved in continuous remodelling throughout adult life. Currently, there is a plethora of different strategies to augment the impaired or “insufficient” bone-regeneration process, including the “gold standard” autologous bone graft, free fibula vascularised graft, allograft implantation, and use of growth factors, osteoconductive scaffolds, osteoprogenitor cells and distraction osteogenesis. Improved “local” strategies in terms of tissue engineering and gene therapy, or even “systemic” enhancement of bone repair, are under intense investigation, in an effort to overcome the limitations of the current methods, to produce bone-graft substitutes with biomechanical properties that are as identical to normal bone as possible, to accelerate the overall regeneration process, or even to address systemic conditions, such as skeletal disorders and osteoporosis. An improved understanding of the molecular and cellular events that occur during bone repair and remodeling has led to the development of biologic agents that can augment the biological microenvironment and enhance bone repair. Orthobiologics, including stem cells, osteoinductive growth factors, osteoconductive matrices, and anabolic agents, are available clinically for accelerating fracture repair and treatment of compromised bone repair situations like delayed unions and nonunions. A lack of standardized outcome measures for comparison of biologic agents in clinical fracture repair trials, frequent off-label use, and a limited understanding of the biological activity of these agents at the bone repair site have limited their efficacy in clinical applications. PMID:26396938

Using the underlying biological organization of the Mycobacterium tuberculosis functional network for protein function prediction.

PubMed

Mazandu, Gaston K; Mulder, Nicola J

2012-07-01

Despite ever-increasing amounts of sequence and functional genomics data, there is still a deficiency of functional annotation for many newly sequenced proteins. For Mycobacterium tuberculosis (MTB), more than half of its genome is still uncharacterized, which hampers the search for new drug targets within the bacterial pathogen and limits our understanding of its pathogenicity. As for many other genomes, the annotations of proteins in the MTB proteome were generally inferred from sequence homology, which is effective but its applicability has limitations. We have carried out large-scale biological data integration to produce an MTB protein functional interaction network. Protein functional relationships were extracted from the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and additional functional interactions from microarray, sequence and protein signature data. The confidence level of protein relationships in the additional functional interaction data was evaluated using a dynamic data-driven scoring system. This functional network has been used to predict functions of uncharacterized proteins using Gene Ontology (GO) terms, and the semantic similarity between these terms measured using a state-of-the-art GO similarity metric. To achieve better trade-off between improvement of quality, genomic coverage and scalability, this prediction is done by observing the key principles driving the biological organization of the functional network. This study yields a new functionally characterized MTB strain CDC1551 proteome, consisting of 3804 and 3698 proteins out of 4195 with annotations in terms of the biological process and molecular function ontologies, respectively. These data can contribute to research into the Development of effective anti-tubercular drugs with novel biological mechanisms of action. Copyright © 2011 Elsevier B.V. All rights reserved.

RAMONA: a Web application for gene set analysis on multilevel omics data.

PubMed

Sass, Steffen; Buettner, Florian; Mueller, Nikola S; Theis, Fabian J

2015-01-01

Decreasing costs of modern high-throughput experiments allow for the simultaneous analysis of altered gene activity on various molecular levels. However, these multi-omics approaches lead to a large amount of data, which is hard to interpret for a non-bioinformatician. Here, we present the remotely accessible multilevel ontology analysis (RAMONA). It offers an easy-to-use interface for the simultaneous gene set analysis of combined omics datasets and is an extension of the previously introduced MONA approach. RAMONA is based on a Bayesian enrichment method for the inference of overrepresented biological processes among given gene sets. Overrepresentation is quantified by interpretable term probabilities. It is able to handle data from various molecular levels, while in parallel coping with redundancies arising from gene set overlaps and related multiple testing problems. The comprehensive output of RAMONA is easy to interpret and thus allows for functional insight into the affected biological processes. With RAMONA, we provide an efficient implementation of the Bayesian inference problem such that ontologies consisting of thousands of terms can be processed in the order of seconds. RAMONA is implemented as ASP.NET Web application and publicly available at http://icb.helmholtz-muenchen.de/ramona. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

An Illness of Power: Gender and the Social Causes of Depression.

PubMed

Neitzke, Alex B

2016-03-01

There is considerable discourse surrounding the disproportionate diagnosis of women with depression as compared to men, often times cited at a rate around 2:1. While this disparity clearly draws attention to gender, a focus on gender tends to fall away in the study and treatment of depression in neuroscience and psychiatry, which largely understand its workings in mechanistic terms of brain chemistry and neurological processes. I first consider how this brain-centered biological model for depression came about. I then argue that the authoritative scientific models for disorder have serious consequences for those diagnosed. Finally, I argue that mechanistic biological models of depression have the effect of silencing women and marginalizing or preventing the examination of social-structural causes of depression, like gender oppression, and therein contribute to the ideological reproduction of oppressive social relations. I argue that depression is best understood in terms of systems of power, including gender, and where a given individual is situated within such social relations. The result is a model of depression that accounts for the influence of biological, psychological, and social factors.

Bioavailability and biotransformation of the mutagenic component of particulate emissions present in motor exhaust samples.

PubMed Central

Vostal, J J

1983-01-01

The pharmacokinetic concepts of bioavailability and biotransformation are introduced into the assessment of public health risk from experimental data concerning the emissions of potentially mutagenic and carcinogenic substances from motor vehicles. The inappropriateness of an automatic application in the risk assessment process of analytical or experimental results, obtained with extracts and procedures incompatible with the biological environment, is illustrated on the discrepancy between short-term laboratory tests predictions that wider use of diesel engines on our roads will increase the risk of respiratory cancer and the widely negative epidemiological evidence. Mutagenic activity of diesel particulates was minimal or negative when tested in extracts obtained with biological fluids, was substantially dependent on the presence of nitroreductase in the microbial tester strain, and disappeared completely 48 hr after the diesel particles had been phagocytized by alveolar macrophages. Similarly, long-term animal inhalation exposures to high concentrations of diesel particles did not induce the activity of hydrocarbon metabolizing enzymes or specific adverse immune response unless organic solvent extracts of diesel particles were administered intratracheally or parenterally in doses that highly exceed the predicted levels of public exposure even by the year 2000. Furthermore, the suspected cancer producing effects of inhaled diesel particles have thus far not been verified by experimental animal models or available long-term epidemiological observations. It is concluded that unless the biological accessibility of the active component on the pollutant as well as its biotransformation and clearance by natural defense mechanisms are considered, lung cancer risk assessment based solely on laboratory microbial tests will remain an arbitrary and unrealistic process and will not provide meaningful information on the potential health hazard of a pollutant. PMID:6186478

Epigenetics: a lasting impression?

PubMed

Biddie, Simon C; Lightman, Stafford L

2011-02-01

Epigenetics is the term that has been classically used to describe inheritable nongenetic factors that regulate genes. Although these factors were originally thought to act in a long time domain only, it is now clear that they can also be highly dynamic, changing over minutes. Transcription factors, including the glucocorticoid, oestrogen and androgen receptors, interact with these epigenetic mechanisms in a very dynamic manner to modify transcription of genes and consequently contribute to physiological processes, health and disease. Modern usage of the term epigenetics encompasses both longer-term and transient changes and is relevant to multiple biological systems. © 2011 The Authors. Journal of Neuroendocrinology © 2011 Blackwell Publishing Ltd.

Population Dynamics of Genetic Regulatory Networks

NASA Astrophysics Data System (ADS)

Braun, Erez

2005-03-01

Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

Non-invasive imaging methods applied to neo- and paleontological cephalopod research

NASA Astrophysics Data System (ADS)

Hoffmann, R.; Schultz, J. A.; Schellhorn, R.; Rybacki, E.; Keupp, H.; Gerden, S. R.; Lemanis, R.; Zachow, S.

2013-11-01

Several non-invasive methods are common practice in natural sciences today. Here we present how they can be applied and contribute to current topics in cephalopod (paleo-) biology. Different methods will be compared in terms of time necessary to acquire the data, amount of data, accuracy/resolution, minimum-maximum size of objects that can be studied, of the degree of post-processing needed and availability. Main application of the methods is seen in morphometry and volumetry of cephalopod shells in order to improve our understanding of diversity and disparity, functional morphology and biology of extinct and extant cephalopods.

Releasing biocontrol agents: Risk assessment and overdue reform

Treesearch

Bob Peterson; Sharlene Sing

2007-01-01

Although the need for universally instituting formal risk assessment (RA) in the screening and approval process for non-native biological control (BC) agent releases has been widely acknowledged for the past several years, little seems to have been accomplished in terms of codifying this practice within a regulatory framework. Given the low success rate of classical BC...

Long-term fragmentation effects on the distribution and dynamics of canopy gaps in a tropical montane forest

Treesearch

Nicholas R. Vaughn; Gregory P. Asner; Christian P. Giardina

2015-01-01

Fragmentation alters forest canopy structure through various mechanisms, which in turn drive subsequent changes to biogeochemical processes and biological diversity. Using repeated airborne LiDAR (Light Detection and Ranging) mappings, we investigated the size distribution and dynamics of forest canopy gaps across a topical montane forest landscape in Hawaii naturally...

Advanced Functional Nanomaterials for Biological Processes

DTIC Science & Technology

2014-01-01

of this project, we performed research in the area of tissue engineering/bone regeneration and cancer nanotechnology . The primary focus of the tissue...photoacoustic approach. 15. SUBJECT TERMS: Tissue Engineering, Cancer detection, Cancer destruction, Nanoparticles 16. SECURITY CLASSIFICATION OF: 17...Nanocomposite Materials with Drug Delivery Capabilities for Tissue Engineering and Bone Regeneration; and B. Multifunctional Nanoparticles for Cancer Early

Multi-Stage Mental Process for Economic Choice in Capuchins

ERIC Educational Resources Information Center

Padoa-Schioppa, Camillo; Jandolo, Lucia; Visalberghi, Elisabetta

2006-01-01

We studied economic choice behavior in capuchin monkeys by offering them to choose between two different foods available in variable amounts. When monkeys selected between familiar foods, their choice patterns were well-described in terms of relative value of the two foods. A leading view in economics and biology is that such behavior results from…

Mind-body interactions in pain: the neurophysiology of anxious and catastrophic pain-related thoughts.

PubMed

Campbell, Claudia M; Edwards, Robert R

2009-03-01

The well-accepted biopsychosocial model proposes that the experience of pain and responses to it result from a complex interaction of biological, psychological, and social factors. However, the separation of these constructs is substantially artificial, and we presume that psychological processes have biological effects, that biological processes affect an individual's psychosocial environment, and so on. Considerable research has demonstrated that pain-coping strategies influence perceived pain intensity and physical functioning, and individual differences in styles of pain coping even shape the persistence of long-term pain complaints in some populations. A good deal of this coping research has focused on catastrophizing, which is a generally maladaptive cognitive and emotional mental set that involves feelings of helplessness when in pain, rumination about pain symptoms, and magnification of pain-related complaints. Collectively, catastrophizing has been consistently associated with heightened experiences of pain across a variety of samples. Although catastrophic thinking regarding pain-related symptoms is often classified under the "psychologic" category within the broader biopsychosocial model, we propose that catastrophizing exerts biologic effects that may account for some of its negative consequences. In general, the cognitive and affective processes captured within the construct of catastrophizing may exert effects on the neuromuscular, cardiovascular, immune, and neuroendocrine systems, and on the activity in the pain neuromatrix within the brain. The interface between pain-related neurobiology and processes such as pain-related catastrophizing represents an important avenue for future pain research.

Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research.

PubMed

An, Gary C

2010-01-01

The greatest challenge facing the biomedical research community is the effective translation of basic mechanistic knowledge into clinically effective therapeutics. This challenge is most evident in attempts to understand and modulate "systems" processes/disorders, such as sepsis, cancer, and wound healing. Formulating an investigatory strategy for these issues requires the recognition that these are dynamic processes. Representation of the dynamic behavior of biological systems can aid in the investigation of complex pathophysiological processes by augmenting existing discovery procedures by integrating disparate information sources and knowledge. This approach is termed Translational Systems Biology. Focusing on the development of computational models capturing the behavior of mechanistic hypotheses provides a tool that bridges gaps in the understanding of a disease process by visualizing "thought experiments" to fill those gaps. Agent-based modeling is a computational method particularly well suited to the translation of mechanistic knowledge into a computational framework. Utilizing agent-based models as a means of dynamic hypothesis representation will be a vital means of describing, communicating, and integrating community-wide knowledge. The transparent representation of hypotheses in this dynamic fashion can form the basis of "knowledge ecologies," where selection between competing hypotheses will apply an evolutionary paradigm to the development of community knowledge.

Comprehensive proteomic profiling of adult Angiostrongylus costaricensis, a human parasitic nematode.

PubMed

Rebello, Karina M; Barros, Juliana S L; Mota, Ester M; Carvalho, Paulo C; Perales, Jonas; Lenzi, Henrique L; Neves-Ferreira, Ana G C

2011-08-24

Angiostrongylus costaricensis is a nematode helminth that causes an intestinal acute inflammatory process known as abdominal angiostrongyliasis, which is a poorly understood human disease occurring in Latin America. Our aim was to study the proteomic profiles of adult parasites focusing on immunogenic proteins. Total cellular extracts from both genders showed similar 2-DE profiles, with 60% of all protein spots focused between pH 5-7 and presenting molecular masses from 20.1 to 66 kDa. A total of 53 different dominant proteins were identified in our dataset and were mainly associated with the following over-represented Gene Ontology Biological Process terms: "macromolecule metabolic process", "developmental process", "response to stress", and "biological regulation". Female and male immunoblots showed similar patterns of reactive proteins. Immunoreactive spots identified by MALDI-PSD were found to represent heat shock proteins, a putative abnormal DAuer Formation family member, and galectins. To date, very few biochemical analyses have focused on the nematode Angiostrongylus costaricensis. As such, our results contribute to a better understanding of its biology and the mechanisms underlying the host-parasite relationship associated with this species. Moreover, our findings represent a first step in the search for candidate proteins for diagnostic assays and the treatment of this parasitic infection. Copyright © 2011 Elsevier B.V. All rights reserved.

Immediate Early Genes Anchor a Biological Pathway of Proteins Required for Memory Formation, Long-Term Depression and Risk for Schizophrenia

PubMed Central

Marballi, Ketan K.; Gallitano, Amelia L.

2018-01-01

While the causes of myriad medical and infectious illnesses have been identified, the etiologies of neuropsychiatric illnesses remain elusive. This is due to two major obstacles. First, the risk for neuropsychiatric disorders, such as schizophrenia, is determined by both genetic and environmental factors. Second, numerous genes influence susceptibility for these illnesses. Genome-wide association studies have identified at least 108 genomic loci for schizophrenia, and more are expected to be published shortly. In addition, numerous biological processes contribute to the neuropathology underlying schizophrenia. These include immune dysfunction, synaptic and myelination deficits, vascular abnormalities, growth factor disruption, and N-methyl-D-aspartate receptor (NMDAR) hypofunction. However, the field of psychiatric genetics lacks a unifying model to explain how environment may interact with numerous genes to influence these various biological processes and cause schizophrenia. Here we describe a biological cascade of proteins that are activated in response to environmental stimuli such as stress, a schizophrenia risk factor. The central proteins in this pathway are critical mediators of memory formation and a particular form of hippocampal synaptic plasticity, long-term depression (LTD). Each of these proteins is also implicated in schizophrenia risk. In fact, the pathway includes four genes that map to the 108 loci associated with schizophrenia: GRIN2A, nuclear factor of activated T-cells (NFATc3), early growth response 1 (EGR1) and NGFI-A Binding Protein 2 (NAB2); each of which contains the “Index single nucleotide polymorphism (SNP)” (most SNP) at its respective locus. Environmental stimuli activate this biological pathway in neurons, resulting in induction of EGR immediate early genes: EGR1, EGR3 and NAB2. We hypothesize that dysfunction in any of the genes in this pathway disrupts the normal activation of Egrs in response to stress. This may result in insufficient electrophysiologic, immunologic, and neuroprotective, processes that these genes normally mediate. Continued adverse environmental experiences, over time, may thereby result in neuropathology that gives rise to the symptoms of schizophrenia. By combining multiple genes associated with schizophrenia susceptibility, in a functional cascade triggered by neuronal activity, the proposed biological pathway provides an explanation for both the polygenic and environmental influences that determine the complex etiology of this mental illness. PMID:29520222

Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets.

PubMed

Salem, Saeed; Ozcaglar, Cagri

2014-01-01

Advances in genomic technologies have enabled the accumulation of vast amount of genomic data, including gene expression data for multiple species under various biological and environmental conditions. Integration of these gene expression datasets is a promising strategy to alleviate the challenges of protein functional annotation and biological module discovery based on a single gene expression data, which suffers from spurious coexpression. We propose a joint mining algorithm that constructs a weighted hybrid similarity graph whose nodes are the coexpression links. The weight of an edge between two coexpression links in this hybrid graph is a linear combination of the topological similarities and co-appearance similarities of the corresponding two coexpression links. Clustering the weighted hybrid similarity graph yields recurrent coexpression link clusters (modules). Experimental results on Human gene expression datasets show that the reported modules are functionally homogeneous as evident by their enrichment with biological process GO terms and KEGG pathways.

Tools for visually exploring biological networks.

PubMed

Suderman, Matthew; Hallett, Michael

2007-10-15

Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond 'static' representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. In view of the first goal, we provide in the Supplementary Material a systematic comparison of more than 35 existing tools in terms of over 25 different features. Supplementary data are available at Bioinformatics online.

Biological embedding of perinatal social relationships in infant stress reactivity.

PubMed

Thomas, Jenna C; Letourneau, Nicole; Bryce, Crystal I; Campbell, Tavis S; Giesbrecht, Gerald F

2017-05-01

Whereas significant advances have been made in understanding how exposure to early adversity "gets under the skin" of children to result in long term changes in developmental outcomes, the processes by which positive social relationships become biologically embedded remain poorly understood. The aim of this study was to understand the pathways by which maternal and infant social environments become biologically embedded in infant cortisol reactivity. Two hundred seventy-two pregnant women and their infants were prospectively assessed during pregnancy and at 6 months postpartum. In serial mediation analyses, higher perceived social support from partners during pregnancy was associated with lower infant cortisol reactivity or larger decreases in cortisol in response to a stressor at 6 months of age via lower self-reported prenatal maternal depression and higher mother-infant interaction quality. The findings add to our understanding of how perinatal social relationships become biologically embedded in child development. © 2017 Wiley Periodicals, Inc.

Drosophila melanogaster and the future of 'evo-devo' biology in space. Challenges and problems in the path of an eventual colonization project outside the earth.

PubMed

Marco, Roberto; Husson, David; Herranz, Raul; Mateos, Jesús; Medina, F Javier

2003-01-01

Space exploration, especially its future phase involving the International Space Station (ISS) makes possible the study of the effects on living systems of long-term expositions to such a strange environment. This phase is being initiated when Biological Sciences are crossing a no-return line into a new territory where the connection between phenotype and genotype may be finally made. We briefly review the paradoxical results obtained in Space experiments performed during the last third of the XX Century. They reveal that simple unicellular systems sense the absence of gravity changing their cytoskeletal organization and the signal transduction pathways, while animal development proceeds unaltered in these conditions, in spite of the fact that these processes are heavily involved in embryogenesis. Longer-term experiments possible in the ISS may solve this apparent contradiction. On the other hand, the current constraints on the scientific use of the ISS makes necessary the development of new hardware and the modification of current techniques to start taking advantage of this extraordinary technological facility. We discuss our advances in this direction using one of the current key biological model systems, Drosophila melanogaster. In addition, the future phase of Space exploration, possibly leading to the exploration and, may be, the colonization of another planet, will provide the means of performing interesting evolutionary experiments, studying how the terrestrial biological systems will change in their long-term adaptation to new, very different environments. In this way, Biological Research in Space may contribute to the advancement of the new Biology, in particular to the branch known as "Evo-Devo". On the other hand, as much as the Space Adventure will continue involving human beings as the main actors in the play, long-term multi-generation experiments using a fast reproducing species, such as Drosophila melanogaster, capable of producing more than 300 generations in 15 years, the useful life foreseen for ISS, will be important. Among other useful information, they will help in detecting the possible changes that a biological species may undergo in such an environment, preventing the uncontrolled occurrence of irreversible deleterious effects with catastrophic consequences on the living beings participating in this endeavour.

Empirical evaluation of the conceptual model underpinning a regional aquatic long-term monitoring program using causal modelling

USGS Publications Warehouse

Irvine, Kathryn M.; Miller, Scott; Al-Chokhachy, Robert K.; Archer, Erik; Roper, Brett B.; Kershner, Jeffrey L.

2015-01-01

Conceptual models are an integral facet of long-term monitoring programs. Proposed linkages between drivers, stressors, and ecological indicators are identified within the conceptual model of most mandated programs. We empirically evaluate a conceptual model developed for a regional aquatic and riparian monitoring program using causal models (i.e., Bayesian path analysis). We assess whether data gathered for regional status and trend estimation can also provide insights on why a stream may deviate from reference conditions. We target the hypothesized causal pathways for how anthropogenic drivers of road density, percent grazing, and percent forest within a catchment affect instream biological condition. We found instream temperature and fine sediments in arid sites and only fine sediments in mesic sites accounted for a significant portion of the maximum possible variation explainable in biological condition among managed sites. However, the biological significance of the direct effects of anthropogenic drivers on instream temperature and fine sediments were minimal or not detected. Consequently, there was weak to no biological support for causal pathways related to anthropogenic drivers’ impact on biological condition. With weak biological and statistical effect sizes, ignoring environmental contextual variables and covariates that explain natural heterogeneity would have resulted in no evidence of human impacts on biological integrity in some instances. For programs targeting the effects of anthropogenic activities, it is imperative to identify both land use practices and mechanisms that have led to degraded conditions (i.e., moving beyond simple status and trend estimation). Our empirical evaluation of the conceptual model underpinning the long-term monitoring program provided an opportunity for learning and, consequently, we discuss survey design elements that require modification to achieve question driven monitoring, a necessary step in the practice of adaptive monitoring. We suspect our situation is not unique and many programs may suffer from the same inferential disconnect. Commonly, the survey design is optimized for robust estimates of regional status and trend detection and not necessarily to provide statistical inferences on the causal mechanisms outlined in the conceptual model, even though these relationships are typically used to justify and promote the long-term monitoring of a chosen ecological indicator. Our application demonstrates a process for empirical evaluation of conceptual models and exemplifies the need for such interim assessments in order for programs to evolve and persist.

Gene Ontology Consortium: going forward.

PubMed

2015-01-01

The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Dynamics of water in strawberry and red onion as studied by dielectric spectroscopy

NASA Astrophysics Data System (ADS)

Jansson, H.; Huldt, C.; Bergman, R.; Swenson, J.

2005-01-01

We have investigated the microscopic dynamics of strawberry and red onion by means of broadband dielectric spectroscopy. In contrast to most of the previous experiments on carbohydrate-rich biological materials, which have mainly considered the more global dynamics of the “biological matrix,” we are here focusing on the microscopic dynamics of mainly the associated water. The results for both strawberry and red onion show that the imaginary part of the permittivity contains one conductivity term and a clear dielectric loss peak, which was found to be similar to the strongest relaxation process of water in carbohydrate solutions. The temperature dependence of the relaxation process was analyzed for different water content. The relaxation process slows down, and its temperature dependence becomes more non-Arrhenius, with decreasing water content. The reason for this is most likely that, on average, the water molecules interact more strongly with carbohydrates and other biological materials at low water content, and the dynamical properties of this biological matrix changes substantially with increasing temperature (from an almost rigid matrix where the water is basically unable to perform long-range diffusion due to confinement effects, to a dynamic matrix with no static confinement effects), which also changes (i.e., reduces) the activation energy of the relaxation process with increasing temperature (i.e., causes a non-Arrhenius temperature dependence). This further changes the conductivity from mainly polarization effects at low temperatures, due to hindered ionic motions, to long-range diffusivity at T>250K . Thus, around this temperature ions in the carbohydrate solution no longer get stuck in confined cavities, since the motion of the biological matrix “opens up” the cavities and the ions are then able to perform long-range migration.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Štys, Dalibor; Urban, Jan; Vaněk, Jan; Císař, Petr

2011-06-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space. This space is reflected as colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them.

Analysis of biological time-lapse microscopic experiment from the point of view of the information theory.

PubMed

Stys, Dalibor; Urban, Jan; Vanek, Jan; Císar, Petr

2010-07-01

We report objective analysis of information in the microscopic image of the cell monolayer. The process of transfer of information about the cell by the microscope is analyzed in terms of the classical Shannon information transfer scheme. The information source is the biological object, the information transfer channel is the whole microscope including the camera chip. The destination is the model of biological system. The information contribution is analyzed as information carried by a point to overall information in the image. Subsequently we obtain information reflection of the biological object. This is transformed in the biological model which, in information terminology, is the destination. This, we propose, should be constructed as state transitions in individual cells modulated by information bonds between the cells. We show examples of detected cell states in multidimensional state space reflected in space an colour channel intensity phenomenological state space. We have also observed information bonds and show examples of them. Copyright 2010 Elsevier Ltd. All rights reserved.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

Removal of fluorescent dissolved organic matter in biologically treated textile effluents by NDMP anion exchange process: efficiency and mechanism.

PubMed

Li, Wen-Tao; Xu, Zi-Xiao; Shuang, Chen-Dong; Zhou, Qing; Li, Hai-Bo; Li, Ai-Min

2016-03-01

The efficiency and mechanism of anion exchange resin Nanda Magnetic Polymer (NDMP) for removal of fluorescent dissolved organic matter in biologically treated textile effluents were studied. The bench-scale experiments showed that as well as activated carbon, anion exchange resin could efficiently remove both aniline-like and humic-like fluorescent components, which can be up to 40 % of dissolved organic matter. The humic-like fluorescent component HS-Em460-Ex3 was more hydrophilic than HS-Em430-Ex2 and contained fewer alkyl chains but more acid groups. As a result, HS-Em460-Ex3 was eliminated more preferentially by NDMP anion exchange. However, compared with adsorption resins, the polarity of fluorescent components had a relatively small effect on the performance of anion exchange resin. The long-term pilot-scale experiments showed that the NDMP anion exchange process could remove approximately 30 % of the chemical oxygen demand and about 90 % of color from the biologically treated textile effluents. Once the issue of waste brine from resin desorption is solved, the NDMP anion exchange process could be a promising alternative for the advanced treatment of textile effluents.

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

Nutrients and ageing: what can we learn about ageing interactions from animal biology?

PubMed

Stenvinkel, Peter; Kooman, Jeroen P; Shiels, Paul G

2016-01-01

Many prevalent clinical conditions, such as chronic kidney disease, diabetes mellitus, chronic obstructive pulmonary, and cardiovascular disease associate with features of premature ageing, such as muscle wasting, hypogonadism, osteoporosis, and arteriosclerosis. Studies on various animal models have shown that caloric restriction prolongs lifespan. Studies of animals with unusual long or short life for their body size may also contribute to better understanding of ageing processes. The aim of the present article is to review what we can learn about nutritional modulations and ageing interactions from animal biology. Caloric restriction is a powerful intervention that increases longevity in animals ranging from short-lived species, such as worms and flies, to primates. As long-term studies on caloric restriction are not feasible to conduct in humans, much interest has focused on the impact of caloric restriction mimetics, such as resveratrol, on ageing processes. Recent data from studies on the long-lived naked mole rat have provided important novel information on metabolic alterations and antioxidative defense mechanisms that characterize longevity. Better understanding of the biology of exceptionally long-lived animals will contribute to better understanding of ageing processes and novel interventions to extend lifespan also in humans.

Consideration of Experimental Approaches in the Physical and Biological Sciences in Designing Long-Term Watershed Studies in Forested Landscapes

NASA Astrophysics Data System (ADS)

Stallard, R. F.

2011-12-01

The importance of biological processes in controlling weathering, erosion, stream-water composition, soil formation, and overall landscape development is generally accepted. The U.S. Geological Survey (USGS) Water, Energy, and Biogeochemical Budgets (WEBB) Project in eastern Puerto Rico and Panama and the Smithsonian Tropical Research Institute (STRI) Panama Canal Watershed Experiment (PCWE) are landscape-scale studies based in the humid tropics where the warm temperatures, moist conditions, and luxuriant vegetation promote especially rapid biological and chemical processes - photosynthesis, respiration, decay, and chemical weathering. In both studies features of small-watershed, large-watershed, and landscape-scale-biology experiments are blended to satisfy the research needs of the physical and biological sciences. The WEBB Project has successfully synthesized its first fifteen years of data, and has addressed the influence of land cover, geologic, topographic, and hydrologic variability, including huge storms on a wide range of hydrologic, physical, and biogeochemical processes. The ongoing PCWE should provide a similar synthesis of a moderate-sized humid tropical watershed. The PCWE and the Agua Salud Project (ASP) within the PCWE are now addressing the role of land cover (mature forests, pasture, invasive-grass dominated, secondary succession, native species plantation, and teak) at scales ranging from small watersheds to the whole Panama Canal watershed. Biologists have participated in the experimental design at both watershed scales, and small (0.1 ha) to large (50 ha) forest-dynamic plots have a central role in interfacing between physical scientists and biologists. In these plots, repeated, high-resolution mapping of all woody plants greater than 1-cm diameter provides a description of population changes through time presumably reflecting individual life histories, interactions with other organisms and the influence of landscape processes and climate, thereby bridging the research needs and conceptual scales of hydrologists and biogeochemists with those of biologists. Both experiments are embedded in larger data-collection networks: the WEBB within the hydrological and meteorological monitoring programs of the USGS and other federal agencies, and the PCWE in the long-term monitoring conducted by the Panama Canal Authority (ACP), its antecedents, and STRI. Examination of landscape-scale processes in a changing world requires the development of detailed landscape-scale data sets, including a formulation of reference states that can act as surrogate experimental controls. For example, the concept of a landscape steady state provides a convenient reference in which present-day observations can be interpreted. Extreme hydrological states must also be described, and both WEBB and PCWE have successfully examined the role of droughts and large storms and their impact on geomorphology, biogeochemistry, and biology. These experiments also have provided platforms for research endeavors never contemplated in the original objectives, a testament to the importance of developing approaches that consider the needs of physical and biological sciences.

Stratigraphy of the Anthropocene.

PubMed

Zalasiewicz, Jan; Williams, Mark; Fortey, Richard; Smith, Alan; Barry, Tiffany L; Coe, Angela L; Bown, Paul R; Rawson, Peter F; Gale, Andrew; Gibbard, Philip; Gregory, F John; Hounslow, Mark W; Kerr, Andrew C; Pearson, Paul; Knox, Robert; Powell, John; Waters, Colin; Marshall, John; Oates, Michael; Stone, Philip

2011-03-13

The Anthropocene, an informal term used to signal the impact of collective human activity on biological, physical and chemical processes on the Earth system, is assessed using stratigraphic criteria. It is complex in time, space and process, and may be considered in terms of the scale, relative timing, duration and novelty of its various phenomena. The lithostratigraphic signal includes both direct components, such as urban constructions and man-made deposits, and indirect ones, such as sediment flux changes. Already widespread, these are producing a significant 'event layer', locally with considerable long-term preservation potential. Chemostratigraphic signals include new organic compounds, but are likely to be dominated by the effects of CO(2) release, particularly via acidification in the marine realm, and man-made radionuclides. The sequence stratigraphic signal is negligible to date, but may become geologically significant over centennial/millennial time scales. The rapidly growing biostratigraphic signal includes geologically novel aspects (the scale of globally transferred species) and geologically will have permanent effects.

Biochemical capacitance of Geobacter sulfurreducens biofilms.

PubMed

Bueno, Paulo R; Schrott, Germán D; Bonanni, Pablo S; Simison, Silvia N; Busalmen, Juan P

2015-08-10

An electrical model able to decouple the electron pathway from microbial cell machinery impedance terms is introduced. In this context, capacitance characteristics of the biofilm are clearly resolved. In other words, the model allows separating, according to the advantage of frequency and spectroscopic response approach, the different terms controlling the performance of the microbial biofilm respiratory process and thus the directly related electricity production process. The model can be accurately fitted to voltammetry measurements obtained under steady-state conditions and also to biofilm discharge amperometric measurements. The implications of biological aspects of the electrochemical or redox capacitance are discussed theoretically in the context of current knowledge with regard to structure and physiological activity of microbial Geobacter biofilms. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

CFD simulation of fluid dynamic and biokinetic processes within activated sludge reactors under intermittent aeration regime.

PubMed

Sánchez, F; Rey, H; Viedma, A; Nicolás-Pérez, F; Kaiser, A S; Martínez, M

2018-08-01

Due to the aeration system, biological reactors are the most energy-consuming facilities of convectional WWTPs. Many biological reactors work under intermittent aeration regime; the optimization of the aeration process (air diffuser layout, air flow rate per diffuser, aeration length …) is necessary to ensure an efficient performance; satisfying the effluent requirements with the minimum energy consumption. This work develops a CFD modelling of an activated sludge reactor (ASR) which works under intermittent aeration regime. The model considers the fluid dynamic and biological processes within the ASR. The biological simulation, which is transient, takes into account the intermittent aeration regime. The CFD modelling is employed for the selection of the aeration system of an ASR. Two different aeration configurations are simulated. The model evaluates the aeration power consumption necessary to satisfy the effluent requirements. An improvement of 2.8% in terms of energy consumption is achieved by modifying the air diffuser layout. An analysis of the influence of the air flow rate per diffuser on the ASR performance is carried out. The results show a reduction of 14.5% in the energy consumption of the aeration system when the air flow rate per diffuser is reduced. The model provides an insight into the aeration inefficiencies produced within ASRs. Copyright © 2018 Elsevier Ltd. All rights reserved.

On inter-tidal transport equation

USGS Publications Warehouse

Cheng, Ralph T.; Feng, Shizuo; Pangen, Xi

1989-01-01

The transports of solutes, sediments, nutrients, and other tracers are fundamental to the interactive physical, chemical, and biological processes in estuaries. The characteristic time scales for most estuarine biological and chemical processes are on the order of several tidal cycles or longer. To address the long-term transport mechanism meaningfully, the formulation of an inter-tidal conservation equation is the main subject of this paper. The commonly used inter-tidal conservation equation takes the form of a convection-dispersion equation in which the convection is represented by the Eulerian residual current, and the dispersion terms are due to the introduction of a Fickian hypothesis, unfortunately, the physical significance of this equation is not clear, and the introduction of a Fickian hypothesis is at best an ad hoc approximation. Some recent research results on the Lagrangian residual current suggest that the long-term transport problem is more closely related to the Lagrangian residual current than to the Eulerian residual current. With the aid of additional insight of residual current, the inter-tidal transport equation has been reformulated in this paper using a small perturbation method for a weakly nonlinear tidal system. When tidal flows can be represented by an M2 system, the new intertidal transport equation also takes the form of a convective-dispersion equation without the introduction of a Fickian hypothesis. The convective velocity turns out to be the first order Lagrangian residual current (the sum of the Eulerian residual current and the Stokes’ drift), and the correlation terms take the form of convection with the Stokes’ drift as the convective velocity. The remaining dispersion terms are perturbations of lower order solution to higher order solutions due to shear effect and turbulent mixing.

ADGO: analysis of differentially expressed gene sets using composite GO annotation.

PubMed

Nam, Dougu; Kim, Sang-Bae; Kim, Seon-Kyu; Yang, Sungjin; Kim, Seon-Young; Chu, In-Sun

2006-09-15

Genes are typically expressed in modular manners in biological processes. Recent studies reflect such features in analyzing gene expression patterns by directly scoring gene sets. Gene annotations have been used to define the gene sets, which have served to reveal specific biological themes from expression data. However, current annotations have limited analytical power, because they are classified by single categories providing only unary information for the gene sets. Here we propose a method for discovering composite biological themes from expression data. We intersected two annotated gene sets from different categories of Gene Ontology (GO). We then scored the expression changes of all the single and intersected sets. In this way, we were able to uncover, for example, a gene set with the molecular function F and the cellular component C that showed significant expression change, while the changes in individual gene sets were not significant. We provided an exemplary analysis for HIV-1 immune response. In addition, we tested the method on 20 public datasets where we found many 'filtered' composite terms the number of which reached approximately 34% (a strong criterion, 5% significance) of the number of significant unary terms on average. By using composite annotation, we can derive new and improved information about disease and biological processes from expression data. We provide a web application (ADGO: http://array.kobic.re.kr/ADGO) for the analysis of differentially expressed gene sets with composite GO annotations. The user can analyze Affymetrix and dual channel array (spotted cDNA and spotted oligo microarray) data for four species: human, mouse, rat and yeast. chu@kribb.re.kr http://array.kobic.re.kr/ADGO.

Disentangling the multigenic and pleiotropic nature of molecular function

PubMed Central

2015-01-01

Background Biological processes at the molecular level are usually represented by molecular interaction networks. Function is organised and modularity identified based on network topology, however, this approach often fails to account for the dynamic and multifunctional nature of molecular components. For example, a molecule engaging in spatially or temporally independent functions may be inappropriately clustered into a single functional module. To capture biologically meaningful sets of interacting molecules, we use experimentally defined pathways as spatial/temporal units of molecular activity. Results We defined functional profiles of Saccharomyces cerevisiae based on a minimal set of Gene Ontology terms sufficient to represent each pathway's genes. The Gene Ontology terms were used to annotate 271 pathways, accounting for pathway multi-functionality and gene pleiotropy. Pathways were then arranged into a network, linked by shared functionality. Of the genes in our data set, 44% appeared in multiple pathways performing a diverse set of functions. Linking pathways by overlapping functionality revealed a modular network with energy metabolism forming a sparse centre, surrounded by several denser clusters comprised of regulatory and metabolic pathways. Signalling pathways formed a relatively discrete cluster connected to the centre of the network. Genetic interactions were enriched within the clusters of pathways by a factor of 5.5, confirming the organisation of our pathway network is biologically significant. Conclusions Our representation of molecular function according to pathway relationships enables analysis of gene/protein activity in the context of specific functional roles, as an alternative to typical molecule-centric graph-based methods. The pathway network demonstrates the cooperation of multiple pathways to perform biological processes and organises pathways into functionally related clusters with interdependent outcomes. PMID:26678917

Identifying ELIXIR Core Data Resources

PubMed Central

Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

2017-01-01

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR’s sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure. PMID:27803796

Identifying ELIXIR Core Data Resources.

PubMed

Durinx, Christine; McEntyre, Jo; Appel, Ron; Apweiler, Rolf; Barlow, Mary; Blomberg, Niklas; Cook, Chuck; Gasteiger, Elisabeth; Kim, Jee-Hyub; Lopez, Rodrigo; Redaschi, Nicole; Stockinger, Heinz; Teixeira, Daniel; Valencia, Alfonso

2016-01-01

The core mission of ELIXIR is to build a stable and sustainable infrastructure for biological information across Europe. At the heart of this are the data resources, tools and services that ELIXIR offers to the life-sciences community, providing stable and sustainable access to biological data. ELIXIR aims to ensure that these resources are available long-term and that the life-cycles of these resources are managed such that they support the scientific needs of the life-sciences, including biological research. ELIXIR Core Data Resources are defined as a set of European data resources that are of fundamental importance to the wider life-science community and the long-term preservation of biological data. They are complete collections of generic value to life-science, are considered an authority in their field with respect to one or more characteristics, and show high levels of scientific quality and service. Thus, ELIXIR Core Data Resources are of wide applicability and usage. This paper describes the structures, governance and processes that support the identification and evaluation of ELIXIR Core Data Resources. It identifies key indicators which reflect the essence of the definition of an ELIXIR Core Data Resource and support the promotion of excellence in resource development and operation. It describes the specific indicators in more detail and explains their application within ELIXIR's sustainability strategy and science policy actions, and in capacity building, life-cycle management and technical actions. The identification process is currently being implemented and tested for the first time. The findings and outcome will be evaluated by the ELIXIR Scientific Advisory Board in March 2017. Establishing the portfolio of ELIXIR Core Data Resources and ELIXIR Services is a key priority for ELIXIR and publicly marks the transition towards a cohesive infrastructure.

Assessing the impact of case sensitivity and term information gain on biomedical concept recognition.

PubMed

Groza, Tudor; Verspoor, Karin

2015-01-01

Concept recognition (CR) is a foundational task in the biomedical domain. It supports the important process of transforming unstructured resources into structured knowledge. To date, several CR approaches have been proposed, most of which focus on a particular set of biomedical ontologies. Their underlying mechanisms vary from shallow natural language processing and dictionary lookup to specialized machine learning modules. However, no prior approach considers the case sensitivity characteristics and the term distribution of the underlying ontology on the CR process. This article proposes a framework that models the CR process as an information retrieval task in which both case sensitivity and the information gain associated with tokens in lexical representations (e.g., term labels, synonyms) are central components of a strategy for generating term variants. The case sensitivity of a given ontology is assessed based on the distribution of so-called case sensitive tokens in its terms, while information gain is modelled using a combination of divergence from randomness and mutual information. An extensive evaluation has been carried out using the CRAFT corpus. Experimental results show that case sensitivity awareness leads to an increase of up to 0.07 F1 against a non-case sensitive baseline on the Protein Ontology and GO Cellular Component. Similarly, the use of information gain leads to an increase of up to 0.06 F1 against a standard baseline in the case of GO Biological Process and Molecular Function and GO Cellular Component. Overall, subject to the underlying token distribution, these methods lead to valid complementary strategies for augmenting term label sets to improve concept recognition.

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

PubMed Central

2013-01-01

Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

Ludwig von Bertalanffy's Organismic View on the Theory of Evolution

PubMed Central

Drack, Manfred

2015-01-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 77–90, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:25727202

Small-scale laser based electron accelerators for biology and medicine: a comparative study of the biological effectiveness

NASA Astrophysics Data System (ADS)

Labate, Luca; Andreassi, Maria Grazia; Baffigi, Federica; Basta, Giuseppina; Bizzarri, Ranieri; Borghini, Andrea; Candiano, Giuliana C.; Casarino, Carlo; Cresci, Monica; Di Martino, Fabio; Fulgentini, Lorenzo; Ghetti, Francesco; Gilardi, Maria Carla; Giulietti, Antonio; Köster, Petra; Lenci, Francesco; Levato, Tadzio; Oishi, Yuji; Russo, Giorgio; Sgarbossa, Antonella; Traino, Claudio; Gizzi, Leonida A.

2013-05-01

Laser-driven electron accelerators based on the Laser Wakefield Acceleration process has entered a mature phase to be considered as alternative devices to conventional radiofrequency linear accelerators used in medical applications. Before entering the medical practice, however, deep studies of the radiobiological effects of such short bunches as the ones produced by laser-driven accelerators have to be performed. Here we report on the setup, characterization and first test of a small-scale laser accelerator for radiobiology experiments. A brief description of the experimental setup will be given at first, followed by an overview of the electron bunch characterization, in particular in terms of dose delivered to the samples. Finally, the first results from the irradiation of biological samples will be briefly discussed.

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks

PubMed Central

Khammash, Mustafa

2014-01-01

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed. PMID:24968191

Biological network motif detection and evaluation

PubMed Central

2011-01-01

Background Molecular level of biological data can be constructed into system level of data as biological networks. Network motifs are defined as over-represented small connected subgraphs in networks and they have been used for many biological applications. Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important. Results We define biological network motifs as biologically significant subgraphs and traditional network motifs are differentiated as structural network motifs in this paper. We develop five algorithms, namely, EDGEGO-BNM, EDGEBETWEENNESS-BNM, NMF-BNM, NMFGO-BNM and VOLTAGE-BNM, for efficient detection of biological network motifs, and introduce several evaluation measures including motifs included in complex, motifs included in functional module and GO term clustering score in this paper. Experimental results show that EDGEGO-BNM and EDGEBETWEENNESS-BNM perform better than existing algorithms and all of our algorithms are applicable to find structural network motifs as well. Conclusion We provide new approaches to finding network motifs in biological networks. Our algorithms efficiently detect biological network motifs and further improve existing algorithms to find high quality structural network motifs, which would be impossible using existing algorithms. The performances of the algorithms are compared based on our new evaluation measures in biological contexts. We believe that our work gives some guidelines of network motifs research for the biological networks. PMID:22784624

The Gene Ontology of eukaryotic cilia and flagella.

PubMed

Roncaglia, Paola; van Dam, Teunis J P; Christie, Karen R; Nacheva, Lora; Toedt, Grischa; Huynen, Martijn A; Huntley, Rachael P; Gibson, Toby J; Lomax, Jane

2017-01-01

Recent research into ciliary structure and function provides important insights into inherited diseases termed ciliopathies and other cilia-related disorders. This wealth of knowledge needs to be translated into a computational representation to be fully exploitable by the research community. To this end, members of the Gene Ontology (GO) and SYSCILIA Consortia have worked together to improve representation of ciliary substructures and processes in GO. Members of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field. The project initially aimed to improve coverage of ciliary parts, and was then broadened to cilia-related biological processes. Discussions were documented in a public tracker. We engaged the broader cilia community via direct consultation and by referring to the literature. Ontology updates were implemented via ontology editing tools. So far, we have created or modified 127 GO terms representing parts and processes related to eukaryotic cilia/flagella or prokaryotic flagella. A growing number of biological pathways are known to involve cilia, and we continue to incorporate this knowledge in GO. The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins. The revised ontology was also used to curate mouse proteins in a collaborative project. The revised GO and annotations, used in comparative 'before and after' analyses of representative ciliary datasets, improve enrichment results significantly. Our work has resulted in a broader and deeper coverage of ciliary composition and function. These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation to interpretation of high-throughput studies. We welcome feedback to further enhance the representation of cilia biology in GO.

Municipal wastewater biological nutrient removal driven by the fermentation liquid of dairy wastewater.

PubMed

Liu, Hui; Chen, Yinguang; Wu, Jiang

2017-11-01

Carbon substrate is required by biological nutrient removal (BNR) microorganism, but it is usually insufficient in the influent of many municipal wastewater treatment plants. In this study the use of ethanol-enriched fermentation liquid, which was derived from dairy wastewater, as the preferred carbon substrate of BNR was reported. First, the application of dairy wastewater and food processing wastewater and their fermentation liquid as the carbon substrate of BNR was compared in the short-term tests. The fermented wastewater showed higher BNR performance than the unfermented one, and the fermentation liquid of dairy wastewater (FL-DW), which was obtained under pH 8 and fermentation time of 6 day, exhibited the highest phosphorus (95.5%) and total nitrogen (97.6%) removal efficiencies due to its high ethanol content (57.9%). Then, the long-term performance of FL-DW acting as the carbon substrate of BNR was compared with that of acetate and ethanol, and the FL-DW showed the greatest phosphorus and total nitrogen removal. Further investigation showed that the use of FL-DW caused the highest polyhydroxyalkanoates (PHAs) synthesis in BNR microbial cells, and more PHAs were used for phosphorus uptake and denitrification rather than glycogen synthesis and microbial growth. The FL-DW can be used as a preferred carbon substrate for BNR microbes. AB: aerobic end sludge active biomass; BNR: biological nutrient removal; DW: dairy wastewater; FL-DW: fermentation liquid of dairy wastewater; FPW: food processing wastewater; FL-FPW: fermentation liquid of food processing wastewater; PHAs: polyhydroxyalkanoates; PHB: poly-3-hydroxybutyrate; PHV: poly-3-hydroxyvalerate; PH2MV: poly-3-hydroxy-2- methylvalerate; PAOs: phosphorus accumulating organisms; SBR: sequencing batch reactor; SOP: soluble ortho-phosphorus; TN: total nitrogen; TSS: total suspended solids; VSS: volatile suspended solids; VFAs: volatile fatty acids; WWTPs: wastewater treatment plants.

WITHDRAWN: The platelet storage lesion: A comparative analysis of six leukoreduction processes in terms of biocompatability, microvesiculation, retention of prions, and generation/removal of biological response modifiers.

PubMed

Seghatchian, Jerard

2005-06-16

The Publisher regrets that this article was an accidental duplication of an article that has already been published in Transfus Apher Sci, 34 (1) 125 - 130, doi:10.1016/j.transci.2005.09.002. The duplicate article has therefore been withdrawn.

Stream nitrogen responses to fire in the Southeastern U.S.

Treesearch

James M. Vose; Stephanie H. Laseter; Steve G. McNulty

2005-01-01

Fire can play a significant role in runoff, sediment yield, and nitrate transport in aquatic and terrestrial ecosystems in the southeast US. The typical impact of fire is an immediate change in the physical properties of the soil and forest floor surface, followed by mid- and long-term changes in biological pools and cycling processes. Depending upon the severity of...

Macroinvertebrates in North American tallgrass prairie soils: effects of fire, mowing, and fertilization on density and biomass

Treesearch

M.A. Callaham; J.M. Blair; T.C. Todd; D.J. Kitchen; M.R. Whiles

2003-01-01

The responses of tallgrass prairie plant communities and ecosystem processes to fire and grazing are well characterized. However, responses of invertebrate consumer groups. and particularly soil-dwelling organisms, to these disturbances are not well known. At Konza Prairie Biological Station. we sampled soil macroinvertebrates in 1994 and 1999 as part of a long-term...

Studying the role of wood-decay fungi in calcium cycling on the Penobscot Experimental Forest: a progress report

Treesearch

Walter C. Shortle; Jody Jellison; Kevin T. Smith; Jonathan S. Schilling

2014-01-01

Depletion of essential mineral nutrients from the rooting zone of trees in northern forests may reduce health and productivity. Long-term field investigations coupled with detailed laboratory studies enhance understanding of the biological processes and suggest means to address potential threats. One such investigation by the U.S. Department of Agriculture, Forest...

Long-term effects of fragmentation and fragment properties on bird species richness in Hawaiian forests

Treesearch

David J. Flaspohler; Christian P. Giardina; Gregory P. Asner; Patrick Hart; Jonathan Price; Cassie Ka’apu Lyons; Xeronimo Castaneda

2010-01-01

Forest fragmentation is a common disturbance affecting biological diversity, yet the impacts of fragmentation on many forest processes remain poorly understood. Forest restoration is likely to be more successful when it proceeds with an understanding of how native and exotic vertebrates utilize forest patches of different size. We used a system of forest fragments...

Differential Vulnerability of Global Motion, Global Form, and Biological Motion Processing in Full-Term and Preterm Children

ERIC Educational Resources Information Center

Taylor, N. M.; Jakobson, L. S.; Maurer, D.; Lewis, T. L.

2009-01-01

Young children born very prematurely show elevated thresholds for global motion and global form [Atkinson, J. & Braddick, O. (2007). "Visual and visuocognitive development in children born very prematurely." "Progress in Brain Research, 164." 123-149; MacKay, T. L., Jakobson, L. S., Ellemberg, D., Lewis, T. L., Maurer, D., & Casiro, O. (2005).…

New Approaches to Evaluate the Biological Degradation of RDX in Groundwater

DTIC Science & Technology

2014-08-27

biodegradation in groundwater. 15. SUBJECT TERMS RDX, hexahydro-1,3,5-trinitro-1,3,5-triazine, bioremediation , biodegradation, groundwater, stable...DoD sites for documenting in situ RDX biodegradation as a natural attenuation process or during bioremediation efforts. Moreover, the CSIA data...and nitroaromatic explosives from surface soils, including enhanced bioremediation , are well documented but there are presently few proven

Biosimilar Monoclonal Antibodies for Inflammatory Bowel Disease: Current Comfort and Future Prospects.

PubMed

Gecse, Krisztina B; Lakatos, Péter L

2016-10-01

Biosimilars are biologic medicines that enter the market after a patent for an original reference product expires. The European Medicines Agency (EMA) developed a stringent legislation process for biosimilar monoclonal antibodies, whereby similarity to the reference medicinal product in terms of quality characteristics, biological activity, clinical safety and efficacy must be demonstrated. Biosimilar infliximab CT-P13 was the first biosimilar monoclonal antibody to receive EMA marketing authorization, and further biosimilar molecules are being developed. The phase I and III clinical trials were conducted in ankylosing spondylitis and rheumatoid arthritis, and the use of CT-P13 in inflammatory bowel disease (IBD) was extrapolated on the results of these trials. Medical professionals were initially concerned about the reversed engineering process, the novel legal framework and the lack of clinical data in IBD. Emerging real-world data have confirmed the similarities between CT-P13 and the reference product in terms of efficacy, safety and immunogenicity in IBD. The cost reduction represented by biosimilars promotes industry competition and improves treatment access with sustained quality of care. This article reviews the existing and emerging clinical data for CT-P13 and a future perspective on biosimilar use in IBD.

Transcriptome differences between enrofloxacin-resistant and enrofloxacin-susceptible strains of Aeromonas hydrophila.

PubMed

Zhu, Fengjiao; Yang, Zongying; Zhang, Yiliu; Hu, Kun; Fang, Wenhong

2017-01-01

Enrofloxacin is the most commonly used antibiotic to control diseases in aquatic animals caused by A. hydrophila. This study conducted de novo transcriptome sequencing and compared the global transcriptomes of enrofloxacin-resistant and enrofloxacin-susceptible strains. We got a total of 4,714 unigenes were assembled. Of these, 4,122 were annotated. A total of 3,280 unigenes were assigned to GO, 3,388 unigenes were classified into Cluster of Orthologous Groups of proteins (COG) using BLAST and BLAST2GO software, and 2,568 were mapped onto pathways using the Kyoto Encyclopedia of Gene and Genomes Pathway database. Furthermore, 218 unigenes were deemed to be DEGs. After enrofloxacin treatment, 135 genes were upregulated and 83 genes were downregulated. The GO terms biological process (126 genes) and metabolic process (136 genes) were the most enriched, and the terms for protein folding, response to stress, and SOS response were also significantly enriched. This study identified enrofloxacin treatment affects multiple biological functions of A. hydrophila. Enrofloxacin resistance in A. hydrophila is closely related to the reduction of intracellular drug accumulation caused by ABC transporters and increased expression of topoisomerase IV.

Transcriptome differences between enrofloxacin-resistant and enrofloxacin-susceptible strains of Aeromonas hydrophila

PubMed Central

Yang, Zongying; Zhang, Yiliu; Hu, Kun; Fang, Wenhong

2017-01-01

Enrofloxacin is the most commonly used antibiotic to control diseases in aquatic animals caused by A. hydrophila. This study conducted de novo transcriptome sequencing and compared the global transcriptomes of enrofloxacin-resistant and enrofloxacin-susceptible strains. We got a total of 4,714 unigenes were assembled. Of these, 4,122 were annotated. A total of 3,280 unigenes were assigned to GO, 3,388 unigenes were classified into Cluster of Orthologous Groups of proteins (COG) using BLAST and BLAST2GO software, and 2,568 were mapped onto pathways using the Kyoto Encyclopedia of Gene and Genomes Pathway database. Furthermore, 218 unigenes were deemed to be DEGs. After enrofloxacin treatment, 135 genes were upregulated and 83 genes were downregulated. The GO terms biological process (126 genes) and metabolic process (136 genes) were the most enriched, and the terms for protein folding, response to stress, and SOS response were also significantly enriched. This study identified enrofloxacin treatment affects multiple biological functions of A. hydrophila. Enrofloxacin resistance in A. hydrophila is closely related to the reduction of intracellular drug accumulation caused by ABC transporters and increased expression of topoisomerase IV. PMID:28708867

Automatic extraction of angiogenesis bioprocess from text

PubMed Central

Wang, Xinglong; McKendrick, Iain; Barrett, Ian; Dix, Ian; French, Tim; Tsujii, Jun'ichi; Ananiadou, Sophia

2011-01-01

Motivation: Understanding key biological processes (bioprocesses) and their relationships with constituent biological entities and pharmaceutical agents is crucial for drug design and discovery. One way to harvest such information is searching the literature. However, bioprocesses are difficult to capture because they may occur in text in a variety of textual expressions. Moreover, a bioprocess is often composed of a series of bioevents, where a bioevent denotes changes to one or a group of cells involved in the bioprocess. Such bioevents are often used to refer to bioprocesses in text, which current techniques, relying solely on specialized lexicons, struggle to find. Results: This article presents a range of methods for finding bioprocess terms and events. To facilitate the study, we built a gold standard corpus in which terms and events related to angiogenesis, a key biological process of the growth of new blood vessels, were annotated. Statistics of the annotated corpus revealed that over 36% of the text expressions that referred to angiogenesis appeared as events. The proposed methods respectively employed domain-specific vocabularies, a manually annotated corpus and unstructured domain-specific documents. Evaluation results showed that, while a supervised machine-learning model yielded the best precision, recall and F1 scores, the other methods achieved reasonable performance and less cost to develop. Availability: The angiogenesis vocabularies, gold standard corpus, annotation guidelines and software described in this article are available at http://text0.mib.man.ac.uk/~mbassxw2/angiogenesis/ Contact: xinglong.wang@gmail.com PMID:21821664

Soil Biological Activity Contributing to Phosphorus Availability in Vertisols under Long-Term Organic and Conventional Agricultural Management

PubMed Central

Bhat, Nisar A.; Riar, Amritbir; Ramesh, Aketi; Iqbal, Sanjeeda; Sharma, Mahaveer P.; Sharma, Sanjay K.; Bhullar, Gurbir S.

2017-01-01

Mobilization of unavailable phosphorus (P) to plant available P is a prerequisite to sustain crop productivity. Although most of the agricultural soils have sufficient amounts of phosphorus, low availability of native soil P remains a key limiting factor to increasing crop productivity. Solubilization and mineralization of applied and native P to plant available form is mediated through a number of biological and biochemical processes that are strongly influenced by soil carbon/organic matter, besides other biotic and abiotic factors. Soils rich in organic matter are expected to have higher P availability potentially due to higher biological activity. In conventional agricultural systems mineral fertilizers are used to supply P for plant growth, whereas organic systems largely rely on inputs of organic origin. The soils under organic management are supposed to be biologically more active and thus possess a higher capability to mobilize native or applied P. In this study we compared biological activity in soil of a long-term farming systems comparison field trial in vertisols under a subtropical (semi-arid) environment. Soil samples were collected from plots under 7 years of organic and conventional management at five different time points in soybean (Glycine max) -wheat (Triticum aestivum) crop sequence including the crop growth stages of reproductive significance. Upon analysis of various soil biological properties such as dehydrogenase, β-glucosidase, acid and alkaline phosphatase activities, microbial respiration, substrate induced respiration, soil microbial biomass carbon, organically managed soils were found to be biologically more active particularly at R2 stage in soybean and panicle initiation stage in wheat. We also determined the synergies between these biological parameters by using the methodology of principle component analysis. At all sampling points, P availability in organic and conventional systems was comparable. Our findings clearly indicate that owing to higher biological activity, organic systems possess equal capabilities of supplying P for crop growth as are conventional systems with inputs of mineral P fertilizers. PMID:28928758

Climate Observing Systems: Where are we and where do we need to be in the future

NASA Astrophysics Data System (ADS)

Baker, B.; Diamond, H. J.

2017-12-01

Climate research and monitoring requires an observational strategy that blends long-term, carefully calibrated measurements as well as short-term, focused process studies. The operation and implementation of operational climate observing networks and the provision of related climate services, both have a significant role to play in assisting the development of national climate adaptation policies and in facilitating national economic development. Climate observing systems will require a strong research element for a long time to come. This requires improved observations of the state variables and the ability to set them in a coherent physical (as well as a chemical and biological) framework with models. Climate research and monitoring requires an integrated strategy of land/ocean/atmosphere observations, including both in situ and remote sensing platforms, and modeling and analysis. It is clear that we still need more research and analysis on climate processes, sampling strategies, and processing algorithms.

Incorporating biodegradation and advanced oxidation processes in the treatment of spent metalworking fluids.

PubMed

MacAdam, Jitka; Ozgencil, Haci; Autin, Olivier; Pidou, Marc; Temple, Clive; Parsons, Simon; Jefferson, Bruce

2012-12-01

The treatment of spent metalworking fluids (MWFs) is difficult due to their complex and variable composition. Small businesses often struggle to meet increasingly stringent legislation and rising costs as they need to treat this wastewater on site annually over a short period. Larger businesses that treat their wastewater continuously can benefit from the use of biological processes, although new MWFs designed to resist biological activity represent a challenge. A three-stage treatment is generally applied, with the oil phase being removed first, followed by a reduction in COD loading and then polishing of the effluent's quality in the final stage. The performance of advanced oxidation processes (AOPs), which could be of benefit to both types of businesses was studied. After assessing the biodegradability of spent MFW, different AOPs were used (UV/H2O2, photo-Fenton and UV/TiO2) to establish the treatability of this wastewater by hydroxyl radicals (*OH). The interactions of both the chemical and biological treatments were also investigated. The wastewater was found to be readily biodegradable in the Zahn-Wellens test with 69% COD and 74% DOC removal. The UV/TiO2 reactor was found to be the cheapest option achieving a very good COD removal (82% at 20 min retention time and 10 L min(-1) aeration rate). The photo-Fenton process was found to be efficient in terms of degradation rate, achieving 84% COD removal (1 M Fe2+, 40 M H2O2, 20.7 J cm(-2), pH 3) and also improving the wastewater's biodegradability. The UV/H202 process was the most effective in removing recalcitrant COD in the post-biological treatment stage.

Biomimetic and Bioinspired Synthesis of Nanomaterials/Nanostructures.

PubMed

Zan, Guangtao; Wu, Qingsheng

2016-03-16

In recent years, due to its unparalleled advantages, the biomimetic and bioinspired synthesis of nanomaterials/nanostructures has drawn increasing interest and attention. Generally, biomimetic synthesis can be conducted either by mimicking the functions of natural materials/structures or by mimicking the biological processes that organisms employ to produce substances or materials. Biomimetic synthesis is therefore divided here into "functional biomimetic synthesis" and "process biomimetic synthesis". Process biomimetic synthesis is the focus of this review. First, the above two terms are defined and their relationship is discussed. Next different levels of biological processes that can be used for process biomimetic synthesis are compiled. Then the current progress of process biomimetic synthesis is systematically summarized and reviewed from the following five perspectives: i) elementary biomimetic system via biomass templates, ii) high-level biomimetic system via soft/hard-combined films, iii) intelligent biomimetic systems via liquid membranes, iv) living-organism biomimetic systems, and v) macromolecular bioinspired systems. Moreover, for these five biomimetic systems, the synthesis procedures, basic principles, and relationships are discussed, and the challenges that are encountered and directions for further development are considered. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Carbon dioxide evolution rate as a method to monitor and control an aerobic biological waste treatment system

NASA Technical Reports Server (NTRS)

Lee, S. S.; Shuler, M. L.

1986-01-01

An experimental system was developed to study the microbial growth kinetic of an undefined mixed culture in an erobic biological waste treatment process. The experimental results were used to develop a mathematical model that can predict the performance of a bioreactor. The bioreactor will be used to regeneratively treat waste material which is expected to be generated during a long term manned space mission. Since the presence of insoluble particles in the chemically undefined complex media made estimating biomass very difficult in the real system, a clean system was devised to study the microbial growth from the soluble substrate.

GPS for QSP: A Summary of the ACoP6 Symposium on Quantitative Systems Pharmacology and a Stage for Near-Term Efforts in the Field.

PubMed

Musante, C J; Abernethy, D R; Allerheiligen, S R; Lauffenburger, D A; Zager, M G

2016-09-01

Quantitative Systems Pharmacology (QSP) is experiencing increased application in the drug discovery and development process. Like its older sibling, systems biology, the QSP field is comprised of a mix of established disciplines and methods, from molecular biology to engineering to pharmacometrics. As a result, there exist critical segments of the discipline that differ dramatically in approach and a need to bring these groups together toward a common goal. © 2016 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

Children Nature Education About Names of Ocean Fish in Banyuwangi

NASA Astrophysics Data System (ADS)

Kartika Santi, Triana

2018-05-01

Children can learn about biology from the nature. Children in fishing area of Muncar sub distric in Banyuwangi learn about name of fish from community in daily life. This research is aimed to identify children learning about the names of ocean fish in Muncar Banyuwangi. The research is conducted by interviewing the children, the fishermen and the local society. The result shows that there are a lot of local names of fish found in learning process. The children tend to be familier with these names rather than biological names. It is also found that names of fishes could be categorized in three different terms.

[Genetics and criminology: a new concept].

PubMed

Jeffery, C R; Jeffery, I A

1975-01-01

The early history of criminology was one of interaction with genetics and biology, but since the sociological school emerged in the 1920's there has occurred a major split between sociological criminology and biology. Behavioral genetics as it has developed since 1950 has great relevance to criminology in terms of neurological and brain functioning, learning processes, violence and the XYY syndrome, and the sociopathy. A new interdisciplinary research effort must be undertaken in order to look at the interaction of genetics, human behavior, criminal law and criminology. If criminology is interested in learning, motivation, aggression and behavior, it must incorporate the new genetics into its theoretical structure.

A Review: Some biological effects of high LET radiations

NASA Technical Reports Server (NTRS)

Wiley, A., Jr.

1972-01-01

There are qualitative and quantitative differences in the biological damage observed after exposure to high LET radiation as compared to that caused by low LET radiations. This review is concerned with these differences, which are ultimately reflected at the biochemical, cellular and even whole animal levels. In general, high LET radiations seem to produce biochemical damage which is more severe and possibly less repairable. Experimental data for those effects are presented in terms of biochemical RBE's with consideration of both early and late manifestations. An LET independent process by which significant biochemical damage may result from protons, neutrons and negative pion mesons is discussed.

clusterProfiler: an R package for comparing biological themes among gene clusters.

PubMed

Yu, Guangchuang; Wang, Li-Gen; Han, Yanyan; He, Qing-Yu

2012-05-01

Increasing quantitative data generated from transcriptomics and proteomics require integrative strategies for analysis. Here, we present an R package, clusterProfiler that automates the process of biological-term classification and the enrichment analysis of gene clusters. The analysis module and visualization module were combined into a reusable workflow. Currently, clusterProfiler supports three species, including humans, mice, and yeast. Methods provided in this package can be easily extended to other species and ontologies. The clusterProfiler package is released under Artistic-2.0 License within Bioconductor project. The source code and vignette are freely available at http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html.

Synthesis of Biomass and Utilization of Plant Wastes in a Physical Model of a Biological Life Support System

NASA Astrophysics Data System (ADS)

Tikhomirov, A. A.; Ushakova, S. A.; Manukovsky, N. S.; Lisovsky, G. M.; Kudenko, Yu A.; Kovalev, V. S.; Gribovksaya, I. V.; Tirranen, L. S.; Zolotukkhin, I. G.; Gros, J. B.; Lasseur, Ch.

Biological life support systems (LSS) with highly closed intrasystem mass ex change mass ex change hold much promise for long-term human life support at planetary stations (Moon, Mars, etc.). The paper considers problems of biosynthesis of higher plants' biomass and "biological incineration" of plant wastes in a working physical model of biological LSS. The plant wastes are "biologically incinerated" in a special heterotroph block involving Californian worms, mushrooms and straw. The block processes plant wastes (straw, haulms) to produce soil-like substrate (SLS) on which plants (wheat, radish) are grown. Gas ex change in such a system consists of respiratory gas ex change of SLS and photosynthesis and respiration of plants. Specifics of gas ex change dynamics of high plants -SLS complex has been considered. Relationship between such a gas ex change and photosynthetic active radiation (PAR) and age of plants has been established. SLS fertility has been shown to depend on its thickness and phase of maturity. The biogenic elements (potassium, phosphorus, nitrogen) in Liebig minimum have been found to include nitrogen which is the first to impair plants' growth in disruption of the process conditions. The SLS microflora has been found to have different kinds of ammonifying and denitrifying bacteria which is indicative of intensive transformation of nitrogen-containing compounds. The number of physiological groups of microorganisms in SLS was, on the whole, steady. As a result, organic substances -products of ex change of plants and microorganisms were not accumulated in the medium, but mineralized and assimilated by the biocenosis. Experiments showed that the developed model of a man-made ecosystem realized complete utilization of plant wastes and involved them into the intrasystem turnover. In multiple recycle of the mat ter (more than 5 cycles) under the irradiance intensity of 150 W/m2 PAR and the SLS mass (dry weight) of 17.7 -19.9 kg/m2 average total harvest of the plant mass was 2.14 kg/m2, the seed harvest was 0.85 kg/m2 (dry weight). The paper considers opportunities of using the technologies considered in biological LSS with long-term human presence.

The NASA Space Radiobiology Risk Assessment Project

NASA Astrophysics Data System (ADS)

Cucinotta, Francis A.; Huff, Janice; Ponomarev, Artem; Patel, Zarana; Kim, Myung-Hee

The current first phase (2006-2011) has the three major goals of: 1) optimizing the conventional cancer risk models currently used based on the double-detriment life-table and radiation quality functions; 2) the integration of biophysical models of acute radiation syndromes; and 3) the development of new systems radiation biology models of cancer processes. The first-phase also includes continued uncertainty assessment of space radiation environmental models and transport codes, and relative biological effectiveness factors (RBE) based on flight data and NSRL results, respectively. The second phase of the (2012-2016) will: 1) develop biophysical models of central nervous system risks (CNS); 2) achieve comphrensive systems biology models of cancer processes using data from proton and heavy ion studies performed at NSRL; and 3) begin to identify computational models of biological countermeasures. Goals for the third phase (2017-2021) include: 1) the development of a systems biology model of cancer risks for operational use at NASA; 2) development of models of degenerative risks, 2) quantitative models of counter-measure impacts on cancer risks; and 3) indiviudal based risk assessments. Finally, we will support a decision point to continue NSRL research in support of NASA's exploration goals beyond 2021, and create an archival of NSRL research results for continued analysis. Details on near term goals, plans for a WEB based data resource of NSRL results, and a space radiation Wikepedia are described.

Decoupling the influence of biological and physical processes on the dissolved oxygen in the Chesapeake Bay

NASA Astrophysics Data System (ADS)

Du, Jiabi; Shen, Jian

2015-01-01

is instructive and essential to decouple the effects of biological and physical processes on the dissolved oxygen condition, in order to understand their contribution to the interannual variability of hypoxia in Chesapeake Bay since the 1980s. A conceptual bottom DO budget model is applied, using the vertical exchange time scale (VET) to quantify the physical condition and net oxygen consumption rate to quantify biological activities. By combining observed DO data and modeled VET values along the main stem of the Chesapeake Bay, the monthly net bottom DO consumption rate was estimated for 1985-2012. The DO budget model results show that the interannual variations of physical conditions accounts for 88.8% of the interannual variations of observed DO. The high similarity between the VET spatial pattern and the observed DO suggests that physical processes play a key role in regulating the DO condition. Model results also show that long-term VET has a slight increase in summer, but no statistically significant trend is found. Correlations among southerly wind strength, North Atlantic Oscillation index, and VET demonstrate that the physical condition in the Chesapeake Bay is highly controlled by the large-scale climate variation. The relationship is most significant during the summer, when the southerly wind dominates throughout the Chesapeake Bay. The seasonal pattern of the averaged net bottom DO consumption rate (B'20) along the main stem coincides with that of the chlorophyll-a concentration. A significant correlation between nutrient loading and B'20 suggests that the biological processes in April-May are most sensitive to the nutrient loading.

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

PubMed

Li, Le; Yip, Kevin Y

2016-12-15

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

Assisted deposition of nano-hydroxyapatite onto exfoliated carbon nanotube oxide scaffolds.

PubMed

Zanin, H; Rosa, C M R; Eliaz, N; May, P W; Marciano, F R; Lobo, A O

2015-06-14

Electrodeposited nano-hydroxyapatite (nHAp) is more similar to biological apatite in terms of microstructure and dimension than apatites prepared by other processes. Reinforcement with carbon nanotubes (CNTs) enhances its mechanical properties and increases adhesion of osteoblasts. Here, we carefully studied nHAp deposited onto vertically aligned multi-walled CNT (VAMWCNT) scaffolds by electrodeposition and soaking in a simulated body fluid (SBF). VAMWCNTs are porous biocompatible scaffolds with nanometric porosity and exceptional mechanical and chemical properties. The VAMWCNT films were prepared on a Ti substrate by a microwave plasma chemical vapour deposition method, and then oxidized and exfoliated by oxygen plasma etching (OPE) to produce graphene oxide (GO) at the VAMWCNT tips. The attachment of oxygen functional groups was found to be crucial for nHAp nucleation during electrodeposition. A thin layer of plate-like and needle-like nHAp with high crystallinity was formed without any need for thermal treatment. This composite (henceforth referred to as nHAp-VAMWCNT-GO) served as the scaffold for in vitro biomineralization when soaked in the SBF, resulting in the formation of both carbonate-rich and carbonate-poor globular-like nHAp. Different steps in the deposition of biological apatite onto VAMWCNT-GO and during the short-term biomineralization process were analysed. Due to their unique structure and properties, such nano-bio-composites may become useful in accelerating in vivo bone regeneration processes.

Assisted deposition of nano-hydroxyapatite onto exfoliated carbon nanotube oxide scaffolds

NASA Astrophysics Data System (ADS)

Zanin, H.; Rosa, C. M. R.; Eliaz, N.; May, P. W.; Marciano, F. R.; Lobo, A. O.

2015-05-01

Electrodeposited nano-hydroxyapatite (nHAp) is more similar to biological apatite in terms of microstructure and dimension than apatites prepared by other processes. Reinforcement with carbon nanotubes (CNTs) enhances its mechanical properties and increases adhesion of osteoblasts. Here, we carefully studied nHAp deposited onto vertically aligned multi-walled CNT (VAMWCNT) scaffolds by electrodeposition and soaking in a simulated body fluid (SBF). VAMWCNTs are porous biocompatible scaffolds with nanometric porosity and exceptional mechanical and chemical properties. The VAMWCNT films were prepared on a Ti substrate by a microwave plasma chemical vapour deposition method, and then oxidized and exfoliated by oxygen plasma etching (OPE) to produce graphene oxide (GO) at the VAMWCNT tips. The attachment of oxygen functional groups was found to be crucial for nHAp nucleation during electrodeposition. A thin layer of plate-like and needle-like nHAp with high crystallinity was formed without any need for thermal treatment. This composite (henceforth referred to as nHAp-VAMWCNT-GO) served as the scaffold for in vitro biomineralization when soaked in the SBF, resulting in the formation of both carbonate-rich and carbonate-poor globular-like nHAp. Different steps in the deposition of biological apatite onto VAMWCNT-GO and during the short-term biomineralization process were analysed. Due to their unique structure and properties, such nano-bio-composites may become useful in accelerating in vivo bone regeneration processes.

A method to identify differential expression profiles of time-course gene data with Fourier transformation.

PubMed

Kim, Jaehee; Ogden, Robert Todd; Kim, Haseong

2013-10-18

Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization.The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics.

Inter-annual variability of transparent exopolymer particles in the Arctic Ocean reveals high sensitivity to ecosystem changes.

PubMed

Engel, Anja; Piontek, Judith; Metfies, Katja; Endres, Sonja; Sprong, Pim; Peeken, Ilka; Gäbler-Schwarz, Steffi; Nöthig, Eva-Maria

2017-06-23

Transparent exopolymer particles (TEP) are a class of marine gel particles and important links between surface ocean biology and atmospheric processes. Derived from marine microorganisms, these particles can facilitate the biological pumping of carbon dioxide to the deep sea, or act as cloud condensation and ice nucleation particles in the atmosphere. Yet, environmental controls on TEP abundance in the ocean are poorly known. Here, we investigated some of these controls during the first multiyear time-series on TEP abundance for the Fram Strait, the Atlantic gateway to the Central Arctic Ocean. Data collected at the Long-Term Ecological Research observatory HAUSGARTEN during 2009 to 2014 indicate a strong biological control with highest abundance co-occurring with the prymnesiophyte Phaeocystis pouchetii. Higher occurrence of P. pouchetii in the Arctic Ocean has previously been related to northward advection of warmer Atlantic waters, which is expected to increase in the future. Our study highlights the role of plankton key species in driving climate relevant processes; thus, changes in plankton distribution need to be accounted for when estimating the ocean's biogeochemical response to global change.

Metallic elements in fossil fuel combustion products: amounts and form of emissions and evaluation of carcinogenicity and mutagenicity.

PubMed

Vouk, V B; Piver, W T

1983-01-01

Metallic elements contained in coal, oil and gasoline are mobilized by combustion processes and may be emitted into the atmosphere, mainly as components of submicron particles. The information about the amounts, composition and form of metal compounds is reviewed for some fuels and combustion processes. Since metal compounds are always contained in urban air pollutants, they have to be considered whenever an evaluation of biological impact of air pollutants is made. The value of currently used bioassays for the evaluation of the role of trace metal compounds, either as major biologically active components or as modifiers of biological effects of organic compounds is assessed. The whole animal bioassays for carcinogenicity do not seem to be an appropriate approach. They are costly, time-consuming and not easily amenable to the testing of complex mixtures. Some problems related to the application and interpretation of short-term bioassays are considered, and the usefulness of such bioassays for the evaluation of trace metal components contained in complex air pollution mixtures is examined.

Systems biomarkers as acute diagnostics and chronic monitoring tools for traumatic brain injury

NASA Astrophysics Data System (ADS)

Wang, Kevin K. W.; Moghieb, Ahmed; Yang, Zhihui; Zhang, Zhiqun

2013-05-01

Traumatic brain injury (TBI) is a significant biomedical problem among military personnel and civilians. There exists an urgent need to develop and refine biological measures of acute brain injury and chronic recovery after brain injury. Such measures "biomarkers" can assist clinicians in helping to define and refine the recovery process and developing treatment paradigms for the acutely injured to reduce secondary injury processes. Recent biomarker studies in the acute phase of TBI have highlighted the importance and feasibilities of identifying clinically useful biomarkers. However, much less is known about the subacute and chronic phases of TBI. We propose here that for a complex biological problem such as TBI, multiple biomarker types might be needed to harness the wide range of pathological and systemic perturbations following injuries, including acute neuronal death, neuroinflammation, neurodegeneration and neuroregeneration to systemic responses. In terms of biomarker types, they range from brain-specific proteins, microRNA, genetic polymorphism, inflammatory cytokines and autoimmune markers and neuro-endocrine hormones. Furthermore, systems biology-driven biomarkers integration can help present a holistic approach to understanding scenarios and complexity pathways involved in brain injury.

Proteomic analysis of Taenia ovis metacestodes by high performance liquid chromatography-coupled tandem mass spectrometry.

PubMed

Zheng, Yadong

2017-03-15

Taenia ovis metacestodes reside in the muscle of sheep and goats, and may cause great economic loss due to condemnation of carcasses if not effectively controlled. Although advances have been made in the control of T. ovis infection, our knowledge of T. ovis biology is limited. Herein the protein profiling of T. ovis metacestodes was determined by liquid chromatography-linked tandem mass spectrometry. A total of 966 proteins were identified and 25.1% (188/748) were annotated to be associated with metabolic pathways. Consistently, GO analysis returned a metabolic process (16.27%) as one of two main biological process terms. Moreover, it was found that 24 proteins, including very low-density lipoprotein receptor, enolase, paramyosin and endophilin B1, were abundant in T. ovis metacestodes. These proteins may be associated with motility, metabolism, signaling, stress, drug resistance and immune responses. Furthermore, comparative analysis of 5 cestodes revealed the presence of Taenia-specific enolases. These data provide clues for better understanding of T. ovis biology, which is informative for effective control of infection. Copyright © 2017 Elsevier B.V. All rights reserved.

Research in progress: FY 1992. Summaries of projects

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

Not Available

1993-08-01

The Biological and Environmental Research (BER) Program of OHER has two main missions: (1) to develop the knowledge base necessary to identify, understand, and anticipate the long-term health and environmental consequences of energy use and development and (2) to utilize the Department`s unique scientific and technological capabilities to solve major scientific problems in medicine, biology, and the environment. These missions reflect a commitment to develop the beneficial uses of advanced energy technologies while at the same time assuring that any potentially adverse health and environmental impacts of the Nation`s energy policies are fully identified and understood. The BER Program includesmore » research in atmospheric, marine, and terrestrial processes, including the linkage between the use in greenhouse gases, carbon dioxide, and regional and global climate change; in molecular and subcellular mechanisms underlying human somatic and genetic processes and their responses to energy-related environmental toxicants; in nuclear medicine, structural biology, the human genome, measurement sciences and instrumentation, and other areas that require the unique capabilities of the Department`s laboratory system. The principal areas of research are Health Research and Environmental Research.« less

Metallic elements in fossil fuel combustion products: amounts and form of emissions and evaluation of carcinogenicity and mutagenicity.

PubMed Central

Vouk, V B; Piver, W T

1983-01-01

Metallic elements contained in coal, oil and gasoline are mobilized by combustion processes and may be emitted into the atmosphere, mainly as components of submicron particles. The information about the amounts, composition and form of metal compounds is reviewed for some fuels and combustion processes. Since metal compounds are always contained in urban air pollutants, they have to be considered whenever an evaluation of biological impact of air pollutants is made. The value of currently used bioassays for the evaluation of the role of trace metal compounds, either as major biologically active components or as modifiers of biological effects of organic compounds is assessed. The whole animal bioassays for carcinogenicity do not seem to be an appropriate approach. They are costly, time-consuming and not easily amenable to the testing of complex mixtures. Some problems related to the application and interpretation of short-term bioassays are considered, and the usefulness of such bioassays for the evaluation of trace metal components contained in complex air pollution mixtures is examined. PMID:6337825

Software Tool for Researching Annotations of Proteins (STRAP): Open-Source Protein Annotation Software with Data Visualization

PubMed Central

Bhatia, Vivek N.; Perlman, David H.; Costello, Catherine E.; McComb, Mark E.

2009-01-01

In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-consuming search for and compilation of information from online protein databases. Furthermore, visualizing this bulk of information can be challenging due to the limited availability of easy-to-use and freely available tools for this process. In response to these constraints, we have undertaken the design of software to automate annotation and visualization of proteomics data in order to accelerate the pace of research. Here we present the Software Tool for Researching Annotations of Proteins (STRAP) – a user-friendly, open-source C# application. STRAP automatically obtains gene ontology (GO) terms associated with proteins in a proteomics results ID list using the freely accessible UniProtKB and EBI GOA databases. Summarized in an easy-to-navigate tabular format, STRAP includes meta-information on the protein in addition to complimentary GO terminology. Additionally, this information can be edited by the user so that in-house expertise on particular proteins may be integrated into the larger dataset. STRAP provides a sortable tabular view for all terms, as well as graphical representations of GO-term association data in pie (biological process, cellular component and molecular function) and bar charts (cross comparison of sample sets) to aid in the interpretation of large datasets and differential analyses experiments. Furthermore, proteins of interest may be exported as a unique FASTA-formatted file to allow for customizable re-searching of mass spectrometry data, and gene names corresponding to the proteins in the lists may be encoded in the Gaggle microformat for further characterization, including pathway analysis. STRAP, a tutorial, and the C# source code are freely available from http://cpctools.sourceforge.net. PMID:19839595

[An increase in efficiency of adaptations and a weakening of organism protective reactions in the process of biological evolution].

PubMed

Ivanov, K P

2014-01-01

The main direction of evolution of living organisms is development of the central nervous system and sense organ, an increase of energy exchange development of homoiothermia, development of the more and more complex forms of behavior, an increase in energy expenditure in connection with an increase of the organism activity, and development of adaptation to the habitat. Such fundamental processes were subjected and have been subjected to numerous studies and discussions. However, in different animals there exist different species peculiarities of evolution of physiological functions, from which finally formed are fundamental evolutionary processes. We studied some of these specific processes by dividing them into two categories. The first category is "Increase of efficiency of adaptation" in development of biological evolution. By this term we mean development of amazing by perfection specific physiological mechanisms of adaptive character. The second category is "Weakening of protective organism reactions". By this we understand disturbance of protective mechanisms of the organism immune system, discoordination of movement of leukocytes along microvessels, the absence of efficient collateral circulation in brain and in heart, etc.

A Search for Signs of Life and Habitability on Europa

NASA Technical Reports Server (NTRS)

Fonda, Mark (Technical Monitor); McKay, Christoper P.; Eicken, H.; Neuer, S.; Sogin, M.; Waite, H.; Warmflash, D.

2003-01-01

Europa is a key target in the search for life beyond the Earth because of consistent evidence that below the icy surface there is liquid water. Future missions to Europa could confirm the presence and nature of the ocean and determine the thickness of the ice layer. Confirming the presence of an ocean and determining the habitability of Europa are key astrobiology science objectives. Nevertheless, the highest priority objective for astrobiology will be a search for life. How could a search for life be accomplished on a near-term mission given the thick ice cover? One answer may lie in the surface materials. If Europa has an ocean, and if that ocean contains life, and if water from the ocean is carried up to the surface, then signs of life may be contained in organic material on the surface. Organics that derive from biological processes (dead organisms) are distinct from organics derived from non-biological processes in several aspects. First, biology is selective and specific in its use of molecules. For example, Earth life uses 20 left-handed amino acids. Second, biology can leave characteristic isotopic patterns. Third, biology often produces large complex molecules in high concentrations, for example lipids. Organic material that has been on the surface of Europa for long periods of time would be reprocessed by the strong radiation field probably erasing any signature of biological origin. Evidence of life in the ocean may be found on the surface of Europa if regions of the surface contained relatively recent material carried up from the ocean through cracks in the icy lithosphere. But organic material that has been on the surface of Europa for long periods of time would be reprocessed by the strong radiation field probably erasing any signature of biological origin. Thus, the detailed analysis required may not be possible via remote sensing but direct sampling of the material below the radiation processed upper meter is probably required.

NetGen: a novel network-based probabilistic generative model for gene set functional enrichment analysis.

PubMed

Sun, Duanchen; Liu, Yinliang; Zhang, Xiang-Sun; Wu, Ling-Yun

2017-09-21

High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as differential expression gene sets derived from microarray or RNA-seq experiments, is still a challenging task. Gene Ontology (GO) is commonly used in the functional enrichment studies. The GO terms identified via current functional enrichment analysis tools often contain direct parent or descendant terms in the GO hierarchical structure. Highly redundant terms make users difficult to analyze the underlying biological processes. In this paper, a novel network-based probabilistic generative model, NetGen, was proposed to perform the functional enrichment analysis. An additional protein-protein interaction (PPI) network was explicitly used to assist the identification of significantly enriched GO terms. NetGen achieved a superior performance than the existing methods in the simulation studies. The effectiveness of NetGen was explored further on four real datasets. Notably, several GO terms which were not directly linked with the active gene list for each disease were identified. These terms were closely related to the corresponding diseases when accessed to the curated literatures. NetGen has been implemented in the R package CopTea publicly available at GitHub ( http://github.com/wulingyun/CopTea/ ). Our procedure leads to a more reasonable and interpretable result of the functional enrichment analysis. As a novel term combination-based functional enrichment analysis method, NetGen is complementary to current individual term-based methods, and can help to explore the underlying pathogenesis of complex diseases.

The Effects of Short-Term Propofol and Dexmedetomidine on Lung Mechanics, Histology, and Biological Markers in Experimental Obesity.

PubMed

Heil, Luciana Boavista Barros; Santos, Cíntia L; Santos, Raquel S; Samary, Cynthia S; Cavalcanti, Vinicius C M; Araújo, Mariana M P N; Poggio, Hananda; Maia, Lígia de A; Trevenzoli, Isis Hara; Pelosi, Paolo; Fernandes, Fatima C; Villela, Nivaldo R; Silva, Pedro L; Rocco, Patricia R M

2016-04-01

Administering anesthetics to the obese population requires caution because of a variety of reasons including possible interactions with the inflammatory process observed in obese patients. Propofol and dexmedetomidine have protective effects on pulmonary function and are widely used in short- and long-term sedation, particularly in intensive care unit settings in lean and obese subjects. However, the functional and biological effects of these drugs in obesity require further elucidation. In a model of diet-induced obesity, we compared the short-term effects of dexmedetomidine versus propofol on lung mechanics and histology, as well as biological markers of inflammation and oxidative stress modulation in obesity. Wistar rats (n = 56) were randomly fed a standard diet (lean) or experimental diet (obese) for 12 weeks. After this period, obese animals received sodium thiopental intraperitoneally and were randomly allocated into 4 subgroups: (1) nonventilated (n = 4) for molecular biology analysis only (control); (2) sodium thiopental (n = 8); (3) propofol (n = 8); and (4) dexmedetomidine (n = 8), which received continuous IV administration of the corresponding agents and were mechanically ventilated (tidal volume = 6 mL/kg body weight, fraction of inspired oxygen = 0.4, positive end-expiratory pressure = 3 cm H2O) for 1 hour. Compared with lean animals, obese rats did not present increased body weight but had higher total body and trunk fat percentages, airway resistance, and interleukin-6 levels in the lung tissue (P = 0.02, P = 0.0027, and P = 0.01, respectively). In obese rats, propofol, but not dexmedetomidine, yielded increased airway resistance, bronchoconstriction index (P = 0.016, P = 0.02, respectively), tumor necrosis factor-α, and interleukin-6 levels, as well as lower levels of nuclear factor-erythroid 2-related factor-2 and glutathione peroxidase (P = 0.001, Bonferroni-corrected t test). In this model of diet-induced obesity, a 1-hour propofol infusion yielded increased airway resistance, atelectasis, and lung inflammation, with depletion of antioxidative enzymes. However, unlike sodium thiopental and propofol, short-term infusion of dexmedetomidine had no impact on lung morphofunctional and biological variables.

The long and short of it: the role of telomeres in fetal origins of adult disease.

PubMed

Hallows, Stephanie E; Regnault, Timothy R H; Betts, Dean H

2012-01-01

Placental insufficiency, maternal malnutrition, and other causes of intrauterine growth restriction (IUGR) can significantly affect short-term growth and long-term health. Following IUGR, there is an increased risk for cardiovascular disease and Type 2 Diabetes. The etiology of these diseases is beginning to be elucidated, and premature aging or cellular senescence through increased oxidative stress and DNA damage to telomeric ends may be initiators of these disease processes. This paper will explore the areas where telomere and telomerase biology can have significant effects on various tissues in the body in IUGR outcomes.

Microbiology and atmospheric processes: research challenges concerning the impact of airborne micro-organisms on the atmosphere and climate

NASA Astrophysics Data System (ADS)

Morris, C. E.; Sands, D. C.; Bardin, M.; Jaenicke, R.; Vogel, B.; Leyronas, C.; Ariya, P. A.; Psenner, R.

2011-01-01

For the past 200 years, the field of aerobiology has explored the abundance, diversity, survival and transport of micro-organisms in the atmosphere. Micro-organisms have been explored as passive and severely stressed riders of atmospheric transport systems. Recently, an interest in the active roles of these micro-organisms has emerged along with proposals that the atmosphere is a global biome for microbial metabolic activity and perhaps even multiplication. As part of a series of papers on the sources, distribution and roles in atmospheric processes of biological particles in the atmosphere, here we describe the pertinence of questions relating to the potential roles that air-borne micro-organisms might play in meteorological phenomena. For the upcoming era of research on the role of air-borne micro-organisms in meteorological phenomena, one important challenge is to go beyond descriptions of abundance of micro-organisms in the atmosphere toward an understanding of their dynamics in terms of both biological and physico-chemical properties and of the relevant transport processes at different scales. Another challenge is to develop this understanding under contexts pertinent to their potential role in processes related to atmospheric chemistry, the formation of clouds, precipitation and radiative forcing. This will require truly interdisciplinary approaches involving collaborators from the biological and physical sciences, from disciplines as disparate as agronomy, microbial genetics and atmosphere physics, for example.

Microbiology and atmospheric processes: an upcoming era of research on bio-meteorology

NASA Astrophysics Data System (ADS)

Morris, C. E.; Sands, D. C.; Bardin, M.; Jaenicke, R.; Vogel, B.; Leyronas, C.; Ariya, P. A.; Psenner, R.

2008-01-01

For the past 200 years, the field of aerobiology has explored the abundance, diversity, survival and transport of micro-organisms in the atmosphere. Micro-organisms have been explored as passive and severely stressed riders of atmospheric transport systems. Recently, an interest in the active roles of these micro-organisms has emerged along with proposals that the atmosphere is a global biome for microbial metabolic activity and perhaps even multiplication. As part of a series of papers on the sources, distribution and roles in atmospheric processes of biological particles in the atmosphere, here we describe the pertinence of questions relating to the potential roles that air-borne micro-organisms might play in meteorological phenomena. For the upcoming era of research on the role of air-borne micro-organisms in meteorological phenomena, one important challenge is to go beyond descriptions of abundance of micro-organisms in the atmosphere toward an understanding of their dynamics in terms of both biological and physico-chemical properties and of the relevant transport processes at different scales. Another challenge is to develop this understanding under contexts pertinent to their potential role in processes related to atmospheric chemistry, the formation of clouds, precipitation and radiative forcing. This will require truly interdisciplinary approaches involving collaborators from the biological and physical sciences, from disciplines as disparate as agronomy, microbial genetics and atmosphere physics, for example.

Analysis of up-flow aerated biological activated carbon filter technology in drinking water treatment.

PubMed

Lu, Shaoming; Liu, Jincui; Li, Shaowen; Biney, Elizabeth

2013-01-01

Problems have been found in the traditional post-positioned down-flow biological activated carbon filter (DBACF), such as microorganism leakage and low biodegradability. A pilot test was carried out to place a BACF between the sediment tank and the sand filter; a new technology of dual media up-flow aerated biological activated carbon filter (UBACF) was developed. Results showed that in terms of the new process, the up-flow mode was better than the down-flow. Compared with the DBACF, the problem of microorganism leakage could be well resolved with the UBACF process by adding disinfectant before the sand filtration, and a similar adsorption effect could be obtained. For the tested raw water, the COD(Mn) and NH3-N removal rate was 54.6% and 85.0%, respectively, similar to the waterworks with the DBACF process. The UBACF greatly enhanced oxygen supply capability and mass transfer rate via aeration, and the NH3-N removal ability was significantly improved from 1.5 mg/L to more than 3 mg/L. Influent to the UBACF with higher turbidity could be coped with through the primary filtration of the ceramisite layer combined with fluid-bed technology, which gave the carbon bed a low-turbidity environment of less than 1.0 NTU. The backwashing parameters and carbon abrasion rate of the two processes were almost the same.

Disappearance of the inversion effect during memory-guided tracking of scrambled biological motion.

PubMed

Jiang, Changhao; Yue, Guang H; Chen, Tingting; Ding, Jinhong

2016-08-01

The human visual system is highly sensitive to biological motion. Even when a point-light walker is temporarily occluded from view by other objects, our eyes are still able to maintain tracking continuity. To investigate how the visual system establishes a correspondence between the biological-motion stimuli visible before and after the disruption, we used the occlusion paradigm with biological-motion stimuli that were intact or scrambled. The results showed that during visually guided tracking, both the observers' predicted times and predictive smooth pursuit were more accurate for upright biological motion (intact and scrambled) than for inverted biological motion. During memory-guided tracking, however, the processing advantage for upright as compared with inverted biological motion was not found in the scrambled condition, but in the intact condition only. This suggests that spatial location information alone is not sufficient to build and maintain the representational continuity of the biological motion across the occlusion, and that the object identity may act as an important information source in visual tracking. The inversion effect disappeared when the scrambled biological motion was occluded, which indicates that when biological motion is temporarily occluded and there is a complete absence of visual feedback signals, an oculomotor prediction is executed to maintain the tracking continuity, which is established not only by updating the target's spatial location, but also by the retrieval of identity information stored in long-term memory.

Advances and bottlenecks in microbial hydrogen production.

PubMed

Stephen, Alan J; Archer, Sophie A; Orozco, Rafael L; Macaskie, Lynne E

2017-09-01

Biological production of hydrogen is poised to become a significant player in the future energy mix. This review highlights recent advances and bottlenecks in various approaches to biohydrogen processes, often in concert with management of organic wastes or waste CO 2 . Some key bottlenecks are highlighted in terms of the overall energy balance of the process and highlighting the need for economic and environmental life cycle analyses with regard also to socio-economic and geographical issues. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

SCICEX Topsounder Data Processing Transition

DTIC Science & Technology

2018-05-29

2011-2014 May 29, 2018 Reporting Period: 12/23/2015 - 03/31/2018 Prepared for: Office of Naval Research 875 North Randolph Street...unlimited. UNCLASSIFIED 2 LONG-TERM GOALS Arctic sea ice thickness is critical to geophysical research into climate change, shipping, biological...productivity and other things. The overall goal of this work is to produce a public archive of ice draft data for research . The data is meant to

Low carbon amendment rates during anaerobic soil disinfestation (ASD) at moderate soil temperatures do not decrease viability of Sclerotinia sclerotiorum sclerotia or Fusarium root rot of common bean

USDA-ARS?s Scientific Manuscript database

Anaerobic soil disinfestation (ASD; also termed biological soil disinfestation) is a non-chemical process which includes 1) soil incorporation of a labile carbon (C) source, 2) mulching with polyethylene film to limit gas exchange, and 3) drip irrigation to saturation of the topsoil or bedded area. ...

[Biological evolution and ancient DNA].

PubMed

Debruyne, Régis; Barriel, Véronique

2006-05-01

Twenty years after the advent of ancient DNA studies, this discipline seems to have reached the maturity formerly lacking to the fulfilment of its objectives. In its early development paleogenetics, as it is now acknowledged, had to cope with very limited data due to the technical limitations of molecular biology. It led to phylogenetic assumptions often limited in their scope and sometimes non-focused or even spurious results that cast the reluctance of the scientific community. This time seems now over and huge amounts of sequences have become available which overcome the former limitations and bridge the gap between paleogenetics, genomics and population biology. The recent studies over the charismatic woolly mammoth (independent sequencing of the whole mitochondrial genome and of millions of base pairs of the nuclear genome) exemplify the growing accuracy of ancient DNA studies thanks to new molecular approaches. From the earliest publications up to now, the number of mammoth nucleotides was multiplied by 100,000. Likewise, populational approaches of ice-age taxa provide new historical scenarios about the diversification and extinction of the Pleistocene megafauna on the one hand, and about the processes of domestication of animal and vegetal species by Man on the other. They also shed light on the differential structure of molecular diversity between short-term populational research (below 2 My) and long-term (over 2 My) phylogenetic approaches. All those results confirm the growing importance of paleogenetics among the evolutionary biology disciplines.

Improvement of organics removal by bio-ceramic filtration of raw water with addition of phosphorus.

PubMed

Sang, Junqiang; Zhang, Xihui; Li, Lingzhi; Wang, Zhansheng

2003-11-01

The purpose of this study was to investigate the effect of phosphorus addition on biological pretreatment of raw water. Experiments were conducted in pilot-scale bio-ceramic filters with raw water from a reservoir located in Beijing, China. The results demonstrated that phosphorus was the limiting nutrient for bacterial growth in the raw water investigated in this study. The measured values of bacterial regrowth potential (BRP) and biodegradable dissolved organic carbon (BDOC) of the raw water increased by 50-65% and 30-40% with addition of 50 microg of PO4(3-)-PL(-1), respectively. Addition of 25 microg of PO4(3-)-PL(-1) to the influent of bio-ceramic filter enhanced the percent removal of organics by 4.6, 5.7 and 15 percentage points in terms of COD(Mn), TOC and BDOC, respectively. Biomass in terms of phospholipid content increased by 13-22% and oxygen uptake rate (OUR) increased by 35-45%. The ratio of C:P for bacteria growth was 100:1.6 for the raw water used in this study. Since change of phosphorus concentrations can influence the performance of biological pretreatment and the biological stability of drinking water, this study is of substantial significance for waterworks in China. The role of phosphorus in biological processes of drinking water should deserve more attention.

Deconstructing (and reconstructing) cell migration.

PubMed

Maheshwari, G; Lauffenburger, D A

1998-12-01

An overriding objective in cell biology is to be able to relate properties of particular molecular components to cell behavioral functions and even physiology. In the "traditional" mode of molecular cell biology, this objective has been tackled on a molecule-by-molecule basis, and in the "future" mode sometimes termed "functional genomics," it might be attacked in a high-throughput, parallel manner. Regardless of the manner of approach, the relationship between molecular-level properties and cell-level function is exceedingly difficult to elucidate because of the large number of relevant components involved, their high degree of interconnectedness, and the inescapable fact that they operate as physico-chemical entities-according to the laws of kinetics and mechanics-in space and time within the cell. Cell migration is a prominent representative example of such a cell behavioral function that requires increased understanding for both scientific and technological advance. This article presents a framework, derived from an engineering perspective regarding complex systems, intended to aid in developing improved understanding of how properties of molecular components influence the function of cell migration. That is, cell population migration behavior can be deconstructed as follows: first in terms of a mathematical model comprising cell population parameters (random motility, chemotaxis/haptotaxis, and chemokinesis/haptokinesis coefficients), which in turn depend on characteristics of individual cell paths that can be analyzed in terms of a mathematical model comprising individual cell parameters (translocation speed, directional persistence time, chemotactic/haptotactic index), which in turn depend on cell-level physical processes underlying motility (membrane extension and retraction, cell/substratum adhesion, cell contractile force, front-vs.-rear asymmetry), which in turn depend on molecular-level properties of the plethora of components involved in governance and regulation of these processes. Hence, the influence of any molecular component on cell population migration can be understood by reconstructing these relationships from the molecular level to the physical process level to the individual cell path level to the cell population distribution level. This approach requires combining experimental, theoretical, and computational methodologies from molecular biology, biochemistry, biophysics, and bioengineering.

Automated Comparative Auditing of NCIT Genomic Roles Using NCBI

PubMed Central

Cohen, Barry; Oren, Marc; Min, Hua; Perl, Yehoshua; Halper, Michael

2008-01-01

Biomedical research has identified many human genes and various knowledge about them. The National Cancer Institute Thesaurus (NCIT) represents such knowledge as concepts and roles (relationships). Due to the rapid advances in this field, it is to be expected that the NCIT’s Gene hierarchy will contain role errors. A comparative methodology to audit the Gene hierarchy with the use of the National Center for Biotechnology Information’s (NCBI’s) Entrez Gene database is presented. The two knowledge sources are accessed via a pair of Web crawlers to ensure up-to-date data. Our algorithms then compare the knowledge gathered from each, identify discrepancies that represent probable errors, and suggest corrective actions. The primary focus is on two kinds of gene-roles: (1) the chromosomal locations of genes, and (2) the biological processes in which genes plays a role. Regarding chromosomal locations, the discrepancies revealed are striking and systematic, suggesting a structurally common origin. In regard to the biological processes, difficulties arise because genes frequently play roles in multiple processes, and processes may have many designations (such as synonymous terms). Our algorithms make use of the roles defined in the NCIT Biological Process hierarchy to uncover many probable gene-role errors in the NCIT. These results show that automated comparative auditing is a promising technique that can identify a large number of probable errors and corrections for them in a terminological genomic knowledge repository, thus facilitating its overall maintenance. PMID:18486558

Cost of biologics in the treatment of juvenile idiopathic arthritis: a factor not to be overlooked.

PubMed

Prince, Femke H M; van Suijlekom-Smit, Lisette W A

2013-08-01

Biologics are a promising treatment option for juvenile idiopathic arthritis (JIA) but drug costs are very high compared to conventional treatment. From a socioeconomic view the additional costs of new interventions should be weighed against their incremental health benefits compared to standard care. Therefore we evaluated data on cost-effectiveness of biologics in JIA. We searched Medline, Embase, and The York Centre for Reviews and Dissemination database for relevant literature. Current data show that biologics are reducing direct and indirect healthcare costs if one excludes the costs of the drug itself. The costs of biologics are more than ten times as high as conventional drug treatment. As a result of limited data, no comparison on cost-effectiveness between biologics could be performed. Although data on long-term cost-effectiveness of biologics are lacking, the expectation is that they will be cost-effective in the long-term. The idea behind this is that biologic treatment should be administered to patients that without these drugs would incur high direct and indirect costs due to continuous severe disease resulting in irreversible disabilities. In our opinion the best cost benefit could be gained if these patients receive biologic treatment introduced early in the disease. This is in order to minimize irreversible damage to the joints and minimize need for long-term biologic therapy by early suppression of the disease. To support these hypotheses future research is needed on long-term cost-effectiveness of all biologics used in JIA.

Enhanced HMAX model with feedforward feature learning for multiclass categorization.

PubMed

Li, Yinlin; Wu, Wei; Zhang, Bo; Li, Fengfu

2015-01-01

In recent years, the interdisciplinary research between neuroscience and computer vision has promoted the development in both fields. Many biologically inspired visual models are proposed, and among them, the Hierarchical Max-pooling model (HMAX) is a feedforward model mimicking the structures and functions of V1 to posterior inferotemporal (PIT) layer of the primate visual cortex, which could generate a series of position- and scale- invariant features. However, it could be improved with attention modulation and memory processing, which are two important properties of the primate visual cortex. Thus, in this paper, based on recent biological research on the primate visual cortex, we still mimic the first 100-150 ms of visual cognition to enhance the HMAX model, which mainly focuses on the unsupervised feedforward feature learning process. The main modifications are as follows: (1) To mimic the attention modulation mechanism of V1 layer, a bottom-up saliency map is computed in the S1 layer of the HMAX model, which can support the initial feature extraction for memory processing; (2) To mimic the learning, clustering and short-term memory to long-term memory conversion abilities of V2 and IT, an unsupervised iterative clustering method is used to learn clusters with multiscale middle level patches, which are taken as long-term memory; (3) Inspired by the multiple feature encoding mode of the primate visual cortex, information including color, orientation, and spatial position are encoded in different layers of the HMAX model progressively. By adding a softmax layer at the top of the model, multiclass categorization experiments can be conducted, and the results on Caltech101 show that the enhanced model with a smaller memory size exhibits higher accuracy than the original HMAX model, and could also achieve better accuracy than other unsupervised feature learning methods in multiclass categorization task.

Novel aspects of endometrial function: a biological sensor of embryo quality and driver of pregnancy success.

PubMed

Sandra, Olivier; Mansouri-Attia, Nadéra; Lea, Richard G

2011-01-01

Successful pregnancy depends on complex biological processes that are regulated temporally and spatially throughout gestation. The molecular basis of these processes have been examined in relation to gamete quality, early blastocyst development and placental function, and data have been generated showing perturbations of these developmental stages by environmental insults or embryo biotechnologies. The developmental period falling between the entry of the blastocyst into the uterine cavity to implantation has also been examined in terms of the biological function of the endometrium. Indeed several mechanisms underlying uterine receptivity, controlled by maternal factors, and the maternal recognition of pregnancy, requiring conceptus-produced signals, have been clarified. Nevertheless, recent data based on experimental perturbations have unveiled unexpected biological properties of the endometrium (sensor/driver) that make this tissue a dynamic and reactive entity. Persistent or transient modifications in organisation and functionality of the endometrium can dramatically affect pre-implantation embryo trajectory through epigenetic alterations with lasting consequences on later stages of pregnancy, including placentation, fetal development, pregnancy outcome and post-natal health. Developing diagnostic and prognostic tools based on endometrial factors may enable the assessment of maternal reproductive capacity and/or the developmental potential of the embryo, particularly when assisted reproductive technologies are applied.

Evaluating a preventive biological control agent applied on grapevines against Botrytis cinerea and its influence on winemaking.

PubMed

Escribano-Viana, Rocío; Portu, Javier; Garijo, Patrocinio; Gutiérrez, Ana Rosa; Santamaría, Pilar; López-Alfaro, Isabel; López, Rosa; González-Arenzana, Lucía

2018-02-25

This research was aimed to study the influence on grape and wine quality and on the fermentation processes of the application of a preventive biological treatment against Botrytis cinerea in Tempranillo Rioja grapevines. For this purpose, a biofungicide containing Bacillus subtilis QST713 was applied twice to the vineyard. Results were compared with non-treated samples from the same vineyard and with samples treated with a chemical fungicide composed of fenhexamid. Data showed that general grape quality and spontaneous alcoholic fermentation performance were not influenced by either fungicide application. The chemical fungicide had a considerable influence on the clonal diversity of Saccharomyces cerevisiae species, which led to the alcoholic fermentation. Furthermore, it caused longer malolactic fermentation than with the biological fungicide and in the control. The biofungicide made malolactic fermentation 1 day shorter because the establishment of the commercial lactic acid bacteria used as a starter culture was total. After malolactic fermentation, the wines did not show significant differences in general oenological parameters. Preventive biofungicide treatment against B. cinerea did not negatively influence the quality of grapes and wines and the fermentation processes. Therefore, biological control of B. cinerea with B. subtilis applied on grapevines could be advisable in oenological terms. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Reduced orienting to audiovisual synchrony in infancy predicts autism diagnosis at 3 years of age.

PubMed

Falck-Ytter, Terje; Nyström, Pär; Gredebäck, Gustaf; Gliga, Teodora; Bölte, Sven

2018-01-23

Effective multisensory processing develops in infancy and is thought to be important for the perception of unified and multimodal objects and events. Previous research suggests impaired multisensory processing in autism, but its role in the early development of the disorder is yet uncertain. Here, using a prospective longitudinal design, we tested whether reduced visual attention to audiovisual synchrony is an infant marker of later-emerging autism diagnosis. We studied 10-month-old siblings of children with autism using an eye tracking task previously used in studies of preschoolers. The task assessed the effect of manipulations of audiovisual synchrony on viewing patterns while the infants were observing point light displays of biological motion. We analyzed the gaze data recorded in infancy according to diagnostic status at 3 years of age (DSM-5). Ten-month-old infants who later received an autism diagnosis did not orient to audiovisual synchrony expressed within biological motion. In contrast, both infants at low-risk and high-risk siblings without autism at follow-up had a strong preference for this type of information. No group differences were observed in terms of orienting to upright biological motion. This study suggests that reduced orienting to audiovisual synchrony within biological motion is an early sign of autism. The findings support the view that poor multisensory processing could be an important antecedent marker of this neurodevelopmental condition. © 2018 Association for Child and Adolescent Mental Health.

Predicted Arabidopsis Interactome Resource and Gene Set Linkage Analysis: A Transcriptomic Analysis Resource.

PubMed

Yao, Heng; Wang, Xiaoxuan; Chen, Pengcheng; Hai, Ling; Jin, Kang; Yao, Lixia; Mao, Chuanzao; Chen, Xin

2018-05-01

An advanced functional understanding of omics data is important for elucidating the design logic of physiological processes in plants and effectively controlling desired traits in plants. We present the latest versions of the Predicted Arabidopsis Interactome Resource (PAIR) and of the gene set linkage analysis (GSLA) tool, which enable the interpretation of an observed transcriptomic change (differentially expressed genes [DEGs]) in Arabidopsis ( Arabidopsis thaliana ) with respect to its functional impact for biological processes. PAIR version 5.0 integrates functional association data between genes in multiple forms and infers 335,301 putative functional interactions. GSLA relies on this high-confidence inferred functional association network to expand our perception of the functional impacts of an observed transcriptomic change. GSLA then interprets the biological significance of the observed DEGs using established biological concepts (annotation terms), describing not only the DEGs themselves but also their potential functional impacts. This unique analytical capability can help researchers gain deeper insights into their experimental results and highlight prospective directions for further investigation. We demonstrate the utility of GSLA with two case studies in which GSLA uncovered how molecular events may have caused physiological changes through their collective functional influence on biological processes. Furthermore, we showed that typical annotation-enrichment tools were unable to produce similar insights to PAIR/GSLA. The PAIR version 5.0-inferred interactome and GSLA Web tool both can be accessed at http://public.synergylab.cn/pair/. © 2018 American Society of Plant Biologists. All Rights Reserved.

The roles of protein expression in synaptic plasticity and memory consolidation

PubMed Central

Rosenberg, Tali; Gal-Ben-Ari, Shunit; Dieterich, Daniela C.; Kreutz, Michael R.; Ziv, Noam E.; Gundelfinger, Eckart D.; Rosenblum, Kobi

2014-01-01

The amount and availability of proteins are regulated by their synthesis, degradation, and transport. These processes can specifically, locally, and temporally regulate a protein or a population of proteins, thus affecting numerous biological processes in health and disease states. Accordingly, malfunction in the processes of protein turnover and localization underlies different neuronal diseases. However, as early as a century ago, it was recognized that there is a specific need for normal macromolecular synthesis in a specific fragment of the learning process, memory consolidation, which takes place minutes to hours following acquisition. Memory consolidation is the process by which fragile short-term memory is converted into stable long-term memory. It is accepted today that synaptic plasticity is a cellular mechanism of learning and memory processes. Interestingly, similar molecular mechanisms subserve both memory and synaptic plasticity consolidation. In this review, we survey the current view on the connection between memory consolidation processes and proteostasis, i.e., maintaining the protein contents at the neuron and the synapse. In addition, we describe the technical obstacles and possible new methods to determine neuronal proteostasis of synaptic function and better explain the process of memory and synaptic plasticity consolidation. PMID:25429258

Collecting, archiving and processing DNA from wildlife samples using FTA® databasing paper

PubMed Central

Smith, LM; Burgoyne, LA

2004-01-01

Background Methods involving the analysis of nucleic acids have become widespread in the fields of traditional biology and ecology, however the storage and transport of samples collected in the field to the laboratory in such a manner to allow purification of intact nucleic acids can prove problematical. Results FTA® databasing paper is widely used in human forensic analysis for the storage of biological samples and for purification of nucleic acids. The possible uses of FTA® databasing paper in the purification of DNA from samples of wildlife origin were examined, with particular reference to problems expected due to the nature of samples of wildlife origin. The processing of blood and tissue samples, the possibility of excess DNA in blood samples due to nucleated erythrocytes, and the analysis of degraded samples were all examined, as was the question of long term storage of blood samples on FTA® paper. Examples of the end use of the purified DNA are given for all protocols and the rationale behind the processing procedures is also explained to allow the end user to adjust the protocols as required. Conclusions FTA® paper is eminently suitable for collection of, and purification of nucleic acids from, biological samples from a wide range of wildlife species. This technology makes the collection and storage of such samples much simpler. PMID:15072582

Complexity Level Analysis Revisited: What Can 30 Years of Hindsight Tell Us about How the Brain Might Represent Visual Information?

PubMed Central

Tsotsos, John K.

2017-01-01

Much has been written about how the biological brain might represent and process visual information, and how this might inspire and inform machine vision systems. Indeed, tremendous progress has been made, and especially during the last decade in the latter area. However, a key question seems too often, if not mostly, be ignored. This question is simply: do proposed solutions scale with the reality of the brain's resources? This scaling question applies equally to brain and to machine solutions. A number of papers have examined the inherent computational difficulty of visual information processing using theoretical and empirical methods. The main goal of this activity had three components: to understand the deep nature of the computational problem of visual information processing; to discover how well the computational difficulty of vision matches to the fixed resources of biological seeing systems; and, to abstract from the matching exercise the key principles that lead to the observed characteristics of biological visual performance. This set of components was termed complexity level analysis in Tsotsos (1987) and was proposed as an important complement to Marr's three levels of analysis. This paper revisits that work with the advantage that decades of hindsight can provide. PMID:28848458

Complexity Level Analysis Revisited: What Can 30 Years of Hindsight Tell Us about How the Brain Might Represent Visual Information?

PubMed

Tsotsos, John K

2017-01-01

Much has been written about how the biological brain might represent and process visual information, and how this might inspire and inform machine vision systems. Indeed, tremendous progress has been made, and especially during the last decade in the latter area. However, a key question seems too often, if not mostly, be ignored. This question is simply: do proposed solutions scale with the reality of the brain's resources? This scaling question applies equally to brain and to machine solutions. A number of papers have examined the inherent computational difficulty of visual information processing using theoretical and empirical methods. The main goal of this activity had three components: to understand the deep nature of the computational problem of visual information processing; to discover how well the computational difficulty of vision matches to the fixed resources of biological seeing systems; and, to abstract from the matching exercise the key principles that lead to the observed characteristics of biological visual performance. This set of components was termed complexity level analysis in Tsotsos (1987) and was proposed as an important complement to Marr's three levels of analysis. This paper revisits that work with the advantage that decades of hindsight can provide.

State-of-the-art and outlook for biomimetic materials

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

Richman, R.H.; Bond, G.M.; McNaughton, W.P.

1994-11-01

A remarkable diversity of structures and molecular functions has evolved in plants and animals. Many of these natural substances have properties or capabilities that belie their origins in humble, everyday, starting materials. Consequently, there is a growing awareness among scientists and engineers that biological systems can be a valuable source of inspiration for man-made materials. Emphasis in this assessment is on biomimetics; that is, the achievement of unusual materials properties or processes by mimicking novel aspects of biological systems. Five broad areas are selected for detailed investigation: Mimicking of Natural Material Designs; Biomimetic Materials Processing; Artificial Photosynthesis; Biomimetic Molecular Electronics;more » and Biomimetic Catalysis. Each of these topics is examined in terms of current activities and approaches, key aspects, unresolved issues, and implications for the power industry. Finally, the researchers, their organizations, the main thrusts of investigation, achievements, and funding agencies are summarized in tabular form.« less

Aging Biology and Novel Targets for Drug Discovery

PubMed Central

McLachlan, Andrew J.; Quinn, Ronald J.; Simpson, Stephen J.; de Cabo, Rafael

2012-01-01

Despite remarkable technological advances in genetics and drug screening, the discovery of new pharmacotherapies has slowed and new approaches to drug development are needed. Research into the biology of aging is generating many novel targets for drug development that may delay all age-related diseases and be used long term by the entire population. Drugs that successfully delay the aging process will clearly become “blockbusters.” To date, the most promising leads have come from studies of the cellular pathways mediating the longevity effects of caloric restriction (CR), particularly target of rapamycin and the sirtuins. Similar research into pathways governing other hormetic responses that influence aging is likely to yield even more targets. As aging becomes a more attractive target for drug development, there will be increasing demand to develop biomarkers of aging as surrogate outcomes for the testing of the effects of new agents on the aging process. PMID:21693687

Atomic force microscopy and spectroscopy to probe single membrane proteins in lipid bilayers.

PubMed

Sapra, K Tanuj

2013-01-01

The atomic force microscope (AFM) has opened vast avenues hitherto inaccessible to the biological scientist. The high temporal (millisecond) and spatial (nanometer) resolutions of the AFM are suited for studying many biological processes in their native conditions. The AFM cantilever stylus is aptly termed as a "lab on a tip" owing to its versatility as an imaging tool as well as a handle to manipulate single bonds and proteins. Recent examples assert that the AFM can be used to study the mechanical properties and monitor processes of single proteins and single cells, thus affording insight into important mechanistic details. This chapter specifically focuses on practical and analytical protocols of single-molecule AFM methodologies related to high-resolution imaging and single-molecule force spectroscopy of membrane proteins. Both these techniques are operator oriented, and require specialized working knowledge of the instrument, theoretical, and practical skills.

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

Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp

We present that challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone–substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperonemore » Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.« less

Natural history of hepatic metastases from colorectal cancer--pathobiological pathways with clinical significance.

PubMed

Paschos, Konstantinos A; Majeed, Ali W; Bird, Nigel C

2014-04-14

Colorectal cancer hepatic metastases represent the final stage of a multi-step biological process. This process starts with a series of mutations in colonic epithelial cells, continues with their detachment from the large intestine, dissemination through the blood and/or lymphatic circulation, attachment to the hepatic sinusoids and interactions with the sinusoidal cells, such as sinusoidal endothelial cells, Kupffer cells, stellate cells and pit cells. The metastatic sequence terminates with colorectal cancer cell invasion, adaptation and colonisation of the hepatic parenchyma. All these events, termed the colorectal cancer invasion-metastasis cascade, include multiple molecular pathways, intercellular interactions and expression of a plethora of chemokines and growth factors, and adhesion molecules, such as the selectins, the integrins or the cadherins, as well as enzymes including matrix metalloproteinases. This review aims to present recent advances that provide insights into these cell-biological events and emphasizes those that may be amenable to therapeutic targeting.

Interplay between social experiences and the genome: epigenetic consequences for behavior.

PubMed

Champagne, Frances A

2012-01-01

Social experiences can have a persistent effect on biological processes leading to phenotypic diversity. Variation in gene regulation has emerged as a mechanism through which the interplay between DNA and environments leads to the biological encoding of these experiences. Epigenetic modifications-molecular pathways through which transcription is altered without altering the underlying DNA sequence-play a critical role in the normal process of development and are being increasingly explored as a mechanism linking environmental experiences to long-term biobehavioral outcomes. In this review, evidence implicating epigenetic factors, such as DNA methylation and histone modifications, in the link between social experiences occurring during the postnatal period and in adulthood and altered neuroendocrine and behavioral outcomes will be highlighted. In addition, the role of epigenetic mechanisms in shaping variation in social behavior and the implications of epigenetics for our understanding of the transmission of traits across generations will be discussed. Copyright © 2012 Elsevier Inc. All rights reserved.

Ocean acidification may increase calcification rates, but at a cost

PubMed Central

Wood, Hannah L; Spicer, John I; Widdicombe, Stephen

2008-01-01

Ocean acidification is the lowering of pH in the oceans as a result of increasing uptake of atmospheric carbon dioxide. Carbon dioxide is entering the oceans at a greater rate than ever before, reducing the ocean's natural buffering capacity and lowering pH. Previous work on the biological consequences of ocean acidification has suggested that calcification and metabolic processes are compromised in acidified seawater. By contrast, here we show, using the ophiuroid brittlestar Amphiura filiformis as a model calcifying organism, that some organisms can increase the rates of many of their biological processes (in this case, metabolism and the ability to calcify to compensate for increased seawater acidity). However, this upregulation of metabolism and calcification, potentially ameliorating some of the effects of increased acidity comes at a substantial cost (muscle wastage) and is therefore unlikely to be sustainable in the long term. PMID:18460426

Synthesis and Biological Response of Size-Specific, Monodisperse Drug-Silica Nanoconjugates

PubMed Central

Tang, Li; Fan, Timothy M.; Borst, Luke B.; Cheng, Jianjun

2012-01-01

Drug-containing nanoparticles (NPs) with monodisperse, controlled particle sizes are highly desirable for drug delivery. Accumulating evidence suggests that NPs with sizes less than 50 nm demonstrate superior performance in vitro and in vivo. However, it is difficult to fabricate monodisperse, drug-containing NPs with discrete and incremental difference in sizes required for studying and characterizing existing relationships among particle size, biologic processing, and therapeutic functionality. Here, we report a scalable process of fabricating drug-silica conjugated nanoparticles, termed drug-silica nanoconjugates (drug-NCs), which possess monodisperse size distributions and desirable particle sizes as small as 20 nm. We found that 20-nm NCs are superior to their 50-nm and 200-nm NC analogues by 2–5 and 10–20 folds, respectively, with regard to tumor accumulation and penetration, and cellular internalization. These fundamental findings underscore the importance and necessity of further miniaturizing nanomedicine size for optimized drug delivery applications. PMID:22494403

A long term glider study of shelf sea oxygen dynamics

NASA Astrophysics Data System (ADS)

Williams, Charlotte; Palmer, Matthew; Mahaffey, Claire; Davis, Clare

2017-04-01

Oxygen is involved in most biogeochemical processes in the ocean, and dissolved oxygen (DO) is a well-established indicator for biological activity via the estimate of apparent oxygen utilisation (AOU). In the deep waters of the open ocean, the AOU provides a valuable insight into the ocean's biological carbon pump. However, in the physically dynamic and highly productive shallow shelf seas, interpretation of the oxygen distribution and the magnitude of AOU is complex. Physical processes, such as diapycnal mixing, entrainment and horizontal advection act to ventilate waters below the thermocline and thus increase oxygen and decrease AOU. In contrast, biological remineralisation of organic material below the thermocline will consume oxygen and increase AOU. We aim to address the following: 1. Does AOU change seasonally in a shelf sea in response to seasonal changes in productivity? 2. How important is turbulence in redistributing oxygen in a shelf sea? Using 9 months of high-resolution data from >20 glider deployments in the seasonally stratified NW European Shelf Sea we identify and quantify the physical and biological processes that control the DO distribution and magnitude of AOU in shelf seas. A 200km transect between the shelf edge and the central Celtic Sea (CCS) was repeated between November 2014 and August 2015, thus capturing key periods in the seasonal cycling in shelf seas, specifically the onset of stratification, the spring bloom, stratified summer period and breakdown of stratification. The gliders collected data for DO, temperature, salinity, chlorophyll fluorescence, CDOM, backscatter and turbulence. In addition, direct measurements of turbulent dissipation from the Ocean Microstructure Glider deployed during the campaign provided estimates of mixing at CCS and the shelf break, allowing accurate quantification of the vertical fluxes of oxygen. We find that oxygen decreases ubiquitously across the shelf as soon as stratification takes hold, though BML oxygen decreases at a slower rate during summer compared to spring at the shelf break and also across the inner shelf. This appears to be due to a stronger oxycline and potentially more efficient, sporadic mixing of oxygen across the thermocline during summer. Biological oxygen consumption is greater at the shelf break than on shelf even when accounting for enhanced oxygen diapycnal fluxes at the shelf break. Gliders prove to be a good tool in monitoring long term oxygen changes in shelf seas and we find that accurate estimation of AOU in the shelf sea requires inclusion of mixing processes.

Assessing anthropogenic impact on boreal lakes with historical fish species distribution data and hydrogeochemical modeling.

PubMed

Valinia, Salar; Englund, Göran; Moldan, Filip; Futter, Martyn N; Köhler, Stephan J; Bishop, Kevin; Fölster, Jens

2014-09-01

Quantifying the effects of human activity on the natural environment is dependent on credible estimates of reference conditions to define the state of the environment before the onset of adverse human impacts. In Europe, emission controls that aimed at restoring ecological status were based on hindcasts from process-based models or paleolimnological reconstructions. For instance, 1860 is used in Europe as the target for restoration from acidification concerning biological and chemical parameters. A more practical problem is that the historical states of ecosystems and their function cannot be observed directly. Therefore, we (i) compare estimates of acidification based on long-term observations of roach (Rutilus rutilus) populations with hindcast pH from the hydrogeochemical model MAGIC; (ii) discuss policy implications and possible scope for use of long-term archival data for assessing human impacts on the natural environment and (iii) present a novel conceptual model for interpreting the importance of physico-chemical and ecological deviations from reference conditions. Of the 85 lakes studied, 78 were coherently classified by both methods. In 1980, 28 lakes were classified as acidified with the MAGIC model, however, roach was present in 14 of these. In 2010, MAGIC predicted chemical recovery in 50% of the lakes, however roach only recolonized in five lakes after 1990, showing a lag between chemical and biological recovery. Our study is the first study of its kind to use long-term archival biological data in concert with hydrogeochemical modeling for regional assessments of anthropogenic acidification. Based on our results, we show how the conceptual model can be used to understand and prioritize management of physico-chemical and ecological effects of anthropogenic stressors on surface water quality. © 2014 The Authors Global Change Biology Published by John Wiley & Sons Ltd.

In Vitro Experimental Model for the Long-Term Analysis of Cellular Dynamics During Bronchial Tree Development from Lung Epithelial Cells

PubMed Central

Maruta, Naomichi; Marumoto, Moegi

2017-01-01

Lung branching morphogenesis has been studied for decades, but the underlying developmental mechanisms are still not fully understood. Cellular movements dynamically change during the branching process, but it is difficult to observe long-term cellular dynamics by in vivo or tissue culture experiments. Therefore, developing an in vitro experimental model of bronchial tree would provide an essential tool for developmental biology, pathology, and systems biology. In this study, we succeeded in reconstructing a bronchial tree in vitro by using primary human bronchial epithelial cells. A high concentration gradient of bronchial epithelial cells was required for branching initiation, whereas homogeneously distributed endothelial cells induced the formation of successive branches. Subsequently, the branches grew in size to the order of millimeter. The developed model contains only two types of cells and it facilitates the analysis of lung branching morphogenesis. By taking advantage of our experimental model, we carried out long-term time-lapse observations, which revealed self-assembly, collective migration with leader cells, rotational motion, and spiral motion of epithelial cells in each developmental event. Mathematical simulation was also carried out to analyze the self-assembly process and it revealed simple rules that govern cellular dynamics. Our experimental model has provided many new insights into lung development and it has the potential to accelerate the study of developmental mechanisms, pattern formation, left–right asymmetry, and disease pathogenesis of the human lung. PMID:28471293

Dynamic Interaction- and Phospho-Proteomics Reveal Lck as a Major Signaling Hub of CD147 in T Cells.

PubMed

Supper, Verena; Hartl, Ingrid; Boulègue, Cyril; Ohradanova-Repic, Anna; Stockinger, Hannes

2017-03-15

Numerous publications have addressed CD147 as a tumor marker and regulator of cytoskeleton, cell growth, stress response, or immune cell function; however, the molecular functionality of CD147 remains incompletely understood. Using affinity purification, mass spectrometry, and phosphopeptide enrichment of isotope-labeled peptides, we examined the dynamic of the CD147 microenvironment and the CD147-dependent phosphoproteome in the Jurkat T cell line upon treatment with T cell stimulating agents. We identified novel dynamic interaction partners of CD147 such as CD45, CD47, GNAI2, Lck, RAP1B, and VAT1 and, furthermore, found 76 CD147-dependent phosphorylation sites on 57 proteins. Using the STRING protein network database, a network between the CD147 microenvironment and the CD147-dependent phosphoproteins was generated and led to the identification of key signaling hubs around the G proteins RAP1B and GNB1, the kinases PKCβ, PAK2, Lck, and CDK1, and the chaperone HSPA5. Gene ontology biological process term analysis revealed that wound healing-, cytoskeleton-, immune system-, stress response-, phosphorylation- and protein modification-, defense response to virus-, and TNF production-associated terms are enriched within the microenvironment and the phosphoproteins of CD147. With the generated signaling network and gene ontology biological process term grouping, we identify potential signaling routes of CD147 affecting T cell growth and function. Copyright © 2017 by The American Association of Immunologists, Inc.

Laser-induced dissociation processes of protonated glucose: dehydration reactions vs cross-ring dissociation

NASA Astrophysics Data System (ADS)

Dyakov, Y. A.; Kazaryan, M. A.; Golubkov, M. G.; Gubanova, D. P.; Bulychev, N. A.; Kazaryan, S. M.

2018-04-01

Studying the processes occurring in biological systems under irradiation is critically important for understanding the principles of working of biological systems. One of the main problems, which stimulate interest to the processes of photo-induced excitation and ionization of biomolecules, is the necessity of their identification by various mass spectrometry (MS) methods. While simple analysis of small molecules became a standard MS technique long time ago, recognition of large molecules, especially carbohydrates, is still a difficult problem, and requires sophisticated techniques and complicated computer analysis. Due to the large variety of substances in the samples, as far as the complexity of the processes occurring after excitation/ionization of the molecules, the recognition efficiency of MS technique in terms of carbohydrates is still not high enough. Additional theoretical and experimental analysis of ionization and dissociation processes in various kinds of polysaccharides, beginning from the simplest ones, is necessary. In our work, we extent previous theoretical and experimental studies of saccharides, and concentrate our attention to protonated glucose. In this article we paid the most attention to the cross-ring dissociation and water loss reactions due to their importance for identification of various isomers of hydrocarbon molecules (for example, distinguish α- and β-glucose).

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

PubMed Central

Li, Le; Yip, Kevin Y.

2016-01-01

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

Severe and acute complications of biologics in psoriasis.

PubMed

Oussedik, Elias; Patel, Nupur U; Cash, Devin R; Gupta, Angela S; Feldman, Steven R

2017-12-01

Biologic therapies have revolutionized the approach to immune-mediated diseases such as psoriasis. Due to their favorable safety profiles and excellent efficacy, biologic agents are considered the gold standard for moderate-to-severe psoriasis. The aim of this paper is to saliently review the severe and acute complications of the Food and Drug Administration (FDA) approved biologic agents for psoriasis. Reviewed agents include tumor necrosis factor alpha inhibitors (etanercept, infliximab, and adalimumab), interleukin 12/23 inhibitors (ustekinumab), and interleukin 17 (IL-17) inhibitors (secukinumab and ixekizumab). While malignancies, serious infections, and major adverse cardiovascular events have been reported, their association with biologic therapy are not hypothesized as causal. However, IL-17 inhibitors appear to cause exacerbations and new cases of inflammatory bowel disease. While more long-term studies are warranted in understanding the biologic's long-term side effect profile, short-term studies have confirmed that the biologics are some of the safest treatment options for psoriasis. Nevertheless, certain populations yield higher risk to acute complications with the biologics than others - physicians must use their judgement and vigilance when monitoring and treating patients undergoing therapy with biological agents.

Hybrid coexpression link similarity graph clustering for mining biological modules from multiple gene expression datasets

PubMed Central

2014-01-01

Background Advances in genomic technologies have enabled the accumulation of vast amount of genomic data, including gene expression data for multiple species under various biological and environmental conditions. Integration of these gene expression datasets is a promising strategy to alleviate the challenges of protein functional annotation and biological module discovery based on a single gene expression data, which suffers from spurious coexpression. Results We propose a joint mining algorithm that constructs a weighted hybrid similarity graph whose nodes are the coexpression links. The weight of an edge between two coexpression links in this hybrid graph is a linear combination of the topological similarities and co-appearance similarities of the corresponding two coexpression links. Clustering the weighted hybrid similarity graph yields recurrent coexpression link clusters (modules). Experimental results on Human gene expression datasets show that the reported modules are functionally homogeneous as evident by their enrichment with biological process GO terms and KEGG pathways. PMID:25221624

Biological and Organic Chemical Decomposition of Silicates. Chapter 7.2

NASA Technical Reports Server (NTRS)

Silverman, M. P.

1979-01-01

The weathering of silicate rocks and minerals, an important concern of geologists and geochemists for many years, traditionally has been approached from strictly physical and chemical points of view. Biological effects were either unrecognized, ignored, or were mentioned in passing to account for such phenomena as the accumulation of organic matter in sediments or the generation of reducing environments. A major exception occurred in soil science where agricultural scientists, studying the factors important in the development of soils and their ability to nourish and sustain various crops, laid the foundation for much of what is known of the biological breakdown of silicate rocks and minerals. The advent of the space age accelerated the realization that many environmental problems and geo- chemical processes on Earth can only be understood in terms of ecosystems. This in turn, spurred renewed interest and activity among modem biologists, geologists and soil scientists attempting to unravel the intimate relations between biology and the weathering of silicate rocks and minerals of the earth surface.

Biological and Organic Chemical Decomposition of Silicates. Chapter 7.2

NASA Technical Reports Server (NTRS)

Sliverman, M. P.

1979-01-01

The weathering of silicate rocks and minerals, an important concern of geologists and geochemists for many years, traditionally has been approached from strictly physical and chemical points of view. Biological effects were either unrecognized, ignored, or were mentioned in passing to account for such phenomena as the accumulation of organic matter in sediments or the generation of reducing environments. A major exception occurred in soil science where agricultural scientists, studying the factors important in the development of soils and their ability to nourish and sustain various crops, laid the foundation for much of what is known of the biological breakdown of silicate rocks and minerals. The advent of the space age accelerated the realization that many environmental problems and geochemical processes on Earth can only be understood in terms of ecosystems. This in turn, spurred renewed interest and activity among modem biologists, geologists and soil scientists attempting to unravel the intimate relations between biology and the weathering of silicate rocks and minerals of the earth's surface.

Exclusivity strategies and opportunities in view of the Biologics Price Competition and Innovation Act.

PubMed

Gaudry, Kate S

2011-01-01

Government-provided exclusivity periods provide pharmaceutical companies with incentives to invest in new drugs. Meanwhile, encouraging competition serves another worthy goal of improving the affordability of medications. Decades ago, the Hatch-Waxman Act set forth provisions attempting to balance these objectives in the context of small-molecule drugs. Recently, the Biologics Price Competition and Innovation Act was enacted to meet similar aims in the context of biologic drugs. This article presents a detailed comparison of these two Acts. While the Acts share many global similarities (e.g., providing exclusivity terms and abbreviated approval processes), many differences are also apparent when analyzing details of the provisions. One area of great departure between the Acts is the requirements of how a generic or follow-on applicant must address patents covering a reference product. After describing these differences, the article presents predictions of how reference product sponsors will adapt their patent-prosecution strategies in view of the new Biologics Act.

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

NASA Astrophysics Data System (ADS)

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.

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

PubMed

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

PubMed Central

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. PMID:28051123

Exponential evolution: implications for intelligent extraterrestrial life.

PubMed

Russell, D A

1983-01-01

Some measures of biologic complexity, including maximal levels of brain development, are exponential functions of time through intervals of 10(6) to 10(9) yrs. Biological interactions apparently stimulate evolution but physical conditions determine the time required to achieve a given level of complexity. Trends in brain evolution suggest that other organisms could attain human levels within approximately 10(7) yrs. The number (N) and longevity (L) terms in appropriate modifications of the Drake Equation, together with trends in the evolution of biological complexity on Earth, could provide rough estimates of the prevalence of life forms at specified levels of complexity within the Galaxy. If life occurs throughout the cosmos, exponential evolutionary processes imply that higher intelligence will soon (10(9) yrs) become more prevalent than it now is. Changes in the physical universe become less rapid as time increases from the Big Bang. Changes in biological complexity may be most rapid at such later times. This lends a unique and symmetrical importance to early and late universal times.

Ontology of physics for biology: representing physical dependencies as a basis for biological processes.

PubMed

Cook, Daniel L; Neal, Maxwell L; Bookstein, Fred L; Gennari, John H

2013-12-02

In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale "physiome" projects such as the EU's Virtual Physiological Human (VPH) and NIH's Virtual Physiological Rat (VPR). Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the "rules" by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm's law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke's law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. We have developed the OPB and annotation methods to represent the meaning-the biophysical semantics-of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes.

Biogeosystem technique as the way to certainty of soil, hydrosphere, environment and climate

NASA Astrophysics Data System (ADS)

Kalinitchenko, Valery; Batukaev, Abdulmalik; Zarmaev, Ali; Startsev, Viktor; Chernenko, Vladimir; Dikaev, Zaurbek; Sushkova, Svetlana

2016-04-01

The modern technological platform awkwardly imitates the Nature. Teaching the Geosciences, development of technology, overcoming the problem of uncertainty of geospheres is impossible on the base of outdated knowledge. An emphasis is to be done not on the natural analogues, but on our new technologies - Biogeosystem Technique (BGT*). BGT* is a transcendental (not imitating the natural processes) approach to soil processing, regulation of fluxes of energy, gas, water, matter and biological productivity of biosphere: Intrasoil milling processing in 20-50 cm soil layer provides new soil disperse system, best conditions for stable evolution of techno-soil and plant growth in period up to 40 years after the single processing. Pulse intrasoil discrete irrigation provides an injection of small discrete dose of water which distributes in vertical soil cylinder. Lateral distance between successive injections is 10-15 cm. The water within 5-10 min after injection spreads in cylinder of diameter 2-4 cm at depth from 5 to 50 cm. The soil carcass around the cylinder is dry and mechanically stable. Mean thermodynamic soil water potential after watering is of -0.2 MPa. Stomatal apparatus is in a regulation mode, transpiration rate is reduced, soil solution concentration increased, plant nutrition rate and biological productivity are high. No excessive plant transpiration, evaporation and seepage of water from soil. Intrasoil environmentally safe waste return during intrasoil milling processing and (or) intrasoil pulse discrete plants watering with nutrition. Is provided the medically, veterinary and environmentally safe recycle of municipal, industrial, biological and agricultural wastes into the soil continuum. All applied substances transform to plant nutrients, not degrade to the greenhouse gas, or become the deposit of waste. Capabilities of intrasoil technologies of BGT* to correct and sustain the Nature: Correct soil evolution, long-term biological productivity of intrasoil processed soil of 150% higher compared to initial. Save of fresh water by intrasoil irrigation up to 20 times. Biological return of matter and high biological productivity of soil by environmentally safe intrasoil waste recycling. On the base of BGT* are opened the opportunities for: controlled, stable, safe, biologically effective soil, environment and landscape; improved equilibriums in soil, environment and landscape; reduced water consumption; improved waste management; reduced flux of nutrients to water systems; carbon transformation into the soil to the state of elements of plant nutrition; reducing degradation of biological matter to the state of greenhouse gases; increasing biologi al consumption of carbon dioxide by photosynthesis in terrestrial system; prolongation of the phase of carbon in terrestrial biological system for greenhouse gases sequestration; extension of the active area of biosphere on terrestrial part of the Earth; high rate oxidation of methane and hydrogen sulfide by oxygen, which is ionized in photosynthesis, and thus is biologically active; high biological product output of biosphere. The higher biomass on the Earth, the more ecologically safe food, raw material and biofuel can be produced, better conditions for technologies of Noosphere. Uncertainty of soil, hydrosphere, environment and climate will be reduced by the BGT* methods. Are available BGT* robotic systems of low cost and minimal consumption of energy and material.

TermGenie – a web-application for pattern-based ontology class generation

DOE PAGES

Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.; ...

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 newmore » classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. Lastly, TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.« less

TermGenie – a web-application for pattern-based ontology class generation

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

Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 newmore » classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. Lastly, TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.« less

TermGenie - a web-application for pattern-based ontology class generation.

PubMed

Dietze, Heiko; Berardini, Tanya Z; Foulger, Rebecca E; Hill, David P; Lomax, Jane; Osumi-Sutherland, David; Roncaglia, Paola; Mungall, Christopher J

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

Why and How We Age, and Is That Process Modifiable?

NASA Astrophysics Data System (ADS)

Arking, R.

Aging is an almost-universal biological process that is better understood in terms of an evolutionary explanation than in terms of a medical or adaptationist explanation. The major advances in human longevity which took place in developed countries during the past century arose from decreases in external (e.g., environmental) sources of mortality, and not from any effect on the aging process. Laboratory studies show that the aging process is under genetic control, can be manipulated, and can be expressed in three different phenotypes. The adult lifespan consists of the health span (ages 20-55 yrs) and the senescent span (ages 55+), with a relatively short but variable transition phase between the two. The most socially desirable phenotype would be that where the transition phase is delayed and the health span extended with little effect on the senescent span. The genetic, nutritional, cell-signaling and pharmecutical interventions inducing this phenotype are discussed. The genetic architecture of senescence is discussed and its stochastic nature made clear. The social and ethical consequences of pharmecutical intervention into the aging process are briefly discussed.

Damage to cellular DNA from particulate radiations, the efficacy of its processing and the radiosensitivity of mammalian cells. Emphasis on DNA double strand breaks and chromatin breaks

NASA Technical Reports Server (NTRS)

Lett, J. T.

1992-01-01

For several years, it has been evident that cellular radiation biology is in a necessary period of consolidation and transition (Lett 1987, 1990; Lett et al. 1986, 1987). Both changes are moving apace, and have been stimulated by studies with heavy charged particles. From the standpoint of radiation chemistry, there is now a consensus of opinion that the DNA hydration shell must be distinguished from bulk water in the cell nucleus and treated as an integral part of DNA (chromatin) (Lett 1987). Concomitantly, sentiment is strengthening for the abandonment of the classical notions of "direct" and "indirect" action (Fielden and O'Neill 1991; O'Neill 1991; O'Neill et al. 1991; Schulte-Frohlinde and Bothe 1991 and references therein). A layer of water molecules outside, or in the outer edge of, the DNA (chromatin) hydration shell influences cellular radiosensitivity in ways not fully understood. Charge and energy transfer processes facilitated by, or involving, DNA hydration must be considered in rigorous theories of radiation action on cells. The induction and processing of double stand breaks (DSBs) in DNA (chromatin) seem to be the predominant determinants of the radiotoxicity of normally radioresistant mammalian cells, the survival curves of which reflect the patterns of damage induced and the damage present after processing ceases, and can be modelled in formal terms by the use of reaction (enzyme) kinetics. Incongruities such as sublethal damage are neither scientifically sound nor relevant to cellular radiation biology (Calkins 1991; Lett 1990; Lett et al. 1987a). Increases in linear energy transfer (LET infinity) up to 100-200 keV micron-1 cause increases in the extents of neighboring chemical and physical damage in DNA denoted by the general term DSB. Those changes are accompanied by decreasing abilities of cells normally radioresistant to sparsely ionizing radiations to process DSBs in DNA and chromatin and to recover from radiation exposure, so they make significant contributions to the relative biological effectiveness (RBE) of a given radiation.(ABSTRACT TRUNCATED AT 400 WORDS).

Cognitive science as an interface between rational and mechanistic explanation.

PubMed

Chater, Nick

2014-04-01

Cognitive science views thought as computation; and computation, by its very nature, can be understood in both rational and mechanistic terms. In rational terms, a computation solves some information processing problem (e.g., mapping sensory information into a description of the external world; parsing a sentence; selecting among a set of possible actions). In mechanistic terms, a computation corresponds to causal chain of events in a physical device (in engineering context, a silicon chip; in biological context, the nervous system). The discipline is thus at the interface between two very different styles of explanation--as the papers in the current special issue well illustrate, it explores the interplay of rational and mechanistic forces. Copyright © 2014 Cognitive Science Society, Inc.

Extinction events can accelerate evolution.

PubMed

Lehman, Joel; Miikkulainen, Risto

2015-01-01

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.

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

PubMed

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.

Distinguishing pathological from constitutional small for gestational age births in population-based studies.

PubMed

Ananth, Cande V; Vintzileos, Anthony M

2009-10-01

Small for gestational age (SGA) can occur following a pathological process or may represent constitutionally small fetuses. However, distinguishing these processes is often difficult, especially in large studies, where the term SGA is often used as a proxy for restricted fetal growth. Since biologic variation in fetal size is largely a third trimester phenomenon, we hypothesized that the definition of SGA at term may include a sizeable proportion of constitutionally small fetuses. In contrast, since biologic variation in fetal size is not fully expressed in (early) preterm gestations, it is plausible that SGA in early preterm gestations would comprise a large proportion of growth restricted fetuses. We compared mortality and morbidity rates between SGA and appropriate for gestational age (AGA) babies. A population-based study of over 19million non-malformed, singleton births (1995-04) in the United States was performed. Gestational age (24-44weeks) was based on a clinical estimate. SGA and AGA were defined as sex-specific birthweight <10th and 25-74th centiles, respectively, for gestational age. All analyses were adjusted for a variety of confounding factors. Excess mortality risk in SGA and AGA babies. On an additive scale, stillbirth and neonatal mortality rates were higher at every preterm gestation among SGA than AGA births, and similar at term gestations. An inverse relationship between gestational age and excess deaths between SGA and AGA babies delivered at <37weeks was evident. In early preterm gestations, the definition of SGA may well be justified as a proxy for IUGR. In contrast, SGA babies that are delivered at term are likely to be constitutionally small.

Clinical, Functional, and Biological Correlates of Cognitive Dimensions in Major Depressive Disorder – Rationale, Design, and Characteristics of the Cognitive Function and Mood Study (CoFaM-Study)

PubMed Central

Baune, Bernhard T.; Air, Tracy

2016-01-01

Cross-sectional and longitudinal studies exploring clinical, functional, and biological correlates of major depressive disorder are frequent. In this type of research, depression is most commonly defined as a categorical diagnosis based on studies using diagnostic instruments. Given the phenotypic and biological heterogeneity of depression, we chose to focus the phenotypic assessments on three cognitive dimensions of depression including (a) cognitive performance, (b) emotion processing, and (c) social cognitive functioning. Hence, the overall aim of the study is to investigate the long-term clinical course of these cognitive dimensions in depression and its functional (psychosocial) correlates. We also aim to identify biological “genomic” correlates of these three cognitive dimensions of depression. To address the above overall aim, we created the Cognition and Mood Study (CoFaMS) with the key objective to investigate the clinical, functional, and biological correlates of cognitive dimensions of depression by employing a prospective study design and including a healthy control group. The study commenced in April 2015, including patients with a primary diagnosis of a major depressive episode of major depressive disorder or bipolar disorder according to DSM-IV-TR criteria. The assessments cover the three cognitive dimensions of depression (cognitive performance, emotion processing, and social cognition), cognitive function screening instrument, plus functional scales to assess general, work place, and psychosocial function, depression symptom scales, and clinical course of illness. Blood is collected for comprehensive genomic discovery analyses of biological correlates of cognitive dimensions of depression. The CoFaM-Study represents an innovative approach focusing on cognitive dimensions of depression and its functional and biological “genomic” correlates. The CoFaMS team welcomes collaborations with both national and international researchers. PMID:27616997

Clinical, Functional, and Biological Correlates of Cognitive Dimensions in Major Depressive Disorder - Rationale, Design, and Characteristics of the Cognitive Function and Mood Study (CoFaM-Study).

PubMed

Baune, Bernhard T; Air, Tracy

2016-01-01

Cross-sectional and longitudinal studies exploring clinical, functional, and biological correlates of major depressive disorder are frequent. In this type of research, depression is most commonly defined as a categorical diagnosis based on studies using diagnostic instruments. Given the phenotypic and biological heterogeneity of depression, we chose to focus the phenotypic assessments on three cognitive dimensions of depression including (a) cognitive performance, (b) emotion processing, and (c) social cognitive functioning. Hence, the overall aim of the study is to investigate the long-term clinical course of these cognitive dimensions in depression and its functional (psychosocial) correlates. We also aim to identify biological "genomic" correlates of these three cognitive dimensions of depression. To address the above overall aim, we created the Cognition and Mood Study (CoFaMS) with the key objective to investigate the clinical, functional, and biological correlates of cognitive dimensions of depression by employing a prospective study design and including a healthy control group. The study commenced in April 2015, including patients with a primary diagnosis of a major depressive episode of major depressive disorder or bipolar disorder according to DSM-IV-TR criteria. The assessments cover the three cognitive dimensions of depression (cognitive performance, emotion processing, and social cognition), cognitive function screening instrument, plus functional scales to assess general, work place, and psychosocial function, depression symptom scales, and clinical course of illness. Blood is collected for comprehensive genomic discovery analyses of biological correlates of cognitive dimensions of depression. The CoFaM-Study represents an innovative approach focusing on cognitive dimensions of depression and its functional and biological "genomic" correlates. The CoFaMS team welcomes collaborations with both national and international researchers.

Perceived Partner Responsiveness Predicts Diurnal Cortisol Profiles 10 Years Later.

PubMed

Slatcher, Richard B; Selcuk, Emre; Ong, Anthony D

2015-07-01

Several decades of research have demonstrated that marital relationships have a powerful influence on physical health. However, surprisingly little is known about how marriage affects health--both in terms of psychological processes and biological ones. Over a 10-year period, we investigated the associations between perceived partner responsiveness--the extent to which people feel understood, cared for, and appreciated by their romantic partners--and diurnal cortisol in a large sample of married and cohabitating couples in the United States. Partner responsiveness predicted higher cortisol values at awakening and steeper (i.e., healthier) cortisol slopes at the 10-year follow-up. These associations remained strong after we controlled for demographic factors, depressive symptoms, agreeableness, and other positive and negative relationship factors. Furthermore, declines in negative affect over the 10-year period mediated the prospective association between responsiveness and cortisol slope. These findings suggest that diurnal cortisol may be a key biological pathway through which social relationships affect long-term health. © The Author(s) 2015.

Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions.

PubMed

Foo, Mathias; Sawlekar, Rucha; Kulkarni, Vishwesh V; Bates, Declan G

2016-08-01

The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators. Here, we propose an alternative design approach that utilises the abstract chemical reactions involved in cellular signalling cycles to implement a biomolecular controller - termed a signalling-cycle (SC) controller. We compare the performance of the PI and SC controllers in closed-loop with a nonlinear second-order chemical process. Our results show that the SC controller outperforms the PI controller in terms of both performance and robustness, and also requires fewer abstract chemical reactions to implement, highlighting its potential usefulness in the construction of biomolecular control circuits.

Dosimetry for photo-coagulation by the use of autofluorescence

NASA Astrophysics Data System (ADS)

Brodzinski, T.

1989-01-01

A basic problem when using lasers in medicine is that of dosimetry. The definition of the terms dose, effective value etc. will be dealt with in Chapter 2. This chapter is intended to give an insight into the problems of basic dosimetry and its technical realization within the field of photocoagulation, an established method used to treat the retina, or some skin diseases. Until now the coagulation process was assessed to be completed when the irradiated area became blanched. However in terms of dosimetry, it must be possible to predict or at least to monitor the biological effect using well-defined parameters for the laser or in achieving an objective measure for a feedback loop. In the case of coagulation, a prediction in this form is not possible. There are two ways of pro- ceeding further see Fig. 1. One can either determine the physical effect, i.e. temperature, by some kind of sensors, or even better, use some biological effect as a direct measure of the effective dose applied.

Repair and tissue engineering techniques for articular cartilage.

PubMed

Makris, Eleftherios A; Gomoll, Andreas H; Malizos, Konstantinos N; Hu, Jerry C; Athanasiou, Kyriacos A

2015-01-01

Chondral and osteochondral lesions due to injury or other pathology commonly result in the development of osteoarthritis, eventually leading to progressive total joint destruction. Although current progress suggests that biologic agents can delay the advancement of deterioration, such drugs are incapable of promoting tissue restoration. The limited ability of articular cartilage to regenerate renders joint arthroplasty an unavoidable surgical intervention. This Review describes current, widely used clinical repair techniques for resurfacing articular cartilage defects; short-term and long-term clinical outcomes of these techniques are discussed. Also reviewed is a developmental pipeline of acellular and cellular regenerative products and techniques that could revolutionize joint care over the next decade by promoting the development of functional articular cartilage. Acellular products typically consist of collagen or hyaluronic-acid-based materials, whereas cellular techniques use either primary cells or stem cells, with or without scaffolds. Central to these efforts is the prominent role that tissue engineering has in translating biological technology into clinical products; therefore, concomitant regulatory processes are also discussed.

Changing social factors and their long-term implications for health.

PubMed

Wadsworthx, M E

1997-01-01

This paper presents findings and arguments to show the power of social factors to affect health at the individual and at the national level. Social factors most strongly and negatively associated with health, at both levels, are those that indicate disorganisation and disruption, perceived helplessness and lack of support, low educational attainment, and poverty. Adverse changes in these social factors and their negative effects on health have been observed in many studies. When such adverse changes affect the lives and health of children, and those who will become parents, they affect the present and long-term future health of individuals because of the processes of biological programming described in this and other papers presented here. Such adverse changes in social factors also adversely affect the social circumstances of childhood, which in turn have a negative impact on health. Because changing social factors affect biological programming and social capitalisation, awareness of the health damaging effects of recent social change provides information on the future health of the population.

Patterns of use and impact of standardised MedDRA query analyses on the safety evaluation and review of new drug and biologics license applications.

PubMed

Chang, Lin-Chau; Mahmood, Riaz; Qureshi, Samina; Breder, Christopher D

2017-01-01

Standardised MedDRA Queries (SMQs) have been developed since the early 2000's and used by academia, industry, public health, and government sectors for detecting safety signals in adverse event safety databases. The purpose of the present study is to characterize how SMQs are used and the impact in safety analyses for New Drug Application (NDA) and Biologics License Application (BLA) submissions to the United States Food and Drug Administration (USFDA). We used the PharmaPendium database to capture SMQ use in Summary Basis of Approvals (SBoAs) of drugs and biologics approved by the USFDA. Characteristics of the drugs and the SMQ use were employed to evaluate the role of SMQ safety analyses in regulatory decisions and the veracity of signals they revealed. A comprehensive search of the SBoAs yielded 184 regulatory submissions approved from 2006 to 2015. Search strategies more frequently utilized restrictive searches with "narrow terms" to enhance specificity over strategies using "broad terms" to increase sensitivity, while some involved modification of search terms. A majority (59%) of 1290 searches used descriptive statistics, however inferential statistics were utilized in 35% of them. Commentary from reviewers and supervisory staff suggested that a small, yet notable percentage (18%) of 1290 searches supported regulatory decisions. The searches with regulatory impact were found in 73 submissions (40% of the submissions investigated). Most searches (75% of 227 searches) with regulatory implications described how the searches were confirmed, indicating prudence in the decision-making process. SMQs have an increasing role in the presentation and review of safety analysis for NDAs/BLAs and their regulatory reviews. This study suggests that SMQs are best used for screening process, with descriptive statistics, description of SMQ modifications, and systematic verification of cases which is crucial for drawing regulatory conclusions.

Reviewing the evidence for biosimilars: key insights, lessons learned and future horizons

PubMed Central

Goll, Guro L.

2017-01-01

Abstract Biologic therapies have become central to the long-term management of many chronic diseases, including inflammatory rheumatic diseases. Over recent years, the development and licensing pathways for biosimilars have become more standardized, and several biosimilars have been made available for patients with inflammatory rheumatic diseases, such as RA. Pre-licensing requirements for biosimilars mandate the demonstration of comparability with reference products in terms of clinical activity, safety and immunogenicity, whereas post-marketing surveillance and risk minimization requirements are set in place to ensure that long-term, real-world safety data are collected to assess biosimilars in clinical practice. These measures should provide a foundation for physician confidence in biosimilars, which can be established further through clinical experience. Biosimilars may help to fill an unmet need by improving patient access to effective biologic treatments for chronic diseases. Greater access may result in additional clinical benefits, with appropriate use of biologic therapies according to treatment guidelines being associated with improved outcomes and the potential for reduced costs of care. Key challenges for the integration of biosimilars into everyday practice include questions about interchangeability, switching and automatic substitution. Several switching studies have shown that biosimilars can be used in place of reference products while maintaining efficacy and safety. Additional ongoing studies and registries may help to optimize the process of switching, and different funding models are examining the optimal mechanisms to ensure effective uptake of these new treatments. PMID:28903542

Biogeography

NASA Technical Reports Server (NTRS)

Quattrochi, Dale A.; Arnold, James E. (Technical Monitor)

2002-01-01

As a field of study, biogeography may be considered a bricolage - it has been constructed from many different facets from an array of research disciplines including biology, botany, zoology, geography, and geology. Biogeography focuses on the study of the constantly changing ranges of plants and animals, over multitude of space and time scales. It also includes the study of the structure and dynamics of biotic communities and ecosystems as they relate to both natural and anthropogenic processes. As it exists today, biogeography is an interdisciplinary research area founded in both the biological and Earth sciences. From a purely biological perspective, biogeography may be perceived as one of two types of studies: 1. biotic distributions and broad scales, and interpretations of the evolutionary and dispersal history of a single taxon or a few taxa; or 2. biotic distributions at local-to-regional scales, and interpretations of these distributions in relation to contemporary environments and rates of immigration or extinction. The first type of study is what is most usually associated with the term "biogeography" as disciplinary research field. It is conventionally termed "classical biogeography" because it reflects the continuity of research foci on which biogeography was founded in the nineteenth-century. The second type of biogeographical study has more modern day roots and is termed "geographical ecology" to reflect the theoretical predilections of ecologists and population biologists. Geographical ecology for all intents has become merged with ecology and exists as a sub discipline within this larger field of study.

Space Biophysics: Accomplishments, Trends, Challenges

NASA Technical Reports Server (NTRS)

Smith, Jeffrey D.

2015-01-01

Physics and biology are inextricably linked. All the chemical and biological processes of life are dutifully bound to follow the rules and laws of physics. In space, these physical laws seem to turn on their head and biological systems, from microbes to humans, adapt and evolve in myriad ways to cope with the changed physical influences of the space environment. Gravity is the most prominent change in space that influences biology. In microgravity, the physical processes of sedimentation, density-driven convective flow, influence of surface tension and fluid pressure profoundly influence biology at the molecular and cellular level as well as at the whole-body level. Gravity sensing mechanisms are altered, structural and functional components of biology (such as bone and muscle) are reduced and changes in the way fluids and gasses behave also drive the way microbial systems and biofilms grow as well as the way plants and animals adapt. The radiation environment also effects life in space. Solar particle events and high energy cosmic radiation can cause serious damage to DNA and other biomolecules. The results can cause mutation, cellular damage or death, leading to health consequences of acute radiation damage or long-term health consequences such as increased cancer risk. Space Biophysics is the study and utilization of physical changes in space that cause changes in biological systems. The unique physical environment in space has been used successfully to grow high-quality protein crystals and 3D tissue cultures that could not be grown in the presence of unidirectional gravitational acceleration here on Earth. All biological processes that change in space have their root in a biophysical alteration due to microgravity and/or the radiation environment of space. In order to fully-understand the risks to human health in space and to fully-understand how humans, plants, animals and microbes can safely and effectively travel and eventually live for long periods beyond the protective environment of Earth, the biophysical properties underlying these changes must be studied, characterized and understood. This lecture reviews the current state of NASA biophysics research accomplishments and identifies future trends and challenges for biophysics research on the International Space Station and beyond.

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

Fraley, John J.; Marotz, Brian L.; DosSantos, Joseph M.

In this document we present fisheries losses, mitigation alternatives, and recommendations to protect, mitigate, and enhance resident fish and aquatic habitat affected by the construction and operation of Hungry Horse Dam. This plan addresses six separate program measures in the 1987 Columbia Basin Fish and Wildlife Program. We designed the plan to be closely coordinated in terms of dam operations, funding, and activities with the Kerr Mitigation Plan presently before the Federal Energy Regulatory Commission. This document represents a mitigation plan for consideration by the Northwest Power Planning Council process; it is not an implementation plan. Flathead Lake is onemore » of the cleanest lakes of its size in the world. The exceptional water quality and unique native fisheries make the Flathead Lake/River system extremely valuable to the economy and quality of life in the basin. The recreational fishery in Flathead Lake has an estimated value of nearly eight million dollars annually. This mitigation process represents our best opportunity to reduce the impacts of hydropower in this valuable aquatic system and increase angling opportunity. We based loss estimates and mitigation alternatives on an extensive data base, agency reports, nationally and internationally peer-reviewed scientific articles, and an innovative biological model for Hungry Horse Reservoir and the Flathead River. We conducted an extensive, 14-month scoping and consultation process with agency representatives, representatives of citizen groups, and the general public. This consultation process helped identify issues, areas of agreement, areas of conflict, and advantages and disadvantages of mitigation alternatives. The results of the scoping and consultation process helped shape our mitigation plan. Our recommended plan is based firmly on principles of adaptive management and recognition of biological uncertainty. After we receive direction from the NPPC, we will add more detailed hypotheses and other features necessary for a long-term implementation plan.« less

Genetic resources for methane production from biomass described with the Gene Ontology.

PubMed

Purwantini, Endang; Torto-Alalibo, Trudy; Lomax, Jane; Setubal, João C; Tyler, Brett M; Mukhopadhyay, Biswarup

2014-01-01

Methane (CH4) is a valuable fuel, constituting 70-95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing "gold standards" for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/).

Genetic resources for methane production from biomass described with the Gene Ontology

PubMed Central

Purwantini, Endang; Torto-Alalibo, Trudy; Lomax, Jane; Setubal, João C.; Tyler, Brett M.; Mukhopadhyay, Biswarup

2014-01-01

Methane (CH4) is a valuable fuel, constituting 70–95% of natural gas, and a potent greenhouse gas. Release of CH4 into the atmosphere contributes to climate change. Biological CH4 production or methanogenesis is mostly performed by methanogens, a group of strictly anaerobic archaea. The direct substrates for methanogenesis are H2 plus CO2, acetate, formate, methylamines, methanol, methyl sulfides, and ethanol or a secondary alcohol plus CO2. In numerous anaerobic niches in nature, methanogenesis facilitates mineralization of complex biopolymers such as carbohydrates, lipids and proteins generated by primary producers. Thus, methanogens are critical players in the global carbon cycle. The same process is used in anaerobic treatment of municipal, industrial and agricultural wastes, reducing the biological pollutants in the wastes and generating methane. It also holds potential for commercial production of natural gas from renewable resources. This process operates in digestive systems of many animals, including cattle, and humans. In contrast, in deep-sea hydrothermal vents methanogenesis is a primary production process, allowing chemosynthesis of biomaterials from H2 plus CO2. In this report we present Gene Ontology (GO) terms that can be used to describe processes, functions and cellular components involved in methanogenic biodegradation and biosynthesis of specialized coenzymes that methanogens use. Some of these GO terms were previously available and the rest were generated in our Microbial Energy Gene Ontology (MENGO) project. A recently discovered non-canonical CH4 production process is also described. We have performed manual GO annotation of selected methanogenesis genes, based on experimental evidence, providing “gold standards” for machine annotation and automated discovery of methanogenesis genes or systems in diverse genomes. Most of the GO-related information presented in this report is available at the MENGO website (http://www.mengo.biochem.vt.edu/). PMID:25520705

Developmental origins of epigenetic transgenerational inheritance

PubMed Central

Hanson, Mark A.; Skinner, Michael K.

2016-01-01

Abstract Environmental factors can induce epigenetic alterations in the germ cells that can potentially be transmitted transgenerationally. This non-genetic form of inheritance is termed epigenetic transgenerational inheritance and has been shown in a variety of species including plants, flies, worms, fish, rodents, pigs, and humans. This phenomenon operates during specific critical windows of exposure, linked to the developmental biology of the germ cells (sperm and eggs). Therefore, concepts of the developmental origins of transgenerational inheritance of phenotypic variation and subsequent disease risk need to include epigenetic processes affecting the developmental biology of the germ cell. These developmental impacts on epigenetic transgenerational inheritance, in contrast to multigenerational exposures, are the focus of this Perspective. PMID:27390622

Advances in the Urinary Exosomes in Renal Diseases.

PubMed

Chen, Pei-Pei; Qin, Yan; Li, Xue-Mei

2016-08-01

Cells secrete around 30- 100 nm membrane-enclosed vesicles that are released into the extracellular spaceis termed exosomes(EXs). EXs widely present in body fluids and incorporated proteins,nucleic acids that reflect the physiological state of their cells of origin and they may play an important role in cell-to-cell communication in various physiological and disease processes. In this article we review the recent basic and clinical studies in urinary EXs in renal diseases,focusing on their biological characteristics and potential roles as new biological markers,intervention treatment goals,and targeted therapy vectors in renal diseases.However,some issues still exist;in particular,the clinical application of EXs as a liquid biopsy technique warrants further investigations.

Introduction to electron crystallography.

PubMed

Kühlbrandt, Werner

2013-01-01

From the earliest work on regular arrays in negative stain, electron crystallography has contributed greatly to our understanding of the structure and function of biological macromolecules. The development of electron cryo-microscopy (cryo-EM) then lead to the first groundbreaking atomic models of the membrane proteins bacteriorhodopsin and light harvesting complex II within lipid bilayers. Key contributions towards cryo-EM and electron crystallography methods included specimen preparation and vitrification, liquid-helium cooling, data collection, and image processing. These methods are now applied almost routinely to both membrane and soluble proteins. Here we outline the advances and the breakthroughs that paved the way towards high-resolution structures by electron crystallography, both in terms of methods development and biological milestones.

A dictionary learning approach for Poisson image deblurring.

PubMed

Ma, Liyan; Moisan, Lionel; Yu, Jian; Zeng, Tieyong

2013-07-01

The restoration of images corrupted by blur and Poisson noise is a key issue in medical and biological image processing. While most existing methods are based on variational models, generally derived from a maximum a posteriori (MAP) formulation, recently sparse representations of images have shown to be efficient approaches for image recovery. Following this idea, we propose in this paper a model containing three terms: a patch-based sparse representation prior over a learned dictionary, the pixel-based total variation regularization term and a data-fidelity term capturing the statistics of Poisson noise. The resulting optimization problem can be solved by an alternating minimization technique combined with variable splitting. Extensive experimental results suggest that in terms of visual quality, peak signal-to-noise ratio value and the method noise, the proposed algorithm outperforms state-of-the-art methods.

A unified anatomy ontology of the vertebrate skeletal system.

PubMed

Dahdul, Wasila M; Balhoff, James P; Blackburn, David C; Diehl, Alexander D; Haendel, Melissa A; Hall, Brian K; Lapp, Hilmar; Lundberg, John G; Mungall, Christopher J; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E; Vickaryous, Matthew K; Westerfield, Monte; Mabee, Paula M

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

A Unified Anatomy Ontology of the Vertebrate Skeletal System

PubMed Central

Dahdul, Wasila M.; Balhoff, James P.; Blackburn, David C.; Diehl, Alexander D.; Haendel, Melissa A.; Hall, Brian K.; Lapp, Hilmar; Lundberg, John G.; Mungall, Christopher J.; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E.; Vickaryous, Matthew K.; Westerfield, Monte; Mabee, Paula M.

2012-01-01

The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity. PMID:23251424

On the Concept of Information and Its Role in Nature

NASA Astrophysics Data System (ADS)

Roederer, Juan G.

2003-03-01

In this article we address some fundamental questions concerning information: Can the existing laws of physics adequately deal with the most striking property of information, namely to cause specific changes in the structure and energy flows of a complex system, without the information in itself representing fields, forces or energy in any of their characteristic forms? Or is information irreducible to the laws of physics and chemistry? Are information and complexity related concepts? Does the Universe, in its evolution, constantly generate new information? Or are information and information-processing exclusive attributes of living systems, related to the very definition of life? If that were the case, what happens with the physical meanings of entropy in statistical mechanics or wave function in quantum mechanics? How many distinct classes of information and information processing do exist in the biological world? How does information appear in Darwinian evolution? Does the human brain have unique properties or capabilities in terms of information processing? In what ways does information processing bring about human self-consciousness? We shall introduce the meaning of "information" in a way that is detached from human technological systems and related algorithms and semantics, and that is not based on any mathematical formula. To accomplish this we turn to the concept of interaction as the basic departing point, and identify two fundamentally different classes, with information and information-processing appearing as the key discriminator: force-field driven interactions between elementary particles and ensembles of particles in the macroscopic physical domain, and information-based interactions between certain kinds of complex systems that form the biological domain. We shall show that in an abiotic world, information plays no role; physical interactions just happen, they are driven by energy exchange between the interacting parts and do not require any operations of information processing. Information only enters the non-living physical world when a living thing interacts with it-and when a scientist extracts information through observation and measurement. But for living organisms, information is the very essence of their existence: to maintain a long-term state of unstable thermodynamic equilibrium with its surroundings, consistently increase its organization and reproduce, an organism has to rely on information-based interactions in which form or pattern, not energy, is the controlling factor. This latter class comprises biomolecular information processes controlling the metabolism, growth, multiplication and differentiation of cells, and neural information processes controlling animal behavior and intelligence. The only way new information can appear is through the process of biological evolution and, in the short term, through sensory acquisition and the manipulation of images in the nervous system. Non-living informational systems such as books, computers, AI systems and other artifacts, as well as living organisms that are the result of breeding or cloning, are planned by human beings and will not be considered here.

The new science of mind and the future of knowledge.

PubMed

Kandel, Eric

2013-10-30

Understanding mental processes in biological terms makes available insights from the new science of the mind to explore connections between philosophy, psychology, the social sciences, the humanities, and studies of disorders of mind. In this Perspective we examine how these linkages might be forged and how the new science of the mind might serve as an inspiration for further exploration. Copyright © 2013 Elsevier Inc. All rights reserved.

The space program's impact on society

NASA Astrophysics Data System (ADS)

Toffler, Alvin

In terms of human evolution, when viewed from 500 or 1000 years from now, today's primitive, still faltering steps beyond the Earth will be recognized as the most important human project of our era, matched only by what is going on in computers and biology. In this paper the social effects of space activity are addressed at three different levels: key social institutions, key social groups, and key social processes.

Physical and Biological Processes Underlying the Sudden Appearance of a Red-Tide Surface Patch in the Nearshore

DTIC Science & Technology

2010-01-01

DISTRIBUTION /AVAILABILITY STATEMENT Approved for public release; distribution unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT 15. SUBJECT TERMS 16...Survey (USGS) programs at Huntington Beach . George Robertson, Marlene Noble, Uwe Send, Steve Weisberg are thanked for their cooperation and assistance...Huntington Beach CA, was dominated by the locally common red-tide 5 forming dinoflagellate Lingulodinium polyedrum (F. Stein). Surface chlorophyll-a

Unified Deep Learning Architecture for Modeling Biology Sequence.

PubMed

Wu, Hongjie; Cao, Chengyuan; Xia, Xiaoyan; Lu, Qiang

2017-10-09

Prediction of the spatial structure or function of biological macromolecules based on their sequence remains an important challenge in bioinformatics. When modeling biological sequences using traditional sequencing models, characteristics, such as long-range interactions between basic units, the complicated and variable output of labeled structures, and the variable length of biological sequences, usually lead to different solutions on a case-by-case basis. This study proposed the use of bidirectional recurrent neural networks based on long short-term memory or a gated recurrent unit to capture long-range interactions by designing the optional reshape operator to adapt to the diversity of the output labels and implementing a training algorithm to support the training of sequence models capable of processing variable-length sequences. Additionally, the merge and pooling operators enhanced the ability to capture short-range interactions between basic units of biological sequences. The proposed deep-learning model and its training algorithm might be capable of solving currently known biological sequence-modeling problems through the use of a unified framework. We validated our model on one of the most difficult biological sequence-modeling problems currently known, with our results indicating the ability of the model to obtain predictions of protein residue interactions that exceeded the accuracy of current popular approaches by 10% based on multiple benchmarks.

Validation of systems biology derived molecular markers of renal donor organ status associated with long term allograft function.

PubMed

Perco, Paul; Heinzel, Andreas; Leierer, Johannes; Schneeberger, Stefan; Bösmüller, Claudia; Oberhuber, Rupert; Wagner, Silvia; Engler, Franziska; Mayer, Gert

2018-05-03

Donor organ quality affects long term outcome after renal transplantation. A variety of prognostic molecular markers is available, yet their validity often remains undetermined. A network-based molecular model reflecting donor kidney status based on transcriptomics data and molecular features reported in scientific literature to be associated with chronic allograft nephropathy was created. Significantly enriched biological processes were identified and representative markers were selected. An independent kidney pre-implantation transcriptomics dataset of 76 organs was used to predict estimated glomerular filtration rate (eGFR) values twelve months after transplantation using available clinical data and marker expression values. The best-performing regression model solely based on the clinical parameters donor age, donor gender, and recipient gender explained 17% of variance in post-transplant eGFR values. The five molecular markers EGF, CD2BP2, RALBP1, SF3B1, and DDX19B representing key molecular processes of the constructed renal donor organ status molecular model in addition to the clinical parameters significantly improved model performance (p-value = 0.0007) explaining around 33% of the variability of eGFR values twelve months after transplantation. Collectively, molecular markers reflecting donor organ status significantly add to prediction of post-transplant renal function when added to the clinical parameters donor age and gender.

Brain mechanisms for perceptual and reward-related decision-making.

PubMed

Deco, Gustavo; Rolls, Edmund T; Albantakis, Larissa; Romo, Ranulfo

2013-04-01

Phenomenological models of decision-making, including the drift-diffusion and race models, are compared with mechanistic, biologically plausible models, such as integrate-and-fire attractor neuronal network models. The attractor network models show how decision confidence is an emergent property; and make testable predictions about the neural processes (including neuronal activity and fMRI signals) involved in decision-making which indicate that the medial prefrontal cortex is involved in reward value-based decision-making. Synaptic facilitation in these models can help to account for sequential vibrotactile decision-making, and for how postponed decision-related responses are made. The randomness in the neuronal spiking-related noise that makes the decision-making probabilistic is shown to be increased by the graded firing rate representations found in the brain, to be decreased by the diluted connectivity, and still to be significant in biologically large networks with thousands of synapses onto each neuron. The stability of these systems is shown to be influenced in different ways by glutamatergic and GABAergic efficacy, leading to a new field of dynamical neuropsychiatry with applications to understanding schizophrenia and obsessive-compulsive disorder. The noise in these systems is shown to be advantageous, and to apply to similar attractor networks involved in short-term memory, long-term memory, attention, and associative thought processes. Copyright © 2012 Elsevier Ltd. All rights reserved.

AIM for Allostery: Using the Ising Model to Understand Information Processing and Transmission in Allosteric Biomolecular Systems.

PubMed

LeVine, Michael V; Weinstein, Harel

2015-05-01

In performing their biological functions, molecular machines must process and transmit information with high fidelity. Information transmission requires dynamic coupling between the conformations of discrete structural components within the protein positioned far from one another on the molecular scale. This type of biomolecular "action at a distance" is termed allostery . Although allostery is ubiquitous in biological regulation and signal transduction, its treatment in theoretical models has mostly eschewed quantitative descriptions involving the system's underlying structural components and their interactions. Here, we show how Ising models can be used to formulate an approach to allostery in a structural context of interactions between the constitutive components by building simple allosteric constructs we termed Allosteric Ising Models (AIMs). We introduce the use of AIMs in analytical and numerical calculations that relate thermodynamic descriptions of allostery to the structural context, and then show that many fundamental properties of allostery, such as the multiplicative property of parallel allosteric channels, are revealed from the analysis of such models. The power of exploring mechanistic structural models of allosteric function in more complex systems by using AIMs is demonstrated by building a model of allosteric signaling for an experimentally well-characterized asymmetric homodimer of the dopamine D2 receptor.

Action verbs are processed differently in metaphorical and literal sentences depending on the semantic match of visual primes

PubMed Central

Troyer, Melissa; Curley, Lauren B.; Miller, Luke E.; Saygin, Ayse P.; Bergen, Benjamin K.

2014-01-01

Language comprehension requires rapid and flexible access to information stored in long-term memory, likely influenced by activation of rich world knowledge and by brain systems that support the processing of sensorimotor content. We hypothesized that while literal language about biological motion might rely on neurocognitive representations of biological motion specific to the details of the actions described, metaphors rely on more generic representations of motion. In a priming and self-paced reading paradigm, participants saw video clips or images of (a) an intact point-light walker or (b) a scrambled control and read sentences containing literal or metaphoric uses of biological motion verbs either closely or distantly related to the depicted action (walking). We predicted that reading times for literal and metaphorical sentences would show differential sensitivity to the match between the verb and the visual prime. In Experiment 1, we observed interactions between the prime type (walker or scrambled video) and the verb type (close or distant match) for both literal and metaphorical sentences, but with strikingly different patterns. We found no difference in the verb region of literal sentences for Close-Match verbs after walker or scrambled motion primes, but Distant-Match verbs were read more quickly following walker primes. For metaphorical sentences, the results were roughly reversed, with Distant-Match verbs being read more slowly following a walker compared to scrambled motion. In Experiment 2, we observed a similar pattern following still image primes, though critical interactions emerged later in the sentence. We interpret these findings as evidence for shared recruitment of cognitive and neural mechanisms for processing visual and verbal biological motion information. Metaphoric language using biological motion verbs may recruit neurocognitive mechanisms similar to those used in processing literal language but be represented in a less-specific way. PMID:25538604

Ordinary differential equations with applications in molecular biology.

PubMed

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

Differential equations are of basic importance in molecular biology mathematics because many biological laws and relations appear mathematically in the form of a differential equation. In this article we presented some applications of mathematical models represented by ordinary differential equations in molecular biology. The vast majority of quantitative models in cell and molecular biology are formulated in terms of ordinary differential equations for the time evolution of concentrations of molecular species. Assuming that the diffusion in the cell is high enough to make the spatial distribution of molecules homogenous, these equations describe systems with many participating molecules of each kind. We propose an original mathematical model with small parameter for biological phospholipid pathway. All the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. If we reduce the size of the solution region the same small epsilon will result in a different condition number. It is clear that the solution for a smaller region is less difficult. We introduce the mathematical technique known as boundary function method for singular perturbation system. In this system, the small parameter is an asymptotic variable, different from the independent variable. In general, the solutions of such equations exhibit multiscale phenomena. Singularly perturbed problems form a special class of problems containing a small parameter which may tend to zero. Many molecular biology processes can be quantitatively characterized by ordinary differential equations. Mathematical cell biology is a very active and fast growing interdisciplinary area in which mathematical concepts, techniques, and models are applied to a variety of problems in developmental medicine and bioengineering. Among the different modeling approaches, ordinary differential equations (ODE) are particularly important and have led to significant advances. Ordinary differential equations are used to model biological processes on various levels ranging from DNA molecules or biosynthesis phospholipids on the cellular level.

Perturbations and 3R in carbon management.

PubMed

Pant, Deepak; Sharma, Virbala; Singh, Pooja; Kumar, Manoj; Giri, Anand; Singh, M P

2017-02-01

Perturbations in various carbon pools like biological, geological, oceanic, and missing carbon sink affect its global data, which are generally neglected or ignored in routine calculations. These natural and anthropogenic events need to be considered before projecting a sustainable carbon management plan. These plans have both general and experimental aspects. General plans should focus on (a) minimizing emission; (b) maximizing environmentally sound reuse, reduce, and recycling; (c) effective treatment; and (d) converting carbon into valuable products with atom economy. Experimental carbon management plans involving various biological and chemical techniques with limitation in terms of research level and economic feasibility. Chemical options have benefits of higher productivity and wider product range, but it suffers from its higher-energy requirements and environmental unfriendliness. In contrast to this, biological options are more selective and less energy intensive, but their productivity is very low. Hence, there is a requirement of hybrid process where the benefits of both the options, i.e., biological and chemical, can be reaped. In view of above, the proposed review targets to highlight the various perturbations in the global carbon cycle and their effects; study the currently practiced options of carbon management, specifically in light of 3R principle; and propose various new hybrid methods by compatible combinations of chemical and biological processes to develop better and safer carbon management. These methods are hypothetical so they may require further research and validations but may provide a comprehensive base for developing such management methods.

Tissue photoablation process with short-pulsed lasers

NASA Astrophysics Data System (ADS)

Mueller, Gerhard J.; Doerschel, Klaus; Kar, Hasan

1992-03-01

Since Hippocrates, physicians have three weapons to fight malignant diseases of the human body: Quae medicamenta non sanat, ferrum sanat; quae ferrum non sanat, ignis sanat; and quae vero ignis non sanat, insanabilia reputari oportet. Today there are various possibilities to use the ''fire'': electrical and optical cauterization; mono- and bipolar rf-surgery; ionizing radiation for tumor treatment; and last but not least, the laser of laser tissue interactions, all can be used to remove malignant tissue either by biological digestion or immediate ablation, i.e., photovaporization or photodecomposition. This paper will discuss a semiempirical theory of the so-called photoablation process and the thermal side effects of the surrounding tissue. The term ''Photoablation; has to be well differentiated with the terms photovaporization, photodisruption and photofragmentation. As will be shown in this paper, photoablation is a microscale fast thermal explosion.

Identification of OBO nonalignments and its implications for OBO enrichment.

PubMed

Bada, Michael; Hunter, Lawrence

2008-06-15

Existing projects that focus on the semiautomatic addition of links between existing terms in the Open Biomedical Ontologies can take advantage of reasoners that can make new inferences between terms that are based on the added formal definitions and that reflect nonalignments between the linked terms. However, these projects require that these definitions be necessary and sufficient, a strong requirement that often does not hold. If such definitions cannot be added, the reasoners cannot point to the nonalignments through the suggestion of new inferences. We describe a methodology by which we have identified over 1900 instances of nonredundant nonalignments between terms from the Gene Ontology (GO) biological process (BP), cellular component (CC) and molecular function (MF) ontologies, Chemical Entities of Biological Interest (ChEBI) and the Cell Type Ontology (CL). Many of the 39.8% of these nonalignments whose object terms are more atomic than the subject terms are not currently examined in other ontology-enrichment projects due to the fact that the necessary and sufficient conditions required for the inferences are not currently examined. Analysis of the ratios of nonalignments to assertions from which the nonalignments were identified suggests that BP-MF, BP-BP, BP-CL and CC-CC terms are relatively well-aligned, while ChEBI-MF, BP-ChEBI and CC-MF terms are relatively not aligned well. We propose four ways to resolve an identified nonalignment and recommend an analogous implementation of our methodology in ontology-enrichment tools to identify types of nonalignments that are currently not detected. The nonalignments discussed in this article may be viewed at http://compbio.uchsc.edu/Hunter_lab/Bada/nonalignments_2008_03_06.html. Code for the generation of these nonalignments is available upon request. mike.bada@uchsc.edu.

A Portal into Biology Education: An Annotated List of Commonly Encountered Terms

ERIC Educational Resources Information Center

Miller, Sarah; Tanner, Kimberly D.

2015-01-01

In an introductory biology course, undergraduate students are expected to become familiar with, and be able to use, hundreds of new terms to navigate the complex ideas in biology. And this is just in the introductory course! Juxtapose this student situation with the common frustration expressed by biologists that there is "just too much…

Public Understanding of Plant Biology: Voices from the Bottom of the Garden

ERIC Educational Resources Information Center

Watts, Mike

2015-01-01

Many household gardeners accumulate considerable knowledge of plant biology through a range of informal learning sources. This knowledge seldom relates to school biology and is driven by interest, keen motivation and what is termed here "vital relevance." A small opportunity sample of 12 gardeners (6 M, 6 F) is interviewed in terms of…

Gender Inequality in Biology Classes in China and Its Effects on Students' Short-Term Outcomes

ERIC Educational Resources Information Center

Liu, Ning; Neuhaus, Birgit

2014-01-01

This study investigated gender inequality in biology lessons and analysed the effects of the observed inequality on students' short-term knowledge achievement, situational interest and students' evaluation of teaching (SET). Twenty-two biology teachers and 803 7th-grade students from rural and urban classrooms in China participated in the study.…

Translational applications of evaluating physiologic variability in human endotoxemia

PubMed Central

Scheff, Jeremy D.; Mavroudis, Panteleimon D.; Calvano, Steve E.; Androulakis, Ioannis P.

2012-01-01

Dysregulation of the inflammatory response is a critical component of many clinically challenging disorders such as sepsis. Inflammation is a biological process designed to lead to healing and recovery, ultimately restoring homeostasis; however, the failure to fully achieve those beneficial results can leave a patient in a dangerous persistent inflammatory state. One of the primary challenges in developing novel therapies in this area is that inflammation is comprised of a complex network of interacting pathways. Here, we discuss our approaches towards addressing this problem through computational systems biology, with a particular focus on how the presence of biological rhythms and the disruption of these rhythms in inflammation may be applied in a translational context. By leveraging the information content embedded in physiologic variability, ranging in scale from oscillations in autonomic activity driving short-term heart rate variability (HRV) to circadian rhythms in immunomodulatory hormones, there is significant potential to gain insight into the underlying physiology. PMID:23203205

Bodily experiences in secondary school biology

NASA Astrophysics Data System (ADS)

Orlander, Auli Arvola; Wickman, Per-Olof

2011-09-01

This is a study of teaching about the human body. It is based on transcribed material from interviews with 15-year-old students and teachers about their experiences of sex education and from recordings of classroom interactions during a dissection. The analysis is focused on the relationship between what students are supposed to learn about the biological body and their expressed experiences and meaning making of bodies in the schoolwork. The results indicate that the negotiations associated with the encounters between the bodies of the classroom (student, teacher, and animal bodies) are important for what directions meaning making takes and what students are afforded to learn about bodies, biologically as well as in terms of values. We suggest that these negotiations should be taken into account at schools, be regarded as an important part of the learning processes in science education and in that way open up for new possibilities for students' meaning making.

Mathematics, structuralism and biology.

PubMed

Saunders, P T

1988-01-01

A new approach is gaining ground in biology, one that has much in common with the structuralist tradition in other fields. It is very much in the spirit of an earlier view of biology and indeed of science in general. It is also, though this is not generally recognized, in the spirit of twentieth century physics. As in modern physics, however, it is not a question of ignoring all the progress that has been made within the former paradigm. On the contrary, the aim is to use it as a basis for setting out in a somewhat different direction. Complex phenomena do not generally lend themselves to reductionist analyses which seek explanation only in terms of detailed mechanisms, but a proper scientific discussion of structure must make full use of what we have already learned - by whatever means - about the processes that underly the phenomena we are trying to understand.

Opportunities in biotechnology.

PubMed

Gartland, Kevan M A; Gartland, Jill S

2018-06-08

Strategies for biotechnology must take account of opportunities for research, innovation and business growth. At a regional level, public-private collaborations provide potential for such growth and the creation of centres of excellence. By considering recent progress in areas such as genomics, healthcare diagnostics, synthetic biology, gene editing and bio-digital technologies, opportunities for smart, strategic and specialised investment are discussed. These opportunities often involve convergent or disruptive technologies, combining for example elements of pharma-science, molecular biology, bioinformatics and novel device development to enhance biotechnology and the life sciences. Analytical applications use novel devices in mobile health, predictive diagnostics and stratified medicine. Synthetic biology provides opportunities for new product development and increased efficiency for existing processes. Successful centres of excellence should promote public-private business partnerships, clustering and global collaborations based on excellence, smart strategies and innovation if they are to remain sustainable in the longer term. Copyright © 2018. Published by Elsevier B.V.

Possible interactions between recirculated landfill leachate and the stabilized organic fraction of municipal solid waste.

PubMed

Calabrò, Paolo S; Mancini, Giuseppe

2012-05-01

The stabilized organic fraction of municipal solid waste (SOFMSW) is a product of the mechanical/biological treatment (MBT) of mixed municipal solid waste (MMSW). SOFMSW is considered a 'grey' compost and the presence of pollutants (particularly heavy metals) and residual glass and plastic normally prevents agricultural use, making landfills the typical final destination for SOFMSW. Recirculation of leachate in landfills can be a cost-effective management option, but the long-term sustainability of such a practice must be verified. Column tests were carried out to examine the effect of SOFMSW on leachate recirculation. The results indicate that organic matter may be biologically degraded and metals (copper and zinc) are effectively entrapped through a combination of physical (adsorption), biological (bacterial sulfate reduction), and chemical (precipitation of metal sulfides) processes, while other chemicals (i.e. ammonia nitrogen and chloride) are essentially unaffected by filtration through SOFMSW.

Mechanistic understanding of nanoparticles' interactions with extracellular matrix: the cell and immune system.

PubMed

Engin, Ayse Basak; Nikitovic, Dragana; Neagu, Monica; Henrich-Noack, Petra; Docea, Anca Oana; Shtilman, Mikhail I; Golokhvast, Kirill; Tsatsakis, Aristidis M

2017-06-24

Extracellular matrix (ECM) is an extraordinarily complex and unique meshwork composed of structural proteins and glycosaminoglycans. The ECM provides essential physical scaffolding for the cellular constituents, as well as contributes to crucial biochemical signaling. Importantly, ECM is an indispensable part of all biological barriers and substantially modulates the interchange of the nanotechnology products through these barriers. The interactions of the ECM with nanoparticles (NPs) depend on the morphological characteristics of intercellular matrix and on the physical characteristics of the NPs and may be either deleterious or beneficial. Importantly, an altered expression of ECM molecules ultimately affects all biological processes including inflammation. This review critically discusses the specific behavior of NPs that are within the ECM domain, and passing through the biological barriers. Furthermore, regenerative and toxicological aspects of nanomaterials are debated in terms of the immune cells-NPs interactions.

Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

PubMed Central

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

2008-01-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

PubMed

Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

2007-05-01

Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.

Synthetic biology in space: considering the broad societal and ethical implications

NASA Astrophysics Data System (ADS)

Race, Margaret S.; Moses, Jacob; McKay, Christopher; Venkateswaran, Kasthuri J.

2012-02-01

Although the field of synthetic biology is still in its infancy, there are expectations for great advances in the coming decades, both on Earth and potentially in space. Promising applications for long duration space missions include a variety of biologically engineered products and biologically aided processes and technologies, which will undoubtedly be scrutinized for risks and benefits in the broad context of ethical, legal and social realms. By comparing and contrasting features of Earth-based and space-applied synthetic biology, it is possible to identify the likely similarities and differences, and to identify possible challenges ahead for space applications that will require additional research, both in the short and long terms. Using an analytical framework associated with synthetic biology and new technologies on Earth, this paper analyses the kinds of issues and concerns ahead, and identifies those areas where space applications may require additional examination. In general, while Earth- and space-based synthetic biology share many commonalities, space applications have additional challenges such as those raised by space microbiology and environmental factors, legal complications, planetary protection, lack of decision-making infrastructure(s), long duration human missions, terraforming and the possible discovery of extraterrestrial (ET) life. For synthetic biology, the way forward offers many exciting opportunities, but is not without legitimate concerns - for life, environments and society, both on Earth and beyond.

Biological imaging in radiation therapy: role of positron emission tomography.

PubMed

Nestle, Ursula; Weber, Wolfgang; Hentschel, Michael; Grosu, Anca-Ligia

2009-01-07

In radiation therapy (RT), staging, treatment planning, monitoring and evaluation of response are traditionally based on computed tomography (CT) and magnetic resonance imaging (MRI). These radiological investigations have the significant advantage to show the anatomy with a high resolution, being also called anatomical imaging. In recent years, so called biological imaging methods which visualize metabolic pathways have been developed. These methods offer complementary imaging of various aspects of tumour biology. To date, the most prominent biological imaging system in use is positron emission tomography (PET), whose diagnostic properties have clinically been evaluated for years. The aim of this review is to discuss the valences and implications of PET in RT. We will focus our evaluation on the following topics: the role of biological imaging for tumour tissue detection/delineation of the gross tumour volume (GTV) and for the visualization of heterogeneous tumour biology. We will discuss the role of fluorodeoxyglucose-PET in lung and head and neck cancer and the impact of amino acids (AA)-PET in target volume delineation of brain gliomas. Furthermore, we summarize the data of the literature about tumour hypoxia and proliferation visualized by PET. We conclude that, regarding treatment planning in radiotherapy, PET offers advantages in terms of tumour delineation and the description of biological processes. However, to define the real impact of biological imaging on clinical outcome after radiotherapy, further experimental, clinical and cost/benefit analyses are required.

TOPICAL REVIEW: Biological imaging in radiation therapy: role of positron emission tomography

NASA Astrophysics Data System (ADS)

Nestle, Ursula; Weber, Wolfgang; Hentschel, Michael; Grosu, Anca-Ligia

2009-01-01

In radiation therapy (RT), staging, treatment planning, monitoring and evaluation of response are traditionally based on computed tomography (CT) and magnetic resonance imaging (MRI). These radiological investigations have the significant advantage to show the anatomy with a high resolution, being also called anatomical imaging. In recent years, so called biological imaging methods which visualize metabolic pathways have been developed. These methods offer complementary imaging of various aspects of tumour biology. To date, the most prominent biological imaging system in use is positron emission tomography (PET), whose diagnostic properties have clinically been evaluated for years. The aim of this review is to discuss the valences and implications of PET in RT. We will focus our evaluation on the following topics: the role of biological imaging for tumour tissue detection/delineation of the gross tumour volume (GTV) and for the visualization of heterogeneous tumour biology. We will discuss the role of fluorodeoxyglucose-PET in lung and head and neck cancer and the impact of amino acids (AA)-PET in target volume delineation of brain gliomas. Furthermore, we summarize the data of the literature about tumour hypoxia and proliferation visualized by PET. We conclude that, regarding treatment planning in radiotherapy, PET offers advantages in terms of tumour delineation and the description of biological processes. However, to define the real impact of biological imaging on clinical outcome after radiotherapy, further experimental, clinical and cost/benefit analyses are required.

Bovine placenta: a review on morphology, components, and defects from terminology and clinical perspectives.

PubMed

Peter, Augustine T

2013-10-15

The bovine placenta has been the subject of many studies. Concurrently, several specialized terms have been developed to describe its development, morphology, components, function, and pathology. Many of these terms are simple, some are difficult to understand and use, and others are antiquated and may not be scientifically accurate. Defining and adopting terminology for the bovine placenta that is clear, precise and understandable, and available in a single source is expected to facilitate exchange of clinical and research information. This review presents a brief overview of the current knowledge regarding the bovine placenta and attempts to define terms. In this process, conventional terminology is presented, and contemporary and novel terms are proposed from a biological perspective. For example, use of terms such as syndesmochorial, retained placenta, and large offspring syndrome should be revisited. Furthermore, the clinical relevance of the structure and function of the bovine placenta is reviewed. Finally, terms discussed in this review are summarized (in table format). Copyright © 2013 Elsevier Inc. All rights reserved.

Long-term Tillage influences on soil carbon, nitrogen, physical, chemical, and biological properties

USDA-ARS?s Scientific Manuscript database

Long-term tillage influences physical, chemical, and biological properties of the soil environment and thereby crop production and quality. We evaluated the effect of long-term (>20 yrs) tillage no-till, spring till, and fall plus spring till under continuous spring wheat (Triticum aestivum L.) on s...

Life's role in environmental regulation

NASA Astrophysics Data System (ADS)

Kump, L. R.

2016-12-01

The fusion of geological and biological perspectives on the operation of the Earth system is revolutionizing the way we think about the interactions of life and environment. No longer does life simply adapt to environmental change; those adaptations in turn modify the environment. Emerging from these interactions is the possibility of environmental regulation, the essence of Lovelock's Gaia Hypothesis. The long-term carbon cycle, for example, reflects a balance between the sources and sinks of carbon including volcanism, weathering of rocks exposed subaerially or on the seafloor, carbonate mineral formation, and the burial of organic carbon. The traditional view of these processes limits biological influences to the production and remineralization of organic matter and the formation of mineral skeletons. With the geobiological revolution we now also recognize the important role biological activity plays in accelerating weathering processes. Weathering rates depend on a variety of factors that we represent in numerical models with rate laws we adapt from inorganic chemistry. These can be characterized as zero-order (independent), first-order (linear), etc. and these functions are all monotonic. Yet one of the hallmark features of life is that it responds to changes in its environment parabolically: rates of physiological processes exhibit minima, optima, and maxima with respect to environment variables (temperature, pH, salinity, pO2, pCO2, . . .). Incorporation of physiological-style rate laws, and in general the explicit representation of life in models of Earth surface processes, demonstrates how the biota influence environmental stability on geologic time scales.

Integrating evolutionary game theory into epigenetic study of embryonic development. Comment on ;Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition; by Qian Wang et al.

NASA Astrophysics Data System (ADS)

Wang, Zuoheng

2017-03-01

DNA methylation is an essential component in the epigenetic regulation of embryonic development, and plays a crucial role in various biological processes, including repression of gene transcription, parent-of-origin genomic imprinting, and X-chromosome inactivation [1-5]. Understanding the epigenetic processes in different stages of embryo development has become an important research topic in the field. It has potential to offer new insight into reproductive medicine and contribute to the improvement of long-term health outcomes.

Land use change impacts on floods at the catchment scale: Challenges and opportunities for future research

NASA Astrophysics Data System (ADS)

Rogger, M.; Agnoletti, M.; Alaoui, A.; Bathurst, J. C.; Bodner, G.; Borga, M.; Chaplot, V.; Gallart, F.; Glatzel, G.; Hall, J.; Holden, J.; Holko, L.; Horn, R.; Kiss, A.; Kohnová, S.; Leitinger, G.; Lennartz, B.; Parajka, J.; Perdigão, R.; Peth, S.; Plavcová, L.; Quinton, J. N.; Robinson, M.; Salinas, J. L.; Santoro, A.; Szolgay, J.; Tron, S.; van den Akker, J. J. H.; Viglione, A.; Blöschl, G.

2017-07-01

Research gaps in understanding flood changes at the catchment scale caused by changes in forest management, agricultural practices, artificial drainage, and terracing are identified. Potential strategies in addressing these gaps are proposed, such as complex systems approaches to link processes across time scales, long-term experiments on physical-chemical-biological process interactions, and a focus on connectivity and patterns across spatial scales. It is suggested that these strategies will stimulate new research that coherently addresses the issues across hydrology, soil and agricultural sciences, forest engineering, forest ecology, and geomorphology.

Land use change impacts on floods at the catchment scale: Challenges and opportunities for future research

PubMed Central

Agnoletti, M.; Alaoui, A.; Bathurst, J. C.; Bodner, G.; Borga, M.; Chaplot, V.; Gallart, F.; Glatzel, G.; Hall, J.; Holden, J.; Holko, L.; Horn, R.; Kiss, A.; Kohnová, S.; Leitinger, G.; Lennartz, B.; Parajka, J.; Perdigão, R.; Peth, S.; Plavcová, L.; Quinton, J. N.; Robinson, M.; Salinas, J. L.; Santoro, A.; Szolgay, J.; Tron, S.; van den Akker, J. J. H.; Viglione, A.; Blöschl, G.

2017-01-01

Abstract Research gaps in understanding flood changes at the catchment scale caused by changes in forest management, agricultural practices, artificial drainage, and terracing are identified. Potential strategies in addressing these gaps are proposed, such as complex systems approaches to link processes across time scales, long‐term experiments on physical‐chemical‐biological process interactions, and a focus on connectivity and patterns across spatial scales. It is suggested that these strategies will stimulate new research that coherently addresses the issues across hydrology, soil and agricultural sciences, forest engineering, forest ecology, and geomorphology. PMID:28919651

Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

PubMed Central

Milacic, Marija; Haw, Robin; Rothfels, Karen; Wu, Guanming; Croft, David; Hermjakob, Henning; D’Eustachio, Peter; Stein, Lincoln

2012-01-01

Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of “cancer” pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics. PMID:24213504

Disentangling physical and biological drivers of phytoplankton dynamics in a coastal system.

PubMed

Cianelli, Daniela; D'Alelio, Domenico; Uttieri, Marco; Sarno, Diana; Zingone, Adriana; Zambianchi, Enrico; d'Alcalà, Maurizio Ribera

2017-11-20

This proof-of-concept study integrates the surface currents measured by high-frequency coastal radars with plankton time-series data collected at a fixed sampling point from the Mediterranean Sea (MareChiara Long Term Ecological Research site in the Gulf of Naples) to characterize the spatial origin of phytoplankton assemblages and to scrutinize the processes ruling their dynamics. The phytoplankton community generally originated from the coastal waters whereby species succession was mainly regulated by biological factors (life-cycle processes, species-specific physiological performances and inter-specific interactions). Physical factors, e.g. the alternation between coastal and offshore waters and the horizontal mixing, were also important drivers of phytoplankton dynamics promoting diversity maintenance by i) advecting species from offshore and ii) diluting the resident coastal community so as to dampen resource stripping by dominant species and thereby increase the numerical importance of rarer species. Our observations highlight the resilience of coastal communities, which may favour their persistence over time and the prevalence of successional events over small time and space scales. Although coastal systems may act differently from one another, our findings provide a conceptual framework to address physical-biological interactions occurring in coastal basins, which can be generalised to other areas.

Biosimilar medicines - Review.

PubMed

Dos Reis, Camila; Teixo, Ricardo; Mendes, Fernando; Cruz, Rui Santos

2016-03-16

By definition, biosimilars are similar to a biological reference that has already received marketing authorization for biologic drugs.The purpose of biosimilars is reducing costs, thus increasing access to this treatment, however, the concerns of health professionals and users refer to the fact that to reduce costs will not neglecting the quality, effectiveness and especially security. The aim of this study is then to assess the degree of similarity between the biosimilar and its reference biopharmaceuticals, trying to understand the production process, requirements necessary for approval, and its impact on the quality, safety, efficacy and costs. For the systematic review without meta-analysis, we researched articles to the b-on, Pubmed and Medscape to 2005-2014, and selected 23 articles that contributed to the verification of the objectives of this study. Several studies indicate that overall the biosimilar and biological reference showed no significant differences except those inherent to the production process, being the first susceptible to comparability tests demonstrating the similarity in terms of clinical efficacy and safety. Biosimilars will be increasingly present in the future as promising therapeutic arsenal and targeted therapy, however, issues related to immunogenicity, interchangeability, automatic substitution and extrapolation of indications should continue to be studied and debated.

Fundamental Principles of Cancer Biology: Does it have relevance to the perioperative period?

PubMed

Jiang, Li; Nick, Alpa M; Sood, Anil K

2015-09-01

Malignant tumors are characterized by their ability to metastasize, which is the main cause of cancer-related mortality. Besides intrinsic alternations in cancer cells, the tumor microenvironment plays a pivotal role in tumor growth and metastasis. Ample evidence suggests that the perioperative period and the excision of the primary tumor can promote the development of metastases and can influence long-term cancer patient outcomes. The role of cancer biology and its impact on the perioperative period are of increasing interest. This review will present evidence regarding fundamental principles of cancer biology, especially tumor microenvironment, and discuss new therapeutic opportunities in the perioperative timeframe. We will also discuss the regulatory signaling that could be relevant to various aspects of surgery and surgical responses, which could facilitate the metastatic process by directly or indirectly affecting malignant tissues and the tumor microenvironment. We address the influences of surgery-related stress, anesthetic and analgesic agents, blood transfusion, hypothermia, and β-adrenergic blockade administration on tumor growth and metastasis. Through an improved understanding of these processes, we will provide suggestions for potential new perioperative approaches aimed at improving treatment outcomes of cancer patients.

Performance of the full-scale biological nutrient removal plant at Noosa in Queensland, Australia: nutrient removal and disinfection.

PubMed

Urbain, V; Wright, P; Thomas, M

2001-01-01

Stringent effluent quality guidelines are progressively implemented in coastal and sensitive areas in Australia. Biological Nutrient Removal (BNR) plants are becoming a standard often including a tertiary treatment for disinfection. The BNR plant in Noosa - Queensland is designed to produce a treated effluent with less than 5 mg/l of BOD5, 5 mg/l of total nitrogen, 1 mg/l of total phosphorus, 5 mg/l of suspended solids and total coliforms of less than 10/100 ml. A flexible multi-stage biological process with a prefermentation stage, followed by sand filtration and UV disinfection was implemented to achieve this level of treatment. Acetic acid is added for phosphorus removal because: i) the volatile fatty acids (VFA) concentration in raw wastewater varies a lot, and ii) the prefermenter had to be turned off due to odor problems on the primary sedimentation tanks. An endogenous anoxic zone was added to the process to further reduce the nitrate concentration. This resulted in some secondary P-release events, a situation that happens when low nitrate and low phosphorus objectives are targeted. Long-term performance data and specific results on nitrogen removal and disinfection are presented in this paper.

A case study of evolutionary computation of biochemical adaptation

NASA Astrophysics Data System (ADS)

François, Paul; Siggia, Eric D.

2008-06-01

Simulations of evolution have a long history, but their relation to biology is questioned because of the perceived contingency of evolution. Here we provide an example of a biological process, adaptation, where simulations are argued to approach closer to biology. Adaptation is a common feature of sensory systems, and a plausible component of other biochemical networks because it rescales upstream signals to facilitate downstream processing. We create random gene networks numerically, by linking genes with interactions that model transcription, phosphorylation and protein-protein association. We define a fitness function for adaptation in terms of two functional metrics, and show that any reasonable combination of them will yield the same adaptive networks after repeated rounds of mutation and selection. Convergence to these networks is driven by positive selection and thus fast. There is always a path in parameter space of continuously improving fitness that leads to perfect adaptation, implying that the actual mutation rates we use in the simulation do not bias the results. Our results imply a kinetic view of evolution, i.e., it favors gene networks that can be learned quickly from the random examples supplied by mutation. This formulation allows for deductive predictions of the networks realized in nature.

Differential Proteome Analysis of a Flor Yeast Strain under Biofilm Formation.

PubMed

Moreno-García, Jaime; Mauricio, Juan Carlos; Moreno, Juan; García-Martínez, Teresa

2017-03-28

Several Saccharomyces cerevisiae strains (flor yeasts) form a biofilm (flor velum) on the surface of Sherry wines after fermentation, when glucose is depleted. This flor velum is fundamental to biological aging of these particular wines. In this study, we identify abundant proteins in the formation of the biofilm of an industrial flor yeast strain. A database search to enrich flor yeast "biological process" and "cellular component" according to Gene Ontology Terminology (GO Terms) and, "pathways" was carried out. The most abundant proteins detected were largely involved in respiration, translation, stress damage prevention and repair, amino acid metabolism (glycine, isoleucine, leucine and arginine), glycolysis/gluconeogenesis and biosynthesis of vitamin B9 (folate). These proteins were located in cellular components as in the peroxisome, mitochondria, vacuole, cell wall and extracellular region; being these two last directly related with the flor formation. Proteins like Bgl2p, Gcv3p, Hyp2p, Mdh1p, Suc2p and Ygp1p were quantified in very high levels. This study reveals some expected processes and provides new and important information for the design of conditions and genetic constructions of flor yeasts for improving the cellular survival and, thus, to optimize biological aging of Sherry wine production.

Fixism and conservation science.

PubMed

Robert, Alexandre; Fontaine, Colin; Veron, Simon; Monnet, Anne-Christine; Legrand, Marine; Clavel, Joanne; Chantepie, Stéphane; Couvet, Denis; Ducarme, Frédéric; Fontaine, Benoît; Jiguet, Frédéric; le Viol, Isabelle; Rolland, Jonathan; Sarrazin, François; Teplitsky, Céline; Mouchet, Maud

2017-08-01

The field of biodiversity conservation has recently been criticized as relying on a fixist view of the living world in which existing species constitute at the same time targets of conservation efforts and static states of reference, which is in apparent disagreement with evolutionary dynamics. We reviewed the prominent role of species as conservation units and the common benchmark approach to conservation that aims to use past biodiversity as a reference to conserve current biodiversity. We found that the species approach is justified by the discrepancy between the time scales of macroevolution and human influence and that biodiversity benchmarks are based on reference processes rather than fixed reference states. Overall, we argue that the ethical and theoretical frameworks underlying conservation research are based on macroevolutionary processes, such as extinction dynamics. Current species, phylogenetic, community, and functional conservation approaches constitute short-term responses to short-term human effects on these reference processes, and these approaches are consistent with evolutionary principles. © 2016 Society for Conservation Biology.

The role of nutraceuticals in anti-aging medicine.

PubMed

Vranesić-Bender, Darija

2010-12-01

'Nutraceuticals' is a wide term including all kinds of food with health or medical effect. Regulations in the world on functional food and nutraceuticals are developed along with the development of new products. This nomenclature is not aligned across legal regulations in different countries. There are several theories trying to interpret the phenomenon of aging and the most interesting theory in terms of nutrition is free radical theory and the possible role of antioxidants in aging process. A large group of substances including vitamins, carotenoids, flavonoids and minerals have in vitro or in vivo clinically significant antioxidant characteristics. There is great interest in anti-aging substances derived from food, and the most popular ingredients are antioxidants, especially coenzyme Q10, phytoestrogens, probiotics and omega-3 fatty acids. These substances have beneficial effect on digestive and immune systems, and modulate inflammatory and degenerative processes in the body. The challenge in the future will be strategic combining of cosmeceuticals and nutraceuticals in order to intervene in biological aging processes and degenerative skin changes.

Persistence of spilled oil on shores and its effects on biota

USGS Publications Warehouse

Irvine, G.V.; ,

2000-01-01

Over two million tonnes of oil are estimated to enter the world's oceans every year. A small percentage, but still a large volume, of this oil strands onshore, where its persistence is governed primarily by the action of physical forces. In some cases, biota influence the persistence of stranded oil or the rate of its weathering. Oil's deleterious effects on biota are frequently related to the persistence and degree of weathering of the oil, with long-lasting effects in low-energy environments such as salt marshes and coastal mangroves, or in higher-energy environments where oil is sequestered. However, an oil spill can have disproportionately large biological effects when it affects key species or processes (e.g., structurally important species, predators, prey, recruitment, or succession). In these cases, the continuing presence of oil is not always a prerequisite for continuing biological effects. There are relatively few long-term studies of the effects of oil spills; data from these suggest that oil can persist for decades in some environments or situations, and that biological effects can be equally persistent. Broad-based, integrated studies have been the most revealing in terms of the importance of direct and indirect effects, spillover effects between different parts of the environment, and continuing linkages between residual oil and biologic effects. Clean-up and treatment techniques applied to spilled or stranded oil can also have significant, long-lasting effects and need to be carefully evaluated prior to use.

On the Materials Science of Nature's Arms Race.

PubMed

Liu, Zengqian; Zhang, Zhefeng; Ritchie, Robert O

2018-06-05

Biological material systems have evolved unique combinations of mechanical properties to fulfill their specific function through a series of ingenious designs. Seeking lessons from Nature by replicating the underlying principles of such biological materials offers new promise for creating unique combinations of properties in man-made systems. One case in point is Nature's means of attack and defense. During the long-term evolutionary "arms race," naturally evolved weapons have achieved exceptional mechanical efficiency with a synergy of effective offense and persistence-two characteristics that often tend to be mutually exclusive in many synthetic systems-which may present a notable source of new materials science knowledge and inspiration. This review categorizes Nature's weapons into ten distinct groups, and discusses the unique structural and mechanical designs of each group by taking representative systems as examples. The approach described is to extract the common principles underlying such designs that could be translated into man-made materials. Further, recent advances in replicating the design principles of natural weapons at differing lengthscales in artificial materials, devices and tools to tackle practical problems are revisited, and the challenges associated with biological and bioinspired materials research in terms of both processing and properties are discussed. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Unraveling Vital Effects: Photosynthesis of Symbiotic Algae in Foraminifera Hosts

NASA Astrophysics Data System (ADS)

Fish, C.; Phelps, S. R.; Goes, J. I.; Hoenisch, B.

2015-12-01

B/Ca and boron isotope proxies recorded in the calcium carbonate shells of planktic foraminifera are sensitive to seawater acidity. We seek to understand how the biology of the organism affects the geochemical signals, as planktic foraminifera shells differ in their chemical composition from inorganic calcite and also between foraminifer species. These differences are most likely related to physiological processes like respiration, calcification, and photosynthesis in symbiont-bearing foraminifera. The modifications of geochemical signals by these biological parameters are termed vital effects. Our study is based on the hypothesis that the B/Ca and δ11B offsets observed in planktic foraminifer shells are primarily due to the photosynthetic activity of their symbionts, which may elevate the microenvironmental pH to different degrees in different foraminifer species. Using fast repetition rate fluorometry, chlorophyll α analyses and symbiont counts, we investigated the symbiont-photosynthetic activity associated with three foraminifera species - Globigerinoides ruber, G. sacculifer, and Orbulina universa. Boron proxy systematics in these species suggest that photosynthetic activity should be greater in G. ruber compared to G. sacculifer and O. universa, but this is not confirmed by our study. While symbiont photosynthesis undoubtedly explains microenvironmental pH-elevation and boron proxy systematics in symbiont-bearing compared to symbiont-barren foraminifer species, additional processes must be responsible for the boron geochemical offsets between symbiont-bearing species. Respiration of the symbiont-host association and the calcification process are most likely candidates that require further analysis. Our study highlights the potential danger of misinterpreting geochemical signals in biological organisms when the biology of the organism in question is not entirely understood.

The Soil Sink for Nitrous Oxide: Trivial Amount but Challenging Question

NASA Astrophysics Data System (ADS)

Davidson, E. A.; Savage, K. E.; Sihi, D.

2015-12-01

Net uptake of atmospheric nitrous oxide (N2O) has been observed sporadically for many years. Such observations have often been discounted as measurement error or noise, but they were reported frequently enough to gain some acceptance as valid. The advent of fast response field instruments with good sensitivity and precision has permitted confirmation that some soils can be small sinks of N2O. With regards to "closing the global N2O budget" the soil sink is trivial, because it is smaller than the error terms of most other budget components. Although not important from a global budget perspective, the existence of a soil sink for atmospheric N2O presents a fascinating challenge for understanding the physical, chemical, and biological processes that explain the sink. Reduction of N2O by classical biological denitrification requires reducing conditions generally found in wet soil, and yet we have measured the N2O sink in well drained soils, where we also simultaneously measure a sink for atmospheric methane (CH4). Co-occurrence of N2O reduction and CH4 oxidation would require a broad range of microsite conditions within the soil, spanning high and low oxygen concentrations. Abiotic sinks for N2O or other biological processes that consume N2O could exist, but have not yet been identified. We are attempting to simulate processes of diffusion of N2O, CH4, and O2 from the atmosphere and within a soil profile to determine if classical biological N2O reduction and CH4 oxidation at rates consistent with measured fluxes are plausible.

Where Do Epigenetics and Developmental Origins Take the Field of Developmental Psychopathology?

PubMed

Nigg, Joel T

2016-04-01

The time is ripe for upgrading or rethinking the assumed paradigms for how we study developmental psychopathology. The classic transactional models appear robust but need specification in terms of biological and psychosocial processes. That specification is increasingly tractable due to developments in genetics, epigenetics, the measurement of psychosocial processes, and theory and data on developmental origins of health and disease. This essay offers a high-level view of where the field has been and where it may be going in regard to nosology and conceptions of etiology. Remarks seek to consider rapidly evolving contexts not only for children, but also for the science itself due to progress in our field and in neighboring fields. Illustrations are provided as to how syndromal nosology can be enriched and advanced by careful integration with biologically relevant behavioral dimensions and application of quantitative methods. It is concluded that a revised, forward-looking, transactional model of abnormal child psychology will incorporate prenatal and postnatal developmental programming, epigenetic mechanisms and their associated genotype x environment interactions, and inflammatory processes as a potential common mediator influencing numerous health and mental health conditions.

Proteases for Processing Proneuropeptides into Peptide Neurotransmitters and Hormones

PubMed Central

Hook, Vivian; Funkelstein, Lydiane; Lu, Douglas; Bark, Steven; Wegrzyn, Jill; Hwang, Shin-Rong

2009-01-01

Peptide neurotransmitters and peptide hormones, collectively known as neuropeptides, are required for cell-cell communication in neurotransmission and for regulation of endocrine functions. Neuropeptides are synthesized from protein precursors (termed proneuropeptides or prohormones) that require proteolytic processing primarily within secretory vesicles that store and secrete the mature neuropeptides to control target cellular and organ systems. This review describes interdisciplinary strategies that have elucidated two primary protease pathways for prohormone processing consisting of the cysteine protease pathway mediated by secretory vesicle cathepsin L and the well-known subtilisin-like proprotein convertase pathway that together support neuropeptide biosynthesis. Importantly, this review discusses important areas of current and future biomedical neuropeptide research with respect to biological regulation, inhibitors, structural features of proneuropeptide and protease interactions, and peptidomics combined with proteomics for systems biological approaches. Future studies that gain in-depth understanding of protease mechanisms for generating active neuropeptides will be instrumental for translational research to develop pharmacological strategies for regulation of neuropeptide functions. Pharmacological applications for neuropeptide research may provide valuable therapeutics in health and disease. PMID:18184105

Data management for JGOFS: Theory and design

NASA Technical Reports Server (NTRS)

Flierl, Glenn R.; Bishop, James K. B.; Glover, David M.; Paranjpe, Satish

1992-01-01

The Joint Global Ocean Flux Study (JGOFS), currently being organized under the auspices of the Scientific Committee for Ocean Research (SCOR), is intended to be a decade long internationally coordinated program. The main goal of JGOFS is to determine and understand on a global scale the processes controlling the time-varying fluxes of carbon and associated biogenic elements in the ocean and to evaluate the related exchanges with the atmosphere, sea floor and continental boundaries. 'A long-term goal of JGOFS will be to establish strategies for observing, on long time scales, changes in ocean biogeochemical cycles in relation to climate change'. Participation from a large number of U.S. and foreign institutions is expected. JGOFS investigators have begun a set of time-series measurements and global surveys of a wide variety of biological, chemical and physical quantities, detailed process-oriented studies, satellite observations of ocean color and wind stress and modeling of the bio-geochemical processes. These experiments will generate data in amounts unprecedented in the biological and chemical communities; rapid and effortless exchange of these data will be important to the success of JGOFS.

Natural photosystems from an engineer's perspective: length, time, and energy scales of charge and energy transfer.

PubMed

Noy, Dror

2008-01-01

The vast structural and functional information database of photosynthetic enzymes includes, in addition to detailed kinetic records from decades of research on physical processes and chemical reaction-pathways, a variety of high and medium resolution crystal structures of key photosynthetic enzymes. Here, it is examined from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in novel biological and non-biological solar-energy conversion systems. This survey reveals that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Furthermore, the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. This underlines a critical challenge for projected de novo designed constructions, that is, the control of spatial organization of cofactor molecules within dense array of different cofactors, some well within 1 nm from each other.

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

ERIC Educational Resources Information Center

Coley, John D.; Tanner, Kimberly

2015-01-01

Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed "misconceptions," among biology students across biological domains. In parallel, cognitive and developmental psychologists…

Biodesalination-On harnessing the potential of nature's desalination processes.

PubMed

Taheri, Reza; Razmjou, Amir; Szekely, Gyorgy; Hou, Jingwei; Ghezelbash, Gholam Reza

2016-07-08

Water scarcity is now one of the major global crises, which has affected many aspects of human health, industrial development and ecosystem stability. To overcome this issue, water desalination has been employed. It is a process to remove salt and other minerals from saline water, and it covers a variety of approaches from traditional distillation to the well-established reverse osmosis. Although current water desalination methods can effectively provide fresh water, they are becoming increasingly controversial due to their adverse environmental impacts including high energy intensity and highly concentrated brine waste. For millions of years, microorganisms, the masters of adaptation, have survived on Earth without the excessive use of energy and resources or compromising their ambient environment. This has encouraged scientists to study the possibility of using biological processes for seawater desalination and the field has been exponentially growing ever since. Here, the term biodesalination is offered to cover all of the techniques which have their roots in biology for producing fresh water from saline solution. In addition to reviewing and categorizing biodesalination processes for the first time, this review also reveals unexplored research areas in biodesalination having potential to be used in water treatment.

Stochastic processes on multiple scales: averaging, decimation and beyond

NASA Astrophysics Data System (ADS)

Bo, Stefano; Celani, Antonio

The recent advances in handling microscopic systems are increasingly motivating stochastic modeling in a large number of physical, chemical and biological phenomena. Relevant processes often take place on widely separated time scales. In order to simplify the description, one usually focuses on the slower degrees of freedom and only the average effect of the fast ones is retained. It is then fundamental to eliminate such fast variables in a controlled fashion, carefully accounting for their net effect on the slower dynamics. We shall present how this can be done by either decimating or coarse-graining the fast processes and discuss applications to physical, biological and chemical examples. With the same tools we will address the fate of functionals of the stochastic trajectories (such as residence times, counting statistics, fluxes, entropy production, etc.) upon elimination of the fast variables. In general, for functionals, such elimination can present additional difficulties. In some cases, it is not possible to express them in terms of the effective trajectories on the slow degrees of freedom but additional details of the fast processes must be retained. We will focus on such cases and show how naive procedures can lead to inconsistent results.

A light-stimulated synaptic device based on graphene hybrid phototransistor

NASA Astrophysics Data System (ADS)

Qin, Shuchao; Wang, Fengqiu; Liu, Yujie; Wan, Qing; Wang, Xinran; Xu, Yongbing; Shi, Yi; Wang, Xiaomu; Zhang, Rong

2017-09-01

Neuromorphic chips refer to an unconventional computing architecture that is modelled on biological brains. They are increasingly employed for processing sensory data for machine vision, context cognition, and decision making. Despite rapid advances, neuromorphic computing has remained largely an electronic technology, making it a challenge to access the superior computing features provided by photons, or to directly process vision data that has increasing importance to artificial intelligence. Here we report a novel light-stimulated synaptic device based on a graphene-carbon nanotube hybrid phototransistor. Significantly, the device can respond to optical stimuli in a highly neuron-like fashion and exhibits flexible tuning of both short- and long-term plasticity. These features combined with the spatiotemporal processability make our device a capable counterpart to today’s electrically-driven artificial synapses, with superior reconfigurable capabilities. In addition, our device allows for generic optical spike processing, which provides a foundation for more sophisticated computing. The silicon-compatible, multifunctional photosensitive synapse opens up a new opportunity for neural networks enabled by photonics and extends current neuromorphic systems in terms of system complexities and functionalities.

Ontology of physics for biology: representing physical dependencies as a basis for biological processes

PubMed Central

2013-01-01

Background In prior work, we presented the Ontology of Physics for Biology (OPB) as a computational ontology for use in the annotation and representations of biophysical knowledge encoded in repositories of physics-based biosimulation models. We introduced OPB:Physical entity and OPB:Physical property classes that extend available spatiotemporal representations of physical entities and processes to explicitly represent the thermodynamics and dynamics of physiological processes. Our utilitarian, long-term aim is to develop computational tools for creating and querying formalized physiological knowledge for use by multiscale “physiome” projects such as the EU’s Virtual Physiological Human (VPH) and NIH’s Virtual Physiological Rat (VPR). Results Here we describe the OPB:Physical dependency taxonomy of classes that represent of the laws of classical physics that are the “rules” by which physical properties of physical entities change during occurrences of physical processes. For example, the fluid analog of Ohm’s law (as for electric currents) is used to describe how a blood flow rate depends on a blood pressure gradient. Hooke’s law (as in elastic deformations of springs) is used to describe how an increase in vascular volume increases blood pressure. We classify such dependencies according to the flow, transformation, and storage of thermodynamic energy that occurs during processes governed by the dependencies. Conclusions We have developed the OPB and annotation methods to represent the meaning—the biophysical semantics—of the mathematical statements of physiological analysis and the biophysical content of models and datasets. Here we describe and discuss our approach to an ontological representation of physical laws (as dependencies) and properties as encoded for the mathematical analysis of biophysical processes. PMID:24295137

Modeling Translation in Protein Synthesis with TASEP: A Tutorial and Recent Developments

NASA Astrophysics Data System (ADS)

Zia, R. K. P.; Dong, J. J.; Schmittmann, B.

2011-07-01

The phenomenon of protein synthesis has been modeled in terms of totally asymmetric simple exclusion processes (TASEP) since 1968. In this article, we provide a tutorial of the biological and mathematical aspects of this approach. We also summarize several new results, concerned with limited resources in the cell and simple estimates for the current (protein production rate) of a TASEP with inhomogeneous hopping rates, reflecting the characteristics of real genes.

The A, C, G, and T of Genome Assembly.

PubMed

Wajid, Bilal; Sohail, Muhammad U; Ekti, Ali R; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.

A unified approach for quantifying invasibility and degree of invasion

Treesearch

Qinfeng Guo; Songlin Fei; Jeffrey S. Dukes; Christopher M. Oswalt; Basil V. Iannone III; Kevin M. Potter

2015-01-01

Habitat invasibility is a central focus of invasion biology, with implications for basic ecological patterns and processes and for effective invasion management. ‘‘Invasibility’’ is, however, one of the most elusive metrics and misused terms in ecology. Empirical studies and meta-analyses of invasibility have produced inconsistent and even conflicting results. This ...

Impact of urban environmental pollution on growth, leaf damage, and chemical constituents of Warsaw urban trees

Treesearch

Waldemar Chmielewski; Wojciech Dmuchowski; Stanislaw Suplat

1998-01-01

In the last 10 years, 3.5 percent of the tree population died annually in PolandÕs largest and most polluted cities, which is a problem of economic importance. Dieback of streetside trees in Warsaw is a long term process. It is an effect of biological reactions of trees to unfavorable conditions in the urban environment, particularly air and soil pollution and water...

Extinction Events Can Accelerate Evolution

PubMed Central

Lehman, Joel; Miikkulainen, Risto

2015-01-01

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term. PMID:26266804

The Role of Lactate-Mediated Metabolic Coupling between Astrocytes and Neurons in Long-Term Memory Formation

PubMed Central

Steinman, Michael Q.; Gao, Virginia; Alberini, Cristina M.

2016-01-01

Long-term memory formation, the ability to retain information over time about an experience, is a complex function that affects multiple behaviors, and is an integral part of an individual’s identity. In the last 50 years many scientists have focused their work on understanding the biological mechanisms underlying memory formation and processing. Molecular studies over the last three decades have mostly investigated, or given attention to, neuronal mechanisms. However, the brain is composed of different cell types that, by concerted actions, cooperate to mediate brain functions. Here, we consider some new insights that emerged from recent studies implicating astrocytic glycogen and glucose metabolisms, and particularly their coupling to neuronal functions via lactate, as an essential mechanism for long-term memory formation. PMID:26973477

Animal Bioacoustics

NASA Astrophysics Data System (ADS)

Fletcher, Neville H.

Animals rely upon their acoustic and vibrational senses and abilities to detect the presence of both predators and prey and to communicate with members of the same species. This chapter surveys the physical bases of these abilities and their evolutionary optimization in insects, birds, and other land animals, and in a variety of aquatic animals other than cetaceans, which are treated in Chap. 20. While there are many individual variations, and some animals devote an immense fraction of their time and energy to acoustic communication, there are also many common features in their sound production and in the detection of sounds and vibrations. Excellent treatments of these matters from a biological viewpoint are given in several notable books [19.1,2] and collections of papers [19.3,4,5,6,7,8], together with other more specialized books to be mentioned in the following sections, but treatments from an acoustical viewpoint [19.9] are rare. The main difference between these two approaches is that biological books tend to concentrate on anatomical and physiological details and on behavioral outcomes, while acoustical books use simplified anatomical models and quantitative analysis to model vocalization frequency scaling in animals hearing sound production animal animal biological biological bioacoustics whole-system behavior. This latter is the approach to be adopted here.

Evolutionary Theory under Fire.

ERIC Educational Resources Information Center

Lewin, Roger

1980-01-01

Summarizes events of a conference on evolutionary biology in Chicago entitled: "Macroevolution." Reviews the theory of modern synthesis, a term used to explain Darwinism in terms of population biology and genetics. Issues presented at the conference are discussed in detail. (CS)

Introduction of Biosimilar Therapeutics Into Nephrology Practice in the United States: Report of a Scientific Workshop Sponsored by the National Kidney Foundation.

PubMed

Wish, Jay B; Charytan, Chaim; Chertow, Glenn M; Kalantar-Zadeh, Kamyar; Kliger, Alan S; Rubin, Robert J; Yee, Jerry; Fishbane, Steven

2016-12-01

Biosimilars are biologic medicines highly similar to the reference product with no meaningful clinical differences in terms of safety, purity, and potency. All biologic medicines are produced by living cells, resulting in an inherent heterogeneity in their higher order structures and post-translational modifications. In 2010, the US Congress enacted legislation to streamline the approval process for biosimilars of products losing patent protection, with the goal of decreasing costs and improving patient access to therapeutically important but expensive biologic agents. In 2015, the US Food and Drug Administration approved the first biosimilar agent through this pathway. Approval of additional biosimilar agents in the United States, including those used by nephrologists, is anticipated. Given the relative lack of knowledge regarding biosimilars and their approval process and a lack of trust by the nephrology community regarding their safety and efficacy, the National Kidney Foundation conducted a symposium, Introduction of Biosimilar Therapeutics Into Nephrology Practice in the U.S., September 17 to 18, 2015. Issues related to manufacturing, the regulatory approval process, interchangeability, substitution/switching, nomenclature, and clinician and patient awareness and acceptance were examined. This report summarizes the main discussions at the symposium, highlights several controversies, and makes recommendations related to public policy, professional and patient education, and research needs. Copyright © 2016 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

A single-stage biological process for municipal sewage treatment in tourist areas.

PubMed

Di Iaconi, C; De Sanctis, M; Lopez, A

2014-11-01

This pilot scale study aims to test the effectiveness of an innovative compact biological system (SBBGR - Sequencing Batch Biofilter Granular Reactor) for treating municipal wastewater in tourist areas characterised by intense seasonal water demand and wastewater discharge. The results obtained after a long term operation of 463 days have shown that the proposed system is able to assure average removal efficiencies higher than 90% for COD (chemical oxygen demand), total suspended solids and TKN (total Kjeldahl nitrogen) independently of the influent concentration values and organic loading, which ranged from 0.2 to 5.1 kgCOD/m(3)biofilter.d Furthermore, the plant showed a high degree of operation flexibility and stability in response to the organic load variations occurring in tourist areas. In fact, no significant deterioration in the plant's effluent quality was observed even during a sudden several-fold increase in organic loading. High nitrogen removal efficiencies (80%, on average) were also achieved thanks to the establishment of simultaneous nitrification-denitrification process favoured by the plant's high biomass concentration and operating conditions. Finally, the system was characterized by an excess sludge production much lower (60-80% lower) than that of conventional biological systems operating without a primary clarifier. An acceptable level of stabilization of excess sludge was also obtained so that a further stabilization process was no longer required. Copyright © 2014 Elsevier Ltd. All rights reserved.

Modelling the Impact of Soil Management on Soil Functions

NASA Astrophysics Data System (ADS)

Vogel, H. J.; Weller, U.; Rabot, E.; Stößel, B.; Lang, B.; Wiesmeier, M.; Urbanski, L.; Wollschläger, U.

2017-12-01

Due to an increasing soil loss and an increasing demand for food and energy there is an enormous pressure on soils as the central resource for agricultural production. Besides the importance of soils for biomass production there are other essential soil functions, i.e. filter and buffer for water, carbon sequestration, provision and recycling of nutrients, and habitat for biological activity. All these functions have a direct feed back to biogeochemical cycles and climate. To render agricultural production efficient and sustainable we need to develop model tools that are capable to predict quantitatively the impact of a multitude of management measures on these soil functions. These functions are considered as emergent properties produced by soils as complex systems. The major challenge is to handle the multitude of physical, chemical and biological processes interacting in a non-linear manner. A large number of validated models for specific soil processes are available. However, it is not possible to simulate soil functions by coupling all the relevant processes at the detailed (i.e. molecular) level where they are well understood. A new systems perspective is required to evaluate the ensemble of soil functions and their sensitivity to external forcing. Another challenge is that soils are spatially heterogeneous systems by nature. Soil processes are highly dependent on the local soil properties and, hence, any model to predict soil functions needs to account for the site-specific conditions. For upscaling towards regional scales the spatial distribution of functional soil types need to be taken into account. We propose a new systemic model approach based on a thorough analysis of the interactions between physical, chemical and biological processes considering their site-specific characteristics. It is demonstrated for the example of soil compaction and the recovery of soil structure, water capacity and carbon stocks as a result of plant growth and biological activity. Coupling of the observed nonlinear interactions allows for modeling the stability and resilience of soil systems in terms of their essential functions.

Biological-Physical Feedbacks Determine Coastal Environmental Response to Climate Change

NASA Astrophysics Data System (ADS)

Moore, L. J.; Duran Vinent, O.; Walters, D.; Fagherazzi, S.; Mariotti, G.; Young, D.; Wolner, C. V.

2012-12-01

As low-lying coastal landforms, transitional between marine and terrestrial realms, barrier islands are especially sensitive to changing environmental conditions. Interactions among biological and physical processes appear to play a critical role in determining how these landscapes will evolve in the future as sea level rises, storm intensity increases and plant species composition changes. Within a new conceptual framework, barrier islands tend to exist in one of two primary states. "Low" islands have little relief above sea level and are dominated by external processes, responding quickly on short time scales to changes in forcing (e.g., storms, sea level rise, etc.), migrating rapidly and generally being low in ecological diversity and productivity. In contrast, "high" islands are less vulnerable to storms, tend to be dominated by internal processes (e.g., sand trapping by vegetation), require long time periods to respond to changes in forcing, migrate slowly (if at all) and host a range of plant species and morphological environments including shrubs, small trees and vegetated secondary and tertiary dunes with intervening swales. The continued existence of barrier island landforms will depend on the degree to which islands can maintain elevation above sea level while also responding to changes in forcing by migrating landward. A long-term morphological-behavior model exploring coupled barrier-marsh evolution and a new ecomorphodynamic model representing the formation/recovery of dunes as a function of storms, shed light on the role of interactions among biological and physical processes on barrier island response to climate change. Results suggest that connections between the marsh and barrier realms, which are mediated by biological processes in the marsh environment, are highly sensitive to factors such as sea level rise rate, antecedent morphology and marsh composition. Results also suggest that feedbacks between sediment transport and vegetation involved in dune building may allow small, gradual changes in storms to cause abrupt, nonlinear transitions from the high to low island state.

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

PubMed

Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

2016-01-01

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.

Subsurface Hydrology: Data Integration for Properties and Processes

NASA Astrophysics Data System (ADS)

Hyndman, David W.; Day-Lewis, Frederick D.; Singha, Kamini

Groundwater is a critical resource and the PrinciPal source of drinking water for over 1.5 billion people. In 2001, the National Research Council cited as a "grand challenge" our need to understand the processes that control water movement in the subsurface. This volume faces that challenge in terms of data integration between complex, multi-scale hydrologie processes, and their links to other physical, chemical, and biological processes at multiple scales. Subsurface Hydrology: Data Integration for Properties and Processes presents the current state of the science in four aspects: • Approaches to hydrologie data integration • Data integration for characterization of hydrologie properties • Data integration for understanding hydrologie processes • Meta-analysis of current interpretations Scientists and researchers in the field, the laboratory, and the classroom will find this work an important resource in advancing our understanding of subsurface water movement.

40 CFR 63.138 - Process wastewater provisions-performance standards for treatment processes managing Group 1...

Code of Federal Regulations, 2010 CFR

2010-07-01

.../or Table 9 compounds are similar and often identical. (3) Biological treatment processes. Biological treatment processes in compliance with this section may be either open or closed biological treatment processes as defined in § 63.111. An open biological treatment process in compliance with this section need...

Using the brain's fight-or-flight response for predicting mental illness on the human space flight program

NASA Astrophysics Data System (ADS)

Losik, L.

A predictive medicine program allows disease and illness including mental illness to be predicted using tools created to identify the presence of accelerated aging (a.k.a. disease) in electrical and mechanical equipment. When illness and disease can be predicted, actions can be taken so that the illness and disease can be prevented and eliminated. A predictive medicine program uses the same tools and practices from a prognostic and health management program to process biological and engineering diagnostic data provided in analog telemetry during prelaunch readiness and space exploration missions. The biological and engineering diagnostic data necessary to predict illness and disease is collected from the pre-launch spaceflight readiness activities and during space flight for the ground crew to perform a prognostic analysis on the results from a diagnostic analysis. The diagnostic, biological data provided in telemetry is converted to prognostic (predictive) data using the predictive algorithms. Predictive algorithms demodulate telemetry behavior. They illustrate the presence of accelerated aging/disease in normal appearing systems that function normally. Mental illness can predicted using biological diagnostic measurements provided in CCSDS telemetry from a spacecraft such as the ISS or from a manned spacecraft in deep space. The measurements used to predict mental illness include biological and engineering data from an astronaut's circadian and ultranian rhythms. This data originates deep in the brain that is also damaged from the long-term exposure to cortisol and adrenaline anytime the body's fight or flight response is activated. This paper defines the brain's FOFR; the diagnostic, biological and engineering measurements needed to predict mental illness, identifies the predictive algorithms necessary to process the behavior in CCSDS analog telemetry to predict and thus prevent mental illness from occurring on human spaceflight missions.

Cancer Systems Biology: a peak into the future of patient care?

PubMed Central

Werner, Henrica M. J.; Mills, Gordon B.; Ram, Prahlad T.

2015-01-01

Traditionally, scientific research has focused on studying individual events, such as single mutations, gene function or the effect of the manipulation of one protein on a biological phenotype. A range of technologies, combined with the ability to develop robust and predictive mathematical models, is beginning to provide information that will enable a holistic view of how the genomic and epigenetic aberrations in cancer cells can alter the homeostasis of signalling networks within these cells, between cancer cells and the local microenvironment, at the organ and organism level. This systems biology process needs to be integrated with an iterative approach wherein hypotheses and predictions that arise from modelling are refined and constrained by experimental evaluation. Systems biology approaches will be vital for developing and implementing effective strategies to deliver personalized cancer therapy. Specifically, these approaches will be important to select those patients most likely to benefit from targeted therapies as well as for the development and implementation of rational combinatorial therapies. Systems biology can help to increase therapy efficacy or bypass the emergence of resistance, thus converting the current (often short term) effects of targeted therapies into durable responses, ultimately to improve quality of life and provide a cure. PMID:24492837

Mechanism and applications of new fluorescent compounds produced by femtosecond laser surgery in biological tissue (Conference Presentation)

NASA Astrophysics Data System (ADS)

Qu, Jianan Y.; Sun, Qiqi

2017-02-01

The single or multi-photon microscopy based on fluorescent labelling and staining is a sensitive and quantitative method that is widely used in molecular biology and medical research for a variety of experimental, analytical, and quality control applications. However, label-free method is highly desirable in biology and medicine when performing long term live imaging of biological system and obtaining instant tissue examination during surgery procedures. Recently, our group found that femtosecond laser surgery turned a variety of biological tissues and protein samples into highly fluorescent substances. The newly formed fluorescent compounds produced during the laser surgery can be excited via single- and two-photon processes over broad wavelength ranges. We developed a combined confocal and two-photon spectroscopic microscope to characterize the fluorescence from the new compound systematically. The structures of the femtosecond laser treated tissue were studied using Raman spectroscopy and transmission electron microscopy. Our study revealed the mechanisms of the fluorescence emission form the new compound. Furthermore, we demonstrated the applications of the fluorescent compounds for instant evaluation of femtosecond laser microsurgery, study of stem cell responses to muscle injury and neuro-regeneration after spinal cord injury.

Modular biological function is most effectively captured by combining molecular interaction data types.

PubMed

Ames, Ryan M; Macpherson, Jamie I; Pinney, John W; Lovell, Simon C; Robertson, David L

2013-01-01

Large-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.

BioModels.net Web Services, a free and integrated toolkit for computational modelling software.

PubMed

Li, Chen; Courtot, Mélanie; Le Novère, Nicolas; Laibe, Camille

2010-05-01

Exchanging and sharing scientific results are essential for researchers in the field of computational modelling. BioModels.net defines agreed-upon standards for model curation. A fundamental one, MIRIAM (Minimum Information Requested in the Annotation of Models), standardises the annotation and curation process of quantitative models in biology. To support this standard, MIRIAM Resources maintains a set of standard data types for annotating models, and provides services for manipulating these annotations. Furthermore, BioModels.net creates controlled vocabularies, such as SBO (Systems Biology Ontology) which strictly indexes, defines and links terms used in Systems Biology. Finally, BioModels Database provides a free, centralised, publicly accessible database for storing, searching and retrieving curated and annotated computational models. Each resource provides a web interface to submit, search, retrieve and display its data. In addition, the BioModels.net team provides a set of Web Services which allows the community to programmatically access the resources. A user is then able to perform remote queries, such as retrieving a model and resolving all its MIRIAM Annotations, as well as getting the details about the associated SBO terms. These web services use established standards. Communications rely on SOAP (Simple Object Access Protocol) messages and the available queries are described in a WSDL (Web Services Description Language) file. Several libraries are provided in order to simplify the development of client software. BioModels.net Web Services make one step further for the researchers to simulate and understand the entirety of a biological system, by allowing them to retrieve biological models in their own tool, combine queries in workflows and efficiently analyse models.

Molecular and Cellular Biology Animations: Development and Impact on Student Learning

PubMed Central

2005-01-01

Educators often struggle when teaching cellular and molecular processes because typically they have only two-dimensional tools to teach something that plays out in four dimensions. Learning research has demonstrated that visualizing processes in three dimensions aids learning, and animations are effective visualization tools for novice learners and aid with long-term memory retention. The World Wide Web Instructional Committee at North Dakota State University has used these research results as an inspiration to develop a suite of high-quality animations of molecular and cellular processes. Currently, these animations represent transcription, translation, bacterial gene expression, messenger RNA (mRNA) processing, mRNA splicing, protein transport into an organelle, the electron transport chain, and the use of a biological gradient to drive adenosine triphosphate synthesis. These animations are integrated with an educational module that consists of First Look and Advanced Look components that feature captioned stills from the animation representing the key steps in the processes at varying levels of complexity. These animation-based educational modules are available via the World Wide Web at http://vcell.ndsu.edu/animations. An in-class research experiment demonstrated that student retention of content material was significantly better when students received a lecture coupled with the animations and then used the animation as an individual study activity. PMID:15917875

Monitoring Anaerobic TCE Degradation by Evanite Cultre in Column Packed with TCE-Contaminated Soil

NASA Astrophysics Data System (ADS)

Ko, J.; Han, K.; Ahn, G.; Park, S.; Kim, N.; Ahn, H.; Kim, Y.

2011-12-01

Trichloroethylene (TCE) is a long-term common groundwater pollutant because the compound with high density is slowly released into groundwater. Physical and chemical remediation processes have been used to clean-up the contaminant, but novel remediation technology is required to overcome a low efficiency of the traditional treatment process. Many researchers focused on biological process using an anaerobic TCE degrading culture, dehalococcoides spp., but it still needs to evaluate whether the process can be applied into field scale under aerobic condition. Therefore, in this work we examined two different types (i.e., Natural attenuation and bioaugmentation) of biological remediation process in anaerobic column packed with TCE-contaminated soil. A TCE degradation by indigenous microorganisms was confirmed by monitoring TCE and the metabolites (c-DCE, VC, ETH). However, TCE was transformed and stoichiometry amount of c-DCE was produced, and VC and ETH was not detected. To test bioaugmentation of Evanite culture containing dehalococcoides spp., Evanite culture was injected into the column and TCE degradation to c-DCE, VC, ETH was monitored. We are evaluating the transport of the Evanite culture in the column by measuring TCE and VC reductases. In the result, the TCE was completely degraded to ETH using hydrogen as electron donor generate by hydrogen-production fermentation from formate.

37 CFR 1.775 - Calculation of patent term extension for a human drug, antibiotic drug or human biological product.

Code of Federal Regulations, 2013 CFR

2013-07-01

... extension for a human drug, antibiotic drug or human biological product. 1.775 Section 1.775 Patents... Review § 1.775 Calculation of patent term extension for a human drug, antibiotic drug or human biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a human drug, antibiotic...

37 CFR 1.775 - Calculation of patent term extension for a human drug, antibiotic drug or human biological product.

Code of Federal Regulations, 2012 CFR

2012-07-01

... extension for a human drug, antibiotic drug or human biological product. 1.775 Section 1.775 Patents... Review § 1.775 Calculation of patent term extension for a human drug, antibiotic drug or human biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a human drug, antibiotic...

37 CFR 1.775 - Calculation of patent term extension for a human drug, antibiotic drug or human biological product.

Code of Federal Regulations, 2014 CFR

2014-07-01

... extension for a human drug, antibiotic drug or human biological product. 1.775 Section 1.775 Patents... Review § 1.775 Calculation of patent term extension for a human drug, antibiotic drug or human biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a human drug, antibiotic...

37 CFR 1.775 - Calculation of patent term extension for a human drug, antibiotic drug or human biological product.

Code of Federal Regulations, 2011 CFR

2011-07-01

... extension for a human drug, antibiotic drug or human biological product. 1.775 Section 1.775 Patents... Review § 1.775 Calculation of patent term extension for a human drug, antibiotic drug or human biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a human drug, antibiotic...

37 CFR 1.775 - Calculation of patent term extension for a human drug, antibiotic drug or human biological product.

Code of Federal Regulations, 2010 CFR

2010-07-01

... extension for a human drug, antibiotic drug or human biological product. 1.775 Section 1.775 Patents... Review § 1.775 Calculation of patent term extension for a human drug, antibiotic drug or human biological product. (a) If a determination is made pursuant to § 1.750 that a patent for a human drug, antibiotic...

Defining contamination control requirements for non-human research on Space Station Freedom

NASA Technical Reports Server (NTRS)

Corbin, Barbara J.; Funk, Glenn A.

1992-01-01

The use of non-human biological specimens for life sciences research on Space Station Freedom has generated concerns about spacecraft internal contamination, crew safety and hardware utility. Various NASA organizations convened to discuss the concerns and determine how they should be addressed. This paper will present the issues raised at this meeting, the process by which safety concerns were identified, and the means by which contamination control requirements for all biological payloads were recommended for incorporation into Space Station Freedom safety requirements. The microbiological, toxicological and particulate contamination criteria for long-term spaceflight will be based on realistic assessment of risk and hardware will be designed to meet established contamination criteria while facilitating crew operations, thereby meeting the needs of the investigator.

Modern morphometry: new perspectives in physical anthropology.

PubMed

Mantini, Simone; Ripani, Maurizio

2009-06-01

In the past one hundred years physical anthropology has recourse to more and more efficient methods, which provide several new information regarding, human evolution and biology. Apart from the molecular approach, the introduction of new computed assisted techniques gave rise to a new concept of morphometry. Computed tomography and 3D-imaging, allowed providing anatomical description of the external and inner structures exceeding the problems encountered with the traditional morphometric methods. Furthermore, the support of geometric morphometrics, allowed creating geometric models to investigate morphological variation in terms of evolution, ontogeny and variability. The integration of these new tools gave rise to the virtual anthropology and to a new image of the anthropologist in which anatomical, biological, mathematical statistical and data processing information are fused in a multidisciplinary approach.

Effects of predation efficiencies on the dynamics of a tritrophic food chain.

PubMed

Cassinari, Maria Paola; Groppi, Maria; Tebaldi, Claudio

2007-07-01

In this paper the dynamics of a tritrophic food chain (resource, consumer, top predator) is investigated, with particular attention not only to equilibrium states but also to cyclic behaviours that the system may exhibit. The analysis is performed in terms of two bifurcation parameters, denoted by p and q, which measure the efficiencies of the interaction processes. The persistence of the system is discussed, characterizing in the (p; q) plane the regions of existence and stability of biologically significant steady states and those of existence of limit cycles. The bifurcations occurring are discussed, and their implications with reference to biological control problems are considered. Examples of the rich dynamics exhibited by the model, including a chaotic regime, are described.

A method to identify differential expression profiles of time-course gene data with Fourier transformation

PubMed Central

2013-01-01

Background Time course gene expression experiments are an increasingly popular method for exploring biological processes. Temporal gene expression profiles provide an important characterization of gene function, as biological systems are both developmental and dynamic. With such data it is possible to study gene expression changes over time and thereby to detect differential genes. Much of the early work on analyzing time series expression data relied on methods developed originally for static data and thus there is a need for improved methodology. Since time series expression is a temporal process, its unique features such as autocorrelation between successive points should be incorporated into the analysis. Results This work aims to identify genes that show different gene expression profiles across time. We propose a statistical procedure to discover gene groups with similar profiles using a nonparametric representation that accounts for the autocorrelation in the data. In particular, we first represent each profile in terms of a Fourier basis, and then we screen out genes that are not differentially expressed based on the Fourier coefficients. Finally, we cluster the remaining gene profiles using a model-based approach in the Fourier domain. We evaluate the screening results in terms of sensitivity, specificity, FDR and FNR, compare with the Gaussian process regression screening in a simulation study and illustrate the results by application to yeast cell-cycle microarray expression data with alpha-factor synchronization. The key elements of the proposed methodology: (i) representation of gene profiles in the Fourier domain; (ii) automatic screening of genes based on the Fourier coefficients and taking into account autocorrelation in the data, while controlling the false discovery rate (FDR); (iii) model-based clustering of the remaining gene profiles. Conclusions Using this method, we identified a set of cell-cycle-regulated time-course yeast genes. The proposed method is general and can be potentially used to identify genes which have the same patterns or biological processes, and help facing the present and forthcoming challenges of data analysis in functional genomics. PMID:24134721

Short-term plasticity and long-term potentiation mimicked in single inorganic synapses

NASA Astrophysics Data System (ADS)

Ohno, Takeo; Hasegawa, Tsuyoshi; Tsuruoka, Tohru; Terabe, Kazuya; Gimzewski, James K.; Aono, Masakazu

2011-08-01

Memory is believed to occur in the human brain as a result of two types of synaptic plasticity: short-term plasticity (STP) and long-term potentiation (LTP; refs , , , ). In neuromorphic engineering, emulation of known neural behaviour has proven to be difficult to implement in software because of the highly complex interconnected nature of thought processes. Here we report the discovery of a Ag2S inorganic synapse, which emulates the synaptic functions of both STP and LTP characteristics through the use of input pulse repetition time. The structure known as an atomic switch, operating at critical voltages, stores information as STP with a spontaneous decay of conductance level in response to intermittent input stimuli, whereas frequent stimulation results in a transition to LTP. The Ag2S inorganic synapse has interesting characteristics with analogies to an individual biological synapse, and achieves dynamic memorization in a single device without the need of external preprogramming. A psychological model related to the process of memorizing and forgetting is also demonstrated using the inorganic synapses. Our Ag2S element indicates a breakthrough in mimicking synaptic behaviour essential for the further creation of artificial neural systems that emulate characteristics of human memory.

Optimal growth trajectories with finite carrying capacity.

PubMed

Caravelli, F; Sindoni, L; Caccioli, F; Ududec, C

2016-08-01

We consider the problem of finding optimal strategies that maximize the average growth rate of multiplicative stochastic processes. For a geometric Brownian motion, the problem is solved through the so-called Kelly criterion, according to which the optimal growth rate is achieved by investing a constant given fraction of resources at any step of the dynamics. We generalize these finding to the case of dynamical equations with finite carrying capacity, which can find applications in biology, mathematical ecology, and finance. We formulate the problem in terms of a stochastic process with multiplicative noise and a nonlinear drift term that is determined by the specific functional form of carrying capacity. We solve the stochastic equation for two classes of carrying capacity functions (power laws and logarithmic), and in both cases we compute the optimal trajectories of the control parameter. We further test the validity of our analytical results using numerical simulations.

Mechanics of active surfaces

NASA Astrophysics Data System (ADS)

Salbreux, Guillaume; Jülicher, Frank

2017-09-01

We derive a fully covariant theory of the mechanics of active surfaces. This theory provides a framework for the study of active biological or chemical processes at surfaces, such as the cell cortex, the mechanics of epithelial tissues, or reconstituted active systems on surfaces. We introduce forces and torques acting on a surface, and derive the associated force balance conditions. We show that surfaces with in-plane rotational symmetry can have broken up-down, chiral, or planar-chiral symmetry. We discuss the rate of entropy production in the surface and write linear constitutive relations that satisfy the Onsager relations. We show that the bending modulus, the spontaneous curvature, and the surface tension of a passive surface are renormalized by active terms. Finally, we identify active terms which are not found in a passive theory and discuss examples of shape instabilities that are related to active processes in the surface.

Optimal growth trajectories with finite carrying capacity

NASA Astrophysics Data System (ADS)

Caravelli, F.; Sindoni, L.; Caccioli, F.; Ududec, C.

2016-08-01

We consider the problem of finding optimal strategies that maximize the average growth rate of multiplicative stochastic processes. For a geometric Brownian motion, the problem is solved through the so-called Kelly criterion, according to which the optimal growth rate is achieved by investing a constant given fraction of resources at any step of the dynamics. We generalize these finding to the case of dynamical equations with finite carrying capacity, which can find applications in biology, mathematical ecology, and finance. We formulate the problem in terms of a stochastic process with multiplicative noise and a nonlinear drift term that is determined by the specific functional form of carrying capacity. We solve the stochastic equation for two classes of carrying capacity functions (power laws and logarithmic), and in both cases we compute the optimal trajectories of the control parameter. We further test the validity of our analytical results using numerical simulations.

Toxicogenomics and cancer risk assessment: a framework for key event analysis and dose-response assessment for nongenotoxic carcinogens.

PubMed

Bercu, Joel P; Jolly, Robert A; Flagella, Kelly M; Baker, Thomas K; Romero, Pedro; Stevens, James L

2010-12-01

In order to determine a threshold for nongenotoxic carcinogens, the traditional risk assessment approach has been to identify a mode of action (MOA) with a nonlinear dose-response. The dose-response for one or more key event(s) linked to the MOA for carcinogenicity allows a point of departure (POD) to be selected from the most sensitive effect dose or no-effect dose. However, this can be challenging because multiple MOAs and key events may exist for carcinogenicity and oftentimes extensive research is required to elucidate the MOA. In the present study, a microarray analysis was conducted to determine if a POD could be identified following short-term oral rat exposure with two nongenotoxic rodent carcinogens, fenofibrate and methapyrilene, using a benchmark dose analysis of genes aggregated in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and Gene Ontology (GO) biological processes, which likely encompass key event(s) for carcinogenicity. The gene expression response for fenofibrate given to rats for 2days was consistent with its MOA and known key events linked to PPARα activation. The temporal response from daily dosing with methapyrilene demonstrated biological complexity with waves of pathways/biological processes occurring over 1, 3, and 7days; nonetheless, the benchmark dose values were consistent over time. When comparing the dose-response of toxicogenomic data to tumorigenesis or precursor events, the toxicogenomics POD was slightly below any effect level. Our results suggest that toxicogenomic analysis using short-term studies can be used to identify a threshold for nongenotoxic carcinogens based on evaluation of potential key event(s) which then can be used within a risk assessment framework. Copyright © 2010 Elsevier Inc. All rights reserved.

FUSE: a profit maximization approach for functional summarization of biological networks.

PubMed

Seah, Boon-Siew; Bhowmick, Sourav S; Dewey, C Forbes; Yu, Hanry

2012-03-21

The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI) using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator) that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL) principle to maximize information gain of the summary graph while satisfying the level of detail constraint. We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

Anal Sphincter Augmentation Using Biological Material.

PubMed

Alam, Nasra N; Narang, Sunil K; Köckerling, Ferdinand; Daniels, Ian R; Smart, Neil J

2015-01-01

The aim of this review is to provide an overview of the use of biological materials in the augmentation of the anal sphincter either as part of an overlapping sphincter repair (OSR) or anal bulking procedure. A systematic search of PubMed was conducted using the search terms "anal bulking agents," "anal sphincter repair," or "overlapping sphincter repair." Five studies using biological material as part of an overlapping sphincter repair (OSR) or as an anal bulking agent were identified. 122 patients underwent anal bulking with a biological material. Anorectal physiology was conducted in 27 patients and demonstrated deterioration in maximum resting pressure, and no significant change in maximum squeeze increment. Quality of life scores (QoLs) demonstrated improvements at 6 weeks and 6 months, but this had deteriorated at 12 months of follow up. Biological material was used in 23 patients to carry out an anal encirclement procedure. Improvements in QoLs were observed in patients undergoing OSR as well as anal encirclement using biological material. Incontinence episodes decreased to an average of one per week from 8 to 10 preoperatively. Sphincter encirclement with biological material has demonstrated improvements in continence and QoLs in the short term compared to traditional repair alone. Long-term studies are necessary to determine if this effect is sustained. As an anal bulking agent the benefits are short-term.

Learning in First-Year Biology: Approaches of Distance and On-Campus Students

NASA Astrophysics Data System (ADS)

Quinn, Frances Catherine

2011-01-01

This paper aims to extend previous research into learning of tertiary biology, by exploring the learning approaches adopted by two groups of students studying the same first-year biology topic in either on-campus or off-campus "distance" modes. The research involved 302 participants, who responded to a topic-specific version of the Study Process Questionnaire, and in-depth interviews with 16 of these students. Several quantitative analytic techniques, including cluster analysis and Rasch differential item functioning analysis, showed that the younger, on-campus cohort made less use of deep approaches, and more use of surface approaches than the older, off-campus group. At a finer scale, clusters of students within these categories demonstrated different patterns of learning approach. Students' descriptions of their learning approaches at interview provided richer complementary descriptions of the approach they took to their study in the topic, showing how deep and surface approaches were manifested in the study context. These findings are critically analysed in terms of recent literature questioning the applicability of learning approaches theory in mass education, and their implications for teaching and research in undergraduate biology.

Recent developments on ultrasound-assisted one-pot multicomponent synthesis of biologically relevant heterocycles.

PubMed

Banerjee, Bubun

2017-03-01

Heterocycles are the backbone of organic compounds. Specially, N- &O-containing heterocycles represent privileged structural subunits well distributed in naturally occurring compounds with immense biological activities. Multicomponent reactions (MCRs) are becoming valuable tool for synthesizing structurally diverse molecular entities. On the other hand, the last decade has seen a tremendous outburst in modifying chemical processes to make them sustainable for the betterment of our environment. The application of ultrasound in organic synthesis is fulfilling some of the goals of 'green and sustainable chemistry' as it has some advantages over the traditional thermal methods in terms of reaction rates, yields, purity of the products, product selectivity, etc. Therefore the synthesis of biologically relevant heterocycles using one-pot multi-component technique coupled with the application of ultrasound is one of the thrusting areas in the 21st Century among the organic chemists. The present review deals with the "up to date" developments on ultrasound assisted one-pot multi-component synthesis of biologically relevant heterocycles reported so far. Copyright © 2016 Elsevier B.V. All rights reserved.

Rational protein design: developing next-generation biological therapeutics and nanobiotechnological tools.

PubMed

Wilson, Corey J

2015-01-01

Proteins are the most functionally diverse macromolecules observed in nature, participating in a broad array of catalytic, biosensing, transport, scaffolding, and regulatory functions. Fittingly, proteins have become one of the most promising nanobiotechnological tools to date, and through the use of recombinant DNA and other laboratory methods we have produced a vast number of biological therapeutics derived from human genes. Our emerging ability to rationally design proteins (e.g., via computational methods) holds the promise of significantly expanding the number and diversity of protein therapies and has opened the gateway to realizing true and uncompromised personalized medicine. In the last decade computational protein design has been transformed from a set of fundamental strategies to stringently test our understanding of the protein structure-function relationship, to practical tools for developing useful biological processes, nano-devices, and novel therapeutics. As protein design strategies improve (i.e., in terms of accuracy and efficiency) clinicians will be able to leverage individual genetic data and biological metrics to develop and deliver personalized protein therapeutics with minimal delay. © 2014 Wiley Periodicals, Inc.

[Valorization of biological resources in tumour libraries].

PubMed

Keelaghan, Thérèse

2006-01-01

The transfer and commercialization of biological materials, whether in the form of tumour samples, tissue samples or chemicals, and of the data base pertaining to such material have become a subject of considerable importance for both the private and public sectors involved in medical research. In order to fully appreciate and apprehend the process for the protection and the valuation of the transferred material, intellectual property law must be taken into account. As a result, a distinction is made between the tangible and intangible elements of the biological material and of the attached data base, thus providing the transferring entity the possibility to claim property rights to future intellectual property arising from the research regarding the transferred material. The transfer of biological material and attached data base without such contractual provisions can lead to the loss of this potential value as well as of physical and legal control over the material transferred by the providing entity. The intentions and the assumptions of the parties must be negotiated and written into terms of contract, at the risk of losing future value due to unexpressed assumptions concerning intangible property rights.

Synergistic effects in the short-term preservation of hides with antiseptics and gamma radiation

NASA Astrophysics Data System (ADS)

Du Plessis, TA; Russell, AE; Stevens, RCB; Galloway, AC

The normal time lapse between the skinning and tanning processes of green hides necessitates the need for a short-term preservation technique to be employed. The most common method of bringing about such preservation is the coarse salting of the flesh side of hides. More recently the antiseptic treatment of hides was introduced to overcome the serious environmental pollution brought about by the salting process. The antiseptic treatment, however, must also be carefully controlled to avoid upsetting the biological breakdown processes in effluent plants. The gamma sterilization of such hides presents a non-polluting alternative to these methods. As the nature of this product demands excessively high radiation doses to be effective, which negatively influences the economics of the process and the physical properties of the resultant leather, a combination process employing radiation and antiseptics was investigated. It was observed that the radiation dose could be lowered from 50 kGy to 8 kGy in combination with certain antiseptics, whilst the required antiseptic concentration could be substantially lowered in the presence of radiation. The resultant leather was of an excellent quality whilst minimizing the environmental pollution problem.

A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics.

PubMed

Somvanshi, Pramod Rajaram; Venkatesh, K V

2014-03-01

Human physiology is an ensemble of various biological processes spanning from intracellular molecular interactions to the whole body phenotypic response. Systems biology endures to decipher these multi-scale biological networks and bridge the link between genotype to phenotype. The structure and dynamic properties of these networks are responsible for controlling and deciding the phenotypic state of a cell. Several cells and various tissues coordinate together to generate an organ level response which further regulates the ultimate physiological state. The overall network embeds a hierarchical regulatory structure, which when unusually perturbed can lead to undesirable physiological state termed as disease. Here, we treat a disease diagnosis problem analogous to a fault diagnosis problem in engineering systems. Accordingly we review the application of engineering methodologies to address human diseases from systems biological perspective. The review highlights potential networks and modeling approaches used for analyzing human diseases. The application of such analysis is illustrated in the case of cancer and diabetes. We put forth a concept of cell-to-human framework comprising of five modules (data mining, networking, modeling, experimental and validation) for addressing human physiology and diseases based on a paradigm of system level analysis. The review overtly emphasizes on the importance of multi-scale biological networks and subsequent modeling and analysis for drug target identification and designing efficient therapies.

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

PubMed

Yi, Ming; Mudunuri, Uma; Che, Anney; Stephens, Robert M

2009-06-29

One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential) gene lists from multiple experiments for common or unique underlying biological themes. A common way to approach this problem is to extract common genes from these gene lists and then subject these genes to enrichment analysis to reveal the underlying biology. However, the capacity of this approach is largely restricted by the limited number of common genes shared by datasets from multiple experiments, which could be caused by the complexity of the biological system itself. We now introduce a new Pathway Pattern Extraction Pipeline (PPEP), which extends the existing WPS application by providing a new pathway-level comparative analysis scheme. To facilitate comparing and correlating results from different studies and sources, PPEP contains new interfaces that allow evaluation of the pathway-level enrichment patterns across multiple gene lists. As an exploratory tool, this analysis pipeline may help reveal the underlying biological themes at both the pathway and gene levels. The analysis scheme provided by PPEP begins with multiple gene lists, which may be derived from different studies in terms of the biological contexts, applied technologies, or methodologies. These lists are then subjected to pathway-level comparative analysis for extraction of pathway-level patterns. This analysis pipeline helps to explore the commonality or uniqueness of these lists at the level of pathways or biological processes from different but relevant biological systems using a combination of statistical enrichment measurements, pathway-level pattern extraction, and graphical display of the relationships of genes and their associated pathways as Gene-Term Association Networks (GTANs) within the WPS platform. As a proof of concept, we have used the new method to analyze many datasets from our collaborators as well as some public microarray datasets. This tool provides a new pathway-level analysis scheme for integrative and comparative analysis of data derived from different but relevant systems. The tool is freely available as a Pathway Pattern Extraction Pipeline implemented in our existing software package WPS, which can be obtained at http://www.abcc.ncifcrf.gov/wps/wps_index.php.

Research and development program, fiscal year 1966

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

Not Available

1964-04-01

The biomedical program of the Laboratory of Nuclear Medicine and Radiation Biology for FY 1966 is conducted within the scope of the following categories: Somatic Effects of Radiation; Combating Detrimental Effects of Radiation; Molecular and Cellular Level Studies; Environmental Radiation Studies; Radiological and Health Physics and Instrumentation; Chemical Toxicity; Cancer Research; and Selected Beneficial Applications. The overall objectives of the Laboratory within these areas of the Biology and Medicine program may be summarized as follows: (1) investigation of the effects of ionizing radiation on living organisms and systems of biological significance; (2) investigation of the dynamic aspects of physiological andmore » biochemical processes in man, animals and plants and how these processes are modified by radiation and related pathological states; (3) the assessment and study of the immediate and long term consequences of the operation or detonation of nuclear devices on the fauna, and flora in man's environment and on man; (4) the development of methods of minimizing or preventing the detrimental effects of ionizing radiation; (5) research in, and development of, beneficial uses of ionizing radiation and radioactive substances in medicine and biology; (6) research in the development of new and more efficient radiation detection devices; (7) research, including field studies, as mutually agreed upon by the Commission and the University, in connection with the conduct of weapon tests and biomedical and civil effects experiments at such tests conducted at continental and overseas test sites; and (8) the conduct of training and educational activities in the biological and medical aspects of radiation and related fields.« less

Future directions in inflammatory bowel disease management.

PubMed

D'Haens, Geert R; Sartor, R Balfour; Silverberg, Mark S; Petersson, Joel; Rutgeerts, Paul

2014-08-01

Clinical management of inflammatory bowel diseases (IBD), new treatment modalities and the potential impact of personalised medicine remain topics of intense interest as our understanding of the pathophysiology of IBD expands. Potential future strategies for IBD management are discussed, based on recent preclinical and clinical research. A top-down approach to medical therapy is increasingly being adopted for patients with risk factors for severe inflammation or an unfavourable disease course in an attempt to halt the inflammatory process as early as possible, prevent complications and induce mucosal healing. In the future, biological therapies for IBD are likely to be used more selectively based on personalised benefit/risk assessment, determined through reliable biomarkers and tissue signatures, and will probably be optimised throughout the course of treatment. Biologics with different mechanisms of action will be available; when one drug fails, patients will be able to switch to another and even combination biologics may become a reality. The role of biotherapeutic products that are similar to currently licensed biologics in terms of quality, safety and efficacy - i.e. biosimilars - is at an early stage and requires further experience. Other therapeutic strategies may involve manipulation of the microbiome using antibiotics, probiotics, prebiotics, diet and combinations of all these approaches. Faecal microbiota transplantation is also a potential option in IBD although controlled data are lacking. The future of classifying, prognosticating and managing IBD involves an outcomes-based approach to identify biomarkers reflecting various biological processes that can be matched with clinically important endpoints. Copyright © 2014 European Crohn's and Colitis Organisation. Published by Elsevier B.V. All rights reserved.

Functional Anthology of Intrinsic Disorder. III. Ligands, Postranslational Modifications and Diseases Associated with Intrinsically Disordered Proteins

PubMed Central

Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

2008-01-01

Currently, the understanding of the relationships between function, amino acid sequence and protein structure continues to represent one of the major challenges of the modern protein science. As much as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bioinformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200,000 proteins from Swiss-Prot database, each annotated with at least one of the 875 functional keywords was described in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Using this tool, we have found that out of the 711 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). The second paper of the series was devoted to the presentation of 87 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions (Vucetic S., Xie H., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. II. Cellular components, domains, technical terms, developmental processes and coding sequence diversities correlated with long disordered regions. J. Proteome Res.). Protein structure and functionality can be modulated by various posttranslational modifications or/and as a result of binding of specific ligands. Numerous human diseases are associated with protein misfolding/misassembly/ misfunctioning. This work concludes the series of papers dedicated to the functional anthology of intrinsic disorder and describes ~80 Swiss-Prot functional keywords that are related to ligands, posttranslational modifications and diseases possessing strong positive or negative correlation with the predicted long disordered regions in proteins. PMID:17391016

Cell cycle regulation by the intrinsically disordered proteins p21 and p27.

PubMed

Yoon, Mi-Kyung; Mitrea, Diana M; Ou, Li; Kriwacki, Richard W

2012-10-01

Today, it is widely accepted that proteins that lack highly defined globular three-dimensional structures, termed IDPs (intrinsically disordered proteins), play key roles in myriad biological processes. Our understanding of how intrinsic disorder mediates biological function is, however, incomplete. In the present paper, we review disorder-mediated cell cycle regulation by two intrinsically disordered proteins, p21 and p27. A structural adaptation mechanism involving a stretchable dynamic linker helix allows p21 to promiscuously recognize the various Cdk (cyclin-dependent kinase)-cyclin complexes that regulate cell division. Disorder within p27 mediates transmission of an N-terminal tyrosine phosphorylation signal to a C-terminal threonine phosphorylation, constituting a signalling conduit. These mechanisms are mediated by folding upon binding p21/p27's regulatory targets. However, residual disorder within the bound state contributes critically to these functional mechanisms. Our studies provide insights into how intrinsic protein disorder mediates regulatory processes and opportunities for designing drugs that target cancer-associated IDPs.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2018-07-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Quantifying evenly distributed states in exclusion and nonexclusion processes

NASA Astrophysics Data System (ADS)

Binder, Benjamin J.; Landman, Kerry A.

2011-04-01

Spatial-point data sets, generated from a wide range of physical systems and mathematical models, can be analyzed by counting the number of objects in equally sized bins. We find that the bin counts are related to the Pólya distribution. New measures are developed which indicate whether or not a spatial data set, generated from an exclusion process, is at its most evenly distributed state, the complete spatial randomness (CSR) state. To this end, we define an index in terms of the variance between the bin counts. Limiting values of the index are determined when objects have access to the entire domain and when there are subregions of the domain that are inaccessible to objects. Using three case studies (Lagrangian fluid particles in chaotic laminar flows, cellular automata agents in discrete models, and biological cells within colonies), we calculate the indexes and verify that our theoretical CSR limit accurately predicts the state of the system. These measures should prove useful in many biological applications.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2017-11-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Circulating Tumor Cell and Cell-free Circulating Tumor DNA in Lung Cancer.

PubMed

Nurwidya, Fariz; Zaini, Jamal; Putra, Andika Chandra; Andarini, Sita; Hudoyo, Achmad; Syahruddin, Elisna; Yunus, Faisal

2016-09-01

Circulating tumor cells (CTCs) are tumor cells that are separated from the primary site or metastatic lesion and disseminate in blood circulation. CTCs are considered to be part of the long process of cancer metastasis. As a 'liquid biopsy', CTC molecular examination and investigation of single cancer cells create an important opportunity for providing an understanding of cancer biology and the process of metastasis. In the last decade, we have seen dramatic development in defining the role of CTCs in lung cancer in terms of diagnosis, genomic alteration determination, treatment response and, finally, prognosis prediction. The aims of this review are to understand the basic biology and to review methods of detection of CTCs that apply to the various types of solid tumor. Furthermore, we explored clinical applications, including treatment monitoring to anticipate therapy resistance as well as biomarker analysis, in the context of lung cancer. We also explored the potential use of cell-free circulating tumor DNA (ctDNA) in the genomic alteration analysis of lung cancer.

Visualizing chaperone-assisted protein folding

DOE PAGES

Horowitz, Scott; Salmon, Loïc; Koldewey, Philipp; ...

2016-05-30

We present that challenges in determining the structures of heterogeneous and dynamic protein complexes have greatly hampered past efforts to obtain a mechanistic understanding of many important biological processes. One such process is chaperone-assisted protein folding. Obtaining structural ensembles of chaperone–substrate complexes would ultimately reveal how chaperones help proteins fold into their native state. To address this problem, we devised a new structural biology approach based on X-ray crystallography, termed residual electron and anomalous density (READ). READ enabled us to visualize even sparsely populated conformations of the substrate protein immunity protein 7 (Im7) in complex with the Escherichia coli chaperonemore » Spy, and to capture a series of snapshots depicting the various folding states of Im7 bound to Spy. The ensemble shows that Spy-associated Im7 samples conformations ranging from unfolded to partially folded to native-like states and reveals how a substrate can explore its folding landscape while being bound to a chaperone.« less

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

PubMed Central

Coley, John D.; Tanner, Kimberly

2015-01-01

Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems—teleological, essentialist, and anthropocentric thinking—that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. PMID:25713093

Green perspective in food industry production line design: A review

NASA Astrophysics Data System (ADS)

Xian, C. Y.; Sin, T. C.; Liyana, M. R. N.; Awang, A.; Fathullah, M.

2017-09-01

The design of green manufacturing process in food industries is currently a hot research topic in the multidisciplinary area of applied chemistry, biology and technology. Several process such as freezing, cutting, drying, tempering, bleaching, sterilization, extraction and filtering have been applied efficiency in the food industry. Due to the rapid development of food and peripheral technology, the use of new physical processing or auxiliary processing methods can maintain food inherent nutrients, texture, color, and freshness and also reduce environmental pollution and energy consumption in food processing. Hence, this review paper will study and summarize the effects of green manufacturing process in food industries in term of waste reduction, materials and sustainability manufacturing. In any case, All the food processing equipment must comply with strict standards and regulation, this action will ensure the securing the food quality and safety of food products to consumers.

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

PubMed

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

2012-03-26

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

Interest in biology. Part I: A multidimensional construct

NASA Astrophysics Data System (ADS)

Gardner, Paul L.; Tamir, Pinchas

Interest in a school subject (e.g., biology) is conceptualized in terms of three components: topics, activities, and motives, each of which has several dimensions. In this study, seven instruments were developed and administered to grade-10 biology students in Israel. Factor analysis provided support for the conceptualization which underlies the development of the instruments. Topic dimensions included biochemical processes, nonhuman organisms, human biology, personal hygiene, and practical applications; the activity dimensions were experiential learning, reception learning, writing/summarizing and group discussion; motives included environmental issues, moral issues, examination success, personal independence, problem solving, and four career dimensions (research, high-status professions, lower-status careers, woodsy-birdsy careers). In an analysis described in Part II of this paper, the students were classified into four groups on the basis of their grade-11 subject enrollment intentions: H (high-level biology), L (low-level biology), P (physical science), and N (no science). Zero-order and multiple correlations were found between interest and other variables and membership/nonmembership of the four groups. Students in Group H were characterized by higher achievement in year-10 biology, higher levels of enjoyment of biology, career orientations towards research or high-status biology-based professions, greater interest in various biology topics, especially reproduction/cell division/genetics, and a greater tendency to regard the Bagrut (grade-12) examination as interesting. Students in Group N displayed lower levels of interest in various topics (especially the microscope, plants, and reproduction), were less motivated to solve problems, had poorer grades in biology (and chemistry), were less likely to perceive biology as useful, were less likely to regard the Bagrut examination as fair, and were less likely to be interested in social modes of learning. There were few associations between interest variables and membership in Groups L or P.

Conceptual Demand of Practical Work in Science Curricula. A Methodological Approach

NASA Astrophysics Data System (ADS)

Ferreira, Sílvia; Morais, Ana M.

2014-02-01

This article addresses the issue of the level of complexity of practical work in science curricula and is focused on the discipline of Biology and Geology at high school. The level of complexity is seen in terms of the emphasis on and types of practical work and, most importantly, in terms of its level of conceptual demand as given by the complexity of scientific knowledge, the degree of inter-relation between knowledges, and the complexity of cognitive skills. The study also analyzes recontextualizing processes that may occur within the official recontextualizing field. The study is psychologically and sociologically grounded, particularly on Bernstein's theory of pedagogic discourse. It uses a mixed methodology. The results show that practical work is poorly represented in the curriculum, particularly in the case of laboratory work. The level of conceptual demand of practical work varies according to the text under analysis, between the two subjects Biology and Geology, and, within each of them, between general and specific guidelines. Aspects studied are not clearly explicated to curriculum receivers (teachers and textbooks authors). The meaning of these findings is discussed in the article. In methodological terms, the study explores assumptions used in the analysis of the level of conceptual demand and presents innovative instruments constructed for developing this analysis.

The A, C, G, and T of Genome Assembly

PubMed Central

Wajid, Bilal; Sohail, Muhammad U.; Ekti, Ali R.; Serpedin, Erchin

2016-01-01

Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research. PMID:27247941