Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions.

PubMed

Zenni, Rafael Dudeque; Dickie, Ian A; Wingfield, Michael J; Hirsch, Heidi; Crous, Casparus J; Meyerson, Laura A; Burgess, Treena I; Zimmermann, Thalita G; Klock, Metha M; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J

2016-12-30

Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics, and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand, and manage biological invasions. Published by Oxford University Press on behalf of the Annals of Botany Company.

Evolutionary dynamics of tree invasions: complementing the unified framework for biological invasions

PubMed Central

Dickie, Ian A.; Wingfield, Michael J.; Hirsch, Heidi; Crous, Casparus J.; Meyerson, Laura A.; Burgess, Treena I.; Zimmermann, Thalita G.; Klock, Metha M.; Siemann, Evan; Erfmeier, Alexandra; Aragon, Roxana; Montti, Lia; Le Roux, Johannes J.

2017-01-01

Abstract Evolutionary processes greatly impact the outcomes of biological invasions. An extensive body of research suggests that invasive populations often undergo phenotypic and ecological divergence from their native sources. Evolution also operates at different and distinct stages during the invasion process. Thus, it is important to incorporate evolutionary change into frameworks of biological invasions because it allows us to conceptualize how these processes may facilitate or hinder invasion success. Here, we review such processes, with an emphasis on tree invasions, and place them in the context of the unified framework for biological invasions. The processes and mechanisms described are pre-introduction evolutionary history, sampling effect, founder effect, genotype-by-environment interactions, admixture, hybridization, polyploidization, rapid evolution, epigenetics and second-genomes. For the last, we propose that co-evolved symbionts, both beneficial and harmful, which are closely physiologically associated with invasive species, contain critical genetic traits that affect the evolutionary dynamics of biological invasions. By understanding the mechanisms underlying invasion success, researchers will be better equipped to predict, understand and manage biological invasions. PMID:28039118

Plant MetGenMAP: an integrative analysis system for plant systems biology

USDA-ARS?s Scientific Manuscript database

We have developed a web-based system, Plant MetGenMAP, which can identify significantly altered biochemical pathways and highly affected biological processes, predict functional roles of pathway genes, and potential pathway-related regulatory motifs from transcript and metabolite profile datasets. P...

Facultative Lagoons. Instructor's Guide. Biological Treatment Process Control.

ERIC Educational Resources Information Center

Andersen, Lorri

This instructor's guide contains materials needed to teach a two-lesson unit on the structure and components of facultative lagoons, the biological theory of their operation, and factors affecting their operation. Control testing recommendations, maintenance guidelines, and troubleshooting hints are also provided. These materials include: (1) an…

Hydrology, phenology and the USA National Phenology Network

USGS Publications Warehouse

Kish, George R.

2010-01-01

Phenology is the study of seasonally-recurring biological events (such as leaf-out, fruit production, and animal reproduction and migration) and how these events are influenced by environmental change. Phenological changes are some of the most sensitive biological indicators of climate change, and also affect nearly all aspects of ecosystem function. Spatially extensive patterns of phenological observations have been closely linked with climate variability. Phenology and hydrology are closely linked and affect one another across a variety of scales, from leaf intercellular spaces to the troposphere, and over periods of seconds to centuries. Ecosystem life cycles and diversity are also influenced by hydrologic processes such as floods and droughts. Therefore, understanding the relationships between hydrology and phenology is increasingly important in understanding how climate change affects biological and physical systems.

Differential physiological responses of dalmatian toadflax, Linaria dalmatica L. Miller, to injury from two insect biological control agents: Implications for decision-making in biological control

Treesearch

Robert K. D. Peterson; Sharlene E. Sing; David K. Weaver

2005-01-01

Successful biological control of invasive weeds with specialist herbivorous insects is predicated on the assumption that the injury stresses the weeds sufficiently to cause reductions in individual fitness. Because plant gas exchange directly impacts growth and fitness, characterizing how injury affects these primary processes may provide a key indicator of...

Understanding the biological underpinnings of ecohydrological processes

NASA Astrophysics Data System (ADS)

Huxman, T. E.; Scott, R. L.; Barron-Gafford, G. A.; Hamerlynck, E. P.; Jenerette, D.; Tissue, D. T.; Breshears, D. D.; Saleska, S. R.

2012-12-01

Climate change presents a challenge for predicting ecosystem response, as multiple factors drive both the physical and life processes happening on the land surface and their interactions result in a complex, evolving coupled system. For example, changes in surface temperature and precipitation influence near-surface hydrology through impacts on system energy balance, affecting a range of physical processes. These changes in the salient features of the environment affect biological processes and elicit responses along the hierarchy of life (biochemistry to community composition). Many of these structural or process changes can alter patterns of soil water-use and influence land surface characteristics that affect local climate. Of the many features that affect our ability to predict the future dynamics of ecosystems, it is this hierarchical response of life that creates substantial complexity. Advances in the ability to predict or understand aspects of demography help describe thresholds in coupled ecohydrological system. Disentangling the physical and biological features that underlie land surface dynamics following disturbance are allowing a better understanding of the partitioning of water in the time-course of recovery. Better predicting the timing of phenology and key seasonal events allow for a more accurate description of the full functional response of the land surface to climate. In addition, explicitly considering the hierarchical structural features of life are helping to describe complex time-dependent behavior in ecosystems. However, despite this progress, we have yet to build an ability to fully account for the generalization of the main features of living systems into models that can describe ecohydrological processes, especially acclimation, assembly and adaptation. This is unfortunate, given that many key ecosystem services are functions of these coupled co-evolutionary processes. To date, both the lack of controlled measurements and experimentation has precluded determination of sufficient theoretical development. Understanding the land-surface response and feedback to climate change requires a mechanistic understanding of the coupling of ecological and hydrological processes and an expansion of theory from the life sciences to appropriately contribute to the broader Earth system science goal.

Capturing extracellular matrix properties in vitro: Microengineering materials to decipher cell and tissue level processes.

PubMed

Abdeen, Amr A; Lee, Junmin; Kilian, Kristopher A

2016-05-01

Rapid advances in biology have led to the establishment of new fields with tremendous translational potential including regenerative medicine and immunoengineering. One commonality to these fields is the need to extract cells for manipulation in vitro; however, results obtained in laboratory cell culture will often differ widely from observations made in vivo. To more closely emulate native cell biology in the laboratory, designer engineered environments have proved a successful methodology to decipher the properties of the extracellular matrix that govern cellular decision making. Here, we present an overview of matrix properties that affect cell behavior, strategies for recapitulating important parameters in vitro, and examples of how these properties can affect cell and tissue level processes, with emphasis on leveraging these tools for immunoengineering. © 2016 by the Society for Experimental Biology and Medicine.

Entrepreneurs and Evolutionary Biology: The Relationship between Testosterone and New Venture Creation

ERIC Educational Resources Information Center

White, Roderick E.; Thornhill, Stewart; Hampson, Elizabeth

2006-01-01

Biological evolutionary processes select for heritable behaviors providing a survival and reproductive advantage. Accordingly, how we behave is, at least in part, affected by the evolutionary history of our species. This research uses evolutionary psychology as the theoretical perspective for exploring the relationship between a heritable…

Factors affecting citrus tree absorption of double-stranded ribonucleic acid, and RNAi delivery to psyllids

USDA-ARS?s Scientific Manuscript database

Modern molecular biological techniques allow for the design of molecules of ribonucleic acid capable of disrupting key biological processes of pests and diseases. A major requirement for the practical application of ribonucleic acid interference (RNAi) against insect pests is an efficient entry path...

Biological invasions in forest ecosystems

Treesearch

Andrew M. Liebhold; Eckehard G. Brockerhoff; Susan Kalisz; Martin A. Nuñez; David A. Wardle; Michael J. Wingfield

2017-01-01

Forests play critical roles in global ecosystem processes and provide numerous services to society. But forests are increasingly affected by a variety of human influences, especially those resulting from biological invasions. Species invading forests include woody and herbaceous plants, many animal species including mammals and invertebrates, as well as a variety of...

Searching the literature for proteins facilitates the identification of biological processes, if advanced methods of analysis are linked: a case study on microgravity-caused changes in cells.

PubMed

Bauer, Johann; Bussen, Markus; Wise, Petra; Wehland, Markus; Schneider, Sabine; Grimm, Daniela

2016-07-01

More than one hundred reports were published about the characterization of cells from malignant and healthy tissues, as well as of endothelial cells and stem cells exposed to microgravity conditions. We retrieved publications about microgravity related studies on each type of cells, extracted the proteins mentioned therein and analyzed them aiming to identify biological processes affected by microgravity culture conditions. The analysis revealed 66 different biological processes, 19 of them were always detected when papers about the four types of cells were analyzed. Since a response to the removal of gravity is common to the different cell types, some of the 19 biological processes could play a role in cellular adaption to microgravity. Applying computer programs, to extract and analyze proteins and genes mentioned in publications becomes essential for scientists interested to get an overview of the rapidly growing fields of gravitational biology and space medicine.

Mutual information estimation reveals global associations between stimuli and biological processes

PubMed Central

Suzuki, Taiji; Sugiyama, Masashi; Kanamori, Takafumi; Sese, Jun

2009-01-01

Background Although microarray gene expression analysis has become popular, it remains difficult to interpret the biological changes caused by stimuli or variation of conditions. Clustering of genes and associating each group with biological functions are often used methods. However, such methods only detect partial changes within cell processes. Herein, we propose a method for discovering global changes within a cell by associating observed conditions of gene expression with gene functions. Results To elucidate the association, we introduce a novel feature selection method called Least-Squares Mutual Information (LSMI), which computes mutual information without density estimaion, and therefore LSMI can detect nonlinear associations within a cell. We demonstrate the effectiveness of LSMI through comparison with existing methods. The results of the application to yeast microarray datasets reveal that non-natural stimuli affect various biological processes, whereas others are no significant relation to specific cell processes. Furthermore, we discover that biological processes can be categorized into four types according to the responses of various stimuli: DNA/RNA metabolism, gene expression, protein metabolism, and protein localization. Conclusion We proposed a novel feature selection method called LSMI, and applied LSMI to mining the association between conditions of yeast and biological processes through microarray datasets. In fact, LSMI allows us to elucidate the global organization of cellular process control. PMID:19208155

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

PubMed

Sakaki, Michiko; Niki, Kazuhisa; Mather, Mara

2012-03-01

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

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

PubMed Central

Sakaki, Michiko; Niki, Kazuhisa; Mather, Mara

2012-01-01

The present study addressed the hypothesis that emotional stimuli relevant to survival or reproduction (biologically emotional stimuli) automatically affect cognitive processing (e.g., attention; memory), while those relevant to social life (socially emotional stimuli) require elaborative processing to modulate attention and memory. Results of our behavioral studies showed that: a) biologically emotional images hold attention more strongly than socially emotional images, b) memory for biologically emotional images was enhanced even with limited cognitive resources, but c) memory for socially emotional images was enhanced only when people had sufficient cognitive resources at encoding. Neither images’ subjective arousal nor their valence modulated these patterns. A subsequent functional magnetic resonance imaging study revealed that biologically emotional images induced stronger activity in visual cortex and greater functional connectivity between amygdala and visual cortex than did socially emotional images. These results suggest that the interconnection between the amygdala and visual cortex supports enhanced attention allocation to biological stimuli. In contrast, socially emotional images evoked greater activity in medial prefrontal cortex (MPFC) and yielded stronger functional connectivity between amygdala and MPFC than biological images. Thus, it appears that emotional processing of social stimuli involves elaborative processing requiring frontal lobe activity. PMID:21964552

Viability analysis in biological evaluations: Concepts of population viability analysis, biological population, and ecological scale

Treesearch

Gregory D. Hayward; John R. Squires

1994-01-01

Environmental protection strategies often rely on environmental impact assessments. As part of the assessment process biologists are routinely asked to evaluate the effects of management actions on plants and animals. This evaluation often requires that biologists make judgments about the viability of affected populations. However, population viability...

Evolution and social epidemiology.

PubMed

Nishi, Akihiro

2015-11-01

Evolutionary biology, which aims to explain the dynamic process of shaping the diversity of life, has not yet significantly affected thinking in social epidemiology. Current challenges in social epidemiology include understanding how social exposures can affect our biology, explaining the dynamics of society and health, and designing better interventions that are mindful of the impact of exposures during critical periods. I review how evolutionary concepts and tools, such as fitness gradient in cultural evolution, evolutionary game theory, and contemporary evolution in cancer, can provide helpful insights regarding social epidemiology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dynamic Biological Functioning Important for Simulating and Stabilizing Ocean Biogeochemistry

NASA Astrophysics Data System (ADS)

Buchanan, P. J.; Matear, R. J.; Chase, Z.; Phipps, S. J.; Bindoff, N. L.

2018-04-01

The biogeochemistry of the ocean exerts a strong influence on the climate by modulating atmospheric greenhouse gases. In turn, ocean biogeochemistry depends on numerous physical and biological processes that change over space and time. Accurately simulating these processes is fundamental for accurately simulating the ocean's role within the climate. However, our simulation of these processes is often simplistic, despite a growing understanding of underlying biological dynamics. Here we explore how new parameterizations of biological processes affect simulated biogeochemical properties in a global ocean model. We combine 6 different physical realizations with 6 different biogeochemical parameterizations (36 unique ocean states). The biogeochemical parameterizations, all previously published, aim to more accurately represent the response of ocean biology to changing physical conditions. We make three major findings. First, oxygen, carbon, alkalinity, and phosphate fields are more sensitive to changes in the ocean's physical state. Only nitrate is more sensitive to changes in biological processes, and we suggest that assessment protocols for ocean biogeochemical models formally include the marine nitrogen cycle to assess their performance. Second, we show that dynamic variations in the production, remineralization, and stoichiometry of organic matter in response to changing environmental conditions benefit the simulation of ocean biogeochemistry. Third, dynamic biological functioning reduces the sensitivity of biogeochemical properties to physical change. Carbon and nitrogen inventories were 50% and 20% less sensitive to physical changes, respectively, in simulations that incorporated dynamic biological functioning. These results highlight the importance of a dynamic biology for ocean properties and climate.

Heterotrimeric G protein alpha subunit controls growth, stress response, extracellular protease activity, and cyclopiazonic acid production in Penicillium camemberti.

PubMed

García-Rico, Ramón O; Gil-Durán, Carlos; Rojas-Aedo, Juan F; Vaca, Inmaculada; Figueroa, Luis; Levicán, Gloria; Chávez, Renato

2017-09-01

The fungus Penicillium camemberti is widely used in the ripening of various bloomy-rind cheeses. Several properties of P. camemberti are important in cheese ripening, including conidiation, growth and enzyme production, among others. However, the production of mycotoxins such as cyclopiazonic acid during the ripening process by P. camemberti has raised concerns among consumers that demand food with minimal contamination. Here we show that overexpressing an α-subunit from the subgroup I of the heterotrimeric G protein (Gαi) influences several of these processes: it negatively affects growth in a media-dependent manner, triggers conidial germination, reduces the rate of sporulation, affects thermal and osmotic stress resistance, and also extracellular protease and cyclopiazonic acid production. Our results contribute to understanding the biological determinants underlying these biological processes in the economically important fungus P. camemberti. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

Adoption: biological and social processes linked to adaptation.

PubMed

Grotevant, Harold D; McDermott, Jennifer M

2014-01-01

Children join adoptive families through domestic adoption from the public child welfare system, infant adoption through private agencies, and international adoption. Each pathway presents distinctive developmental opportunities and challenges. Adopted children are at higher risk than the general population for problems with adaptation, especially externalizing, internalizing, and attention problems. This review moves beyond the field's emphasis on adoptee-nonadoptee differences to highlight biological and social processes that affect adaptation of adoptees across time. The experience of stress, whether prenatal, postnatal/preadoption, or during the adoption transition, can have significant impacts on the developing neuroendocrine system. These effects can contribute to problems with physical growth, brain development, and sleep, activating cascading effects on social, emotional, and cognitive development. Family processes involving contact between adoptive and birth family members, co-parenting in gay and lesbian adoptive families, and racial socialization in transracially adoptive families affect social development of adopted children into adulthood.

Fate of acetone in water

USGS Publications Warehouse

Rathbun, R.E.; Stephens, D.W.; Shultz, D.J.

1982-01-01

The physical, chemical, and biological processes that might affect the concentration of acetone in water were investigated in laboratory studies. Processes considered included volatilization, adsorption by sediments, photodecomposition, bacterial degradation, and absorption by algae and molds. It was concluded that volatilization and bacterial degradation were the dominant processes determining the fate of acetone in streams and rivers. ?? 1982.

Aerobic Digestion. Biological Treatment Process Control. Instructor's Guide.

ERIC Educational Resources Information Center

Klopping, Paul H.

This unit on aerobic sludge digestion covers the theory of the process, system components, factors that affect the process performance, standard operational concerns, indicators of steady-state operations, and operational problems. The instructor's guide includes: (1) an overview of the unit; (2) lesson plan; (3) lecture outline (keyed to a set of…

Reversible modulation of SIRT1 activity in a mouse strain

PubMed Central

Clark-Knowles, Katherine V.; He, Xiaohong; Jardine, Karen; Coulombe, Josée; Dewar-Darch, Danielle; Caron, Annabelle Z.

2017-01-01

The SIRT1 protein deacetylase is reported to have a remarkably wide spectrum of biological functions affecting such varied processes as aging, cancer, metabolism, neurodegeneration and immunity. However, the SIRT1 literature is also full of contradictions. To help establish the role(s) of SIRT1 in these and other biological processes, we set out to create a mouse in which the SIRT1 activity could be toggled between on and off states by fusing the estrogen receptor ligand-binding domain (ER) to the C terminus of the SIRT1 protein. We found that the catalytic activity of the SIRT1-ER fusion protein increased 4–5 fold in cells treated with its ligand, 4-hydroxy-tamoxifen (4OHT). The 4OHT-induced activation of SIRT1-ER was due in large part to a 2 to 4-fold increase in abundance of the SIRT1-ER protein in cells in culture and in tissues in vivo. This increase is reversible and is a consequence of 4OHT-induced stabilization of the SIRT1-ER protein. Since changes in SIRT1 level or activity of 2–4 fold are frequently reported to be sufficient to affect its biological functions, this mouse should be helpful in establishing the causal relationships between SIRT1 and the diseases and processes it affects. PMID:28273169

Status and trends of the nation's biological resources

USGS Publications Warehouse

Mac, Michael J.; Opler, Paul A.; Puckett Haecker, Catherine E.; Doran, Peter D.

1998-01-01

This report is a comprehensive summary of the status and trends of our nation’s biological resources. The report describes the major processes and factors affecting biological resources, and it treats regional status and trends. Authors of the chapters and boxes in this two-volume report were drawn from federal and state agencies, universities, and private organizations, reflecting the U.S. Geological Survey’s national partnership approach to providing comprehensive, reliable information about our biological resources. Following scientific tradition, each chapter and box was peer-reviewed by anonymous scientific reviewers.

40 CFR 233.31 - Coordination requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... discharge may affect the biological, chemical, or physical integrity of the waters of any State(s) other... coordinated with Federal and Federal-State water related planning and review processes. ...

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.

Culture, Urbanism and Changing Human Biology.

PubMed

Schell, L M

2014-04-03

Anthropologists have long known that human activity driven by culture changes the environment. This is apparent in the archaeological record and through the study of the modern environment. Perhaps the largest change since the paleolithic era is the organization of human populations in cities. New environments can reshape human biology through evolution as shown by the evolution of the hominid lineage. Evolution is not the only process capable of reshaping our biology. Some changes in our human biology are adaptive and evolutionary while others are pathological. What changes in human biology may be wrought by the modern urban environment? One significant new change in the environment is the introduction of pollutants largely through urbanization. Pollutants can affect human biology in myriad ways. Evidence shows that human growth, reproduction, and cognitive functioning can be altered by some pollutants, and altered in different ways depending on the pollutant. Thus, pollutants have significance for human biologists and anthropologists generally. Further, they illustrate the bio-cultural interaction characterizing human change. Humans adapt by changing the environment, a cultural process, and then change biologically to adjust to that new environment. This ongoing, interactive process is a fundamental characteristic of human change over the millennia.

Culture, Urbanism and Changing Human Biology

PubMed Central

Schell, L.M.

2014-01-01

Anthropologists have long known that human activity driven by culture changes the environment. This is apparent in the archaeological record and through the study of the modern environment. Perhaps the largest change since the paleolithic era is the organization of human populations in cities. New environments can reshape human biology through evolution as shown by the evolution of the hominid lineage. Evolution is not the only process capable of reshaping our biology. Some changes in our human biology are adaptive and evolutionary while others are pathological. What changes in human biology may be wrought by the modern urban environment? One significant new change in the environment is the introduction of pollutants largely through urbanization. Pollutants can affect human biology in myriad ways. Evidence shows that human growth, reproduction, and cognitive functioning can be altered by some pollutants, and altered in different ways depending on the pollutant. Thus, pollutants have significance for human biologists and anthropologists generally. Further, they illustrate the bio-cultural interaction characterizing human change. Humans adapt by changing the environment, a cultural process, and then change biologically to adjust to that new environment. This ongoing, interactive process is a fundamental characteristic of human change over the millennia. PMID:25598655

Predicting plot soil loss by empirical and process-oriented approaches: A review

USDA-ARS?s Scientific Manuscript database

Soil erosion directly affects the quality of the soil, its agricultural productivity and its biological diversity. Many mathematical models have been developed to estimate plot soil erosion at different temporal scales. At present, empirical soil loss equations and process-oriented models are consid...

EVALUATION OF MULTIPLE PHARMACOKINETIC MODELING STRUCTURES FOR TRICHLOROETHYLENE

EPA Science Inventory

A series of PBPK models were developed for trichloroethylene (TCE) to evaluate biological processes that may affect the absorption, distribution, metabolism and excretion (ADME) of TCE and its metabolites.

Learning cell biology as a team: a project-based approach to upper-division cell biology.

PubMed

Wright, Robin; Boggs, James

2002-01-01

To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular and molecular biology of the disease, and recent research focused on understanding the cellular mechanisms of the disease process. To support effective teamwork and to help students develop collaboration skills useful for their future careers, we provide training in working in small groups. A final poster presentation, held in a public forum, summarizes what students have learned throughout the quarter. Although student satisfaction with the course is similar to that of standard lecture-based classes, a project-based class offers unique benefits to both the student and the instructor.

Ecosystem management and its role in linking science, policy, and management

Treesearch

Matthew Skroch

2005-01-01

The scientific community has recently emphasized the importance of ecological process, structure, and scale in the maintenance of biological diversity. Humans have affected most natural landscapes, and many naturally occurring processes, structures, and species may not rebound to naturally sustaining function without intervention. Ecosystem management relies on science...

Overnight Therapy? The Role of Sleep in Emotional Brain Processing

ERIC Educational Resources Information Center

Walker, Matthew P.; van Der Helm, Els

2009-01-01

Cognitive neuroscience continues to build meaningful connections between affective behavior and human brain function. Within the biological sciences, a similar renaissance has taken place, focusing on the role of sleep in various neurocognitive processes and, most recently, on the interaction between sleep and emotional regulation. This review…

Indicators: Sediment Enzymes

EPA Pesticide Factsheets

Sediment enzymes are proteins that are produced by microorganisms living in the sediment or soil. They are indicators of key ecosystem processes and can help determine which nutrients are affecting the biological community of a waterbody.

Classification of climate-change-induced stresses on biological diversity.

PubMed

Geyer, Juliane; Kiefer, Iris; Kreft, Stefan; Chavez, Veronica; Salafsky, Nick; Jeltsch, Florian; Ibisch, Pierre L

2011-08-01

Conservation actions need to account for and be adapted to address changes that will occur under global climate change. The identification of stresses on biological diversity (as defined in the Convention on Biological Diversity) is key in the process of adaptive conservation management. We considered any impact of climate change on biological diversity a stress because such an effect represents a change (negative or positive) in key ecological attributes of an ecosystem or parts of it. We applied a systemic approach and a hierarchical framework in a comprehensive classification of stresses to biological diversity that are caused directly by global climate change. Through analyses of 20 conservation sites in 7 countries and a review of the literature, we identified climate-change-induced stresses. We grouped the identified stresses according to 3 levels of biological diversity: stresses that affect individuals and populations, stresses that affect biological communities, and stresses that affect ecosystem structure and function. For each stress category, we differentiated 3 hierarchical levels of stress: stress class (thematic grouping with the coarsest resolution, 8); general stresses (thematic groups of specific stresses, 21); and specific stresses (most detailed definition of stresses, 90). We also compiled an overview of effects of climate change on ecosystem services using the categories of the Millennium Ecosystem Assessment and 2 additional categories. Our classification may be used to identify key climate-change-related stresses to biological diversity and may assist in the development of appropriate conservation strategies. The classification is in list format, but it accounts for relations among climate-change-induced stresses. © 2011 Society for Conservation Biology.

Controlled ecological life support system - biological problems

NASA Technical Reports Server (NTRS)

Moore, B., III (Editor); Macelroy, R. D. (Editor)

1982-01-01

The general processes and controls associated with two distinct experimental paradigms are examined. Specific areas for research related to biotic production (food production) and biotic decomposition (waste management) are explored. The workshop discussions were directed toward Elemental cycles and the biological factors that affect the transformations of nutrients into food, of food material into waste, and of waste into nutrients were discussed. To focus on biological issues, the discussion assumed that (1) food production would be by biological means (thus excluding chemical synthesis), (2) energy would not be a limiting factor, and (3) engineering capacity for composition and leak rate would be adequate.

A Multidisciplinary, Open Access Platform for Research on Biomolecules.

PubMed

Bähler, Jürg

2011-08-22

I am pleased to introduce Biomolecules, a new journal to report on all aspects of science that focuses on biologically derived substances, from small molecules to complex polymers. Some examples are lipids, carbohydrates, vitamins, hormones, amino acids, nucleotides, peptides, RNA and polysaccharides, but this list is far from exhaustive. Research on biomolecules encompasses multiple fascinating questions. How are biomolecules synthesized and modified? What are their structures and interactions with other biomolecules? How do biomolecules function in biological processes, at the level of organelles, cells, organs, organisms, or even ecosystems? How do biomolecules affect either the organism that produces them or other organisms of the same or different species? How are biomolecules shaped by evolution, and how in turn do they affect cellular phenotypes? What is the systems-level contribution of biomolecules to biological function? [...].

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation.

PubMed

Yang, Feng; Waters, Katrina M; Miller, John H; Gritsenko, Marina A; Zhao, Rui; Du, Xiuxia; Livesay, Eric A; Purvine, Samuel O; Monroe, Matthew E; Wang, Yingchun; Camp, David G; Smith, Richard D; Stenoien, David L

2010-11-30

High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health.

Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation

PubMed Central

Yang, Feng; Waters, Katrina M.; Miller, John H.; Gritsenko, Marina A.; Zhao, Rui; Du, Xiuxia; Livesay, Eric A.; Purvine, Samuel O.; Monroe, Matthew E.; Wang, Yingchun; Camp, David G.; Smith, Richard D.; Stenoien, David L.

2010-01-01

Background High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation. Principal Findings We have identified 7117 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts 1 h post-exposure. Semi-quantitative label-free analyses were performed to identify phosphopeptides that are apparently altered by radiation exposure. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation-responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatic analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role for MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conclusions Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provide a basis for the systems-level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low-dose radiation exposure on human health. PMID:21152398

Gray Wave of the Great Transformation: A Satellite View of Urbanization, Climate, and Food Security

NASA Technical Reports Server (NTRS)

Imhoff, Marc L.

2007-01-01

Land cover change driven by human activity is profoundly affecting Earth's natural systems with impacts ranging from a loss of biological productivity to changes in atmospheric chemistry and regional and global climate. This change has been so pervasive and progressed so rapidly, compared to natural processes, scientists refer to it as 'the great transformation'. Urbanization or the 'gray wave' of this transformation is being increasingly recognized as an important process in global climate change. A hallmark of our success as a species, large urban conglomerates do in fact alter their environments so profoundly that the local climate, atmospheric composition, and the basic ecology of the landscape are affected in ways that have consequences to human health and economic well-being. Fortunately we have incredible new tools to observe and understand these processes in ways that can be used to plan and develop enjoyable and sustainable urban places. A suite of Earth observing satellites is making it possible to study the interactions between urbanization, biological processes, and the atmosphere including weather and climate. Using these Earth Observatories we are learning how urban heat islands form and potentially ameliorate them, how urbanization can affect rainfall, pollution, surface water recharge at the local level, and climate and food security globally.

Multiple dimensions of biodiversity and ecosystem processes: Exploring the joint influence of intraspecific, specific and interspecific diversity.

PubMed

Eduardo, Anderson A

2016-09-07

The positive influence of biodiversity on ecosystem processes was the focus of intense debate in ecology throughout the recent decades, becoming accepted and treated as a new paradigm in contemporary ecology. However, the available literature in this research field extensively explores species richness as an unidimensional measure for biodiversity. The present study explores how different components of biological diversity (number of genotypes, species, and functional groups) can influence an ecosystem process (biomass fixation). A mathematical model was employed and the simulation results showed that species richness per se does not affect the ecosystem productivity. Genotypic richness affected positively the ecosystem, but only if the genotypes are functionally complementary. The functional groups richness always affected positively the simulated ecosystem process. When together, richness at the different components of biological diversity showed stronger effect on ecosystem, and the scenarios with high species, genotypes and functional groups richness were the most productive ones. The results also allowed to observe that the ecosystems which are diverse in terms of functional groups and genotypes can be less susceptible to species loss. Finally, it is argued that a multiple dimension approach to biodiversity is relevant to advance the current knowledge on the relation between biodiversity and ecosystem functioning. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Psychosocial analysis of the health-disease process].

PubMed

Sawaia, B B

1994-04-01

This article is a reflection about the transdisciplinary paradigmas of the health-illness process noting the symbolic mediation between the reactions of the biological organism and the socio-environment factors including the pathogenic ones. The symbolic-affective mediation is analyzed from the perspective of Social Representation theory allowing one to comprehend the references of individual and collective actions in the health-illness process.

Gray Wave of the Great Transformation: A Satellite View of Urbanization, Climate Change, and Food Security

NASA Technical Reports Server (NTRS)

Imhoff, Marc Lee; Kamiell, Arnon Menahem

2010-01-01

Land cover change driven by human activity is profoundly affecting Earth's natural systems with impacts ranging from a loss of biological diversity to changes in regional and global climate. This change has been so pervasive and progressed so rapidly, compared to natural processes, scientists refer to it as "the great transformation". Urbanization or the 'gray wave' of land transformation is being increasingly recognized as an important process in global climate change. A hallmark of our success as a species, large urban conglomerates do in fact alter the land surface so profoundly that both local climate and the basic ecology of the landscape are affected in ways that have consequences to human health and economic well-being. Fortunately we have incredible new tools for planning and developing urban places that are both enjoyable and sustainable. A suite of Earth observing satellites is making it possible to study the interactions between urbanization, biological processes, and weather and climate. Using these Earth Observatories we are learning how urban heat islands form and potentially ameliorate them, how urbanization can affect rainfall, pollution, and surface water recharge at the local level and climate and food security globally.

Does scale matter? A systematic review of incorporating biological realism when predicting changes in species distributions.

PubMed

Record, Sydne; Strecker, Angela; Tuanmu, Mao-Ning; Beaudrot, Lydia; Zarnetske, Phoebe; Belmaker, Jonathan; Gerstner, Beth

2018-01-01

There is ample evidence that biotic factors, such as biotic interactions and dispersal capacity, can affect species distributions and influence species' responses to climate change. However, little is known about how these factors affect predictions from species distribution models (SDMs) with respect to spatial grain and extent of the models. Understanding how spatial scale influences the effects of biological processes in SDMs is important because SDMs are one of the primary tools used by conservation biologists to assess biodiversity impacts of climate change. We systematically reviewed SDM studies published from 2003-2015 using ISI Web of Science searches to: (1) determine the current state and key knowledge gaps of SDMs that incorporate biotic interactions and dispersal; and (2) understand how choice of spatial scale may alter the influence of biological processes on SDM predictions. We used linear mixed effects models to examine how predictions from SDMs changed in response to the effects of spatial scale, dispersal, and biotic interactions. There were important biases in studies including an emphasis on terrestrial ecosystems in northern latitudes and little representation of aquatic ecosystems. Our results suggest that neither spatial extent nor grain influence projected climate-induced changes in species ranges when SDMs include dispersal or biotic interactions. We identified several knowledge gaps and suggest that SDM studies forecasting the effects of climate change should: 1) address broader ranges of taxa and locations; and 1) report the grain size, extent, and results with and without biological complexity. The spatial scale of analysis in SDMs did not affect estimates of projected range shifts with dispersal and biotic interactions. However, the lack of reporting on results with and without biological complexity precluded many studies from our analysis.

Evaporative losses from soils covered by physical and different types of biological soil crusts

USGS Publications Warehouse

Chamizo, S.; Cantón, Y.; Domingo, F.; Belnap, J.

2013-01-01

Evaporation of soil moisture is one of the most important processes affecting water availability in semiarid ecosystems. Biological soil crusts, which are widely distributed ground cover in these ecosystems, play a recognized role on water processes. Where they roughen surfaces, water residence time and thus infiltration can be greatly enhanced, whereas their ability to clog soil pores or cap the soil surface when wetted can greatly decrease infiltration rate, thus affecting evaporative losses. In this work, we compared evaporation in soils covered by physical crusts, biological crusts in different developmental stages and in the soils underlying the different biological crust types. Our results show that during the time of the highest evaporation (Day 1), there was no difference among any of the crust types or the soils underlying them. On Day 2, when soil moisture was moderately low (11%), evaporation was slightly higher in well-developed biological soil crusts than in physical or poorly developed biological soil crusts. However, crust removal did not cause significant changes in evaporation compared with the respective soil crust type. These results suggest that the small differences we observed in evaporation among crust types could be caused by differences in the properties of the soil underneath the biological crusts. At low soil moisture (<6%), there was no difference in evaporation among crust types or the underlying soils. Water loss for the complete evaporative cycle (from saturation to dry soil) was similar in both crusted and scraped soils. Therefore, we conclude that for the specific crust and soil types tested, the presence or the type of biological soil crust did not greatly modify evaporation with respect to physical crusts or scraped soils.

Meaning Making: What Reflective Essays Reveal about Biology Students' Conceptions about Natural Selection

ERIC Educational Resources Information Center

Balgopal, Meena M.; Montplaisir, Lisa M.

2011-01-01

The process of reflective writing can play a central role in making meaning as learners process new information and connect it to prior knowledge. An examination of the written discourse can therefore be revealing of learners' cognitive understanding and affective (beliefs, feelings, motivation to learn) responses to concepts. Despite reflective…

Ecological and geographical regularities of changes in the biological activity of automorphic soils on the foothills and adjacent plains of the Central Caucasus region (Kabardino-Balkarian Republic)

NASA Astrophysics Data System (ADS)

Gorobtsova, O. N.; Khezheva, F. V.; Uligova, T. S.; Tembotov, R. Kh.

2015-03-01

The biochemical properties inherent to the main types of automorphic soils developed in different bioclimatic conditions of Elbrus and Terek variants of the vertical zonality within Kabardino-Balkaria were compared. The natural-climatic conditions of these variants noticeably affect the soil cover pattern. The ratio of the oxidase and hydrolase activities is sensitive to the moisture conditions in which these soils are formed. The redox processes are more active in drier conditions, whereas hydrolytic processes are more active under higher moisture. The level of the biological activity of the automorphic soils is estimated using the integral index of the ecological-biological soil status.

A Preliminary Experimental Examination of Worldview Verification, Perceived Racism, and Stress Reactivity in African Americans

PubMed Central

Lucas, Todd; Lumley, Mark A.; Flack, John M.; Wegner, Rhiana; Pierce, Jennifer; Goetz, Stefan

2016-01-01

Objective According to worldview verification theory, inconsistencies between lived experiences and worldviews are psychologically threatening. These inconsistencies may be key determinants of stress processes that influence cardiovascular health disparities. This preliminary examination considers how experiencing injustice can affect perceived racism and biological stress reactivity among African Americans. Guided by worldview verification theory, it was hypothesized that responses to receiving an unfair outcome would be moderated by fairness of the accompanying decision process, and that this effect would further depend on the consistency of the decision process with preexisting justice beliefs. Method A sample of 118 healthy African American adults completed baseline measures of justice beliefs, followed by a laboratory-based social-evaluative stressor task. Two randomized fairness manipulations were implemented during the task: participants were given either high or low levels of distributive (outcome) and procedural (decision process) justice. Glucocorticoid (cortisol) and inflammatory (C-reactive protein) biological responses were measured in oral fluids, and attributions of racism were also measured. Results The hypothesized 3-way interaction was generally obtained. Among African Americans with a strong belief in justice, perceived racism, cortisol and C-reactive protein responses to low distributive justice were higher when procedural justice was low. Among African Americans with a weak belief in justice however, these responses were higher when a low level of distributive justice was coupled with high procedural justice. Conclusions Biological and psychological processes that contribute to cardiovascular health disparities are affected by consistency between individual-level and contextual justice factors. PMID:27018728

Fairness influences early signatures of reward-related neural processing.

PubMed

Massi, Bart; Luhmann, Christian C

2015-12-01

Many humans exhibit a strong preference for fairness during decision-making. Although there is evidence that social factors influence reward-related and affective neural processing, it is unclear if this effect is mediated by compulsory outcome evaluation processes or results from slower deliberate cognition. Here we show that the feedback-related negativity (FRN) and late positive potential (LPP), two signatures of early hedonic processing, are modulated by the fairness of rewards during a passive rating task. We find that unfair payouts elicit larger FRNs than fair payouts, whereas fair payouts elicit larger LPPs than unfair payouts. This is true both in the time-domain, where the FRN and LPP are related, and in the time-frequency domain, where the two signals are largely independent. Ultimately, this work demonstrates that fairness affects the early stages of reward and affective processing, suggesting a common biological mechanism for social and personal reward evaluation.

[Construction of individual-based ecological model for Scomber japonicas at its early growth stages in East China Sea].

PubMed

Li, Yue-Song; Chen, Xin-Jun; Yang, Hong

2012-06-01

By adopting FVCOM-simulated 3-D physical field and based on the biological processes of chub mackerel (Scomber japonicas) in its early life history from the individual-based biological model, the individual-based ecological model for S. japonicas at its early growth stages in the East China Sea was constructed through coupling the physical field in March-July with the biological model by the method of Lagrange particle tracking. The model constructed could well simulate the transport process and abundance distribution of S. japonicas eggs and larvae. The Taiwan Warm Current, Kuroshio, and Tsushima Strait Warm Current directly affected the transport process and distribution of the eggs and larvae, and indirectly affected the growth and survive of the eggs and larvae through the transport to the nursery grounds with different water temperature and foods. The spawning grounds in southern East China Sea made more contributions to the recruitment to the fishing grounds in northeast East China Sea, but less to the Yangtze estuary and Zhoushan Island. The northwestern and southwestern parts of spawning grounds had strong connectivity with the nursery grounds of Cheju and Tsushima Straits, whereas the northeastern and southeastern parts of the spawning ground had strong connectivity with the nursery grounds of Kyushu and Pacific Ocean.

Is chronic insomnia a precursor to major depression? Epidemiological and biological findings.

PubMed

Baglioni, Chiara; Riemann, Dieter

2012-10-01

Insomnia has been found to be a clinical predictor of subsequent depression. Nevertheless the biological processes underlying this causal relationship are yet not fully understood. Both conditions share a common imbalance of the arousal system. Patients with insomnia present fragmented REM sleep, which probably interferes with basal processes of emotion regulation. The interaction between the arousal and the affective system with the persistence of the disorder could slowly alter also the cognitive system and lead to depression. Although preliminary results seem to support this hypothesis, data are still too few to make valid conclusions.

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.

Use of maize wastewater for the cultivation of the Pleurotus spp. mushroom and optimization of its biological efficiency.

PubMed

Loss, Edenes; Royer, Andrea Rafaela; Barreto-Rodrigues, Marcio; Barana, Ana Claudia

2009-07-30

This study evaluated the Pleurotus spp. mushroom production process using an effluent from the maize agroindustrial process as a carbon and nitrogen source and as a wetting agent. A complete experimental design based on factorial planning was used to optimize the biological efficiency and evaluate the effect of the concentration of effluent, pH and species of Pleurotus. The results indicated that the effluent affects the biological efficiency for the production of both species of mushrooms at all pH values studied. The maximum biological efficiency predicted by the model (81.36%) corresponded to the point defined by the effluent contents (X(1)=1), pH (X(2)=-1) and fungus species (X(3)=1), specifically 50%, 5.0 and P. floridae, respectively. The results demonstrated that the effluent is a good alternative for the production of Pleurotus mushrooms.

Spectroscopic study of the effect of biological treatment on the humification process of sewage sludge

NASA Astrophysics Data System (ADS)

Polak, J.; Sułkowski, W. W.; Bartoszek, M.; Luty, A.; Pentak, D.; Sułkowska, A.

2007-05-01

In 2005 the treatment plant in Sosnowiec Zagórze was modernized and the processes of nitrification and denitrification were introduced. The study of the biological treatment influence on the course of the humification process was conducted for the sewage sludge received from each stage of sewage purification. The extracted humic-like substances (HA) were investigated by the use of the spectroscopic and analytical methods. The concentration of free radicals and the g-factor was determined with EPR, the presence of the characteristic functional groups was confirmed with IR spectroscopy, whereas the aromatisation of HA was estimated by 13C NMR method. The results obtained were compared with those for HA extracted from sewage sludge before modernization [1]. It was found that the processes of biological treatment have a significant influence on the changes of the chemical elements in the extracted HA. The HA obtained after modernization are nitrogen-rich (about 9%), in particular after the nitrification and denitrification processes. However, nitrification and denitrification processes only slightly affect the free radical concentration and the g-factor values.

Biological causal links on physiological and evolutionary time scales.

PubMed

Karmon, Amit; Pilpel, Yitzhak

2016-04-26

Correlation does not imply causation. If two variables, say A and B, are correlated, it could be because A causes B, or that B causes A, or because a third factor affects them both. We suggest that in many cases in biology, the causal link might be bi-directional: A causes B through a fast-acting physiological process, while B causes A through a slowly accumulating evolutionary process. Furthermore, many trained biologists tend to consistently focus at first on the fast-acting direction, and overlook the slower process in the opposite direction. We analyse several examples from modern biology that demonstrate this bias (codon usage optimality and gene expression, gene duplication and genetic dispensability, stem cell division and cancer risk, and the microbiome and host metabolism) and also discuss an example from linguistics. These examples demonstrate mutual effects between the fast physiological processes and the slow evolutionary ones. We believe that building awareness of inference biases among biologists who tend to prefer one causal direction over another could improve scientific reasoning.

Biomarker-driven phenotyping in Parkinson disease: a translational missing link in disease-modifying clinical trials

PubMed Central

Espay, Alberto J.; Schwarzschild, Michael A.; Tanner, Caroline M.; Fernandez, Hubert H; Simon, David K.; Leverenz, James B.; Merola, Aristide; Chen-Plotkin, Alice; Brundin, Patrik; Kauffman, Marcelo A.; Erro, Roberto; Kieburtz, Karl; Woo, Daniel; Macklin, Eric A.; Standaert, David G.; Lang, Anthony E.

2016-01-01

Past clinical trials of putative neuroprotective therapies have targeted Parkinson disease (PD) as a single pathogenic disease entity. From an Oslerian clinico-pathologic perspective, the wide complexity of PD converges into Lewy bodies and justifies a reductionist approach to PD: a single-mechanism therapy can affect most of those sharing the classic pathologic hallmark. From a systems-biology perspective, PD is a group of disorders that, while related by sharing the feature of nigral dopamine-neuron degeneration, exhibit unique genetic, biological and molecular abnormalities, which probably respond differentially to a given therapeutic approach, particularly for strategies aimed at neuroprotection. Under this model, only biomarker-defined, homogenous subtypes of PD are likely to respond optimally to therapies proven to affect the biological processes within each subtype. Therefore, we suggest that precision medicine applied to PD requires a reevaluation of the biomarker-discovery effort. This effort is currently centered on correlating biological measures to clinical features of PD and on identifying factors that predict whether various prodromal states will convert into the classical movement disorder. We suggest, instead, that subtyping of PD requires the reverse view, where abnormal biological signals (i.e., biomarkers) rather than clinical definitions are used to define disease phenotypes. Successful development of disease-modifying strategies will depend on how relevant the specific biological processes addressed by an intervention are to the pathogenetic mechanisms in the subgroup of targeted patients. This precision-medicine approach will likely yield smaller but well-defined subsets of PD amenable to successful neuroprotection. PMID:28233927

Treatment of winery wastewater by physicochemical, biological and advanced processes: a review.

PubMed

Ioannou, L A; Li Puma, G; Fatta-Kassinos, D

2015-04-09

Winery wastewater is a major waste stream resulting from numerous cleaning operations that occur during the production stages of wine. The resulting effluent contains various organic and inorganic contaminants and its environmental impact is notable, mainly due to its high organic/inorganic load, the large volumes produced and its seasonal variability. Several processes for the treatment of winery wastewater are currently available, but the development of alternative treatment methods is necessary in order to (i) maximize the efficiency and flexibility of the treatment process to meet the discharge requirements for winery effluents, and (ii) decrease both the environmental footprint, as well as the investment/operational costs of the process. This review, presents the state-of-the-art of the processes currently applied and/or tested for the treatment of winery wastewater, which were divided into five categories: i.e., physicochemical, biological, membrane filtration and separation, advanced oxidation processes, and combined biological and advanced oxidation processes. The advantages and disadvantages, as well as the main parameters/factors affecting the efficiency of winery wastewater treatment are discussed. Both bench- and pilot/industrial-scale processes have been considered for this review. Copyright © 2014 Elsevier B.V. All rights reserved.

A Multimodal Approach to Counselor Supervision.

ERIC Educational Resources Information Center

Ponterotto, Joseph G.; Zander, Toni A.

1984-01-01

Represents an initial effort to apply Lazarus's multimodal approach to a model of counselor supervision. Includes continuously monitoring the trainee's behavior, affect, sensations, images, cognitions, interpersonal functioning, and when appropriate, biological functioning (diet and drugs) in the supervisory process. (LLL)

The use of acoustic doppler meters to estimate sediment and nutrient concentrations in freshwater inflows to Texas coastal ecosystems

Treesearch

Zullmar Lucena; Micheal Lee

2016-01-01

Excessive sediment and nutrient loading are among the leading causes of impairment in water bodies of the United States due to their effect on biologic productivity, water quality, and aquatic food webs. Understanding the nutrient and suspended sediment loads affecting estuarine waters is fundamental to the assessment of the physical, chemical, and biological processes...

Electrophysiological differences in the processing of affective information in words and pictures.

PubMed

Hinojosa, José A; Carretié, Luis; Valcárcel, María A; Méndez-Bértolo, Constantino; Pozo, Miguel A

2009-06-01

It is generally assumed that affective picture viewing is related to higher levels of physiological arousal than is the reading of emotional words. However, this assertion is based mainly on studies in which the processing of either words or pictures has been investigated under heterogenic conditions. Positive, negative, relaxing, neutral, and background (stimulus fragments) words and pictures were presented to subjects in two experiments under equivalent experimental conditions. In Experiment 1, neutral words elicited an enhanced late positive component (LPC) that was associated with an increased difficulty in discriminating neutral from background stimuli. In Experiment 2, high-arousing pictures elicited an enhanced early negativity and LPC that were related to a facilitated processing for these stimuli. Thus, it seems that under some circumstances, the processing of affective information captures attention only with more biologically relevant stimuli. Also, these data might be better interpreted on the basis of those models that postulate a different access to affective information for words and pictures.

Gene Expression Profile Change and Associated Physiological and Pathological Effects in Mouse Liver Induced by Fasting and Refeeding

PubMed Central

Zhang, Fang; Xu, Xiang; Zhou, Ben; He, Zhishui; Zhai, Qiwei

2011-01-01

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed, fasted and refed states. Totally 12162 genes were detected, and 2305 genes were significantly regulated by food availability. Biological process and pathway analysis showed that fasting mainly affected lipid and carboxylic acid metabolic processes in liver. Moreover, the genes regulated by fasting and refeeding in liver were mainly enriched in lipid metabolic process or fatty acid metabolism. Network analysis demonstrated that fasting mainly regulated Drug Metabolism, Small Molecule Biochemistry and Endocrine System Development and Function, and the networks including Lipid Metabolism, Small Molecule Biochemistry and Gene Expression were affected by refeeding. In addition, FunDo analysis showed that liver cancer and diabetes mellitus were most likely to be affected by food availability. This study provides the digital gene expression profile of mouse liver regulated by food availability, and demonstrates the main biological processes, pathways, gene networks and potential hepatic diseases regulated by fasting and refeeding. These results show that food availability mainly regulates hepatic lipid metabolism and is highly correlated with liver-related diseases including liver cancer and diabetes. PMID:22096593

Gene expression profile change and associated physiological and pathological effects in mouse liver induced by fasting and refeeding.

PubMed

Zhang, Fang; Xu, Xiang; Zhou, Ben; He, Zhishui; Zhai, Qiwei

2011-01-01

Food availability regulates basal metabolism and progression of many diseases, and liver plays an important role in these processes. The effects of food availability on digital gene expression profile, physiological and pathological functions in liver are yet to be further elucidated. In this study, we applied high-throughput sequencing technology to detect digital gene expression profile of mouse liver in fed, fasted and refed states. Totally 12162 genes were detected, and 2305 genes were significantly regulated by food availability. Biological process and pathway analysis showed that fasting mainly affected lipid and carboxylic acid metabolic processes in liver. Moreover, the genes regulated by fasting and refeeding in liver were mainly enriched in lipid metabolic process or fatty acid metabolism. Network analysis demonstrated that fasting mainly regulated Drug Metabolism, Small Molecule Biochemistry and Endocrine System Development and Function, and the networks including Lipid Metabolism, Small Molecule Biochemistry and Gene Expression were affected by refeeding. In addition, FunDo analysis showed that liver cancer and diabetes mellitus were most likely to be affected by food availability. This study provides the digital gene expression profile of mouse liver regulated by food availability, and demonstrates the main biological processes, pathways, gene networks and potential hepatic diseases regulated by fasting and refeeding. These results show that food availability mainly regulates hepatic lipid metabolism and is highly correlated with liver-related diseases including liver cancer and diabetes.

Regulatory effects of cotranscriptional RNA structure formation and transitions.

PubMed

Liu, Sheng-Rui; Hu, Chun-Gen; Zhang, Jin-Zhi

2016-09-01

RNAs, which play significant roles in many fundamental biological processes of life, fold into sophisticated and precise structures. RNA folding is a dynamic and intricate process, which conformation transition of coding and noncoding RNAs form the primary elements of genetic regulation. The cellular environment contains various intrinsic and extrinsic factors that potentially affect RNA folding in vivo, and experimental and theoretical evidence increasingly indicates that the highly flexible features of the RNA structure are affected by these factors, which include the flanking sequence context, physiochemical conditions, cis RNA-RNA interactions, and RNA interactions with other molecules. Furthermore, distinct RNA structures have been identified that govern almost all steps of biological processes in cells, including transcriptional activation and termination, transcriptional mutagenesis, 5'-capping, splicing, 3'-polyadenylation, mRNA export and localization, and translation. Here, we briefly summarize the dynamic and complex features of RNA folding along with a wide variety of intrinsic and extrinsic factors that affect RNA folding. We then provide several examples to elaborate RNA structure-mediated regulation at the transcriptional and posttranscriptional levels. Finally, we illustrate the regulatory roles of RNA structure and discuss advances pertaining to RNA structure in plants. WIREs RNA 2016, 7:562-574. doi: 10.1002/wrna.1350 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Comprehensive evaluation of gene expression signatures in response to electroacupuncture stimulation at Zusanli (ST36) acupoint by transcriptomic analysis.

PubMed

Wu, Jing-Shan; Lo, Hsin-Yi; Li, Chia-Cheng; Chen, Feng-Yuan; Hsiang, Chien-Yun; Ho, Tin-Yun

2017-08-15

Electroacupuncture (EA) has been applied to treat and prevent diseases for years. However, molecular events happened in both the acupunctured site and the internal organs after EA stimulation have not been clarified. Here we applied transcriptomic analysis to explore the gene expression signatures after EA stimulation. Mice were applied EA stimulation at ST36 for 15 min and nine tissues were collected three hours later for microarray analysis. We found that EA affected the expression of genes not only in the acupunctured site but also in the internal organs. EA commonly affected biological networks involved in cytoskeleton and cell adhesion, and also regulated unique process networks in specific organs, such as γ-aminobutyric acid-ergic neurotransmission in brain and inflammation process in lung. In addition, EA affected the expression of genes related to various diseases, such as neurodegenerative diseases in brain and obstructive pulmonary diseases in lung. This report applied, for the first time, a global comprehensive genome-wide approach to analyze the gene expression profiling of acupunctured site and internal organs after EA stimulation. The connection between gene expression signatures, biological processes, and diseases might provide a basis for prediction and explanation on the therapeutic potentials of acupuncture in organs.

Action spectra affect variability of the climatology of biologically effective ultraviolet radiation on cloud-free days.

PubMed

Grifoni, D; Zipoli, G; Sabatini, F; Messeri, G; Bacci, L

2013-12-01

Action spectrum (AS) describes the relative effectiveness of ultraviolet (UV) radiation in producing biological effects and allows spectral UV irradiance to be weighted in order to compute biologically effective UV radiation (UVBE). The aim of this research was to study the seasonal and latitudinal distribution over Europe of daily UVBE doses responsible for various biological effects on humans and plants. Clear sky UV radiation spectra were computed at 30-min time intervals for the first day of each month of the year for Rome, Potsdam and Trondheim using a radiative transfer model fed with climatological data. Spectral data were weighted using AS for erythema, vitamin D synthesis, cataract and photokeratitis for humans, while the generalised plant damage and the plant damage AS were used for plants. The daily UVBE doses for the above-mentioned biological processes were computed and are analysed in this study. The patterns of variation due to season (for each location) and latitude (for each date) resulted as being specific for each adopted AS. The biological implications of these results are briefly discussed highlighting the importance of a specific UVBE climatology for each biological process.

High Mobility Group N Proteins Modulate the Fidelity of the Cellular Transcriptional Profile in a Tissue- and Variant-specific Manner*

PubMed Central

Kugler, Jamie E.; Horsch, Marion; Huang, Di; Furusawa, Takashi; Rochman, Mark; Garrett, Lillian; Becker, Lore; Bohla, Alexander; Hölter, Sabine M.; Prehn, Cornelia; Rathkolb, Birgit; Racz, Ildikó; Aguilar-Pimentel, Juan Antonio; Adler, Thure; Adamski, Jerzy; Beckers, Johannes; Busch, Dirk H.; Eickelberg, Oliver; Klopstock, Thomas; Ollert, Markus; Stöger, Tobias; Wolf, Eckhard; Wurst, Wolfgang; Yildirim, Ali Önder; Zimmer, Andreas; Gailus-Durner, Valérie; Fuchs, Helmut; Hrabě de Angelis, Martin; Garfinkel, Benny; Orly, Joseph; Ovcharenko, Ivan; Bustin, Michael

2013-01-01

The nuclei of most vertebrate cells contain members of the high mobility group N (HMGN) protein family, which bind specifically to nucleosome core particles and affect chromatin structure and function, including transcription. Here, we study the biological role of this protein family by systematic analysis of phenotypes and tissue transcription profiles in mice lacking functional HMGN variants. Phenotypic analysis of Hmgn1tm1/tm1, Hmgn3tm1/tm1, and Hmgn5tm1/tm1 mice and their wild type littermates with a battery of standardized tests uncovered variant-specific abnormalities. Gene expression analysis of four different tissues in each of the Hmgntm1/tm1 lines reveals very little overlap between genes affected by specific variants in different tissues. Pathway analysis reveals that loss of an HMGN variant subtly affects expression of numerous genes in specific biological processes. We conclude that within the biological framework of an entire organism, HMGNs modulate the fidelity of the cellular transcriptional profile in a tissue- and HMGN variant-specific manner. PMID:23620591

Extraversion and reward-related processing: probing incentive motivation in affective priming tasks.

PubMed

Robinson, Michael D; Moeller, Sara K; Ode, Scott

2010-10-01

Based on an incentive motivation theory of extraversion (Depue & Collins, 1999), it was hypothesized that extraverts (relative to introverts) would exhibit stronger positive priming effects in affective priming tasks, whether involving words or pictures. This hypothesis was systematically supported in four studies involving 229 undergraduates. In each of the four studies, and in a subsequent combined analysis, extraversion was positively predictive of positive affective priming effects, but was not predictive of negative affective priming effects. The results bridge an important gap in the literature between biological and trait models of incentive motivation and do so in a way that should be informative to subsequent efforts to understand the processing basis of extraversion as well as incentive motivation. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

Putting Connectivity in Context: Overview on Geographically Isolated Wetland Research

EPA Science Inventory

Geographically isolated wetlands (GIWs) affect and contribute to the integrity of other waters through biological, chemical, and hydrological (or physical) processes that vary in timing, duration, and magnitude of their impact. Research quantifying contributions and effects of so...

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

Olsen, C.R.; Larsen, I.L.; Lowry, P.D.

Radionuclides released into the Susquehanna--Chesapeake System from the Three Mile Island, Peach Bottom, and Calvert Cliffs nuclear power plants are partitioned among dissolved, particulate, and biological phases and may thus exist in a number of physical and chemical forms. In this project, we have measured the dissolved and particulate distributions of fallout /sup 137/Cs; reactor-released /sup 137/Cs, /sup 134/Cs, /sup 65/Zn, /sup 60/Co, and /sup 58/Co; and naturally occurring /sup 7/Be and /sup 210/Pb in the lower Susquehanna River and Upper Chesapeake Bay. In addition, we chemically leached suspended particles and bottom sediments in the laboratory to determine radionuclide partitioningmore » among different particulate-sorbing phases to complement the site-specific field data. This information has been used to document the important geochemical processes that affect the transport, sorption, distribution, and fate of reactor-released radionuclides (and by analogy, other trace contaminants) in this river-estuarine system. Knowledge of the mechanisms, kinetic factors, and processes that affect radionuclide distributions is crucial for predicting their biological availability, toxicity, chemical behavior, physical transport, and accumulation in aquatic systems. The results from this project provide the information necessary for developing accurate radionuclide-transport and biological-uptake models. 76 refs., 12 figs.« less

A preliminary experimental examination of worldview verification, perceived racism, and stress reactivity in African Americans.

PubMed

Lucas, Todd; Lumley, Mark A; Flack, John M; Wegner, Rhiana; Pierce, Jennifer; Goetz, Stefan

2016-04-01

According to worldview verification theory, inconsistencies between lived experiences and worldviews are psychologically threatening. These inconsistencies may be key determinants of stress processes that influence cardiovascular health disparities. This preliminary examination considers how experiencing injustice can affect perceived racism and biological stress reactivity among African Americans. Guided by worldview verification theory, it was hypothesized that responses to receiving an unfair outcome would be moderated by fairness of the accompanying decision process, and that this effect would further depend on the consistency of the decision process with preexisting justice beliefs. A sample of 118 healthy African American adults completed baseline measures of justice beliefs, followed by a laboratory-based social-evaluative stressor task. Two randomized fairness manipulations were implemented during the task: participants were given either high or low levels of distributive (outcome) and procedural (decision process) justice. Glucocorticoid (cortisol) and inflammatory (C-reactive protein) biological responses were measured in oral fluids, and attributions of racism were also measured. The hypothesized 3-way interaction was generally obtained. Among African Americans with a strong belief in justice, perceived racism, cortisol, and C-reactive protein responses to low distributive justice were higher when procedural justice was low. Among African Americans with a weak belief in justice however, these responses were higher when a low level of distributive justice was coupled with high procedural justice. Biological and psychological processes that contribute to cardiovascular health disparities are affected by consistency between individual-level and contextual justice factors. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Gene expression profile change and growth inhibition in Drosophila larvae treated with azadirachtin.

PubMed

Lai, Duo; Jin, Xiaoyong; Wang, Hao; Yuan, Mei; Xu, Hanhong

2014-09-20

Azadirachtin is a botanical insecticide that affects various biological processes. The effects of azadirachtin on the digital gene expression profile and growth inhibition in Drosophila larvae have not been investigated. In this study, we applied high-throughput sequencing technology to detect the differentially expressed genes of Drosophila larvae regulated by azadirachtin. A total of 15,322 genes were detected, and 28 genes were found to be significantly regulated by azadirachtin. Biological process and pathway analysis showed that azadirachtin affected starch and sucrose metabolism, defense response, signal transduction, instar larval or pupal development, and chemosensory behavior processes. The genes regulated by azadirachtin were mainly enriched in starch and sucrose metabolism. This study provided a general digital gene expression profile of dysregulated genes in response to azadirachtin and showed that azadirachtin provoked potent growth inhibitory effects in Drosophila larvae by regulating the genes of cuticular protein, amylase, and odorant-binding protein. Finally, we propose a potential mechanism underlying the dysregulation of the insulin/insulin-like growth factor signaling pathway by azadirachtin. Copyright © 2014 Elsevier B.V. All rights reserved.

Mammals' response and adaptation to static magnetic fields as a nonspecific stressor

NASA Astrophysics Data System (ADS)

Nakagawa, Masayoshi

1990-06-01

Biological effects of static magnetic fields are still unclear and sometimes contradictory, and it has not been possible to connect this situation directly to some explanations of the mechanisms of the effects of static magnetic fields at the molecular level. Some researchers have pointed out that the process through which animals respond at the whole-body level to static magnetic fields follows the same pattern as the GAS (general adaptation syndrome) described by Selye. This biological or behavioral pattern is considered to be a common process followed by animals which are affected by environmental stimulants; they are depressed first, then surpass the deteriorated conditions and recover their normal conditions, or sometimes overshoot it. When this process is observed with mammals subjected to the magnetic fields, it can be concluded that magnetism has affected the organism. In this paper, the author reviews reports in which magnetic field density and minimum exposure time were determined with certain effects produced under certain conditions, and proposes a regression model for estimating the minimum amount of exposure which produces some effect on mammals.

Primary thermosensory events in cells.

PubMed

Digel, Ilya

2011-01-01

Temperature sensing is essential for the survival of living organisms. Since thermal gradients are almost everywhere, thermoreception could represent one of the oldest sensory transduction processes that evolved in organisms. There are many examples of temperature changes affecting the physiology of living cells. Almost all classes of biological macromolecules in a cell (nucleic acids, lipids, proteins) can serve as a target of the temperature-related stimuli. This review is devoted to some common features of different classes of temperature-sensing molecules as well as molecular and biological processes involved in thermosensation. Biochemical, structural and thermodynamic approaches are discussed in order to overview the existing knowledge on molecular mechanisms of thermosensation.

Can entomophagous nematodes slow the spread of invasive pest populations? The case study of Beddingia siricidicola released for the management of Sirex noctilio

Treesearch

Juan C. Corley; José M. Villacide; Andrew M. Liebhold

2014-01-01

Though rarely used in this way, biological control could potentially be exploited for managing spread of invasive species. Because spread of invasive species emerges from the combined action of population growth and dispersal, natural enemies that affect either of these processes should also affect spread. Dispersal of parasitoid species plays a key role in determining...

Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation

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

Yang, Feng; Waters, Katrina M.; Miller, John H.

2010-11-30

Background: High doses of ionizing radiation result in biological damage, however the precise relationships between long term health effects, including cancer, and low dose exposures remain poorly understood and are currently extrapolated using high dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose dependent responses to radiation. Principle Findings: We have identified 6845 unique phosphopeptides (2566 phosphoproteins) from control and irradiated (2 and 50 cGy) primary human skin fibroblasts one hour post-exposure. Dual statistical analyses based on spectral counts and peakmore » intensities identified 287 phosphopeptides (from 231 proteins) and 244 phosphopeptides (from 182 proteins) that varied significantly following exposure to 2 and 50 cGy respectively. This screen identified phosphorylation sites on proteins with known roles in radiation responses including TP53BP1 as well as previously unidentified radiation responsive proteins such as the candidate tumor suppressor SASH1. Bioinformatics analyses suggest that low and high doses of radiation affect both overlapping and unique biological processes and suggest a role of MAP kinase and protein kinase A (PKA) signaling in the radiation response as well as differential regulation of p53 networks at low and high doses of radiation. Conlcusions: Our results represent the most comprehensive analysis of the phosphoproteomes of human primary fibroblasts exposed to multiple doses of ionizing radiation published to date and provides a basis for the systems level identification of biological processes, molecular pathways and individual proteins regulated in a dose dependent manner by ionizing radiation. Further study of these modified proteins and affected networks should help to define the molecular mechanisms that regulate biological responses to radiation at different radiation doses and elucidate the impact of low dose radiation exposure on human health.« less

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.

Evidence of opposing fitness effects of parental heterozygosity and relatedness in a critically endangered marine turtle?

PubMed

Phillips, K P; Jorgensen, T H; Jolliffe, K G; Richardson, D S

2017-11-01

How individual genetic variability relates to fitness is important in understanding evolution and the processes affecting populations of conservation concern. Heterozygosity-fitness correlations (HFCs) have been widely used to study this link in wild populations, where key parameters that affect both variability and fitness, such as inbreeding, can be difficult to measure. We used estimates of parental heterozygosity and genetic similarity ('relatedness') derived from 32 microsatellite markers to explore the relationship between genetic variability and fitness in a population of the critically endangered hawksbill turtle, Eretmochelys imbricata. We found no effect of maternal MLH (multilocus heterozygosity) on clutch size or egg success rate, and no single-locus effects. However, we found effects of paternal MLH and parental relatedness on egg success rate that interacted in a way that may result in both positive and negative effects of genetic variability. Multicollinearity in these tests was within safe limits, and null simulations suggested that the effect was not an artefact of using paternal genotypes reconstructed from large samples of offspring. Our results could imply a tension between inbreeding and outbreeding depression in this system, which is biologically feasible in turtles: female-biased natal philopatry may elevate inbreeding risk and local adaptation, and both processes may be disrupted by male-biased dispersal. Although this conclusion should be treated with caution due to a lack of significant identity disequilibrium, our study shows the importance of considering both positive and negative effects when assessing how variation in genetic variability affects fitness in wild systems. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Fetal growth restriction promotes physical inactivity and obesity in female mice

USDA-ARS?s Scientific Manuscript database

Environmental exposures during critical periods of prenatal and early postnatal life affect the development of mammalian body weight regulatory mechanisms, influencing lifelong risk of obesity. The specific biological processes that mediate the persistence of such effects, however, remain poorly und...

Effect of sex, age, and breed on genetic recombination features in cattle

USDA-ARS?s Scientific Manuscript database

Meiotic recombination is a fundamental biological process which generates genetic diversity, affects fertility, and influences evolvability. Here we investigate the roles of sex, age, and breed in cattle recombination features, including recombination rate, location and crossover interference. Usin...

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.

A novel rotating experimental platform in a superconducting magnet.

PubMed

Chen, Da; Cao, Hui-Ling; Ye, Ya-Jing; Dong, Chen; Liu, Yong-Ming; Shang, Peng; Yin, Da-Chuan

2016-08-01

This paper introduces a novel platform designed to be used in a strong static magnetic field (in a superconducting magnet). The platform is a sample holder that rotates in the strong magnetic field. Any samples placed in the platform will rotate due to the rotation of the sample holder. With this platform, a number of experiments such as material processing, culture of biological systems, chemical reactions, or other processes can be carried out. In this report, we present some preliminary experiments (protein crystallization, cell culture, and seed germination) conducted using this platform. The experimental results showed that the platform can affect the processes, indicating that it provides a novel environment that has not been investigated before and that the effects of such an environment on many different physical, chemical, or biological processes can be potentially useful for applications in many fields.

Aesthetic episodes, domains, and the mind. Comment on: "Move me, astonish me... delight my eyes and brain: The Vienna Integrated Model of top-down and bottom-up processes in Art Perception (VIMAP) and corresponding affective, evaluative, and neurophysiological correlates" by Matthew Pelowski et al.

NASA Astrophysics Data System (ADS)

Jacobsen, Thomas

2017-07-01

Aesthetic episodes, as all behavior, are situated. They take place as an interaction of person and situation variables [1]. There are different artistic and aesthetic domains that afford, in part, mutual mental processes, but also fundamentally different, e.g., modality-specific ones [2]. For the infinite number of possible aesthetic episodes a plethora of component processes can be selectively combined and dynamically configured. Following psychophysics' pragmatic dualism of mind and body, this results in dynamically configured (neuro-) biological networks subserving these mental processes [1]. These are, of course, also subject to evolutionary, biological, historical, cultural, and social change [1,3].

Remotely controlled fusion of selected vesicles and living cells: a key issue review

NASA Astrophysics Data System (ADS)

Bahadori, Azra; Moreno-Pescador, Guillermo; Oddershede, Lene B.; Bendix, Poul M.

2018-03-01

Remote control over fusion of single cells and vesicles has a great potential in biological and chemical research allowing both transfer of genetic material between cells and transfer of molecular content between vesicles. Membrane fusion is a critical process in biology that facilitates molecular transport and mixing of cellular cytoplasms with potential formation of hybrid cells. Cells precisely regulate internal membrane fusions with the aid of specialized fusion complexes that physically provide the energy necessary for mediating fusion. Physical factors like membrane curvature, tension and temperature, affect biological membrane fusion by lowering the associated energy barrier. This has inspired the development of physical approaches to harness the fusion process at a single cell level by using remotely controlled electromagnetic fields to trigger membrane fusion. Here, we critically review various approaches, based on lasers or electric pulses, to control fusion between individual cells or between individual lipid vesicles and discuss their potential and limitations for present and future applications within biochemistry, biology and soft matter.

Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity.

PubMed

Hateley, Shannon; Hosamani, Ravikumar; Bhardwaj, Shilpa R; Pachter, Lior; Bhattacharya, Sharmila

2016-10-01

Altered gravity can perturb normal development and induce corresponding changes in gene expression. Understanding this relationship between the physical environment and a biological response is important for NASA's space travel goals. We use RNA-Seq and qRT-PCR techniques to profile changes in early Drosophila melanogaster pupae exposed to chronic hypergravity (3g, or three times Earth's gravity). During the pupal stage, D. melanogaster rely upon gravitational cues for proper development. Assessing gene expression changes in the pupae under altered gravity conditions helps highlight gravity-dependent genetic pathways. A robust transcriptional response was observed in hypergravity-treated pupae compared to controls, with 1513 genes showing a significant (q<0.05) difference in gene expression. Five major biological processes were affected: ion transport, redox homeostasis, immune response, proteolysis, and cuticle development. This outlines the underlying molecular and biological changes occurring in Drosophila pupae in response to hypergravity; gravity is important for many biological processes on Earth. Published by Elsevier Inc.

Biological and Psychosocial Predictors of Postpartum Depression: Systematic Review and Call for Integration

PubMed Central

Tanner Stapleton, Lynlee R.; Guardino, Christine M.; Hahn-Holbrook, Jennifer; Schetter, Christine Dunkel

2017-01-01

Postpartum depression (PPD) adversely affects the health and well being of many new mothers, their infants, and their families. A comprehensive understanding of biopsychosocial precursors to PPD is needed to solidify the current evidence base for best practices in translation. We conducted a systematic review of research published from 2000 through 2013 on biological and psychosocial factors associated with PPD and postpartum depressive symptoms. Two hundred fourteen publications based on 199 investigations of 151,651 women in the first postpartum year met inclusion criteria. The biological and psychosocial literatures are largely distinct, and few studies provide integrative analyses. The strongest PPD risk predictors among biological processes are hypothalamic-pituitary-adrenal dysregulation, inflammatory processes, and genetic vulnerabilities. Among psychosocial factors, the strongest predictors are severe life events, some forms of chronic strain, relationship quality, and support from partner and mother. Fully integrated biopsychosocial investigations with large samples are needed to advance our knowledge of PPD etiology. PMID:25822344

How input fluctuations reshape the dynamics of a biological switching system

NASA Astrophysics Data System (ADS)

Hu, Bo; Kessler, David A.; Rappel, Wouter-Jan; Levine, Herbert

2012-12-01

An important task in quantitative biology is to understand the role of stochasticity in biochemical regulation. Here, as an extension of our recent work [Phys. Rev. Lett.PRLTAO0031-900710.1103/PhysRevLett.107.148101 107, 148101 (2011)], we study how input fluctuations affect the stochastic dynamics of a simple biological switch. In our model, the on transition rate of the switch is directly regulated by a noisy input signal, which is described as a non-negative mean-reverting diffusion process. This continuous process can be a good approximation of the discrete birth-death process and is much more analytically tractable. Within this setup, we apply the Feynman-Kac theorem to investigate the statistical features of the output switching dynamics. Consistent with our previous findings, the input noise is found to effectively suppress the input-dependent transitions. We show analytically that this effect becomes significant when the input signal fluctuates greatly in amplitude and reverts slowly to its mean.

Producing Seed Crops to Naturally Regenerate Southern Pines

Treesearch

James P. Barnett; Ronald O. Haugen

1995-01-01

The biological processes that affect seed production in natural southern pine are documented, and information that will allow foresters to manipulate stands in a manner to improve and predict seed production is provided. As a result, natural regeneration should become a more reliable technique.

Hybridization affects life-history traits and host specificity in Diorhabda spp

USDA-ARS?s Scientific Manuscript database

Hybridization is an influential evolutionary process that has been viewed alternatively as an evolutionary dead-end or as an important creative evolutionary force. In colonizing species, such as introduced biological control agents, hybridization can negate the effects of bottlenecks and genetic dri...

The growing significance of probiotics on health

USDA-ARS?s Scientific Manuscript database

The confluence of all food-dependent life sustaining processes is in the gastrointestinal tract where the gut resident and food introduced microbes mix. Healthy living is conditioned on the proper functioning of the digestive ecosystem which is biologically affected by the state of the microbial loa...

How to Train a Cell - Cutting-Edge Molecular Tools

NASA Astrophysics Data System (ADS)

Czapiński, Jakub; Kiełbus, Michał; Kałafut, Joanna; Kos, Michał; Stepulak, Andrzej; Rivero-Müller, Adolfo

2017-03-01

In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.

Soft-Bodied Fossils Are Not Simply Rotten Carcasses - Toward a Holistic Understanding of Exceptional Fossil Preservation: Exceptional Fossil Preservation Is Complex and Involves the Interplay of Numerous Biological and Geological Processes.

PubMed

Parry, Luke A; Smithwick, Fiann; Nordén, Klara K; Saitta, Evan T; Lozano-Fernandez, Jesus; Tanner, Alastair R; Caron, Jean-Bernard; Edgecombe, Gregory D; Briggs, Derek E G; Vinther, Jakob

2018-01-01

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes that remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant (e.g., the notochord) are rarely preserved (even where carbonaceous components survive), and decay-prone structures (e.g., nervous systems) can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils. © 2017 The Authors. BioEssays Published by WILEY Periodicals, Inc.

Brownian dynamics simulation of protein diffusion in crowded environments

NASA Astrophysics Data System (ADS)

Mereghetti, Paolo; Wade, Rebecca C.

2013-02-01

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. We first describe the development of a Brownian dynamics simulation methodology to investigate the dynamic and structural properties of protein solutions using atomic-detail protein structures. We then discuss insights obtained from applying this approach to simulation of solutions of a range of types of proteins.

Agent-based models in translational systems biology

PubMed Central

An, Gary; Mi, Qi; Dutta-Moscato, Joyeeta; Vodovotz, Yoram

2013-01-01

Effective translational methodologies for knowledge representation are needed in order to make strides against the constellation of diseases that affect the world today. These diseases are defined by their mechanistic complexity, redundancy, and nonlinearity. Translational systems biology aims to harness the power of computational simulation to streamline drug/device design, simulate clinical trials, and eventually to predict the effects of drugs on individuals. The ability of agent-based modeling to encompass multiple scales of biological process as well as spatial considerations, coupled with an intuitive modeling paradigm, suggests that this modeling framework is well suited for translational systems biology. This review describes agent-based modeling and gives examples of its translational applications in the context of acute inflammation and wound healing. PMID:20835989

Biological Remediation of Petroleum Contaminants

NASA Astrophysics Data System (ADS)

Kuhad, Ramesh Chander; Gupta, Rishi

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

Modeling biochemical transformation processes and information processing with Narrator.

PubMed

Mandel, Johannes J; Fuss, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

2007-03-27

Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from http://www.narrator-tool.org.

Modeling biochemical transformation processes and information processing with Narrator

PubMed Central

Mandel, Johannes J; Fuß, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

2007-01-01

Background Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Results Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Conclusion Narrator is a flexible and intuitive systems biology tool. It is specifically intended for users aiming to construct and simulate dynamic models of biology without recourse to extensive mathematical detail. Its design facilitates mappings to different formal languages and frameworks. The combined set of features makes Narrator unique among tools of its kind. Narrator is implemented as Java software program and available as open-source from . PMID:17389034

An overview of surface radiance and biology studies in FIFE

NASA Astrophysics Data System (ADS)

Blad, B. L.; Schimel, D. S.

1992-11-01

The use of satellite data to study and to understand energy and mass exchanges between the land surface and the atmosphere requires information about various biological processes and how various reflected or emitted spectral radiances are influenced by or manifested in these processes. To obtain such information, studies were conducted by the First ISLSCP Field Experiment (FIFE) surface radiances and biology (SRB) group using surface, near-surface, helicopter, and aircraft measurements. The two primary objectives of this group were to relate radiative fluxes to biophysical parameters and physiological processes and to assess how various management treatments affect important biological processes. This overview paper summarizes the results obtained by various SRB teams working in nine different areas: (1) measurement of bidirectional reflectance and estimation of hemispherical albedo; (2) evaluation of spatial and seasonal variability of spectral reflectance and vegetation indices; (3) determination of surface and radiational factors and their effects on vegetation indices and PAR relationships; (4) use of surface temperatures to estimate sensible heat flux; (5) controls over photosynthesis and respiration at small scales; (6) soil surface CO2 fluxes and grassland carbon budget; (7) landscape variations in controls over gas exchange and energy partitioning; (8) radiometric response of prairie to management and topography; and (9) determination of nitrogen gas exchanges in a tallgrass prairie.

The micro and macro of nutrients across biological scales.

PubMed

Warne, Robin W

2014-11-01

During the past decade, we have gained new insights into the profound effects that essential micronutrients and macronutrients have on biological processes ranging from cellular function, to whole-organism performance, to dynamics in ecological communities, as well as to the structure and function of ecosystems. For example, disparities between intake and organismal requirements for specific nutrients are known to strongly affect animal physiological performance and impose trade-offs in the allocations of resources. However, recent findings have demonstrated that life-history allocation trade-offs and even microevolutionary dynamics may often be a result of molecular-level constraints on nutrient and metabolic processing, in which limiting reactants are routed among competing biochemical pathways. In addition, recent work has shown that complex ecological interactions between organismal physiological states such as exposure to environmental stressors and infectious pathogens can alter organismal requirements for, and, processing of, nutrients, and even alter subsequent nutrient cycling in ecosystems. Furthermore, new research is showing that such interactions, coupled with evolutionary and biogeographical constraints on the biosynthesis and availability of essential nutrients and micronutrients play an important, but still under-studied role in the structuring and functioning of ecosystems. The purpose of this introduction to the symposium "The Micro and Macro of Nutrient Effects in Animal Physiology and Ecology" is to briefly review and highlight recent research that has dramatically advanced our understanding of how nutrients in their varied forms profoundly affect and shape ecological and evolutionary processes. © The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

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

SOLAR ULTRAVIOLET RADIATION AND AQUATIC CARBON, NITROGEN, SULFUR AND METALS CYCLES

EPA Science Inventory

Solar ultraviolet radiation (290-400 nm) has a wide-ranging impact on biological and chemical processes that affect the cycling of elements in aquatic environments. This chapter uses recent field and laboratory observations along with models to assess these impacts on carbon, nit...

Apple miRNAs and tasiRNAs with novel regulatory networks

USDA-ARS?s Scientific Manuscript database

MiRNAs, negatively affecting gene expression at the post-transcriptional levels, have been shown to control numerous genes involved in various biological and metabolic processes. To date, the identification of miRNAs in plants focused on certain model plants, such as Arabidopsis and rice. Investig...

Concordance in Genomic Changes Between Mouse Lungs and Human Airway Epithelial Cells Exposed to Diesel Exhaust Particles

EPA Science Inventory

Human and animal toxicity studies have shown that exposure to diesel exhaust particles (DEP) or their constituents affect multiple biological processes including immune and inflammatory pathways, mutagenesis and in some cases carcinogenesis. This study compared genomic changes by...

Analysis of miRNA expression profiles in melatonin-exposed GC-1 spg cell line.

PubMed

Zhu, Xiaoling; Chen, Shuxiong; Jiang, Yanwen; Xu, Ying; Zhao, Yun; Chen, Lu; Li, Chunjin; Zhou, Xu

2018-02-05

Melatonin is an endocrine neurohormone secreted by pinealocytes in the pineal gland. It exerts diverse physiological effects, such as circadian rhythm regulator and antioxidant. However, the functional importance of melatonin in spermatogenesis regulation remains unclear. The objectives of this study are to: (1) detect melatonin affection on miRNA expression profiles in GC-1 spg cells by miRNA deep sequencing (DeepSeq) and (2) define melatonin affected miRNA-mRNA interactions and associated biological processes using bioinformatics analysis. GC-1 spg cells were cultured with melatonin (10 -7 M) for 24h. DeepSeq data were validated using quantitative real-time reverse transcription polymerase chain reaction analysis (qRT-PCR). A total of 176 miRNA expressions were found to be significantly different between two groups (fold change of >2 or <0.5 and FDR<0.05). Among these expressions, 171 were up-regulated, and 5 were down-regulated. Ontology analysis of biological processes of these targets indicated a variety of biological functions. Pathway analysis indicated that the predicted targets were involved in cancers, apoptosis and signaling pathways, such as VEGF, TNF, Ras and Notch. Results implicated that melatonin could regulate the expression of miRNA to perform its physiological effects in GC-1 spg cells. These results should be useful to investigate the biological function of miRNAs regulated by melatonin in spermatogenesis and testicular germ cell tumor. Copyright © 2017 Elsevier B.V. All rights reserved.

Possible Impact of Cosmochemistry on Terrestrial Biology: Historical Introduction

NASA Astrophysics Data System (ADS)

Pirie, N. W.

1981-12-01

Until the middle of the nineteenth century most philosophers, scientists and theologians assumed that life, even intelligent life, was not confined to Earth. Few of them, however, assumed that these organisms affected, or had affected, life here. The absence of human remains in ancient strata led, at the beginning of that century, to the suggestion that people were late intruders: later it was suggested that all life had come from Space. These speculations now seem quaint; our own may seem as quaint to our descendants. A few thoughtful scientists pointed out that these `explanations' did not explain anything: they merely transferred problems. The presence of organic matter in meteorites was well known in the nineteenth century. There is now abundant quantitative evidence that molecules of many different types come here from Space; there is no unequivocal evidence that any have a biological origin. Nor is there evidence for the arrival of molecules of types that could not have been synthesized in the probiotic environment here by non-biological processes.

Anatomy of ageing face.

PubMed

Ilankovan, V

2014-03-01

Ageing is a biological process that results from changes at a cellular level, particularly modification of mRNA. The face is affected by the same physiological process and results in skeletal, muscular, and cutaneous ageing; ligamentous attenuation, descent of fat, and ageing of the appendages. I describe these changes on a structural and clinical basis and summarise possible solutions for a rejuvenation surgeon. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Biology of teeth and implants: Host factors - pathology, regeneration, and the role of stem cells.

PubMed

Eggert, F-Michael; Levin, Liran

2018-01-01

In chronic periodontitis and peri-implantitis, cells of the innate and adaptive immune systems are involved directly in the lesions within the tissues of the patient. Absence of a periodontal ligament around implants does not prevent a biologic process similar to that of periodontitis from affecting osseointegration. Our first focus is on factors in the biology of individuals that are responsible for the susceptibility of such individuals to chronic periodontitis and to peri-implantitis. Genetic factors are of significant importance in susceptibility to these diseases. Genetic factors of the host affect the composition of the oral microbiome in the same manner that they influence other microbiomes, such as those of the intestines and of the lungs. Our second focus is on the central role of stem cells in tissue regeneration, in the functioning of innate and adaptive immune systems, and in metabolism of bone. Epithelial cell rests of Malassez (ERM) are stem cells of epithelial origin that maintain the periodontal ligament as well as the cementum and alveolar bone associated with the ligament. The tissue niche within which ERM are found extends into the supracrestal areas of collagen fiber-containing tissues of the gingivae above the bony alveolar crest. Maintenance and regeneration of all periodontal tissues involves the activity of a variety of stem cells. The success of dental implants indicates that important groups of stem cells in the periodontium are active to enable that biologic success. Successful replantation of avulsed teeth and auto-transplantation of teeth is comparable to placing dental implants, and so must also involve periodontal stem cells. Biology of teeth and biology of implants represents the biology of the various stem cells that inhabit specialized niches within the periodontal tissues. Diverse biologic processes must function together successfully to maintain periodontal health. Osseointegration of dental implants does not involve formation of cementum or collagen fibers inserted into cementum - indicating that some stem cells are not active around dental implants or their niches are not available. Investigation of these similarities and differences between teeth and implants will help to develop a better understanding of the biology and physiologic functioning of the periodontium.

Biodiversity of Total Phenolics, Antioxidant Capacity, and Juice Quality in Apple Cider Taxa

USDA-ARS?s Scientific Manuscript database

Apples are known to contain antioxidants that may play an important role in human health by providing protection against reactive free radicals affecting a wide range of biological molecules including nucleic acids, lipids, and proteins. While fresh apple juice is a main product of processed apples,...

A Treatise on the Application of Life Cycle Management Principles in Agricultural & Biological Engineering

USDA-ARS?s Scientific Manuscript database

Life Cycle Management (LCM) is a systematic approach, mindset and culture that considers economic, social, and environmental factors among other factors in the decision making process throughout various business or organizational decisions that affect both inputs and outputs of a product or service...

The role of gut peptides in the gut-brain-axis of livestock

USDA-ARS?s Scientific Manuscript database

Gut peptides are small hormones produced within the gut that are involved in many biological processes including, but not limited to, appetite regulation, mucosal growth, and metabolism regulation. Some peptides, such as cholecystokinin (CCK) and xenin-25 may affect appetite by altering gut motilit...

36 CFR 9.86 - Application review process and approval standards.

Code of Federal Regulations, 2011 CFR

2011-07-01

... applicable laws, Executive Orders and regulations, the Regional Director will promptly notify the AMRAP... impacts that appreciably alter the natural character of the units or the integrity of the biological or... established; and (3) Does not adversely affect the natural and cultural resources, visitor use, or...

36 CFR 9.86 - Application review process and approval standards.

Code of Federal Regulations, 2013 CFR

2013-07-01

... applicable laws, Executive Orders and regulations, the Regional Director will promptly notify the AMRAP... impacts that appreciably alter the natural character of the units or the integrity of the biological or... established; and (3) Does not adversely affect the natural and cultural resources, visitor use, or...

Quantitative profiling of oxylipins through comprehensive lc-ms/ms analysis: Application in cardiac surgery

USDA-ARS?s Scientific Manuscript database

Oxylipins, including eicosanoids, affect a broad range of biological processes, such as the initiation and resolution of inflammation. These compounds, also referred to as lipid mediators, are (non-) enzymatically generated by oxidation of polyunsaturated fatty acids such as arachidonic acid (AA). A...

Understanding Personality Development: An Integrative State Process Model

ERIC Educational Resources Information Center

Geukes, Katharina; van Zalk, Maarten; Back, Mitja D.

2018-01-01

While personality is relatively stable over time, it is also subject to change across the entire lifespan. On a macro-analytical level, empirical research has identified patterns of normative and differential development that are affected by biological and environmental factors, specific life events, and social role investments. On a…

Alteration in gene expression in Nile tilapia (Oreochromis niloticus) juveniles submitted to fasting and refeeding.

USDA-ARS?s Scientific Manuscript database

One of the most important biological processes in living organisms that are affected by environmental fluctuations is growth, and the skeletal muscle growth in fish is dependent on proliferation and differentiation of myogenic precursor cells that are activated by Myogenic Regulatory Factors or inhi...

The emotive nature of conflict monitoring in the medial prefrontal cortex.

PubMed

Saunders, Blair; Lin, Hause; Milyavskaya, Marina; Inzlicht, Michael

2017-09-01

The detection of conflict between incompatible impulses, thoughts, and actions is a ubiquitous source of motivation across theories of goal-directed action. In this overview, we explore the hypothesis that conflict is emotive, integrating perspectives from affective science and cognitive neuroscience. Initially, we review evidence suggesting that the mental and biological processes that monitor for information processing conflict-particularly those generated by the anterior midcingulate cortex-track the affective significance of conflict and use this signal to motivate increased control. In this sense, variation in control resembles a form of affect regulation in which control implementation counteracts the aversive experience of conflict. We also highlight emerging evidence proposing that states and dispositions associated with acceptance facilitate control by tuning individuals to the emotive nature of conflict, before proposing avenues for future research, including investigating the role of affect in reinforcement learning and decision making. Copyright © 2017 Elsevier B.V. All rights reserved.

Sources, mechanisms, and consequences of chemical-induced mitochondrial toxicity

PubMed Central

Meyer, Joel N.; Chan, Sherine S. L.

2017-01-01

Mitochondrial function is critical for health, as demonstrated by the effects of mitochondrial toxicity, mutations in genes encoding mitochondrial proteins, and the role of mitochondrial dysfunction in many chronic diseases. However, much basic mitochondrial biology is still being discovered. Furthermore, the details of how different environmental exposures affect mitochondria, how mitochondria respond to stressors, and how genetic variation affecting mitochondrial function alters response to exposures are areas of rapid research growth. This Special Issue was created to highlight and review cutting-edge areas of research into chemical effects on mitochondrial function. We anticipate that it will stimulate additional research into the mechanisms by which chemical exposures impact mitochondria, the biological processes that protect mitochondria from such impacts, and the health consequences that result when defense and homeostatic mechanisms are overcome. PMID:28627407

Processing of face identity in the affective flanker task: a diffusion model analysis.

PubMed

Mueller, Christina J; Kuchinke, Lars

2016-11-01

Affective flanker tasks often present affective facial expressions as stimuli. However, it is not clear whether the identity of the person on the target picture needs to be the same for the flanker stimuli or whether it is better to use pictures of different persons as flankers. While Grose-Fifer, Rodrigues, Hoover & Zottoli (Advances in Cognitive Psychology 9(2):81-91, 2013) state that attentional focus might be captured by processing the differences between faces, i.e. the identity, and therefore use pictures of the same individual as target and flanker stimuli, Munro, Dywan, Harris, McKee, Unsal & Segalowitz (Biological Psychology, 76:31-42, 2007) propose an advantage in presenting pictures of a different individual as flankers. They state that participants might focus only on small visual changes when targets and flankers are from the same individual instead of processing the affective content of the stimuli. The present study manipulated face identity in a between-subject design. Through investigation of behavioral measures as well as diffusion model parameters, we conclude that both types of flankers work equally efficient. This result seems best supported by recent accounts that propose an advantage of emotional processing over identity processing in face recognition. In the present study, there is no evidence that the processing of the face identity attracts sufficient attention to interfere with the affective evaluation of the target and flanker faces.

The Effect of Inkjet Printing over Polymeric Films as Potential Buccal Biologics Delivery Systems.

PubMed

Montenegro-Nicolini, Miguel; Reyes, Patricio E; Jara, Miguel O; Vuddanda, Parameswara R; Neira-Carrillo, Andrónico; Butto, Nicole; Velaga, Sitaram; Morales, Javier O

2018-06-22

The buccal mucosa appears as a promissory route for biologic drug administration, and pharmaceutical films are flexible dosage forms that can be used in the buccal mucosa as drug delivery systems for either a local or systemic effect. Recently, thin films have been used as printing substrates to manufacture these dosage forms by inkjet printing. As such, it is necessary to investigate the effects of printing biologics on films as substrates in terms of their physical and mucoadhesive properties. Here, we explored solvent casting as a conventional method with two biocompatible polymers, hydroxypropyl methylcellulose, and chitosan, and we used electrospinning process as an electrospun film fabrication of polycaprolactone fibers due to its potential to elicit mucoadhesion. Lysozyme was used as biologic drug model and was formulated as a solution for printing by thermal inkjet printing. Films were characterized before and after printing by mechanical and mucoadhesive properties, surface, and ultrastructure morphology through scanning electron microscopy and solid state properties by thermal analysis. Although minor differences were detected in micrographs and thermograms in all polymeric films tested, neither mechanical nor mucoadhesive properties were affected by these differences. Thus, biologic drug printing on films was successful without affecting their mechanical or mucoadhesive properties. These results open way to explore biologics loading on buccal films by inkjet printing, and future efforts will include further in vitro and in vivo evaluations.

Visual processing and social cognition in schizophrenia: relationships among eye movements, biological motion perception, and empathy.

PubMed

Matsumoto, Yukiko; Takahashi, Hideyuki; Murai, Toshiya; Takahashi, Hidehiko

2015-01-01

Schizophrenia patients have impairments at several levels of cognition including visual attention (eye movements), perception, and social cognition. However, it remains unclear how lower-level cognitive deficits influence higher-level cognition. To elucidate the hierarchical path linking deficient cognitions, we focused on biological motion perception, which is involved in both the early stage of visual perception (attention) and higher social cognition, and is impaired in schizophrenia. Seventeen schizophrenia patients and 18 healthy controls participated in the study. Using point-light walker stimuli, we examined eye movements during biological motion perception in schizophrenia. We assessed relationships among eye movements, biological motion perception and empathy. In the biological motion detection task, schizophrenia patients showed lower accuracy and fixated longer than healthy controls. As opposed to controls, patients exhibiting longer fixation durations and fewer numbers of fixations demonstrated higher accuracy. Additionally, in the patient group, the correlations between accuracy and affective empathy index and between eye movement index and affective empathy index were significant. The altered gaze patterns in patients indicate that top-down attention compensates for impaired bottom-up attention. Furthermore, aberrant eye movements might lead to deficits in biological motion perception and finally link to social cognitive impairments. The current findings merit further investigation for understanding the mechanism of social cognitive training and its development. Copyright © 2014 Elsevier Ireland Ltd and the Japan Neuroscience Society. All rights reserved.

Fractal Scaling of Particle Size Distribution and Relationships with Topsoil Properties Affected by Biological Soil Crusts

PubMed Central

Gao, Guang-Lei; Ding, Guo-Dong; Wu, Bin; Zhang, Yu-Qing; Qin, Shu-Gao; Zhao, Yuan-Yuan; Bao, Yan-Feng; Liu, Yun-Dong; Wan, Li; Deng, Ji-Feng

2014-01-01

Background Biological soil crusts are common components of desert ecosystem; they cover ground surface and interact with topsoil that contribute to desertification control and degraded land restoration in arid and semiarid regions. Methodology/Principal Findings To distinguish the changes in topsoil affected by biological soil crusts, we compared topsoil properties across three types of successional biological soil crusts (algae, lichens, and mosses crust), as well as the referenced sandland in the Mu Us Desert, Northern China. Relationships between fractal dimensions of soil particle size distribution and selected soil properties were discussed as well. The results indicated that biological soil crusts had significant positive effects on soil physical structure (P<0.05); and soil organic carbon and nutrients showed an upward trend across the successional stages of biological soil crusts. Fractal dimensions ranged from 2.1477 to 2.3032, and significantly linear correlated with selected soil properties (R2 = 0.494∼0.955, P<0.01). Conclusions/Significance Biological soil crusts cause an important increase in soil fertility, and are beneficial to sand fixation, although the process is rather slow. Fractal dimension proves to be a sensitive and useful index for quantifying changes in soil properties that additionally implies desertification. This study will be essential to provide a firm basis for future policy-making on optimal solutions regarding desertification control and assessment, as well as degraded ecosystem restoration in arid and semiarid regions. PMID:24516668

Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series

PubMed Central

Ferguson, Jake M; Ponciano, José M

2014-01-01

Predicting population extinction risk is a fundamental application of ecological theory to the practice of conservation biology. Here, we compared the prediction performance of a wide array of stochastic, population dynamics models against direct observations of the extinction process from an extensive experimental data set. By varying a series of biological and statistical assumptions in the proposed models, we were able to identify the assumptions that affected predictions about population extinction. We also show how certain autocorrelation structures can emerge due to interspecific interactions, and that accounting for the stochastic effect of these interactions can improve predictions of the extinction process. We conclude that it is possible to account for the stochastic effects of community interactions on extinction when using single-species time series. PMID:24304946

Toxicological effects of the different substances in tobacco smoke on human embryonic development by a systems chemo-biology approach.

PubMed

Feltes, Bruno César; de Faria Poloni, Joice; Notari, Daniel Luis; Bonatto, Diego

2013-01-01

The physiological and molecular effects of tobacco smoke in adult humans and the development of cancer have been well described. In contrast, how tobacco smoke affects embryonic development remains poorly understood. Morphological studies of the fetuses of smoking pregnant women have shown various physical deformities induced by constant fetal exposure to tobacco components, especially nicotine. In addition, nicotine exposure decreases fetal body weight and bone/cartilage growth in addition to decreasing cranial diameter and tibia length. Unfortunately, the molecular pathways leading to these morphological anomalies are not completely understood. In this study, we applied interactome data mining tools and small compound interaction networks to elucidate possible molecular pathways associated with the effects of tobacco smoke components during embryonic development in pregnant female smokers. Our analysis showed a relationship between nicotine and 50 additional harmful substances involved in a variety of biological process that can cause abnormal proliferation, impaired cell differentiation, and increased oxidative stress. We also describe how nicotine can negatively affect retinoic acid signaling and cell differentiation through inhibition of retinoic acid receptors. In addition, nicotine causes a stress reaction and/or a pro-inflammatory response that inhibits the agonistic action of retinoic acid. Moreover, we show that the effect of cigarette smoke on the developing fetus could represent systemic and aggressive impacts in the short term, causing malformations during certain stages of development. Our work provides the first approach describing how different tobacco constituents affect a broad range of biological process in human embryonic development.

Toxicological Effects of the Different Substances in Tobacco Smoke on Human Embryonic Development by a Systems Chemo-Biology Approach

PubMed Central

Feltes, Bruno César; Poloni, Joice de Faria; Notari, Daniel Luis; Bonatto, Diego

2013-01-01

The physiological and molecular effects of tobacco smoke in adult humans and the development of cancer have been well described. In contrast, how tobacco smoke affects embryonic development remains poorly understood. Morphological studies of the fetuses of smoking pregnant women have shown various physical deformities induced by constant fetal exposure to tobacco components, especially nicotine. In addition, nicotine exposure decreases fetal body weight and bone/cartilage growth in addition to decreasing cranial diameter and tibia length. Unfortunately, the molecular pathways leading to these morphological anomalies are not completely understood. In this study, we applied interactome data mining tools and small compound interaction networks to elucidate possible molecular pathways associated with the effects of tobacco smoke components during embryonic development in pregnant female smokers. Our analysis showed a relationship between nicotine and 50 additional harmful substances involved in a variety of biological process that can cause abnormal proliferation, impaired cell differentiation, and increased oxidative stress. We also describe how nicotine can negatively affect retinoic acid signaling and cell differentiation through inhibition of retinoic acid receptors. In addition, nicotine causes a stress reaction and/or a pro-inflammatory response that inhibits the agonistic action of retinoic acid. Moreover, we show that the effect of cigarette smoke on the developing fetus could represent systemic and aggressive impacts in the short term, causing malformations during certain stages of development. Our work provides the first approach describing how different tobacco constituents affect a broad range of biological process in human embryonic development. PMID:23637898

Experimental study on the impact of temperature on the dissipation process of supersaturated total dissolved gas.

PubMed

Shen, Xia; Liu, Shengyun; Li, Ran; Ou, Yangming

2014-09-01

Water temperature not only affects the solubility of gas in water but can also be an important factor in the dissipation process of supersaturated total dissolved gas (TDG). The quantitative relationship between the dissipation process and temperature has not been previously described. This relationship affects the accurate evaluation of the dissipation process and the subsequent biological effects. This article experimentally investigates the impact of temperature on supersaturated TDG dissipation in static and turbulent conditions. The results show that the supersaturated TDG dissipation coefficient increases with the temperature and turbulence intensity. The quantitative relationship was verified by straight flume experiments. This study enhances our understanding of the dissipation of supersaturated TDG. Furthermore, it provides a scientific foundation for the accurate prediction of the dissipation process of supersaturated TDG in the downstream area and the negative impacts of high dam projects on aquatic ecosystems. Copyright © 2014. Published by Elsevier B.V.

Potentials of biological oxidation processes for the treatment of spent sulfidic caustics containing thiols.

PubMed

Sipma, Jan; Svitelskaya, Anna; van der Mark, Bart; Pol, Look W Hulshoff; Lettinga, Gatze; Buisman, Cees J N; Janssen, Albert J H

2004-12-01

This research focused on the biological treatment of sulfidic spent caustics from refineries, which contain mainly hydrogen sulfide, methanethiol (MT) and ethanethiol (ET). Also various organic compounds can be present such as BTEX. Biological oxidation of 2.5 mM MT in batch experiments occurred after MT was first auto-oxidized into dimethyldisulfide (DMDS) whereafter oxidation into sulfate was completed in 350 h. DMDS as sole substrate was completely oxidized within 40 h. Therefore, DMDS formation seems to play an important role in detoxification of MT. Biological oxidation of ET and buthanethiol was not successful in batch experiments. Complete oxidation of MT and ET was observed in flow-through reactor experiments. Simultaneous oxidation of sulfide and MT was achieved when treating a synthetic spent caustic, containing 10 mM sulfide and 2.5 mM MT, in a bubble column reactor with carrier material at a hydraulic retention time of 6 h. Addition of 7.5 mM phenol, a common pollutant of spent caustics, did not adversely affect the biological oxidation process and phenol was completely removed from the effluent. Finally, three different spent caustics solutions from refineries were successfully treated.

Developmental biology in marine invertebrate symbioses.

PubMed

McFall-Ngai, M J; Ruby, E G

2000-12-01

Associations between marine invertebrates and their cooperative bacterial symbionts offer access to an understanding of the roots of host-microbe interaction; for example, several symbioses like the squid-vibrio light organ association serve as models for investigating how each partner affects the developmental biology of the other. Previous results have identified a program of specific developmental events that unfolds as the association is initiated. In the past year, published studies have focused primarily on describing the mechanisms underlying the signaling processes that occur between the juvenile squid and the luminous bacteria that colonize it.

Effects of amendment of different biochars on soil physical and biological properties related to carbon mineralization

NASA Astrophysics Data System (ADS)

Zhang, Renduo; Zhu, Shuzhi; Ouyang, Lei

2014-05-01

Biochar addition to soils potentially affects various soil properties, and these effects are dependent on biochars derived from different feedstock materials and pyrolysis processes. The objective of this study was to investigate the effects of amendment of different biochars on soil physical and biological properties. Biochars were produced with dairy manure and woodchip at temperatures of 300, 500, and 700°C, respectively. Each biochar was mixed at 5% (w/w) with a forest soil and the mixture was incubated for 180 days, during which soil physical and biological properties, and soil respiration rates were measured. Results showed that the biochar addition significantly enhanced the formation of soil macroaggregates at the early incubation time. The biochar application significantly reduced soil bulk density, increased the amount of soil organic matter, and stimulated microbial activity and soil respiration rates at the early incubation stage. Biochar applications improved water retention capacity, with stronger effects by biochars produced at higher pyrolysis temperatures. At the same suction, the soil with woodchip biochars possessed higher water content than with the dairy manure biochars. Biochar addition significantly affected the soil physical and biological properties, which resulted in different soil carbon mineralization rates.

Borderline personality disorder and childhood trauma: exploring the affected biological systems and mechanisms.

PubMed

Cattane, Nadia; Rossi, Roberta; Lanfredi, Mariangela; Cattaneo, Annamaria

2017-06-15

According to several studies, the onset of the Borderline Personality Disorder (BPD) depends on the combination between genetic and environmental factors (GxE), in particular between biological vulnerabilities and the exposure to traumatic experiences during childhood. We have searched for studies reporting possible alterations in several biological processes and brain morphological features in relation to childhood trauma experiences and to BPD. We have also looked for epigenetic mechanisms as they could be mediators of the effects of childhood trauma in BPD vulnerability. We prove the role of alterations in Hypothalamic-Pituitary-Adrenal (HPA) axis, in neurotrasmission, in the endogenous opioid system and in neuroplasticity in the childhood trauma-associated vulnerability to develop BPD; we also confirm the presence of morphological changes in several BPD brain areas and in particular in those involved in stress response. Not so many studies are available on epigenetic changes in BPD patients, although these mechanisms are widely investigated in relation to stress-related disorders. A better comprehension of the biological and epigenetic mechanisms, affected by childhood trauma and altered in BPD patients, could allow to identify "at high risk" subjects and to prevent or minimize the development of the disease later in life.

Ethical issues in dementia

PubMed Central

Whitehouse, Peter J.

2000-01-01

The growing number of individuals affected by dementia will intensify the ethical issues that emerge in clinical practice and research, issues early in disease relate to genetic testing, use of medications in mildly affected persons, and diagnostic disclosure. Research issues relate to appropriate informed consent processes, conflict of interests, and research design issues, such as the use of placebos and the use of biological tissues, in the later stages of disease concern about appropriate therapeutic goals and end-of-life care is appropriate. PMID:22033828

Antiproliferative effects of fresh and thermal processed green and red cultivars of curly kale (Brassica oleracea L. convar. acephala var. sabellica).

PubMed

Olsen, Helle; Grimmer, Stine; Aaby, Kjersti; Saha, Shikha; Borge, Grethe Iren A

2012-08-01

Brassica vegetables contain a diverse range of phytochemicals with biological properties such as antioxidant and anticancer activity. However, knowledge about how biological activities are affected by processing is lacking. A green cultivar and a red cultivar of curly kale were evaluated for water/methanol-soluble phytochemicals before and after processing involving blanching, freeze storage, and boil-in-bag heat treatment. In both kale cultivars, processing resulted in a significant decrease of total phenolics, antioxidant capacity, and content and distribution of flavonols, anthocyanins, hydroxycinnamic acids, glucosinolates, and vitamin C. Interestingly, the red curly kale cultivar had a higher capacity to withstand thermal loss of phytochemicals. The extracts of both green and red curly kale inhibited the cell proliferation of three human colon cancer cell lines (Caco-2, HT-29, and HCT 116). However, extracts from fresh plant material had a significantly stronger antiproliferative effect than extracts from processed plant material.

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.

Why genes don't count (for racial differences in health).

PubMed Central

Goodman, A H

2000-01-01

There is a paradoxical relationship between "race" and genetics. Whereas genetic data were first used to prove the validity of race, since the early 1970s they have been used to illustrate the invalidity of biological races. Indeed, race does not account for human genetic variation, which is continuous, complexly structured, constantly changing, and predominantly within "races." Despite the disproof of race-as-biology, genetic variation continues to be used to explain racial differences. Such explanations require the acceptance of 2 disproved assumptions: that genetic variation explains variation in disease and that genetic variation explains racial variation in disease. While the former is a form of geneticization, the notion that genes are the primary determinants of biology and behavior, the latter represents a form of racialization, an exaggeration of the salience of race. Using race as a proxy for genetic differences limits understandings of the complex interactions among political-economic processes, lived experiences, and human biologies. By moving beyond studies of racialized genetics, we can clarify the processes by which varied and interwoven forms of racialization and racism affect individuals "under the skin." PMID:11076233

Why genes don't count (for racial differences in health).

PubMed

Goodman, A H

2000-11-01

There is a paradoxical relationship between "race" and genetics. Whereas genetic data were first used to prove the validity of race, since the early 1970s they have been used to illustrate the invalidity of biological races. Indeed, race does not account for human genetic variation, which is continuous, complexly structured, constantly changing, and predominantly within "races." Despite the disproof of race-as-biology, genetic variation continues to be used to explain racial differences. Such explanations require the acceptance of 2 disproved assumptions: that genetic variation explains variation in disease and that genetic variation explains racial variation in disease. While the former is a form of geneticization, the notion that genes are the primary determinants of biology and behavior, the latter represents a form of racialization, an exaggeration of the salience of race. Using race as a proxy for genetic differences limits understandings of the complex interactions among political-economic processes, lived experiences, and human biologies. By moving beyond studies of racialized genetics, we can clarify the processes by which varied and interwoven forms of racialization and racism affect individuals "under the skin."

Advances of Molecular Imaging for Monitoring the Anatomical and Functional Architecture of the Olfactory System.

PubMed

Zhang, Xintong; Bi, Anyao; Gao, Quansheng; Zhang, Shuai; Huang, Kunzhu; Liu, Zhiguo; Gao, Tang; Zeng, Wenbin

2016-01-20

The olfactory system of organisms serves as a genetically and anatomically model for studying how sensory input can be translated into behavior output. Some neurologic diseases are considered to be related to olfactory disturbance, especially Alzheimer's disease, Parkinson's disease, multiple sclerosis, and so forth. However, it is still unclear how the olfactory system affects disease generation processes and olfaction delivery processes. Molecular imaging, a modern multidisciplinary technology, can provide valid tools for the early detection and characterization of diseases, evaluation of treatment, and study of biological processes in living subjects, since molecular imaging applies specific molecular probes as a novel approach to produce special data to study biological processes in cellular and subcellular levels. Recently, molecular imaging plays a key role in studying the activation of olfactory system, thus it could help to prevent or delay some diseases. Herein, we present a comprehensive review on the research progress of the imaging probes for visualizing olfactory system, which is classified on different imaging modalities, including PET, MRI, and optical imaging. Additionally, the probes' design, sensing mechanism, and biological application are discussed. Finally, we provide an outlook for future studies in this field.

How to Train a Cell–Cutting-Edge Molecular Tools

PubMed Central

Czapiński, Jakub; Kiełbus, Michał; Kałafut, Joanna; Kos, Michał; Stepulak, Andrzej; Rivero-Müller, Adolfo

2017-01-01

In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications. PMID:28344971

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.

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

Modelling fungal growth in heterogeneous soil: analyses of the effect of soil physical structure on fungal community dynamics

NASA Astrophysics Data System (ADS)

Falconer, R.; Radoslow, P.; Grinev, D.; Otten, W.

2009-04-01

Fungi play a pivital role in soil ecosystems contributing to plant productivity. The underlying soil physical and biological processes responsible for community dynamics are interrelated and, at present, poorly understood. If these complex processes can be understood then this knowledge can be managed with an aim to providing more sustainable agriculture. Our understanding of microbial dynamics in soil has long been hampered by a lack of a theoretical framework and difficulties in observation and quantification. We will demonstrate how the spatial and temporal dynamics of fungi in soil can be understood by linking mathematical modelling with novel techniques that visualise the complex structure of the soil. The combination of these techniques and mathematical models opens up new possibilities to understand how the physical structure of soil affects fungal colony dynamics and also how fungal dynamics affect soil structure. We will quantify, using X ray tomography, soil structure for a range of artificially prepared microcosms. We characterise the soil structures using soil metrics such as porosity, fractal dimension, and the connectivity of the pore volume. Furthermore we will use the individual based fungal colony growth model of Falconer et al. 2005, which is based on the physiological processes of fungi, to assess the effect of soil structure on microbial dynamics by qualifying biomass abundances and distributions. We demonstrate how soil structure can critically affect fungal species interactions with consequences for biological control and fungal biodiversity.

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.

Dispersal polymorphism in an invasive forest pest affects its ability to establish

Treesearch

Christelle Robinet; Andrew M. Liebhold

2009-01-01

Given the increasing number of biological invasions, there is a crucial need to identify life history traits that promote invasion. Invasiveness reflects capabilities for both establishment after introduction and spread following establishment. In this paper, we explore, via simulation, the interacting effects of dispersal and Allee effects on both invasion processes....

Grassland restoration with and without fire: evidence from a tree-removal experiment

Treesearch

C.B. Halpern; R.D. Haugo; J.A. Antos; S.S. Kaas; A.L. Kilanowski

2012-01-01

Forest encroachment threatens the biological diversity of grasslands globally. Positive feedbacks can reinforce the process, affecting soils and ground vegetation, ultimately leading to replacement of grassland by forest species. We tested whether restoration treatments (tree removal, with or without fire) reversed effects of nearly two centuries of encroachment by...

Water quality and irrigation [Chapter 10

Treesearch

Thomas D. Landis; Kim M. Wilkinson

2009-01-01

Water is the single most important biological factor affecting plant growth and health. Water is essential for almost every plant process: photosynthesis, nutrient transport, and cell expansion and development. In fact, 80 to 90 percent of a seedling's weight is made up of water. Therefore, irrigation management is the most critical aspect of nursery operations....

Wood properties affecting finish service life

Treesearch

R. Sam Williams; Charles Jourdain; George I. Daisey; Robert W. Springate

2000-01-01

Wood is a biological material that has widely different properties depending on species, geographic area where the tree grew, the growth conditions, size of the tree at harvest, sawing, and other manufacturing processes. Some of the more important wood properties as they relate to wood finishing are discussed, e.g., growth rate, density, knots, extractives, juvenile...

PHYSICAL AND BIOLOGICAL CONTROLS ON DISSOLVED OXYGEN DYNAMICS IN A NORTHEASTERN GULF OF MEXICO ESTUARY

EPA Science Inventory

Nutrient over-enrichment is one of the most often cited causes of 305b impairment in coastal waters. Excessive nutrients affect designated uses of the nation's aquatic resources, and pose risks to human health and the environment. The process of developing nutrient criteria for e...

Predictors of Student Success in Entry-Level Science Courses

ERIC Educational Resources Information Center

Singh, Mamta K.

2009-01-01

Although the educational evaluation process is useful and valuable and is supported by the Higher Education Act, a strong research base for program evaluation of college entry-level science courses is still lacking. Studies in science disciplines such as, biology, chemistry, and physics have addressed various affective and demographic factors and…

Alpha-Tocopherol modulates transcriptional activities that affect essential biological processes in Bovine Cells

USDA-ARS?s Scientific Manuscript database

Alpha-tocopherol is the major isoform of vitamin E. after nearly 100 years of research and countless publications, the physiological functions of vitamin E remain mysterious to a certain degree. Nevertheless, vitamin E is one of the most commonly used single nutrient supplements. Recent data has su...

Toward a U.S. National Phenological Assessment

NASA Astrophysics Data System (ADS)

Henebry, Geoffrey M.; Betancourt, Julio L.

2010-01-01

Third USA National Phenology Network (USA-NPN) and Research Coordination Network (RCN) Annual Meeting; Milwaukee, Wisconsin, 5-9 October 2009; Directional climate change will have profound and lasting effects throughout society that are best understood through fundamental physical and biological processes. One such process is phenology: how the timing of recurring biological events is affected by biotic and abiotic forces. Phenology is an early and integrative indicator of climate change readily understood by nonspecialists. Phenology affects the planting, maturation, and harvesting of food and fiber; pollination; timing and magnitude of allergies and disease; recreation and tourism; water quantity and quality; and ecosystem function and resilience. Thus, phenology is the gateway to climatic effects on both managed and unmanaged ecosystems. Adaptation to climatic variability and change will require integration of phenological data and models with climatic forecasts at seasonal to decadal time scales. Changes in phenologies have already manifested myriad effects of directional climate change. As these changes continue, it is critical to establish a comprehensive suite of benchmarks that can be tracked and mapped at local to continental scales with observations and climate models.

Lactobacillus acidophilus—Rutin Interplay Investigated by Proteomics

PubMed Central

Mazzeo, Maria Fiorella; Lippolis, Rosa; Sorrentino, Alida; Liberti, Sarah; Fragnito, Federica; Siciliano, Rosa Anna

2015-01-01

Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes.This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus. PMID:26544973

Lactobacillus acidophilus-Rutin Interplay Investigated by Proteomics.

PubMed

Mazzeo, Maria Fiorella; Lippolis, Rosa; Sorrentino, Alida; Liberti, Sarah; Fragnito, Federica; Siciliano, Rosa Anna

2015-01-01

Dietary polyphenols are bioactive molecules that beneficially affect human health, due to their anti-oxidant, anti-inflammatory, cardio-protective and chemopreventive properties. They are absorbed in a very low percentage in the small intestine and reach intact the colon, where they are metabolized by the gut microbiota. Although it is well documented a key role of microbial metabolism in the absorption of polyphenols and modulation of their biological activity, molecular mechanisms at the basis of the bacteria-polyphenols interplay are still poorly understood. In this context, differential proteomics was applied to reveal adaptive response mechanisms that enabled a potential probiotic Lactobacillus acidophilus strain to survive in the presence of the dietary polyphenol rutin. The response to rutin mainly modulated the expression level of proteins involved in general stress response mechanisms and, in particular, induced the activation of protein quality control systems, and affected carbohydrate and amino acid metabolism, protein synthesis and cell wall integrity. Moreover, rutin triggered the expression of proteins involved in oxidation-reduction processes.This study provides a first general view of the impact of dietary polyphenols on metabolic and biological processes of L. acidophilus.

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.

Critical operational parameters for zero sludge production in biological wastewater treatment processes combined with sludge disintegration.

PubMed

Yoon, Seong-Hoon; Lee, Sangho

2005-09-01

Mathematical models were developed to elucidate the relationships among process control parameters and the effect of these parameters on the performance of anoxic/oxic biological wastewater processes combined with sludge disintegrators (A/O-SD). The model equations were also applied for analyses of activated sludge processes hybrid with sludge disintegrators (AS-SD). Solubilization ratio of sludge in the sludge disintegrator, alpha, hardly affected sludge reduction efficiencies if the biomass was completely destructed to smaller particulates. On the other hand, conversion efficiency of non-biodegradable particulates to biodegradable particulates, beta, significantly affected sludge reduction efficiencies because beta was directly related to the accumulation of non-biodegradable particulates in bioreactors. When 30% of sludge in the oxic tank was disintegrated everyday and beta was 0.5, sludge reduction was expected to be 78% and 69% for the A/O-SD and AS-SD processes, respectively. Under this condition, the sludge disintegration number (SDN), which is the amount of sludge disintegrated divided by the reduced sludge, was calculated to be around 4. Due to the sludge disintegration, live biomass concentration decreased while other non-biodegradable particulates concentration increased. As a consequence, the real F/M ratio was expected to be much higher than the apparent F/M. The effluent COD was maintained almost constant for the range of sludge disintegration rate considered in this study. Nitrogen removal efficiencies of the A/O-SD process was hardly affected by the sludge disintegration until daily sludge disintegration reaches 40% of sludge in the oxic tank. Above this level of sludge disintegration, autotrophic biomass concentration decreases overly and TKN in the effluent increases abruptly in both the A/O-SD and AS-SD processes. Overall, the trends of sludge reduction and effluent quality according to operation parameters matched well with experimental results found in literatures.

Biomorphodynamics: Physical-biological feedbacks that shape landscapes

USGS Publications Warehouse

Murray, A.B.; Knaapen, M.A.F.; Tal, M.; Kirwan, M.L.

2008-01-01

Plants and animals affect morphological evolution in many environments. The term "ecogeomorphology" describes studies that address such effects. In this opinion article we use the term "biomorphodynamics" to characterize a subset of ecogeomorphologic studies: those that investigate not only the effects of organisms on physical processes and morphology but also how the biological processes depend on morphology and physical forcing. The two-way coupling precipitates feedbacks, leading to interesting modes of behavior, much like the coupling between flow/sediment transport and morphology leads to rich morphodynamic behaviors. Select examples illustrate how even the basic aspects of some systems cannot be understood without considering biomorphodynamic coupling. Prominent examples include the dynamic interactions between vegetation and flow/sediment transport that can determine river channel patterns and the multifaceted biomorphodynamic feedbacks shaping tidal marshes and channel networks. These examples suggest that the effects of morphology and physical processes on biology tend to operate over the timescale of the evolution of the morphological pattern. Thus, in field studies, which represent a snapshot in the pattern evolution, these effects are often not as obvious as the effects of biology on physical processes. However, numerical modeling indicates that the influences on biology from physical processes can play a key role in shaping landscapes and that even local and temporary vegetation disturbances can steer large-scale, long-term landscape evolution. The prevalence of biomorphodynamic research is burgeoning in recent years, driven by societal need and a confluence of complex systems-inspired modeling approaches in ecology and geomorphology. To make fundamental progress in understanding the dynamics of many landscapes, our community needs to increasingly learn to look for two-way, biomorphodynamic feedbacks and to collect new types of data to support the modeling of such emergent interactions. Copyright 2008 by the American Geophysical Union.

Limits on reliable information flows through stochastic populations.

PubMed

Boczkowski, Lucas; Natale, Emanuele; Feinerman, Ofer; Korman, Amos

2018-06-06

Biological systems can share and collectively process information to yield emergent effects, despite inherent noise in communication. While man-made systems often employ intricate structural solutions to overcome noise, the structure of many biological systems is more amorphous. It is not well understood how communication noise may affect the computational repertoire of such groups. To approach this question we consider the basic collective task of rumor spreading, in which information from few knowledgeable sources must reliably flow into the rest of the population. We study the effect of communication noise on the ability of groups that lack stable structures to efficiently solve this task. We present an impossibility result which strongly restricts reliable rumor spreading in such groups. Namely, we prove that, in the presence of even moderate levels of noise that affect all facets of the communication, no scheme can significantly outperform the trivial one in which agents have to wait until directly interacting with the sources-a process which requires linear time in the population size. Our results imply that in order to achieve efficient rumor spread a system must exhibit either some degree of structural stability or, alternatively, some facet of the communication which is immune to noise. We then corroborate this claim by providing new analyses of experimental data regarding recruitment in Cataglyphis niger desert ants. Finally, in light of our theoretical results, we discuss strategies to overcome noise in other biological systems.

Predicting the process of extinction in experimental microcosms and accounting for interspecific interactions in single-species time series.

PubMed

Ferguson, Jake M; Ponciano, José M

2014-02-01

Predicting population extinction risk is a fundamental application of ecological theory to the practice of conservation biology. Here, we compared the prediction performance of a wide array of stochastic, population dynamics models against direct observations of the extinction process from an extensive experimental data set. By varying a series of biological and statistical assumptions in the proposed models, we were able to identify the assumptions that affected predictions about population extinction. We also show how certain autocorrelation structures can emerge due to interspecific interactions, and that accounting for the stochastic effect of these interactions can improve predictions of the extinction process. We conclude that it is possible to account for the stochastic effects of community interactions on extinction when using single-species time series. © 2013 The Authors. Ecology Letters published by John Wiley & Sons Ltd and CNRS.

Reduce oil and grease content in wastewater

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

Capps, R.W.; Matelli, G.N.; Bradford, M.L.

Poor water quality is often blamed on biological oxidation unit malfunction. However, poorly treated water entering the bio-unit is more often the problem. At the microscopic level, oil/water-separation dynamics are influenced by pH, fluid velocity, temperature, and unit volumes. Oily water's physical and chemical properties affect pretreatment systems such as API separators, corrugated plate interception (CPI) separators, air flotation and equalization systems. A better understanding of pretreatment systems' limits and efficiencies can improve wastewater quality before it upsets the biological oxidation (BIOX). Oil contamination in refinery wastewater originates from desalting, steam stripping, product treating, tank drains, sample drains and equipmentmore » washdown. The largest volumetric contributors are cooling tower blowdowns and contaminated stormwater. The paper describes the BIOX process; oil/water separation; oil/water emulsions and colloidal solutions; air flotation; surfactants; DAF (dissolved air flotation) process; IAF (induced air flotation) process; equalization; load factors; salts; and system design.« less

Induced Fit in Protein Multimerization: The HFBI Case

PubMed Central

Riccardi, Laura

2016-01-01

Hydrophobins, produced by filamentous fungi, are small amphipathic proteins whose biological functions rely on their unique surface-activity properties. Understanding the mechanistic details of the multimerization process is of primary importance to clarify the interfacial activity of hydrophobins. We used free energy calculations to study the role of a flexible β-hairpin in the multimerization process in hydrophobin II from Trichoderma reesei (HFBI). We characterized how the displacement of this β-hairpin controls the stability of the monomers/dimers/tetramers in solution. The regulation of the oligomerization equilibrium of HFBI will necessarily affect its interfacial properties, fundamental for its biological function and for technological applications. Moreover, we propose possible routes for the multimerization process of HFBI in solution. This is the first case where a mechanism by which a flexible loop flanking a rigid patch controls the protein-protein binding equilibrium, already known for proteins with charged binding hot-spots, is described within a hydrophobic patch. PMID:27832079

Investigating cholesterol metabolism and ageing using a systems biology approach.

PubMed

Morgan, A E; Mooney, K M; Wilkinson, S J; Pickles, N A; Mc Auley, M T

2017-08-01

CVD accounted for 27 % of all deaths in the UK in 2014, and was responsible for 1·7 million hospital admissions in 2013/2014. This condition becomes increasingly prevalent with age, affecting 34·1 and 29·8 % of males and females over 75 years of age respectively in 2011. The dysregulation of cholesterol metabolism with age, often observed as a rise in LDL-cholesterol, has been associated with the pathogenesis of CVD. To compound this problem, it is estimated by 2050, 22 % of the world's population will be over 60 years of age, in culmination with a growing resistance and intolerance to pre-existing cholesterol regulating drugs such as statins. Therefore, it is apparent research into additional therapies for hypercholesterolaemia and CVD prevention is a growing necessity. However, it is also imperative to recognise this complex biological system cannot be studied using a reductionist approach; rather its biological uniqueness necessitates a more integrated methodology, such as that offered by systems biology. In this review, we firstly discuss cholesterol metabolism and how it is affected by diet and the ageing process. Next, we describe therapeutic strategies for hypercholesterolaemia, and finally how the systems biology paradigm can be utilised to investigate how ageing interacts with complex systems such as cholesterol metabolism. We conclude by emphasising the need for nutritionists to work in parallel with the systems biology community, to develop novel approaches to studying cholesterol metabolism and its interaction with ageing.

Environmental Stress-mediated EPS Production Shape Microbial Activity on Various Hydrated Rough Surfaces

NASA Astrophysics Data System (ADS)

Wang, G.; Liu, L.; Chen, G.

2016-12-01

The complex environmental physical and chemical processes and interplay with the associating biological responses are keys to understanding the environmental microbiology ensconced in environmental remediation, water quality control, food safety, nutrient cycling, and etc., yet remain poorly understood. Using experimental micromodels, we study how environmental conditions (e.g., hydration fluctuation, nutrient limitation, pH variation, etc.) affect microbial extracellular polymeric substances (EPS) production and their configuration within various hydrated surfaces, and impacts on microbial motility, surface attachment, aggregation, and other bioremediation activities. To elucidate the potential mechanisms underlying the complex bio-physicochemical processes, we developed an individual-based and spatio-temporally resolved modeling platform that explicitly considers microscale aqueous-phase configuration and nutrient transport/diffusion and associated biophysical processes affecting individual microbial cell life history. We quantitatively explore the effects of the above microscale environmental processes on bio-physicochemical interactions affecting microbial growth, motility, surface attachment and aggregation, and shaping population interactions and functions. Simulation scenarios of microbial induced pollutant (e.g., roxarsone) biotransformation on various hydrated rough surfaces will also be present.

The importance of benthic-pelagic coupling for marine ecosystem functioning in a changing world.

PubMed

Griffiths, Jennifer R; Kadin, Martina; Nascimento, Francisco J A; Tamelander, Tobias; Törnroos, Anna; Bonaglia, Stefano; Bonsdorff, Erik; Brüchert, Volker; Gårdmark, Anna; Järnström, Marie; Kotta, Jonne; Lindegren, Martin; Nordström, Marie C; Norkko, Alf; Olsson, Jens; Weigel, Benjamin; Žydelis, Ramunas; Blenckner, Thorsten; Niiranen, Susa; Winder, Monika

2017-06-01

Benthic-pelagic coupling is manifested as the exchange of energy, mass, or nutrients between benthic and pelagic habitats. It plays a prominent role in aquatic ecosystems, and it is crucial to functions from nutrient cycling to energy transfer in food webs. Coastal and estuarine ecosystem structure and function are strongly affected by anthropogenic pressures; however, there are large gaps in our understanding of the responses of inorganic nutrient and organic matter fluxes between benthic habitats and the water column. We illustrate the varied nature of physical and biological benthic-pelagic coupling processes and their potential sensitivity to three anthropogenic pressures - climate change, nutrient loading, and fishing - using the Baltic Sea as a case study and summarize current knowledge on the exchange of inorganic nutrients and organic material between habitats. Traditionally measured benthic-pelagic coupling processes (e.g., nutrient exchange and sedimentation of organic material) are to some extent quantifiable, but the magnitude and variability of biological processes are rarely assessed, preventing quantitative comparisons. Changing oxygen conditions will continue to have widespread effects on the processes that govern inorganic and organic matter exchange among habitats while climate change and nutrient load reductions may have large effects on organic matter sedimentation. Many biological processes (predation, bioturbation) are expected to be sensitive to anthropogenic drivers, but the outcomes for ecosystem function are largely unknown. We emphasize how improved empirical and experimental understanding of benthic-pelagic coupling processes and their variability are necessary to inform models that can quantify the feedbacks among processes and ecosystem responses to a changing world. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Integration of Biological and Physical Sciences to Advance Ecological Understanding of Aquatic Ecosystems

NASA Astrophysics Data System (ADS)

Luce, C. H.; Buffington, J. M.; Rieman, B. E.; Dunham, J. B.; McKean, J. A.; Thurow, R. F.; Gutierrez-Teira, B.; Rosenberger, A. E.

2005-05-01

Conservation and restoration of freshwater stream and river habitats are important goals for land management and natural resources research. Several examples of research have emerged showing that many species are adapted to temporary habitat disruptions, but that these adaptations are sensitive to the spatial grain and extent of disturbance as well as to its duration. When viewed from this perspective, questions of timing, spatial pattern, and relevant scales emerge as critical issues. In contrast, much regulation, management, and research remains tied to pollutant loading paradigms that are insensitive to either time or space scales. It is becoming clear that research is needed to examine questions and hypotheses about how physical processes affect ecological processes. Two overarching questions concisely frame the scientific issues: 1) How do we quantify physical watershed processes in a way that is meaningful to biological and ecological processes, and 2) how does the answer to that question vary with changing spatial and temporal scales? A joint understanding of scaling characteristics of physical process and the plasticity of aquatic species will be needed to accomplish this research; hence a strong need exists for integrative and collaborative development. Considering conservation biology problems in this fashion can lead to creative and non-obvious solutions because the integrated system has important non-linearities and feedbacks related to a biological system that has responded to substantial natural variability in the past. We propose that research beginning with ecological theories and principles followed with a structured examination of each physical process as related to the specific ecological theories is a strong approach to developing the necessary science, and such an approach may form a basis for development of scaling theories of hydrologic and geomorphic process. We illustrate the approach with several examples.

Harnessing Preclinical Molecular Imaging to Inform Advances in Personalized Cancer Medicine.

PubMed

Clark, Peter M; Ebiana, Victoria A; Gosa, Laura; Cloughesy, Timothy F; Nathanson, David A

2017-05-01

Comprehensive molecular analysis of individual tumors provides great potential for personalized cancer therapy. However, the presence of a particular genetic alteration is often insufficient to predict therapeutic efficacy. Drugs with distinct mechanisms of action can affect the biology of tumors in specific and unique ways. Therefore, assays that can measure drug-induced perturbations of defined functional tumor properties can be highly complementary to genomic analysis. PET provides the capacity to noninvasively measure the dynamics of various tumor biologic processes in vivo. Here, we review the underlying biochemical and biologic basis for a variety of PET tracers and how they may be used to better optimize cancer therapy. © 2017 by the Society of Nuclear Medicine and Molecular Imaging.

Clinical, functional, behavioural and epigenomic biomarkers of obesity.

PubMed

Lafortuna, Claudio L; Tovar, Armando R; Rastelli, Fabio; Tabozzi, Sarah A; Caramenti, Martina; Orozco-Ruiz, Ximena; Aguilar-Lopez, Miriam; Guevara-Cruz, Martha; Avila-Nava, Azalia; Torres, Nimbe; Bertoli, Gloria

2017-06-01

Overweight and obesity are highly prevalent conditions worldwide, linked to an increased risk for death, disability and disease due to metabolic and biochemical abnormalities affecting the biological human system throughout different domains. Biomarkers, defined as indicators of biological processes in health and disease, relevant for body mass excess management have been identified according to different criteria, including anthropometric and molecular indexes, as well as physiological and behavioural aspects. Analysing these different biomarkers, we identified their potential role in diagnosis, prognosis and treatment. Epigenetic biomarkers, cellular mediators of inflammation and factors related to microbiota-host interactions may be considered to have a theranostic value. Though, the molecular processes responsible for the biological phenomenology detected by the other analysed markers, is not clear yet. Nevertheless, these biomarkers possess valuable diagnostic and prognostic power. A new frontier for theranostic biomarkers can be foreseen in the exploitation of parameters defining behaviours and lifestyles linked to the risk of obesity, capable to describe the effects of interventions for obesity prevention and treatment which include also behaviour change strategies.

Using Student Writing and Lexical Analysis to Reveal Student Thinking about the Role of Stop Codons in the Central Dogma.

PubMed

Prevost, Luanna B; Smith, Michelle K; Knight, Jennifer K

2016-01-01

Previous work has shown that students have persistent difficulties in understanding how central dogma processes can be affected by a stop codon mutation. To explore these difficulties, we modified two multiple-choice questions from the Genetics Concept Assessment into three open-ended questions that asked students to write about how a stop codon mutation potentially impacts replication, transcription, and translation. We then used computer-assisted lexical analysis combined with human scoring to categorize student responses. The lexical analysis models showed high agreement with human scoring, demonstrating that this approach can be successfully used to analyze large numbers of student written responses. The results of this analysis show that students' ideas about one process in the central dogma can affect their thinking about subsequent and previous processes, leading to mixed models of conceptual understanding. © 2016 L. B. Prevost et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

An extension of ASM2d including pH calculation.

PubMed

Serralta, J; Ferrer, J; Borrás, L; Seco, A

2004-11-01

This paper presents an extension of the Activated Sludge Model No. 2d (ASM2d) including a chemical model able to calculate the pH value in biological processes. The developed chemical model incorporates the complete set of chemical species affecting the pH value to ASM2d describing non-equilibrium biochemical processes. It considers the system formed by one aqueous phase, in which biochemical processes take place, and one gaseous phase, and is based on the assumptions of instantaneous chemical equilibrium under liquid phase and kinetically governed mass transport between the liquid and gas phase. The ASM2d enlargement comprises the addition of every component affecting the pH value and an ion-balance for the calculation of the pH value and the dissociation species. The significant pH variations observed in a sequencing batch reactor operated for enhanced biological phosphorus removal were used to verify the capability of the extended model for predicting the dynamics of pH jointly with concentrations of acetic acid and phosphate. A pH inhibition function for polyphosphate accumulating bacteria has also been included in the model to simulate the behaviour observed. Experimental data obtained in four different experiments (with different sludge retention time and influent phosphorus concentrations) were accurately reproduced.

Biological nutrient removal and molecular biological characteristics in an anaerobic-multistage anaerobic/oxic (A-MAO) process to treat municipal wastewater.

PubMed

Huang, Xiao; Dong, Wenyi; Wang, Hongjie; Jiang, Shilong

2017-10-01

This study aimed to present an anaerobic-multistage anaerobic/oxic (A-MAO) process to treat municipal wastewater. The average COD, NH 4 + -N, TN, and TP removal efficiency were 91.81%, 96.26%, 83.73% and 94.49%, respectively. Temperature plunge and C/N decrease have a certain impact on the modified process. Characteristics of microbial community, function microorganism, and correlation of microbial community with environmental variables in five compartments were carried out by Illumina Miseq high-throughput sequencing. The differences of microbial community were observed and Blastocatella, Flavobacterium and Pseudomonas were the dominant genus. Nitrosomonas and Nitrospira occupied a dominant position in AOB and NOB, respectively. Rhodospirillaceae and Rhodocyclaceae owned a considerable proportion in phosphorus removal bacteria. DO and COD played significant roles on affecting the microbial components. The A-MAO process in this study demonstrated a high potential for nutrient removal from municipal wastewater. Copyright © 2017 Elsevier Ltd. All rights reserved.

MicroRNA expression profiles from eggs of different qualities associated with post-ovulatory ageing in rainbow trout (Oncorhynchus mykiss)

USDA-ARS?s Scientific Manuscript database

Background: Egg quality is an important aspect in rainbow trout farming. Post-ovulatory aging is one of the most important factors affecting egg quality. MicroRNAs (miRNAs) are the major regulators in various biological processes and their expression profiles could serve as reliable biomarkers for v...

Factors affecting ammonium uptake in streams - an inter-biome perspective

Treesearch

Jackson R Webster; Partick J. Mulholland; Jennifer L. Tanks; H. Maurice Valett; Walter K. Dodds; Bruce J. Peterson; William B. Bowden; Clifford N. Dahm; Stuart Findlay; Stanley V. Gregory; Nancy B. Grimm; Stephen K. Hamilton; Sherri L. Johnson; Eugenia Marti; William H. McDowell; Judy L. Meyer; Donna D. Morrall; Steven A. Thomas; Wilfred M. Wollhem

2003-01-01

1. The Lotic Intersite Nitrogen experiment (LINX) was a coordinated study of the relationships between North American biomes and factors governing ammonium uptake in streams. Our objective was to relate inter-biome variability of ammonium uptake to physical, chemical and biological processes. 2. Data were collected from 11 streams ranging from arctic to tropical and...

Estimating daily Landsat-scale evapotranspiration over a managed pine plantation in North Carolina, USA using a data fusion method

USDA-ARS?s Scientific Manuscript database

As a primary flux in the global water cycle, evapotranspiration (ET) connects hydrologic and biological processes and is directly affected by water management, land use change and climate change. The two source energy balance (TSEB) model has been widely applied to quantify field scale ET using sate...

Daily Landsat-scale evapotranspiration estimation over a managed pine plantation in North Carolina, USA using multi-satellite data fusion

USDA-ARS?s Scientific Manuscript database

As a primary flux in the global water cycle, evapotranspiration (ET) connects hydrologic and biological processes and is directly affected by water and land management, land use change and climate variability. The Two Source Energy Balance (TSEB) model has been widely applied to quantify field- to g...

The Politics of Invasive Weed Management: Gender, Race, and Risk Perception in Rural California

ERIC Educational Resources Information Center

Norgaard, Kari Marie

2007-01-01

"Biological invasions" are now recognized as the cause of significant ecological and economic damage. They also raise a series of less visible social issues. Management of invasive species is often a political process raising questions such as who decides which organisms are to be managed, and who benefits or is affected by different…

The theory, direction, and magnitude of ecosystem fire probability as constrained by precipitation and temperature

Treesearch

Richard Guyette; Michael C. Stambaugh; Daniel Dey; Rose Marie Muzika; Ben Bond-Lamberty

2017-01-01

The effects of climate on wildland fire confronts society across a range of different ecosystems. Water and temperature affect the combustion dynamics, irrespective of whether those are associated with carbon fueled motors or ecosystems, but through different chemical, physical, and biological processes. We use an ecosystem combustion equation developed with the...

Tree harvest in an experimental sand ecosystem: plant effects on nutrient dynamics and solute generation.

Treesearch

C. K. Keller; R. O' Brien; J. R. Havig; J. L. Smith; B. T. Bormann; D. Wang

2006-01-01

The hydrochemical signatures of forested ecosystems are known to be determined by a time-variant combination of physical-hydrologic, geochemical, and biologic processes. We studied subsurface potassium (K), calcium (Ca), and nitrate (NO3) in an experimental red-pine mesocosm to determine how trees affect the behavior of these nutrients in soil...

Identification of Students' Content Mastery and Cognitive and Affective Percepts of a Bioinformatics Miniunit: A Case Study with Recommendations for Teacher Education

ERIC Educational Resources Information Center

Wefer, Stephen H.; Anderson, O. Roger

2008-01-01

Bioinformatics, merging biological data with computer science, is increasingly incorporated into school curricula at all levels. This case study of 10 secondary school students highlights student individual differences (especially the way they processed information and integrated procedural and analytical thought) and summarizes a variety of…

Effects of species biological traits and environmental heterogeneity on simulated tree species distribution shifts under climate change.

PubMed

Wang, Wen J; He, Hong S; Thompson, Frank R; Spetich, Martin A; Fraser, Jacob S

2018-09-01

Demographic processes (fecundity, dispersal, colonization, growth, and mortality) and their interactions with environmental changes are not well represented in current climate-distribution models (e.g., niche and biophysical process models) and constitute a large uncertainty in projections of future tree species distribution shifts. We investigate how species biological traits and environmental heterogeneity affect species distribution shifts. We used a species-specific, spatially explicit forest dynamic model LANDIS PRO, which incorporates site-scale tree species demography and competition, landscape-scale dispersal and disturbances, and regional-scale abiotic controls, to simulate the distribution shifts of four representative tree species with distinct biological traits in the central hardwood forest region of United States. Our results suggested that biological traits (e.g., dispersal capacity, maturation age) were important for determining tree species distribution shifts. Environmental heterogeneity, on average, reduced shift rates by 8% compared to perfect environmental conditions. The average distribution shift rates ranged from 24 to 200myear -1 under climate change scenarios, implying that many tree species may not able to keep up with climate change because of limited dispersal capacity, long generation time, and environmental heterogeneity. We suggest that climate-distribution models should include species demographic processes (e.g., fecundity, dispersal, colonization), biological traits (e.g., dispersal capacity, maturation age), and environmental heterogeneity (e.g., habitat fragmentation) to improve future predictions of species distribution shifts in response to changing climates. Copyright © 2018 Elsevier B.V. All rights reserved.

Zebrafish: A marvel of high-throughput biology for 21st century toxicology.

PubMed

Bugel, Sean M; Tanguay, Robert L; Planchart, Antonio

2014-09-07

The evolutionary conservation of genomic, biochemical and developmental features between zebrafish and humans is gradually coming into focus with the end result that the zebrafish embryo model has emerged as a powerful tool for uncovering the effects of environmental exposures on a multitude of biological processes with direct relevance to human health. In this review, we highlight advances in automation, high-throughput (HT) screening, and analysis that leverage the power of the zebrafish embryo model for unparalleled advances in our understanding of how chemicals in our environment affect our health and wellbeing.

Zebrafish: A marvel of high-throughput biology for 21st century toxicology

PubMed Central

Bugel, Sean M.; Tanguay, Robert L.; Planchart, Antonio

2015-01-01

The evolutionary conservation of genomic, biochemical and developmental features between zebrafish and humans is gradually coming into focus with the end result that the zebrafish embryo model has emerged as a powerful tool for uncovering the effects of environmental exposures on a multitude of biological processes with direct relevance to human health. In this review, we highlight advances in automation, high-throughput (HT) screening, and analysis that leverage the power of the zebrafish embryo model for unparalleled advances in our understanding of how chemicals in our environment affect our health and wellbeing. PMID:25678986

Hypericin-mediated selective photomodification of connective tissues

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

Hovhannisyan, V., E-mail: hovv@phys.ntu.edu.tw; Guo, H. W.; Chen, Y. F., E-mail: yfchen@phys.ntu.edu.tw

2014-12-29

Controllable modification of biological molecules and supramolecular components of connective tissue are important for biophysical and biomedical applications. Through the use of second harmonic generation imaging, two-photon fluorescence microscopy, and spectrofluorimetry, we found that hypericin, a natural pigment, induces photosensitized destruction of collagen fibers but does not affect elastic fibers and lipids in chicken tendon, skin, and blood vessels. We demonstrated the dynamics and efficiency of collagen photomodification and investigated mechanisms of this processes. Our results suggest that hypericin–mediated photoprocesses in biological tissues may be useful in biomedical applications that require selective modification of connective tissues.

Impact of hydrothermalism on the ocean iron cycle

PubMed Central

Resing, Joseph

2016-01-01

As the iron supplied from hydrothermalism is ultimately ventilated in the iron-limited Southern Ocean, it plays an important role in the ocean biological carbon pump. We deploy a set of focused sensitivity experiments with a state of the art global model of the ocean to examine the processes that regulate the lifetime of hydrothermal iron and the role of different ridge systems in governing the hydrothermal impact on the Southern Ocean biological carbon pump. Using GEOTRACES section data, we find that stabilization of hydrothermal iron is important in some, but not all regions. The impact on the Southern Ocean biological carbon pump is dominated by poorly explored southern ridge systems, highlighting the need for future exploration in this region. We find inter-basin differences in the isopycnal layer onto which hydrothermal Fe is supplied between the Atlantic and Pacific basins, which when combined with the inter-basin contrasts in oxidation kinetics suggests a muted influence of Atlantic ridges on the Southern Ocean biological carbon pump. Ultimately, we present a range of processes, operating at distinct scales, that must be better constrained to improve our understanding of how hydrothermalism affects the ocean cycling of iron and carbon. This article is part of the themed issue ‘Biological and climatic impacts of ocean trace element chemistry’. PMID:29035256

Impact of hydrothermalism on the ocean iron cycle.

PubMed

Tagliabue, Alessandro; Resing, Joseph

2016-11-28

As the iron supplied from hydrothermalism is ultimately ventilated in the iron-limited Southern Ocean, it plays an important role in the ocean biological carbon pump. We deploy a set of focused sensitivity experiments with a state of the art global model of the ocean to examine the processes that regulate the lifetime of hydrothermal iron and the role of different ridge systems in governing the hydrothermal impact on the Southern Ocean biological carbon pump. Using GEOTRACES section data, we find that stabilization of hydrothermal iron is important in some, but not all regions. The impact on the Southern Ocean biological carbon pump is dominated by poorly explored southern ridge systems, highlighting the need for future exploration in this region. We find inter-basin differences in the isopycnal layer onto which hydrothermal Fe is supplied between the Atlantic and Pacific basins, which when combined with the inter-basin contrasts in oxidation kinetics suggests a muted influence of Atlantic ridges on the Southern Ocean biological carbon pump. Ultimately, we present a range of processes, operating at distinct scales, that must be better constrained to improve our understanding of how hydrothermalism affects the ocean cycling of iron and carbon.This article is part of the themed issue 'Biological and climatic impacts of ocean trace element chemistry'. © 2016 The Author(s).

Ocean Biological Pump Sensitivities and Implications for Climate Change Impacts

NASA Technical Reports Server (NTRS)

Romanou, Anastasia

2013-01-01

The ocean is one of the principal reservoirs of CO2, a greenhouse gas, and therefore plays a crucial role in regulating Earth's climate. Currently, the ocean sequesters about a third of anthropogenic CO2 emissions, mitigating the human impact on climate. At the same time, the deeper ocean represents the largest carbon pool in the Earth System and processes that describe the transfer of carbon from the surface of the ocean to depth are intimately linked to the effectiveness of carbon sequestration.The ocean biological pump (OBP), which involves several biogeochemical processes, is a major pathway for transfer of carbon from the surface mixed layer into the ocean interior. About 75 of the carbon vertical gradient is due to the carbon pump with only 25 attributed to the solubility pump. However, the relative importance and role of the two pumps is poorly constrained. OBP is further divided to the organic carbon pump (soft tissue pump) and the carbonate pump, with the former exporting about 10 times more carbon than the latter through processes like remineralization.Major uncertainties about OBP, and hence in the carbon uptake and sequestration, stem from uncertainties in processes involved in OBP such as particulate organicinorganic carbon sinkingsettling, remineralization, microbial degradation of DOC and uptakegrowth rate changes of the ocean biology. The deep ocean is a major sink of atmospheric CO2 in scales of hundreds to thousands of years, but how the export efficiency (i.e. the fraction of total carbon fixation at the surface that is transported at depth) is affected by climate change remains largely undetermined. These processes affect the ocean chemistry (alkalinity, pH, DIC, particulate and dissolved organic carbon) as well as the ecology (biodiversity, functional groups and their interactions) in the ocean. It is important to have a rigorous, quantitative understanding of the uncertainties involved in the observational measurements, the models and the projections of future changes.

Comprehensive Expression Profiling and Functional Network Analysis of Porphyra-334, One Mycosporine-Like Amino Acid (MAA), in Human Keratinocyte Exposed with UV-radiation.

PubMed

Suh, Sung-Suk; Lee, Sung Gu; Youn, Ui Joung; Han, Se Jong; Kim, Il-Chan; Kim, Sanghee

2017-06-24

Mycosporine-like amino acids (MAAs) have been highlighted as pharmacologically active secondary compounds to protect cells from harmful UV-radiation by absorbing its energy. Previous studies have mostly focused on characterizing their physiological properties such as antioxidant activity and osmotic regulation. However, molecular mechanisms underlying their UV-protective capability have not yet been revealed. In the present study, we investigated the expression profiling of porphyra-334-modulated genes or microRNA (miRNAs) in response to UV-exposure and their functional networks, using cDNA and miRNAs microarray. Based on our data, we showed that porphyra-334-regulated genes play essential roles in UV-affected biological processes such as Wnt (Wingless/integrase-1) and Notch pathways which exhibit antagonistic relationship in various biological processes; the UV-repressed genes were in the Wnt signaling pathway, while the activated genes were in the Notch signaling. In addition, porphyra-334-regulated miRNAs can target many genes related with UV-mediated biological processes such as apoptosis, cell proliferation and translational elongation. Notably, we observed that functional roles of the target genes for up-regulated miRNAs are inversely correlated with those for down-regulated miRNAs; the former genes promote apoptosis and translational elongation, whereas the latter function as inhibitors in these processes. Taken together, these data suggest that porphyra-334 protects cells from harmful UV radiation through the comprehensive modulation of expression patterns of genes involved in UV-mediated biological processes, and that provide a new insight to understand its functional molecular networks.

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.

Global Change: A Biogeochemical Perspective

NASA Technical Reports Server (NTRS)

Mcelroy, M.

1983-01-01

A research program that is designed to enhance our understanding of the Earth as the support system for life is described. The program change, both natural and anthropogenic, that might affect the habitability of the planet on a time scale roughly equal to that of a human life is studied. On this time scale the atmosphere, biosphere, and upper ocean are treated as a single coupled system. The need for understanding the processes affecting the distribution of essential nutrients--carbon, nitrogen, phosphorous, sulfur, and water--within this coupled system is examined. The importance of subtle interactions among chemical, biological, and physical effects is emphasized. The specific objectives are to define the present state of the planetary life-support system; to ellucidate the underlying physical, chemical, and biological controls; and to provide the body of knowledge required to assess changes that might impact the future habitability of the Earth.

Factors Affecting Wound Healing

PubMed Central

Guo, S.; DiPietro, L.A.

2010-01-01

Wound healing, as a normal biological process in the human body, is achieved through four precisely and highly programmed phases: hemostasis, inflammation, proliferation, and remodeling. For a wound to heal successfully, all four phases must occur in the proper sequence and time frame. Many factors can interfere with one or more phases of this process, thus causing improper or impaired wound healing. This article reviews the recent literature on the most significant factors that affect cutaneous wound healing and the potential cellular and/or molecular mechanisms involved. The factors discussed include oxygenation, infection, age and sex hormones, stress, diabetes, obesity, medications, alcoholism, smoking, and nutrition. A better understanding of the influence of these factors on repair may lead to therapeutics that improve wound healing and resolve impaired wounds. PMID:20139336

Factors affecting wound healing.

PubMed

Guo, S; Dipietro, L A

2010-03-01

Wound healing, as a normal biological process in the human body, is achieved through four precisely and highly programmed phases: hemostasis, inflammation, proliferation, and remodeling. For a wound to heal successfully, all four phases must occur in the proper sequence and time frame. Many factors can interfere with one or more phases of this process, thus causing improper or impaired wound healing. This article reviews the recent literature on the most significant factors that affect cutaneous wound healing and the potential cellular and/or molecular mechanisms involved. The factors discussed include oxygenation, infection, age and sex hormones, stress, diabetes, obesity, medications, alcoholism, smoking, and nutrition. A better understanding of the influence of these factors on repair may lead to therapeutics that improve wound healing and resolve impaired wounds.

Soluble microbial products (SMPs) release in activated sludge systems: a review

PubMed Central

2012-01-01

This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as “the pool of organic compounds that are released into solution from substrate metabolism and biomass decay”'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process. PMID:23369231

Soluble microbial products (SMPs) release in activated sludge systems: a review.

PubMed

Azami, Hamed; Sarrafzadeh, Mohammad Hossein; Mehrnia, Mohammad Reza

2012-12-18

This review discusses the characterization, production and implications of soluble microbial products (SMPs) in biological wastewater treatment. The precise definition of SMPs is open to talk about, but is currently regarded as "the pool of organic compounds that are released into solution from substrate metabolism and biomass decay"'. Some of the SMPs have been identified as humic acids, polysaccharides, proteins, amino acids, antibiotics, extracellular enzymes and structural components of cells and products of energy metabolism. They adversely affect the kinetic activity, flocculating and settling properties of sludge. This review outlines some important findings with regard to biodegradability and treatability of SMPs and also the effect of process parameters on their production. As SMPs are produced during biological treatment process, their trace amounts normally remain in the effluent that defines the highest COD removal efficiency. Their presence in effluent represents a high potential risk of toxic by-product formation during chlorine disinfection. Studies have indicated that among all wastewater post-treatment processes, the adsorption by granular activated carbon combined with biologically induced degradation is the most effective method for removal of SMPs. However, it may be concludes that the knowledge regarding SMPs is still under progress and more work is required to fully understand their contribution to the treatment process.

Biohydrogen Production: Strategies to Improve Process Efficiency through Microbial Routes

PubMed Central

Chandrasekhar, Kuppam; Lee, Yong-Jik; Lee, Dong-Woo

2015-01-01

The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H2), a clean energy carrier with high-energy yields; upon the combustion of H2, H2O is the only major by-product. In recent decades, the attractive and renewable characteristics of H2 led us to develop a variety of biological routes for the production of H2. Based on the mode of H2 generation, the biological routes for H2 production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H2. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications. PMID:25874756

Biohydrogen production: strategies to improve process efficiency through microbial routes.

PubMed

Chandrasekhar, Kuppam; Lee, Yong-Jik; Lee, Dong-Woo

2015-04-14

The current fossil fuel-based generation of energy has led to large-scale industrial development. However, the reliance on fossil fuels leads to the significant depletion of natural resources of buried combustible geologic deposits and to negative effects on the global climate with emissions of greenhouse gases. Accordingly, enormous efforts are directed to transition from fossil fuels to nonpolluting and renewable energy sources. One potential alternative is biohydrogen (H2), a clean energy carrier with high-energy yields; upon the combustion of H2, H2O is the only major by-product. In recent decades, the attractive and renewable characteristics of H2 led us to develop a variety of biological routes for the production of H2. Based on the mode of H2 generation, the biological routes for H2 production are categorized into four groups: photobiological fermentation, anaerobic fermentation, enzymatic and microbial electrolysis, and a combination of these processes. Thus, this review primarily focuses on the evaluation of the biological routes for the production of H2. In particular, we assess the efficiency and feasibility of these bioprocesses with respect to the factors that affect operations, and we delineate the limitations. Additionally, alternative options such as bioaugmentation, multiple process integration, and microbial electrolysis to improve process efficiency are discussed to address industrial-level applications.

Biological Oceanography

NASA Technical Reports Server (NTRS)

Abbott, M. R.

1984-01-01

Within the framework of global biogeochemical cycles and ocean productivity, there are two areas that will be of particular interest to biological oceanography in the 1990s. The first is the mapping in space time of the biomass and productivity of phytoplankton in the world ocean. The second area is the coupling of biological and physical processes as it affects the distribution and growth rate of phytoplankton biomass. Certainly other areas will be of interest to biological oceanographers, but these two areas are amenable to observations from satellites. Temporal and spatial variability is a regular feature of marine ecosystems. The temporal and spatial variability of phytoplankton biomass and productivity which is ubiquitous at all time and space scales in the ocean must be characterized. Remote sensing from satellites addresses these problems with global observations of mesocale (2 to 20 days, 10 to 200 km) features over a long period of time.

Culture and biology in the origins of linguistic structure.

PubMed

Kirby, Simon

2017-02-01

Language is systematically structured at all levels of description, arguably setting it apart from all other instances of communication in nature. In this article, I survey work over the last 20 years that emphasises the contributions of individual learning, cultural transmission, and biological evolution to explaining the structural design features of language. These 3 complex adaptive systems exist in a network of interactions: individual learning biases shape the dynamics of cultural evolution; universal features of linguistic structure arise from this cultural process and form the ultimate linguistic phenotype; the nature of this phenotype affects the fitness landscape for the biological evolution of the language faculty; and in turn this determines individuals' learning bias. Using a combination of computational simulation, laboratory experiments, and comparison with real-world cases of language emergence, I show that linguistic structure emerges as a natural outcome of cultural evolution once certain minimal biological requirements are in place.

Sources and sinks of plastic debris in estuaries: A conceptual model integrating biological, physical and chemical distribution mechanisms.

PubMed

Vermeiren, Peter; Muñoz, Cynthia C; Ikejima, Kou

2016-12-15

Micro- and macroplastic accumulation threatens estuaries worldwide because of the often dense human populations, diverse plastic inputs and high potential for plastic degradation and storage in these ecosystems. Nonetheless, our understanding of plastic sources and sinks remains limited. We designed conceptual models of the local and estuary-wide transport of plastics. We identify processes affecting the position of plastics in the water column; processes related to the mixing of fresh and salt water; and processes resulting from the influences of wind, topography, and organism-plastic interactions. The models identify gaps in the spatial context of plastic-organisms interactions, the chemical behavior of plastics in estuaries, effects of wind on plastic suspension-deposition cycles, and the relative importance of processes affecting the position in the water column. When interpreted in the context of current understanding, sinks with high management potential can be identified. However, source-sink patterns vary among estuary types and with local scale processes. Copyright © 2016 Elsevier Ltd. All rights reserved.

Gendering Genetics: Biological Contingencies in the Protective Effects of Social Integration for Men and Women.

PubMed

Perry, Brea L

2016-05-01

Evidence that social and biological processes are intertwined in producing health and human behavior is rapidly accumulating. Using a feminist approach, this research explores how gender moderates the interaction between biological processes and men's and women's behavioral and emotional responses to similar social environments. Using data from the Collaborative Study on the Genetics of Alcoholism, the influence of gender, social integration, and genetic risk on nicotine and alcohol dependence is examined. Three-way interaction models reveal gender-specific moderation of interactions between genetic risk score and social integration. Namely, being currently married and reporting positive social psychological integration are predictive of reduced risk of nicotine dependence among men with genetic susceptibility to strong nicotine cravings in the presence of social cues like stress. In contrast, the protective effects of marital status and social integration are substantially attenuated and absent, respectively, among women with high-risk genotypes. This pattern reflects the dualism (i.e., simultaneous costs and benefits) inherent in social integration for women, which may disproportionately affect those with a genetic sensitivity to stress. These findings contest the notion of genotype as static biological hardwiring that is independent from social and cultural systems of gender difference.

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.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Do Social Ties Affect Our Health? Exploring the Biology of Relationships

MedlinePlus

... Do Social Ties Affect Our Health? Exploring the Biology of Relationships En español Send us your comments ... neighbors, or others, social connections can influence our biology and well-being. Wide-ranging research suggests that ...

Bioactive Compounds of Blueberries: Post-Harvest Factors Influencing the Nutritional Value of Products

PubMed Central

Michalska, Anna; Łysiak, Grzegorz

2015-01-01

Blueberries, besides having commonly-recognized taste properties, are also a valuable source of health-promoting bioactive compounds. For several decades, blueberries have gained in popularity all over the world, and recent years have seen not only an increase in fresh consumption, but also in the importance of blueberries for the processing industry. Blueberry processing mostly consists of freezing and juicing. Recently, more attention has been drawn to dewatering and drying, which are promising areas for developing novel blueberry products. Processing affects each biologically-active compound in a different way, and it is still unknown what changes those compounds undergo at the molecular level after the application of different processing technologies. This work presents the most recent state of knowledge about the pre-treatment and processing methods applied to blueberries and their influence on the content of biologically-active compounds. The presentation of methods is preceded by a brief overview of the characteristics of the blueberry species, a description of the chemical composition of the fruit and a short note about the main growing areas, production volumes and the management of fruit crops. PMID:26266408

Bioactive Compounds of Blueberries: Post-Harvest Factors Influencing the Nutritional Value of Products.

PubMed

Michalska, Anna; Łysiak, Grzegorz

2015-08-10

Blueberries, besides having commonly-recognized taste properties, are also a valuable source of health-promoting bioactive compounds. For several decades, blueberries have gained in popularity all over the world, and recent years have seen not only an increase in fresh consumption, but also in the importance of blueberries for the processing industry. Blueberry processing mostly consists of freezing and juicing. Recently, more attention has been drawn to dewatering and drying, which are promising areas for developing novel blueberry products. Processing affects each biologically-active compound in a different way, and it is still unknown what changes those compounds undergo at the molecular level after the application of different processing technologies. This work presents the most recent state of knowledge about the pre-treatment and processing methods applied to blueberries and their influence on the content of biologically-active compounds. The presentation of methods is preceded by a brief overview of the characteristics of the blueberry species, a description of the chemical composition of the fruit and a short note about the main growing areas, production volumes and the management of fruit crops.

Subcortical encoding of sound is enhanced in bilinguals and relates to executive function advantages

PubMed Central

Krizman, Jennifer; Marian, Viorica; Shook, Anthony; Skoe, Erika; Kraus, Nina

2012-01-01

Bilingualism profoundly affects the brain, yielding functional and structural changes in cortical regions dedicated to language processing and executive function [Crinion J, et al. (2006) Science 312:1537–1540; Kim KHS, et al. (1997) Nature 388:171–174]. Comparatively, musical training, another type of sensory enrichment, translates to expertise in cognitive processing and refined biological processing of sound in both cortical and subcortical structures. Therefore, we asked whether bilingualism can also promote experience-dependent plasticity in subcortical auditory processing. We found that adolescent bilinguals, listening to the speech syllable [da], encoded the stimulus more robustly than age-matched monolinguals. Specifically, bilinguals showed enhanced encoding of the fundamental frequency, a feature known to underlie pitch perception and grouping of auditory objects. This enhancement was associated with executive function advantages. Thus, through experience-related tuning of attention, the bilingual auditory system becomes highly efficient in automatically processing sound. This study provides biological evidence for system-wide neural plasticity in auditory experts that facilitates a tight coupling of sensory and cognitive functions. PMID:22547804

Method Designed to Respect Molecular Heterogeneity Can Profoundly Correct Present Data Interpretations for Genome-Wide Expression Analysis

PubMed Central

Chen, Chih-Hao; Hsu, Chueh-Lin; Huang, Shih-Hao; Chen, Shih-Yuan; Hung, Yi-Lin; Chen, Hsiao-Rong; Wu, Yu-Chung

2015-01-01

Although genome-wide expression analysis has become a routine tool for gaining insight into molecular mechanisms, extraction of information remains a major challenge. It has been unclear why standard statistical methods, such as the t-test and ANOVA, often lead to low levels of reproducibility, how likely applying fold-change cutoffs to enhance reproducibility is to miss key signals, and how adversely using such methods has affected data interpretations. We broadly examined expression data to investigate the reproducibility problem and discovered that molecular heterogeneity, a biological property of genetically different samples, has been improperly handled by the statistical methods. Here we give a mathematical description of the discovery and report the development of a statistical method, named HTA, for better handling molecular heterogeneity. We broadly demonstrate the improved sensitivity and specificity of HTA over the conventional methods and show that using fold-change cutoffs has lost much information. We illustrate the especial usefulness of HTA for heterogeneous diseases, by applying it to existing data sets of schizophrenia, bipolar disorder and Parkinson’s disease, and show it can abundantly and reproducibly uncover disease signatures not previously detectable. Based on 156 biological data sets, we estimate that the methodological issue has affected over 96% of expression studies and that HTA can profoundly correct 86% of the affected data interpretations. The methodological advancement can better facilitate systems understandings of biological processes, render biological inferences that are more reliable than they have hitherto been and engender translational medical applications, such as identifying diagnostic biomarkers and drug prediction, which are more robust. PMID:25793610

Evaluation of the simultaneous removal of recalcitrant drugs (bezafibrate, gemfibrozil, indomethacin and sulfamethoxazole) and biodegradable organic matter from synthetic wastewater by electro-oxidation coupled with a biological system.

PubMed

Rodríguez-Nava, Odín; Ramírez-Saad, Hugo; Loera, Octavio; González, Ignacio

2016-12-01

Pharmaceutical degradation in conventional wastewater treatment plants (WWTP) represents a challenge since municipal wastewater and hospital effluents contain pharmaceuticals in low concentrations (recalcitrant and persistent in WWTP) and biodegradable organic matter (BOM) is the main pollutant. This work shows the feasibility of coupling electro-oxidation with a biological system for the simultaneous removal of recalcitrant drugs (bezafibrate, gemfibrozil, indomethacin and sulfamethoxazole (BGIS)) and BOM from wastewater. High removal efficiencies were attained without affecting the performance of activated sludge. BGIS degradation was performed by advanced electrochemical oxidation and the activated sludge process for BOM degradation in a continuous reactor. The selected electrochemical parameters from microelectrolysis tests (1.2 L s(-1) and 1.56 mA cm(-2)) were maintained to operate a filter press laboratory reactor FM01-LC using boron-doped diamond as the anode. The low current density was chosen in order to remove drugs without decreasing BOM and chlorine concentration control, so as to avoid bulking formation in the biological process. The wastewater previously treated by FM01-LC was fed directly (without chemical modification) to the activated sludge reactor to remove 100% of BGIS and 83% of BOM; conversely, the BGIS contained in wastewater without electrochemical pre-treatment were persistent in the biological process and promoted bulking formation.

Classical biological control of an invasive forest pest: a world perspective of the management of Sirex noctilio using the parasitoid Ibalia leucospoides (Hymenoptera: Ibaliidae).

PubMed

Fischbein, D; Corley, J C

2015-02-01

Classical biological control is a key method for managing populations of pests in long-lived crops such as plantation forestry. The execution of biological control programmes in general, as the evaluation of potential natural enemies remains, to a large extent, an empirical endeavour. Thus, characterizing specific cases to determine patterns that may lead to more accurate predictions of success is an important goal of the much applied ecological research. We review the history of introduction, ecology and behaviour of the parasitoid Ibalia leucospoides. The species is a natural enemy of Sirex noctilio, one of the most important pests of pine afforestation worldwide. We use an invasion ecology perspective given the analogy between the main stages involved in classical biological control and the biological invasion processes. We conclude that success in the establishment, a common reason of failure in biocontrol, is not a limiting factor of success by I. leucospoides. A mismatch between the spread capacity of the parasitoid and that of its host could nevertheless affect control at a regional scale. In addition, we suggest that given its known life history traits, this natural enemy may be a better regulator than suppressor of the host population. Moreover, spatial and temporal refuges of the host population that may favour the local persistence of the interaction probably reduce the degree to which S. noctilio population is suppressed by the parasitoid. We emphasize the fact that some of the biological attributes that promote establishment may negatively affect suppression levels achieved. Studies on established non-native pest-parasitoid interactions may contribute to defining selection criteria for classical biological control which may prove especially useful in integrated pest management IPM programmes of invasive forest insects.

Astrobiological stoichiometry.

PubMed

Young, Patrick A; Desch, Steven J; Anbar, Ariel D; Barnes, Rory; Hinkel, Natalie R; Kopparapu, Ravikumar; Madhusudhan, Nikku; Monga, Nikhil; Pagano, Michael D; Riner, Miriam A; Scannapieco, Evan; Shim, Sang-Heon; Truitt, Amanda

2014-07-01

Chemical composition affects virtually all aspects of astrobiology, from stellar astrophysics to molecular biology. We present a synopsis of the research results presented at the "Stellar Stoichiometry" Workshop Without Walls hosted at Arizona State University April 11-12, 2013, under the auspices of the NASA Astrobiology Institute. The results focus on the measurement of chemical abundances and the effects of composition on processes from stellar to planetary scales. Of particular interest were the scientific connections between processes in these normally disparate fields. Measuring the abundances of elements in stars and giant and terrestrial planets poses substantial difficulties in technique and interpretation. One of the motivations for this conference was the fact that determinations of the abundance of a given element in a single star by different groups can differ by more than their quoted errors. The problems affecting the reliability of abundance estimations and their inherent limitations are discussed. When these problems are taken into consideration, self-consistent surveys of stellar abundances show that there is still substantial variation (factors of ∼ 2) in the ratios of common elements (e.g., C, O, Na, Al, Mg, Si, Ca) important in rock-forming minerals, atmospheres, and biology. We consider how abundance variations arise through injection of supernova nucleosynthesis products into star-forming material and through photoevaporation of protoplanetary disks. The effects of composition on stellar evolution are substantial, and coupled with planetary atmosphere models can result in predicted habitable zone extents that vary by many tens of percent. Variations in the bulk composition of planets can affect rates of radiogenic heating and substantially change the mineralogy of planetary interiors, affecting properties such as convection and energy transport.

The importance of trace element speciation in biomedical science.

PubMed

Templeton, Douglas M

2003-04-01

According to IUPAC terminology, trace element speciation reflects differences in chemical composition at multiple levels from nuclear and electronic structure to macromolecular complexation. In the medical sciences, all levels of composition are important in various circumstances, and each can affect the bioavailability, distribution, physiological function, toxicity, diagnostic utility, and therapeutic potential of an element. Here we discuss, with specific examples, three biological principles in the intimate relation between speciation and biological behavior: i) the kinetics of interconversion of species determines distribution within the organism, ii) speciation governs transport across various biological barriers, and iii) speciation can limit potentially undesirable interactions between physiologically essential elements. We will also describe differences in the speciation of iron in states of iron overload, to illustrate how speciation analysis can provide insight into cellular processes in human disease.

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...

Daily Landsat-scale evapotranspiration estimation over a forested landscape in North Carolina, USA, using multi-satellite data fusion

Treesearch

Yun Yang; Martha C. Anderson; Feng Gao; Christopher R. Hain; Kathryn A. Semmens; William P. Kustas; Asko Noormets; Randolph H. Wynne; Valerie A. Thomas; Ge Sun

2017-01-01

As a primary flux in the global water cycle, evapotranspiration (ET) connects hydrologic and biological processes and is directly affected by water and land management, land use change and climate variability. Satellite remote sensing provides an effective means for diagnosing ET patterns over heterogeneous landscapes; however, limitations on the spatial and temporal...

Tensegrity II. How structural networks influence cellular information processing networks

NASA Technical Reports Server (NTRS)

Ingber, Donald E.

2003-01-01

The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

Autophagy and its effects: making sense of double-edged swords.

PubMed

Thorburn, Andrew

2014-10-01

Autophagy is the mechanism by which cellular material is delivered to lysosomes and degraded. This process has become a major focus of biological and biomedical research with thousands of papers published each year and rapidly growing appreciation that autophagy affects many normal and pathological processes. However, as we learn more about this evolutionarily ancient process, we are discovering that autophagy's effects may work for both the good and the bad of an organism. Here, I discuss some of these context-dependent findings and how, as we make sense of them, we can try to apply our knowledge for practical purposes.

Towards a heterarchical approach to biology and cognition.

PubMed

Bruni, Luis Emilio; Giorgi, Franco

2015-12-01

In this article we challenge the pervasive notion of hierarchy in biological and cognitive systems and delineate the basis for a complementary heterarchical approach starting from the seminal ideas of Warren McCullock and Gregory Bateson. We intend these considerations as a contribution to the different scientific disciplines working towards a multilevel integrative perspective of biological and cognitive processes, such as systems and integrative biology and neuroscience, social and cultural neuroscience, social signal transduction and psychoneuroimmunology, for instance. We argue that structures and substrates are by necessity organized hierarchically, while communication processes - and their embeddedness - are rather organized heterarchically. Before getting into the implications of the heterarchical approach and its congeniality with the semiotic perspective to biology and cognition, we introduce a set of notions and concepts in order to advance a framework that considers the heterarchical embeddedness of different layers of physiological, behavioral, affective, cognitive, technological and socio-cultural levels implicit in networks of interacting minds, considering the dynamic complementarity of bottom-up and top-down causal links. This should contribute to account for the integration, interpretation and response to complex aggregates of information at different levels of organization in a developmental context. We illustrate the dialectical nature of embedded heterarchical processes by addressing the simultaneity and circularity of cognition and volition, and how such dialectics can be present in primitive instances of proto-cognition and proto-volition, giving rise to our claim that subjectivity and semiotic freedom are scalar properties. We collate the framework with recent empirical systemic approaches to biology and integrative neuroscience, and conclude with a reflection on its implications to the understanding of the emergence of pathological conditions in multi-level semiotic systems. Copyright © 2015. Published by Elsevier Ltd.

Dietary modification of brain function: effects on neuroendocrine and psychological determinants of mental health- and stress-related disorders.

PubMed

Waladkhani, A R; Hellhammer, J

2008-01-01

Stress is associated with both psychological and biological adaptation. Chronic stress, however, impairs adaptation, and may finally lead to illness, in part through unhealthy changes in nutritional behavior. This chapter shows how physiological and psychological stress responses are affected by different food ingredients, and how stress affects health behavior, for example food choice. It becomes obvious that nutrition is closely linked to food choice and that food ingredients affect a broad range of neuroendocrine and related psychological processes, which regulate adaptation to chronic stress. Thus, dietary modification may become a valuable tool to modify the susceptibility to stress and stress-related disorders.

Maximum Drawdown of Atmospheric CO2 due to Biological Uptake in the Ocean and the Ocean Temperature Effect

NASA Astrophysics Data System (ADS)

Odalen, M.; Nycander, J.; Oliver, K. I. C.; Nilsson, J.; Brodeau, L.; Ridgwell, A.

2016-02-01

During glacials, atmospheric CO2 is significantly lowered; the decrease is about 1/3 or 90 ppm during the last four glacial cycles. Since the ocean reservoir of carbon, and hence the ocean capacity for storing carbon, is substantially larger than the atmospheric and terrestrial counterparts, it is likely that this lowering was caused by ocean processes, drawing the CO2 into the deep ocean. The Southern Ocean circulation and biological efficiency are widely accepted as having played an important part in this CO2 drawdown. However, the relative effects of different processes contributing to this oceanic uptake have not yet been well constrained. In this work, we focus on better constraining two of these processes; 1) the effect of increased efficiency of the biological carbon uptake, and 2) the effect of changes in global mean ocean temperature on the abiotic ocean-atmosphere CO2 equilibrium. By performing ensemble runs using an Earth System Model of Intermediate Complexity (EMIC) we examine the changes in atmospheric pCO2 achieved by 100% nutrient utilization efficiency of biology. The simulations display different ocean circulation patterns and hence different global ocean mean temperatures. By restoring the atmospheric pCO2 to a target value during the spin-up phase, the total carbon content differs between each of the ensemble members. The difference is due to circulation having direct effects on biology, but also on global ocean mean temperature, changing the solubility of CO2. This study reveals the relative importance of of the processes 1 and 2 (mentioned above) for atmospheric pCO2 in a changed climate. The results of this study also show that a difference in carbon content after spin-up can have a significant effect on the drawdown potential of a maximised biological efficiency. Thus, the choice of spin-up characteristics in a model study of climate change CO2 dynamics may significantly affect the outcome of the study.

Can modular psychological concepts like affect and emotion be assigned to a distinct subset of regional neural circuits?. Comment on "The quartet theory of human emotions: An integrative and neurofunctional model" by S. Koelsch et al.

NASA Astrophysics Data System (ADS)

Fehr, Thorsten; Herrmann, Manfred

2015-06-01

The proposed Quartet Theory of Human Emotions by Koelsch and co-workers [11] adumbrates evidence from various scientific sources to integrate and assign the psychological concepts of 'affect' and 'emotion' to four brain circuits or to four neuronal core systems for affect-processing in the brain. The authors differentiate between affect and emotion and assign several facultative, or to say modular, psychological domains and principles of information processing, such as learning and memory, antecedents of affective activity, emotion satiation, cognitive complexity, subjective quality feelings, degree of conscious appraisal, to different affect systems. Furthermore, they relate orbito-frontal brain structures to moral affects as uniquely human, and the hippocampus to attachment-related affects. An additional feature of the theory describes 'emotional effector-systems' for motor-related processes (e.g., emotion-related actions), physiological arousal, attention and memory that are assumed to be cross-linked with the four proposed affect systems. Thus, higher principles of emotional information processing, but also modular affect-related issues, such as moral and attachment related affects, are thought to be handled by these four different physiological sub-systems that are on the other side assumed to be highly interwoven at both physiological and functional levels. The authors also state that the proposed sub-systems have many features in common, such as the selection and modulation of biological processes related to behaviour, perception, attention and memory. The latter aspect challenges an ongoing discussion about the mind-body problem: To which degree do the proposed sub-systems 'sufficiently' cover the processing of complex modular or facultative emotional/affective and/or cognitive phenomena? There are current models and scientific positions that almost completely reject the idea that modular psychological phenomena are handled by a distinct selection of regional brain systems or neural modules, but rather suggest highly complex and cross-linked neural networks individually shaped by livelong learning and experience [e.g., 6,7,10,13]. This holds in particular true for complex emotional phenomena such as aggression or empathy in social interaction [8,13]. It thus remains questionable, whether - beyond primary sensory and motor-processing - a small number of modular sub-systems sufficiently cover the organisation of specific phenomenological and social features of perception and behaviour [7,10].

Harnessing the apoptotic programs in cancer stem-like cells

PubMed Central

Wang, Ying-Hua; Scadden, David T

2015-01-01

Elimination of malignant cells is an unmet challenge for most human cancer types even with therapies targeting specific driver mutations. Therefore, a multi-pronged strategy to alter cancer cell biology on multiple levels is increasingly recognized as essential for cancer cure. One such aspect of cancer cell biology is the relative apoptosis resistance of tumor-initiating cells. Here, we provide an overview of the mechanisms affecting the apoptotic process in tumor cells emphasizing the differences in the tumor-initiating or stem-like cells of cancer. Further, we summarize efforts to exploit these differences to design therapies targeting that important cancer cell population. PMID:26253117

Non-thermal plasma activates human keratinocytes by stimulation of antioxidant and phase II pathways.

PubMed

Schmidt, Anke; Dietrich, Stephan; Steuer, Anna; Weltmann, Klaus-Dieter; von Woedtke, Thomas; Masur, Kai; Wende, Kristian

2015-03-13

Non-thermal atmospheric pressure plasma provides a novel therapeutic opportunity to control redox-based processes, e.g. wound healing, cancer, and inflammatory diseases. By spatial and time-resolved delivery of reactive oxygen and nitrogen species, it allows stimulation or inhibition of cellular processes in biological systems. Our data show that both gene and protein expression is highly affected by non-thermal plasma. Nuclear factor erythroid-related factor 2 (NRF2) and phase II enzyme pathway components were found to act as key controllers orchestrating the cellular response in keratinocytes. Additionally, glutathione metabolism, which is a marker for NRF2-related signaling events, was affected. Among the most robustly increased genes and proteins, heme oxygenase 1, NADPH-quinone oxidoreductase 1, and growth factors were found. The roles of NRF2 targets, investigated by siRNA silencing, revealed that NRF2 acts as an important switch for sensing oxidative stress events. Moreover, the influence of non-thermal plasma on the NRF2 pathway prepares cells against exogenic noxae and increases their resilience against oxidative species. Via paracrine mechanisms, distant cells benefit from cell-cell communication. The finding that non-thermal plasma triggers hormesis-like processes in keratinocytes facilitates the understanding of plasma-tissue interaction and its clinical application. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

Slowly switching between environments facilitates reverse evolution in small populations

NASA Astrophysics Data System (ADS)

Tan, Longzhi; Gore, Jeff

2011-03-01

The rate at which a physical process occurs usually changes the behavior of a system. In thermodynamics, the reversibility of a process generally increases when it occurs at an infinitely slow rate. In biological evolution, adaptations to a new environment may be reversed by evolution in the ancestral environment. Such fluctuating environments are ubiquitous in nature, although how the rate of switching affects reverse evolution is unknown. Here we use a computational approach to quantify evolutionary reversibility as a function of the rate of switching between two environments. For small population sizes, which travel on landscapes as random walkers, we find that both genotypic and phenotypic reverse evolution increase at slow switching rates. However, slow switching of environments decreases evolutionary reversibility for a greedy walker, corresponding to large populations (extensive clonal interference). We conclude that the impact of the switching rate for biological evolution is more complicated than other common physical processes, and that a quantitative approach may yield significant insight into reverse evolution.

Albumin microspheres as an ocular delivery system for pilocarpine nitrate.

PubMed

Rathod, Sudha; Deshpande, S G

2008-01-01

Pilocarpine nitrate loaded egg albumin microspheres were prepared by thermal denaturation process in the size range of 1-12 mum. A series of batches were prepared to study factors, which may affect the size and entrapment efficiency of drug in microspheres and optimized the process. Drug loaded microspheres so obtained were evaluated for their size, entrapment efficiency, release rate and biological response. Electron photomicrographs were taken (8000X) to study the morphological characteristics of microspheres. The entrapment and encapsulation of pilocarpine after process optimization was found to be 82.63% and 62.5% respectively. In vitro dissolution rate studies revealed that the release of drug from the microspheres followed spherical matrix mechanism. Biological response of microspheric suspension was measured by reduction in intraocular pressure in albino rabbit eyes and compared with marketed eye drops. Various pharmacokinetic parameters viz. onset of action, duration of action, Tmax and AUC were studied. A measurable difference was found in the mean miotic response, duration and AUC of pilocarpine nitrate microspheric suspension.

Parameters affecting the photocatalytic degradation of dyes using TiO2: a review

NASA Astrophysics Data System (ADS)

Reza, Khan Mamun; Kurny, ASW; Gulshan, Fahmida

2017-07-01

Traditional chemical, physical and biological processes for treating wastewater containing textile dye have such disadvantages as high cost, high energy requirement and generation of secondary pollution during treatment process. The advanced oxidation processes technology has been attracting growing attention for the decomposition of organic dyes. Such processes are based on the light-enhanced generation of highly reactive hydroxyl radicals, which oxidize the organic matter in solution and convert it completely into water, CO2 and inorganic compounds. In this presentation, the photocatalytic degradation of dyes in aqueous solution using TiO2 as photocatalyst under solar and UV irradiation has been reviewed. It is observed that the degradation of dyes depends on several parameters such as pH, catalyst concentration, substrate concentration and the presence of oxidants. Reaction temperature and the intensity of light also affect the degradation of dyes. Particle size, BET-surface area and different mineral forms of TiO2 also have influence on the degradation rate.

Curriculum in biomedical optics and laser-tissue interactions

NASA Astrophysics Data System (ADS)

Jacques, Steven L.

2003-10-01

A graduate student level curriculum has been developed for teaching the basic principles of how lasers and light interact with biological tissues and materials. The field of Photomedicine can be divided into two topic areas: (1) where tissue affects photons, used for diagnostic sensing, imaging, and spectroscopy of tissues and biomaterials, and (2) where photons affect tissue, used for surgical and therapeutic cutting, dissecting, machining, processing, coagulating, welding, and oxidizing tissues and biomaterials. The courses teach basic principles of tissue optical properties and light transport in tissues, and interaction of lasers and conventional light sources with tissues via photochemical, photothermal and photomechanical mechanisms.

RARE EARTH ELEMENT IMPACTS ON BIOLOGICAL WASTEWATER TREATMENT

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

Fujita, Y.; Barnes, J.; Fox, S.

Increasing demand for rare earth elements (REE) is expected to lead to new development and expansion in industries processing and or recycling REE. For some industrial operators, sending aqueous waste streams to a municipal wastewater treatment plant, or publicly owned treatment works (POTW), may be a cost effective disposal option. However, wastewaters that adversely affect the performance of biological wastewater treatment at the POTW will not be accepted. The objective of our research is to assess the effects of wastewaters that might be generated by new rare earth element (REE) beneficiation or recycling processes on biological wastewater treatment systems. Wemore » have been investigating the impact of yttrium and europium on the biological activity of activated sludge collected from an operating municipal wastewater treatment plant. We have also examined the effect of an organic complexant that is commonly used in REE extraction and separations; similar compounds may be a component of newly developed REE recycling processes. Our preliminary results indicate that in the presence of Eu, respiration rates for the activated sludge decrease relative to the no-Eu controls, at Eu concentrations ranging from <10 to 660 µM. Yttrium appears to inhibit respiration as well, although negative impacts have been observed only at the highest Y amendment level tested (660 µM). The organic complexant appears to have a negative impact on activated sludge activity as well, although results are variable. Ultimately the intent of this research is to help REE industries to develop environmentally friendly and economically sustainable beneficiation and recycling processes.« less

Sterilization by oxygen plasma

NASA Astrophysics Data System (ADS)

Moreira, Adir José; Mansano, Ronaldo Domingues; Andreoli Pinto, Terezinha de Jesus; Ruas, Ronaldo; Zambon, Luis da Silva; da Silva, Mônica Valero; Verdonck, Patrick Bernard

2004-07-01

The use of polymeric medical devices has stimulated the development of new sterilization methods. The traditional techniques rely on ethylene oxide, but there are many questions concerning the carcinogenic properties of the ethylene oxide residues adsorbed on the materials after processing. Another common technique is the gamma irradiation process, but it is costly, its safe operation requires an isolated site and it also affects the bulk properties of the polymers. The use of a gas plasma is an elegant alternative sterilization technique. The plasma promotes an efficient inactivation of the micro-organisms, minimises the damage to the materials and presents very little danger for personnel and the environment. Pure oxygen reactive ion etching type of plasmas were applied to inactivate a biologic indicator, the Bacillus stearothermophilus, to confirm the efficiency of this process. The sterilization processes took a short time, in a few minutes the mortality was complete. In situ analysis of the micro-organisms' inactivating time was possible using emission spectrophotometry. The increase in the intensity of the 777.5 nm oxygen line shows the end of the oxidation of the biologic materials. The results were also observed and corroborated by scanning electron microscopy.

Hydrocarbon Degradation and Lead Solubility in a Soil Polluted with Lead and Used Motor Oil Treated by Composting and Phytoremediation.

PubMed

Escobar-Alvarado, L F; Vaca-Mier, M; López, R; Rojas-Valencia, M N

2018-02-01

Used lubricant oils and metals can be common soil pollutants in abandoned sites. When soil is contaminated with various hazardous wastes, the efficiency of biological treatments could be affected. The purpose of this work was to investigate the effect of combining phytoremediation and composting on the efficiency of hydrocarbon degradation and lead solubility in a soil contaminated with 31,823 mg/kg of total petroleum hydrocarbon (TPH) from used motor oil and 8260 mg/kg of lead. Mexican cactus (Opuntia ficus indica) and yard trimmings were added in the composting process, and lucerne (Medicago sativa) was used in the phytoremediation process. After a 9 week composting process, only 13% of the initial TPH concentration was removed. The following 20 week phytoremediation process removed 48% of TPH. The highest TPH degradation percentage (66%), was observed in the experiment with phytoremediation only. This work demonstrates sustainable technologies, such as biological treatments, represent low-cost options for remediation; however, they are not frequently used because they require long periods of time for success.

Blending ecology and evolution using emerging technologies to determine species distributions with a non-native pathogen in a changing climate

Treesearch

K. Waring; S. Cushman; A. Eckert; L. Flores-Renteria; H. Lintz; R. Sniezko; C. Still; C. Wehenkel; A. Whipple; M. Wing

2017-01-01

A collaborative team of researchers from the United States and Mexico has begun an exciting new research project funded by The National Science Foundation’s Macrosystems Biology program. The project will study ecological and evolutionary processes affecting the distribution of southwestern white pine (Pinus strobiformis), an important tree species of mixed conifer...

Being fruitful: genetics of reproduction in Arabidopsis.

PubMed

Preuss, D

1995-04-01

Reproduction in flowering plants requires a series of interactions between the haploid and diploid phases of the life cycle of the plant. Mutations that affect these interactions have been identified in Arabidopsis, thus giving insight into the processes of gamete development and pollination. These studies promise to yield new information on diverse topics in plant biology, from cell-cell recognition to the evolution of mating interactions.

The effectiveness of vegetation management practices for prevention and control of bark beetle infestations in coniferous forests of the western and southern United States

Treesearch

Christopher J. Fettig; Kier D. Klepzig; Ronald f. Billings; A. Steven Munson; T. Evan Nebeker; Jose F. Negron; John T. Nowak

2007-01-01

Insects are major components of forest ecosystems, representing most of the biological diversity and affecting virtually all processes and uses. In the USA, bark beetles (Coleoptera: Curculionidae, Scolytinae) heavily influence the structure and function of these ecosystems by regulating certain aspects of primary production, nutrient cycling, ecological succession and...

Deformational mass transport and invasive processes in soil evolution

NASA Technical Reports Server (NTRS)

Brimhall, George H.; Chadwick, Oliver A.; Lewis, Chris J.; Compston, William; Williams, Ian S.; Danti, Kathy J.; Dietrich, William E.; Power, Mary E.; Hendricks, David; Bratt, James

1992-01-01

Channels left in soil by decayed roots and burrowing animals allow organic and inorganic precipitates and detritus to move through soil from above, to depths at which the minuteness of pores restricts further passage. Consecutive translocation-and-root-growth phases stir the soil, constituting an invasive, dilatational process which generates cumulative strains. Below the depths thus affected, mineral dissolution by descending organic acids leads to internal collapse; this softened/condensed precursor horizon is then transformed into soil via biological activity that mixes and expands the evolving residuum through root and micropore-network invasion.

[Research progress on the degradation mechanisms and restoration of riparian ecosystem].

PubMed

Huang, Kai; Guo, Huai-cheng; Liu, Yong; Yu, Ya-juan; Zhou, Feng

2007-06-01

Restoration and reconstruction of degraded riparian ecosystem caused by natural and anthropogenic disturbances is one of the important issues in restoration ecology and watershed ecology. The disturbances on riparian ecosystem include flow regime alteration, direct modification and watershed disturbance, which have different affecting mechanisms. Flow regime alteration affects riparian ecosystem by changing riparian soil humidity, oxidation-reduction potential, biotaliving environment, and sediment transfer; direct modification affects riparian vegetation diversity through human activities and exotic plants invasion; and watershed disturbance mainly manifests in the channel degradation, aggradation or widening, the lowering of groundwater table, and the modification in fluvial process. The assessment objects of riparian restoration are riparian ecosystem components, and the assessment indicators are shifted from ecological to synthetic indices. Riparian restoration should be based on the detailed understanding of the biological and physical processes which affect riparian ecosystem, and implemented by vegetation restoration and hydrological adjustment at watershed or landscape scale. To extend the research scales and objects and to apply interdisciplinary approaches should be the key points in the further studies on the degradation mechanisms and restoration of riparian ecosystem.

High-resolution modeling of a marine ecosystem using the FRESCO hydroecological model

NASA Astrophysics Data System (ADS)

Zalesny, V. B.; Tamsalu, R.

2009-02-01

The FRESCO (Finnish Russian Estonian Cooperation) mathematical model describing a marine hydroecosystem is presented. The methodology of the numerical solution is based on the method of multicomponent splitting into physical and biological processes, spatial coordinates, etc. The model is used for the reproduction of physical and biological processes proceeding in the Baltic Sea. Numerical experiments are performed with different spatial resolutions for four marine basins that are enclosed into one another: the Baltic Sea, the Gulf of Finland, the Tallinn-Helsinki water area, and Tallinn Bay. Physical processes are described by the equations of nonhydrostatic dynamics, including the k-ω parametrization of turbulence. Biological processes are described by the three-dimensional equations of an aquatic ecosystem with the use of a size-dependent parametrization of biochemical reactions. The main goal of this study is to illustrate the efficiency of the developed numerical technique and to demonstrate the importance of a high spatial resolution for water basins that have complex bottom topography, such as the Baltic Sea. Detailed information about the atmospheric forcing, bottom topography, and coastline is very important for the description of coastal dynamics and specific features of a marine ecosystem. Experiments show that the spatial inhomogeneity of hydroecosystem fields is caused by the combined effect of upwelling, turbulent mixing, surface-wave breaking, and temperature variations, which affect biochemical reactions.

Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis

NASA Astrophysics Data System (ADS)

Liang, J.; Qi, X.; Souza, L.; Luo, Y.

2015-10-01

Nitrogen (N) cycle has the potential to regulate climate change through its influence on carbon (C) sequestration. Although extensive researches have been done to explore whether or not progressive N limitation (PNL) occurs under CO2 enrichment, a comprehensive assessment of the processes that regulate PNL is still lacking. Here, we quantitatively synthesized the responses of all major processes and pools in terrestrial N cycle with meta-analysis of CO2 experimental data available in the literature. The results showed that CO2 enrichment significantly increased N sequestration in plant and litter pools but not in soil pool. Thus, the basis of PNL occurrence partially exists. However, CO2 enrichment also significantly increased the N influx via biological N fixation, but decreased the N efflux via leaching. In addition, no general diminished CO2 fertilization effect on plant growth over time was observed. Overall, our analyses suggest that the extra N supply by the increased biological N fixation and decreased leaching may potentially alleviate PNL under elevated CO2 conditions. Moreover, our synthesis showed that CO2 enrichment increased soil ammonium (NH4+) but decreased nitrate (NO3-). The different responses of NH4+ and NO3-, and the consequent biological processes, may result in changes in soil microenvironment, community structures and above-belowground interactions, which could potentially affect the terrestrial biogeochemical cycles and the feedback to climate change.

The epigenetic impacts of social stress: how does social adversity become biologically embedded?

PubMed Central

Cunliffe, Vincent T

2016-01-01

Epigenetic mechanisms are implicated in the processes through which social stressors erode health in humans and other animals. Here I review progress in elucidating the biological pathways underlying the social gradient in health, with particular emphasis on how behavioral stresses influence epigenomic variation linked to health. The evidence that epigenetic changes are involved in embedding of social status-linked chronic stress is reviewed in the context of current knowledge about behavior within animal dominance hierarchies and the impacts of social position on behaviors that affect health. The roles of epigenetic mechanisms in responses to trauma and the evidence for their involvement in intergenerational transmission of the biological impacts of traumatic stress are also considered. Taken together, the emerging insights have important implications for development of strategies to improve societal health and well-being. PMID:27869483

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.

Novel Transcriptional Activities of Vitamin E: Inhibition of Cholesterol Biosynthesis

PubMed Central

Valastyan, Scott; Thakur, Varsha; Johnson, Amy; Kumar, Karan; Manor, Danny

2008-01-01

Vitamin E is a dietary lipid that is essential for vertebrate health and fertility. The biological activity of vitamin E is thought to reflect its ability to quench oxygen- and carbon- based free radicals, and thus to protect the organism from oxidative damage. However, recent reports suggest that vitamin E may also display other biological activities. Here, to examine possible mechanisms that may underlie such non-classical activities of vitamin E, we investigated the possibility that it functions as a specific modulator of gene expression. We show that treatment of cultured hepatocytes with RRR-α-tocopherol alters the expression of multiple genes and that these effects are distinct from those elicited by another antioxidant. Genes modulated by vitamin E include those that encode key enzymes in the cholesterol biosynthetic pathway. Correspondingly, vitamin E caused a pronounced inhibition of de novo cholesterol biosynthesis. The transcriptional activities of vitamin E were mediated by attenuating the post-translational processing of the transcription factor SREBP-2 that, in turn, led to a decreased transcriptional activity of sterol responsive elements in the promoters of target genes. These observations indicate that vitamin E possesses novel transcriptional activities that affect fundamental biological processes. Cross talk between tocopherol levels and cholesterol status may be an important facet of the biological activities of vitamin E. PMID:18095660

Onset of meso-scale turbulence in active nematics

NASA Astrophysics Data System (ADS)

Doostmohammadi, Amin; Shendruk, Tyler N.; Thijssen, Kristian; Yeomans, Julia M.

2017-05-01

Meso-scale turbulence is an innate phenomenon, distinct from inertial turbulence, that spontaneously occurs at low Reynolds number in fluidized biological systems. This spatiotemporal disordered flow radically changes nutrient and molecular transport in living fluids and can strongly affect the collective behaviour in prominent biological processes, including biofilm formation, morphogenesis and cancer invasion. Despite its crucial role in such physiological processes, understanding meso-scale turbulence and any relation to classical inertial turbulence remains obscure. Here we show how the motion of active matter along a micro-channel transitions to meso-scale turbulence through the evolution of locally disordered patches (active puffs) from an ordered vortex-lattice flow state. We demonstrate that the stationary critical exponents of this transition to meso-scale turbulence in a channel coincide with the directed percolation universality class. This finding bridges our understanding of the onset of low-Reynolds-number meso-scale turbulence and traditional scale-invariant turbulence in confinement.

Spring Meeting Preview: Joint Assembly Sessions Focus on Urbanization

NASA Astrophysics Data System (ADS)

Zielinski, Sarah

2006-04-01

The urban environment has grown to encompass not just the downtown area of a city but also the suburbs and rapidly growing exurban areas. This growth can affect a wide range of geological, physical, and biological processes. Several sessions at the 23-26 May 2006 Joint Assembly in Baltimore, Md., will explore this topic. Two union sessions on the ``Impact of Urbanization on Environmental Systems'' (U31A and U32A) will take place on Wednesday morning, 24 May, at 8:30 A.M. and 10:45 A.M. The sessions are designed to be a wide-ranging exploration of the different, multiple roles that urbanization, and the changes in the environment that accompany urbanization, have on biological and geophysical processes, said session co-convener Larry Band. Brand is Voit Gilmore distinguished professor and chair of the department of geography at the University of North Carolina, Chapel Hill.

Biomarkers of Aging: From Function to Molecular Biology

PubMed Central

Wagner, Karl-Heinz; Cameron-Smith, David; Wessner, Barbara; Franzke, Bernhard

2016-01-01

Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a single biomarker or gold standard tool that can monitor successful or healthy aging. Within this short review the current knowledge of putative biomarkers is presented, focusing on their application to the major physiological mechanisms affected by the aging process including physical capability, nutritional status, body composition, endocrine and immune function. This review emphasizes molecular and DNA-based biomarkers, as well as recent advances in other biomarkers such as microRNAs, bilirubin or advanced glycation end products. PMID:27271660

Applicability of discovery science approach to determine biological effects of mobile phone radiation.

PubMed

Leszczynski, Dariusz; Nylund, Reetta; Joenväärä, Sakari; Reivinen, Jukka

2004-02-01

We argue that the use of high-throughput screening techniques, although expensive and laborious, is justified and necessary in studies that examine biological effects of mobile phone radiation. The "case of hsp27 protein" presented here suggests that even proteins with only modestly altered (by exposure to mobile phone radiation) expression and activity might have an impact on cell physiology. However, this short communication does not attempt to present the full scientific evidence that is far too large to be presented in a single article and that is being prepared for publication in three separate research articles. Examples of the experimental evidence presented here were designed to show the flow of experimental process demonstrating that the use of high-throughput screening techniques might help in rapid identification of the responding proteins. This, in turn, can help in speeding up of the process of determining whether these changes might affect human health.*

Does a prosocial-selfish distinction help explain the biological affects? Comment on Buck (1999).

PubMed

Gray, Jeremy R

2002-10-01

R. Buck (1999) argued that a conceptual distinction between prosocial and selfish motivation is necessary to understand the biological affects (consciously experienced feelings and desires having an innate neurochemical basis). However, at a biological level of analysis, a prosocial-selfish distinction is doubtful empirically and conceptually. For this reason, Buck's proposed typology of biological affects is unclear. Moreover, a prosocial-selfish distinction is not necessary to explain hemispheric differences in brain activity associated with affect. In contrast, an approach-withdrawal distinction explains some data uniquely well, although numerous exceptions imply that simple models are inadequate. To extend hemispheric models of experienced emotion, a prosocial-selfish distinction is unlikely to be explanatory, whereas an alternative account based on a distinction between verbal and nonverbal working memory may be useful.

Lost at sea: ocean acidification undermines larval fish orientation via altered hearing and marine soundscape modification

PubMed Central

Rossi, Tullio; Nagelkerken, Ivan; Connell, Sean D.

2016-01-01

The dispersal of larvae and their settlement to suitable habitat is fundamental to the replenishment of marine populations and the communities in which they live. Sound plays an important role in this process because for larvae of various species, it acts as an orientational cue towards suitable settlement habitat. Because marine sounds are largely of biological origin, they not only carry information about the location of potential habitat, but also information about the quality of habitat. While ocean acidification is known to affect a wide range of marine organisms and processes, its effect on marine soundscapes and its reception by navigating oceanic larvae remains unknown. Here, we show that ocean acidification causes a switch in role of present-day soundscapes from attractor to repellent in the auditory preferences in a temperate larval fish. Using natural CO2 vents as analogues of future ocean conditions, we further reveal that ocean acidification can impact marine soundscapes by profoundly diminishing their biological sound production. An altered soundscape poorer in biological cues indirectly penalizes oceanic larvae at settlement stage because both control and CO2-treated fish larvae showed lack of any response to such future soundscapes. These indirect and direct effects of ocean acidification put at risk the complex processes of larval dispersal and settlement. PMID:26763221

Parsing Heterogeneity in the Brain Connectivity of Depressed and Healthy Adults During Positive Mood.

PubMed

Price, Rebecca B; Lane, Stephanie; Gates, Kathleen; Kraynak, Thomas E; Horner, Michelle S; Thase, Michael E; Siegle, Greg J

2017-02-15

There is well-known heterogeneity in affective mechanisms in depression that may extend to positive affect. We used data-driven parsing of neural connectivity to reveal subgroups present across depressed and healthy individuals during positive processing, informing targets for mechanistic intervention. Ninety-two individuals (68 depressed patients, 24 never-depressed control subjects) completed a sustained positive mood induction during functional magnetic resonance imaging. Directed functional connectivity paths within a depression-relevant network were characterized using Group Iterative Multiple Model Estimation (GIMME), a method shown to accurately recover the direction and presence of connectivity paths in individual participants. During model selection, individuals were clustered using community detection on neural connectivity estimates. Subgroups were externally tested across multiple levels of analysis. Two connectivity-based subgroups emerged: subgroup A, characterized by weaker connectivity overall, and subgroup B, exhibiting hyperconnectivity (relative to subgroup A), particularly among ventral affective regions. Subgroup predicted diagnostic status (subgroup B contained 81% of patients; 50% of control subjects; χ 2 = 8.6, p = .003) and default mode network connectivity during a separate resting-state task. Among patients, subgroup B members had higher self-reported symptoms, lower sustained positive mood during the induction, and higher negative bias on a reaction-time task. Symptom-based depression subgroups did not predict these external variables. Neural connectivity-based categorization travels with diagnostic category and is clinically predictive, but not clinically deterministic. Both patients and control subjects showed heterogeneous, and overlapping, profiles. The larger and more severely affected patient subgroup was characterized by ventrally driven hyperconnectivity during positive processing. Data-driven parsing suggests heterogeneous substrates of depression and possible resilience in control subjects in spite of biological overlap. Copyright © 2016 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

Defining age- and lactocrine-sensitive elements of the neonatal porcine uterine microRNA–mRNA interactome†,‡

PubMed Central

George, Ashley F.; Rahman, Kathleen M.; Camp, Meredith E.; Prasad, Nripesh; Bartol, Frank F.; Bagnell, Carol A.

2017-01-01

Abstract Factors delivered to offspring in colostrum within 2 days of birth support neonatal porcine uterine development. The uterine mRNA transcriptome is affected by age and nursing during this period. Whether uterine microRNA (miRNA) expression is affected similarly is unknown. Objectives were to (1) determine effects of age and nursing on porcine uterine miRNA expression between birth and postnatal day (PND) 2 using miRNA sequencing (miRNAseq) and; (2) define affected miRNA–mRNA interactions and associated biological processes using integrated target prediction analysis. At birth (PND 0), gilts were euthanized, nursed ad libitum, or gavage-fed milk replacer for 48 h. Uteri were collected at birth or 50 h postnatal. MicroRNAseq data were validated using quantitative real-time PCR. Targets were predicted using an established mRNA database generated from the same tissues. For PND 2 versus PND 0 comparisons, 31 differentially expressed (DE) miRNAs were identified for nursed, and 42 DE miRNAs were identified for replacer-fed gilts. Six DE miRNAs were identified for nursed versus replacer-fed gilts on PND 2. Target prediction for inversely correlated DE miRNA–mRNA pairings indicated 20 miRNAs targeting 251 mRNAs in nursed, versus 29 miRNAs targeting 585 mRNAs in replacer-fed gilts for PND 2 versus PND 0 comparisons, and 5 miRNAs targeting 81 mRNAs for nursed versus replacer-fed gilts on PND 2. Biological processes predicted to be affected by age and nursing included cell-to-cell signaling, cell morphology, and tissue morphology. Results indicate novel age- and lactocrine-sensitive miRNA–mRNA relationships associated with porcine neonatal uterine development between birth and PND 2. PMID:28203709

Analysis of THG modes for femtosecond laser pulse

NASA Astrophysics Data System (ADS)

Trofimov, Vyacheslav A.; Sidorov, Pavel S.

2017-05-01

THG is used nowadays in many practical applications such as a substance diagnostics, and biological objects imaging, and etc. With developing of new materials and technology (for example, photonic crystal) an attention to THG process analysis grow. Therefore, THG features understanding are a modern problem. Early we have developed new analytical approach based on using the problem invariant for analytical solution construction of the THG process. It should be stressed that we did not use a basic wave non-depletion approximation. Nevertheless, a long pulse duration approximation and plane wave approximation has applied. The analytical solution demonstrates, in particular, an optical bistability property (and may other regimes of frequency tripling) for the third harmonic generation process. But, obviously, this approach does not reflect an influence of a medium dispersion on the frequency tripling. Therefore, in this paper we analyze THG efficiency of a femtosecond laser pulse taking into account a second order dispersion affect as well as self- and crossmodulation of the interacting waves affect on the frequency conversion process. Analysis is made using a computer simulation on the base of Schrödinger equations describing the process under consideration.

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing

PubMed Central

Pantazatos, Spiro P.; Talati, Ardesheer; Pavlidis, Paul; Hirsch, Joy

2012-01-01

It is currently unclear to what extent cortical structures are required for and engaged during subconscious processing of biologically salient affective stimuli (i.e. the ‘low-road’ vs. ‘many-roads’ hypotheses). Here we show that cortical-cortical and cortical-subcortical functional connectivity (FC) contain substantially more information, relative to subcortical-subcortical FC (i.e. ‘subcortical alarm’ and other limbic regions), that predicts subliminal fearful face processing within individuals using training data from separate subjects. A plot of classification accuracy vs. number of selected whole-brain FC features revealed 92% accuracy when learning was based on the top 8 features from each training set. The most informative FC was between right amygdala and precuneus, which increased during subliminal fear conditions, while left and right amygdala FC decreased, suggesting a bilateral decoupling of this key limbic region during processing of subliminal fear-related stimuli. Other informative FC included angular gyrus, middle temporal gyrus and cerebellum. These findings identify FC that decodes subliminally perceived, task-irrelevant affective stimuli, and suggest that cortical structures are actively engaged by and appear to be essential for subliminal fear processing. PMID:22484206

Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing.

PubMed

Pantazatos, Spiro P; Talati, Ardesheer; Pavlidis, Paul; Hirsch, Joy

2012-07-16

It is currently unclear to what extent cortical structures are required for and engaged during subconscious processing of biologically salient affective stimuli (i.e. the 'low-road' vs. 'many-roads' hypotheses). Here we show that cortical-cortical and cortical-subcortical functional connectivity (FC) contain substantially more information, relative to subcortical-subcortical FC (i.e. 'subcortical alarm' and other limbic regions), that predicts subliminal fearful face processing within individuals using training data from separate subjects. A plot of classification accuracy vs. number of selected whole-brain FC features revealed 92% accuracy when learning was based on the top 8 features from each training set. The most informative FC was between right amygdala and precuneus, which increased during subliminal fear conditions, while left and right amygdala FC decreased, suggesting a bilateral decoupling of this key limbic region during processing of subliminal fear-related stimuli. Other informative FC included angular gyrus, middle temporal gyrus and cerebellum. These findings identify FC that decodes subliminally perceived, task-irrelevant affective stimuli, and suggest that cortical structures are actively engaged by and appear to be essential for subliminal fear processing. Published by Elsevier Inc.

How emotions affect eating: a five-way model.

PubMed

Macht, Michael

2008-01-01

Despite the importance of affective processes in eating behaviour, it remains difficult to predict how emotions affect eating. Emphasizing individual differences, previous research did not pay full attention to the twofold variability of emotion-induced changes of eating (variability across both individuals and emotions). By contrast, the present paper takes into account both individual characteristics and emotion features, and specifies five classes of emotion-induced changes of eating: (1) emotional control of food choice, (2) emotional suppression of food intake, (3) impairment of cognitive eating controls, (4) eating to regulate emotions, and (5) emotion-congruent modulation of eating. These classes are distinguished by antecedent conditions, eating responses and mediating mechanisms. They point to basic functional principles underlying the relations between emotions and biologically based motives: interference, concomitance and regulation. Thus, emotion-induced changes of eating can be a result of interference of eating by emotions, a by-product of emotions, and a consequence of regulatory processes (i.e., emotions may regulate eating, and eating may regulate emotions).

Barth Syndrome (BTHS)

MedlinePlus

... mitochondrial diseases through a better understanding of mitochondrial biology. Because people affected by mitochondrial disease often have ... mitochondrial diseases through a better understanding of mitochondrial biology. Because people affected by mitochondrial disease often have ...

Evaluating the administration costs of biologic drugs: development of a cost algorithm.

PubMed

Tetteh, Ebenezer K; Morris, Stephen

2014-12-01

Biologic drugs, as with all other medical technologies, are subject to a number of regulatory, marketing, reimbursement (financing) and other demand-restricting hurdles applied by healthcare payers. One example is the routine use of cost-effectiveness analyses or health technology assessments to determine which medical technologies offer value-for-money. The manner in which these assessments are conducted suggests that, holding all else equal, the economic value of biologic drugs may be determined by how much is spent on administering these drugs or trade-offs between drug acquisition and administration costs. Yet, on the supply-side, it seems very little attention is given to how manufacturing and formulation choices affect healthcare delivery costs. This paper evaluates variations in the administration costs of biologic drugs, taking care to ensure consistent inclusion of all relevant cost resources. From this, it develops a regression-based algorithm with which manufacturers could possibly predict, during process development, how their manufacturing and formulation choices may impact on the healthcare delivery costs of their products.

Bridging the physical scales in evolutionary biology: From protein sequence space to fitness of organisms and populations

PubMed Central

Bershtein, Shimon; Serohijos, Adrian W.R.; Shakhnovich, Eugene I.

2016-01-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. PMID:27810574

Bridging the physical scales in evolutionary biology: from protein sequence space to fitness of organisms and populations.

PubMed

Bershtein, Shimon; Serohijos, Adrian Wr; Shakhnovich, Eugene I

2017-02-01

Bridging the gap between the molecular properties of proteins and organismal/population fitness is essential for understanding evolutionary processes. This task requires the integration of the several physical scales of biological organization, each defined by a distinct set of mechanisms and constraints, into a single unifying model. The molecular scale is dominated by the constraints imposed by the physico-chemical properties of proteins and their substrates, which give rise to trade-offs and epistatic (non-additive) effects of mutations. At the systems scale, biological networks modulate protein expression and can either buffer or enhance the fitness effects of mutations. The population scale is influenced by the mutational input, selection regimes, and stochastic changes affecting the size and structure of populations, which eventually determine the evolutionary fate of mutations. Here, we summarize the recent advances in theory, computer simulations, and experiments that advance our understanding of the links between various physical scales in biology. Copyright © 2016 Elsevier Ltd. All rights reserved.

The brain's emotional foundations of human personality and the Affective Neuroscience Personality Scales.

PubMed

Davis, Kenneth L; Panksepp, Jaak

2011-10-01

Six of the primary-process subcortical brain emotion systems - SEEKING, RAGE, FEAR, CARE, GRIEF and PLAY - are presented as foundational for human personality development, and hence as a potentially novel template for personality assessment as in the Affective Neurosciences Personality Scales (ANPS), described here. The ANPS was conceptualized as a potential clinical research tool, which would help experimentalists and clinicians situate subjects and clients in primary-process affective space. These emotion systems are reviewed in the context of a multi-tiered framing of consciousness spanning from primary affect, which encodes biological valences, to higher level tertiary (thought mediated) processing. Supporting neuroscience research is presented along with comparisons to Cloninger's Temperament and Character Inventory and the Five Factor Model (FFM). Suggestions are made for grounding the internal structure of the FFM on the primal emotional systems recognized in affective neuroscience, which may promote substantive dialog between human and animal research traditions. Personality is viewed in the context of Darwinian "continuity" with the inherited subcortical brain emotion systems being foundational, providing major forces for personality development in both humans and animals, and providing an affective infrastructure for an expanded five factor descriptive model applying to normal and clinical human populations as well as mammals generally. Links with ontogenetic and epigenetic models of personality development are also presented. Potential novel clinical applications of the CARE maternal-nurturance system and the PLAY system are also discussed. Copyright © 2011 Elsevier Ltd. All rights reserved.

Interactive effects of global climate change and pollution on marine microbes: the way ahead.

PubMed

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Angela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-06-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

Interactive effects of global climate change and pollution on marine microbes: the way ahead

PubMed Central

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Ângela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-01-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future. PMID:23789087

Bipolar disorder diagnosis: challenges and future directions

PubMed Central

Phillips, Mary L; Kupfer, David J

2018-01-01

Bipolar disorder refers to a group of affective disorders, which together are characterised by depressive and manic or hypomanic episodes. These disorders include: bipolar disorder type I (depressive and manic episodes: this disorder can be diagnosed on the basis of one manic episode); bipolar disorder type II (depressive and hypomanic episodes); cyclothymic disorder (hypomanic and depressive symptoms that do not meet criteria for depressive episodes); and bipolar disorder not otherwise specified (depressive and hypomanic-like symptoms that do not meet the diagnostic criteria for any of the aforementioned disorders). Bipolar disorder type II is especially difficult to diagnose accurately because of the difficulty in differentiation of this disorder from recurrent unipolar depression (recurrent depressive episodes) in depressed patients. The identification of objective biomarkers that represent pathophysiologic processes that differ between bipolar disorder and unipolar depression can both inform bipolar disorder diagnosis and provide biological targets for the development of new and personalised treatments. Neuroimaging studies could help the identification of biomarkers that differentiate bipolar disorder from unipolar depression, but the problem in detection of a clear boundary between these disorders suggests that they might be better represented as a continuum of affective disorders. Innovative combinations of neuroimaging and pattern recognition approaches can identify individual patterns of neural structure and function that accurately ascertain where a patient might lie on a behavioural scale. Ultimately, an integrative approach, with several biological measurements using different scales, could yield patterns of biomarkers (biosignatures) to help identify biological targets for personalised and new treatments for all affective disorders. PMID:23663952

Precambrian evolution of the climate system.

PubMed

Walker, J C

1990-01-01

Climate is an important environmental parameter of the early Earth, likely to have affected the origin and evolution of life, the composition and mineralogy of sedimentary rocks, and stable isotope ratios in sedimentary minerals. There is little observational evidence constraining Precambrian climates. Most of our knowledge is at present theoretical. Factors that must have affected the climate include reduced solar luminosity, enhanced rotation rate of the Earth, an area of land that probably increased with time, and biological evolution, particularly as it affected the composition of the atmosphere and the greenhouse effect. Cloud cover is a major uncertainty about the early Earth. Carbon dioxide and its greenhouse effect are the factors that have been most extensively studied. This paper presents a new examination of the biogeochemical cycles of carbon as they may have changed between an Archean Earth deficient in land, sedimentary rocks, and biological activity, and a Proterozoic Earth much like the modern Earth, but lacking terrestrial life and carbonate-secreting plankton. Results of a numerical simulation of this transition show how increasing biological activity could have drawn down atmospheric carbon dioxide by extracting sedimentary organic carbon from the system. Increasing area of continents could further have drawn down carbon dioxide by encouraging the accumulation of carbonate sediments. An attempt to develop a numerical simulation of the carbon cycles of the Precambrian raises questions about sources and sinks of marine carbon and alkalinity on a world without continents. More information is needed about sea-floor weathering processes.

Diverse structures, functions and uses of FK506 binding proteins.

PubMed

Bonner, Julia Maeve; Boulianne, Gabrielle L

2017-10-01

FK506 (Tacrolimus), isolated from Streptomyces tsukubaenis is a powerful immunosuppressant shown to inhibit T cell activation. FK506 mediated immunosuppression requires the formation of a complex between FK506, a FK506 binding protein (FKBP) and calcineurin. Numerous FKBPs have been identified in a wide range of species, from single celled organisms to humans. FKBPs show peptidylprolyl cis/trans isomerase (PPIase) activity and have been shown to affect a wide range of cellular processes including protein folding, receptor signaling and apoptosis. FKBPs also affect numerous biological functions in addition to immunosuppression including regulation of cardiac function, neuronal function and development and have been implicated in several diseases including cardiac disease, cancer and neurodegenerative diseases such as Alzheimer's disease. More recently, FKBPs have proven useful as molecular tools for studying protein interactions, localization and functions. This review provides an overview of the current state of knowledge of FKBPs and their numerous biological functions and uses. Copyright © 2017 Elsevier Inc. All rights reserved.

Fate of Engineered Nanoparticles: Implications in the ...

EPA Pesticide Factsheets

The increased flux of the engineered nanoparticles (ENPs) in consumer and commercial products has become a viable threat, particularly if their release affects the environment. The aim of this paper is to review the recent literature results pertaining to the underlying mechanisms initiating the transformations of ENPs for both, the biotic and abiotic processes. The transformation of ENPs is necessarily interrelated to multiple environmental aspects and many concepts overlap. Physicochemical, macromolecular, and biological pathways contribute to assessing the impact of the altered activities of ENPs on the surrounding environmental matrices. Transformations involving both organic and inorganic ligands are vital in soil and water systems. Energy-efficient biocatalytic pathways can easily facilitate biotransformation involving enzymatic reactions and biomolecules. The relationship between physicochemical and biological parameters triggers transformation, greatly affecting the bioavailability and aging of ENPs to various extents. Therefore, the interaction of ENPs in environmental matrices is significant in understanding the risk of potential exposure and/or uptake by biota. Submitted to Elsevier journal, Coordination Chemistry Reviews

Direct detection and measurement of wall shear stress using a filamentous bio-nanoparticle

PubMed Central

Lobo, Daniela P.; Wemyss, Alan M.; Smith, David J.; Straube, Anne; Betteridge, Kai B.; Salmon, Andrew H. J.; Foster, Rebecca R.; Elhegni, Hesham E.; Satchell, Simon C.; Little, Haydn A.; Pacheco-Gómez, Raúl; Simmons, Mark J.; Hicks, Matthew R.; Bates, David O.; Dafforn, Timothy R.; Arkill, Kenton P.

2016-01-01

The wall shear stress (WSS) that a moving fluid exerts on a surface affects many processes including those relating to vascular function. WSS plays an important role in normal physiology (e.g. angiogenesis) and affects the microvasculature’s primary function of molecular transport. Points of fluctuating WSS show abnormalities in a number of diseases; however, there is no established technique for measuring WSS directly in physiological systems. All current methods rely on estimates obtained from measured velocity gradients in bulk flow data. In this work, we report a nanosensor that can directly measure WSS in microfluidic chambers with sub-micron spatial resolution by using a specific type of virus, the bacteriophage M13, which has been fluorescently labeled and anchored to a surface. It is demonstrated that the nanosensor can be calibrated and adapted for biological tissue, revealing WSS in micro-domains of cells that cannot be calculated accurately from bulk flow measurements. This method lends itself to a platform applicable to many applications in biology and microfluidics. PMID:27570611

Introducing the Global Register of Introduced and Invasive Species

PubMed Central

Pagad, Shyama; Genovesi, Piero; Carnevali, Lucilla; Schigel, Dmitry; McGeoch, Melodie A.

2018-01-01

Harmonised, representative data on the state of biological invasions remain inadequate at country and global scales, particularly for taxa that affect biodiversity and ecosystems. Information is not readily available in a form suitable for policy and reporting. The Global Register of Introduced and Invasive Species (GRIIS) provides the first country-wise checklists of introduced (naturalised) and invasive species. GRIIS was conceived to provide a sustainable platform for information delivery to support national governments. We outline the rationale and methods underpinning GRIIS, to facilitate transparent, repeatable analysis and reporting. Twenty country checklists are presented as exemplars; GRIIS Checklists for close to all countries globally will be submitted through the same process shortly. Over 11000 species records are currently in the 20 country exemplars alone, with environmental impact evidence for just over 20% of these. GRIIS provides significant support for countries to identify and prioritise invasive alien species, and establishes national and global baselines. In future this will enable a global system for sustainable monitoring of trends in biological invasions that affect the environment. PMID:29360103

Differential Network Analyses of Alzheimer’s Disease Identify Early Events in Alzheimer’s Disease Pathology

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

Xia, Jing; Rocke, David M.; Perry, George

In late-onset Alzheimer’s disease (AD), multiple brain regions are not affected simultaneously. Comparing the gene expression of the affected regions to identify the differences in the biological processes perturbed can lead to greater insight into AD pathogenesis and early characteristics. We identified differentially expressed (DE) genes from single cell microarray data of four AD affected brain regions: entorhinal cortex (EC), hippocampus (HIP), posterior cingulate cortex (PCC), and middle temporal gyrus (MTG). We organized the DE genes in the four brain regions into region-specific gene coexpression networks. Differential neighborhood analyses in the coexpression networks were performed to identify genes with lowmore » topological overlap (TO) of their direct neighbors. The low TO genes were used to characterize the biological differences between two regions. Our analyses show that increased oxidative stress, along with alterations in lipid metabolism in neurons, may be some of the very early events occurring in AD pathology. Cellular defense mechanisms try to intervene but fail, finally resulting in AD pathology as the disease progresses. Furthermore, disease annotation of the low TO genes in two independent protein interaction networks has resulted in association between cancer, diabetes, renal diseases, and cardiovascular diseases.« less

Differential Network Analyses of Alzheimer’s Disease Identify Early Events in Alzheimer’s Disease Pathology

DOE PAGES

Xia, Jing; Rocke, David M.; Perry, George; ...

2014-01-01

In late-onset Alzheimer’s disease (AD), multiple brain regions are not affected simultaneously. Comparing the gene expression of the affected regions to identify the differences in the biological processes perturbed can lead to greater insight into AD pathogenesis and early characteristics. We identified differentially expressed (DE) genes from single cell microarray data of four AD affected brain regions: entorhinal cortex (EC), hippocampus (HIP), posterior cingulate cortex (PCC), and middle temporal gyrus (MTG). We organized the DE genes in the four brain regions into region-specific gene coexpression networks. Differential neighborhood analyses in the coexpression networks were performed to identify genes with lowmore » topological overlap (TO) of their direct neighbors. The low TO genes were used to characterize the biological differences between two regions. Our analyses show that increased oxidative stress, along with alterations in lipid metabolism in neurons, may be some of the very early events occurring in AD pathology. Cellular defense mechanisms try to intervene but fail, finally resulting in AD pathology as the disease progresses. Furthermore, disease annotation of the low TO genes in two independent protein interaction networks has resulted in association between cancer, diabetes, renal diseases, and cardiovascular diseases.« less

Quantitative evaluations of mechanisms of radiofrequency interactions with biological molecules and processes.

PubMed

Sheppard, Asher R; Swicord, Mays L; Balzano, Quirino

2008-10-01

The complexity of interactions of electromagnetic fields up to 10(12) Hz with the ions, atoms, and molecules of biological systems has given rise to a large number of established and proposed biophysical mechanisms applicable over a wide range of time and distance scales, field amplitudes, frequencies, and waveforms. This review focuses on the physical principles that guide quantitative assessment of mechanisms applicable for exposures at or below the level of endogenous electric fields associated with development, wound healing, and excitation of muscles and the nervous system (generally, 1 to 10(2) V m(-1)), with emphasis on conditions where temperature increases are insignificant (<1 K). Experiment and theory demonstrate possible demodulation at membrane barriers for frequencies < or =10 MHz, but not at higher frequencies. Although signal levels somewhat below system noise can be detected, signal-to-noise ratios substantially less than 0.1 cannot be overcome by cooperativity, signal averaging, coherent detection, or by nonlinear dynamical systems. Sensory systems and possible effects on biological magnetite suggest paradigms for extreme sensitivity at lower frequencies, but there are no known radiofrequency (RF) analogues. At the molecular level, vibrational modes are so overdamped by water molecules that excitation of molecular modes below the far infrared cannot occur. Two RF mechanisms plausibly may affect biological matter under common exposure conditions. For frequencies below approximately 150 MHz, shifts in the rate of chemical reactions can be mediated by radical pairs and, at all frequencies, dielectric and resistive heating can raise temperature and increase the entropy of the affected biological system.

Effects of intense magnetic fields on sedimentation pattern and gene expression profile in budding yeast

NASA Astrophysics Data System (ADS)

Ikehata, Masateru; Iwasaka, Masakazu; Miyakoshi, Junji; Ueno, Shoogo; Koana, Takao

2003-05-01

Effects of magnetic fields (MFs) on biological systems are usually investigated using biological indices such as gene expression profiles. However, to precisely evaluate the biological effects of MF, the effects of intense MFs on systematic material transport processes including experimental environment must be seriously taken into consideration. In this study, a culture of the budding yeast, Saccharomyces cerevisiae, was used as a model for an in vitro biological test system. After exposure to 5 T static vertical MF, we found a difference in the sedimentation pattern of cells depending on the location of the dish in the magnet bore. Sedimented cells were localized in the center of the dish when they were placed in the lower part of the magnet bore while the sedimentation of the cells was uniform in dishes placed in the upper part of the bore because of the diamagnetic force. Genome wide gene expression profile of the yeast cells after exposure to 5 T static MF for 2 h suggested that the MF did not affect the expression level of any gene in yeast cells although the sedimentation pattern was altered. In addition, exposure to 10 T for 1 h and 5 T for 24 h also did not affect the gene expression. On the other hand, a slight change in expressions of several genes which are related to respiration was observed by exposure to a 14 T static MF for 24 h. The necessity of estimating the indirect effects of MFs on a study of its biological effect of MF in vitro will be discussed.

Neural circuits underlying mother’s voice perception predict social communication abilities in children

PubMed Central

Abrams, Daniel A.; Chen, Tianwen; Odriozola, Paola; Cheng, Katherine M.; Baker, Amanda E.; Padmanabhan, Aarthi; Ryali, Srikanth; Kochalka, John; Feinstein, Carl; Menon, Vinod

2016-01-01

The human voice is a critical social cue, and listeners are extremely sensitive to the voices in their environment. One of the most salient voices in a child’s life is mother's voice: Infants discriminate their mother’s voice from the first days of life, and this stimulus is associated with guiding emotional and social function during development. Little is known regarding the functional circuits that are selectively engaged in children by biologically salient voices such as mother’s voice or whether this brain activity is related to children’s social communication abilities. We used functional MRI to measure brain activity in 24 healthy children (mean age, 10.2 y) while they attended to brief (<1 s) nonsense words produced by their biological mother and two female control voices and explored relationships between speech-evoked neural activity and social function. Compared to female control voices, mother’s voice elicited greater activity in primary auditory regions in the midbrain and cortex; voice-selective superior temporal sulcus (STS); the amygdala, which is crucial for processing of affect; nucleus accumbens and orbitofrontal cortex of the reward circuit; anterior insula and cingulate of the salience network; and a subregion of fusiform gyrus associated with face perception. The strength of brain connectivity between voice-selective STS and reward, affective, salience, memory, and face-processing regions during mother’s voice perception predicted social communication skills. Our findings provide a novel neurobiological template for investigation of typical social development as well as clinical disorders, such as autism, in which perception of biologically and socially salient voices may be impaired. PMID:27185915

Neural circuits underlying mother's voice perception predict social communication abilities in children.

PubMed

Abrams, Daniel A; Chen, Tianwen; Odriozola, Paola; Cheng, Katherine M; Baker, Amanda E; Padmanabhan, Aarthi; Ryali, Srikanth; Kochalka, John; Feinstein, Carl; Menon, Vinod

2016-05-31

The human voice is a critical social cue, and listeners are extremely sensitive to the voices in their environment. One of the most salient voices in a child's life is mother's voice: Infants discriminate their mother's voice from the first days of life, and this stimulus is associated with guiding emotional and social function during development. Little is known regarding the functional circuits that are selectively engaged in children by biologically salient voices such as mother's voice or whether this brain activity is related to children's social communication abilities. We used functional MRI to measure brain activity in 24 healthy children (mean age, 10.2 y) while they attended to brief (<1 s) nonsense words produced by their biological mother and two female control voices and explored relationships between speech-evoked neural activity and social function. Compared to female control voices, mother's voice elicited greater activity in primary auditory regions in the midbrain and cortex; voice-selective superior temporal sulcus (STS); the amygdala, which is crucial for processing of affect; nucleus accumbens and orbitofrontal cortex of the reward circuit; anterior insula and cingulate of the salience network; and a subregion of fusiform gyrus associated with face perception. The strength of brain connectivity between voice-selective STS and reward, affective, salience, memory, and face-processing regions during mother's voice perception predicted social communication skills. Our findings provide a novel neurobiological template for investigation of typical social development as well as clinical disorders, such as autism, in which perception of biologically and socially salient voices may be impaired.

Ant-mediated ecosystem processes are driven by trophic community structure but mainly by the environment.

PubMed

Salas-Lopez, Alex; Mickal, Houadria; Menzel, Florian; Orivel, Jérôme

2017-01-01

The diversity and functional identity of organisms are known to be relevant to the maintenance of ecosystem processes but can be variable in different environments. Particularly, it is uncertain whether ecosystem processes are driven by complementary effects or by dominant groups of species. We investigated how community structure (i.e., the diversity and relative abundance of biological entities) explains the community-level contribution of Neotropical ant communities to different ecosystem processes in different environments. Ants were attracted with food resources representing six ant-mediated ecosystem processes in four environments: ground and vegetation strata in cropland and forest habitats. The exploitation frequencies of the baits were used to calculate the taxonomic and trophic structures of ant communities and their contribution to ecosystem processes considered individually or in combination (i.e., multifunctionality). We then investigated whether community structure variables could predict ecosystem processes and whether such relationships were affected by the environment. We found that forests presented a greater biodiversity and trophic complementarity and lower dominance than croplands, but this did not affect ecosystem processes. In contrast, trophic complementarity was greater on the ground than on vegetation and was followed by greater resource exploitation levels. Although ant participation in ecosystem processes can be predicted by means of trophic-based indices, we found that variations in community structure and performance in ecosystem processes were best explained by environment. We conclude that determining the extent to which the dominance and complementarity of communities affect ecosystem processes in different environments requires a better understanding of resource availability to different species.

Systems Biology and Biomarkers of Early Effects for Occupational Exposure Limit Setting

PubMed Central

DeBord, D. Gayle; Burgoon, Lyle; Edwards, Stephen W.; Haber, Lynne T.; Kanitz, M. Helen; Kuempel, Eileen; Thomas, Russell S.; Yucesoy, Berran

2015-01-01

In a recent National Research Council document, new strategies for risk assessment were described to enable more accurate and quicker assessments.( 1 ) This report suggested that evaluating individual responses through increased use of bio-monitoring could improve dose-response estimations. Identi-fication of specific biomarkers may be useful for diagnostics or risk prediction as they have the potential to improve exposure assessments. This paper discusses systems biology, biomarkers of effect, and computational toxicology approaches and their relevance to the occupational exposure limit setting process. The systems biology approach evaluates the integration of biological processes and how disruption of these processes by chemicals or other hazards affects disease outcomes. This type of approach could provide information used in delineating the mode of action of the response or toxicity, and may be useful to define the low adverse and no adverse effect levels. Biomarkers of effect are changes measured in biological systems and are considered to be preclinical in nature. Advances in computational methods and experimental -omics methods that allow the simultaneous measurement of families of macromolecules such as DNA, RNA, and proteins in a single analysis have made these systems approaches feasible for broad application. The utility of the information for risk assessments from -omics approaches has shown promise and can provide information on mode of action and dose-response relationships. As these techniques evolve, estimation of internal dose and response biomarkers will be a critical test of these new technologies for application in risk assessment strategies. While proof of concept studies have been conducted that provide evidence of their value, challenges with standardization and harmonization still need to be overcome before these methods are used routinely. PMID:26132979

Systems Biology and Biomarkers of Early Effects for Occupational Exposure Limit Setting.

PubMed

DeBord, D Gayle; Burgoon, Lyle; Edwards, Stephen W; Haber, Lynne T; Kanitz, M Helen; Kuempel, Eileen; Thomas, Russell S; Yucesoy, Berran

2015-01-01

In a recent National Research Council document, new strategies for risk assessment were described to enable more accurate and quicker assessments. This report suggested that evaluating individual responses through increased use of bio-monitoring could improve dose-response estimations. Identification of specific biomarkers may be useful for diagnostics or risk prediction as they have the potential to improve exposure assessments. This paper discusses systems biology, biomarkers of effect, and computational toxicology approaches and their relevance to the occupational exposure limit setting process. The systems biology approach evaluates the integration of biological processes and how disruption of these processes by chemicals or other hazards affects disease outcomes. This type of approach could provide information used in delineating the mode of action of the response or toxicity, and may be useful to define the low adverse and no adverse effect levels. Biomarkers of effect are changes measured in biological systems and are considered to be preclinical in nature. Advances in computational methods and experimental -omics methods that allow the simultaneous measurement of families of macromolecules such as DNA, RNA, and proteins in a single analysis have made these systems approaches feasible for broad application. The utility of the information for risk assessments from -omics approaches has shown promise and can provide information on mode of action and dose-response relationships. As these techniques evolve, estimation of internal dose and response biomarkers will be a critical test of these new technologies for application in risk assessment strategies. While proof of concept studies have been conducted that provide evidence of their value, challenges with standardization and harmonization still need to be overcome before these methods are used routinely.

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

Activity of alkaloids on peptic ulcer: what's new?

PubMed

do Nascimento, Raphaela Francelino; de Sales, Igor Rafael Praxedes; de Oliveira Formiga, Rodrigo; Barbosa-Filho, José Maria; Sobral, Marianna Vieira; Tavares, Josean Fechine; Diniz, Margareth de Fátima Formiga Melo; Batista, Leônia Maria

2015-01-08

Peptic ulcer is a common disease characterized by lesions that affect the mucosa of the esophagus, stomach and/or duodenum, and may extend into the muscular layer of the mucosa. Natural products have played an important role in the process of development and discovery of new drugs, due to their wide structural diversity and present, mostly specific and selective biological activities. Among natural products the alkaloids, biologically active secondary metabolites, that can be found in plants, animals or microorganisms stand out. The alkaloids are compounds consisting of a basic nitrogen atom that may or may not be part of a heterocyclic ring. This review will describe 15 alkaloids with antiulcer activity in animal models and in vitro studies.

Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees.

Treesearch

Lijun Liu; V. Missirian; Matthew S. Zinkgraf; Andrew Groover; V. Filkov

2014-01-01

Background: One of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms. It should be possible, in turn, to apply advanced computational approaches to these datasets to develop models of biological processes. In a practical sense, working with non-model organisms...

Biological Processes Affecting Bioaccumulation, Transfer, and Toxicity of Metal Contaminants in Estuarine Sediments

DTIC Science & Technology

2011-12-01

ER-1503 December 2011 Celia Y. Chen Dartmouth College Nicholas S. Fisher Stonybrook University Joseph R. Shaw Indiana University...and Cd because of their importance in DoD sites and other industrial point sources. Hg comes from the combustion of fossil fuels, cadmium from...investigate the trophic transfer of cadmium , inorganic mercury and methylmercury from phytoplankton to a benthic amphipod to fish, simulating a

Environmental Impact Analysis Process. Supplement to Final Environmental Impact Statement Space Shuttle Program, Vandenberg AFB, California

DTIC Science & Technology

1983-07-01

problems . Six appendices offer more detailed environmental assessments for the key issues of air quality impacts, inadvertent weather modification...research studies in problem areas, and newly- acquired knowledge of the affected environment. The physical, chemi- cal, biological, and...Shuttle program, in conjunction with other projects within the county, will aggravate short-tenm problems concerning housing, and the quality and quantity

Land Cover Land Use Change and Soil Organic Carbon under Climate Variability in the Semi-Arid West African Sahel (1960-2050)

ERIC Educational Resources Information Center

Dieye, Amadou M.

2016-01-01

Land Cover Land Use (LCLU) change affects land surface processes recognized to influence climate change at local, national and global levels. Soil organic carbon is a key component for the functioning of agro-ecosystems and has a direct effect on the physical, chemical and biological characteristics of the soil. The capacity to model and project…

[Cognitive/affective processes, social interaction and social structure].

PubMed

Cicourel, Aaron V

2012-01-01

Research on brain and structural analysis are overlapping but developed most often in independent ways. Here we consider biological mechanisms and environmental pressures for survival as simultaneously creating a gradual intersection of these various registers and changes in collaborative social interaction and communicative skills. We consider the ways humans have learned to characterize their brain life often depend on unexamined "representational redescriptions" that facilitate the depiction of practices.

Effect of chronic mild stress on hippocampal transcriptome in mice selected for high and low stress-induced analgesia and displaying different emotional behaviors.

PubMed

Lisowski, Pawel; Juszczak, Grzegorz R; Goscik, Joanna; Wieczorek, Marek; Zwierzchowski, Lech; Swiergiel, Artur H

2011-01-01

There is increasing evidence that mood disorders may derive from the impact of environmental pressure on genetically susceptible individuals. Stress-induced hippocampal plasticity has been implicated in depression. We studied hippocampal transcriptomes in strains of mice that display high (HA) and low (LA) swim stress-induced analgesia and that differ in emotional behaviors and responses to different classes of antidepressants. Chronic mild stress (CMS) affected expression of a number of genes common for both strains. CMS also produced strain specific changes in expression suggesting that hippocampal responses to stress depend on genotype. Considerably larger number of genes, biological processes, molecular functions, biochemical pathways, and gene networks were affected by CMS in LA than in HA mice. The results suggest that potential drug targets against detrimental effects of stress include glutamate transporters, and cholinergic, cholecystokinin (CCK), glucocorticoids, and thyroid hormones receptors. Furthermore, some biological processes evoked by stress and different between the strains, such as apoptosis, neurogenesis and chromatin modifications, may be responsible for the long-term, irreversible effects of stress and suggest a role for epigenetic regulation of mood related stress responses. Copyright © 2010 Elsevier B.V. and ECNP. All rights reserved.

A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors

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

Webb-Robertson, Bobbie-Jo M.; Matzke, Melissa M.; Jacobs, Jon M.

2011-12-01

Quantification of LC-MS peak intensities assigned during peptide identification in a typical comparative proteomics experiment will deviate from run-to-run of the instrument due to both technical and biological variation. Thus, normalization of peak intensities across a LC-MS proteomics dataset is a fundamental step in pre-processing. However, the downstream analysis of LC-MS proteomics data can be dramatically affected by the normalization method selected . Current normalization procedures for LC-MS proteomics data are presented in the context of normalization values derived from subsets of the full collection of identified peptides. The distribution of these normalization values is unknown a priori. If theymore » are not independent from the biological factors associated with the experiment the normalization process can introduce bias into the data, which will affect downstream statistical biomarker discovery. We present a novel approach to evaluate normalization strategies, where a normalization strategy includes the peptide selection component associated with the derivation of normalization values. Our approach evaluates the effect of normalization on the between-group variance structure in order to identify candidate normalization strategies that improve the structure of the data without introducing bias into the normalized peak intensities.« less

Climate change and coastal environmental risk perceptions in Florida.

PubMed

Carlton, Stuart J; Jacobson, Susan K

2013-11-30

Understanding public perceptions of climate change risks is a prerequisite for effective climate communication and adaptation. Many studies of climate risk perceptions have either analyzed a general operationalization of climate change risk or employed a case-study approach of specific adaptive processes. This study takes a different approach, examining attitudes toward 17 specific, climate-related coastal risks and cognitive, affective, and risk-specific predictors of risk perception. A survey of 558 undergraduates revealed that risks to the physical environment were a greater concern than economic or biological risks. Perceptions of greater physical environment risks were significantly associated with having more pro-environmental attitudes, being female, and being more Democratic-leaning. Perceptions of greater economic risks were significantly associated with having more negative environmental attitudes, being female, and being more Republican-leaning. Perceptions of greater biological risks were significantly associated with more positive environmental attitudes. The findings suggest that focusing on physical environment risks maybe more salient to this audience than communications about general climate change adaptation. The results demonstrate that climate change beliefs and risk perceptions are multifactorial and complex and are shaped by individuals' attitudes and basic beliefs. Climate risk communications need to apply this knowledge to better target cognitive and affective processes of specific audiences, rather than providing simple characterizations of risks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Identification of copy number variants in horses.

PubMed

Doan, Ryan; Cohen, Noah; Harrington, Jessica; Veazey, Kylee; Veazy, Kylee; Juras, Rytis; Cothran, Gus; McCue, Molly E; Skow, Loren; Dindot, Scott V

2012-05-01

Copy number variants (CNVs) represent a substantial source of genetic variation in mammals. However, the occurrence of CNVs in horses and their subsequent impact on phenotypic variation is unknown. We performed a study to identify CNVs in 16 horses representing 15 distinct breeds (Equus caballus) and an individual gray donkey (Equus asinus) using a whole-exome tiling array and the array comparative genomic hybridization methodology. We identified 2368 CNVs ranging in size from 197 bp to 3.5 Mb. Merging identical CNVs from each animal yielded 775 CNV regions (CNVRs), involving 1707 protein- and RNA-coding genes. The number of CNVs per animal ranged from 55 to 347, with median and mean sizes of CNVs of 5.3 kb and 99.4 kb, respectively. Approximately 6% of the genes investigated were affected by a CNV. Biological process enrichment analysis indicated CNVs primarily affected genes involved in sensory perception, signal transduction, and metabolism. CNVs also were identified in genes regulating blood group antigens, coat color, fecundity, lactation, keratin formation, neuronal homeostasis, and height in other species. Collectively, these data are the first report of copy number variation in horses and suggest that CNVs are common in the horse genome and may modulate biological processes underlying different traits observed among horses and horse breeds.

Effect of ozone on the performance of a hybrid ceramic membrane-biological activated carbon process.

PubMed

Guo, Jianning; Hu, Jiangyong; Tao, Yi; Zhu, Jia; Zhang, Xihui

2014-04-01

Two hybrid processes including ozonation-ceramic membrane-biological activated carbon (BAC) (Process A) and ceramic membrane-BAC (Process B) were compared to treat polluted raw water. The performance of hybrid processes was evaluated with the removal efficiencies of turbidity, ammonia and organic matter. The results indicated that more than 99% of particle count was removed by both hybrid processes and ozonation had no significant effect on its removal. BAC filtration greatly improved the removal of ammonia. Increasing the dissolved oxygen to 30.0 mg/L could lead to a removal of ammonia with concentrations as high as 7.80 mg/L and 8.69 mg/L for Processes A and B, respectively. The average removal efficiencies of total organic carbon and ultraviolet absorbance at 254 nm (UV254, a parameter indicating organic matter with aromatic structure) were 49% and 52% for Process A, 51% and 48% for Process B, respectively. Some organic matter was oxidized by ozone and this resulted in reduced membrane fouling and increased membrane flux by 25%-30%. However, pre-ozonation altered the components of the raw water and affected the microorganisms in the BAC, which may impact the removals of organic matter and nitrite negatively. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

ISS Flight 2A.2B (STS-106): Commercial Generic Bioprocessing Apparatus (CGBA) Payload BioServe Space Technologies

NASA Technical Reports Server (NTRS)

Stodieck, Louis; Klaus, David

2001-01-01

The two experiments housed in the Commercial Generic Bioprocessing Apparatus (CGBA) during STS-106 were designed to explore how biological processes are affected by microgravity. The first was a developmental study into the effects of microgravity on motor-neuronal growth in the fruit fly species Drosophila melanogaster and the second study was designed to characterize changes in kidney cell gene expression. The objective of the primary experiment, called NIH-B1, was to determine how gravity affects neuronal development of the D. melanogaster embryo and larvae in microgravity, specifically observing the neural connections to muscle fibers.

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.

Nicotine increases neural response to unpleasant stimuli and anxiety in non-smokers.

PubMed

Kobiella, Andrea; Ulshöfer, Dorothea E; Vollmert, Christian; Vollstädt-Klein, Sabine; Bühler, Mira; Esslinger, Christine; Smolka, Michael N

2011-04-01

Studies in smokers suggest that nicotine might exert anxiolytic, stress-dampening and mood-enhancing effects and beneficially influences neural processing of affective information. Regarding non-smokers, results are inconsistent, and no data exist on the effect of nicotine on neural emotion processing. We applied functional magnetic resonance imaging (fMRI) to assess the influence of nicotine on brain activation during processing of emotional stimuli in 31 non-smokers with a maximum lifetime cigarette consumption of 20 cigarettes. Participants were subjected to two fMRI scans with event-related presentations of images taken from the International Affective Picture System, receiving nicotine (2 mg) and placebo gums in a double-blinded, randomized cross-over design. Furthermore, subjective affect was assessed. Nicotine increased brain activity in response to unpleasant stimuli in the amygdala, anterior cingulate cortex (ACC) and basal ganglia, whereas processing of pleasant stimuli was not altered. Psychophysiological interaction (PPI) analyses revealed that nicotine increased connectivity between the amygdala and the perigenual ACC (pACC) during processing of unpleasant stimuli and decreased connectivity between those structures during processing of pleasant stimuli. Participants reported higher state anxiety under nicotine than placebo. A single dose of nicotine acted as a stressor in non-smokers, leading to increased anxiety and neural activation elicited by unpleasant stimuli as well as altered connectivity within the amygdala-pACC circuit. Besides the possibility that reactions to nicotine may differ between non-smokers and smokers due to tolerance and neuroadaptive processes that occur during prolonged nicotine use, a priori differences in smokers and non-smokers might potentially explain diverse effects of nicotine on affect and emotional reactivity. © 2010 The Authors, Addiction Biology © 2010 Society for the Study of Addiction.

How a High-Gradient Magnetic Field Could Affect Cell Life

NASA Astrophysics Data System (ADS)

Zablotskii, Vitalii; Polyakova, Tatyana; Lunov, Oleg; Dejneka, Alexandr

2016-11-01

The biological effects of high-gradient magnetic fields (HGMFs) have steadily gained the increased attention of researchers from different disciplines, such as cell biology, cell therapy, targeted stem cell delivery and nanomedicine. We present a theoretical framework towards a fundamental understanding of the effects of HGMFs on intracellular processes, highlighting new directions for the study of living cell machinery: changing the probability of ion-channel on/off switching events by membrane magneto-mechanical stress, suppression of cell growth by magnetic pressure, magnetically induced cell division and cell reprograming, and forced migration of membrane receptor proteins. By deriving a generalized form for the Nernst equation, we find that a relatively small magnetic field (approximately 1 T) with a large gradient (up to 1 GT/m) can significantly change the membrane potential of the cell and thus have a significant impact on not only the properties and biological functionality of cells but also cell fate.

How a High-Gradient Magnetic Field Could Affect Cell Life

PubMed Central

Zablotskii, Vitalii; Polyakova, Tatyana; Lunov, Oleg; Dejneka, Alexandr

2016-01-01

The biological effects of high-gradient magnetic fields (HGMFs) have steadily gained the increased attention of researchers from different disciplines, such as cell biology, cell therapy, targeted stem cell delivery and nanomedicine. We present a theoretical framework towards a fundamental understanding of the effects of HGMFs on intracellular processes, highlighting new directions for the study of living cell machinery: changing the probability of ion-channel on/off switching events by membrane magneto-mechanical stress, suppression of cell growth by magnetic pressure, magnetically induced cell division and cell reprograming, and forced migration of membrane receptor proteins. By deriving a generalized form for the Nernst equation, we find that a relatively small magnetic field (approximately 1 T) with a large gradient (up to 1 GT/m) can significantly change the membrane potential of the cell and thus have a significant impact on not only the properties and biological functionality of cells but also cell fate. PMID:27857227

Small Molecule Signaling Agents: The Integrated Chemistry and Biochemistry of Nitrogen Oxides, Oxides of Carbon, Dioxygen, Hydrogen Sulfide, and Their Derived Species

PubMed Central

Fukuto, Jon M.; Carrington, Samantha J.; Tantillo, Dean J.; Harrison, Jason G.; Ignarro, Louis J.; Freeman, Bruce A.; Chen, Andrew; Wink, David A.

2014-01-01

Several small molecule species formally known primarily as toxic gases have, over the past 20 years, been shown to be endogenously generated signaling molecules. The biological signaling associated with the small molecules NO, CO, H2S (and the nonendogenously generated O2), and their derived species have become a topic of extreme interest. It has become increasingly clear that these small molecule signaling agents form an integrated signaling web that affects/regulates numerous physiological processes. The chemical interactions between these species and each other or biological targets is an important factor in their roles as signaling agents. Thus, a fundamental understanding of the chemistry of these molecules is essential to understanding their biological/physiological utility. This review focuses on this chemistry and attempts to establish the chemical basis for their signaling functions. PMID:22263838

The magnitude of linear dichroism of biological tissues as a result of cancer changes

NASA Astrophysics Data System (ADS)

Bojchuk, T. M.; Yermolenko, S. B.; Fedonyuk, L. Y.; Petryshen, O. I.; Guminetsky, S. G.; Prydij, O. G.

2012-01-01

The results of studies of linear dichroism values of different types of biological tissues (human prostate, esophageal epithelial human muscle tissue in rats) both healthy and infected tumor at different stages of development are shown here. The significant differences in magnitude of linear dichroism and its spectral dependence in the spectral range λ = 330 - 750 nm both among the objects of study, and between biotissues: healthy (or affected by benign tumors) and cancer patients are established. It is researched that in all cases in biological tissues (prostate gland, esophagus, human muscle tissue in rats) with cancer the linear dichroism arises, the value of which depends on the type of tissue and time of the tumor process. As for healthy tissues linear dichroism is absent, the results may have diagnostic value for detecting and assessing the degree of development of cancer.

Population biological principles of drug-resistance evolution in infectious diseases.

PubMed

zur Wiesch, Pia Abel; Kouyos, Roger; Engelstädter, Jan; Regoes, Roland R; Bonhoeffer, Sebastian

2011-03-01

The emergence of resistant pathogens in response to selection pressure by drugs and their possible disappearance when drug use is discontinued are evolutionary processes common to many pathogens. Population biological models have been used to study the dynamics of resistance in viruses, bacteria, and eukaryotic microparasites both at the level of the individual treated host and of the treated host population. Despite the existence of generic features that underlie such evolutionary dynamics, different conclusions have been reached about the key factors affecting the rate of resistance evolution and how to best use drugs to minimise the risk of generating high levels of resistance. Improved understanding of generic versus specific population biological aspects will help to translate results between different studies, and allow development of a more rational basis for sustainable drug use than exists at present. Copyright © 2011 Elsevier Ltd. All rights reserved.

The magnitude of linear dichroism of biological tissues as a result of cancer changes

NASA Astrophysics Data System (ADS)

Bojchuk, T. M.; Yermolenko, S. B.; Fedonyuk, L. Y.; Petryshen, O. I.; Guminetsky, S. G.; Prydij, O. G.

2011-09-01

The results of studies of linear dichroism values of different types of biological tissues (human prostate, esophageal epithelial human muscle tissue in rats) both healthy and infected tumor at different stages of development are shown here. The significant differences in magnitude of linear dichroism and its spectral dependence in the spectral range λ = 330 - 750 nm both among the objects of study, and between biotissues: healthy (or affected by benign tumors) and cancer patients are established. It is researched that in all cases in biological tissues (prostate gland, esophagus, human muscle tissue in rats) with cancer the linear dichroism arises, the value of which depends on the type of tissue and time of the tumor process. As for healthy tissues linear dichroism is absent, the results may have diagnostic value for detecting and assessing the degree of development of cancer.

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.

Neuronal coding of implicit emotion categories in the subcallosal cortex in patients with depression.

PubMed

Laxton, Adrian W; Neimat, Joseph S; Davis, Karen D; Womelsdorf, Thilo; Hutchison, William D; Dostrovsky, Jonathan O; Hamani, Clement; Mayberg, Helen S; Lozano, Andres M

2013-11-15

The subcallosal cingulate and adjacent ventromedial prefrontal cortex (collectively referred to here as the subcallosal cortex or SCC) have been identified as key brain areas in emotional processing. The SCC's role in affective valuation as well as severe mood and motivational disturbances, such as major depression, has been largely inferred from measures of neuronal population activity using functional neuroimaging. On the basis of imaging studies, it is unclear whether the SCC predominantly processes 1) negatively valenced affective content, 2) affective arousal, or 3) category-specific affective information. To clarify these putative functional roles of the SCC, we measured single neuron activity in the SCC of 15 human subjects undergoing deep brain stimulation for depression while they viewed emotionally evocative images grouped into categories that varied in emotional valence (pleasantness) and arousal. We found that the majority of responsive neurons were modulated by specific emotion categories, rather than by valence or arousal alone. Moreover, although these emotion-category-specific neurons responded to both positive and negative emotion categories, a significant majority were selective for negatively valenced emotional content. These findings reveal that single SCC neuron activity reflects the automatic valuational processing and implicit emotion categorization of visual stimuli. Furthermore, because of the predominance of neuronal signals in SCC conveying negative affective valuations and the increased activity in this region among depressed people, the effectiveness of depression therapies that alter SCC neuronal activity may relate to the down-regulation of a previously negative emotional processing bias. © 2013 Society of Biological Psychiatry.

Associations of genetic risk scores based on adult adiposity pathways with childhood growth and adiposity measures.

PubMed

Monnereau, Claire; Vogelezang, Suzanne; Kruithof, Claudia J; Jaddoe, Vincent W V; Felix, Janine F

2016-08-18

Results from genome-wide association studies (GWAS) identified many loci and biological pathways that influence adult body mass index (BMI). We aimed to identify if biological pathways related to adult BMI also affect infant growth and childhood adiposity measures. We used data from a population-based prospective cohort study among 3,975 children with a mean age of 6 years. Genetic risk scores were constructed based on the 97 SNPs associated with adult BMI previously identified with GWAS and on 28 BMI related biological pathways based on subsets of these 97 SNPs. Outcomes were infant peak weight velocity, BMI at adiposity peak and age at adiposity peak, and childhood BMI, total fat mass percentage, android/gynoid fat ratio, and preperitoneal fat area. Analyses were performed using linear regression models. A higher overall adult BMI risk score was associated with infant BMI at adiposity peak and childhood BMI, total fat mass, android/gynoid fat ratio, and preperitoneal fat area (all p-values < 0.05). Analyses focused on specific biological pathways showed that the membrane proteins genetic risk score was associated with infant peak weight velocity, and the genetic risk scores related to neuronal developmental processes, hypothalamic processes, cyclicAMP, WNT-signaling, membrane proteins, monogenic obesity and/or energy homeostasis, glucose homeostasis, cell cycle, and muscle biology pathways were associated with childhood adiposity measures (all p-values <0.05). None of the pathways were associated with childhood preperitoneal fat area. A genetic risk score based on 97 SNPs related to adult BMI was associated with peak weight velocity during infancy and general and abdominal fat measurements at the age of 6 years. Risk scores based on genetic variants linked to specific biological pathways, including central nervous system and hypothalamic processes, influence body fat development from early life onwards.

Characterizing and predicting species distributions across environments and scales: Argentine ant occurrences in the eye of the beholder

USGS Publications Warehouse

Menke, S.B.; Holway, D.A.; Fisher, R.N.; Jetz, W.

2009-01-01

Aim: Species distribution models (SDMs) or, more specifically, ecological niche models (ENMs) are a useful and rapidly proliferating tool in ecology and global change biology. ENMs attempt to capture associations between a species and its environment and are often used to draw biological inferences, to predict potential occurrences in unoccupied regions and to forecast future distributions under environmental change. The accuracy of ENMs, however, hinges critically on the quality of occurrence data. ENMs often use haphazardly collected data rather than data collected across the full spectrum of existing environmental conditions. Moreover, it remains unclear how processes affecting ENM predictions operate at different spatial scales. The scale (i.e. grain size) of analysis may be dictated more by the sampling regime than by biologically meaningful processes. The aim of our study is to jointly quantify how issues relating to region and scale affect ENM predictions using an economically important and ecologically damaging invasive species, the Argentine ant (Linepithema humile). Location: California, USA. Methods: We analysed the relationship between sampling sufficiency, regional differences in environmental parameter space and cell size of analysis and resampling environmental layers using two independently collected sets of presence/absence data. Differences in variable importance were determined using model averaging and logistic regression. Model accuracy was measured with area under the curve (AUC) and Cohen's kappa. Results: We first demonstrate that insufficient sampling of environmental parameter space can cause large errors in predicted distributions and biological interpretation. Models performed best when they were parametrized with data that sufficiently sampled environmental parameter space. Second, we show that altering the spatial grain of analysis changes the relative importance of different environmental variables. These changes apparently result from how environmental constraints and the sampling distributions of environmental variables change with spatial grain. Conclusions: These findings have clear relevance for biological inference. Taken together, our results illustrate potentially general limitations for ENMs, especially when such models are used to predict species occurrences in novel environments. We offer basic methodological and conceptual guidelines for appropriate sampling and scale matching. ?? 2009 The Authors Journal compilation ?? 2009 Blackwell Publishing.

Effects of Biochar Amendment on Soil Properties and Soil Carbon Sequestration

NASA Astrophysics Data System (ADS)

Zhang, R.; Zhu, S.

2015-12-01

Biochar addition to soils potentially affects various soil properties and soil carbon sequestration, and these effects are dependent on biochars derived from different feedstock materials and pyrolysis processes. The objective of this study was to investigate the effects of amendment of different biochars on soil physical and biological properties as well as soil carbon sequestration. Biochars were produced with dairy manure and woodchip at temperatures of 300, 500, and 700°C, respectively. Each biochar was mixed at 5% (w/w) with a forest soil and the mixture was incubated for 180 days, during which soil physical and biological properties, and soil respiration rates were measured. Results showed that the biochar addition significantly enhanced the formation of soil macroaggregates at the early incubation time. The biochar application significantly reduced soil bulk density, increased the amount of soil organic matter, and stimulated microbial activity and soil respiration rates at the early incubation stage. Biochar applications improved water retention capacity, with stronger effects by biochars produced at higher pyrolysis temperatures. At the same suction, the soil with woodchip biochars possessed higher water content than with the dairy manure biochars. Biochar addition significantly affected the soil physical and biological properties, which resulted in different soil carbon mineralization rates and the amount of soil carbon storage.

The effect of music performance on the transcriptome of professional musicians.

PubMed

Kanduri, Chakravarthi; Kuusi, Tuire; Ahvenainen, Minna; Philips, Anju K; Lähdesmäki, Harri; Järvelä, Irma

2015-03-25

Music performance by professional musicians involves a wide-spectrum of cognitive and multi-sensory motor skills, whose biological basis is unknown. Several neuroscientific studies have demonstrated that the brains of professional musicians and non-musicians differ structurally and functionally and that musical training enhances cognition. However, the molecules and molecular mechanisms involved in music performance remain largely unexplored. Here, we investigated the effect of music performance on the genome-wide peripheral blood transcriptome of professional musicians by analyzing the transcriptional responses after a 2-hr concert performance and after a 'music-free' control session. The up-regulated genes were found to affect dopaminergic neurotransmission, motor behavior, neuronal plasticity, and neurocognitive functions including learning and memory. Particularly, candidate genes such as SNCA, FOS and DUSP1 that are involved in song perception and production in songbirds, were identified, suggesting an evolutionary conservation in biological processes related to sound perception/production. Additionally, modulation of genes related to calcium ion homeostasis, iron ion homeostasis, glutathione metabolism, and several neuropsychiatric and neurodegenerative diseases implied that music performance may affect the biological pathways that are otherwise essential for the proper maintenance of neuronal function and survival. For the first time, this study provides evidence for the candidate genes and molecular mechanisms underlying music performance.

Dissociative semantic breakdown in Alzheimer's disease: evidence from multiple category fluency test.

PubMed

Ting, Simon Kang Seng; Hameed, Shahul; Earnest, Arul; Tan, Eng-King

2013-07-01

Category-specific semantic dissociation particularly in terms of biological and non-biological dichotomy has been described in Alzheimer's disease (AD). We re-examine above finding by performing multiple superordinate category verbal fluency test in AD patients. We analyze the baseline neuropsychological assessment performance of food and animal fluency test of AD patients from a tertiary hospital that collected prospectively over 5 years period and correlation was calculated by Kappa test. The analysis is stratified according to literacy level (primary: 0-6 years education and secondary: >6 years education) and disease severity (MMSE score: mild 19-24, moderate 13-18 and severe <13). A total of 296 AD patients were analyzed and only fair to moderate agreement between food and animal category fluency test was found especially in the mild AD cases (primary: kappa 0.42; secondary: kappa 0.40). Kappa agreement level increases when disease progress especially in the secondary education group. Food category, which is a more relevant semantic knowledge to Singapore population, is generally more affected. Higher educated subjects appeared to have less semantic dissociation effect when disease progress. Despite less primed in daily life, biological category of semantic knowledge appears to be affected less during AD process in highly urbanized Singapore society. Brain appears to have special protective mechanism towards living things. However, education level seems have a modulation effect towards the biological protective mechanism. Copyright © 2012 Elsevier B.V. All rights reserved.

THERMOREGULATION AND ITS INFLUENCE ON TOXICITY ASSESSMENT

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

Gordon, Christopher J.; Spencer, Pamela J.; Hotchkiss, Jon

2008-02-28

The thermoregulatory system of laboratory rodents is susceptible to a variety of chemical toxicants. Because temperature directly affects the reaction of virtually all biological processes, it is critical to consider how changes in the thermoregulatory response to a toxicant may affect physiological, behavioral, and pathological endpoints. Researchers in industry and government laboratories are often faced with addressing how changes in body temperature of their experimental subjects may affect the outcome of a particular toxicity test and/or screening panel. However, many toxicologists are either unaware of the importance or ignore the potential impact of a toxic-induced change in body temperature. Thismore » paper endeavors to summarize the importance of thermoregulation in the study of toxicology and propose recommendations for thermometry that researchers may utilize in their toxicological studies.« less

Effects of wastewater effluent discharge and treatment facility upgrades on environmental and biological conditions of Indian Creek, Johnson County, Kansas, June 2004 through June 2013

USGS Publications Warehouse

Graham, Jennifer L.; Stone, Mandy L.; Rasmussen, Teresa J.; Foster, Guy M.; Poulton, Barry C.; Paxson, Chelsea R.; Harris, Theodore D.

2014-01-01

Indian Creek is one of the most urban drainage basins in Johnson County, Kansas, and environmental and biological conditions of the creek are affected by contaminants from point and other urban sources. The Johnson County Douglas L. Smith Middle Basin (hereafter referred to as the “Middle Basin”) and Tomahawk Creek Wastewater Treatment Facilities (WWTFs) discharge to Indian Creek. In summer 2010, upgrades were completed to increase capacity and include biological nutrient removal at the Middle Basin facility. There have been no recent infrastructure changes at the Tomahawk Creek facility; however, during 2009, chemically enhanced primary treatment was added to the treatment process for better process settling before disinfection and discharge with the added effect of enhanced phosphorus removal. The U.S. Geological Survey, in cooperation with Johnson County Wastewater, assessed the effects of wastewater effluent on environmental and biological conditions of Indian Creek by comparing two upstream sites to four sites located downstream from the WWTFs using data collected during June 2004 through June 2013. Environmental conditions were evaluated using previously and newly collected discrete and continuous data and were compared with an assessment of biological community composition and ecosystem function along the upstream-downstream gradient. This study improves the understanding of the effects of wastewater effluent on stream-water and streambed sediment quality, biological community composition, and ecosystem function in urban areas. After the addition of biological nutrient removal to the Middle Basin WWTF in 2010, annual mean total nitrogen concentrations in effluent decreased by 46 percent, but still exceeded the National Pollutant Discharge Elimination System (NPDES) wastewater effluent permit concentration goal of 8.0 milligrams per liter (mg/L); however, the NPDES wastewater effluent permit total phosphorus concentration goal of 1.5 mg/L or less was achieved at the Middle Basin WWTF. At the Tomahawk Creek WWTF, after the addition of chemically enhanced primary treatment in 2009, effluent discharges also had total phosphorus concentrations below 1.5 mg/L. After the addition of biological nutrient removal, annual total nitrogen and phosphorus loads from the Middle Basin WWTF decreased by 42 and 54 percent, respectively, even though effluent volume increased by 11 percent. Annual total phosphorus loads from the Tomahawk Creek WWTF after the addition of chemically enhanced primary treatment decreased by 54 percent despite a 33-percent increase in effluent volume. Total nitrogen and phosphorus from the WWTFs contributed between 30 and nearly 100 percent to annual nutrient loads in Indian Creek depending on streamflow conditions. In-stream total nitrogen primarily came from wastewater effluent except during years with the highest streamflows. Most of the in-stream total phosphorus typically came from effluent during dry years and from other urban sources during wet years. During 2010 through 2013, annual mean discharge from the Middle Basin WWTF was about 75 percent of permitted design capacity. Annual nutrient loads likely will increase when the facility is operated at permitted design capacity; however, estimated maximum annual nutrient loads from the Middle Basin WWTF were 27 to 38 percent lower than before capacity upgrades and the addition of biological nutrient removal to treatment processes. Thus, the addition of biological nutrient removal to the Middle Basin wastewater treatment process should reduce overall nutrient loads from the facility even when the facility is operated at permitted design capacity. The effects of wastewater effluent on the water quality of Indian Creek were most evident during below-normal and normal streamflows (about 75 percent of the time) when wastewater effluent represented about 24 percent or more of total streamflow. Wastewater effluent had the most substantial effect on nutrient concentrations in Indian Creek. Total and inorganic nutrient concentrations at the downstream sites during below-normal and normal streamflows were 10 to 100 times higher than at the upstream sites, even after changes in treatment practices at the WWTFs. Median total phosphorus concentrations during below-normal and normal streamflows at a downstream site were 43 percent lower following improvements in wastewater treatment processes. Similar decreases in total nitrogen were not observed, likely because total nitrogen concentrations only decreased in Middle Basin effluent and wastewater contributed a higher percentage to streamflows when nutrient samples were collected during the after-upgrade period. The wastewater effluent discharges to Indian Creek caused changes in stream-water quality that may affect biological community structure and ecosystem processes, including higher concentrations of bioavailable nutrients (nitrate and orthophosphorus) and warmer water temperatures during winter months. Other urban sources of contaminants also caused changes in stream-water quality that may affect biological community structure and ecosystem processes, including higher turbidities downstream from construction areas and higher specific conductance and chloride concentrations during winter months. Chloride concentrations exceeded acute and chronic exposure criteria at all Indian Creek study sites, regardless of wastewater influence, for weeks or months during winter. Streambed sediment chemistry was affected by wastewater (elevated nutrient and organic wastewater-indicator compound concentrations) and other contaminants from urban sources (elevated polyaromatic hydrocarbon concentrations). Overall habitat conditions were suboptimal or marginal at all sites; general decline in habitat conditions along the upstream-downstream gradient likely was caused by the cumulative effects of urbanization with increasing drainage basin size. Wastewater effluent likely affected algal periphyton biomass and community composition, primary production, and community respiration in Indian Creek. Functional stream health, evaluated using a preliminary framework based on primary production and community respiration, was mildly or severely impaired at most downstream sites relative to an urban upstream Indian Creek site. The mechanistic cause of the changes in these biological variables are unclear, though elevated nutrient concentrations were positively correlated with algal biomass, primary production, and community respiration. Macroinvertebrate communities indicated impairment at all sites, and Kansas Department of Health and Environment aquatic life support scores indicated conditions nonsupporting of aquatic life, regardless of wastewater influences. Urban influences, other than wastewater effluent discharge, likely control macroinvertebrate community structure in Indian Creek. Changes in treatment processes at the Middle Basin and Tomahawk Creek WWTFs improved wastewater effluent quality and decreased nutrient loads, but wastewater effluent discharges still had negative effects on the environmental and biological conditions at downstream Indian Creek sites. Wastewater effluent discharge into Indian Creek likely contributed to changes in measures of ecosystem structure (streamflow, water and streambed-sediment chemistry, algal biomass, and algal periphyton community composition) and function (primary production and community respiration) along the upstream-downstream gradient. Wastewater effluent discharges maintained streamflows and increased nutrient concentrations, algal biomass, primary production, and community respiration at the downstream sites. Functional stream health was severely impaired downstream from the Middle Basin WWTF and mildly impaired downstream from the Tomahawk WWTF relative to the urban upstream site. As distance from the Middle Basin WWTF increased, nutrient concentrations, algal biomass, primary production, and community respiration decreased, and functional stream health was no longer impaired 9.5 kilometers downstream from the discharge relative to the urban upstream site. Therefore, although wastewater effluent caused persistent changes in environmental and biological conditions and functional stream health at sites located immediately downstream from WWTF effluent discharges, some recovery to conditions more similar to the urban upstream site occurred within a relatively short distance.

When time affects space: Dispersal ability and extreme weather events determine metacommunity organization in marine sediments.

PubMed

Corte, Guilherme N; Gonçalves-Souza, Thiago; Checon, Helio H; Siegle, Eduardo; Coleman, Ross A; Amaral, A Cecília Z

2018-05-01

Community ecology has traditionally assumed that the distribution of species is mainly influenced by environmental processes. There is, however, growing evidence that environmental (habitat characteristics and biotic interactions) and spatial processes (factors that affect a local assemblage regardless of environmental conditions - typically related to dispersal and movement of species) interactively shape biological assemblages. A metacommunity, which is a set of local assemblages connected by dispersal of individuals, is spatial in nature and can be used as a straightforward approach for investigating the interactive and independent effects of both environmental and spatial processes. Here, we examined (i) how environmental and spatial processes affect the metacommunity organization of marine macroinvertebrates inhabiting the intertidal sediments of a biodiverse coastal ecosystem; (ii) whether the influence of these processes is constant through time or is affected by extreme weather events (storms); and (iii) whether the relative importance of these processes depends on the dispersal abilities of organisms. We found that macrobenthic assemblages are influenced by each of environmental and spatial variables; however, spatial processes exerted a stronger role. We also found that this influence changes through time and is modified by storms. Moreover, we observed that the influence of environmental and spatial processes varies according to the dispersal capabilities of organisms. More effective dispersers (i.e., species with planktonic larvae) are more affected by spatial processes whereas environmental variables had a stronger effect on weaker dispersers (i.e. species with low motility in larval and adult stages). These findings highlight that accounting for spatial processes and differences in species life histories is essential to improve our understanding of species distribution and coexistence patterns in intertidal soft-sediments. Furthermore, it shows that storms modify the structure of coastal assemblages. Given that the influence of spatial and environmental processes is not consistent through time, it is of utmost importance that future studies replicate sampling over different periods so the influence of temporal and stochastic factors on macrobenthic metacommunities can be better understood. Copyright © 2018 Elsevier Ltd. All rights reserved.

Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

PubMed

Hu, Xiaotang; Li, Hongbin

2014-10-01

Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

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.

Microbiological Safety of Animal Wastes Processed by Physical Heat Treatment: An Alternative To Eliminate Human Pathogens in Biological Soil Amendments as Recommended by the Food Safety Modernization Act.

PubMed

Chen, Zhao; Jiang, Xiuping

2017-03-01

Animal wastes have high nutritional value as biological soil amendments of animal origin for plant cultivation in sustainable agriculture; however, they can be sources of some human pathogens. Although composting is an effective way to reduce pathogen levels in animal wastes, pathogens may still survive under certain conditions and persist in the composted products, which potentially could lead to fresh produce contamination. According to the U.S. Food and Drug Administration Food Safety Modernization Act, alternative treatments are recommended for reducing or eliminating human pathogens in raw animal manure. Physical heat treatments can be considered an effective method to inactivate pathogens in animal wastes. However, microbial inactivation in animal wastes can be affected by many factors, such as composition of animal wastes, type and physiological stage of the tested microorganism, and heat source. Following some current processing guidelines for physical heat treatments may not be adequate for completely eliminating pathogens from animal wastes. Therefore, this article primarily reviews the microbiological safety and economic value of physically heat-treated animal wastes as biological soil amendments.

Carbon Cycling and Biosequestration Integrating Biology and Climate Through Systems Science Report from the March 2008 Workshop

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

Graber, J.; Amthor, J.; Dahlman, R.

2008-12-01

One of the most daunting challenges facing science in the 21st Century is to predict how Earth's ecosystems will respond to global climate change. The global carbon cycle plays a central role in regulating atmospheric carbon dioxide (CO{sub 2}) levels and thus Earth's climate, but our basic understanding of the myriad of tightly interlinked biological processes that drive the global carbon cycle remains limited at best. Whether terrestrial and ocean ecosystems will capture, store, or release carbon is highly dependent on how changing climate conditions affect processes performed by the organisms that form Earth's biosphere. Advancing our knowledge of biologicalmore » components of the global carbon cycle is thus crucial to predicting potential climate change impacts, assessing the viability of climate change adaptation and mitigation strategies, and informing relevant policy decisions. Global carbon cycling is dominated by the paired biological processes of photosynthesis and respiration. Photosynthetic plants and microbes of Earth's land-masses and oceans use solar energy to transform atmospheric CO{sub 2} into organic carbon. The majority of this organic carbon is rapidly consumed by plants or microbial decomposers for respiration and returned to the atmosphere as CO{sub 2}. Coupling between the two processes results in a near equilibrium between photosynthesis and respiration at the global scale, but some fraction of organic carbon also remains in stabilized forms such as biomass, soil, and deep ocean sediments. This process, known as carbon biosequestration, temporarily removes carbon from active cycling and has thus far absorbed a substantial fraction of anthropogenic carbon emissions.« less

Transcriptomic characterization of temperature stress responses in larval zebrafish.

PubMed

Long, Yong; Li, Linchun; Li, Qing; He, Xiaozhen; Cui, Zongbin

2012-01-01

Temperature influences nearly all biochemical, physiological and life history activities of fish, but the molecular mechanisms underlying the temperature acclimation remains largely unknown. Previous studies have identified many temperature-regulated genes in adult tissues; however, the transcriptional responses of fish larvae to temperature stress are not well understood. In this study, we characterized the transcriptional responses in larval zebrafish exposed to cold or heat stress using microarray analysis. In comparison with genes expressed in the control at 28 °C, a total of 2680 genes were found to be affected in 96 hpf larvae exposed to cold (16 °C) or heat (34 °C) for 2 and 48h and most of these genes were expressed in a temperature-specific and temporally regulated manner. Bioinformatic analysis identified multiple temperature-regulated biological processes and pathways. Biological processes overrepresented among the earliest genes induced by temperature stress include regulation of transcription, nucleosome assembly, chromatin organization and protein folding. However, processes such as RNA processing, cellular metal ion homeostasis and protein transport and were enriched in genes up-regulated under cold exposure for 48 h. Pathways such as mTOR signalling, p53 signalling and circadian rhythm were enriched among cold-induced genes, while adipocytokine signalling, protein export and arginine and praline metabolism were enriched among heat-induced genes. Although most of these biological processes and pathways were specifically regulated by cold or heat, common responses to both cold and heat stresses were also found. Thus, these findings provide new interesting clues for elucidation of mechanisms underlying the temperature acclimation in fish.

Activation and Resolution of Periodontal Inflammation and Its Systemic Impact

PubMed Central

Hasturk, Hatice; Kantarci, Alpdogan

2015-01-01

Inflammation is a highly organized event impacting upon organs, tissues and biological systems. Periodontal diseases are characterized by dysregulation or dysfunction of resolution pathways of inflammation resulting in a failure of healing and a dominant chronic, progressive, destructive and predominantly unresolved inflammation. The biological consequences of inflammatory processes may be independent of the etiological agents such as trauma, microbial organisms and stress. The impact of the inflammatory pathological process depends upon the affected tissues or organ system. Whilst mediators are similar, there is a tissue specificity for the inflammatory events. It is plausible that inflammatory processes in one organ could directly lead to pathologies in another organ or tissue. Communication between distant parts of the body and their inflammatory status is also mediated by common signaling mechanisms mediated via cells and soluble mediators. This review focuses on periodontal inflammation, its systemic associations and advances in therapeutic approaches based on mediators acting through orchestration of natural pathway to resolution of inflammation. We also discuss a new treatment concept where natural pathways of resolution of periodontal inflammation can be used to limit systemic inflammation and promote healing and regeneration. PMID:26252412

Developmental mechanisms underlying variation in craniofacial disease and evolution.

PubMed

Fish, Jennifer L

2016-07-15

Craniofacial disease phenotypes exhibit significant variation in penetrance and severity. Although many genetic contributions to phenotypic variation have been identified, genotype-phenotype correlations remain imprecise. Recent work in evolutionary developmental biology has exposed intriguing developmental mechanisms that potentially explain incongruities in genotype-phenotype relationships. This review focuses on two observations from work in comparative and experimental animal model systems that highlight how development structures variation. First, multiple genetic inputs converge on relatively few developmental processes. Investigation of when and how variation in developmental processes occurs may therefore help predict potential genetic interactions and phenotypic outcomes. Second, genetic mutation is typically associated with an increase in phenotypic variance. Several models outlining developmental mechanisms underlying mutational increases in phenotypic variance are discussed using Satb2-mediated variation in jaw size as an example. These data highlight development as a critical mediator of genotype-phenotype correlations. Future research in evolutionary developmental biology focusing on tissue-level processes may help elucidate the "black box" between genotype and phenotype, potentially leading to novel treatment, earlier diagnoses, and better clinical consultations for individuals affected by craniofacial anomalies. Copyright © 2015 Elsevier Inc. All rights reserved.

[Effect of pineal peptide on parameters of the biological age and life span in mice].

PubMed

Anisimov, V N; Khavinson, V Kh; Zavarzina, N Iu; Zabezhinskiĭ, M A; Zimina, O A; Popovich, I G; Shtylik, A V; Arutiunian, A V; Oparina, T I; Prokopenko, V M

2001-01-01

Female CBA mice were injected with s.c. synthetic tetrapeptide Epithalon from a 6-month age until death. The drug failed to affect the body weight or food consumption, physical activity or behavioural parameters. However, it slowed down the age-related switching off of the estrus function, decreased body temperature, decelerated free redical processes, prolonged the mice life span with an accompanying drop in spontaneous tumour incidence.

A horizon scan of global conservation issues for 2013.

PubMed

Sutherland, William J; Bardsley, Sarah; Clout, Mick; Depledge, Michael H; Dicks, Lynn V; Fellman, Liz; Fleishman, Erica; Gibbons, David W; Keim, Brandon; Lickorish, Fiona; Margerison, Ceri; Monk, Kathryn A; Norris, Kenneth; Peck, Lloyd S; Prior, Stephanie V; Scharlemann, Jörn P W; Spalding, Mark D; Watkinson, Andrew R

2013-01-01

This paper presents the findings of our fourth annual horizon-scanning exercise, which aims to identify topics that increasingly may affect conservation of biological diversity. The 15 issues were identified via an iterative, transferable process by a team of professional horizon scanners, researchers, practitioners, and a journalist. The 15 topics include the commercial use of antimicrobial peptides, thorium-fuelled nuclear power, and undersea oil production. Copyright © 2012 Elsevier Ltd. All rights reserved.

Biogeochemistry of hypersaline microbial mats illustrates the dynamics of modern microbial ecosystems and the early evolution of the biosphere

NASA Technical Reports Server (NTRS)

Des Marais, David J.

2003-01-01

Photosynthetic microbial mats are remarkably complete self-sustaining ecosystems at the millimeter scale, yet they have substantially affected environmental processes on a planetary scale. These mats may be direct descendents of the most ancient biological communities in which even oxygenic photosynthesis might have developed. Photosynthetic mats are excellent natural laboratories to help us to learn how microbial populations associate to control dynamic biogeochemical gradients.

Mechanical Adaptivity as a Process: Implications to New Materials and Material System Design

DTIC Science & Technology

2012-08-01

Deliver. Rev. 2004 Microactuators and valves Uses: • Drug delivery • Microfluidic actuators, valves , and pumps • Chemical and biological Sensors... paper where they did a study with f the stoichiometric parameter involved in the reduction step, and they looked at 2 X* - both far away from the...through strain? How do varying material properties affect behavior? Smith, Vaia et al. submitted 2012 23 Fibrous Paper Next Step: Heterogeneous

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.

Enhanced biological phosphorus removal with different carbon sources.

PubMed

Shen, Nan; Zhou, Yan

2016-06-01

Enhanced biological phosphorus removal (EBPR) process is one of the most economical and sustainable methods for phosphorus removal from wastewater. However, the performance of EBPR can be affected by available carbon sources types in the wastewater that may induce different functional microbial communities in the process. Glycogen accumulating organisms (GAOs) and polyphosphate accumulating organisms (PAOs) are commonly found by coexisting in the EBPR process. Predominance of GAO population may lead to EBPR failure due to the competition on carbon source with PAO without contributing phosphorus removal. Carbon sources indeed play an important role in alteration of PAOs and GAOs in EBPR processes. Various types of carbon sources have been investigated for EBPR performance. Certain carbon sources tend to enrich specific groups of GAOs and/or PAOs. This review summarizes the types of carbon sources applied in EBPR systems and highlights the roles of these carbon sources in PAO and GAO competition. Both single (e.g., acetate, propionate, glucose, ethanol, and amino acid) and complex carbon sources (e.g., yeast extract, peptone, and mixed carbon sources) are discussed in this review. Meanwhile, the environmental friendly and economical carbon sources that are derived from waste materials, such as crude glycerol and wasted sludge, are also discussed and compared.

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.

Meat science: From proteomics to integrated omics towards system biology.

PubMed

D'Alessandro, Angelo; Zolla, Lello

2013-01-14

Since the main ultimate goal of farm animal raising is the production of proteins for human consumption, research tools to investigate proteins play a major role in farm animal and meat science. Indeed, proteomics has been applied to the field of farm animal science to monitor in vivo performances of livestock animals (growth performances, fertility, milk quality etc.), but also to further our understanding of the molecular processes at the basis of meat quality, which are largely dependent on the post mortem biochemistry of the muscle, often in a species-specific way. Post mortem alterations to the muscle proteome reflect the biological complexity of the process of "muscle to meat conversion," a process that, despite decades of advancements, is all but fully understood. This is mainly due to the enormous amounts of variables affecting meat tenderness per se, including biological factors, such as animal species, breed specific-characteristic, muscle under investigation. However, it is rapidly emerging that the tender meat phenotype is not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as the rearing environment, feeding conditions, physical activity, administration of hormonal growth promotants, pre-slaughter handling and stress, post mortem handling. From this intricate scenario, biochemical approaches and systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion. The growing integration of omics disciplines in the field of systems biology will soon contribute to take further steps forward. Copyright © 2012 Elsevier B.V. All rights reserved.

The complexities of skeletal biology

NASA Technical Reports Server (NTRS)

Karsenty, Gerard

2003-01-01

For a long time, the skeleton was seen as an amorphous tissue of little biological interest. But such a view ignored the large number of genetic and degenerative diseases affecting this organ. Over the past 15 years, molecular and genetic studies have modified our understanding of skeletal biology. By so doing this progress has affected our understanding of diseases and suggested in many instances new therapeutic opportunities.

Pre-Treatment effects of peripheral tumors on brain and behavior: Neuroinflammatory mechanisms in humans and rodents

PubMed Central

Schrepf, Andrew; Lutgendorf, Susan K.; Pyter, Leah M.

2015-01-01

Cancer patients suffer high levels of affective and cognitive disturbances, which have been attributed to diagnosis-related distress, impairment of quality of life, and side effects of primary treatment. An inflammatory microenvironment is also a feature of the vast majority of solid tumors. However, the ability of tumor-associated biological processes to affect the central nervous system (CNS) has only recently been explored in the context of symptoms of depression and cognitive disturbances. In this review, we summarize the burgeoning evidence from rodent cancer models that solid tumors alter neurobiological pathways and subsequent behavioral processes with relevance to affective and cognitive disturbances reported in human cancer populations. We consider, in parallel, the evidence from human clinical cancer research demonstrating that affective and cognitive disturbances are common in some malignancies prior to diagnosis and treatment. We further consider the underlying neurobiological pathways, including altered neuroinflammation, tryptophan metabolism, prostaglandin synthesis and associated neuroanatomical changes, that are most strongly implicated in the rodent literature and supported by analogous evidence from human cancer populations. We focus on the implications of these findings for behavioral researchers and clinicians, with particular emphasis on methodological issues and areas of future research. PMID:25958011

Familial Transmission of Hospital-Treated Varicose Veins in Adoptees: A Swedish Family Study.

PubMed

Kohno, Kunie; Niihara, Hiroyuki; Li, Xinjun; Hamano, Tsuyoshi; Nabika, Toru; Shiwaku, Kuninori; Isomura, Minoru; Morita, Eishin; Sundquist, Kristina; Zöller, Bengt

2016-09-01

Varicose veins (VVs) cluster in families, but the familial risk of VVs has not been determined among adoptees. The aim was to estimate whether the familial transmission of VVs is related to disease in biological and/or adoptive parents. The Swedish Multi-Generation Register and the Swedish Patient Register were used to follow all Swedish-born adoptees (born 1932 through 2004) that could be linked to both their biological and their adoptive parents (n = 80,214; 50% females). The risk of VVs was estimated in adoptees with at least 1 biological parent with VVs, but no adoptive parent with VVs (n = 187) compared with adoptees without a biological or adoptive parent with VVs (n = 1,758). The risk of VVs was also determined in adoptees with at least 1 adoptive parent, but no biological parent with VVs (n = 87), and in adoptees with both biological and adoptive parents affected (n = 21). Adoptees from an affected biological parent, but no adoptive parent, were more likely to have VVs than adoptees from an unaffected biological or adoptive parent (standard incidence ratio [SIR] = 2.21; 95% CI, 1.91-2.55). The familial SIR for adoptees with both an affected biological parent and an adoptive parent was 4.58 (95% CI, 2.83-7.01). Adoptees with an affected adoptive parent but no biological parent were not at increased risk of VVs (SIR = 1.15; 95% CI, 0.92-1.42). These novel findings suggest that genetic factors make a strong contribution to the familial transmission of VVs from parents to offspring, although familial environmental factors might contribute. Copyright © 2016 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Metabolic Free Energy and Biological Codes: A 'Data Rate Theorem' Aging Model.

PubMed

Wallace, Rodrick

2015-06-01

A famous argument by Maturana and Varela (Autopoiesis and cognition. Reidel, Dordrecht, 1980) holds that the living state is cognitive at every scale and level of organization. Since it is possible to associate many cognitive processes with 'dual' information sources, pathologies can sometimes be addressed using statistical models based on the Shannon Coding, the Shannon-McMillan Source Coding, the Rate Distortion, and the Data Rate Theorems, which impose necessary conditions on information transmission and system control. Deterministic-but-for-error biological codes do not directly invoke cognition, but may be essential subcomponents within larger cognitive processes. A formal argument, however, places such codes within a similar framework, with metabolic free energy serving as a 'control signal' stabilizing biochemical code-and-translator dynamics in the presence of noise. Demand beyond available energy supply triggers punctuated destabilization of the coding channel, affecting essential biological functions. Aging, normal or prematurely driven by psychosocial or environmental stressors, must interfere with the routine operation of such mechanisms, initiating the chronic diseases associated with senescence. Amyloid fibril formation, intrinsically disordered protein logic gates, and cell surface glycan/lectin 'kelp bed' logic gates are reviewed from this perspective. The results generalize beyond coding machineries having easily recognizable symmetry modes, and strip a layer of mathematical complication from the study of phase transitions in nonequilibrium biological systems.

Dissimilatory perchlorate reduction: a review.

PubMed

Bardiya, Nirmala; Bae, Jae-Ho

2011-05-20

In the United States anthropogenic activities are mainly responsible for the wide spread perchlorate contamination of drinking water, surface water, groundwater, and soil. Even at microgram levels, perchlorate causes toxicity to flora and fauna and affects growth, metabolism and reproduction in humans and animals. Reports of antithyroid effects of perchlorate and its detection in common food items have raised serious public health concerns, leading to extensive decontamination efforts in recent years. Several physico-chemical removal and biological decontamination processes are being developed. Although promising, ion exchange is a non-selective and incomplete process as it merely transfers perchlorate from water to the resin. The perchlorate-laden spent resins (perchlorate 200-500 mg L(-1)) require regeneration resulting in production of concentrated brine (6-12% NaCl) or caustic waste streams. On the contrary, biological reduction completely degrades perchlorate into O(2) and innocuous Cl(-). High reduction potential of ClO(4)(-)/Cl(-) (E° =∼ 1.28 V) and ClO(3)(-)/Cl(-) pairs (E° =1.03 V) makes these contaminants thermodynamically ideal e(-) acceptors for microbial reduction. In recent years unique dissimilatory perchlorate reducing bacteria have been isolated and detailed studies pertaining to their microbiological, biochemical, genetics and phylogenetic aspects have been undertaken which is the subject of this review article while the various physico-chemical removal and biological reduction processes have been reviewed by others. Copyright © 2010 Elsevier GmbH. All rights reserved.

Parasite-mediated predation between native and invasive amphipods.

PubMed Central

MacNeil, Calum; Dick, Jaimie T A; Hatcher, Melanie J; Terry, Rebecca S; Smith, Judith E; Dunn, Alison M

2003-01-01

Parasites can structure biological communities directly through population regulation and indirectly by processes such as apparent competition. However, the role of parasites in the process of biological invasion is less well understood and mechanisms of parasite mediation of predation among hosts are unclear. Mutual predation between native and invading species is an important factor in determining the outcome of invasions in freshwater amphipod communities. Here, we show that parasites mediate mutual intraguild predation among native and invading species and may thereby facilitate the invasion process. We find that the native amphipod Gammarus duebeni celticus is host to a microsporidian parasite, Pleistophora sp. (new species), with a frequency of infection of 0-90%. However, the parasite does not infect three invading species, G. tigrinus, G. pulex and Crangonyx pseudogracilis. In field and laboratory manipulations, we show that the parasite exhibits cryptic virulence: the parasite does not affect host fitness in single-species populations, but virulence becomes apparent when the native and invading species interact. That is, infection has no direct effect on G. d. celticus survivorship, size or fecundity; however, in mixed-species experiments, parasitized natives show a reduced capacity to prey on the smaller invading species and are more likely to be preyed upon by the largest invading species. Thus, by altering dominance relationships and hierarchies of mutual predation, parasitism strongly influences, and has the potential to change, the outcome of biological invasions. PMID:12816645

Lost at sea: ocean acidification undermines larval fish orientation via altered hearing and marine soundscape modification.

PubMed

Rossi, Tullio; Nagelkerken, Ivan; Pistevos, Jennifer C A; Connell, Sean D

2016-01-01

The dispersal of larvae and their settlement to suitable habitat is fundamental to the replenishment of marine populations and the communities in which they live. Sound plays an important role in this process because for larvae of various species, it acts as an orientational cue towards suitable settlement habitat. Because marine sounds are largely of biological origin, they not only carry information about the location of potential habitat, but also information about the quality of habitat. While ocean acidification is known to affect a wide range of marine organisms and processes, its effect on marine soundscapes and its reception by navigating oceanic larvae remains unknown. Here, we show that ocean acidification causes a switch in role of present-day soundscapes from attractor to repellent in the auditory preferences in a temperate larval fish. Using natural CO2 vents as analogues of future ocean conditions, we further reveal that ocean acidification can impact marine soundscapes by profoundly diminishing their biological sound production. An altered soundscape poorer in biological cues indirectly penalizes oceanic larvae at settlement stage because both control and CO2-treated fish larvae showed lack of any response to such future soundscapes. These indirect and direct effects of ocean acidification put at risk the complex processes of larval dispersal and settlement. © 2016 The Author(s).

Contaminants of emerging concern presence and adverse effects in fish: A case study in the Laurentian Great Lakes.

PubMed

Jorgenson, Zachary G; Thomas, Linnea M; Elliott, Sarah M; Cavallin, Jenna E; Randolph, Eric C; Choy, Steven J; Alvarez, David A; Banda, Jo A; Gefell, Daniel J; Lee, Kathy E; Furlong, Edward T; Schoenfuss, Heiko L

2018-05-01

The Laurentian Great Lakes are a valuable natural resource that is affected by contaminants of emerging concern (CECs), including sex steroid hormones, personal care products, pharmaceuticals, industrial chemicals, and new generation pesticides. However, little is known about the fate and biological effects of CECs in tributaries to the Great Lakes. In the current study, 16 sites on three rivers in the Great Lakes basin (Fox, Cuyahoga, and Raquette Rivers) were assessed for CEC presence using polar organic chemical integrative samplers (POCIS) and grab water samplers. Biological activity was assessed through a combination of in vitro bioassays (focused on estrogenic activity) and in vivo assays with larval fathead minnows. In addition, resident sunfish, largemouth bass, and white suckers were assessed for changes in biological endpoints associated with CEC exposure. CECs were present in all water samples and POCIS extracts. A total of 111 and 97 chemicals were detected in at least one water sample and POCIS extract, respectively. Known estrogenic chemicals were detected in water samples at all 16 sites and in POCIS extracts at 13 sites. Most sites elicited estrogenic activity in bioassays. Ranking sites and rivers based on water chemistry, POCIS chemistry, or total in vitro estrogenicity produced comparable patterns with the Cuyahoga River ranking as most and the Raquette River as least affected by CECs. Changes in biological responses grouped according to physiological processes, and differed between species but not sex. The Fox and Cuyahoga Rivers often had significantly different patterns in biological response Our study supports the need for multiple lines of evidence and provides a framework to assess CEC presence and effects in fish in the Laurentian Great Lakes basin. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Multi-isotope Tracer Approach Linking Land Use With Carbon and Nitrogen Cycling in the San Joaquin River System

NASA Astrophysics Data System (ADS)

Young, M. B.; Kendall, C.; Silva, S. R.; Dahlgren, R. A.; Stringfellow, W. T.

2008-12-01

The San Joaquin River (SJR) is a large hypereutrophic river located in the Central Valley, California, a major agricultural region. Nutrient subsidies, algae, and other organic material from the San Joaquin River contribute to periods of low dissolved oxygen in the Stockton Deep Water Ship Channel, inhibiting salmon migration. We used a multi-isotope approach to link nitrate and particulate organic matter (POM) to different sources and related land uses. The isotope data was also used to better understand the physical and biological processes controlling the distribution of nitrate and POM throughout the river system. Samples collected from the mainstem SJR and tributaries twice-monthly to monthly between March 2005 and December 2007 were analyzed for nitrate, POM, and water isotopes. There are many land uses surrounding the SJR and its tributaries, including multiple types of agriculture, dairies, wetlands, and urban areas. Samples from SJR tributaries containing both major and minor contributions of wetland discharge generally had distinct nitrate and POM isotope signatures compared to other tributaries. Unique nitrate and POM isotope signatures associated with wetland discharges may reflect anaerobic biological processes occurring in flooded soils. For the mainstem SJR, we applied an isotope mass balance approach using nitrate and water isotopes to calculate the expected downstream isotope values based upon measured inputs from known water sources such as drains and tributaries. Differences between the calculated downstream isotope values and the measured values indicate locations and time periods when either biological processes such as algal uptake, or physical process such as the input of unidentified water sources, significantly altered the isotope signatures of water, POM, or nitrate within the SJR. This research will provide a better understanding of how different land uses affect the delivery of carbon and nitrogen to the SJR, and will provide a better understanding of the physical and biological processes occurring within the mainstem SJR.

Systems Genetics Analysis of GWAS reveals Novel Associations between Key Biological Processes and Coronary Artery Disease

PubMed Central

Ghosh, Sujoy; Vivar, Juan; Nelson, Christopher P; Willenborg, Christina; Segrè, Ayellet V; Mäkinen, Ville-Petteri; Nikpay, Majid; Erdmann, Jeannette; Blankenberg, Stefan; O'Donnell, Christopher; März, Winfried; Laaksonen, Reijo; Stewart, Alexandre FR; Epstein, Stephen E; Shah, Svati H; Granger, Christopher B; Hazen, Stanley L; Kathiresan, Sekar; Reilly, Muredach P; Yang, Xia; Quertermous, Thomas; Samani, Nilesh J; Schunkert, Heribert; Assimes, Themistocles L; McPherson, Ruth

2016-01-01

Objective Genome-wide association (GWA) studies have identified multiple genetic variants affecting the risk of coronary artery disease (CAD). However, individually these explain only a small fraction of the heritability of CAD and for most, the causal biological mechanisms remain unclear. We sought to obtain further insights into potential causal processes of CAD by integrating large-scale GWA data with expertly curated databases of core human pathways and functional networks. Approaches and Results Employing pathways (gene sets) from Reactome, we carried out a two-stage gene set enrichment analysis strategy. From a meta-analyzed discovery cohort of 7 CADGWAS data sets (9,889 cases/11,089 controls), nominally significant gene-sets were tested for replication in a meta-analysis of 9 additional studies (15,502 cases/55,730 controls) from the CARDIoGRAM Consortium. A total of 32 of 639 Reactome pathways tested showed convincing association with CAD (replication p<0.05). These pathways resided in 9 of 21 core biological processes represented in Reactome, and included pathways relevant to extracellular matrix integrity, innate immunity, axon guidance, and signaling by PDRF, NOTCH, and the TGF-β/SMAD receptor complex. Many of these pathways had strengths of association comparable to those observed in lipid transport pathways. Network analysis of unique genes within the replicated pathways further revealed several interconnected functional and topologically interacting modules representing novel associations (e.g. semaphorin regulated axonal guidance pathway) besides confirming known processes (lipid metabolism). The connectivity in the observed networks was statistically significant compared to random networks (p<0.001). Network centrality analysis (‘degree’ and ‘betweenness’) further identified genes (e.g. NCAM1, FYN, FURIN etc.) likely to play critical roles in the maintenance and functioning of several of the replicated pathways. Conclusions These findings provide novel insights into how genetic variation, interpreted in the context of biological processes and functional interactions among genes, may help define the genetic architecture of CAD. PMID:25977570

A statistical approach to quasi-extinction forecasting.

PubMed

Holmes, Elizabeth Eli; Sabo, John L; Viscido, Steven Vincent; Fagan, William Fredric

2007-12-01

Forecasting population decline to a certain critical threshold (the quasi-extinction risk) is one of the central objectives of population viability analysis (PVA), and such predictions figure prominently in the decisions of major conservation organizations. In this paper, we argue that accurate forecasting of a population's quasi-extinction risk does not necessarily require knowledge of the underlying biological mechanisms. Because of the stochastic and multiplicative nature of population growth, the ensemble behaviour of population trajectories converges to common statistical forms across a wide variety of stochastic population processes. This paper provides a theoretical basis for this argument. We show that the quasi-extinction surfaces of a variety of complex stochastic population processes (including age-structured, density-dependent and spatially structured populations) can be modelled by a simple stochastic approximation: the stochastic exponential growth process overlaid with Gaussian errors. Using simulated and real data, we show that this model can be estimated with 20-30 years of data and can provide relatively unbiased quasi-extinction risk with confidence intervals considerably smaller than (0,1). This was found to be true even for simulated data derived from some of the noisiest population processes (density-dependent feedback, species interactions and strong age-structure cycling). A key advantage of statistical models is that their parameters and the uncertainty of those parameters can be estimated from time series data using standard statistical methods. In contrast for most species of conservation concern, biologically realistic models must often be specified rather than estimated because of the limited data available for all the various parameters. Biologically realistic models will always have a prominent place in PVA for evaluating specific management options which affect a single segment of a population, a single demographic rate, or different geographic areas. However, for forecasting quasi-extinction risk, statistical models that are based on the convergent statistical properties of population processes offer many advantages over biologically realistic models.

Food supply confers calcifiers resistance to ocean acidification.

PubMed

Ramajo, Laura; Pérez-León, Elia; Hendriks, Iris E; Marbà, Núria; Krause-Jensen, Dorte; Sejr, Mikael K; Blicher, Martin E; Lagos, Nelson A; Olsen, Ylva S; Duarte, Carlos M

2016-01-18

Invasion of ocean surface waters by anthropogenic CO2 emitted to the atmosphere is expected to reduce surface seawater pH to 7.8 by the end of this century compromising marine calcifiers. A broad range of biological and mineralogical mechanisms allow marine calcifiers to cope with ocean acidification, however these mechanisms are energetically demanding which affect other biological processes (trade-offs) with important implications for the resilience of the organisms against stressful conditions. Hence, food availability may play a critical role in determining the resistance of calcifiers to OA. Here we show, based on a meta-analysis of existing experimental results assessing the role of food supply in the response of organisms to OA, that food supply consistently confers calcifiers resistance to ocean acidification.

Food supply confers calcifiers resistance to ocean acidification

NASA Astrophysics Data System (ADS)

Ramajo, Laura; Pérez-León, Elia; Hendriks, Iris E.; Marbà, Núria; Krause-Jensen, Dorte; Sejr, Mikael K.; Blicher, Martin E.; Lagos, Nelson A.; Olsen, Ylva S.; Duarte, Carlos M.

2016-01-01

Invasion of ocean surface waters by anthropogenic CO2 emitted to the atmosphere is expected to reduce surface seawater pH to 7.8 by the end of this century compromising marine calcifiers. A broad range of biological and mineralogical mechanisms allow marine calcifiers to cope with ocean acidification, however these mechanisms are energetically demanding which affect other biological processes (trade-offs) with important implications for the resilience of the organisms against stressful conditions. Hence, food availability may play a critical role in determining the resistance of calcifiers to OA. Here we show, based on a meta-analysis of existing experimental results assessing the role of food supply in the response of organisms to OA, that food supply consistently confers calcifiers resistance to ocean acidification.

Regulation of the Rhythmic Emission of Plant Volatiles by the Circadian Clock.

PubMed

Zeng, Lanting; Wang, Xiaoqin; Kang, Ming; Dong, Fang; Yang, Ziyin

2017-11-13

Like other organisms, plants have endogenous biological clocks that enable them to organize their metabolic, physiological, and developmental processes. The representative biological clock is the circadian system that regulates daily (24-h) rhythms. Circadian-regulated changes in growth have been observed in numerous plants. Evidence from many recent studies indicates that the circadian clock regulates a multitude of factors that affect plant metabolites, especially emitted volatiles that have important ecological functions. Here, we review recent progress in research on plant volatiles showing rhythmic emission under the regulation of the circadian clock, and on how the circadian clock controls the rhythmic emission of plant volatiles. We also discuss the potential impact of other factors on the circadian rhythmic emission of plant volatiles.

Space Station Centrifuge: A Requirement for Life Science Research

NASA Technical Reports Server (NTRS)

Smith, Arthur H.; Fuller, Charles A.; Johnson, Catherine C.; Winget, Charles M.

1992-01-01

A centrifuge with the largest diameter that can be accommodated on Space Station Freedom is required to conduct life science research in the microgravity environment of space. (This was one of the findings of a group of life scientists convened at the University of California, Davis, by Ames Research Center.) The centrifuge will be used as a research tool to understand how gravity affects biological processes; to provide an on-orbit one-g control; and to assess the efficacy of using artificial gravity to counteract the deleterious biological effect of space flight. The rationale for the recommendation and examples of using ground-based centrifugation for animal and plant acceleration studies are presented. Included are four appendixes and an extensive bibliography of hypergravity studies.

Nutrition and skin.

PubMed

Pappas, Apostolos; Liakou, Aikaterini; Zouboulis, Christos C

2016-09-01

Nutrition has long been associated with skin health, including all of its possible aspects from beauty to its integrity and even the aging process. Multiple pathways within skin biology are associated with the onset and clinical course of various common skin diseases, such as acne, atopic dermatitis, aging, or even photoprotection. These conditions have been shown to be critically affected by nutritional patterns and dietary interventions where well-documented studies have demonstrated beneficial effects of essential nutrients on impaired skin structural and functional integrity and have restored skin appearance and health. Although the subject could be vast, the intention of this review is to provide the most relevant and the most well-documented information on the role of nutrition in common skin conditions and its impact on skin biology.

Food supply confers calcifiers resistance to ocean acidification

PubMed Central

Ramajo, Laura; Pérez-León, Elia; Hendriks, Iris E.; Marbà, Núria; Krause-Jensen, Dorte; Sejr, Mikael K.; Blicher, Martin E.; Lagos, Nelson A.; Olsen, Ylva S.; Duarte, Carlos M.

2016-01-01

Invasion of ocean surface waters by anthropogenic CO2 emitted to the atmosphere is expected to reduce surface seawater pH to 7.8 by the end of this century compromising marine calcifiers. A broad range of biological and mineralogical mechanisms allow marine calcifiers to cope with ocean acidification, however these mechanisms are energetically demanding which affect other biological processes (trade-offs) with important implications for the resilience of the organisms against stressful conditions. Hence, food availability may play a critical role in determining the resistance of calcifiers to OA. Here we show, based on a meta-analysis of existing experimental results assessing the role of food supply in the response of organisms to OA, that food supply consistently confers calcifiers resistance to ocean acidification. PMID:26778520

Carbon Nanotubes Facilitate Oxidation of Cysteine Residues of Proteins.

PubMed

Hirano, Atsushi; Kameda, Tomoshi; Wada, Momoyo; Tanaka, Takeshi; Kataura, Hiromichi

2017-10-19

The adsorption of proteins onto nanoparticles such as carbon nanotubes (CNTs) governs the early stages of nanoparticle uptake into biological systems. Previous studies regarding these adsorption processes have primarily focused on the physical interactions between proteins and nanoparticles. In this study, using reduced lysozyme and intact human serum albumin in aqueous solutions, we demonstrated that CNTs interact chemically with proteins. The CNTs induce the oxidation of cysteine residues of the proteins, which is accounted for by charge transfer from the sulfhydryl groups of the cysteine residues to the CNTs. The redox reaction simultaneously suppresses the intermolecular association of proteins via disulfide bonds. These results suggest that CNTs can affect the folding and oxidation degree of proteins in biological systems such as blood and cytosol.

Temperature of surface waters in the conterminous United States

USGS Publications Warehouse

Blakey, James F.

1966-01-01

Temperature is probably the most important, but least discussed, parameter in determining water quality. The purpose of this report is to present the average or most probable temperatures of surface waters in the conterminous United States and to cite factors that affect and are affected by water temperature. Temperature is related, usually directly, to all the chemical, physical, and biological properties of water. The ability of water to dissolve or precipitate materials is temperature dependent, the ability of water to transport or deposit suspended material is temperature dependent, and the aquatic life of a lake or stream may thrive or die because of the water temperature.Everyone is concerned, though often unknowingly, about water temperature. The amount and type of treatment necessary for a municipal supply are temperature dependent; therefore it affects the consumer cost. Temperature determines the volume of cooling water needed for industrial processes and steampower generation. Conservation and recreation practices are affected by water temperature, and the farmers' irrigation practices and livestock production may be affected by the water temperature.

Brain disorders and the biological role of music.

PubMed

Clark, Camilla N; Downey, Laura E; Warren, Jason D

2015-03-01

Despite its evident universality and high social value, the ultimate biological role of music and its connection to brain disorders remain poorly understood. Recent findings from basic neuroscience have shed fresh light on these old problems. New insights provided by clinical neuroscience concerning the effects of brain disorders promise to be particularly valuable in uncovering the underlying cognitive and neural architecture of music and for assessing candidate accounts of the biological role of music. Here we advance a new model of the biological role of music in human evolution and the link to brain disorders, drawing on diverse lines of evidence derived from comparative ethology, cognitive neuropsychology and neuroimaging studies in the normal and the disordered brain. We propose that music evolved from the call signals of our hominid ancestors as a means mentally to rehearse and predict potentially costly, affectively laden social routines in surrogate, coded, low-cost form: essentially, a mechanism for transforming emotional mental states efficiently and adaptively into social signals. This biological role of music has its legacy today in the disordered processing of music and mental states that characterizes certain developmental and acquired clinical syndromes of brain network disintegration. © The Author (2014). Published by Oxford University Press.

Brain disorders and the biological role of music

PubMed Central

Clark, Camilla N.; Downey, Laura E.

2015-01-01

Despite its evident universality and high social value, the ultimate biological role of music and its connection to brain disorders remain poorly understood. Recent findings from basic neuroscience have shed fresh light on these old problems. New insights provided by clinical neuroscience concerning the effects of brain disorders promise to be particularly valuable in uncovering the underlying cognitive and neural architecture of music and for assessing candidate accounts of the biological role of music. Here we advance a new model of the biological role of music in human evolution and the link to brain disorders, drawing on diverse lines of evidence derived from comparative ethology, cognitive neuropsychology and neuroimaging studies in the normal and the disordered brain. We propose that music evolved from the call signals of our hominid ancestors as a means mentally to rehearse and predict potentially costly, affectively laden social routines in surrogate, coded, low-cost form: essentially, a mechanism for transforming emotional mental states efficiently and adaptively into social signals. This biological role of music has its legacy today in the disordered processing of music and mental states that characterizes certain developmental and acquired clinical syndromes of brain network disintegration. PMID:24847111

Post-traumatic stress disorder.

PubMed

Yehuda, Rachel; Hoge, Charles W; McFarlane, Alexander C; Vermetten, Eric; Lanius, Ruth A; Nievergelt, Caroline M; Hobfoll, Stevan E; Koenen, Karestan C; Neylan, Thomas C; Hyman, Steven E

2015-10-08

Post-traumatic stress disorder (PTSD) occurs in 5-10% of the population and is twice as common in women as in men. Although trauma exposure is the precipitating event for PTSD to develop, biological and psychosocial risk factors are increasingly viewed as predictors of symptom onset, severity and chronicity. PTSD affects multiple biological systems, such as brain circuitry and neurochemistry, and cellular, immune, endocrine and metabolic function. Treatment approaches involve a combination of medications and psychotherapy, with psychotherapy overall showing greatest efficacy. Studies of PTSD pathophysiology initially focused on the psychophysiology and neurobiology of stress responses, and the acquisition and the extinction of fear memories. However, increasing emphasis is being placed on identifying factors that explain individual differences in responses to trauma and promotion of resilience, such as genetic and social factors, brain developmental processes, cumulative biological and psychological effects of early childhood and other stressful lifetime events. The field of PTSD is currently challenged by fluctuations in diagnostic criteria, which have implications for epidemiological, biological, genetic and treatment studies. However, the advent of new biological methodologies offers the possibility of large-scale approaches to heterogeneous and genetically complex brain disorders, and provides optimism that individualized approaches to diagnosis and treatment will be discovered.

Proteome Analysis of Human Sebaceous Follicle Infundibula Extracted from Healthy and Acne-Affected Skin

PubMed Central

Bek-Thomsen, Malene; Lomholt, Hans B.; Scavenius, Carsten; Enghild, Jan J.; Brüggemann, Holger

2014-01-01

Acne vulgaris is a very common disease of the pilosebaceous unit of the human skin. The pathological processes of acne are not fully understood. To gain further insight sebaceous follicular casts were extracted from 18 healthy and 20 acne-affected individuals by cyanoacrylate-gel biopsies and further processed for mass spectrometry analysis, aiming at a proteomic analysis of the sebaceous follicular casts. Human as well as bacterial proteins were identified. Human proteins enriched in acne and normal samples were detected, respectively. Normal follicular casts are enriched in proteins such as prohibitins and peroxiredoxins which are involved in the protection from various stresses, including reactive oxygen species. By contrast, follicular casts extracted from acne-affected skin contained proteins involved in inflammation, wound healing and tissue remodeling. Among the most distinguishing proteins were myeloperoxidase, lactotransferrin, neutrophil elastase inhibitor and surprisingly, vimentin. The most significant biological process among all acne-enriched proteins was ‘response to a bacterium’. Identified bacterial proteins were exclusively from Propionibacterium acnes. The most abundant P. acnes proteins were surface-exposed dermatan sulphate adhesins, CAMP factors, and a so far uncharacterized lipase in follicular casts extracted from normal as well as acne-affected skin. This is a first proteomic study that identified human proteins together with proteins of the skin microbiota in sebaceous follicular casts. PMID:25238151

Different pathways but same result? Comparing chemistry and biological effects of burned and decomposed litter

NASA Astrophysics Data System (ADS)

Mazzoleni, Stefano; Bonanomi, Giuliano; Incerti, Guido; El-Gawad, Ahmed M. Abd; Sarker, Tushar Chandra; Cesarano, Gaspare; Saulino, Luigi; Saracino, Antonio; Castro Rego, Francisco

2017-04-01

Litter burning and biological decomposition are oxidative processes co-occurring in many terrestrial ecosystems, producing organic matter with different chemical properties and differently affecting plant growth and soil microbial activity. Here, we tested the chemical convergence hypothesis (i.e. materials with different initial chemistry tend to converge towards a common profile, with similar biological effects, as the oxidative process advances) for burning and decomposition. We compared the molecular composition of 63 organic materials - 7 litter types either fresh, decomposed for 30, 90, 180 days, or heated at 100, 200, 300, 400, 500 °C - as assessed by 13C NMR. We used litter water extracts (5% dw) as treatments in bioassays on plant (Lepidium sativum) and fungal (Aspergillus niger) growth, and a washed quartz sand amended with litter materials (0.5 % dw) to assess heterotrophic respiration by CO2 flux chamber. We observed different molecular variations for materials either burning (i.e. a sharp increase of aromatic C and a decrease of most other fractions above 200 °C) or decomposing (i.e. early increase of alkyl, methoxyl and N-alkyl C and decrease of O-alkyl and di-O-alkyl C fractions). Soil respiration and fungal growth progressively decreased with litter age and temperature. Plant growth underwent an inhibitory effect by untreated litter, more and less rapidly released over decomposing and burning materials, respectively. Correlation analysis between NMR and bioassay data showed that opposite responses for soil respiration and fungi, compared to plants, are related to essentially the same C molecular types. Our findings suggest a functional convergence of decomposed and burnt organic substrates, emerging from the balance between the bioavailability of labile C sources and the presence of recalcitrant and pyrogenic compounds, oppositely affecting different trophic levels.

The natural chlorine cycle - Formation of the carcinogenic and greenhouse gas compound chloroform in drinking water reservoirs.

PubMed

Forczek, Sándor T; Pavlík, Milan; Holík, Josef; Rederer, Luděk; Ferenčík, Martin

2016-08-01

Chlorine cycle in natural ecosystems involves formation of low and high molecular weight organic compounds of living organisms, soil organic matter and atmospherically deposited chloride. Chloroform (CHCl3) and adsorbable organohalogens (AOX) are part of the chlorine cycle. We attempted to characterize the dynamical changes in the levels of total organic carbon (TOC), AOX, chlorine and CHCl3 in a drinking water reservoir and in its tributaries, mainly at its spring, and attempt to relate the presence of AOX and CHCl3 with meteorological, chemical or biological factors. Water temperature and pH influence the formation and accumulation of CHCl3 and affect the conditions for biological processes, which are demonstrated by the correlation between CHCl3 and ΣAOX/Cl(-) ratio, and also by CHCl3/ΣAOX, CHCl3/AOXLMW, CHCl3/ΣTOC, CHCl3/TOCLMW and CHCl3/Cl(-) ratios in different microecosystems (e.g. old spruce forest, stagnant acidic water, humid and warm conditions with high biological activity). These processes start with the biotransformation of AOX from TOC, continue via degradation of AOX to smaller molecules and further chlorination, and finish with the formation of small chlorinated molecules, and their subsequent volatilization and mineralization. The determined concentrations of chloroform result from a dynamic equilibrium between its formation and degradation in the water; in the Hamry water reservoir, this results in a total amount of 0.1-0.7 kg chloroform and 5.2-15.4 t chloride. The formation of chloroform is affected by Cl(-) concentration, by concentrations and ratios of biogenic substrates (TOC and AOX), and by the ratios of the substrates and the product (feedback control by chloroform itself). Copyright © 2016 Elsevier Ltd. All rights reserved.

Hierarchy of responses to resource pulses in arid and semi-arid ecosystems.

PubMed

Schwinning, Susanne; Sala, Osvaldo E

2004-10-01

In arid/semi-arid ecosystems, biological resources, such as water, soil nutrients, and plant biomass, typically go through periods of high and low abundance. Short periods of high resource abundance are usually triggered by rainfall events, which, despite of the overall scarcity of rain, can saturate the resource demand of some biological processes for a time. This review develops the idea that there exists a hierarchy of soil moisture pulse events with a corresponding hierarchy of ecological responses, such that small pulses only trigger a small number of relatively minor ecological events, and larger pulses trigger a more inclusive set and some larger ecological events. This framework hinges on the observation that many biological state changes, where organisms transition from a state of lower to higher physiological activity, require a minimal triggering event size. Response thresholds are often determined by the ability of organisms to utilize soil moisture pulses of different infiltration depth or duration. For example, brief, shallow pulses can only affect surface dwelling organisms with fast response times and high tolerance for low resource levels, such as some species of the soil micro-fauna and -flora, while it takes more water and deeper infiltration to affect the physiology, growth or reproduction of higher plants. This review first discusses how precipitation, climate and site factors translate into soil moisture pulses of varying magnitude and duration. Next, the idea of the response hierarchy for ecosystem processes is developed, followed by an exploration of the possible evolutionary background for the existence of response thresholds to resource pulses. The review concludes with an outlook on global change: does the hierarchical view of precipitation effects in ecosystems provide new perspectives on the future of arid/semiarid lands?

Peatlands as a unique climatic hotspots

NASA Astrophysics Data System (ADS)

Slowinska, S.; Marcisz, K.; Slowinski, M. M.; Blazejczyk, K.; Lamentowicz, M.

2017-12-01

Peatlands are unique environments, often acting as microrefugia of various taxa. High groundwater table, organic soils, specific vegetation and topography are important determinants of their local climatic conditions. However, relations between those determinants are not stable. For example, seasonal changes in weather patterns, hydrological dynamics, and local vegetation may alter microclimate. Additionally, long-term changes are important factor, as for example overgrowing due to significant change of microclimate conditions, what in turn changes geochemical and biological processes in the peat layer. We have been investigating interactions between abiotic and biotic factors of a small Sphagnum mire (ca. 6.0 ha) for over ten years now. The mire is located in Poland in transitional temperate climate and is the only place in polish lowlands where glacial relict Betula nana occurs. Identification of local climate of the mire, its microclimatic differentiation and its influence on surroundings were objectives of the study. We recorded water level fluctuations, photosynthetically active radiation (PAR), air temperature and humidity, and peat temperature at five monitoring plots at the mire and observed significant differences between them. We also investigated Sphagnum mosses growth and testate amoeba diversity and community structure to understand biological response of those differences. We observed that local climate of the mire was significantly different from open area reference place, it was much colder especially during nights. The average minimal temperature at the height 30 cm for growing seasons 2010-2012 was 3.7oC lower there and ground frosts occurred even in the summer. The climate of the mire affected the forest directly adjacent to it, and depending on weather conditions the strength and the distance of this interaction was different. Our results show that micro-environmental changes affects on biological processes and should be taken into consideration in palaeoecological investigations.

The chaperone role of the pyridoxal 5'-phosphate and its implications for rare diseases involving B6-dependent enzymes.

PubMed

Cellini, Barbara; Montioli, Riccardo; Oppici, Elisa; Astegno, Alessandra; Voltattorni, Carla Borri

2014-02-01

The biologically active form of the B6 vitamers is pyridoxal 5'-phosphate (PLP), which plays a coenzymatic role in several distinct enzymatic activities ranging from the synthesis, interconversion and degradation of amino acids to the replenishment of one-carbon units, synthesis and degradation of biogenic amines, synthesis of tetrapyrrolic compounds and metabolism of amino-sugars. In the catalytic process of PLP-dependent enzymes, the substrate amino acid forms a Schiff base with PLP and the electrophilicity of the PLP pyridine ring plays important roles in the subsequent catalytic steps. While the essential role of PLP in the acquisition of biological activity of many proteins is long recognized, the finding that some PLP-enzymes require the coenzyme for refolding in vitro points to an additional role of PLP as a chaperone in the folding process. Mutations in the genes encoding PLP-enzymes are causative of several rare inherited diseases. Patients affected by some of these diseases (AADC deficiency, cystathionuria, homocystinuria, gyrate atrophy, primary hyperoxaluria type 1, xanthurenic aciduria, X-linked sideroblastic anaemia) can benefit, although at different degrees, from the administration of pyridoxine, a PLP precursor. The effect of the coenzyme is not limited to mutations that affect the enzyme-coenzyme interaction, but also to those that cause folding defects, reinforcing the idea that PLP could play a chaperone role and improve the folding efficiency of misfolded variants. In this review, recent biochemical and cell biology studies highlighting the chaperoning activity of the coenzyme on folding-defective variants of PLP-enzymes associated with rare diseases are presented and discussed. Copyright © 2013 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Economic evaluation of a combined photo-Fenton/MBR process using pesticides as model pollutant. Factors affecting costs.

PubMed

Sánchez Pérez, José Antonio; Román Sánchez, Isabel María; Carra, Irene; Cabrera Reina, Alejandro; Casas López, José Luis; Malato, Sixto

2013-01-15

The aim of this paper is to carry out an economic assessment on a solar photo-Fenton/MBR combined process to treat industrial ecotoxic wastewater. This study focuses on the impact of the contamination present in wastewater, the photochemical oxidation, the use of an MBR as biological process and the plant size on operating and amortization costs. As example of ecotoxic pollutant, a mixture of five commercial pesticides commonly used in the Mediterranean area has been used, ranging from 500 mg/L to 50mg/L, expressed as dissolved organic carbon concentration. The economic evaluation shows that (i) the increase in pollution load does not always involve an increase in photo-Fenton costs because they also depend on organic matter mineralization; (ii) the use of an MBR process permits lower photochemical oxidation requirements than other biological treatments, resulting in approximately 20% photo-Fenton cost reduction for highly polluted wastewater; (iii) when pollution load decreases, the contribution of reactant consumption to the photo-Fenton process costs increase with regard to amortization costs; (iv) 30% total cost reduction can be gained treating higher daily volumes, obtaining competitive costs that vary from 1.1-1.9 €/m(3), depending on the pollution load. Copyright © 2012 Elsevier B.V. All rights reserved.

Are Plasma Oxytocin and Vasopressin Levels Reflective of Amygdala Activation during the Processing of Negative Emotions? A Preliminary Study.

PubMed

Motoki, Kosuke; Sugiura, Motoaki; Takeuchi, Hikaru; Kotozaki, Yuka; Nakagawa, Seishu; Yokoyama, Ryoichi; Kawashima, Ryuta

2016-01-01

Plasma oxytocin (OT) and arginine vasopressin (AVP) are associated with individual differences in emotional responses and behaviors. The amygdala is considered to be an important brain region for regulating emotion-based behavior, with OT and AVP modulating activity in the amygdala during the processing of negative emotions. In particular, increased OT levels may diminish amygdala activation (anxiolytic effects) and enhanced AVP levels may augment amygdala activation (anxiogenic effects) when negative emotions are processed. A growing body of research has shown that the effects of OT and AVP are modulated by sex: the aforementioned anxiolytic effects of OT and the anxiogenic effects of AVP occur in men, but not in women. However, we have little knowledge regarding the biological mechanisms underlying OT and AVP plasma levels or their respective anxiogenic and anxiolytic effects; similarly, little is known about the causes and nature of sex differences related to these neuropeptides and their effects on emotional processing. In the current study, we focused on the neural functions associated with the biological mechanisms underlying such effects. We hypothesized that amygdala activation would correlate with trait plasma OT (anxiolytic effects) and AVP (anxiogenic effects) levels because the amygdala is thought to affect the coordinated release of these neuropeptides following affective experiences. We further hypothesized that the effects would be modulated by sex. We assessed 51 participants (male and female) using a paradigm involving negative emotion in conjunction with functional magnetic resonance imaging and measurements of plasma OT and AVP levels. We determined that increased plasma AVP levels were positively associated with amygdala activation (anxiogenic effects) in men, but not in women. These findings highlight the potential underlying neural mechanisms of plasma AVP levels in men.

Downstream processing of biopharmaceutical proteins produced in plants: the pros and cons of flocculants.

PubMed

Buyel, Johannes Felix; Fischer, Rainer

2014-01-01

All biological platforms for the manufacture of biopharmaceutical proteins produce an initially turbid extract that must be clarified to avoid fouling sensitive media such as chromatography resins. Clarification is more challenging if the feed stream contains large amounts of dispersed particles, because these rapidly clog the filter media typically used to remove suspended solids. Charged polymers (flocculants) can increase the apparent size of the dispersed particles by aggregation, facilitating the separation of solids and liquids, and thus reducing process costs. However, many different factors can affect the behavior of flocculants, including the pH and conductivity of the medium, the size and charge distribution of the particulates, and the charge density and molecular mass of the polymer. Importantly, these properties can also affect the recovery of the target protein and the overall safety profile of the process. We therefore used a design of experiments approach to establish reliable predictive models that characterize the impact of flocculants during the downstream processing of biopharmaceutical proteins. We highlight strategies for the selection of flocculants during process optimization. These strategies will contribute to the quality by design aspects of process development and facilitate the development of safe and efficient downstream processes for plant-derived pharmaceutical proteins.

[Regeneration and repair of peripheral nerves: clinical implications in facial paralysis surgery].

PubMed

Hontanilla, B; Vidal, A

2000-01-01

Peripheral nerve lesions are one of the most frequent causes of chronic incapacity. Upper or lower limb palsies due to brachial or lumbar plexus injuries, facial paralysis and nerve lesions caused by systemic diseases are one of the major goals of plastic and reconstructive surgery. However, the poor results obtained in repaired peripheral nerves during the Second World War lead to a pessimist vision of peripheral nerve repair. Nevertheless, a well understanding of microsurgical principles in reconstruction and molecular biology of nerve regeneration have improved the clinical results. Thus, although the results obtained are quite far from perfect, these procedures give to patients a hope in the recuperation of their lesions and then on function. Technical aspects in nerve repair are well established; the next step is to manipulate the biology. In this article we will comment the biological processes which appear in peripheral nerve regeneration, we will establish the main concepts on peripheral nerve repair applied in facial paralysis cases and, finally, we will proportionate some ideas about how clinical practice could be affected by manipulation of the peripheral nerve biology.

[Sample preparation and bioanalysis in mass spectrometry].

PubMed

Bourgogne, Emmanuel; Wagner, Michel

2015-01-01

The quantitative analysis of compounds of clinical interest of low molecular weight (<1000 Da) in biological fluids is currently in most cases performed by liquid chromatography-mass spectrometry (LC-MS). Analysis of these compounds in biological fluids (plasma, urine, saliva, hair...) is a difficult task requiring a sample preparation. Sample preparation is a crucial part of chemical/biological analysis and in a sense is considered the bottleneck of the whole analytical process. The main objectives of sample preparation are the removal of potential interferences, analyte preconcentration, and converting (if needed) the analyte into a more suitable form for detection or separation. Without chromatographic separation, endogenous compounds, co-eluted products may affect a quantitative method in mass spectrometry performance. This work focuses on three distinct parts. First, quantitative bioanalysis will be defined, different matrices and sample preparation techniques currently used in bioanalysis by mass spectrometry of/for small molecules of clinical interest in biological fluids. In a second step the goals of sample preparation will be described. Finally, in a third step, sample preparation strategies will be made either directly ("dilute and shoot") or after precipitation.

An open future for ecological and evolutionary data?

PubMed

Kenall, Amye; Harold, Simon; Foote, Christopher

2014-04-02

As part of BioMed Central's open science mission, we are pleased to announce that two of our journals have integrated with the open data repository Dryad. Authors submitting their research to either BMC Ecology or BMC Evolutionary Biology will now have the opportunity to deposit their data directly into the Dryad archive and will receive a permanent, citable link to their dataset. Although this does not affect any of our current data deposition policies at these journals, we hope to encourage a more widespread adoption of open data sharing in the fields of ecology and evolutionary biology by facilitating this process for our authors. We also take this opportunity to discuss some of the wider issues that may concern researchers when making their data openly available. Although we offer a number of positive examples from different fields of biology, we also recognise that reticence to data sharing still exists, and that change must be driven from within research communities in order to create future science that is fit for purpose in the digital age. This editorial was published jointly in both BMC Ecology and BMC Evolutionary Biology.

[Polyvalence of bacteriophages isolated from fruit trees, affected by bacterial fire blight].

PubMed

Tovkach, F I; Moroz, S N; Korol', N A; Faĭdiuk, Iu V; Kushkina, A I

2013-01-01

Phage populations appearing as a result of a pathogenic process caused by Erwinia amylovora have been discovered and described. They accompany bacterial fire blight development in the process of quince, pear and apple trees vegetation in Zakarpattya region of Ukraine. Phage isolates of the affected pear and quince include polyvalent virulent phages able to develop on bacterial strains associated with plants--E. amylovora. E. "horticola" and Pantoea agglomerans. E. amylovora isolated from the plant tissues affected by the fire blight and detected at the same time as phages proved to be resistant to the viral infection. It is hard to explain now this characteristic however it was noticed that resistance to phages can change drastically in case of dissociation, lysogenization and mutagenesis of erwinia in laboratory conditions. Phage population study shows that they are heterogeneous and can obviously include not only polyvalent but also specific viruses. Further studies of biology and molecular genetics of pure lines of isolated phages will help to get closer to understanding the place and role of bacteriophages in the complicated network of relations between bacterial pathogens and plants.

How electrostatic networks modulate specificity and stability of collagen.

PubMed

Zheng, Hongning; Lu, Cheng; Lan, Jun; Fan, Shilong; Nanda, Vikas; Xu, Fei

2018-06-12

One-quarter of the 28 types of natural collagen exist as heterotrimers. The oligomerization state of collagen affects the structure and mechanics of the extracellular matrix, providing essential cues to modulate biological and pathological processes. A lack of high-resolution structural information limits our mechanistic understanding of collagen heterospecific self-assembly. Here, the 1.77-Å resolution structure of a synthetic heterotrimer demonstrates the balance of intermolecular electrostatics and hydrogen bonding that affects collagen stability and heterospecificity of assembly. Atomistic simulations and mutagenesis based on the solved structure are used to explore the contributions of specific interactions to energetics. A predictive model of collagen stability and specificity is developed for engineering novel collagen structures.

Persistence of the Intuitive Conception of Living Things in Adolescence

NASA Astrophysics Data System (ADS)

Babai, Reuven; Sekal, Rachel; Stavy, Ruth

2010-02-01

This study investigated whether intuitive, naive conceptions of "living things" based on objects' mobility (movement = alive) persist into adolescence and affect 10th graders' accuracy of responses and reaction times during object classification. Most of the 58 students classified the test objects correctly as living/nonliving, yet they demonstrated significantly longer reaction times for classifying plants compared to animals and for classifying dynamic objects compared to static inanimate objects. Findings indicated that, despite prior learning in biology, the intuitive conception of living things persists up to age 15-16 years, affecting related reasoning processes. Consideration of these findings may help educators in their decisions about the nature of examples they use in their classrooms.

Pathophysiological significance and therapeutic applications of snake venom protease inhibitors.

PubMed

Thakur, Rupamoni; Mukherjee, Ashis K

2017-06-01

Protease inhibitors are important constituents of snake venom and play important roles in the pathophysiology of snakebite. Recently, research on snake venom protease inhibitors has provided valuable information to decipher the molecular details of various biological processes and offer insight for the development of some therapeutically important molecules from snake venom. The process of blood coagulation and fibrinolysis, in addition to affecting platelet function, are well known as the major targets of several snake venom protease inhibitors. This review summarizes the structure-functional aspects of snake venom protease inhibitors that have been described to date. Because diverse biological functions have been demonstrated by protease inhibitors, a comparative overview of their pharmacological and pathophysiological properties is also highlighted. In addition, since most snake venom protease inhibitors are non-toxic on their own, this review evaluates the different roles of individual protease inhibitors that could lead to the identification of drug candidates and diagnostic molecules. Copyright © 2017 Elsevier Ltd. All rights reserved.

Changes in carbon and nitrogen pool during in-situ aeration of old landfills under varying conditions.

PubMed

Prantl, R; Tesar, M; Huber-Humer, M; Lechner, P

2006-01-01

Emissions from old landfills via leachate and the gas phase are influenced by state and stability of the organic matter in the solid waste and by environmental conditions within the landfill. Remediation of landfills by means of in-situ aeration is one possibility to reduce these emissions. By establishing aerobic conditions, biological processes in the landfill are accelerated. To investigate the effects of this remediation technology, lab-scale experiments with column tests have been carried out. The main goal of the present work is to characterize the changes of the carbon and nitrogen compounds in the aerated solid waste, the leachate and the gas phase under varying conditions. The results demonstrate a clear reduction of emissions and a stabilization of the organic matter. Furthermore, it is shown that both the intensity of aeration and the amount of water affect biological processes to a certain extent. Even when columns were operated under anaerobic conditions after a long running period of aeration, the emissions remained low.

Insects and low temperatures: from molecular biology to distributions and abundance.

PubMed Central

Bale, J S

2002-01-01

Insects are the most diverse fauna on earth, with different species occupying a range of terrestrial and aquatic habitats from the tropics to the poles. Species inhabiting extreme low-temperature environments must either tolerate or avoid freezing to survive. While much is now known about the synthesis, biochemistry and function of the main groups of cryoprotectants involved in the seasonal processes of acclimatization and winter cold hardiness (ice-nucleating agents, polyols and antifreeze proteins), studies on the structural biology of these compounds have been more limited. The recent discovery of rapid cold-hardening, ice-interface desiccation and the daily resetting of critical thermal thresholds affecting mortality and mobility have emphasized the role of temperature as the most important abiotic factor, acting through physiological processes to determine ecological outcomes. These relationships are seen in key areas such as species responses to climate warming, forecasting systems for pest outbreaks and the establishment potential of alien species in new environments. PMID:12171648

Modifications of pancreatic diffusion MRI by tissue characteristics: what are we weighting for?

PubMed

Nissan, Noam

2017-08-01

Diffusion-weighted imaging holds the potential to improve the diagnosis and biological characterization of pancreatic disease, and in particular pancreatic cancer, which exhibits decreased values of the apparent diffusion coefficient (ADC). Yet, variable and overlapping ADC values have been reported for the healthy and the pathological pancreas, including for cancer and other benign conditions. This controversy reflects the complexity of probing the water-diffusion process in the pancreas, which is dependent upon multiple biological factors within this organ's unique physiological environment. In recent years, extensive studies have investigated the correlation between tissue properties including cellularity, vascularity, fibrosis, secretion and microstructure and pancreatic diffusivity. Understanding how the various physiological and pathological features and the underlying functional processes affect the diffusion measurement may serve to optimize the method for improved diagnostic gain. Therefore, the aim of the present review article is to elucidate the relationship between pancreatic tissue characteristics and diffusion MRI measurement. Copyright © 2017 John Wiley & Sons, Ltd.

Communities of microorganisms and invertebrates in soil-like bodies of soccer fields in Moscow oblast

NASA Astrophysics Data System (ADS)

Kutovaya, O. V.; Zamotaev, I. V.; Belobrov, V. P.

2014-11-01

Artificially created soil-like technogenic formations (STFs) of soccer fields are developed under combined action of intense technogenic and natural factors and processes, which cannot but affect the structure and biological activity of their microbial communities and mesofauna. The microflora of the STFs is very similar to the microflora of the background soddy-podzolic soils of Moscow oblast with respect to the composition of the physiological groups of microorganisms. However, they are drastically different in their quantitative characteristics. The numbers of all the trophic groups of microorganisms, except for the microscopic fungi, in the STFs are much higher than those in the zonal soils. An increased biological activity of the STFs is due to regular watering, heating, application of sand and mineral fertilizers, and technogenic turbation processes. The mesofauna of the STFs is represented by several ecological groups of earthworms, including soildwelling (endogeic) earthworms ( Aporrectodea caliginosa), epigeic earthworms dwelling at the soil-litter interface ( Lumbricus rubellus), and litter-dwelling earthworms ( Eisenia foetida).

Division of energy biosciences: Annual report and summaries of FY 1995 activities

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

NONE

1996-04-01

The mission of the Division of Energy Biosciences is to support research that advances the fundamental knowledge necessary for the future development of biotechnologies related to the Department of Energy`s mission. The departmental civilian objectives include effective and efficient energy production, energy conservation, environmental restoration, and waste management. The Energy Biosciences program emphasizes research in the microbiological and plant sciences, as these understudied areas offer numerous scientific opportunities to dramatically influence environmentally sensible energy production and conservation. The research supported is focused on the basic mechanisms affecting plant productivity, conversion of biomass and other organic materials into fuels and chemicalsmore » by microbial systems, and the ability of biological systems to replace energy-intensive or pollutant-producing processes. The Division also addresses the increasing number of new opportunities arising at the interface of biology with other basic energy-related sciences such as biosynthesis of novel materials and the influence of soil organisms on geological processes.« less

Early nutritional programming affects liver transcriptome in diploid and triploid Atlantic salmon, Salmo salar.

PubMed

Vera, L M; Metochis, C; Taylor, J F; Clarkson, M; Skjærven, K H; Migaud, H; Tocher, D R

2017-11-17

To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutrient utilisation of fish. The application of nutritional stimuli during early development can induce long-term changes in animal physiology. Recently, we successfully used this approach to improve the utilisation of plant-based diets in diploid and triploid Atlantic salmon. In the present study we explored the molecular mechanisms occurring in the liver of salmon when challenged with a plant-based diet in order to determine the metabolic processes affected, and the effect of ploidy. Microarray analysis revealed that nutritional history had a major impact on the expression of genes. Key pathways of intermediary metabolism were up-regulated, including oxidative phosphorylation, pyruvate metabolism, TCA cycle, glycolysis and fatty acid metabolism. Other differentially expressed pathways affected by diet included protein processing in endoplasmic reticulum, RNA transport, endocytosis and purine metabolism. The interaction between diet and ploidy also had an effect on the hepatic transcriptome of salmon. The biological pathways with the highest number of genes affected by this interaction were related to gene transcription and translation, and cell processes such as proliferation, differentiation, communication and membrane trafficking. The present study revealed that nutritional programming induced changes in a large number of metabolic processes in Atlantic salmon, which may be associated with the improved fish performance and nutrient utilisation demonstrated previously. In addition, differences between diploid and triploid salmon were found, supporting recent data that indicate nutritional requirements of triploid salmon may differ from those of their diploid counterparts.

Contributions of in situ microscopy to the current understanding of stone biodeterioration.

PubMed

de Los Ríos, Asunción; Ascaso, Carmen

2005-09-01

In situ microscopy consists of simultaneously applying several microscopy techniques without separating the biological component from its habitat. Over the past few years, this strategy has allowed characterization of the biofilms involved in biodeterioration processes affecting stone monuments and has revealed the biogeophysical and biogeochemical impact of the microbiota present. In addition, through in situ microscopy diagnosis, appropriate treatments can be designed to resolve the problems related to microbial colonization of stone monuments.

The Importance of Fine-Scale Flow Processes and Food Availability in the Maintenance of Soft-Sediment Communities

DTIC Science & Technology

1993-02-01

of the bottom sediments at a given site. From long time -series measurements of the flow and sediment-transport environment on Georges Bank...significantly affect flows and sediment transport depends, in part, on timing . Biological effects on seafloor stability may be more pronounced, for example...potentially can enhance particle retention time within the tube bed via skimming flow (described earlier), although it is unclear if natural populations of

The Role of Dynamic m6 A RNA Methylation in Photobiology.

PubMed

Robinson, Myles; Shah, Palak; Cui, Yan-Hong; He, Yu-Ying

2018-05-04

N 6 -methyladenosine (m 6 A) is the most abundant internal RNA modification among numerous post-transcriptional modifications identified in eukaryotic mRNA. m 6 A modification of RNA is catalyzed by the "writer" m 6 A methyltransferase enzyme complex, consisting of METTL3, METTL14, WTAP and KIAA1429. The m 6 A modification is reversible and can be removed by "eraser" m 6 A demethylase enzymes, namely, FTO and ALKBH5. The biological function of m 6 A modification on RNA is carried out by RNA-binding effector proteins called "readers." Varied functions of the reader proteins regulate mRNA metabolism by affecting stability, translation, splicing or nuclear export. The epitranscriptomic gene regulation by m 6 A RNA methylation regulates various pathways, which contribute to basic cellular processes essential for cell maintenance, development and cell fate, and affect response to external stimuli and stressors. In this review, we summarize the recent advances in the regulation and function of m 6 A RNA methylation, with a focus on UV-induced DNA damage response and the circadian clock machinery. Insights into the mechanisms of m 6 A RNA regulation and post-transcriptional regulatory function in these biological processes may facilitate the development of new preventive and therapeutic strategies for various diseases related to dysregulation of UV damage response and circadian rhythm. © 2018 The American Society of Photobiology.

Cannabinoid-like anti-inflammatory compounds from flax fiber.

PubMed

Styrczewska, Monika; Kulma, Anna; Ratajczak, Katarzyna; Amarowicz, Ryszard; Szopa, Jan

2012-09-01

Flax is a valuable source of fibers, linseed and oil. The compounds of the latter two products have already been widely examined and have been proven to possess many health-beneficial properties. In the course of analysis of fibers extract from previously generated transgenic plants overproducing phenylpropanoids a new terpenoid compound was discovered.The UV spectra and the retention time in UPLC analysis of this new compound reveal similarity to a cannabinoid-like compound, probably cannabidiol (CBD). This was confirmed by finding two ions at m/z 174.1 and 231.2 in mass spectra analysis. Further confirmation of the nature of the compound was based on a biological activity assay. It was found that the compound affects the expression of genes involved in inflammatory processes in mouse and human fibroblasts and likely the CBD from Cannabis sativa activates the specific peripheral cannabinoid receptor 2 (CB2) gene expression. Besides fibers, the compound was also found in all other flax tissues. It should be pointed out that the industrial process of fabric production does not affect CBD activity.The presented data suggest for the first time that flax products can be a source of biologically active cannabinoid-like compounds that are able to influence the cell immunological response. These findings might open up many new applications for medical flax products, especially for the fabric as a material for wound dressing with anti-inflammatory properties.

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...

Ventral aspect of the visual form pathway is not critical for the perception of biological motion

PubMed Central

Gilaie-Dotan, Sharon; Saygin, Ayse Pinar; Lorenzi, Lauren J.; Rees, Geraint; Behrmann, Marlene

2015-01-01

Identifying the movements of those around us is fundamental for many daily activities, such as recognizing actions, detecting predators, and interacting with others socially. A key question concerns the neurobiological substrates underlying biological motion perception. Although the ventral “form” visual cortex is standardly activated by biologically moving stimuli, whether these activations are functionally critical for biological motion perception or are epiphenomenal remains unknown. To address this question, we examined whether focal damage to regions of the ventral visual cortex, resulting in significant deficits in form perception, adversely affects biological motion perception. Six patients with damage to the ventral cortex were tested with sensitive point-light display paradigms. All patients were able to recognize unmasked point-light displays and their perceptual thresholds were not significantly different from those of three different control groups, one of which comprised brain-damaged patients with spared ventral cortex (n > 50). Importantly, these six patients performed significantly better than patients with damage to regions critical for biological motion perception. To assess the necessary contribution of different regions in the ventral pathway to biological motion perception, we complement the behavioral findings with a fine-grained comparison between the lesion location and extent, and the cortical regions standardly implicated in biological motion processing. This analysis revealed that the ventral aspects of the form pathway (e.g., fusiform regions, ventral extrastriate body area) are not critical for biological motion perception. We hypothesize that the role of these ventral regions is to provide enhanced multiview/posture representations of the moving person rather than to represent biological motion perception per se. PMID:25583504

Error cascades in the biological sciences: the unwanted consequences of using bad taxonomy in ecology.

PubMed

Bortolus, Alejandro

2008-03-01

Why do ecologists seem to underestimate the consequences of using bad taxonomy? Is it because the consequences of doing so have not been yet scrutinized well enough? Is it because these consequences are irrelevant? In this paper I examine and discuss these questions, focusing on the fact that because ecological works provide baseline information for many other biological disciplines, they play a key role in spreading and magnifying the abundance of a variety of conceptual and methodological errors. Although overlooked and underestimated, this cascade-like process originates from trivial taxonomical problems that affect hypotheses and ideas, but it soon shifts into a profound practical problem affecting our knowledge about nature, as well as the ecosystem structure and functioning and the efficiency of human health care programs. In order to improve the intercommunication among disciplines, I propose a set of specific requirements that peer reviewed journals should request from all authors, and I also advocate for urgent institutional and financial support directed at reinvigorating the formation of scientific collections that integrate taxonomy and ecology.

Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

PubMed

Mereghetti, Paolo; Wade, Rebecca C

2012-07-26

High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

Can a systems biology approach unlock the mysteries of Kawasaki disease?

PubMed

Rowley, Anne H

2013-01-01

Kawasaki disease (KD) is a systemic inflammatory illness of childhood that particularly affects the coronary arteries. It can lead to coronary artery aneurysms, myocardial infarction, and sudden death. Clinical and epidemiologic data support an infectious cause, and the etiology remains unknown, but recent data support infection with a 'new' virus. Genetic factors influence KD susceptibility; the incidence is 10-fold higher in children of Asian when compared with Caucasian ethnicity. Recent research has identified genes affecting immune response that are associated with KD susceptibility and outcome. A re-examination of the pathologic features of KD has yielded a three process model of KD vasculopathy, providing a framework for understanding the KD arterial immune response and the damage it inflicts and for identifying new therapeutic targets for KD patients with coronary artery abnormalities. The researcher is faced with many challenges in determining the pathogenesis of KD. A systems biology approach incorporating genomics, proteomics, transcriptomics, and microbial bioinformatics analysis of high-throughput sequence data from KD tissues could provide the keys to unlocking the mysteries of this potentially fatal illness of childhood. Copyright © 2013 Wiley Periodicals, Inc.

On-Line Monitoring the Growth of E. coli or HeLa Cells Using an Annular Microelectrode Piezoelectric Biosensor.

PubMed

Tong, Feifei; Lian, Yan; Han, Junliang

2016-12-18

Biological information is obtained from the interaction between the series detection electrode and the organism or the physical field of biological cultures in the non-mass responsive piezoelectric biosensor. Therefore, electric parameter of the electrode will affect the biosensor signal. The electric field distribution of the microelectrode used in this study was simulated using the COMSOL Multiphysics analytical tool. This process showed that the electric field spatial distribution is affected by the width of the electrode finger or the space between the electrodes. In addition, the characteristic response of the piezoelectric sensor constructed serially with an annular microelectrode was tested and applied for the continuous detection of Escherichia coli culture or HeLa cell culture. Results indicated that the piezoelectric biosensor with an annular microelectrode meets the requirements for the real-time detection of E. coli or HeLa cells in culture. Moreover, this kind of piezoelectric biosensor is more sensitive than the sensor with an interdigital microelectrode. Thus, the piezoelectric biosensor acts as an effective analysis tool for acquiring online cell or microbial culture information.

How life affects the geochemical cycle of carbon

NASA Technical Reports Server (NTRS)

Walker, James C. G.

1992-01-01

Developing a quantitative understanding of the biogeochemical cycles of carbon as they have worked throughout Earth history on various time scales, how they have been affected by biological evolution, and how changes in the carbon content of ocean and atmosphere may have affected climate and the evolution of life are the goals of the research. Theoretical simulations were developed that can be tuned to reproduce such data as exist and, once tuned, can be used to predict properties that have not yet been observed. This is an ongoing process, in which models and results are refined as new data and interpretations become available and as understanding of the global system improves. Results of the research are described in several papers which were published or submitted for publication. These papers are summarized. Future research plans are presented.

Effect of different professions' clothing on children's height perception.

PubMed

Rashidi, Mahmoud; Keshtkaran, Katayoun; Zabihidan, Sahar; Hosseinchari, Masoud; Pazhoohi, Farid

2012-11-01

Height is a biological factor that can affect how others perceive and behave toward an individual. Height is a biological factor that can affect how others perceive and behave toward an individual. Clothing, as a non-biological factor, can affect these perceptions of height. In this study weClothing, as a non-biological factor, can affect these perceptions of height. In this study we investigated the effect of different professions' clothing on children's perceptions of height. One investigated the effect of different professions' clothing on children's perceptions of height. One hundred and eighty primary school students participated in this study and estimated the height of an actor in the clothing of four different professions which differed in terms of prestige. The results of study showed that the difference between the perceived and actual height was larger when participants estimated the height of socially esteemed professions. Also there was no difference between girls' and boys' estimation of different professions' height. The implications of these findings are discussed.

Patient Understanding of the Risks and Benefits of Biologic Therapies in Inflammatory Bowel Disease: Insights from a Large-scale Analysis of Social Media Platforms.

PubMed

Martinez, Bibiana; Dailey, Francis; Almario, Christopher V; Keller, Michelle S; Desai, Mansee; Dupuy, Taylor; Mosadeghi, Sasan; Whitman, Cynthia; Lasch, Karen; Ursos, Lyann; Spiegel, Brennan M R

2017-07-01

Few studies have examined inflammatory bowel disease (IBD) patients' knowledge and understanding of biologic therapies outside traditional surveys. Here, we used social media data to examine IBD patients' understanding of the risks and benefits associated with biologic therapies and how this affects decision-making. We collected posts from Twitter and e-forum discussions from >3000 social media sites posted between June 27, 2012 and June 27, 2015. Guided by natural language processing, we identified posts with specific IBD keywords that discussed the risks and/or benefits of biologics. We then manually coded the resulting posts and performed qualitative analysis using ATLAS.ti software. A hierarchical coding structure was developed based on the keyword list and relevant themes were identified through manual coding. We examined 1598 IBD-related posts, of which 452 (28.3%) centered on the risks and/or benefits of biologics. There were 5 main themes: negative experiences and concerns with biologics (n = 247; 54.6%), decision-making surrounding biologic use (n = 169; 37.4%), positive experiences with biologics (n = 168; 37.2%), information seeking from peers (n = 125; 27.7%), and cost (n = 38; 8.4%). Posts describing negative experiences primarily commented on side effects from biologics, concerns about potential side effects and increased cancer risk, and pregnancy safety concerns. Posts on decision-making focused on nonbiologic treatment options, hesitation to initiate biologics, and concerns about changing or discontinuing regimens. Social media reveals a wide range of themes governing patients' experience and choice with IBD biologics. The complexity of navigating their risk-benefit profiles suggests merit in creating online tailored decision tools to support IBD patients' decision-making with biologic therapies.

Red blood cell vesiculation in hereditary hemolytic anemia

PubMed Central

Alaarg, Amr; Schiffelers, Raymond M.; van Solinge, Wouter W.; van Wijk, Richard

2013-01-01

Hereditary hemolytic anemia encompasses a heterogeneous group of anemias characterized by decreased red blood cell survival because of inherited membrane, enzyme, or hemoglobin disorders. Affected red blood cells are more fragile, less deformable, and more susceptible to shear stress and oxidative damage, and show increased vesiculation. Red blood cells, as essentially all cells, constitutively release phospholipid extracellular vesicles in vivo and in vitro in a process known as vesiculation. These extracellular vesicles comprise a heterogeneous group of vesicles of different sizes and intracellular origins. They are described in literature as exosomes if they originate from multi-vesicular bodies, or as microvesicles when formed by a one-step budding process directly from the plasma membrane. Extracellular vesicles contain a multitude of bioactive molecules that are implicated in intercellular communication and in different biological and pathophysiological processes. Mature red blood cells release in principle only microvesicles. In hereditary hemolytic anemias, the underlying molecular defect affects and determines red blood cell vesiculation, resulting in shedding microvesicles of different compositions and concentrations. Despite extensive research into red blood cell biochemistry and physiology, little is known about red cell deformability and vesiculation in hereditary hemolytic anemias, and the associated pathophysiological role is incompletely assessed. In this review, we discuss recent progress in understanding extracellular vesicles biology, with focus on red blood cell vesiculation. Also, we review recent scientific findings on the molecular defects of hereditary hemolytic anemias, and their correlation with red blood cell deformability and vesiculation. Integrating bio-analytical findings on abnormalities of red blood cells and their microvesicles will be critical for a better understanding of the pathophysiology of hereditary hemolytic anemias. PMID:24379786

Temporal variations of low molecular mass organic acids during vegetation period in temperate forest soil affected by acidification

NASA Astrophysics Data System (ADS)

Tejnecky, V.; Drabek, O.; Bradová, M.; Němeček, K.; Šebek, O.; Zenáhlíková, J.; Boruvka, L.

2011-12-01

The Low Molecular Mass Organic Acids (LMMOA) are essential in processes affecting the soils and represent reactive fraction of dissolved organic carbon (DOC). LMMOA influence soil-chemistry behaviour, participate in transport of mineral nutrition and reduce potential toxicity of selected elements like Al. The aim of this research was to assess behaviour, amount and composition of LMMOA in forest soil under different vegetation cover. The researched area is located in the naturally acid Jizera Mountains (Czech Republic), which was further affected by acid deposition and improper forest management. Soil samples from organic F and H horizons, organo-mineral A horizon and spodic or cambic mineral B horizons were taken under beech and spruce stands monthly (from April to October). Both stands were located immediately next to each other. The collected soil samples were analyzed immediately in a "fresh" state. Contents of LMMOA in deionised water extract were determined by means of ion-exchange chromatography (ICS-1600, Dionex, USA) with suppressed conductivity and gradient elution of KOH mobile phase. The contents of LMMOAS were also determined in precipitation samples. In addition, other selected elements (Al, Fe, Ca, Na, Mg and K), Al speciation and main inorganic anions were determined in water extract and precipitation samples. The highest amounts of LMMOA (mainly lactic, acetic, formic, malic and oxalic acid) were observed in organic F and H horizons and measured amounts decreased with increasing soil profile depth. Higher contents were determined in soil under spruce forest than under beech forest. External inputs of LMMOA in a form of precipitation were assessed as less significant in comparison with the soil processes (e.g. soil biological activity, soil organic matter decomposition processes). LMMOA amounts were higher in spring and summer (from April to August), caused by increased biological activity, while lower amounts were observed during the autumn period. Soil LMMOA were influencing also Al behaviour and Al species representation to less potentially toxic Al species.

Biomachining - A new approach for micromachining of metals

NASA Astrophysics Data System (ADS)

Vigneshwaran, S. C. Sakthi; Ramakrishnan, R.; Arun Prakash, C.; Sashank, C.

2018-04-01

Machining is the process of removal of material from workpiece. Machining can be done by physical, chemical or biological methods. Though physical and chemical methods have been widely used in machining process, they have their own disadvantages such as development of heat affected zone and usage of hazardous chemicals. Biomachining is the machining process in which bacteria is used to remove material from the metal parts. Chemolithotrophic bacteria such as Acidothiobacillus ferroxidans has been used in biomachining of metals like copper, iron etc. These bacteria are used because of their property of catalyzing the oxidation of inorganic substances. Biomachining is a suitable process for micromachining of metals. This paper reviews the biomachining process and various mechanisms involved in biomachining. This paper also briefs about various parameters/factors to be considered in biomachining and also the effect of those parameters on metal removal rate.

Advanced glycation end-products: a biological consequence of lifestyle contributing to cancer disparity.

PubMed

Turner, David P

2015-05-15

Low income, poor diet, obesity, and a lack of exercise are interrelated lifestyle factors that can profoundly alter our biologic make up to increase cancer risk, growth, and development. We recently reported a potential mechanistic link between carbohydrate-derived metabolites and cancer, which may provide a biologic consequence of lifestyle that can directly affect tumor biology. Advanced glycation end-products (AGE) are reactive metabolites produced as a by-product of sugar metabolism. Failure to remove these highly reactive metabolites can lead to protein damage, aberrant cell signaling, increased stress responses, and decreased genetic fidelity. Critically, AGE accumulation is also directly affected by our lifestyle choices and shows a race-specific, tumor-dependent pattern of accumulation in cancer patients. This review will discuss the contribution of AGEs to the cancer phenotype, with a particular emphasis on their biologic links with the socioeconomic and environmental risk factors that drive cancer disparity. Given the potential benefits of lifestyle changes and the potential biologic role of AGEs in promoting cancer, opportunities exist for collaborations affecting basic, translational, epidemiologic, and cancer prevention initiatives. ©2015 American Association for Cancer Research.

[Nutrigenomics--bioactive dietary components].

PubMed

Gętek, Monika; Czech, Natalia; Fizia, Katarzyna; Białek-Dratwa, Agnieszka; Muc-Wierzgoń, Małgorzata; Kokot, Teresa; Nowakowska-Zajdel, Ewa

2013-04-05

Nutrigenomics analyzes relations between diet and genes, and identifies mechanisms in which food and nutrition affect health and lifestyles and noncommunicable diseases (R. Chadwick, 2004). Bioactive dietary components are signal molecules that carry information from the external environment and affect in terms of quantity and quality in the process of gene expression. The biological effect of bioactive dietary components depends on various of physiological processes that can occur within a few genes. Polymorphism of genes can change their function and physiological response of the body for nutrients. Bioactive dietary components work on at least two levels of the expression of genes as factors regulating chromatin structure and as factors directly regulate the activity of nuclear receptors. The processes of synthesis and DNA repair are regulated by some of vitamins, macro-and micro-elements. They provide, among others, cofactors of enzymes that catalyze the replication of DNA methylation and its repair. DNA methylation profile may change under the influence of diet, single nucleotide polymorphisms and environmental factors. Bioactive dietary components may directly affect the process of gene expression by acting as ligands for nuclear receptors. Sensitive to dietary group of nuclear receptors are sensory receptors. This group includes, among others receptor PPAR (peroxisome proliferator activated), responsible for energy metabolism and receptors LXR (liver X receptor), FXR (farnesoid X receptor) and RXR, which is responsible for the metabolism of cholesterol.

Anaerobic gaseous biofuel production using microalgal biomass - A review.

PubMed

Wirth, Roland; Lakatos, Gergely; Böjti, Tamás; Maróti, Gergely; Bagi, Zoltán; Rákhely, Gábor; Kovács, Kornél L

2018-05-24

Most photosynthetic organisms store and convert solar energy in an aerobic process and produce biomass for various uses. Utilization of biomass for the production of renewable energy carriers employs anaerobic conditions. This review focuses on microalgal biomass and its use for biological hydrogen and methane production. Microalgae offer several advantages compared to terrestrial plants. Strategies to maintain anaerobic environment for biohydrogen production are summarized. Efficient biogas production via anaerobic digestion is significantly affected by the biomass composition, pretreatment strategies and the parameters of the digestion process. Coupled biohydrogen and biogas production increases the efficiency and sustainability of renewable energy production. Copyright © 2018. Published by Elsevier Ltd.

Octamer-binding protein 4 affects the cell biology and phenotypic transition of lung cancer cells involving β-catenin/E-cadherin complex degradation.

PubMed

Chen, Zhong-Shu; Ling, Dong-Jin; Zhang, Yang-De; Feng, Jian-Xiong; Zhang, Xue-Yu; Shi, Tian-Sheng

2015-03-01

Clinical studies have reported evidence for the involvement of octamer‑binding protein 4 (Oct4) in the tumorigenicity and progression of lung cancer; however, the role of Oct4 in lung cancer cell biology in vitro and its mechanism of action remain to be elucidated. Mortality among lung cancer patients is more frequently due to metastasis rather than their primary tumors. Epithelial‑mesenchymal transition (EMT) is a prominent biological event for the induction of epithelial cancer metastasis. The aim of the present study was to investigate whether Oct4 had the capacity to induce lung cancer cell metastasis via the promoting the EMT in vitro. Moreover, the effect of Oct4 on the β‑catenin/E‑cadherin complex, associated with EMT, was examined using immunofluorescence and immunoprecipitation assays as well as western blot analysis. The results demonstrated that Oct4 enhanced cell invasion and adhesion accompanied by the downregulation of epithelial marker cytokeratin, and upregulation of the mesenchymal markers vimentin and N‑cadherin. Furthermore, Oct4 induced EMT of lung cancer cells by promoting β‑catenin/E‑cadherin complex degradation and regulating nuclear localization of β‑catenin. In conclusion, the present study indicated that Oct4 affected the cell biology of lung cancer cells in vitro through promoting lung cancer cell metastasis via EMT; in addition, the results suggested that the association and degradation of the β‑catenin/E‑cadherin complex was regulated by Oct4 during the process of EMT.

Greek Secondary School Students' Views about Biology

ERIC Educational Resources Information Center

Mavrikaki, Evangelia; Koumparou, Helen; Kyriakoudi, Margarita; Papacharalampous, Irene; Trimandili, Maria

2012-01-01

This paper aims to give a picture of Greek students' views about biology and some of the factors that affect them. A questionnaire measuring students' intrinsic motivation to learn biology, individual interest in biology and perceived difficulty of biology, along with information about students' gender, level, parents' occupation and educational…

Validating Experimental Bedform Dynamics on Cohesive Sand-Mud Beds in the Dee Estuary

NASA Astrophysics Data System (ADS)

Baas, Jaco H.; Baker, Megan; Hope, Julie; Malarkey, Jonathan; Rocha, Renata

2014-05-01

Recent laboratory experiments and field measurements have shown that small quantities of cohesive clay, and in particular 'sticky' biological polymers, within a sandy substrate dramatically reduce the development rate of sedimentary bedforms, with major implications for sediment transport rate calculations and process interpretations from the sedimentary record. FURTHER INFORMATION Flow and sediment transport predictions from sedimentary structures found in modern estuaries and within estuarine geological systems are impeded by an almost complete lack of process-based knowledge of the behaviour of natural sediments that consist of mixtures of cohesionless sand and biologically-active cohesive mud. Indeed, existing predictive models are largely based on non-organic cohesionless sands, despite the fact that mud, in pure form or mixed with sand, is the most common sediment on Earth and also the most biologically active interface across a range of Earth-surface environments, including rivers and shallow seas. The multidisciplinary COHBED project uses state-of-the-art laboratory and field technologies to measure the erosional properties of mixed cohesive sediment beds and the formation and stability of sedimentary bedforms on these beds, integrating the key physical and biological processes that govern bed evolution. The development of current ripples on cohesive mixed sediment beds was investigated as a function of physical control on bed cohesion versus biological control on bed cohesion. These investigations included laboratory flume experiments in the Hydrodynamics Laboratory (Bangor University) and field experiments in the Dee estuary (at West Kirby near Liverpool). The flume experiments showed that winnowing of fine-grained cohesive sediment, including biological stabilisers, is an important process affecting the development rate, size and shape of the cohesive bedforms. The ripples developed progressively slower as the kaolin clay fraction in the sandy substrate bed was increased. The same result was obtained for xanthan gum, which is a proxy for biological polymers produced by microphytobenthos. Yet, the xanthan gum was several orders more effective in slowing down ripple development than kaolin clay, suggesting that the cohesive forces for biological polymers are much higher than for clay minerals, and that sedimentological process models should refocus on biostabilisation processes. The first results of the field experiments show that the winnowing of fines from developing ripples and the slowing down of current ripple development in mixed cohesive sediment is mimicked on intertidal flats in the Dee estuary. In particular, these field data revealed that current ripples in cohesive sediment are smaller with more two-dimensional crestlines than in non-cohesive sand. The wider implications of these findings will be discussed. COHBED Project Team (NERC): Alan Davies (Bangor University); Daniel Parsons, Leiping Ye (University of Hull); Jeffrey Peakall (University of Leeds); Dougal Lichtman, Louise O'Boyle, Peter Thorne (NOC Liverpool); Sarah Bass, Andrew Manning, Robert Schindler (University of Plymouth); Rebecca Aspden, Emma Defew, Julie Hope, David Paterson (University of St Andrews)

Long-Term Trends in the Global Carbon Cycle: Biogeochemical Records of the Past 205 myrs

NASA Astrophysics Data System (ADS)

Katz, M. E.; Fennel, K.; Berner, R. A.; Falkowski, P. G.

2005-12-01

Atmospheric and seawater chemistry are modified through time by both geological and biological processes: tectonic outgassing in combination with erosional processes are the primary suppliers of most major elements in geochemical cycles; biologically-mediated redox processes alter mobile elemental reservoirs before geologic processes sequester (remove) elements from these mobile reservoirs. We present Jurassic-Cenozoic carbon isotope records for carbonates and organic matter generated from bulk sediment samples from the Atlantic (sample resolution of 200 kyrs), and infer from these records changes in redox conditions and biological processes that affected atmospheric and seawater chemistry through time. We use our carbon isotope records with published sulfur isotopes of sulfates in model simulations to reconstruct carbon burial, pCO2 and pO2 over the past 205 myrs; our model results indicate that organic C burial and pO2 have increased, while pCO2 has decreased. The evolution and expansion of the larger-celled eucaryotic phytoplankton of the red-plastid lineage, coupled with the opening of the Atlantic Ocean basin and global sea-level rise, led to this increase in organic carbon burial beginning in the Early Jurassic as the supercontinent Pangea broke apart. This organic C burial increased the oxidation state of Earth's surface reservoirs while drawing down atmospheric CO2, which in turn acted as a strong selective agent in both marine and terrestrial primary producers, resulting in the rise in C4 and beta-carboxylation photosynthetic pathways in the latter part of the Cenozoic. At the same time, O2 levels approximately doubled, with relatively fast increases in the Early Jurassic and the Eocene. The rise of oxygen may have been a key factor in the evolution, radiation, and subsequent increase in the average size of placental mammals during the Cenozoic.

Impact of Release Rates on the Effectiveness of Augmentative Biological Control Agents

PubMed Central

Crowder, David W.

2007-01-01

To access the effect of augmentative biological control agents, 31 articles were reviewed that investigated the impact of release rates of 35 augmentative biological control agents on the control of 42 arthropod pests. In 64% of the cases, the release rate of the biological control agent did not significantly affect the density or mortality of the pest insect. Results where similar when parasitoidsor predators were utilized as the natural enemy. Within any order of natural enemy, there were more cases where release rates did not affect augmentative biological control than cases where release rates were significant. There were more cases in which release rates did not affect augmentative biological control when pests were from the orders Hemiptera, Acari, or Diptera, but not with pests from the order Lepidoptera. In most cases, there was an optimal release rate that produced effective control of a pest species. This was especially true when predators were used as a biological control agent. Increasing the release rate above the optimal rate did not improve control of the pest and thus would be economically detrimental. Lower release rates were of ten optimal when biological control was used in conjunction with insecticides. In many cases, the timing and method of biological control applications were more significant factors impacting the effectiveness of biological control than the release rate. Additional factors that may limit the relative impact of release rates include natural enemy fecundity, establishment rates, prey availability, dispersal, and cannibalism. PMID:20307240

Global processing in amblyopia: a review

PubMed Central

Hamm, Lisa M.; Black, Joanna; Dai, Shuan; Thompson, Benjamin

2014-01-01

Amblyopia is a neurodevelopmental disorder of the visual system that is associated with disrupted binocular vision during early childhood. There is evidence that the effects of amblyopia extend beyond the primary visual cortex to regions of the dorsal and ventral extra-striate visual cortex involved in visual integration. Here, we review the current literature on global processing deficits in observers with either strabismic, anisometropic, or deprivation amblyopia. A range of global processing tasks have been used to investigate the extent of the cortical deficit in amblyopia including: global motion perception, global form perception, face perception, and biological motion. These tasks appear to be differentially affected by amblyopia. In general, observers with unilateral amblyopia appear to show deficits for local spatial processing and global tasks that require the segregation of signal from noise. In bilateral cases, the global processing deficits are exaggerated, and appear to extend to specialized perceptual systems such as those involved in face processing. PMID:24987383

Design modification and optimisation of the perfusion system of a tri-axial bioreactor for tissue engineering.

PubMed

Hussein, Husnah; Williams, David J; Liu, Yang

2015-07-01

A systematic design of experiments (DOE) approach was used to optimize the perfusion process of a tri-axial bioreactor designed for translational tissue engineering exploiting mechanical stimuli and mechanotransduction. Four controllable design parameters affecting the perfusion process were identified in a cause-effect diagram as potential improvement opportunities. A screening process was used to separate out the factors that have the largest impact from the insignificant ones. DOE was employed to find the settings of the platen design, return tubing configuration and the elevation difference that minimise the load on the pump and variation in the perfusion process and improve the controllability of the perfusion pressures within the prescribed limits. DOE was very effective for gaining increased knowledge of the perfusion process and optimizing the process for improved functionality. It is hypothesized that the optimized perfusion system will result in improved biological performance and consistency.

Statistical modelling of variability in sediment-water nutrient and oxygen fluxes

NASA Astrophysics Data System (ADS)

Serpetti, Natalia; Witte, Ursula; Heath, Michael

2016-06-01

Organic detritus entering, or produced, in the marine environment is re-mineralised to inorganic nutrient in the seafloor sediments. The flux of dissolved inorganic nutrient between the sediment and overlying water column is a key process in the marine ecosystem, which binds the biogeochemical sub-system to the living food web. These fluxes are potentially affected by a wide range of physical and biological factors and disentangling these is a significant challenge. Here we develop a set of General Additive Models (GAM) of nitrate, nitrite, ammonia, phosphate, silicate and oxygen fluxes, based on a year-long campaign of field measurements off the north-east coast of Scotland. We show that sediment grain size, turbidity due to sediment re-suspension, temperature, and biogenic matter content were the key factors affecting oxygen consumption, ammonia and silicate fluxes. However, phosphate fluxes were only related to suspended sediment concentrations, whilst nitrate fluxes showed no clear relationship to any of the expected drivers of change, probably due to the effects of denitrification. Our analyses show that the stoichiometry of nutrient regeneration in the ecosystem is not necessarily constant and may be affected by combinations of processes. We anticipate that our statistical modelling results will form the basis for testing the functionality of process-based mathematical models of whole-sediment biogeochemistry.

Lysine acetylation stoichiometry and proteomics analyses reveal pathways regulated by sirtuin 1 in human cells.

PubMed

Gil, Jeovanis; Ramírez-Torres, Alberto; Chiappe, Diego; Luna-Peñaloza, Juan; Fernandez-Reyes, Francis C; Arcos-Encarnación, Bolivar; Contreras, Sandra; Encarnación-Guevara, Sergio

2017-11-03

Lysine acetylation is a widespread posttranslational modification affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make it difficult to confidently assign these numbers, limiting understanding of their biological significance. Here, we tested three common sample preparation methods to determine their suitability for assessing acetylation stoichiometry in three human cell lines, identifying the acetylation occupancy in more than 1,300 proteins from each cell line. The stoichiometric analysis in combination with quantitative proteomics also enabled us to explore their functional roles. We found that higher abundance of the deacetylase sirtuin 1 (SIRT1) correlated with lower acetylation occupancy and lower levels of ribosomal proteins, including those involved in ribosome biogenesis and rRNA processing. Treatment with the SIRT1 inhibitor EX-527 confirmed SIRT1's role in the regulation of pre-rRNA synthesis and processing. Specifically, proteins involved in pre-rRNA transcription, including subunits of the polymerase I and SL1 complexes and the RNA polymerase I-specific transcription initiation factor RRN3, were up-regulated after SIRT1 inhibition. Moreover, many protein effectors and regulators of pre-rRNA processing needed for rRNA maturation were also up-regulated after EX-527 treatment with the outcome that pre-rRNA and 28S rRNA levels also increased. More generally, we found that SIRT1 inhibition down-regulates metabolic pathways, including glycolysis and pyruvate metabolism. Together, these results provide the largest data set thus far of lysine acetylation stoichiometry (available via ProteomeXchange with identifier PXD005903) and set the stage for further biological investigations of this central posttranslational modification. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning.

PubMed

Wilcox, Jennifer L; Bevilacqua, Philip C

2013-10-22

Shifting of pKa's in RNA is important for many biological processes; however, the driving forces responsible for shifting are not well understood. Herein, we determine how structural environments surrounding protonated bases affect pKa shifting in double-stranded RNA (dsRNA). Using (31)P NMR, we determined the pKa of the adenine in an A(+)·C base pair in various sequence and structural environments. We found a significant dependence of pKa on the base pairing strength of nearest neighbors and the location of a nearby bulge. Increasing nearest neighbor base pairing strength shifted the pKa of the adenine in an A(+)·C base pair higher by an additional 1.6 pKa units, from 6.5 to 8.1, which is well above neutrality. The addition of a bulge two base pairs away from a protonated A(+)·C base pair shifted the pKa by only ~0.5 units less than a perfectly base paired hairpin; however, positioning the bulge just one base pair away from the A(+)·C base pair prohibited formation of the protonated base pair as well as several flanking base pairs. Comparison of data collected at 25 °C and 100 mM KCl to biological temperature and Mg(2+) concentration revealed only slight pKa changes, suggesting that similar sequence contexts in biological systems have the potential to be protonated at biological pH. We present a general model to aid in the determination of the roles protonated bases may play in various dsRNA-mediated processes including ADAR editing, miRNA processing, programmed ribosomal frameshifting, and general acid-base catalysis in ribozymes.

Discovery of Transcriptional Targets Regulated by Nuclear Receptors Using a Probabilistic Graphical Model

PubMed Central

Lee, Mikyung; Huang, Ruili; Tong, Weida

2016-01-01

Nuclear receptors (NRs) are ligand-activated transcriptional regulators that play vital roles in key biological processes such as growth, differentiation, metabolism, reproduction, and morphogenesis. Disruption of NRs can result in adverse health effects such as NR-mediated endocrine disruption. A comprehensive understanding of core transcriptional targets regulated by NRs helps to elucidate their key biological processes in both toxicological and therapeutic aspects. In this study, we applied a probabilistic graphical model to identify the transcriptional targets of NRs and the biological processes they govern. The Tox21 program profiled a collection of approximate 10 000 environmental chemicals and drugs against a panel of human NRs in a quantitative high-throughput screening format for their NR disruption potential. The Japanese Toxicogenomics Project, one of the most comprehensive efforts in the field of toxicogenomics, generated large-scale gene expression profiles on the effect of 131 compounds (in its first phase of study) at various doses, and different durations, and their combinations. We applied author-topic model to these 2 toxicological datasets, which consists of 11 NRs run in either agonist and/or antagonist mode (18 assays total) and 203 in vitro human gene expression profiles connected by 52 shared drugs. As a result, a set of clusters (topics), which consists of a set of NRs and their associated target genes were determined. Various transcriptional targets of the NRs were identified by assays run in either agonist or antagonist mode. Our results were validated by functional analysis and compared with TRANSFAC data. In summary, our approach resulted in effective identification of associated/affected NRs and their target genes, providing biologically meaningful hypothesis embedded in their relationships. PMID:26643261

Effect of location in the canopy on the colour development of three apple cultivars during growth.

PubMed

Unuk, Tatjana; Tijskens, L M M Pol; Germšek, Blaž; Zadravec, Peter; Vogrin, Andrej; Hribar, Janez; Simčič, Marjan; Tojnko, Stanislav

2012-09-01

Homogeneity in appearance is one of the quality aspects asked for in the supply chain. Decreasing the biological variation in batches of harvested apples (cultivars Braeburn, Fuji and Gala) becomes increasingly important. Skin colour is one of the aspects that determine both optimal harvest and stage of development. Skin colour is affected by location in the canopy. The rules of development of biological variation are now established and will be used on skin colour data. The Minolta colour aspects a*, b* and L* measured before commercial harvest change in a sigmoidal fashion and can be analysed including the biological variation, with a logistic model in indexed nonlinear regression, obtaining explained parts of above 90%. The mechanism of colour change is not affected by state of development or location in the canopy. The location in the canopy affects the intensity of both red and green colouring compounds. The variation in colouration is not affected by the location in the canopy. The red-coloured apple cultivar (Gala) depends more on the location in the canopy than the less-coloured cultivars (Fuji and Braeburn). The colour development in Fuji apples is considerably slower, with a much larger variation in stage of development. The location in the canopy affects all aspects of biological variation (biological shift factor and asymptotic starting level of colouration) for all three colour aspects L*, a* and b*, but only the mean value, not the standard deviation. The biological shift factors per colour aspects are linearly related. Once induced, variation remains constant during development. Copyright © 2012 Society of Chemical Industry.

[Factors affecting biological removal of iron and manganese in groundwater].

PubMed

Xue, Gang; He, Sheng-Bing; Wang, Xin-Ze

2006-01-01

Factors affecting biological process for removing iron and manganese in groundwater were analyzed. When DO and pH in groundwater after aeration were 7.0 - 7.5 mg/L and 6.8 - 7.0 respectively, not only can the activation of Mn2+ oxidizing bacteria be maintained, but also the demand of iron and manganese removal can be satisfied. A novel inoculating approach of grafting mature filter material into filter bed, which is easier to handle than selective culture media, was employed in this research. However, this approach was only suitable to the filter material of high-quality manganese sand with strong Mn2+ adsorption capacity. For the filter material of quartz sand with weak adsorption capacity, only culturing and domesticating Mn2+ oxidizing bacteria by selective culture media can be adopted as inoculation in filter bed. The optimal backwashing rate of biological filter bed filled with manganese sand and quartz sand should be kept at a relatively low level of 6 - 9 L/(m2 x s) and 7 -11 L/( m2 x s), respectively. Then the stability of microbial phase in filter bed was not disturbed, and iron and manganese removal efficiency recovered in less than 5h. Moreover, by using filter material with uniform particle size of 1.0 - 1.2 mm in filter bed, the filtration cycle reached as long as 35 - 38h.

Biogeochemical cycling in the ocean. Part 1: Introduction to the effects of upwelling along the west coast of North America

NASA Technical Reports Server (NTRS)

Howe, John T.

1986-01-01

Coastal upwelling is examined as it relates to the cycling of chemical species in coastal waters along the west coast of North America. The temporal and spatial features of upwelling phenomena in the Eastern boundary regions of the North Pacific Ocean are presented and discussed in terms of upwelling episodes. Climate conditions affecting upwelling include: thermal effects, wind-induced shear stress which moves surface layers, and the curl of the wind stress vector which is thought to affect the extent and nature of upwelling and the formation of offshore convergent downwelling fronts. These effects and the interaction of sunlight and upwelled nutrients which result in a biological bloom in surface waters is modeled analytically. The roles of biological and chemical species, including the effects of predation, are discussed in that context, and relevant remote sensing and in situ observations are presented. Climatological, oceanographic, biological, physical, chemical events, and processes that pertain to biogeochemical cycling are presented and described by a set of partial differential equations. Simple preliminary results are obtained and are compared with data. Thus a fairly general framework has been laid where the many facets of biogeochemical cycling in coastal upwelled waters can be examined in their relationship to one another, and to the whole, to whatever level of detail or approximation is warranted or desired.

Analysis of a dynamic model of guard cell signaling reveals the stability of signal propagation

NASA Astrophysics Data System (ADS)

Gan, Xiao; Albert, RéKa

Analyzing the long-term behaviors (attractors) of dynamic models of biological systems can provide valuable insight into biological phenotypes and their stability. We identified the long-term behaviors of a multi-level, 70-node discrete dynamic model of the stomatal opening process in plants. We reduce the model's huge state space by reducing unregulated nodes and simple mediator nodes, and by simplifying the regulatory functions of selected nodes while keeping the model consistent with experimental observations. We perform attractor analysis on the resulting 32-node reduced model by two methods: 1. converting it into a Boolean model, then applying two attractor-finding algorithms; 2. theoretical analysis of the regulatory functions. We conclude that all nodes except two in the reduced model have a single attractor; and only two nodes can admit oscillations. The multistability or oscillations do not affect the stomatal opening level in any situation. This conclusion applies to the original model as well in all the biologically meaningful cases. We further demonstrate the robustness of signal propagation by showing that a large percentage of single-node knockouts does not affect the stomatal opening level. Thus, we conclude that the complex structure of this signal transduction network provides multiple information propagation pathways while not allowing extensive multistability or oscillations, resulting in robust signal propagation. Our innovative combination of methods offers a promising way to analyze multi-level models.

Climate change and alpine stream biology: progress, challenges, and opportunities for the future.

PubMed

Hotaling, Scott; Finn, Debra S; Joseph Giersch, J; Weisrock, David W; Jacobsen, Dean

2017-11-01

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems. © 2017 Cambridge Philosophical Society.

Climate change and alpine stream biology: progress, challenges, and opportunities for the future

USGS Publications Warehouse

Hotaling, Scott; Finn, Debra S.; Giersch, J. Joseph; Weisrock, David W.; Jacobsen, Dean

2017-01-01

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro- to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism-focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward-looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.

Effects of insufficient sleep on circadian rhythmicity and expression amplitude of the human blood transcriptome.

PubMed

Möller-Levet, Carla S; Archer, Simon N; Bucca, Giselda; Laing, Emma E; Slak, Ana; Kabiljo, Renata; Lo, June C Y; Santhi, Nayantara; von Schantz, Malcolm; Smith, Colin P; Dijk, Derk-Jan

2013-03-19

Insufficient sleep and circadian rhythm disruption are associated with negative health outcomes, including obesity, cardiovascular disease, and cognitive impairment, but the mechanisms involved remain largely unexplored. Twenty-six participants were exposed to 1 wk of insufficient sleep (sleep-restriction condition 5.70 h, SEM = 0.03 sleep per 24 h) and 1 wk of sufficient sleep (control condition 8.50 h sleep, SEM = 0.11). Immediately following each condition, 10 whole-blood RNA samples were collected from each participant, while controlling for the effects of light, activity, and food, during a period of total sleep deprivation. Transcriptome analysis revealed that 711 genes were up- or down-regulated by insufficient sleep. Insufficient sleep also reduced the number of genes with a circadian expression profile from 1,855 to 1,481, reduced the circadian amplitude of these genes, and led to an increase in the number of genes that responded to subsequent total sleep deprivation from 122 to 856. Genes affected by insufficient sleep were associated with circadian rhythms (PER1, PER2, PER3, CRY2, CLOCK, NR1D1, NR1D2, RORA, DEC1, CSNK1E), sleep homeostasis (IL6, STAT3, KCNV2, CAMK2D), oxidative stress (PRDX2, PRDX5), and metabolism (SLC2A3, SLC2A5, GHRL, ABCA1). Biological processes affected included chromatin modification, gene-expression regulation, macromolecular metabolism, and inflammatory, immune and stress responses. Thus, insufficient sleep affects the human blood transcriptome, disrupts its circadian regulation, and intensifies the effects of acute total sleep deprivation. The identified biological processes may be involved with the negative effects of sleep loss on health, and highlight the interrelatedness of sleep homeostasis, circadian rhythmicity, and metabolism.

Gene expression of corals in response to macroalgal competitors.

PubMed

Shearer, Tonya L; Snell, Terry W; Hay, Mark E

2014-01-01

As corals decline and macroalgae proliferate on coral reefs, coral-macroalgal competition becomes more frequent and ecologically important. Whether corals are damaged by these interactions depends on susceptibility of the coral and traits of macroalgal competitors. Investigating changes in gene expression of corals and their intracellular symbiotic algae, Symbiodinium, in response to contact with different macroalgae provides insight into the biological processes and cellular pathways affected by competition with macroalgae. We evaluated the gene expression profiles of coral and Symbiodinium genes from two confamilial corals, Acropora millepora and Montipora digitata, after 6 h and 48 h of contact with four common macroalgae that differ in their allelopathic potency to corals. Contacts with macroalgae affected different biological pathways in the more susceptible (A. millepora) versus the more resistant (M. digitata) coral. Genes of coral hosts and of their associated Symbiodinium also responded in species-specific and time-specific ways to each macroalga. Changes in number and expression intensity of affected genes were greater after 6 h compared to 48 h of contact and were greater following contact with Chlorodesmis fastigiata and Amphiroa crassa than following contact with Galaxaura filamentosa or Turbinaria conoides. We documented a divergence in transcriptional responses between two confamilial corals and their associated Symbiodinium, as well as a diversity of dynamic responses within each coral species with respect to the species of macroalgal competitor and the duration of exposure to that competitor. These responses included early initiation of immune processes by Montipora, which is more resistant to damage after long-term macroalgal contact. Activation of the immune response by corals that better resist algal competition is consistent with the hypothesis that some macroalgal effects on corals may be mediated by microbial pathogens.

Conservation implications of anthropogenic impacts on visual communication and camouflage.

PubMed

Delhey, Kaspar; Peters, Anne

2017-02-01

Anthropogenic environmental impacts can disrupt the sensory environment of animals and affect important processes from mate choice to predator avoidance. Currently, these effects are best understood for auditory and chemosensory modalities, and recent reviews highlight their importance for conservation. We examined how anthropogenic changes to the visual environment (ambient light, transmission, and backgrounds) affect visual communication and camouflage and considered the implications of these effects for conservation. Human changes to the visual environment can increase predation risk by affecting camouflage effectiveness, lead to maladaptive patterns of mate choice, and disrupt mutualistic interactions between pollinators and plants. Implications for conservation are particularly evident for disrupted camouflage due to its tight links with survival. The conservation importance of impaired visual communication is less documented. The effects of anthropogenic changes on visual communication and camouflage may be severe when they affect critical processes such as pollination or species recognition. However, when impaired mate choice does not lead to hybridization, the conservation consequences are less clear. We suggest that the demographic effects of human impacts on visual communication and camouflage will be particularly strong when human-induced modifications to the visual environment are evolutionarily novel (i.e., very different from natural variation); affected species and populations have low levels of intraspecific (genotypic and phenotypic) variation and behavioral, sensory, or physiological plasticity; and the processes affected are directly related to survival (camouflage), species recognition, or number of offspring produced, rather than offspring quality or attractiveness. Our findings suggest that anthropogenic effects on the visual environment may be of similar importance relative to conservation as anthropogenic effects on other sensory modalities. © 2016 Society for Conservation Biology.

Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome.

PubMed

Folly, Brenda B; Weffort-Santos, Almeriane M; Fathman, C G; Soares, Luis R B

2011-01-31

Dengue virus infection is a public health threat to hundreds of millions of individuals in the tropical regions of the globe. Although Dengue infection usually manifests itself in its mildest, though often debilitating clinical form, dengue fever, life-threatening complications commonly arise in the form of hemorrhagic shock and encephalitis. The etiological basis for the virus-induced pathology in general, and the different clinical manifestations in particular, are not well understood. We reasoned that a detailed knowledge of the global biological processes affected by virus entry into a cell might help shed new light on this long-standing problem. A bacterial two-hybrid screen using DENV2 structural proteins as bait was performed, and the results were used to feed a manually curated, global dengue-human protein interaction network. Gene ontology and pathway enrichment, along with network topology and microarray meta-analysis, were used to generate hypothesis regarding dengue disease biology. Combining bioinformatic tools with two-hybrid technology, we screened human cDNA libraries to catalogue proteins physically interacting with the DENV2 virus structural proteins, Env, cap and PrM. We identified 31 interacting human proteins representing distinct biological processes that are closely related to the major clinical diagnostic feature of dengue infection: haemostatic imbalance. In addition, we found dengue-binding human proteins involved with additional key aspects, previously described as fundamental for virus entry into cells and the innate immune response to infection. Construction of a DENV2-human global protein interaction network revealed interesting biological properties suggested by simple network topology analysis. Our experimental strategy revealed that dengue structural proteins interact with human protein targets involved in the maintenance of blood coagulation and innate anti-viral response processes, and predicts that the interaction of dengue proteins with a proposed human protein interaction network produces a modified biological outcome that may be behind the hallmark pathologies of dengue infection.

Creating the Chemistry in Cellular Respiration Concept Inventory (CCRCI)

NASA Astrophysics Data System (ADS)

Forshee, Jay Lance, II

Students at our institution report cellular respiration to be the most difficult concept they encounter in undergraduate biology, but why students find this difficult is unknown. Students may find cellular respiration difficult because there is a large amount of steps, or because there are persistent, long-lasting misconceptions and misunderstandings surrounding their knowledge of chemistry, which affect their performance on cellular respiration assessments. Most studies of cellular respiration focus on student macro understanding of the process related to breathing, and matter and energy. To date, no studies identify which chemistry concepts are most relevant to students' development of an understanding of the process of cellular respiration or have developed an assessment to measure student understanding of them. Following the Delphi method, the researchers conducted expert interviews with faculty members from four-year, masters-, and PhD-granting institutions who teach undergraduate general biology, and are experts in their respective fields of biology. From these interviews, researchers identified twelve chemistry concepts important to understanding cellular respiration and using surveys, these twelve concepts were refined into five (electron transfer, energy transfer, thermodynamics (law/conservation), chemical reactions, and gradients). The researchers then interviewed undergraduate introductory biology students at a large Midwestern university to identify their knowledge and misconceptions of the chemistry concepts that the faculty had identified previously as important. The CCRCI was developed using the five important chemistry concepts underlying cellular respiration. The final version of the CCRCI was administered to n=160 introductory biology students during the spring 2017 semester. Reliability of the CCRCI was evaluated using Cronbach's alpha (=.7) and split-half reliability (=.769), and validity of the instrument was assessed through content validity via expert agreement, response process validity through student think-aloud interviews, and via the Delphi survey methodology. Included is a discussion of item function (difficulty, discrimination, and point-biserial correlation), persistent misconceptions and the interpretation, uses, and future directions of the CCRCI.

The roles of the amygdala in the affective regulation of body, brain, and behaviour

NASA Astrophysics Data System (ADS)

Mirolli, Marco; Mannella, Francesco; Baldassarre, Gianluca

2010-09-01

Despite the great amount of knowledge produced by the neuroscientific literature on affective phenomena, current models tackling non-cognitive aspects of behaviour are often bio-inspired but rarely bio-constrained. This paper presents a theoretical account of affective systems centred on the amygdala (Amg). This account aims to furnish a general framework and specific pathways to implement models that are more closely related to biological evidence. The Amg, which receives input from brain areas encoding internal states, innately relevant stimuli, and innately neutral stimuli, plays a fundamental role in the motivational and emotional processes of organisms. This role is based on the fact that Amg implements the two associative processes at the core of Pavlovian learning (conditioned stimulus (CS)-unconditioned stimulus (US) and CS-unconditioned response (UR) associations), and that it has the capacity of modulating these associations on the basis of internal states. These functionalities allow the Amg to play an important role in the regulation of the three fundamental classes of affective responses (namely, the regulation of body states, the regulation of brain states via neuromodulators, and the triggering of a number of basic behaviours fundamental for adaptation) and in the regulation of three high-level cognitive processes (namely, the affective labelling of memories, the production of goal-directed behaviours, and the performance of planning and complex decision-making). Our analysis is conducted within a methodological approach that stresses the importance of understanding the brain within an evolutionary/adaptive framework and with the aim of isolating general principles that can potentially account for the wider possible empirical evidence in a coherent fashion.

Culture and biology interplay: An introduction.

PubMed

Causadias, José M; Telzer, Eva H; Lee, Richard M

2017-01-01

Culture and biology have evolved together, influence each other, and concurrently shape behavior, affect, cognition, and development. This special section highlights 2 major domains of the interplay between culture and biology. The first domain is neurobiology of cultural experiences-how cultural, ethnic, and racial experiences influence limbic systems and neuroendocrine functioning-and the second domain is cultural neuroscience-the connections between cultural processes and brain functioning. We include 3 studies on neurobiology of cultural experiences that examine the associations between racial discrimination and heart rate variability (Hill et al., 2016), economic and sociocultural stressors and cortisol levels (Mendoza, Dmitrieva, Perreira, & Watamura, 2016), and unfair treatment and allostatic load (Ong, Williams, Nwizu, & Gruenewald, 2016). We also include 2 studies on cultural neuroscience that investigate cultural group differences and similarities in beliefs, practices, and neural basis of emotion regulation (Qu & Telzer, 2016), and reflected and direct self-appraisals (Pfeifer et al., 2016). We discuss pending challenges and future directions for this emerging field. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Radiation-Related Treatment Effects across the Age Spectrum: Differences and Similarities or What The Old and Young Can Learn From Each Other

PubMed Central

Krasin, Matthew J.; Constine, Louis S.; Friedman, Debra; Marks, Lawrence B.

2010-01-01

Radiation related effects in children and adults limit the delivery of effective radiation doses and result in long-term morbidity affecting function and quality of life. Improvements in our understanding of the etiology and biology of these effects, including the influence of clinical variables, dosimetric factors, and the underlying biologic processes has made treatment safer and more efficacious. However, the approach to studying and understanding these effects differs between children and adults. By using the pulmonary and skeletal organ systems as examples, comparisons are made across the age spectrum for radiation related effects including pneumonitis, pulmonary fibrosis, osteonecrosis and fracture. Methods for dosimetric analysis, incorporation of imaging and biology as well a length of follow-up are compared, contrasted and discussed for both organ systems in children and adults. Better understanding of each age specific approach and how it differs may improve our ability to study late effects of radiation across the ages PMID:19959028

Extraction, Characterization, Stability and Biological Activity of Flavonoids Isolated from Chamomile Flowers

PubMed Central

Srivastava, Janmejai K; Gupta, Sanjay

2009-01-01

Dried flowers of Chamomile (Matricaria chamomilla) are largely used for their medicinal properties. In the present study, we examined the pharmacological properties of aqueous and methanolic fraction isolated from two varieties of German chamomile. HPLC-MS analysis of chamomile extract confirmed apigenin-7-O-glucoside as the major constituent of chamomile; some minor glycoside components were observed along with essential oils. These glucosides are highly stable in solution at different temperature range and their degradation occurs after long-term storage and extraction conditions at different pH and solvent. Methanolic fraction isolated from chamomile flowers demonstrated higher biologic response in inhibiting cell growth and causing induction of apoptosis in various human cancer cell lines compared to aqueous chamomile fraction. Apigenin glucosides inhibited cancer cell growth through deconjugation of glycosides that occurs in the cellular compartment to produce aglycone, apigenin. Taken together, the pharmacological profile of chamomile extract was dependent upon extraction process, storage conditions which affected the biological activity. PMID:20098626

Effects of various pretreatments on biological sulfate reduction with waste activated sludge as electron donor and waste activated sludge diminution under biosulfidogenic condition.

PubMed

Sheng, Yuxing; Cao, Hongbin; Li, Yuping; Zhang, Yi

2010-07-15

The current study focused on the influences of various pretreatments, including alkaline, ultrasonic and thermal pretreatments on biological sulfate reduction with waste activated sludge (WAS) as sole electron donor. Our results showed that thermal and ultrasonic pretreatments increased the sulfate reduction percentage by 14.8% and 7.1%, respectively, compared with experiment with raw WAS, while alkaline pretreatment decreased the sulfate reduction percentage by 46%. By analyzing the WAS structure, particle size distribution, organic component, and enzyme activity after different pretreatments, we studied the effects of these pretreatments on WAS as well as on the mechanisms of how biological sulfate reduction was affected. The reduction of WAS and variation of WAS structure in the process of sulfate reduction were investigated. Our results showed that biosulfidogenesis was an efficient method of diminishing WAS, and various pretreatments could enhance the reduction efficiency of volatile solid in the WAS. 2010 Elsevier B.V. All rights reserved.

Non-coding RNAs in Prostate Cancer: From Discovery to Clinical Applications.

PubMed

Ceder, Yvonne

2016-01-01

Prostate cancer is a heterogeneous disease for which the molecular mechanisms are still not fully elucidated. Prostate cancer research has traditionally focused on genomic and epigenetic alterations affecting the proteome, but over the last decade non-coding RNAs, especially microRNAs, have been recognized to play a key role in prostate cancer progression. A considerable number of individual microRNAs have been found to be deregulated in prostate cancer and their biological significance elucidated in functional studies. This review will delineate the current advances regarding the involvement of microRNAs and their targets in prostate cancer biology as well as their potential usage in the clinical management of the disease. The main focus will be on microRNAs contributing to initiation and progression of prostate cancer, including androgen signalling, cellular plasticity, stem cells biology and metastatic processes. To conclude, implications on potential future microRNA-based therapeutics based on the recent advances regarding the interplay between microRNAs and their targets are discussed.

Heterologous vaccine effects.

PubMed

Saadatian-Elahi, Mitra; Aaby, Peter; Shann, Frank; Netea, Mihai G; Levy, Ofer; Louis, Jacques; Picot, Valentina; Greenberg, Michael; Warren, William

2016-07-25

The heterologous or non-specific effects (NSEs) of vaccines, at times defined as "off-target effects" suggest that they can affect the immune response to organisms other than their pathogen-specific intended purpose. These NSEs have been the subject of clinical, immunological and epidemiological studies and are increasingly recognized as an important biological process by a growing group of immunologists and epidemiologists. Much remain to be learned about the extent and underlying mechanisms for these effects. The conference "Off-target effects of vaccination" held in Annecy-France (June 8-10 2015) intended to take a holistic approach drawing from the fields of immunology, systems biology, epidemiology, bioinformatics, public health and regulatory science to address fundamental questions of immunological mechanisms, as well as translational questions about vaccines NSEs. NSE observations were examined using case-studies on live attenuated vaccines and non-live vaccines followed by discussion of studies of possible biological mechanisms. Some possible pathways forward in the study of vaccines NSE were identified and discussed by the expert group. Copyright © 2016.

Biodistribution mechanisms of therapeutic monoclonal antibodies in health and disease.

PubMed

Tabrizi, Mohammad; Bornstein, Gadi Gazit; Suria, Hamza

2010-03-01

The monoclonal antibody market continues to witness an impressive rate of growth and has become the leading source of expansion in the biologic segment within the pharmaceutical industry. Currently marketed monoclonal antibodies target a diverse array of antigens. These antigens are distributed in a variety of tissues such as tumors, lungs, synovial fluid, psoriatic plaques, and lymph nodes. As the concentration of drug at the proximity of the biological receptor determines the magnitude of the observed pharmacological responses, a significant consideration in effective therapeutic application of monoclonal antibodies is a thorough understanding of the processes that regulate antibody biodistribution. Monoclonal antibody distribution is affected by factors such as molecular weight, blood flow, tissue and tumor heterogeneity, structure and porosity, target antigen density, turnover rate, and the target antigen expression profile.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

PubMed Central

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Assessing potential abiotic and biotic complications of crayfish-induced gravel transport in experimental streams

NASA Astrophysics Data System (ADS)

Statzner, Bernhard; Peltret, Odile

2006-03-01

Biogeomorphology adds the element "biological dynamics" (of populations or communities) to chemical and physical geomorphic factors and thus complicates the framework of geomorphic processes. Such biological complications of the animal-induced transport of solids in streams should be particularly important in crayfish, as crayfish affect this transport through their overall activity and intraspecific aggression levels, which could be modified by shelter availability or the establishment of dominance hierarchies among individuals not knowing each other. Using experimental streams, we tested these hypotheses by measuring how shelter availability or residential crayfish group invasion by unknown individuals affected the impact of the crayfish Orconectes limosus on the (i) transport of gravel at baseflow (during 12 experimental days); (ii) sediment surface characteristics (after 12 days); and (iii) critical shear stress causing incipient gravel motion during simulated floods (after 12 days). The two potentially important factors shelter availability or residential group invasion negligibly affected the crayfish impact on gravel sediments, suggesting that habitat unfamiliarity (a third potentially important factor affecting crayfish activity) should increase the crayfish-induced sediment transport. Because habitat unfamiliarity is associated with sporadic long-distance migrations of a few crayfish individuals, this third factor should play a minor role in real streams, where crayfish biomass should be a key factor in relations with crayfish effects on sediments. Therefore, we combined the results of this study with those of previous crayfish experiments to assess how crayfish biomass could serve in modelling the gravel transport. Crayfish biomass explained 47% of the variability in the baseflow gravel transport and, in combination with the coefficient of variation of the bed elevation and algal cover, 72% of the variability in the critical gravel shear stress. These results encourage more research on the topic, as an increasing number of eliminations of abiotic and biotic factors that could complicate the animal-induced sediment transport in streams would facilitate the use of biological variables (e.g., bioturbator biomass) in future modelling of the transport of solids.

Fluid models and simulations of biological cell phenomena

NASA Technical Reports Server (NTRS)

Greenspan, H. P.

1982-01-01

The dynamics of coated droplets are examined within the context of biofluids. Of specific interest is the manner in which the shape of a droplet, the motion within it as well as that of aggregates of droplets can be controlled by the modulation of surface properties and the extent to which such fluid phenomena are an intrinsic part of cellular processes. From the standpoint of biology, an objective is to elucidate some of the general dynamical features that affect the disposition of an entire cell, cell colonies and tissues. Conventionally averaged field variables of continuum mechanics are used to describe the overall global effects which result from the myriad of small scale molecular interactions. An attempt is made to establish cause and effect relationships from correct dynamical laws of motion rather than by what may have been unnecessary invocation of metabolic or life processes. Several topics are discussed where there are strong analogies droplets and cells including: encapsulated droplets/cell membranes; droplet shape/cell shape; adhesion and spread of a droplet/cell motility and adhesion; and oams and multiphase flows/cell aggregates and tissues. Evidence is presented to show that certain concepts of continuum theory such as suface tension, surface free energy, contact angle, bending moments, etc. are relevant and applicable to the study of cell biology.

The developing framework of marine ecotoxicology: Pollutants as a variable in marine ecosystems?

USGS Publications Warehouse

Luoma, Samuel N.

1996-01-01

Marine ecosystems include a subset in which at least some interrelated geochemical, biochemical, physiological, population and community characteristics are changed by pollutants. Moderate contamination is relatively widespread in coastal and estuarine ecosystems, so the subset of ecosystems with at least some processes affected could be relatively large. Pollutant influences have changed and will probably continue to change on time scales of decades. Biological exposures and dose in such ecosystems are species-specific and determined by how the species is exposed to different environmental media and the geochemistry of individual pollutants within those media. Bioaccumulation models offer significant promise for interpreting such exposures. Biological responses to pollutants need to be more directly linked to exposure and dose. At the level of the individual this might be improved by better understanding relationships between tissue concentrations of pollutants and responses to pollutants. Multi-discipline field and laboratory studies combined with advanced understanding of some basic processes have reduced the ambiguities in interpreting a few physiological/organismic responses to pollutants in nature. Recognition of pollutant-induced patterns in population responses could lead to similar advances. A rational framework for ecotoxicology is developing, but its further advance is dependent upon better integration of ecotoxicology with basic marine ecology and biology.

Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

PubMed

Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

2016-01-01

Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Impacts of climate change on marine organisms and ecosystems.

PubMed

Brierley, Andrew S; Kingsford, Michael J

2009-07-28

Human activities are releasing gigatonnes of carbon to the Earth's atmosphere annually. Direct consequences of cumulative post-industrial emissions include increasing global temperature, perturbed regional weather patterns, rising sea levels, acidifying oceans, changed nutrient loads and altered ocean circulation. These and other physical consequences are affecting marine biological processes from genes to ecosystems, over scales from rock pools to ocean basins, impacting ecosystem services and threatening human food security. The rates of physical change are unprecedented in some cases. Biological change is likely to be commensurately quick, although the resistance and resilience of organisms and ecosystems is highly variable. Biological changes founded in physiological response manifest as species range-changes, invasions and extinctions, and ecosystem regime shifts. Given the essential roles that oceans play in planetary function and provision of human sustenance, the grand challenge is to intervene before more tipping points are passed and marine ecosystems follow less-buffered terrestrial systems further down a spiral of decline. Although ocean bioengineering may alleviate change, this is not without risk. The principal brake to climate change remains reduced CO(2) emissions that marine scientists and custodians of the marine environment can lobby for and contribute to. This review describes present-day climate change, setting it in context with historical change, considers consequences of climate change for marine biological processes now and in to the future, and discusses contributions that marine systems could play in mitigating the impacts of global climate change.

A single preovulatory administration of ulipristal acetate affects the decidualization process of the human endometrium during the receptive period of the menstrual cycle.

PubMed

Lira-Albarrán, Saúl; Durand, Marta; Barrera, David; Vega, Claudia; Becerra, Rocio García; Díaz, Lorenza; García-Quiroz, Janice; Rangel, Claudia; Larrea, Fernando

2018-04-27

In order to get further information on the effects of ulipristal acetate (UPA) upon the process of decidualization of endometrium, a functional analysis of the differentially expressed genes in endometrium (DEG) from UPA treated-versus control-cycles of normal ovulatory women was performed. A list of 1183 endometrial DEG, from a previously published study by our group, was submitted to gene ontology, gene enrichment and ingenuity pathway analyses (IPA). This functional analysis showed that decidualization was a biological process overrepresented. Gene set enrichment analysis identified LIF, PRL, IL15 and STAT3 among the most down-regulated genes within the JAK STAT canonical pathway. IPA showed that decidualization of uterus was a bio-function predicted as inhibited by UPA. The results demonstrated that this selective progesterone receptor modulator, when administered during the periovulatory phase of the menstrual cycle, may affect the molecular mechanisms leading to endometrial decidualization in response to progesterone during the period of maximum embryo receptivity. Copyright © 2018 Elsevier B.V. All rights reserved.

The Design and Analysis of Transposon-Insertion Sequencing Experiments

PubMed Central

Chao, Michael C.; Abel, Sören; Davis, Brigid M.; Waldor, Matthew K.

2016-01-01

Preface Transposon-insertion sequencing (TIS) is a powerful approach that can be widely applied to genome-wide definition of loci that are required for growth in diverse conditions. However, experimental design choices and stochastic biological processes can heavily influence the results of TIS experiments and affect downstream statistical analysis. Here, we discuss TIS experimental parameters and how these factors relate to the benefits and limitations of the various statistical frameworks that can be applied to computational analysis of TIS data. PMID:26775926

Water - The key to global change. [of weather and climate

NASA Technical Reports Server (NTRS)

Soffen, Gerald A.

1988-01-01

The role of water in processes of global change is discussed. The importance of water in global warming, the loss of biological diversity, the activity of the El Nino southern oscillation, and the melting of polar ice are examined. Plans for a mission to measure tropical rainfall using a two frequency radar, a visible/IR radiometer and a passive microwave radiometer are noted. The way in which global change is affected by changes in patterns of available water is considered.

Trident Biological Surveys: SUBASE Bangor (July 1977 and June 1978) and Indian Island Annex (January, May 1974 and June 1978). Supplement 2.

DTIC Science & Technology

1979-12-01

or critical marine habitats affected by construction activities. Adverse impact has been limited to the biota physically disrupted by the mechanical ...Adverse impact has been limited to the biota physically disrupted by the mechanical process of pier construction. Commercial clam densities, standing crop...such as those at SUBASE Bangor. Samples are often expensive and time consuming to obtain: however, the reliability of one’s results depends heavily upon

Focus Issue: Cell biology meets cancer therapy.

PubMed

Gough, Nancy R

2016-02-16

Cells are the targets of anticancer therapy, whether the therapy is directed at the tumor cells themselves or the cells of the immune system. Articles in this issue and in the 2015 Science Signaling archives provide insights into what makes a cell responsive to therapy and how understanding the cellular processes affected by the drugs (including endosomal trafficking and response to proteotoxic stress) can lead to personalized cancer therapies, thereby minimizing side effects and ineffective treatment strategies. Copyright © 2016, American Association for the Advancement of Science.

Worldwide Emerging Environmental Issues Affecting the U.S. Military

DTIC Science & Technology

2010-09-01

scale, biological process to remove CO2 from the environment and transform it into solid carbonate. The procedure produces approximately two pounds of...Resources Fuel Violence in Eastern D.R. Congo……………………………..5 7.2 Protests in Peru over Dam Irrigation and Hydroelectric Project Part of a Regional...the synergies developed among the three on chemicals and waste — the Basel, Rotterdam and Stockholm Conventions (see First Joint Meeting of the Main

Summing up the noise in gene networks

NASA Astrophysics Data System (ADS)

Paulsson, Johan

2004-01-01

Random fluctuations in genetic networks are inevitable as chemical reactions are probabilistic and many genes, RNAs and proteins are present in low numbers per cell. Such `noise' affects all life processes and has recently been measured using green fluorescent protein (GFP). Two studies show that negative feedback suppresses noise, and three others identify the sources of noise in gene expression. Here I critically analyse these studies and present a simple equation that unifies and extends both the mathematical and biological perspectives.

Visual Information Processing Based on Spatial Filters Constrained by Biological Data.

DTIC Science & Technology

1978-12-01

was provided by Pantie and Sekuler ( 19681. They found that the detection (if gratings was affected most by adapting isee Section 6.1. 11 to square...evidence for certain eye scans being directed by spatial information in filtered images is given. Eye scan paths of a portrait of a young girl I Figure 08...multistable objects to more complex objects such as the man- girl figure of Fisher 119681, decision boundaries that are a natural concomitant to any pattern

Student perceptions of their biology teacher's interpersonal teaching behaviors and student achievement and affective learning outcomes

NASA Astrophysics Data System (ADS)

Smith, Wade Clay, Jr.

The primary goals of this dissertation were to determine the relationships between interpersonal teaching behaviors and student achievement and affective learning outcomes. The instrument used to collect student perceptions of teacher interpersonal teaching behaviors was the Questionnaire on Teacher Interactions (QTI). The instrument used to assess student affective learning outcomes was the Biology Student Affective Instrument (BSAI). The interpersonal teaching behavior data were collected using students as the observers. 111 students in an urban influenced, rural high school answered the QTI and BSAI in September 1997 and again in April 1998. At the same time students were pre and post tested using the Biology End of Course Examination (BECE). The QTI has been used primarily in European and Oceanic areas. The instrument was also primarily used in educational stratified environment. This was the first time the BSAI was used to assess student affective learning outcomes. The BECE is a Texas normed cognitive assessment test and it is used by Texas schools districts as the end of course examination in biology. The interpersonal teaching behaviors model was tested to ascertain if predictive power in the USA and in a non-stratified educational environment. Findings indicate that the QTI is an adequate predictor of student achievement in biology. The results were not congruent with the non-USA data and results, this indicates that the QTI is a society/culturally sensitive instrument and the instrument needs to be normed to a particular society/culture before it is used to affect teachers' and students' educational environments.

Inflammation, Self-Regulation, and Health: An Immunologic Model of Self-Regulatory Failure.

PubMed

Shields, Grant S; Moons, Wesley G; Slavich, George M

2017-07-01

Self-regulation is a fundamental human process that refers to multiple complex methods by which individuals pursue goals in the face of distractions. Whereas superior self-regulation predicts better academic achievement, relationship quality, financial and career success, and lifespan health, poor self-regulation increases a person's risk for negative outcomes in each of these domains and can ultimately presage early mortality. Given its centrality to understanding the human condition, a large body of research has examined cognitive, emotional, and behavioral aspects of self-regulation. In contrast, relatively little attention has been paid to specific biologic processes that may underlie self-regulation. We address this latter issue in the present review by examining the growing body of research showing that components of the immune system involved in inflammation can alter neural, cognitive, and motivational processes that lead to impaired self-regulation and poor health. Based on these findings, we propose an integrated, multilevel model that describes how inflammation may cause widespread biobehavioral alterations that promote self-regulatory failure. This immunologic model of self-regulatory failure has implications for understanding how biological and behavioral factors interact to influence self-regulation. The model also suggests new ways of reducing disease risk and enhancing human potential by targeting inflammatory processes that affect self-regulation.

Resilience among children and adolescents at risk for depression: Mediation and moderation across social and neurobiological contexts.

PubMed

Silk, Jennifer S; Vanderbilt-Adriance, Ella; Shaw, Daniel S; Forbes, Erika E; Whalen, Diana J; Ryan, Neal D; Dahl, Ronald E

2007-01-01

This article offers a multilevel perspective on resilience to depression, with a focus on interactions among social and neurobehavioral systems involved in emotional reactivity and regulation. We discuss models of cross-contextual mediation and moderation by which the social context influences or modifies the effects of resilience processes at the biological level, or the biological context influences or modifies the effects of resilience processes at the social level. We highlight the socialization of emotion regulation as a candidate process contributing to resilience against depression at the social context level. We discuss several factors and their interactions across levels-including genetic factors, stress reactivity, positive affect, neural systems of reward, and sleep-as candidate processes contributing to resilience against depression at the neurobehavioral level. We then present some preliminary supportive findings from two studies of children and adolescents at high risk for depression. Study 1 shows that elevated neighborhood level adversity has the potential to constrain or limit the benefits of protective factors at other levels. Study 2 indicates that ease and quickness in falling asleep and a greater amount of time in deep Stage 4 sleep may be protective against the development of depressive disorders for children. The paper concludes with a discussion of clinical implications of this approach.

Rising tides, cumulative impacts and cascading changes to estuarine ecosystem functions.

PubMed

O'Meara, Theresa A; Hillman, Jenny R; Thrush, Simon F

2017-08-31

In coastal ecosystems, climate change affects multiple environmental factors, yet most predictive models are based on simple cause-and-effect relationships. Multiple stressor scenarios are difficult to predict because they can create a ripple effect through networked ecosystem functions. Estuarine ecosystem function relies on an interconnected network of physical and biological processes. Estuarine habitats play critical roles in service provision and represent global hotspots for organic matter processing, nutrient cycling and primary production. Within these systems, we predicted functional changes in the impacts of land-based stressors, mediated by changing light climate and sediment permeability. Our in-situ field experiment manipulated sea level, nutrient supply, and mud content. We used these stressors to determine how interacting environmental stressors influence ecosystem function and compared results with data collected along elevation gradients to substitute space for time. We show non-linear, multi-stressor effects deconstruct networks governing ecosystem function. Sea level rise altered nutrient processing and impacted broader estuarine services ameliorating nutrient and sediment pollution. Our experiment demonstrates how the relationships between nutrient processing and biological/physical controls degrade with environmental stress. Our results emphasise the importance of moving beyond simple physically-forced relationships to assess consequences of climate change in the context of ecosystem interactions and multiple stressors.

Habitat connectivity and in-stream vegetation control temporal variability of benthic invertebrate communities.

PubMed

Huttunen, K-L; Mykrä, H; Oksanen, J; Astorga, A; Paavola, R; Muotka, T

2017-05-03

One of the key challenges to understanding patterns of β diversity is to disentangle deterministic patterns from stochastic ones. Stochastic processes may mask the influence of deterministic factors on community dynamics, hindering identification of the mechanisms causing variation in community composition. We studied temporal β diversity (among-year dissimilarity) of macroinvertebrate communities in near-pristine boreal streams across 14 years. To assess whether the observed β diversity deviates from that expected by chance, and to identify processes (deterministic vs. stochastic) through which different explanatory factors affect community variability, we used a null model approach. We observed that at the majority of sites temporal β diversity was low indicating high community stability. When stochastic variation was unaccounted for, connectivity was the only variable explaining temporal β diversity, with weakly connected sites exhibiting higher community variability through time. After accounting for stochastic effects, connectivity lost importance, suggesting that it was related to temporal β diversity via random colonization processes. Instead, β diversity was best explained by in-stream vegetation, community variability decreasing with increasing bryophyte cover. These results highlight the potential of stochastic factors to dampen the influence of deterministic processes, affecting our ability to understand and predict changes in biological communities through time.

Steroidogenesis in the skin: implications for local immune functions

PubMed Central

Slominski, Andrzej; Zbytek, Bazej; Nikolakis, Georgios; Manna, Pulak R.; Skobowiat, Cezary; Zmijewski, Michal; Li, Wei; Janjetovic, Zorica; Postlethwaite, Arnold; Zouboulis, Christos C.; Tuckey, Robert C.

2013-01-01

The skin has developed a hierarchy of systems that encompasses the skin immune and local steroidogenic activities in order to protect the body against the external environment and biological factors and to maintain local homeostasis. Most recently it has been established that skin cells contain the entire biochemical apparatus necessary for production of glucocorticoids, androgens and estrogens either from precursors of systemic origin or, alternatively, through the conversion of cholesterol to pregnenolone and its subsequent transformation to biologically active steroids. Examples of these products are corticosterone, cortisol, testosterone, dihydrotesterone and estradiol. Their local production can be regulated by locally produced corticotropin releasing hormone (CRH), adrenocorticotropic hormone (ACTH) or cytokines. Furthermore the production of glucocorticoids is affected by ultraviolet B radiation. The level of production and nature of the final steroid products are dependent on the cell type or cutaneous compartment, e.g., epidermis, dermis, adnexal structures or adipose tissue. Locally produced glucocorticoids, androgens and estrogens affect functions of the epidermis and adnexal structures as well as local immune activity. Malfunction of these steroidogenic activities can lead to inflammatory disorders or autoimmune diseases. The cutaneous steroidogenic system can also have systemic effects, which are emphasized by significant skin contribution to circulating androgens and/or estrogens. Furthermore, local activity of CYP11A1 can produce novel 7 -steroids and secosteroids that are biologically active. Therefore, modulation of local steroidogenic activity may serve as a new therapeutic approach for treatment of inflammatory disorders, autoimmune processes or other skin disorders. In conclusion, the skin can be defined as an independent steroidogenic organ, whose activity can affect its functions and the development of local or systemic inflammatory or autoimmune diseases. PMID:23435015

Pathway Analysis Revealed Potential Diverse Health Impacts of Flavonoids that Bind Estrogen Receptors

PubMed Central

Ye, Hao; Ng, Hui Wen; Sakkiah, Sugunadevi; Ge, Weigong; Perkins, Roger; Tong, Weida; Hong, Huixiao

2016-01-01

Flavonoids are frequently used as dietary supplements in the absence of research evidence regarding health benefits or toxicity. Furthermore, ingested doses could far exceed those received from diet in the course of normal living. Some flavonoids exhibit binding to estrogen receptors (ERs) with consequential vigilance by regulatory authorities at the U.S. EPA and FDA. Regulatory authorities must consider both beneficial claims and potential adverse effects, warranting the increases in research that has spanned almost two decades. Here, we report pathway enrichment of 14 targets from the Comparative Toxicogenomics Database (CTD) and the Herbal Ingredients’ Targets (HIT) database for 22 flavonoids that bind ERs. The selected flavonoids are confirmed ER binders from our earlier studies, and were here found in mainly involved in three types of biological processes, ER regulation, estrogen metabolism and synthesis, and apoptosis. Besides cancers, we conjecture that the flavonoids may affect several diseases via apoptosis pathways. Diseases such as amyotrophic lateral sclerosis, viral myocarditis and non-alcoholic fatty liver disease could be implicated. More generally, apoptosis processes may be importantly evolved biological functions of flavonoids that bind ERs and high dose ingestion of those flavonoids could adversely disrupt the cellular apoptosis process. PMID:27023590

Application of Moving Bed Biofilm Reactor (MBBR) and Integrated Fixed Activated Sludge (IFAS) for Biological River Water Purification System: A Short Review

NASA Astrophysics Data System (ADS)

Lariyah, M. S.; Mohiyaden, H. A.; Hayder, G.; Hayder, G.; Hussein, A.; Basri, H.; Sabri, A. F.; Noh, MN

2016-03-01

This review paper present the MBBR and IFAS technology for urban river water purification including both conventional methods and new emerging technologies. The aim of this paper is to present the MBBR and IFAS technology as an alternative and successful method for treating different kinds of effluents under different condition. There are still current treatment technologies being researched and the outcomes maybe available in a while. The review also includes many relevant researches carried out at the laboratory and pilot scales. This review covers the important processes on MBBR and IFAS basic treatment process, affecting of carrier type and influent types. However, the research concluded so far are compiled herein and reported for the first time to acquire a better perspective and insight on the subject with a view of meeting the news approach. The research concluded so far are compiled herein and reported for the first time to acquire a better perspective and insight on the subject with a view of meeting the news approach. To this end, the most feasible technology could be the combination of advanced biological process (bioreactor systems) including MBBR and IFAS system.

Re-use of winery wastewaters for biological nutrient removal.

PubMed

Rodríguez, L; Villaseñor, J; Buendía, I M; Fernández, F J

2007-01-01

The aim of this study was to evaluate the feasibility of the re-use of the winery wastewater to enhance the biological nutrient removal (BNR) process. In batch experiments it was observed that the addition of winery wastewater mainly enhanced the nitrogen removal process because of the high denitrification potential (DNP), of about 130 mg N/g COD, of the contained substrates. This value is very similar to that obtained by using pure organic substrates such as acetate. The addition of winery wastewater did not significantly affect either phosphorus or COD removal processes. Based on the experimental results obtained, the optimum dosage to remove each mg of N-NO3 was determined, being a value of 6.7 mg COD/mg N-NO3. Because of the good properties of the winery wastewater to enhance the nitrogen removal, the viability of its continuous addition in an activated sludge pilot-scale plant for BNR was studied. Dosing the winery wastewater to the pilot plant a significant increase in the nitrogen removal was detected, from 58 to 75%. The COD removal was slightly increased, from 89 to 95%, and the phosphorus removal remained constant.

Amygdala in action: relaying biological and social significance to autobiographical memory.

PubMed

Markowitsch, Hans J; Staniloiu, Angelica

2011-03-01

The human amygdala is strongly embedded in numerous other structures of the limbic system, but is also a hub for a multitude of other brain regions it is connected with. Its major involvement in various kinds of integrative sensory and emotional functions makes it a cornerstone for self-relevant biological and social appraisals of the environment and consequently also for the processing of autobiographical events. Given its contribution to the integration of emotion, perception and cognition (including memory for past autobiographical events) the amygdala also forges the establishment and maintenance of an integrated self. Damage or disturbances of amygdalar connectivity may therefore lead to disconnection syndromes, in which the synchronous processing of affective and cognitive aspects of memory is impaired. We will provide support for this thesis by reviewing data from patients with a rare experiment of nature - Urbach-Wiethe disease - as well as other conditions associated with amygdala abnormalities. With respect to memory processing, we propose that the amygdala's role is to charge cues so that mnemonic events of a specific emotional significance can be successfully searched within the appropriate neural nets and re-activated. Copyright © 2010 Elsevier Ltd. All rights reserved.

Global transcriptome analysis of eukaryotic genes affected by gromwell extract.

PubMed

Bang, Soohyun; Lee, Dohyun; Kim, Hanhe; Park, Jiyong; Bahn, Yong-Sun

2014-02-01

Gromwell is known to have diverse pharmacological, cosmetic and nutritional benefits for humans. Nevertheless, the biological influence of gromwell extract (GE) on the general physiology of eukaryotic cells remains unknown. In this study a global transcriptome analysis was performed to identify genes affected by the addition of GE with Cryptococcus neoformans as the model system. In response to GE treatment, genes involved in signal transduction were immediately regulated, and the evolutionarily conserved sets of genes involved in the core cellular functions, including DNA replication, RNA transcription/processing and protein translation/processing, were generally up-regulated. In contrast, a number of genes involved in carbohydrate metabolism and transport, inorganic ion transport and metabolism, post-translational modification/protein turnover/chaperone functions and signal transduction were down-regulated. Among the GE-responsive genes that are also evolutionarily conserved in the human genome, the expression patterns of YSA1, TPO2, CFO1 and PZF1 were confirmed by northern blot analysis. Based on the functional characterization of some GE-responsive genes, it was found that GE treatment may promote cellular tolerance against a variety of environmental stresses in eukaryotes. GE treatment affects the expression levels of a significant portion of the Cryptococcus genome, implying that GE significantly affects the general physiology of eukaryotic cells. © 2013 Society of Chemical Industry.

Modifications of the chemical structure of phenolics differentially affect physiological activities in pulvinar cells of Mimosa pudica L. II. Influence of various molecular properties in relation to membrane transport.

PubMed

Rocher, Françoise; Roblin, Gabriel; Chollet, Jean-François

2017-03-01

Early prediction of compound absorption by cells is of considerable importance in the building of an integrated scheme describing the impact of a compound on intracellular biological processes. In this scope, we study the structure-activity relationships of several benzoic acid-related phenolics which are involved in many plant biological phenomena (growth, flowering, allelopathy, defense processes). Using the partial least squares (PLS) regression method, the impact of molecular descriptors that have been shown to play an important role concerning the uptake of pharmacologically active compounds by animal cells was analyzed in terms of the modification of membrane potential, variations in proton flux, and inhibition of the osmocontractile reaction of pulvinar cells of Mimosa pudica leaves. The hydrogen bond donors (HBD) and hydrogen bond acceptors (HBA), polar surface area (PSA), halogen ratio (Hal ratio), number of rotatable bonds (FRB), molar volume (MV), molecular weight (MW), and molar refractivity (MR) were considered in addition to two physicochemical properties (logD and the amount of non-dissociated form in relation to pKa). HBD + HBA and PSA predominantly impacted the three biological processes compared to the other descriptors. The coefficient of determination in the quantitative structure-activity relationship (QSAR) models indicated that a major part of the observed seismonasty inhibition and proton flux modification can be explained by the impact of these descriptors, whereas this was not the case for membrane potential variations. These results indicate that the transmembrane transport of the compounds is a predominant component. An increasing number of implicated descriptors as the biological processes become more complex may reflect their impacts on an increasing number of sites in the cell. The determination of the most efficient effectors may lead to a practical use to improve drugs in the control of microbial attacks on plants.

Biological properties of dehydrated human amnion/chorion composite graft: implications for chronic wound healing

PubMed Central

Koob, Thomas J; Rennert, Robert; Zabek, Nicole; Massee, Michelle; Lim, Jeremy J; Temenoff, Johnna S; Li, William W; Gurtner, Geoffrey

2013-01-01

Human amnion/chorion tissue derived from the placenta is rich in cytokines and growth factors known to promote wound healing; however, preservation of the biological activities of therapeutic allografts during processing remains a challenge. In this study, PURION® (MiMedx, Marietta, GA) processed dehydrated human amnion/chorion tissue allografts (dHACM, EpiFix®, MiMedx) were evaluated for the presence of growth factors, interleukins (ILs) and tissue inhibitors of metalloproteinases (TIMPs). Enzyme-linked immunosorbent assays (ELISA) were performed on samples of dHACM and showed quantifiable levels of the following growth factors: platelet-derived growth factor-AA (PDGF-AA), PDGF-BB, transforming growth factor α (TGFα), TGFβ1, basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), placental growth factor (PLGF) and granulocyte colony-stimulating factor (GCSF). The ELISA assays also confirmed the presence of IL-4, 6, 8 and 10, and TIMP 1, 2 and 4. Moreover, the relative elution of growth factors into saline from the allograft ranged from 4% to 62%, indicating that there are bound and unbound fractions of these compounds within the allograft. dHACM retained biological activities that cause human dermal fibroblast proliferation and migration of human mesenchymal stem cells (MSCs) in vitro. An in vivo mouse model showed that dHACM when tested in a skin flap model caused mesenchymal progenitor cell recruitment to the site of implantation. The results from both the in vitro and in vivo experiments clearly established that dHACM contains one or more soluble factors capable of stimulating MSC migration and recruitment. In summary, PURION® processed dHACM retains its biological activities related to wound healing, including the potential to positively affect four distinct and pivotal physiological processes intimately involved in wound healing: cell proliferation, inflammation, metalloproteinase activity and recruitment of progenitor cells. This suggests a paracrine mechanism of action for dHACM when used for wound healing applications. PMID:23902526

The impact of temporal sampling resolution on parameter inference for biological transport models.

PubMed

Harrison, Jonathan U; Baker, Ruth E

2018-06-25

Imaging data has become an essential tool to explore key biological questions at various scales, for example the motile behaviour of bacteria or the transport of mRNA, and it has the potential to transform our understanding of important transport mechanisms. Often these imaging studies require us to compare biological species or mutants, and to do this we need to quantitatively characterise their behaviour. Mathematical models offer a quantitative description of a system that enables us to perform this comparison, but to relate mechanistic mathematical models to imaging data, we need to estimate their parameters. In this work we study how collecting data at different temporal resolutions impacts our ability to infer parameters of biological transport models; performing exact inference for simple velocity jump process models in a Bayesian framework. The question of how best to choose the frequency with which data is collected is prominent in a host of studies because the majority of imaging technologies place constraints on the frequency with which images can be taken, and the discrete nature of observations can introduce errors into parameter estimates. In this work, we mitigate such errors by formulating the velocity jump process model within a hidden states framework. This allows us to obtain estimates of the reorientation rate and noise amplitude for noisy observations of a simple velocity jump process. We demonstrate the sensitivity of these estimates to temporal variations in the sampling resolution and extent of measurement noise. We use our methodology to provide experimental guidelines for researchers aiming to characterise motile behaviour that can be described by a velocity jump process. In particular, we consider how experimental constraints resulting in a trade-off between temporal sampling resolution and observation noise may affect parameter estimates. Finally, we demonstrate the robustness of our methodology to model misspecification, and then apply our inference framework to a dataset that was generated with the aim of understanding the localization of RNA-protein complexes.

Process analysis and economics of drinking water production from coastal aquifers containing chromophoric dissolved organic matter and bromide using nanofiltration and ozonation.

PubMed

Sobhani, R; McVicker, R; Spangenberg, C; Rosso, D

2012-01-01

In regions characterized by water scarcity, such as coastal Southern California, groundwater containing chromophoric dissolved organic matter is a viable source of water supply. In the coastal aquifer of Orange County in California, seawater intrusion driven by coastal groundwater pumping increased the concentration of bromide in extracted groundwater from 0.4 mg l⁻¹ in 2000 to over 0.8 mg l⁻¹ in 2004. Bromide, a precursor to bromate formation is regulated by USEPA and the California Department of Health as a potential carcinogen and therefore must be reduced to a level below 10 μg l⁻¹. This paper compares two processes for treatment of highly coloured groundwater: nanofiltration and ozone injection coupled with biologically activated carbon. The requirement for bromate removal decreased the water production in the ozonation process to compensate for increased maintenance requirements, and required the adoption of catalytic carbon with associated increase in capital and operating costs per unit volume. However, due to the absence of oxidant addition in nanofiltration processes, this process is not affected by bromide. We performed a process analysis and a comparative economic analysis of capital and operating costs for both technologies. Our results show that for the case studied in coastal Southern California, nanofiltration has higher throughput and lower specific capital and operating cost, when compared to ozone injection with biologically activate carbon. Ozone injection with biologically activated carbon, compared to nanofiltration, has 14% higher capital cost and 12% higher operating costs per unit water produced while operating at the initial throughput. Due to reduced ozone concentration required to accommodate for bromate reduction, the ozonation process throughput is reduced and the actual cost increase (per unit water produced) is 68% higher for capital cost and 30% higher for operations. Copyright © 2011 Elsevier Ltd. All rights reserved.

The NASA Space Biology Program

NASA Technical Reports Server (NTRS)

Halstead, T. W.

1982-01-01

A discussion is presented of the research conducted under the auspices of the NASA Space Biology Program. The objectives of this Program include the determination of how gravity affects and how it has shaped life on earth, the use of gravity as a tool to investigate relevant biological questions, and obtaining an understanding of how near-weightlessness affects both plants and animals in order to enhance the capability to use and explore space. Several areas of current developmental research are discussed and the future focus of the Program is considered.

Inclusion of Biological Foundations of Human Behavior in Counselor Education.

ERIC Educational Resources Information Center

Panther, Edward E.

1987-01-01

Reports that textbooks and counseling approaches studied by prospective counselors largely omit information on biological foundations of human behavior, although biological factors often affect human behavior profoundly. Uses case study examples to show importance of biological factors. Recommends that counselor educators understand biological…

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.

HMGN proteins modulate chromatin regulatory sites and gene expression during activation of naïve B cells

PubMed Central

Zhang, Shaofei; Zhu, Iris; Deng, Tao; Furusawa, Takashi; Rochman, Mark; Vacchio, Melanie S.; Bosselut, Remy; Yamane, Arito; Casellas, Rafael; Landsman, David; Bustin, Michael

2016-01-01

The activation of naïve B lymphocyte involves rapid and major changes in chromatin organization and gene expression; however, the complete repertoire of nuclear factors affecting these genomic changes is not known. We report that HMGN proteins, which bind to nucleosomes and affect chromatin structure and function, co-localize with, and maintain the intensity of DNase I hypersensitive sites genome wide, in resting but not in activated B cells. Transcription analyses of resting and activated B cells from wild-type and Hmgn−/− mice, show that loss of HMGNs dampens the magnitude of the transcriptional response and alters the pattern of gene expression during the course of B-cell activation; defense response genes are most affected at the onset of activation. Our study provides insights into the biological function of the ubiquitous HMGN chromatin binding proteins and into epigenetic processes that affect the fidelity of the transcriptional response during the activation of B cell lymphocytes. PMID:27112571

Black pepper (Piper nigrum) essential oil demonstrates tissue remodeling and metabolism modulating potential in human cells.

PubMed

Han, Xuesheng; Beaumont, Cody; Rodriguez, Damian; Bahr, Tyler

2018-05-17

Very few studies have investigated the biological activities of black pepper essential oil (BPEO) in human cells. Therefore, in the current study, we examined the biological activities of BPEO in cytokine-stimulated human dermal fibroblasts by analyzing the levels of 17 important protein biomarkers pertinent to inflammation and tissue remodeling. BPEO exhibited significant antiproliferative activity in these skin cells and significantly inhibited the production of Collagen I, Collagen III, and plasminogen activator inhibitor 1. In addition, we studied the effect of BPEO on the regulation of genome-wide expression and found that BPEO diversely modulated global gene expression. Further analysis showed that BPEO affected many important genes and signaling pathways closely related to metabolism, inflammation, tissue remodeling, and cancer signaling. This study is the first to provide evidence of the biological activities of BPEO in human dermal fibroblasts. The data suggest that BPEO possesses promising potential to modulate the biological processes of tissue remodeling, wound healing, and metabolism. Although further research is required, BPEO appears to be a good therapeutic candidate for a variety of health conditions including wound care and metabolic diseases. Research into the biological and pharmacological mechanisms of action of BPEO and its major active constituents is recommended. Copyright © 2018 John Wiley & Sons, Ltd.

Understanding system dynamics of an adaptive enzyme network from globally profiled kinetic parameters.

PubMed

Chiang, Austin W T; Liu, Wei-Chung; Charusanti, Pep; Hwang, Ming-Jing

2014-01-15

A major challenge in mathematical modeling of biological systems is to determine how model parameters contribute to systems dynamics. As biological processes are often complex in nature, it is desirable to address this issue using a systematic approach. Here, we propose a simple methodology that first performs an enrichment test to find patterns in the values of globally profiled kinetic parameters with which a model can produce the required system dynamics; this is then followed by a statistical test to elucidate the association between individual parameters and different parts of the system's dynamics. We demonstrate our methodology on a prototype biological system of perfect adaptation dynamics, namely the chemotaxis model for Escherichia coli. Our results agreed well with those derived from experimental data and theoretical studies in the literature. Using this model system, we showed that there are motifs in kinetic parameters and that these motifs are governed by constraints of the specified system dynamics. A systematic approach based on enrichment statistical tests has been developed to elucidate the relationships between model parameters and the roles they play in affecting system dynamics of a prototype biological network. The proposed approach is generally applicable and therefore can find wide use in systems biology modeling research.

Sex differences in depression and anxiety disorders: potential biological determinants.

PubMed

Altemus, Margaret

2006-11-01

The phenomenon of higher rates of affective disorders in women illustrates many of the difficulties as well as promises of translating preclinical models to human disorders. Abnormalities in the regulation of the hypothalamic-pituitary adrenal axis and the sympathoadrenomedullary system have been identified in depression and anxiety disorders, and these disorders are clearly precipitated and exacerbated by stress. Despite the striking sex difference in the prevalence of depression and anxiety disorders, attempts to identify corresponding sex differences in stress response reactivity in animal models have met with limited success. Processes which may contribute to increased rates of affective disorders in women are greater fluxes in reproductive hormones across the life span, and increased sensitivity to catecholamine augmentation of emotional memory consolidation.

Case Report: Evaluation strategies and cognitive intervention: the case of a monovular twin child affected by selective mutism

PubMed Central

Capobianco, Micaela; Cerniglia, Luca

2018-01-01

The present work describes the assessment process, evaluation strategies, and cognitive intervention on a 9 years old child with selective mutism (SM), a monovular twin of a child also affected by mutism. Currently, the cognitive behavioral multimodal treatment seems the most effective therapeutic approach for children diagnosed with selective mutism (Capobianco & Cerniglia, 2018). The illustrated case confirms the role of biological factors involved in mutacic disorder but also highlights the importance of environmental influences in the maintenance of the disorder with respect to relational and contextual dynamics (e.g. complicity between sisters, family relationships). The article discusses furthermore the importance of an early diagnosis as a predictor of positive treatment outcomes. PMID:29568498

Case Report: Evaluation strategies and cognitive intervention: the case of a monovular twin child affected by selective mutism.

PubMed

Capobianco, Micaela; Cerniglia, Luca

2018-01-01

The present work describes the assessment process, evaluation strategies, and cognitive intervention on a 9 years old child with selective mutism (SM), a monovular twin of a child also affected by mutism. Currently, the cognitive behavioral multimodal treatment seems the most effective therapeutic approach for children diagnosed with selective mutism (Capobianco & Cerniglia, 2018). The illustrated case confirms the role of biological factors involved in mutacic disorder but also highlights the importance of environmental influences in the maintenance of the disorder with respect to relational and contextual dynamics (e.g. complicity between sisters, family relationships). The article discusses furthermore the importance of an early diagnosis as a predictor of positive treatment outcomes.

Daily water-temperature records for Utah streams, 1944-68

USGS Publications Warehouse

Whitaker, G.L.

1970-01-01

Temperature is an important and sometimes critical factor for many uses of water. Temperature affects the usefulness of the water for recreation, fish and wildlife propagation, industrial cooling, food processing, and manufacturing. Temperature also affects the ability of the water to accommodate biologic and vegetative types of life.The purpose of this report is to summarize in tabular form the water- temperature data that have been collected by the U.S. Geological Survey on a daily basis for streams in Utah. A few stream sites near the boundaries of Utah in neighboring States have been included. These sites are on streams which either flow out of or into Utah, and they may provide information of value in studies dealing with water quality in the State.

S-Nitrosothiol measurements in biological systems⋄

PubMed Central

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

2007-01-01

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

The epigenomic landscape of African rainforest hunter-gatherers and farmers.

PubMed

Fagny, Maud; Patin, Etienne; MacIsaac, Julia L; Rotival, Maxime; Flutre, Timothée; Jones, Meaghan J; Siddle, Katherine J; Quach, Hélène; Harmant, Christine; McEwen, Lisa M; Froment, Alain; Heyer, Evelyne; Gessain, Antoine; Betsem, Edouard; Mouguiama-Daouda, Patrick; Hombert, Jean-Marie; Perry, George H; Barreiro, Luis B; Kobor, Michael S; Quintana-Murci, Lluis

2015-11-30

The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation--particularly that correlated with historical lifestyle--shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.

Perception of Biological Motion in Schizophrenia and Healthy Individuals: A Behavioral and fMRI Study

PubMed Central

Kim, Jejoong; Park, Sohee; Blake, Randolph

2011-01-01

Background Anomalous visual perception is a common feature of schizophrenia plausibly associated with impaired social cognition that, in turn, could affect social behavior. Past research suggests impairment in biological motion perception in schizophrenia. Behavioral and functional magnetic resonance imaging (fMRI) experiments were conducted to verify the existence of this impairment, to clarify its perceptual basis, and to identify accompanying neural concomitants of those deficits. Methodology/Findings In Experiment 1, we measured ability to detect biological motion portrayed by point-light animations embedded within masking noise. Experiment 2 measured discrimination accuracy for pairs of point-light biological motion sequences differing in the degree of perturbation of the kinematics portrayed in those sequences. Experiment 3 measured BOLD signals using event-related fMRI during a biological motion categorization task. Compared to healthy individuals, schizophrenia patients performed significantly worse on both the detection (Experiment 1) and discrimination (Experiment 2) tasks. Consistent with the behavioral results, the fMRI study revealed that healthy individuals exhibited strong activation to biological motion, but not to scrambled motion in the posterior portion of the superior temporal sulcus (STSp). Interestingly, strong STSp activation was also observed for scrambled or partially scrambled motion when the healthy participants perceived it as normal biological motion. On the other hand, STSp activation in schizophrenia patients was not selective to biological or scrambled motion. Conclusion Schizophrenia is accompanied by difficulties discriminating biological from non-biological motion, and associated with those difficulties are altered patterns of neural responses within brain area STSp. The perceptual deficits exhibited by schizophrenia patients may be an exaggerated manifestation of neural events within STSp associated with perceptual errors made by healthy observers on these same tasks. The present findings fit within the context of theories of delusion involving perceptual and cognitive processes. PMID:21625492

The solusphere-its inferences and study

USGS Publications Warehouse

Rainwater, F.H.; White, W.F.

1958-01-01

Water is a fundamental geologic agent active in rock decomposition, erosion, and synthesis. Solutes in water are of particular interest to geochemists as sources of raw material for synthesis or as products of decomposition. When geochemical studies move from the laboratory into natural environment many variables relating to solute hydrology must be considered. As a focal point there has been designed a graphical representation of solute hydrology, the solusphere, which embodies the concepts of land-water occurrence and movement on which are superimposed geologic, biologic, physical, chemical, and cultural processes affecting solutes. The solusphere is demonstrated by passing an imaginary plane through the centre of the earth. This plane intercepts concentric zones designated as rock flowage, saturation, aeration, surface activity, and atmosphere. Transport processes carry solutes within and between zones without alteration or conversion. However, whether stationary or in motion, the water's solute character is constantly subject to (1) alteration processes that change concentration by addition or subtraction of solutes or solvent without loss of solute identities, and (2) conversion processes that change the chemical state and form of solutes. The geochemist is concerned with specific conversion processes, but he also must consider transport, alteration, and other conversion processes that are continually modifying the materials with which he is dealing in nature. The solusphere is an attempt to organize processes affecting the chemical quality of land waters into a unified field of science much like the field of marine chemistry. ?? 1958.

Biology of Healthy Aging and Longevity.

PubMed

Carmona, Juan José; Michan, Shaday

2016-01-01

As human life expectancy is prolonged, age-related diseases are thriving. Aging is a complex multifactorial process of molecular and cellular decline that affects tissue function over time, rendering organisms frail and susceptible to disease and death. Over the last decades, a growing body of scientific literature across different biological models, ranging from yeast, worms, flies, and mice to primates, humans and other long-lived animals, has contributed greatly towards identifying conserved biological mechanisms that ward off structural and functional deterioration within living systems. Collectively, these data offer powerful insights into healthy aging and longevity. For example, molecular integrity of the genome, telomere length, epigenetic landscape stability, and protein homeostasis are all features linked to "youthful" states. These molecular hallmarks underlie cellular functions associated with aging like mitochondrial fitness, nutrient sensing, efficient intercellular communication, stem cell renewal, and regenerative capacity in tissues. At present, calorie restriction remains the most robust strategy for extending health and lifespan in most biological models tested. Thus, pathways that mediate the beneficial effects of calorie restriction by integrating metabolic signals to aging processes have received major attention, such as insulin/insulin growth factor-1, sirtuins, mammalian target of rapamycin, and 5' adenosine monophosphate-activated protein kinase. Consequently, small-molecule targets of these pathways have emerged in the impetuous search for calorie restriction mimetics, of which resveratrol, metformin, and rapamycin are the most extensively studied. A comprehensive understanding of the molecular and cellular mechanisms that underlie age-related deterioration and repair, and how these pathways interconnect, remains a major challenge for uncovering interventions to slow human aging while extending molecular and physiological youthfulness, vitality, and health. This review summarizes key molecular mechanisms underlying the biology of healthy aging and longevity.

Can we manage for biological diversity in the absence of science?

USGS Publications Warehouse

Trauger, D.L.; Hall, R.J.

1995-01-01

Conservation of biological diversity is dependent on sound scientific information about underlying ecological processes. Current knowledge of the composition, distribution, abundance and life cycles of most species of plants and animals is incomplete, insufficient, unreliable, or nonexistent. Contemporary managers are also confronted with additional levels of complexity related to varying degrees of knowledge and understanding about interactions of species and ecosystems. Consequently, traditional species-oriented management schemes may have unintended consequences and ecosystem-oriented management initiatives may fail in the face of inadequate or fragmentary information on the structure, function, and dynamics of biotic communities and ecological systems. Nevertheless, resource managers must make decisions and manage based on the best biological information currently available. Adaptive resource management may represent a management paradigm that allows managers to learn something about the species or systems that they are managing while they are managing, but potential pitfalls lurk for such approaches. In addition to lack of control over the primary physical, chemical, and ecological processes, managers also lack control over social, economic, and political parameters affecting resource management options. Moreover, appropriate goals may be difficult to identify and criteria for determining success may be elusive. Some management responsibilities do not lend themselves to adaptive strategies. Finally, the lessons learned from adaptive management are usually obtained from a highly situational context that may limit applicability in a wider range of situations or undermine confidence that problems and solutions were properly diagnosed and addressed. Several scenarios are critically examined where adaptive management approaches may be inappropriate or ineffective and where management for biological diversity may be infeasible or inefficient without a sound scientific basis. Whereas some level of management must exist to meet agency responsibilities, more research is needed to conserve biological diversity.

Translating Mendelian and complex inheritance of Alzheimer's disease genes for predicting unique personal genome variants

PubMed Central

Regan, Kelly; Wang, Kanix; Doughty, Emily; Li, Haiquan; Li, Jianrong; Lee, Younghee; Kann, Maricel G

2012-01-01

Objective Although trait-associated genes identified as complex versus single-gene inheritance differ substantially in odds ratio, the authors nonetheless posit that their mechanistic concordance can reveal fundamental properties of the genetic architecture, allowing the automated interpretation of unique polymorphisms within a personal genome. Materials and methods An analytical method, SPADE-gen, spanning three biological scales was developed to demonstrate the mechanistic concordance between Mendelian and complex inheritance of Alzheimer's disease (AD) genes: biological functions (BP), protein interaction modeling, and protein domain implicated in the disease-associated polymorphism. Results Among Gene Ontology (GO) biological processes (BP) enriched at a false detection rate <5% in 15 AD genes of Mendelian inheritance (Online Mendelian Inheritance in Man) and independently in those of complex inheritance (25 host genes of intragenic AD single-nucleotide polymorphisms confirmed in genome-wide association studies), 16 overlapped (empirical p=0.007) and 45 were similar (empirical p<0.009; information theory). SPAN network modeling extended the canonical pathway of AD (KEGG) with 26 new protein interactions (empirical p<0.0001). Discussion The study prioritized new AD-associated biological mechanisms and focused the analysis on previously unreported interactions associated with the biological processes of polymorphisms that affect specific protein domains within characterized AD genes and their direct interactors using (1) concordant GO-BP and (2) domain interactions within STRING protein–protein interactions corresponding to the genomic location of the AD polymorphism (eg, EPHA1, APOE, and CD2AP). Conclusion These results are in line with unique-event polymorphism theory, indicating how disease-associated polymorphisms of Mendelian or complex inheritance relate genetically to those observed as ‘unique personal variants’. They also provide insight for identifying novel targets, for repositioning drugs, and for personal therapeutics. PMID:22319180

Assessing the dynamics of the upper soil layer relative to soil management practices

NASA Astrophysics Data System (ADS)

Hatfield, J.; Wacha, K.; Dold, C.

2017-12-01

The upper layer of the soil is the critical interface between the soil and the atmosphere and is the most dynamic in response to management practices. One of the soil properties most reflective to changes in management is the stability of the aggregates because this property controls infiltration of water and exchange of gases. An aggregation model has been developed based on the factors that control how aggregates form and the forces which degrade aggregates. One of the major factors for this model is the storage of carbon into the soil and the interaction with the soil biological component. To increase soil biology requires a stable microclimate that provides food, water, shelter, and oxygen which in turn facilitates the incorporation of organic material into forms that can be combined with soil particles to create stable aggregates. The processes that increase aggregate size and stability are directly linked the continual functioning of the biological component which in turn changes the physical and chemical properties of the soil. Soil aggregates begin to degrade as soon as there is no longer a supply of organic material into the soil. These processes can range from removal of organic material and excessive tillage. To increase aggregation of the upper soil layer requires a continual supply of organic material and the biological activity that incorporates organic material into substances that create a stable aggregate. Soils that exhibit stable soil aggregates at the surface have a prolonged infiltration rate with less runoff and a gas exchange that ensures adequate oxygen for maximum biological activity. Quantifying the dynamics of the soil surface layer provides a quantitative understanding of how management practices affect aggregate stability.

Characterization of Biogenic Gas and Mineral Formation Process by Denitrification in Porous Media

NASA Astrophysics Data System (ADS)

Hall, C. A.; Kim, D.; Mahabadi, N.; van Paassen, L. A.

2017-12-01

Biologically mediated processes have been regarded and developed as an alternative approach to traditional ground improvement techniques. Denitrification has been investigated as a potential ground improvement process towards liquefaction hazard mitigation. During denitrification, microorganisms reduce nitrate to dinitrogen gas and facilitate calcium carbonate precipitation as a by-product under adequate environmental conditions. The formation of dinitrogen gas desaturates soils and allows for potential pore pressure dampening during earthquake events. While, precipitation of calcium carbonate can improve the mechanical properties by filling the voids and cementing soil particles. As a result of small changes in gas and mineral phases, the mechanical properties of soils can be significantly affected. Prior research has primarily focused on quantitative analysis of overall residual calcium carbonate mineral and biogenic gas products in lab-scale porous media. However, the distribution of these products at the pore-scale has not been well-investigated. In this research, denitrification is activated in a microfluidic chip simulating a homogenous pore structure. The denitrification process is monitored by sequential image capture, where gas and mineral phase changes are evaluated by image processing. Analysis of these images correspond with previous findings, which demonstrate that biogenic gas behaviour at the pore scale is affected by the balance between reaction, diffusion, and convection rates.

Reward and affective regulation in depression-prone smokers.

PubMed

Audrain-McGovern, Janet; Wileyto, E Paul; Ashare, Rebecca; Cuevas, Jocelyn; Strasser, Andrew A

2014-11-01

There is a disproportionately high smoking prevalence among individuals who are prone to depression. While depression has been conceptualized as a disorder of dysregulated positive affect and disrupted reward processing, little research has been conducted to determine the role of smoking in these processes among depression-prone smokers. Depression-prone smokers (DP+; n = 34) and smokers not depression-prone (DP-; n = 49) underwent two laboratory sessions, one while smoking abstinent and one while smoking ad libitum, to assess the relative reinforcing value of smoking and reward sensitivity. Using experience sampling methods, participants completed self-report measures of subjective reward, positive affect, and negative affect across 3 days while smoking as usual and 3 days while smoking abstinent. DP+ were two times more likely to work for cigarette puffs versus money in a progressive ratio, choice task (odds ratio 2.05; 95% confidence interval 1.04 to 4.06, p = .039) compared with DP-. Reward sensitivity as measured by the signal detection task did not yield any significant findings. Mixed models regressions revealed a three-way interaction (depression group, smoking phase, and time) for subjective reward, negative affect, and positive affect. For all three of these outcomes, the slopes for DP- and DP+ differed significantly from each other (ps < .05) and the effect of smoking (versus abstinence) over time was greater for DP+ than DP- smokers (ps < .05). These findings indicate that the effects of smoking on reward and positive affect regulation are specific to DP+ smokers and highlight novel targets for smoking cessation treatment in this population. Copyright © 2014 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

A Comparison of Biological and Adoptive Mothers and Fathers: The Relevance of Biological Kinship and Gendered Constructs of Parenthood.

ERIC Educational Resources Information Center

Miall, Charlene E.; March, Karen

2003-01-01

Used qualitative interviews to examine beliefs and values about biological and adoptive parents. Considered how biological kinship, gender, and actual parenting behavior affect the assessments respondents made of the emotional bonding between parents and children. Found that biological and adoptive parents viewed motherhood as instinctive and…

The dark side of creativity: biological vulnerability and negative emotions lead to greater artistic creativity.

PubMed

Akinola, Modupe; Mendes, Wendy Berry

2008-12-01

Historical and empirical data have linked artistic creativity to depression and other affective disorders. This study examined how vulnerability to experiencing negative affect, measured with biological products, and intense negative emotions influenced artistic creativity. The authors assessed participants' baseline levels of an adrenal steroid (dehydroepiandrosterone-sulfate, or DHEAS), previously linked to depression, as a measure of affective vulnerability. They then manipulated emotional responses by randomly assigning participants to receive social rejection or social approval or to a nonsocial situation. Participants then completed artistic collages, which were later evaluated by artists. Results confirmed a person-by-situation interaction. Social rejection was associated with greater artistic creativity; however, the interaction between affective vulnerability (lower baseline DHEAS) and condition was significant, suggesting that situational triggers of negative affect were especially influential among those lower in DHEAS, which resulted in the most creative products. These data provide evidence of possible biological and social pathways to artistic creativity.

The Dark Side of Creativity: Biological Vulnerability and Negative Emotions Lead to Greater Artistic Creativity

PubMed Central

Akinola, Modupe; Mendes, Wendy Berry

2009-01-01

Historical and empirical data have linked artistic creativity to depression and other affective disorders. This study examined how vulnerability to experiencing negative affect, measured with biological products, and intense negative emotions influenced artistic creativity. The authors assessed participants' baseline levels of an adrenal steroid (dehydroepiandrosterone-sulfate, or DHEAS), previously linked to depression, as a measure of affective vulnerability. They then manipulated emotional responses by randomly assigning participants to receive social rejection or social approval or to a nonsocial situation. Participants then completed artistic collages, which were later evaluated by artists. Results confirmed a person-by-situation interaction. Social rejection was associated with greater artistic creativity; however, the interaction between affective vulnerability (lower baseline DHEAS) and condition was significant, suggesting that situational triggers of negative affect were especially influential among those lower in DHEAS, which resulted in the most creative products. These data provide evidence of possible biological and social pathways to artistic creativity. PMID:18832338

Topsoil structure stability in a restored floodplain: Impacts of fluctuating water levels, soil parameters and ecosystem engineers.

PubMed

Schomburg, A; Schilling, O S; Guenat, C; Schirmer, M; Le Bayon, R C; Brunner, P

2018-10-15

Ecosystem services provided by floodplains are strongly controlled by the structural stability of soils. The development of a stable structure in floodplain soils is affected by a complex and poorly understood interplay of hydrological, physico-chemical and biological processes. This paper aims at analysing relations between fluctuating groundwater levels, soil physico-chemical and biological parameters on soil structure stability in a restored floodplain. Water level fluctuations in the soil are modelled using a numerical surface-water-groundwater flow model and correlated to soil physico-chemical parameters and abundances of plants and earthworms. Causal relations and multiple interactions between the investigated parameters are tested through structural equation modelling (SEM). Fluctuating water levels in the soil did not directly affect the topsoil structure stability, but indirectly through affecting plant roots and soil parameters that in turn determine topsoil structure stability. These relations remain significant for mean annual days of complete and partial (>25%) water saturation. Ecosystem functioning of a restored floodplain might already be affected by the fluctuation of groundwater levels alone, and not only through complete flooding by surface water during a flood period. Surprisingly, abundances of earthworms did not show any relation to other variables in the SEM. These findings emphasise that earthworms have efficiently adapted to periodic stress and harsh environmental conditions. Variability of the topsoil structure stability is thus stronger driven by the influence of fluctuating water levels on plants than by the abundance of earthworms. This knowledge about the functional network of soil engineering organisms, soil parameters and fluctuating water levels and how they affect soil structural stability is of fundamental importance to define management strategies of near-natural or restored floodplains in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Arbuscular mycorrhizal fungal assemblages in biological crusts from a Neotropical savanna are not related to the dominant perennial Trachypogon.

PubMed

Hernández-Hernández, R M; Roldán, A; Caravaca, F; Rodriguez-Caballero, G; Torres, M P; Maestre, F T; Alguacil, M M

2017-01-01

Knowledge of the arbuscular mycorrhizal fungal assemblages in the Trachypogon savanna ecosystems is very important to a better understanding of the ecological processes mediated by this soil microbial group that affects multiple ecosystem functions. Considering the hypothesis that the biocrusts can be linked to vegetation through the arbuscular fungi mycelial network, the objectives proposed in this study were to determine (i) whether there are arbuscular mycorrhizal fungi (AMF) in the biocrusts (ii) whether arbuscular mycorrhizal fungal assemblages are linked to the Trachypogon patches, and (iii) whether the composition of the assemblages is related to soil properties affected by microbiological activity. The community structure of the AMF was investigated in three habitats: rhizospheric soil and roots of Trachypogon vestitus, biological soil crusts, and bare soil. The canonical correspondence analysis showed that two soil properties related to enzymatic activity (protease and β-glucosidase) significantly affected the community composition of the AMF. The biocrusts in the Venezuelan savanna are colonized by an AM fungal community linked to that of the bare soil and significantly different from that hosted by the roots of the surrounding T. vestitus, suggesting that assemblages of AMF in biocrusts might be related more closely to those of annual plant species appearing in favorable conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Nanotechnology, nanotoxicology, and neuroscience

PubMed Central

Suh, Won Hyuk; Suslick, Kenneth S.; Stucky, Galen D.; Suh, Yoo-Hun

2009-01-01

Nanotechnology, which deals with features as small as a 1 billionth of a meter, began to enter into mainstream physical sciences and engineering some 20 years ago. Recent applications of nanoscience include the use of nanoscale materials in electronics, catalysis, and biomedical research. Among these applications, strong interest has been shown to biological processes such as blood coagulation control and multimodal bioimaging, which has brought about a new and exciting research field called nanobiotechnology. Biotechnology, which itself also dates back ∼30 years, involves the manipulation of macroscopic biological systems such as cells and mice in order to understand why and how molecular level mechanisms affect specific biological functions, e.g., the role of APP (amyloid precursor protein) in Alzheimer’s disease (AD). This review aims (1) to introduce key concepts and materials from nanotechnology to a non-physical sciences community; (2) to introduce several state-of-the-art examples of current nanotechnology that were either constructed for use in biological systems or that can, in time, be utilized for biomedical research; (3) to provide recent excerpts in nanotoxicology and multifunctional nanoparticle systems (MFNPSs); and (4) to propose areas in neuroscience that may benefit from research at the interface of neurobiologically important systems and nanostructured materials. PMID:18926873

Computer-aided discovery of biological activity spectra for anti-aging and anti-cancer olive oil oleuropeins.

PubMed

Corominas-Faja, Bruna; Santangelo, Elvira; Cuyàs, Elisabet; Micol, Vicente; Joven, Jorge; Ariza, Xavier; Segura-Carretero, Antonio; García, Jordi; Menendez, Javier A

2014-09-01

Aging is associated with common conditions, including cancer, diabetes, cardiovascular disease, and Alzheimer's disease. The type of multi-targeted pharmacological approach necessary to address a complex multifaceted disease such as aging might take advantage of pleiotropic natural polyphenols affecting a wide variety of biological processes. We have recently postulated that the secoiridoids oleuropein aglycone (OA) and decarboxymethyl oleuropein aglycone (DOA), two complex polyphenols present in health-promoting extra virgin olive oil (EVOO), might constitute a new family of plant-produced gerosuppressant agents. This paper describes an analysis of the biological activity spectra (BAS) of OA and DOA using PASS (Prediction of Activity Spectra for Substances) software. PASS can predict thousands of biological activities, as the BAS of a compound is an intrinsic property that is largely dependent on the compound's structure and reflects pharmacological effects, physiological and biochemical mechanisms of action, and specific toxicities. Using Pharmaexpert, a tool that analyzes the PASS-predicted BAS of substances based on thousands of "mechanism-effect" and "effect-mechanism" relationships, we illuminate hypothesis-generating pharmacological effects, mechanisms of action, and targets that might underlie the anti-aging/anti-cancer activities of the gerosuppressant EVOO oleuropeins.

ARTS: automated randomization of multiple traits for study design.

PubMed

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

2014-06-01

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

Drawing-to-Learn: A Framework for Using Drawings to Promote Model-Based Reasoning in Biology

PubMed Central

Quillin, Kim; Thomas, Stephen

2015-01-01

The drawing of visual representations is important for learners and scientists alike, such as the drawing of models to enable visual model-based reasoning. Yet few biology instructors recognize drawing as a teachable science process skill, as reflected by its absence in the Vision and Change report’s Modeling and Simulation core competency. Further, the diffuse research on drawing can be difficult to access, synthesize, and apply to classroom practice. We have created a framework of drawing-to-learn that defines drawing, categorizes the reasons for using drawing in the biology classroom, and outlines a number of interventions that can help instructors create an environment conducive to student drawing in general and visual model-based reasoning in particular. The suggested interventions are organized to address elements of affect, visual literacy, and visual model-based reasoning, with specific examples cited for each. Further, a Blooming tool for drawing exercises is provided, as are suggestions to help instructors address possible barriers to implementing and assessing drawing-to-learn in the classroom. Overall, the goal of the framework is to increase the visibility of drawing as a skill in biology and to promote the research and implementation of best practices. PMID:25713094

Roles of the oviduct in mammalian fertilization

PubMed Central

Coy, P; García-Vázquez, FA; Visconti, PE; Avilés, M

2014-01-01

The oviduct or Fallopian tube is the anatomical region where every new life begins in mammalian species. After a long journey, the spermatozoa meet the oocyte in the specific site of the oviduct named ampulla, and fertilization takes place. The successful fertilization depends on several biological processes which occur in the oviduct some hours before this rendezvous and affect both gametes. Estrogen and progesterone, released from the ovary, orchestrate a series of changes by genomic- and non-genomic pathways in the oviductal epithelium affecting gene expression, proteome and secretion of its cells into the fluid bathing the oviductal lumen. In addition, new regulatory molecules are being discovered playing important roles in oviductal physiology and fertilization. The present review tries to describe these processes, building a comprehensive map of the physiology of the oviduct, to better understand the importance of this organ in reproduction. With this purpose, gamete transport, sperm and oocyte changes in the oviductal environment and other interactions between gametes and oviduct are discussed in light of recent publications in the field. PMID:23028122

[Endocrine orbitopathy - the topic still alive].

PubMed

Fryšák, Zdeněk; Karásek, David; Halenka, Milan

Endocrine orbitopathy (EO) must be understood mainly as a result of oxidative stress. The pathological process finally affects both the appearance and vision of the patient. In the case of inappropriate or late treatment or lack of patient cooperation, it significantly influences the quality of life of those affected. In spite of the sophisticated dia-gnostic algorithms, in some cases it is difficult to confirm the diagnosis of EO. The range of laboratory methods, the essential part of the diagnostic process, has only recently been extended by the possibility of quantification of specific, stimulating immunoglobulins (TSI). A major shortcoming may be seen in an undervalued importance of orbital ultrasonography, in particular of the eye muscles (US).Key words: biological treatment - endocrine orbitopathy (EO) - Graves-Basedow disease (GB) - "hashitoxicosis" (HTX) - hyaluronan synthase 2 (HAS2) - thyroid-blocking immunoglobulins (TBI) - thyroid-stimulating immunoglobulins (TSI) - hyaluronic acid (HA) - lymphocytary, Hashimotos thyroiditis (HT) - pulse therapy - TSH-receptor - transcription factors FOXOs - orbital ultrasonography, mainly of the eye muscles (US).

Measuring biogeochemical responses to pulses of water

NASA Astrophysics Data System (ADS)

Balcerak, Ernie

2012-05-01

Hydrologic pulses, temporary increases in water inputs such as bouts of precipitation, can affect biogeochemical processes in ecosystems by providing water and nutrient resources. However, ecosystem responses to the water vary. Harms and Grimm conducted experiments to determine how hydrologic pulses and existing moisture conditions interact to affect the biogeochemistry of desert floodplains. During dry and monsoon seasons at their study site in the floodplains of the San Pedro River in Arizona, the researchers experimentally added pulses of water and then measured emissions of several trace gases that are indicators of biological processes. They found that the size of the added hydrologic pulse strongly interacted with existing soil moisture conditions in determining emissions of some trace gases. For instance, following dry conditions, pulses of water stimulated carbon dioxide, methane, and nitric oxide emissions, with larger water pulses stimulating more emissions. However, when soil was already wet, the addition of water pulses had less effect on the emission of these gases. (Journal of Geophysical Research-Biogeosciences, doi:10.1029/2011JG001775, 2012)

Temperature modelling and prediction for activated sludge systems.

PubMed

Lippi, S; Rosso, D; Lubello, C; Canziani, R; Stenstrom, M K

2009-01-01

Temperature is an important factor affecting biomass activity, which is critical to maintain efficient biological wastewater treatment, and also physiochemical properties of mixed liquor as dissolved oxygen saturation and settling velocity. Controlling temperature is not normally possible for treatment systems but incorporating factors impacting temperature in the design process, such as aeration system, surface to volume ratio, and tank geometry can reduce the range of temperature extremes and improve the overall process performance. Determining how much these design or up-grade options affect the tank temperature requires a temperature model that can be used with existing design methodologies. This paper presents a new steady state temperature model developed by incorporating the best aspects of previously published models, introducing new functions for selected heat exchange paths and improving the method for predicting the effects of covering aeration tanks. Numerical improvements with embedded reference data provide simpler formulation, faster execution, easier sensitivity analyses, using an ordinary spreadsheet. The paper presents several cases to validate the model.

Defining "adverse environmental impact" and making paragraph 316(b) decisions: a fisheries management approach.

PubMed

Bailey, David E; Bulleit, Kristy A N

2002-05-17

The electric utility industry has developed an approach for decisionmaking that includes a definition of Adverse Environmental Impact (AEI) and an implementation process. The definition of AEI is based on lessons from fishery management science and analysis of the statutory term "adverse environmental impact" and is consistent with current natural resource management policy. The industry has proposed a definition focusing on "unacceptable risk to the population"s ability to sustain itself, to support reasonably anticipated commercial or recreational harvests, or to perform its normal ecological function." This definition focuses not on counting individual fish or eggs cropped by the various uses of a water body, but on preserving populations of aquatic organisms and their functions in the aquatic community. The definition recognizes that assessment of AEI should be site-specific and requires both a biological decision and a balancing of diverse societal values. The industry believes that the definition of AEI should be implemented in a process that will maximize the overall societal benefit of the paragraph 316(b) decision by considering the facility"s physical location, design, and operation, as well as the local biology. The approach considers effects on affected fish and shellfish populations and the benefits of any necessary best technology available (BTA) alternatives. This is accomplished through consideration of population impacts, which conversely allows consideration of the benefits of any necessary BTA modifications. This in turn allows selection of BTAs that will protect potentially affected populations in a cost-effective manner. The process also employs risk assessment with stakeholder participation, in accordance with EPA's Guidelines for Ecological Risk Assessment. The information and tools are now available to make informed decisions about site-specific impacts that will ensure protection of aquatic ecosystems and best serve the public interest.

Ecological linkages between headwaters and downstream ecosystems: Transport of organic matter, invertebrates, and wood down headwater channels

USGS Publications Warehouse

Wipfli, M.S.; Richardson, J.S.; Naiman, R.J.

2007-01-01

Headwater streams make up a large proportion of the total length and watershed area of fluvial networks, and are partially characterized by the large volume of organic matter (large wood, detritus, and dissolved organic matter) and invertebrate inputs from the riparian forest, relative to stream size. Much of those inputs are exported to downstream reaches through time where they potentially subsidize river communities. The relative rates, timing, and conversion processes that carry inputs from small streams to downstream reaches are reasonably well quantified. For example, larger particles are converted to smaller particles, which are more easily exported. Also, dissolved organic matter and surface biofilms are converted to larger particles which can be more easily intercepted by consumers. However, the quality of these materials as it affects biological activity downstream is not well known, nor is the extent to which timing permits biological use of those particles. These ecological unknowns need to be resolved. Further, land uses may disrupt and diminish material transport to downstream reaches by removing sources (e.g., forest harvest), by affecting transport and decomposition processes (e.g., flow regulation, irrigation, changes in biotic communities), and by altering mechanisms of storage within headwaters (e.g., channelization). We present conceptual models of energy and nutrient fluxes that outline small stream processes and pathways important to downstream communities, and we identify informational gaps that, if filled, could significantly advance the understanding of linkages between headwater streams and larger rivers. The models, based on empirical evidence and best professional judgment, suggest that navigable waters are significantly influenced by headwater streams through hydrological and ecological connectivities, and land use can dramatically influence these natural connectivities, impacting downstream riverine ecosystems. ?? 2007 American Water Resources Association.

Treatment of raw and ozonated oil sands process-affected water under decoupled denitrifying anoxic and nitrifying aerobic conditions: a comparative study.

PubMed

Xue, Jinkai; Zhang, Yanyan; Liu, Yang; Gamal El-Din, Mohamed

2016-11-01

Batch experiments were performed to evaluate biodegradation of raw and ozonated oil sands process-affected water (OSPW) under denitrifying anoxic and nitrifying aerobic conditions for 33 days. The results showed both the anoxic and aerobic conditions are effective in degrading OSPW classical and oxidized naphthenic acids (NAs) with the aerobic conditions demonstrating higher removal efficiency. The reactors under nitrifying aerobic condition reduced the total classical NAs of raw OSPW by 69.1 %, with better efficiency for species of higher hydrophobicity. Compared with conventional aerobic reactor, nitrifying aerobic condition substantially shortened the NA degradation half-life to 16 days. The mild-dose ozonation remarkably accelerated the subsequent aerobic biodegradation of classical NAs within the first 14 days, especially for those with long carbon chains. Moreover, the ozone pretreatment enhanced the biological removal of OSPW classical NAs by leaving a considerably lower final residual concentration of 10.4 mg/L under anoxic conditions, and 5.7 mg/L under aerobic conditions. The combination of ozonation and nitrifying aerobic biodegradation removed total classical NAs by 76.5 % and total oxy-NAs (O3-O6) by 23.6 %. 454 Pyrosequencing revealed that microbial species capable of degrading recalcitrant hydrocarbons were dominant in all reactors. The most abundant genus in the raw and ozonated anoxic reactors was Thauera (~56 % in the raw OSPW anoxic reactor, and ~65 % in the ozonated OSPW anoxic reactor); whereas Rhodanobacter (~40 %) and Pseudomonas (~40 %) dominated the raw and ozonated aerobic reactors, respectively. Therefore, the combination of mild-dose ozone pretreatment and subsequent biological process could be a competent choice for OSPW treatment.

Warming reduces the growth and diversity of biological soil crusts in a semi-arid environment: implications for ecosystem structure and functioning

PubMed Central

Escolar, Cristina; Martínez, Isabel; Bowker, Matthew A.; Maestre, Fernando T.

2012-01-01

Biological soil crusts (BSCs) are key biotic components of dryland ecosystems worldwide that control many functional processes, including carbon and nitrogen cycling, soil stabilization and infiltration. Regardless of their ecological importance and prevalence in drylands, very few studies have explicitly evaluated how climate change will affect the structure and composition of BSCs, and the functioning of their constituents. Using a manipulative experiment conducted over 3 years in a semi-arid site from central Spain, we evaluated how the composition, structure and performance of lichen-dominated BSCs respond to a 2.4°C increase in temperature, and to an approximately 30 per cent reduction of total annual rainfall. In areas with well-developed BSCs, warming promoted a significant decrease in the richness and diversity of the whole BSC community. This was accompanied by important compositional changes, as the cover of lichens suffered a substantial decrease with warming (from 70 to 40% on average), while that of mosses increased slightly (from 0.3 to 7% on average). The physiological performance of the BSC community, evaluated using chlorophyll fluorescence, increased with warming during the first year of the experiment, but did not respond to rainfall reduction. Our results indicate that ongoing climate change will strongly affect the diversity and composition of BSC communities, as well as their recovery after disturbances. The expected changes in richness and composition under warming could reduce or even reverse the positive effects of BSCs on important soil processes. Thus, these changes are likely to promote an overall reduction in ecosystem processes that sustain and control nutrient cycling, soil stabilization and water dynamics. PMID:23045707

From biofilm ecology to reactors: a focused review.

PubMed

Boltz, Joshua P; Smets, Barth F; Rittmann, Bruce E; van Loosdrecht, Mark C M; Morgenroth, Eberhard; Daigger, Glen T

2017-04-01

Biofilms are complex biostructures that appear on all surfaces that are regularly in contact with water. They are structurally complex, dynamic systems with attributes of primordial multicellular organisms and multifaceted ecosystems. The presence of biofilms may have a negative impact on the performance of various systems, but they can also be used beneficially for the treatment of water (defined herein as potable water, municipal and industrial wastewater, fresh/brackish/salt water bodies, groundwater) as well as in water stream-based biological resource recovery systems. This review addresses the following three topics: (1) biofilm ecology, (2) biofilm reactor technology and design, and (3) biofilm modeling. In so doing, it addresses the processes occurring in the biofilm, and how these affect and are affected by the broader biofilm system. The symphonic application of a suite of biological methods has led to significant advances in the understanding of biofilm ecology. New metabolic pathways, such as anaerobic ammonium oxidation (anammox) or complete ammonium oxidation (comammox) were first observed in biofilm reactors. The functions, properties, and constituents of the biofilm extracellular polymeric substance matrix are somewhat known, but their exact composition and role in the microbial conversion kinetics and biochemical transformations are still to be resolved. Biofilm grown microorganisms may contribute to increased metabolism of micro-pollutants. Several types of biofilm reactors have been used for water treatment, with current focus on moving bed biofilm reactors, integrated fixed-film activated sludge, membrane-supported biofilm reactors, and granular sludge processes. The control and/or beneficial use of biofilms in membrane processes is advancing. Biofilm models have become essential tools for fundamental biofilm research and biofilm reactor engineering and design. At the same time, the divergence between biofilm modeling and biofilm reactor modeling approaches is recognized.

Scientific assessment of animal welfare.

PubMed

Hemsworth, P H; Mellor, D J; Cronin, G M; Tilbrook, A J

2015-01-01

Animal welfare is a state within the animal and a scientific perspective provides methodologies for evidence-based assessment of an animal's welfare. A simplistic definition of animal welfare might be how the animal feels now. Affective experiences including emotions, are subjective states so cannot be measured directly in animals, but there are informative indirect physiological and behavioural indices that can be cautiously used to interpret such experiences. This review enunciates several key science-based frameworks for understanding animal welfare. The biological functioning and affective state frameworks were initially seen as competing, but a recent more unified approach is that biological functioning is taken to include affective experiences and affective experiences are recognised as products of biological functioning, and knowledge of the dynamic interactions between the two is considered to be fundamental to managing and improving animal welfare. The value of these two frameworks in understanding the welfare of group-housed sows is reviewed. The majority of studies of the welfare of group-housed sows have employed the biological functioning framework to infer compromised sow welfare, on the basis that suboptimal biological functioning accompanies negative affective states such as sow hunger, pain, fear, helplessness, frustration and anger. Group housing facilitates social living, but group housing of gestating sows raises different welfare considerations to stall housing, such as high levels of aggression, injuries and stress, at least for several days after mixing, as well as subordinate sows being underfed due to competition at feeding. This paper highlights the challenges and potential opportunities for the continued improvement in sow management through well-focused research and multidisciplinary assessment of animal welfare. In future the management of sentient animals will require the promotion of positive affective experiences in animals and this is likely to be a major focus for animal welfare science activity in the early twenty-first century.

Research About the Corosive Effects of FeCl3 in the Aeration Wastewater Basin

NASA Astrophysics Data System (ADS)

Panaitescu, C.; Petrescu, M. G.

2018-01-01

Biological aeration of industrial wastewater is a very impressive process in the treatment of wastewater. The involvement of chemical reagents in this process, however, implies the intensification of the corrosion processes due to both pollutants in the wastewater and the chemical reactions that occur when the coagulation / flocculation reagents are added. This paper explores the action of ferric chloride (FeCl3) on metallic parts in the aeration basin. The most affected structures are metal. At the classical basins the aeration systems were made of P295GH materials. The corrosion produced is uneven. The analysis of the high degree of corrosion was done according to the national and international standards. Finally, the paper supports the replacement of the existing aeration system with an anticorrosive material.

Tissue Engineering the Cornea: The Evolution of RAFT

PubMed Central

Levis, Hannah J.; Kureshi, Alvena K.; Massie, Isobel; Morgan, Louise; Vernon, Amanda J.; Daniels, Julie T.

2015-01-01

Corneal blindness affects over 10 million people worldwide and current treatment strategies often involve replacement of the defective layer with healthy tissue. Due to a worldwide donor cornea shortage and the absence of suitable biological scaffolds, recent research has focused on the development of tissue engineering techniques to create alternative therapies. This review will detail how we have refined the simple engineering technique of plastic compression of collagen to a process we now call Real Architecture for 3D Tissues (RAFT). The RAFT production process has been standardised, and steps have been taken to consider Good Manufacturing Practice compliance. The evolution of this process has allowed us to create biomimetic epithelial and endothelial tissue equivalents suitable for transplantation and ideal for studying cell-cell interactions in vitro. PMID:25809689

[Kinetic model and simulation of the adsorption-biofilm theory for the process of biopurifying VOC waste gases].

PubMed

Sun, Peishi; Huang, Bing; Huang, Ruohua; Yang, Ping

2002-05-01

For the process of biopurifying waste gas containing VOC in low concentration by using a biological trickling filter, the related kinetic model and simulation of the new Adsorption-Biofilm theory were investigated in this study. By using the lab test data and the industrial test data, the results of contrast and validation indicated that the model had a good applicability for describing the practical bio-purification process of VOC waste gas. In the simulation study for the affection of main factor, such as the concentration of toluene in inlet gas, the gas flow and the height of biofilm-packing, a good pertinence was showed between calculated data and test dada, the interrelation coefficients were in 0.80-0.97.

Mechanism of biological denitrification inhibition: procyanidins induce an allosteric transition of the membrane-bound nitrate reductase through membrane alteration.

PubMed

Bardon, Clément; Poly, Franck; Piola, Florence; Pancton, Muriel; Comte, Gilles; Meiffren, Guillaume; Haichar, Feth el Zahar

2016-05-01

Recently, it has been shown that procyanidins from Fallopia spp. inhibit bacterial denitrification, a phenomenon called biological denitrification inhibition (BDI). However, the mechanisms involved in such a process remain unknown. Here, we investigate the mechanisms of BDI involving procyanidins, using the model strain Pseudomonas brassicacearum NFM 421. The aerobic and anaerobic (denitrification) respiration, cell permeability and cell viability of P. brassicacearum were determined as a function of procyanidin concentration. The effect of procyanidins on the bacterial membrane was observed using transmission electronic microscopy. Bacterial growth, denitrification, NO3- and NO2-reductase activity, and the expression of subunits of NO3- (encoded by the gene narG) and NO2-reductase (encoded by the gene nirS) under NO3 or NO2 were measured with and without procyanidins. Procyanidins inhibited the denitrification process without affecting aerobic respiration at low concentrations. Procyanidins also disturbed cell membranes without affecting cell viability. They specifically inhibited NO3- but not NO2-reductase.Pseudomonas brassicacearum responded to procyanidins by over-expression of the membrane-bound NO3-reductase subunit (encoded by the gene narG). Our results suggest that procyanidins can specifically inhibit membrane-bound NO3-reductase inducing enzymatic conformational changes through membrane disturbance and that P. brassicacearum responds by over-expressing membrane-bound NO3-reductase. Our results lead the way to a better understanding of BDI. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Interspecies Systems Biology Uncovers Metabolites Affecting C. elegans Gene Expression and Life History Traits

PubMed Central

Watson, Emma; MacNeil, Lesley T.; Ritter, Ashlyn D.; Yilmaz, L. Safak; Rosebrock, Adam P.; Caudy, Amy A.; Walhout, Albertha J. M.

2014-01-01

SUMMARY Diet greatly influences gene expression and physiology. In mammals, elucidating the effects and mechanisms of individual nutrients is challenging due to the complexity of both the animal and its diet. Here we used an interspecies systems biology approach with Caenorhabditis elegans and two if its bacterial diets, Escherichia coli and Comamonas aquatica, to identify metabolites that affect the animal’s gene expression and physiology. We identify vitamin B12 as the major dilutable metabolite provided by Comamonas aq. that regulates gene expression, accelerates development and reduces fertility, but does not affect lifespan. We find that vitamin B12 has a dual role in the animal: it affects development and fertility via the methionine/S-Adenosylmethionine (SAM) cycle and breaks down the short-chain fatty acid propionic acid preventing its toxic buildup. Our interspecies systems biology approach provides a paradigm for understanding complex interactions between diet and physiology. PMID:24529378

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

NASA Astrophysics Data System (ADS)

Maskiewicz, April Lee

Educational studies report that secondary and college level students have developed only limited understandings of the most basic biological processes and their interrelationships from typical classroom experiences. Furthermore, students have developed undesirable reasoning schemes and beliefs that directly affect how they make sense of and account for biological phenomena. For these reasons, there exists a need to rethink instructional practices in biology. This dissertation discusses how the principles of Harel's (1998, 2001) DNR-based instruction in mathematics could be applied to the teaching and learning of biology. DNR is an acronym for the three foundational principles of the system: Duality, Necessity, and Repeated-reasoning. This study examines the application of these three principles to ecology instruction. Through clinical and teaching interviews, I developed models of students' existing ways of understanding in ecology and inferred their ways of thinking. From these models a hypothetical learning trajectory was developed for 16 college level freshmen enrolled in a 10-week ecology teaching experiment. Through cyclical, interpretive analysis I documented and analyzed the evolution of the participants' progress. The results provide empirical evidence to support the claim that the DNR principles are applicable to ecology instruction. With respect to the Duality Principle, helping students develop specific ways of understanding led to the development of model-based reasoning---a way of thinking and the cognitive objective guiding instruction. Through carefully structured problem solving tasks, the students developed a biological understanding of the relationship between matter cycling, energy flow, and cellular processes such as photosynthesis and respiration, and used this understanding to account for observable phenomena in nature. In the case of intellectual necessity, the results illuminate how problem situations can be developed for biology learners that create cognitive disequilibrium-equilibrium phases and thus lead to modification or refinement of existing schemes. Elements that contributed to creating intellectual need include (a) problem tasks that built on students' existing knowledge; (b) problem tasks that challenged students; (c) a routine in which students presented their group's solution to the class; and (d) the didactical contract (Brousseau, 1997) established in the classroom.

[Neuroscientific basic in addiction].

PubMed

Johann-Ridinger, Monika

2014-10-01

The growing evidence of Neuroscience leads to a better understanding of cerebral processes in cases of acute or chronic intake of psychotropic substances (ps). Predominantly, structures of the "reward system" contributed to the development of addiction. Chronic consumption of ps provides changing in brain equilibrium and leads to adaptations in the brain architecture. In this article, the complex responses of neurons and neuronal networks are presented in cases of chronic intake of ps. The alterations affect the cognitive, emotional and behavioral processings and influence learning and stress regulation. In summary, all cerebral adaptations are integrated in a complex model of biological, psychological and social factors and therefore, addiction arises as a consequence of combination of individual protecting and risk factors.