Profile of science process skills of Preservice Biology Teacher in General Biology Course

Science.gov (United States)

Susanti, R.; Anwar, Y.; Ermayanti

2018-04-01

This study aims to obtain portrayal images of science process skills among preservice biology teacher. This research took place in Sriwijaya University and involved 41 participants. To collect the data, this study used multiple choice test comprising 40 items to measure the mastery of science process skills. The data were then analyzed in descriptive manner. The results showed that communication aspect outperfomed the other skills with that 81%; while the lowest one was identifying variables and predicting (59%). In addition, basic science process skills was 72%; whereas for integrated skills was a bit lower, 67%. In general, the capability of doing science process skills varies among preservice biology teachers.

Degrading organic micropollutants: The next challenge in the evolution of biological wastewater treatment processes

Directory of Open Access Journals (Sweden)

Naresh eSinghal

2016-05-01

Full Text Available Global water scarcity is driving the need for identifying new water source. Wastewater could be a potential water resource if appropriate treatment technologies could be developed. One of the barriers to obtaining high quality water from wastewater arises from the presence of organic micropollutants, which are biologically active at trace levels. Removal of these compounds from wastewater by current physico-chemical technologies is prohibitively expensive. While biological treatment processes are comparatively cheap, current systems are not capable of degrading the wide range of organic micropollutants present in wastewater. As current wastewater treatment processes were developed for treating conventional pollutants present at mg/L levels, degrading the ng/L levels of micropollutants will require a different approach to system design and operation. In this paper we discuss strategies that could be employed to develop biological wastewater treatment systems capable of degrading organic micropollutants.

Advanced oxidation process-biological system for wastewater containing a recalcitrant pollutant.

Science.gov (United States)

Oller, I; Malato, S; Sánchez-Pérez, J A; Maldonado, M I; Gernjak, W; Pérez-Estrada, L A

2007-01-01

Two advanced oxidation processes (AOPs), ozonation and photo-Fenton, combined with a pilot aerobic biological reactor at field scale were employed for the treatment of industrial non-biodegradable saline wastewater (TOC around 200 mgL(-1)) containing a biorecalcitrant compound, alpha-methylphenylglycine (MPG), at a concentration of 500 mgL(-1). Ozonation experiments were performed in a 50-L reactor with constant inlet ozone of 21.9 g m(-3). Solar photo-Fenton tests were carried out in a 75-L pilot plant made up of four compound parabolic collector (CPC) units. The catalyst concentration employed in this system was 20 mgL(-1) of Fe2+ and the H2O2 concentration was kept in the range of 200-500mgL(-1). Complete degradation of MPG was attained after 1,020 min of ozone treatment, while only 195 min were required for photo-Fenton. Samples from different stages of both AOPs were taken for Zahn-Wellens biocompatibility tests. Biodegradability enhancement of the industrial saline wastewater was confirmed (>70% biodegradability). Biodegradable compounds generated during the preliminary oxidative processes were biologically mineralised in a 170-L aerobic immobilised biomass reactor (IBR). The global efficiency of both AOP/biological combined systems was 90% removal of an initial TOC of over 500 mgL(-1).

Evolution of density-dependent movement during experimental range expansions.

Science.gov (United States)

Fronhofer, E A; Gut, S; Altermatt, F

2017-12-01

Range expansions and biological invasions are prime examples of transient processes that are likely impacted by rapid evolutionary changes. As a spatial process, range expansions are driven by dispersal and movement behaviour. Although it is widely accepted that dispersal and movement may be context-dependent, for instance density-dependent, and best represented by reaction norms, the evolution of density-dependent movement during range expansions has received little experimental attention. We therefore tested current theory predicting the evolution of increased movement at low densities at range margins using highly replicated and controlled range expansion experiments across multiple genotypes of the protist model system Tetrahymena thermophila. Although rare, we found evolutionary changes during range expansions even in the absence of initial standing genetic variation. Range expansions led to the evolution of negatively density-dependent movement at range margins. In addition, we report the evolution of increased intrastrain competitive ability and concurrently decreased population growth rates in range cores. Our findings highlight the importance of understanding movement and dispersal as evolving reaction norms and plastic life-history traits of central relevance for range expansions, biological invasions and the dynamics of spatially structured systems in general. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Comparing ecohydrological processes in alien vs. native ranges: perspectives from the endangered shrub Myricaria germanica

Science.gov (United States)

Michielon, Bruno; Campagnaro, Thomas; Porté, Annabel; Hoyle, Jo; Picco, Lorenzo; Sitzia, Tommaso

2017-04-01

Comparing the ecology of woody species in their alien and native ranges may provide interesting insights for theoretical ecology, invasion biology, restoration ecology and forestry. The literature which describes the biological evolution of successful plant invaders is rich and increasing. However, no general theories have been developed about the geomorphic settings which may limit or favour the alien woody species expansion along rivers. The aim of this contribution is to explore the research opportunities in the comparison of ecohydrological processes occurring in the alien vs. the native ranges of invasive tree and shrub species along the riverine corridor. We use the endangered shrub Myricaria germanica as an example. Myricaria germanica is an Euro-Asiatic pioneer species that, in the native range, develops along natural rivers, wide and dynamic. These conditions are increasingly limited by anthropogenic constraints in most European rivers. This species has been recently introduced in New Zealand, where it is spreading in some natural rivers of the Canterbury region (South Island). We present the current knowledge about the natural and anthropogenic factors influencing this species in its native range. We compare this information with the current knowledge about the same factors influencing M. germanica invasiveness and invasibility of riparian habitats in New Zealand. We stress the need to identify potential factors which could drive life-traits and growing strategies divergence which may hinder the application to the alien ranges of existing ecohydrological knowledge from native ranges. Moreover, the pattern of expansion of the alien range of species endangered in their native ranges opens new windows for research.

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research. PMID:20150964

Synthetic Biology: Tools to Design, Build, and Optimize Cellular Processes

Directory of Open Access Journals (Sweden)

Eric Young

2010-01-01

Full Text Available The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1 the process units and associated streams of the central dogma, (2 the intrinsic regulatory mechanisms, and (3 the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Synthetic biology: tools to design, build, and optimize cellular processes.

Science.gov (United States)

Young, Eric; Alper, Hal

2010-01-01

The general central dogma frames the emergent properties of life, which make biology both necessary and difficult to engineer. In a process engineering paradigm, each biological process stream and process unit is heavily influenced by regulatory interactions and interactions with the surrounding environment. Synthetic biology is developing the tools and methods that will increase control over these interactions, eventually resulting in an integrative synthetic biology that will allow ground-up cellular optimization. In this review, we attempt to contextualize the areas of synthetic biology into three tiers: (1) the process units and associated streams of the central dogma, (2) the intrinsic regulatory mechanisms, and (3) the extrinsic physical and chemical environment. Efforts at each of these three tiers attempt to control cellular systems and take advantage of emerging tools and approaches. Ultimately, it will be possible to integrate these approaches and realize the vision of integrative synthetic biology when cells are completely rewired for biotechnological goals. This review will highlight progress towards this goal as well as areas requiring further research.

Biological processes influencing contaminant release from sediments

International Nuclear Information System (INIS)

Reible, D.D.

1996-01-01

The influence of biological processes, including bioturbation, on the mobility of contaminants in freshwater sediments is described. Effective mass coefficients are estimated for tubificid oligochaetes as a function of worm behavior and biomass density. The mass transfer coefficients were observed to be inversely proportional to water oxygen content and proportional to the square root of biomass density. The sediment reworking and contaminant release are contrasted with those of freshwater amphipods. The implications of these and other biological processes for contaminant release and i n-situ remediation of soils and sediments are summarized. 4 figs., 1 tab

Processing scarce biological samples for light and transmission electron microscopy

Directory of Open Access Journals (Sweden)

P Taupin

2008-06-01

Full Text Available Light microscopy (LM and transmission electron microscopy (TEM aim at understanding the relationship structure-function. With advances in biology, isolation and purification of scarce populations of cells or subcellular structures may not lead to enough biological material, for processing for LM and TEM. A protocol for preparation of scarce biological samples is presented. It is based on pre-embedding the biological samples, suspensions or pellets, in bovine serum albumin (BSA and bis-acrylamide (BA, cross-linked and polymerized. This preparation provides a simple and reproducible technique to process biological materials, present in limited quantities that can not be amplified, for light and transmission electron microscopy.

An introduction to stochastic processes with applications to biology

CERN Document Server

Allen, Linda J S

2010-01-01

An Introduction to Stochastic Processes with Applications to Biology, Second Edition presents the basic theory of stochastic processes necessary in understanding and applying stochastic methods to biological problems in areas such as population growth and extinction, drug kinetics, two-species competition and predation, the spread of epidemics, and the genetics of inbreeding. Because of their rich structure, the text focuses on discrete and continuous time Markov chains and continuous time and state Markov processes.New to the Second EditionA new chapter on stochastic differential equations th

Nanomaterial processing using self-assembly-bottom-up chemical and biological approaches

International Nuclear Information System (INIS)

Thiruvengadathan, Rajagopalan; Gangopadhyay, Keshab; Gangopadhyay, Shubhra; Korampally, Venumadhav; Ghosh, Arkasubhra; Chanda, Nripen

2013-01-01

Nanotechnology is touted as the next logical sequence in technological evolution. This has led to a substantial surge in research activities pertaining to the development and fundamental understanding of processes and assembly at the nanoscale. Both top-down and bottom-up fabrication approaches may be used to realize a range of well-defined nanostructured materials with desirable physical and chemical attributes. Among these, the bottom-up self-assembly process offers the most realistic solution toward the fabrication of next-generation functional materials and devices. Here, we present a comprehensive review on the physical basis behind self-assembly and the processes reported in recent years to direct the assembly of nanoscale functional blocks into hierarchically ordered structures. This paper emphasizes assembly in the synthetic domain as well in the biological domain, underscoring the importance of biomimetic approaches toward novel materials. In particular, two important classes of directed self-assembly, namely, (i) self-assembly among nanoparticle–polymer systems and (ii) external field-guided assembly are highlighted. The spontaneous self-assembling behavior observed in nature that leads to complex, multifunctional, hierarchical structures within biological systems is also discussed in this review. Recent research undertaken to synthesize hierarchically assembled functional materials have underscored the need as well as the benefits harvested in synergistically combining top-down fabrication methods with bottom-up self-assembly. (review article)

A study on the ranges of low energy ions in biological samples and its mechanism of biological effects

International Nuclear Information System (INIS)

Lu Ting; Xie Liqing; Li Junping; Xia Ji

1993-01-01

The seeds of wheat and bean are irradiated by iron ion beam with energy 100 keV. The RBS spectra of the samples are observed and the ranges and distributions of the iron ions in the wheat and bean are calculated theoretically by means of Monte Carlo method. The results of theory and experiment are compared and the mechanism of biological effects induced by ion is discussed

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

Science.gov (United States)

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

2015-09-04

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

Stochastic transport processes in discrete biological systems

CERN Document Server

Frehland, Eckart

1982-01-01

These notes are in part based on a course for advanced students in the applications of stochastic processes held in 1978 at the University of Konstanz. These notes contain the results of re­ cent studies on the stochastic description of ion transport through biological membranes. In particular, they serve as an introduction to an unified theory of fluctuations in complex biological transport systems. We emphasize that the subject of this volume is not to introduce the mathematics of stochastic processes but to present a field of theoretical biophysics in which stochastic methods are important. In the last years the study of membrane noise has become an important method in biophysics. Valuable information on the ion transport mechanisms in membranes can be obtained from noise analysis. A number of different processes such as the opening and closing of ion channels have been shown to be sources of the measured current or voltage fluctuations. Bio­ logical 'transport systems can be complex. For example, the tr...

Students’ learning activities while studying biological process diagrams

NARCIS (Netherlands)

Kragten, M.; Admiraal, W.; Rijlaarsdam, G.

2015-01-01

Process diagrams describe how a system functions (e.g. photosynthesis) and are an important type of representation in Biology education. In the present study, we examined students’ learning activities while studying process diagrams, related to their resulting comprehension of these diagrams. Each

Students' Ability to Solve Process-Diagram Problems in Secondary Biology Education

Science.gov (United States)

Kragten, Marco; Admiraal, Wilfried; Rijlaarsdam, Gert

2015-01-01

Process diagrams are important tools in biology for explaining processes such as protein synthesis, compound cycles and the like. The aim of the present study was to measure the ability to solve process-diagram problems in biology and its relationship with prior knowledge, spatial ability and working memory. For this purpose, we developed a test…

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

Science.gov (United States)

List, Johann-Mattis; Pathmanathan, Jananan Sylvestre; Lopez, Philippe; Bapteste, Eric

2016-08-20

For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir's drift). Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to

Boolean Models of Biological Processes Explain Cascade-Like Behavior.

Science.gov (United States)

Chen, Hao; Wang, Guanyu; Simha, Rahul; Du, Chenghang; Zeng, Chen

2016-01-29

Biological networks play a key role in determining biological function and therefore, an understanding of their structure and dynamics is of central interest in systems biology. In Boolean models of such networks, the status of each molecule is either "on" or "off" and along with the molecules interact with each other, their individual status changes from "on" to "off" or vice-versa and the system of molecules in the network collectively go through a sequence of changes in state. This sequence of changes is termed a biological process. In this paper, we examine the common perception that events in biomolecular networks occur sequentially, in a cascade-like manner, and ask whether this is likely to be an inherent property. In further investigations of the budding and fission yeast cell-cycle, we identify two generic dynamical rules. A Boolean system that complies with these rules will automatically have a certain robustness. By considering the biological requirements in robustness and designability, we show that those Boolean dynamical systems, compared to an arbitrary dynamical system, statistically present the characteristics of cascadeness and sequentiality, as observed in the budding and fission yeast cell- cycle. These results suggest that cascade-like behavior might be an intrinsic property of biological processes.

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

Science.gov (United States)

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

2014-12-01

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

Redox processes in radiation biology and cancer

International Nuclear Information System (INIS)

Greenstock, C.L.

1981-01-01

Free-radical intermediates, particularly the activated oxygen species OH, O - 2 , and 1 O 2 , are implicated in many types of radiation damage to biological systems. In addition, these same species may be formed, either directly or indirectly through biochemical redox reactions, in both essential and aberrant metabolic processes. Cell survival and adaptation to an environment containing ionizing radiation and other physical and chemical carcinogens ultimately depend upon the cell's ability to maintain optimal function in response to free-radical damage at the chemical level. Many of these feedback control mechanisms are redox controlled. Radiation chemical techniques using selective radical scavengers, such as product analysis and pulse radiolysis, enable us to generate, observe, and characterize individually the nature and reactivity of potentially damaging free radicals. From an analysis of the chemical kinetics of free-radical involvement in biological damage, redox mechanisms are proposed to describe the early processes of radiation damage, redox mechanisms are proposed to describe the early processes of radiation damage, its protection and sensitization, and the role of free radicals in radiation and chemical carcinogenesis

Biology and host range of Tecmessa elegans (Lepidoptera: Notodontidae), a leaf-feeding moth evaluated as a potential biological control agent for Schinus terebinthifolius (Sapindales: Anacardiaceae) in the United States.

Science.gov (United States)

Oleiro, Marina; Mc Kay, Fernando; Wheeler, Gregory S

2011-06-01

During surveys for natural enemies that could be used as classical biological control agents of Schinus terebinthifolius Raddi (Brazilian pepper), the caterpillar, Tecmessa elegans Schaus (Lepidoptera: Notodontidae), was recorded feeding on the leaves of the shrub in South America. The biology and larval and adult host range of this species were examined to determine the insect's suitability for biological control of this invasive weed in North America and Hawaii. Biological observations indicate that the larvae have five instars. When disturbed, the late instar larvae emit formic acid from a prothoracic gland that may protect larvae from generalist predators. Larval host range tests conducted both in South and North America indicated that this species feeds and completes development primarily on members of the Anacardiaceae within the tribe Rhoeae. Oviposition tests indicated that when given a choice in large cages the adults will select the target weed over Pistacia spp. However, considering the many valued plant species in its host range, especially several North American natives, this species will not be considered further for biological control of S. terebinthifolius in North America.

Mathematical methods in biology and neurobiology

CERN Document Server

Jost, Jürgen

2014-01-01

Mathematical models can be used to meet many of the challenges and opportunities offered by modern biology. The description of biological phenomena requires a range of mathematical theories. This is the case particularly for the emerging field of systems biology. Mathematical Methods in Biology and Neurobiology introduces and develops these mathematical structures and methods in a systematic manner. It studies:   • discrete structures and graph theory • stochastic processes • dynamical systems and partial differential equations • optimization and the calculus of variations.   The biological applications range from molecular to evolutionary and ecological levels, for example:   • cellular reaction kinetics and gene regulation • biological pattern formation and chemotaxis • the biophysics and dynamics of neurons • the coding of information in neuronal systems • phylogenetic tree reconstruction • branching processes and population genetics • optimal resource allocation • sexual recombi...

Biologic phosphorus elimination - influencing parameters, boundary conditions, process optimation

International Nuclear Information System (INIS)

Dai Xiaohu.

1992-01-01

This paper first presents a systematic study of the basic process of biologic phosphorus elimination as employed by the original 'Phoredox (Main Stream) Process'. The conditions governing the process and the factors influencing its performance were determined by trial operation. A stationary model was developed for the purpose of modelling biologic phosphorus elimination in such a main stream process and optimising the dimensioning. The validity of the model was confirmed by operational data given in the literature and by operational data from the authors' own semitechnical-scale experimental plant. The model permits simulation of the values to be expected for effluent phosphorus and phosphate concentrations for given influent data and boundary conditions. It is thus possible to dimension a plant for accomodation of the original Phoredox (Main Stream) Process or any similar phosphorus eliminating plant that is to work according to the principle of the main stream process. (orig./EF) [de

Finite Range Decomposition of Gaussian Processes

CERN Document Server

Brydges, C D; Mitter, P K

2003-01-01

Let $D$ be the finite difference Laplacian associated to the lattice $bZ^{d}$. For dimension $dge 3$, $age 0$ and $L$ a sufficiently large positive dyadic integer, we prove that the integral kernel of the resolvent $G^{a}:=(a-D)^{-1}$ can be decomposed as an infinite sum of positive semi-definite functions $ V_{n} $ of finite range, $ V_{n} (x-y) = 0$ for $|x-y|ge O(L)^{n}$. Equivalently, the Gaussian process on the lattice with covariance $G^{a}$ admits a decomposition into independent Gaussian processes with finite range covariances. For $a=0$, $ V_{n} $ has a limiting scaling form $L^{-n(d-2)}Gamma_{ c,ast }{bigl (frac{x-y}{ L^{n}}bigr )}$ as $nrightarrow infty$. As a corollary, such decompositions also exist for fractional powers $(-D)^{-alpha/2}$, $0

Process for sewage biological treatment from uranium

International Nuclear Information System (INIS)

Popa, K.; Cecal, A.; Craciun, I.

2004-01-01

The invention relates to the sewage treatment, in particular to the sewage biological treatmen from radioactive waste, namely from uranium. The process dor sewage biological treatment from uranium includes cultivation in the sewage of the aquatic plants Lemna minor and Spirulina platensis. The plants cultivation is carried out in two stages. In the first stage for cultivation is used Lemna minor in the second stage - Spirulina platensis . After finishing the plant cultivation it is carried out separation of their biomass. The result of the invention consists in increasing the uranyl ions by the biomass of plants cultivated in the sewage

Process for sewage biological treatment from uranium

International Nuclear Information System (INIS)

Popa, Karin; Cecal, Alexandru; Craciun, Iftimie Ionel; Rudic, Valeriu; Gulea, Aurelian; Cepoi, Liliana

2004-01-01

The invention relates to the sewage treatment, in particular to the sewage biological treatment from radioactive waste, namely from uranium. The process for sewage biological treatment from uranium includes cultivation in the sewage of the aquatic plants Lemna minor and Spirulina platensis. The plant cultivation is carried out in two stages. In the first stage for cultivation is used Lemna minor and in the second stage - Spirulina platensis. After finishing the plant cultivation it is carried out separation of their biomass. The result of the invention consists in increasing the uranyl ions accumulation by the biomass of plants cultivated in the sewage.

Combination of Advanced Oxidation Processes and biological treatments for wastewater decontamination-A review

International Nuclear Information System (INIS)

Oller, I.; Malato, S.; Sanchez-Perez, J.A.

2011-01-01

Nowadays there is a continuously increasing worldwide concern for development of alternative water reuse technologies, mainly focused on agriculture and industry. In this context, Advanced Oxidation Processes (AOPs) are considered a highly competitive water treatment technology for the removal of those organic pollutants not treatable by conventional techniques due to their high chemical stability and/or low biodegradability. Although chemical oxidation for complete mineralization is usually expensive, its combination with a biological treatment is widely reported to reduce operating costs. This paper reviews recent research combining AOPs (as a pre-treatment or post-treatment stage) and bioremediation technologies for the decontamination of a wide range of synthetic and real industrial wastewater. Special emphasis is also placed on recent studies and large-scale combination schemes developed in Mediterranean countries for non-biodegradable wastewater treatment and reuse. The main conclusions arrived at from the overall assessment of the literature are that more work needs to be done on degradation kinetics and reactor modeling of the combined process, and also dynamics of the initial attack on primary contaminants and intermediate species generation. Furthermore, better economic models must be developed to estimate how the cost of this combined process varies with specific industrial wastewater characteristics, the overall decontamination efficiency and the relative cost of the AOP versus biological treatment.

Stochastic processes, multiscale modeling, and numerical methods for computational cellular biology

CERN Document Server

2017-01-01

This book focuses on the modeling and mathematical analysis of stochastic dynamical systems along with their simulations. The collected chapters will review fundamental and current topics and approaches to dynamical systems in cellular biology. This text aims to develop improved mathematical and computational methods with which to study biological processes. At the scale of a single cell, stochasticity becomes important due to low copy numbers of biological molecules, such as mRNA and proteins that take part in biochemical reactions driving cellular processes. When trying to describe such biological processes, the traditional deterministic models are often inadequate, precisely because of these low copy numbers. This book presents stochastic models, which are necessary to account for small particle numbers and extrinsic noise sources. The complexity of these models depend upon whether the biochemical reactions are diffusion-limited or reaction-limited. In the former case, one needs to adopt the framework of s...

Test of Science Process Skills of Biology Students towards Developing of Learning Exercises

Directory of Open Access Journals (Sweden)

Judith S. Rabacal

2016-11-01

Full Text Available This is a descriptive study aimed to determine the academic achievement on science process skills of the BS Biology Students of Northern Negros State College of Science and Technology, Philippines with the end view of developing learning exercises which will enhance their academic achievement on basic and integrated science process skills. The data in this study were obtained using a validated questionnaire. Mean was the statistical tool used to determine the academic achievement on the above mentioned science process skills; t-test for independent means was used to determine significant difference on the academic achievement of science process skills of BS Biology students while Pearson Product Moment of Correlation Coefficient was used to determine the significant relationship between basic and integrated science process skills of the BS Biology students. A 0.05 level of significance was used to determine whether the hypothesis set in the study will be rejected or accepted. Findings revealed that the academic achievement on basic and integrated science process skills of the BS Biology students was average. Findings revealed that there are no significant differences on the academic performance of the BS Biology students when grouped according to year level and gender. Findings also revealed that there is a significant difference on the academic achievement between basic and integrated science process skills of the BS Biology students. Findings revealed that there is a significant relationship between academic achievement on the basic and integrated science process skills of the BS Biology students.

Active Interaction Mapping as a tool to elucidate hierarchical functions of biological processes.

Science.gov (United States)

Farré, Jean-Claude; Kramer, Michael; Ideker, Trey; Subramani, Suresh

2017-07-03

Increasingly, various 'omics data are contributing significantly to our understanding of novel biological processes, but it has not been possible to iteratively elucidate hierarchical functions in complex phenomena. We describe a general systems biology approach called Active Interaction Mapping (AI-MAP), which elucidates the hierarchy of functions for any biological process. Existing and new 'omics data sets can be iteratively added to create and improve hierarchical models which enhance our understanding of particular biological processes. The best datatypes to further improve an AI-MAP model are predicted computationally. We applied this approach to our understanding of general and selective autophagy, which are conserved in most eukaryotes, setting the stage for the broader application to other cellular processes of interest. In the particular application to autophagy-related processes, we uncovered and validated new autophagy and autophagy-related processes, expanded known autophagy processes with new components, integrated known non-autophagic processes with autophagy and predict other unexplored connections.

Gene-ontology enrichment analysis in two independent family-based samples highlights biologically plausible processes for autism spectrum disorders.

LENUS (Irish Health Repository)

Anney, Richard J L

2012-02-01

Recent genome-wide association studies (GWAS) have implicated a range of genes from discrete biological pathways in the aetiology of autism. However, despite the strong influence of genetic factors, association studies have yet to identify statistically robust, replicated major effect genes or SNPs. We apply the principle of the SNP ratio test methodology described by O\\'Dushlaine et al to over 2100 families from the Autism Genome Project (AGP). Using a two-stage design we examine association enrichment in 5955 unique gene-ontology classifications across four groupings based on two phenotypic and two ancestral classifications. Based on estimates from simulation we identify excess of association enrichment across all analyses. We observe enrichment in association for sets of genes involved in diverse biological processes, including pyruvate metabolism, transcription factor activation, cell-signalling and cell-cycle regulation. Both genes and processes that show enrichment have previously been examined in autistic disorders and offer biologically plausibility to these findings.

iBiology: communicating the process of science.

Science.gov (United States)

Goodwin, Sarah S

2014-08-01

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

Biological Effects of Osteoblast-Like Cells on Nanohydroxyapatite Particles at a Low Concentration Range

Directory of Open Access Journals (Sweden)

Xiaochen Liu

2011-01-01

Full Text Available The biological effects of osteoblast-like MG-63 cells on nanohydroxyapatite (n-HA at the low concentration range (5–25 g/mL for 5 days was investigated. The results showed the viability and actin cytoskeleton of the cells descended with the increase of the concentration of n-HA, and the actin cytoskeleton of cells was depolymerised and became more disordered. Apoptotic rate of cells (1.85%, 1.99%, and 2.29% increased with the increase of n-HA concentration (5, 15, and 25 g/mL and become significantly higher than the control. Total intracellular protein content decreased with n-HA concentration increase, showing significant difference between 25 g/mL and the control, and no significant change of ALP activity was observed at the 5th day. The results revealed that the cell growth was inhibited by n-HA in a concentration-dependent manner, and the obvious biological effects of MG-63 cells on n-HA existed at the low concentration range from 5 to 25 g/mL.

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

Science.gov (United States)

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

2007-01-01

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

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

Science.gov (United States)

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

2017-11-01

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

Influence of different natural physical fields on biological processes

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Mashinsky, A. L.

2001-01-01

In space flight conditions gravity, magnetic, and electrical fields as well as ionizing radiation change both in size, and in direction. This causes disruptions in the conduct of some physical processes, chemical reactions, and metabolism in living organisms. In these conditions organisms of different phylogenetic level change their metabolic reactions undergo changes such as disturbances in ionic exchange both in lower and in higher plants, changes in cell morphology for example, gyrosity in Proteus ( Proteus vulgaris), spatial disorientation in coleoptiles of Wheat ( Triticum aestivum) and Pea ( Pisum sativum) seedlings, mutational changes in Crepis ( Crepis capillaris) and Arabidopsis ( Arabidopsis thaliana) seedling. It has been found that even in the absence of gravity, gravireceptors determining spatial orientation in higher plants under terrestrial conditions are formed in the course of ontogenesis. Under weightlessness this system does not function and spatial orientation is determined by the light flux gradient or by the action of some other factors. Peculiarities of the formation of the gravireceptor apparatus in higher plants, amphibians, fish, and birds under space flight conditions have been observed. It has been found that the system in which responses were accompanied by phase transition have proven to be gravity-sensitive under microgravity conditions. Such reactions include also the process of photosynthesis which is the main energy production process in plants. In view of the established effects of microgravity and different natural physical fields on biological processes, it has been shown that these processes change due to the absence of initially rigid determination. The established biological effect of physical fields influence on biological processes in organisms is the starting point for elucidating the role of gravity and evolutionary development of various organisms on Earth.

100 years after Smoluchowski: stochastic processes in cell biology

International Nuclear Information System (INIS)

Holcman, D; Schuss, Z

2017-01-01

100 years after Smoluchowski introduced his approach to stochastic processes, they are now at the basis of mathematical and physical modeling in cellular biology: they are used for example to analyse and to extract features from a large number (tens of thousands) of single molecular trajectories or to study the diffusive motion of molecules, proteins or receptors. Stochastic modeling is a new step in large data analysis that serves extracting cell biology concepts. We review here Smoluchowski’s approach to stochastic processes and provide several applications for coarse-graining diffusion, studying polymer models for understanding nuclear organization and finally, we discuss the stochastic jump dynamics of telomeres across cell division and stochastic gene regulation. (topical review)

The dielectric constant and its role in the long range coherence in biological systems

International Nuclear Information System (INIS)

Paul, R.; Chatterjee, R.

1984-01-01

An expression for the dielectric constant has been derived, for the Froehlich model of long-range coherence in biological cells. These theoretical expressions are employed to interpret the observed rouleaux formation of red blood cells (erythrocytes). It is concluded that this unusual behaviour of the erythrocytes can be interpreted satisfactorilly by the extended Froehlich model developed by us. (Author) [pt

Magnetic Nanotweezers for Interrogating Biological Processes in Space and Time.

Science.gov (United States)

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

2018-04-17

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

Diffusion processes and related topics in biology

CERN Document Server

Ricciardi, Luigi M

1977-01-01

These notes are based on a one-quarter course given at the Department of Biophysics and Theoretical Biology of the University of Chicago in 1916. The course was directed to graduate students in the Division of Biological Sciences with interests in population biology and neurobiology. Only a slight acquaintance with probability and differential equations is required of the reader. Exercises are interwoven with the text to encourage the reader to play a more active role and thus facilitate his digestion of the material. One aim of these notes is to provide a heuristic approach, using as little mathematics as possible, to certain aspects of the theory of stochastic processes that are being increasingly employed in some of the population biol­ ogy and neurobiology literature. While the subject may be classical, the nov­ elty here lies in the approach and point of view, particularly in the applica­ tions such as the approach to the neuronal firing problem and its related dif­ fusion approximations. It is a ple...

Classical and spatial stochastic processes with applications to biology

CERN Document Server

Schinazi, Rinaldo B

2014-01-01

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

Fundamental host range of Leptoypha hospita (Hemiptera: Tingidae), a potential biological control agent of Chinese privet

Science.gov (United States)

Yanzhuo Zhang; James L. Hanula; Scott Horn; Cera Jones; S. Kristine Braman; Jianghua Sun

2016-01-01

Chinese privet, Ligustrum sinense Lour., is an invasive shrub within riparian areas of the southeastern United States. Biological control is considered the most suitable management option for Chinese privet. The potential host range of the lace bug, Leptoypha hospita Drake et...

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

Science.gov (United States)

Somogyi, Endre; Glazier, James A

2017-04-01

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

State of the art of biological hydrogen production processes

International Nuclear Information System (INIS)

Loubette, N.; Junker, M.

2006-01-01

Our report gives an overview of hydrogen production processes with bacteria or algae. 4 main processes are described: water biophotolysis, photo- fermentation biological CO conversion and dark fermentation. Chemical phenomena which lead to hydrogen generation are exp/aired. Performances, limits and outlook are given for each process. Main projects, programs and key players involved in this field of research have been listed. This paper resumes few results of this report. (authors)

State of the art of biological hydrogen production processes

International Nuclear Information System (INIS)

Nicolas Loubette; Michel Junker

2006-01-01

Our report gives an overview of hydrogen production processes with bacteria or algae. 4 main processes are described: water bio-photolysis, photo-fermentation biological CO conversion and dark fermentation. Chemical phenomena which lead to hydrogen generation are explained. Performances, limits and outlook are given for each process. Main projects, programs and key players involved in this field of research have been listed. This paper resumes few results of this report. (authors)

Topographic laser ranging and scanning principles and processing

CERN Document Server

Shan, Jie

2008-01-01

A systematic, in-depth introduction to theories and principles of Light Detection and Ranging (LiDAR) technology is long overdue, as it is the most important geospatial data acquisition technology to be introduced in recent years. An advanced discussion, this text fills the void.Professionals in fields ranging from geology, geography and geoinformatics to physics, transportation, and law enforcement will benefit from this comprehensive discussion of topographic LiDAR principles, systems, data acquisition, and data processing techniques. The book covers ranging and scanning fundamentals, and broad, contemporary analysis of airborne LiDAR systems, as well as those situated on land and in space. The authors present data collection at the signal level in terms of waveforms and their properties; at the system level with regard to calibration and georeferencing; and at the data level to discuss error budget, quality control, and data organization. They devote the bulk of the book to LiDAR data processing and inform...

Processing laboratory of radio sterilized biological tissues

International Nuclear Information System (INIS)

Aguirre H, Paulina; Zarate S, Herman; Silva R, Samy; Hitschfeld, Mario

2005-01-01

The nuclear development applications have also reached those areas related to health. The risk of getting contagious illnesses through applying biological tissues has been one of the paramount worries to be solved since infectious illnesses might be provoked by virus, fungis or bacterias coming from donors or whether they have been introduced by means of intermediate stages before the use of these tissues. Therefore it has been concluded that the tissue allografts must be sterilized. The sterilization of medical products has been one of the main applications of the ionizing radiations and that it is why the International Organization of Atomic Energy began in the 70s promoting works related to the biological tissue sterilization and pharmaceutical products. The development of different tissue preservation methods has made possible the creation of tissue banks in different countries, to deal with long-term preservation. In our country, a project was launched in 1998, 'Establishment of a Tissue Bank in Latino america', this project was supported by the OIEA through the project INT/ 6/ 049, and was the starting of the actual Processing Laboratory of Radioesterilized Biological Tissues (LPTR), leaded by the Chilean Nuclear Energy Commission (CCHEN). This first organization is part of a number of entities compounding the Tissue Bank in Chile, organizations such as the Transplantation Promotion Corporation hospitals and the LPTR. The working system is carried out by means of the interaction between the hospitals and the laboratory. The medical professionals perform the procuring of tissues in the hospitals, then send them to the LPTR where they are processed and sterilized with ionizing radiation. The cycle ends up with the tissues return released to the hospitals, where they are used, and then the result information is sent to the LPTR as a form of feedback. Up to now, human skin has been processed (64 donors), amniotic membranes (35 donors) and pig skin (175 portions

Rhizosphere Biological Processes of Legume//Cereal Intercropping Systems: A Review

Directory of Open Access Journals (Sweden)

JIANG Yuan-yuan

2016-09-01

Full Text Available Intercropping, a sustainable planting pattern, was widely used in the wordwide. It not only has the advantages of yield and nutrient acquisition, but also can ensure food security and reduce the risk of crop failures. The majority of intercropping systems involve legume//cereal combinations because of interspecific facilitation or complementarity. The rhizosphere is the interface between plants and soil where there are interactions among a myriad of microorganisms and affect the uptake of nutrients, water and harmful substances. The rhizosphere biologi-cal processes not only determine the amount of nutrients and the availability of nutrients, but also affect crop productivity and nutrient use efficiency. Hence, this paper summarized the progress made on root morphology, rhizosphere microorganisms, root exudates and ecological ef-fect in the perspective of the rhizosphere biological process,which would provide theoretical basis for improving nutrient availability, remov-ing heavy metals, and plant genetic improvements.

Stochastic processes and long range dependence

CERN Document Server

Samorodnitsky, Gennady

2016-01-01

This monograph is a gateway for researchers and graduate students to explore the profound, yet subtle, world of long-range dependence (also known as long memory). The text is organized around the probabilistic properties of stationary processes that are important for determining the presence or absence of long memory. The first few chapters serve as an overview of the general theory of stochastic processes which gives the reader sufficient background, language, and models for the subsequent discussion of long memory. The later chapters devoted to long memory begin with an introduction to the subject along with a brief history of its development, followed by a presentation of what is currently the best known approach, applicable to stationary processes with a finite second moment. The book concludes with a chapter devoted to the author’s own, less standard, point of view of long memory as a phase transition, and even includes some novel results. Most of the material in the book has not previously been publis...

Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors.

Science.gov (United States)

Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

2013-05-01

In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors are absorbed in sufficient quantity, and then reach target organs while maintaining beneficial effects. These are the reasons why the bioavailability of functional food factors has been well investigated using rodent models. Recently, many of the biological processes have been reported to follow diurnal rhythms recurring every 24 h. Therefore, absorption and metabolism of functional food factors influenced by the biological processes may vary with time of day. Consequently, the evaluation of the bioavailability of functional food factors using rodent models should take into consideration the timing of consumption. In this review, we provide a perspective overview of the diurnal rhythm of biological processes involved in the bioavailability of functional food factors, particularly flavonoids.

Advances in downstream processing of biologics - Spectroscopy: An emerging process analytical technology.

Science.gov (United States)

Rüdt, Matthias; Briskot, Till; Hubbuch, Jürgen

2017-03-24

Process analytical technologies (PAT) for the manufacturing of biologics have drawn increased interest in the last decade. Besides being encouraged by the Food and Drug Administration's (FDA's) PAT initiative, PAT promises to improve process understanding, reduce overall production costs and help to implement continuous manufacturing. This article focuses on spectroscopic tools for PAT in downstream processing (DSP). Recent advances and future perspectives will be reviewed. In order to exploit the full potential of gathered data, chemometric tools are widely used for the evaluation of complex spectroscopic information. Thus, an introduction into the field will be given. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

A novel theory: biological processes mostly involve two types of mediators, namely general and specific mediators Endogenous small radicals such as superoxide and nitric oxide may play a role of general mediator in biological processes.

Science.gov (United States)

Mo, Jian

2005-01-01

A great number of papers have shown that free radicals as well as bioactive molecules can play a role of mediator in a wide spectrum of biological processes, but the biological actions and chemical reactivity of the free radicals are quite different from that of the bioactive molecules, and that a wide variety of bioactive molecules can be easily modified by free radicals due to having functional groups sensitive to redox, and the significance of the interaction between the free radicals and the bioactive molecules in biological processes has been confirmed by the results of some in vitro and in vivo studies. Based on these evidence, this article presented a novel theory about the mediators of biological processes. The essentials of the theory are: (a) mediators of biological processes can be classified into general and specific mediators; the general mediators include two types of free radicals, namely superoxide and nitric oxide; the specific mediators include a wide variety of bioactive molecules, such as specific enzymes, transcription factors, cytokines and eicosanoids; (b) a general mediator can modify almost any class of the biomolecules, and thus play a role of mediator in nearly every biological process via diverse mechanisms; a specific mediator always acts selectively on certain classes of the biomolecules, and may play a role of mediator in different biological processes via a same mechanism; (c) biological processes are mostly controlled by networks of their mediators, so the free radicals can regulate the last consequence of a biological process by modifying some types of the bioactive molecules, or in cooperation with these bioactive molecules; the biological actions of superoxide and nitric oxide may be synergistic or antagonistic. According to this theory, keeping the integrity of these networks and the balance between the free radicals and the bioactive molecules as well as the balance between the free radicals and the free radical scavengers

Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

Science.gov (United States)

Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

2016-10-20

The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

Biclustering with Flexible Plaid Models to Unravel Interactions between Biological Processes.

Science.gov (United States)

Henriques, Rui; Madeira, Sara C

2015-01-01

Genes can participate in multiple biological processes at a time and thus their expression can be seen as a composition of the contributions from the active processes. Biclustering under a plaid assumption allows the modeling of interactions between transcriptional modules or biclusters (subsets of genes with coherence across subsets of conditions) by assuming an additive composition of contributions in their overlapping areas. Despite the biological interest of plaid models, few biclustering algorithms consider plaid effects and, when they do, they place restrictions on the allowed types and structures of biclusters, and suffer from robustness problems by seizing exact additive matchings. We propose BiP (Biclustering using Plaid models), a biclustering algorithm with relaxations to allow expression levels to change in overlapping areas according to biologically meaningful assumptions (weighted and noise-tolerant composition of contributions). BiP can be used over existing biclustering solutions (seizing their benefits) as it is able to recover excluded areas due to unaccounted plaid effects and detect noisy areas non-explained by a plaid assumption, thus producing an explanatory model of overlapping transcriptional activity. Experiments on synthetic data support BiP's efficiency and effectiveness. The learned models from expression data unravel meaningful and non-trivial functional interactions between biological processes associated with putative regulatory modules.

Is nanotechnology the key to unravel and engineer biological processes?

Science.gov (United States)

Navarro, Melba; Planell, Josep A

2012-01-01

Regenerative medicine is an emerging field aiming to the development of new reparative strategies to treat degenerative diseases, injury, and trauma through developmental pathways in order to rebuild the architecture of the original injured organ and take over its functionality. Most of the processes and interactions involved in the regenerative process take place at subcellular scale. Nanotechnology provides the tools and technology not only to detect, to measure, or to image the interactions between the different biomolecules and biological entities, but also to control and guide the regenerative process. The relevance of nanotechnology for the development of regenerative medicine as well as an overview of the different tools that contribute to unravel and engineer biological systems are presented in this chapter. In addition, general data about the social impact and global investment in nanotechnology are provided.

Conserving forest biological diversity: How the Montreal Process helps achieve sustainability

Science.gov (United States)

Mark Nelson; Guy Robertson; Kurt. Riitters

2015-01-01

Forests support a variety of ecosystems, species and genes — collectively referred to as biological diversity — along with important processes that tie these all together. With the growing recognition that biological diversity contributes to human welfare in a number of important ways such as providing food, medicine and fiber (provisioning services...

PERMITTIVITY RESEARCH OF BIOLOGICAL SOLUTIONS IN GIGAHERTZ FREQUENCY RANGE

Directory of Open Access Journals (Sweden)

Anton S. Demin

2017-07-01

Full Text Available Subject of Research. We present results of permittivity research in gigahertz frequency range for saline and glucose solutions used in medical practice. Experiment results are substantiated theoretically on the basis of Debye-Cole model. Method. Researches have been carried out on blood plasma of healthy donor, water, normal saline and glucose solutions with different concentration from 3 to 12 mmol/l. Experiments have been performed by an active nearfield method based on measuring the impedance of a plane air-liquid boundary with open end of coaxial waveguide in the frequency range from 1 to 12 GHz. Measurement results have been processed with the use of vector analyzer computer system from Rohde & Schwarz. Transmittance spectra have been determined by means of IR-spectrometer from TENZOR-Bruker. Main Results. Simulation results have shown good agreement between the experimental results and the model, as well as the choice of the main parameters of the Debye-Cole model in the studied frequency range for all media. It has been shown that the range of 3-6 GHz can be considered as the main one in the development of diagnostic sensors for the non-invasive analysis of the glucose concentration in the human blood. Practical Relevance. Electrodynamic models of test fluid replacing human blood give the possibility to simulate the sensor basic characteristics for qualitative and quantitative estimation of glucose concentration in human blood and can be used to create an experimental sample of a non- invasive glucometer.

Biological features produced by additive manufacturing processes using vat photopolymerization method

DEFF Research Database (Denmark)

Davoudinejad, Ali; Mendez Ribo, Macarena; Pedersen, David Bue

2017-01-01

of micro biological features by Additive Manufacturing (AM) processes. The study characterizes the additive manufacturing processes for polymeric micro part productions using the vat photopolymerization method. A specifically designed vat photopolymerization AM machine suitable for precision printing...

Mineralization of 2-chlorophenol by sequential electrochemical reductive dechlorination and biological processes

Energy Technology Data Exchange (ETDEWEB)

Arellano-González, Miguel Ángel; González, Ignacio [Universidad Autónoma Metropolitana-Iztapalapa, Departamento de Química, Av. San Rafael Atlixco No. 186, Col. Vicentina, 09340 Mexico D.F. (Mexico); Texier, Anne-Claire, E-mail: actx@xanum.uam.mx [Universidad Autónoma Metropolitana-Iztapalapa, Departamento de Biotecnología, Av. San Rafael Atlixco No. 186, Col. Vicentina, 09340 Mexico, D.F. (Mexico)

2016-08-15

Highlights: • Dechlorination of 2-chlorophenol to phenol was 100% efficient on Pd-Ni/Ti electrode. • An ECCOCEL reactor was efficient and selective to obtain phenol from 2-chlorophenol. • Phenol was totally mineralized in a coupled denitrifying biorreactor. • Global time of 2-chlorophenol mineralization in the combined system was 7.5 h. - Abstract: In this work, a novel approach was applied to obtain the mineralization of 2-chlorophenol (2-CP) in an electrochemical-biological combined system where an electrocatalytic dehydrogenation process (reductive dechlorination) was coupled to a biological denitrification process. Reductive dechlorination of 2-CP was conducted in an ECCOCEL-type reactor on a Pd-Ni/Ti electrode at a potential of −0.40 V vs Ag/AgCl{sub (s)}/KCl{sub (sat)}, achieving 100 percent transformation of 2-CP into phenol. The electrochemically pretreated effluent was fed to a rotating cylinder denitrifying bioreactor where the totality of phenol was mineralized by denitrification, obtaining CO{sub 2} and N{sub 2} as the end products. The total time required for 2-CP mineralization in the combined electrochemical-biological process was 7.5 h. This value is close to those previously reported for electrochemical and advanced oxidation processes but in this case, an efficient process was obtained without accumulation of by-products or generation of excessive energy costs due to the selective electrochemical pretreatment. This study showed that the use of electrochemical reductive pretreatment combined with biological processes could be a promising technology for the removal of recalcitrant molecules, such as chlorophenols, from wastewaters by more efficient, rapid, and environmentally friendly processes.

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

International Nuclear Information System (INIS)

McMahon, S.

2016-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-15

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

Radiation processing of biological tissues for nuclear disaster management

International Nuclear Information System (INIS)

Singh, Rita

2012-01-01

A number of surgical procedures require tissue substitutes to repair or replace damaged or diseased tissues. Biological tissues from human donor like bone, skin, amniotic membrane and other soft tissues can be used for repair or reconstruction of the injured part of the body. Tissues from human donor can be processed and banked for orthopaedic, spinal, trauma and other surgical procedures. Allograft tissues provide an excellent alternative to autografts. The use of allograft tissue avoids the donor site morbidity and reduces the operating time, expense and trauma associated with the acquisition of autografts. Further, allografts have the added advantage of being available in large quantities. This has led to a global increase in allogeneic transplantation and development of tissue banking. However, the risk of infectious disease transmission via tissue allografts is a major concern. Therefore, tissue allografts should be sterilized to make them safe for clinical use. Radiation processing has well appreciated technological advantages and is the most suitable method for sterilization of biological tissues. Radiation processed biological tissues can be provided by the tissue banks for the management of injuries due to a nuclear disaster. A nuclear detonation will result in a large number of casualties due to the heat, blast and radiation effects of the weapon. Skin dressings or skin substitutes like allograft skin, xenograft skin and amniotic membrane can be used for the treatment of thermal burns and radiation induced skin injuries. Bone grafts can be employed for repairing fracture defects, filling in destroyed regions of bone, management of open fractures and joint injuries. Radiation processed tissues have the potential to repair or reconstruct damaged tissues and can be of great assistance in the treatment of injuries due to the nuclear weapon. (author)

Combined heterogeneous Electro-Fenton and biological process for the treatment of stabilized landfill leachate.

Science.gov (United States)

Baiju, Archa; Gandhimathi, R; Ramesh, S T; Nidheesh, P V

2018-03-15

Treatment of stabilized landfill leachate is a great challenge due to its poor biodegradability. Present study made an attempt to treat this wastewater by combining electro-Fenton (E-Fenton) and biological process. E-Fenton treatment was applied prior to biological process to enhance the biodegradability of leachate, which will be beneficial for the subsequent biological process. This study also investigates the efficiency of iron molybdophosphate (FeMoPO) nanoparticles as a heterogeneous catalyst in E-Fenton process. The effects of initial pH, catalyst dosage, applied voltage and electrode spacing on Chemical Oxygen Demand (COD) removal efficiency were analyzed to determine the optimum conditions. Heterogeneous E-Fenton process gave 82% COD removal at pH 2, catalyst dosage of 50 mg/L, voltage 5 V, electrode spacing 3 cm and electrode area 25 cm 2 . Combined E-Fenton and biological treatment resulted an overall COD removal of 97%, bringing down the final COD to 192 mg/L. Copyright © 2018 Elsevier Ltd. All rights reserved.

Simulation and Analysis of Complex Biological Processes: an Organisation Modelling Perspective

NARCIS (Netherlands)

Bosse, T.; Jonker, C.M.; Treur, J.

2005-01-01

This paper explores how the dynamics of complex biological processes can be modelled and simulated as an organisation of multiple agents. This modelling perspective identifies organisational structure occurring in complex decentralised processes and handles complexity of the analysis of the dynamics

Using Simple Manipulatives to Improve Student Comprehension of a Complex Biological Process: Protein Synthesis

Science.gov (United States)

Guzman, Karen; Bartlett, John

2012-01-01

Biological systems and living processes involve a complex interplay of biochemicals and macromolecular structures that can be challenging for undergraduate students to comprehend and, thus, misconceptions abound. Protein synthesis, or translation, is an example of a biological process for which students often hold many misconceptions. This article…

Irradiation of biological molecules (DNA and RNA bases) by proton impact in the velocity range of the Bragg peak (20-150 keV/amu)

International Nuclear Information System (INIS)

Tabet, J.

2007-11-01

The aim of this work was to study the ionization of DNA and RNA base molecules by proton impact at energies between 20 and 150 keV/amu. The experiments developed over the course of this project made it possible not only to study the fragmentation of uracil, thymine, adenine, and cytosine, but also to measure absolute cross sections for different ionization processes initiated by proton interactions with these important biological molecules. Firstly, the experimental system enabled the contributions of two key ionization processes to be separated: direct ionization and electron capture. The corresponding mass spectra were measured and analyzed on an event-by-event basis. For uracil, the branching ratios for these two processes were measured as function of the projectile velocity. Secondly, we have developed a system to measure absolute cross sections for the electron capture process. The production rate of neutral atoms compared to protons was measured for the four biological molecules: uracil, cytosine, thymine, and adenine at different vaporization temperatures. This production rate varies as a function of the thickness of the target jet traversed by the protons. Accordingly, a deposit experiment was developed in order to characterize the density of molecules in the targeted gas jets. Theoretical and experimental study of the total effusion and density-profile of the gaseous molecular beams enabled us to deduce the thickness of the target jets traversed by the protons. Thus it was possible to determine absolute cross sections for the ionization of each of the four isolated biological molecules by 80 keV protons impact. To our knowledge, this work provides the first experimental absolute cross sections for DNA and RNA base ionization processes initiated by proton impact in the velocity range corresponding to the Bragg peak. (author)

Trait-Dependent Biogeography: (Re)Integrating Biology into Probabilistic Historical Biogeographical Models.

Science.gov (United States)

Sukumaran, Jeet; Knowles, L Lacey

2018-04-20

The development of process-based probabilistic models for historical biogeography has transformed the field by grounding it in modern statistical hypothesis testing. However, most of these models abstract away biological differences, reducing species to interchangeable lineages. We present here the case for reintegration of biology into probabilistic historical biogeographical models, allowing a broader range of questions about biogeographical processes beyond ancestral range estimation or simple correlation between a trait and a distribution pattern, as well as allowing us to assess how inferences about ancestral ranges themselves might be impacted by differential biological traits. We show how new approaches to inference might cope with the computational challenges resulting from the increased complexity of these trait-based historical biogeographical models. Copyright © 2018 Elsevier Ltd. All rights reserved.

Moving beyond a descriptive aquatic toxicology: the value of biological process and trait information.

Science.gov (United States)

Segner, Helmut

2011-10-01

In order to improve the ability to link chemical exposure to toxicological and ecological effects, aquatic toxicology will have to move from observing what chemical concentrations induce adverse effects to more explanatory approaches, that are concepts which build on knowledge of biological processes and pathways leading from exposure to adverse effects, as well as on knowledge on stressor vulnerability as given by the genetic, physiological and ecological (e.g., life history) traits of biota. Developing aquatic toxicology in this direction faces a number of challenges, including (i) taking into account species differences in toxicant responses on the basis of the evolutionarily developed diversity of phenotypic vulnerability to environmental stressors, (ii) utilizing diversified biological response profiles to serve as biological read across for prioritizing chemicals, categorizing them according to modes of action, and for guiding targeted toxicity evaluation; (iii) prediction of ecological consequences of toxic exposure from knowledge of how biological processes and phenotypic traits lead to effect propagation across the levels of biological hierarchy; and (iv) the search for concepts to assess the cumulative impact of multiple stressors. An underlying theme in these challenges is that, in addition to the question of what the chemical does to the biological receptor, we should give increasing emphasis to the question how the biological receptor handles the chemicals, i.e., through which pathways the initial chemical-biological interaction extends to the adverse effects, how this extension is modulated by adaptive or compensatory processes as well as by phenotypic traits of the biological receptor. 2011 Elsevier B.V. All rights reserved.

Image processing and recognition for biological images.

Science.gov (United States)

Uchida, Seiichi

2013-05-01

This paper reviews image processing and pattern recognition techniques, which will be useful to analyze bioimages. Although this paper does not provide their technical details, it will be possible to grasp their main tasks and typical tools to handle the tasks. Image processing is a large research area to improve the visibility of an input image and acquire some valuable information from it. As the main tasks of image processing, this paper introduces gray-level transformation, binarization, image filtering, image segmentation, visual object tracking, optical flow and image registration. Image pattern recognition is the technique to classify an input image into one of the predefined classes and also has a large research area. This paper overviews its two main modules, that is, feature extraction module and classification module. Throughout the paper, it will be emphasized that bioimage is a very difficult target for even state-of-the-art image processing and pattern recognition techniques due to noises, deformations, etc. This paper is expected to be one tutorial guide to bridge biology and image processing researchers for their further collaboration to tackle such a difficult target. © 2013 The Author Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Morphogenesis and pattern formation in biological systems experiments and models

CERN Document Server

Noji, Sumihare; Ueno, Naoto; Maini, Philip

2003-01-01

A central goal of current biology is to decode the mechanisms that underlie the processes of morphogenesis and pattern formation. Concerned with the analysis of those phenomena, this book covers a broad range of research fields, including developmental biology, molecular biology, plant morphogenesis, ecology, epidemiology, medicine, paleontology, evolutionary biology, mathematical biology, and computational biology. In Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, experimental and theoretical aspects of biology are integrated for the construction and investigation of models of complex processes. This collection of articles on the latest advances by leading researchers not only brings together work from a wide spectrum of disciplines, but also provides a stepping-stone to the creation of new areas of discovery.

Microbiological control of sterilization efficiency by irradiation. Biological indicators. [Medical supplies

Energy Technology Data Exchange (ETDEWEB)

Bates, C [Institut National des Radioelements, Brussels (Belgium)

1977-01-01

The microbiological efficiency of the radiosterilization process was tested by means of biological indicators such as Micrococcus radiodurans R1 and Bacillus pumilus E601 for gamma and electron radiation doses ranging from 0.5 to 6 Mrad. The response of the biological indicators was studied in terms of conservation time, initial concentration of biological material, and sources of used radiation. Both the biological dosimetry of the process and the sterility after treatment were studied on the basis of inactivation curves.

DEMONSTRATION OF AN INTEGRATED, PASSIVE BIOLOGICAL TREATMENT PROCESS FOR AMD

Science.gov (United States)

An innovative, cost-effective, biological treatment process has been designed by MSE Technology Applications, Inc. to treat acid mine drainage (AMD). A pilot-scale demonstration is being conducted under the Mine Waste Technology Program using water flowing from an abandoned mine ...

Effect of Process-Oriented Guided-Inquiry Learning on Non-majors Biology Students' Understanding of Biological Classification

Science.gov (United States)

Wozniak, Breann M.

The purpose of this study was to examine the effect of process-oriented guided-inquiry learning (POGIL) on non-majors college biology students' understanding of biological classification. This study addressed an area of science instruction, POGIL in the non-majors college biology laboratory, which has yet to be qualitatively and quantitatively researched. A concurrent triangulation mixed methods approach was used. Students' understanding of biological classification was measured in two areas: scores on pre and posttests (consisting of 11 multiple choice questions), and conceptions of classification as elicited in pre and post interviews and instructor reflections. Participants were Minnesota State University, Mankato students enrolled in BIOL 100 Summer Session. One section was taught with the traditional curriculum (n = 6) and the other section in the POGIL curriculum (n = 10) developed by the researcher. Three students from each section were selected to take part in pre and post interviews. There were no significant differences within each teaching method (p familiar animal categories and aquatic habitats, unfamiliar organisms, combining and subdividing initial groupings, and the hierarchical nature of classification. The POGIL students were the only group to surpass these challenges after the teaching intervention. This study shows that POGIL is an effective technique at eliciting students' misconceptions, and addressing these misconceptions, leading to an increase in student understanding of biological classification.

Single-Nanoparticle Resolved Biomimetic Long-Range Electron Transfer and Electrocatalysis of Mixed-Valence Nanoparticles

DEFF Research Database (Denmark)

Zhu, Nan; Hao, Xian; Ulstrup, Jens

2016-01-01

Long-range electron transfer (LRET) is a core elementary step in a wealth of processes central to chemistry and biology, including photosynthesis, respiration, and catalysis. In nature, biological catalysis is performed by enzymes. However, enzymes are structurally fragile and have limited stabil...

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

Science.gov (United States)

Rey, Alejandro D; Herrera-Valencia, Edtson E

2012-06-01

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

Selection platforms for directed evolution in synthetic biology.

Science.gov (United States)

Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

2016-08-15

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).

Simulating biological processes: stochastic physics from whole cells to colonies

Science.gov (United States)

Earnest, Tyler M.; Cole, John A.; Luthey-Schulten, Zaida

2018-05-01

The last few decades have revealed the living cell to be a crowded spatially heterogeneous space teeming with biomolecules whose concentrations and activities are governed by intrinsically random forces. It is from this randomness, however, that a vast array of precisely timed and intricately coordinated biological functions emerge that give rise to the complex forms and behaviors we see in the biosphere around us. This seemingly paradoxical nature of life has drawn the interest of an increasing number of physicists, and recent years have seen stochastic modeling grow into a major subdiscipline within biological physics. Here we review some of the major advances that have shaped our understanding of stochasticity in biology. We begin with some historical context, outlining a string of important experimental results that motivated the development of stochastic modeling. We then embark upon a fairly rigorous treatment of the simulation methods that are currently available for the treatment of stochastic biological models, with an eye toward comparing and contrasting their realms of applicability, and the care that must be taken when parameterizing them. Following that, we describe how stochasticity impacts several key biological functions, including transcription, translation, ribosome biogenesis, chromosome replication, and metabolism, before considering how the functions may be coupled into a comprehensive model of a ‘minimal cell’. Finally, we close with our expectation for the future of the field, focusing on how mesoscopic stochastic methods may be augmented with atomic-scale molecular modeling approaches in order to understand life across a range of length and time scales.

Transmission as a basic process in microbial biology. Lwoff Award Prize Lecture.

Science.gov (United States)

Baquero, Fernando

2017-11-01

Transmission is a basic process in biology and evolution, as it communicates different biological entities within and across hierarchical levels (from genes to holobionts) both in time and space. Vertical descent, replication, is transmission of information across generations (in the time dimension), and horizontal descent is transmission of information across compartments (in the space dimension). Transmission is essentially a communication process that can be studied by analogy of the classic information theory, based on 'emitters', 'messages' and 'receivers'. The analogy can be easily extended to the triad 'emigration', 'migration' and 'immigration'. A number of causes (forces) determine the emission, and another set of causes (energies) assures the reception. The message in fact is essentially constituted by 'meaningful' biological entities. A DNA sequence, a cell and a population have a semiotic dimension, are 'signs' that are eventually recognized (decoded) and integrated by receiver biological entities. In cis-acting or unenclosed transmission, the emitters and receivers correspond to separated entities of the same hierarchical level; in trans-acting or embedded transmission, the information flows between different, but frequently nested, hierarchical levels. The result (as in introgressive events) is constantly producing innovation and feeding natural selection, influencing also the evolution of transmission processes. This review is based on the concepts presented at the André Lwoff Award Lecture in the FEMS Microbiology Congress in Maastricht in 2015. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Biological effects of tritium on fish cells in the concentration range of international drinking water standards.

Science.gov (United States)

Stuart, Marilyne; Festarini, Amy; Schleicher, Krista; Tan, Elizabeth; Kim, Sang Bog; Wen, Kendall; Gawlik, Jilian; Ulsh, Brant

2016-10-01

To evaluate whether the current Canadian tritium drinking water limit is protective of aquatic biota, an in vitro study was designed to assess the biological effects of low concentrations of tritium, similar to what would typically be found near a Canadian nuclear power station, and higher concentrations spanning the range of international tritium drinking water standards. Channel catfish peripheral blood B-lymphoblast and fathead minnow testis cells were exposed to 10-100,000 Bq l(-1) of tritium, after which eight molecular and cellular endpoints were assessed. Increased numbers of DNA strand breaks were observed and ATP levels were increased. There were no increases in γH2AX-mediated DNA repair. No differences in cell growth were noted. Exposure to the lowest concentrations of tritium were associated with a modest increase in the viability of fathead minnow testicular cells. Using the micronucleus assay, an adaptive response was observed in catfish B-lymphoblasts. Using molecular endpoints, biological responses to tritium in the range of Canadian and international drinking water standards were observed. At the cellular level, no detrimental effects were noted on growth or cycling, and protective effects were observed as an increase in cell viability and an induced resistance to a large challenge dose.

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

Science.gov (United States)

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.

Facilitating a More Efficient Commercial Review Process for Pediatric Drugs and Biologics

Directory of Open Access Journals (Sweden)

Ryan D. Rykhus

2017-12-01

Full Text Available Over the past two decades, the biopharmaceutical industry has seen unprecedented expansion and innovation in concert with significant technological advancements. While the industry has experienced marked growth, the regulatory system in the United States still operates at a capacity much lower than the influx of new drug and biologic candidates. As a result, it has become standard for months or even years of waiting for commercial approval by the U.S. Food and Drug Administration. These regulatory delays have generated a system that stifles growth and innovation due to the exorbitant costs associated with awaiting approval from the nation’s sole regulatory agency. The recent re-emergence of diseases that impact pediatric demographics represents one particularly acute reason for developing a regulatory system that facilitates a more efficient commercial review process. Herein, we present a range of initiatives that could represent early steps toward alleviating the delays in approving life-saving therapeutics.

Dense range images from sparse point clouds using multi-scale processing

NARCIS (Netherlands)

Do, Q.L.; Ma, L.; With, de P.H.N.

2013-01-01

Multi-modal data processing based on visual and depth/range images has become relevant in computer vision for 3D reconstruction applications such as city modeling, robot navigation etc. In this paper, we generate highaccuracy dense range images from sparse point clouds to facilitate such

Applications of Structural Biology and Bioinformatics in the Investigation of Oxidative Stress-Related Processes

NARCIS (Netherlands)

Bersch, Beate; Groves, Matthew; Johann, Klare; Torda, Andrew; Ortiz, Dario; Laher, I.

2014-01-01

Reactive oxygen species (ROS)-mediated dysfunction of certain biological processes is implicated in different diseases in humans, including cardiovascular, cancer, or neurodegenerative disorders. Not only human cells and tissues are affected by ROS but also all other biological systems, including

High speed, wide dynamic range analog signal processing for avalanche photodiode

CERN Document Server

Walder, J P; Pangaud, P

2000-01-01

A wide dynamic range multi-gain analog transimpedance amplifier integrated circuit has been developed for avalanche photodiode signal processing. The 96 dB input dynamic range is divided into four ranges of 12-bits each in order to provide 40 MHz analog sampled data to a 12-bits ADC. This concept which has been integrated in both BiCMOS and full complementary bipolar technology along with fitted design techniques will be presented.

High speed, wide dynamic range analog signal processing for avalanche photodiode

International Nuclear Information System (INIS)

Walder, J.P.; El Mamouni, Houmani; Pangaud, Patrick

2000-01-01

A wide dynamic range multi-gain analog transimpedance amplifier integrated circuit has been developed for avalanche photodiode signal processing. The 96 dB input dynamic range is divided into four ranges of 12-bits each in order to provide 40 MHz analog sampled data to a 12-bits ADC. This concept which has been integrated in both BiCMOS and full complementary bipolar technology along with fitted design techniques will be presented

High speed, wide dynamic range analog signal processing for avalanche photodiode

Energy Technology Data Exchange (ETDEWEB)

Walder, J.P. E-mail: walder@in2p3.fr; El Mamouni, Houmani; Pangaud, Patrick

2000-03-11

A wide dynamic range multi-gain analog transimpedance amplifier integrated circuit has been developed for avalanche photodiode signal processing. The 96 dB input dynamic range is divided into four ranges of 12-bits each in order to provide 40 MHz analog sampled data to a 12-bits ADC. This concept which has been integrated in both BiCMOS and full complementary bipolar technology along with fitted design techniques will be presented.

Genomic Signal Processing: Predicting Basic Molecular Biological Principles

Science.gov (United States)

Alter, Orly

2005-03-01

Advances in high-throughput technologies enable acquisition of different types of molecular biological data, monitoring the flow of biological information as DNA is transcribed to RNA, and RNA is translated to proteins, on a genomic scale. Future discovery in biology and medicine will come from the mathematical modeling of these data, which hold the key to fundamental understanding of life on the molecular level, as well as answers to questions regarding diagnosis, treatment and drug development. Recently we described data-driven models for genome-scale molecular biological data, which use singular value decomposition (SVD) and the comparative generalized SVD (GSVD). Now we describe an integrative data-driven model, which uses pseudoinverse projection (1). We also demonstrate the predictive power of these matrix algebra models (2). The integrative pseudoinverse projection model formulates any number of genome-scale molecular biological data sets in terms of one chosen set of data samples, or of profiles extracted mathematically from data samples, designated the ``basis'' set. The mathematical variables of this integrative model, the pseudoinverse correlation patterns that are uncovered in the data, represent independent processes and corresponding cellular states (such as observed genome-wide effects of known regulators or transcription factors, the biological components of the cellular machinery that generate the genomic signals, and measured samples in which these regulators or transcription factors are over- or underactive). Reconstruction of the data in the basis simulates experimental observation of only the cellular states manifest in the data that correspond to those of the basis. Classification of the data samples according to their reconstruction in the basis, rather than their overall measured profiles, maps the cellular states of the data onto those of the basis, and gives a global picture of the correlations and possibly also causal coordination of

Automated force volume image processing for biological samples.

Directory of Open Access Journals (Sweden)

Pavel Polyakov

2011-04-01

Full Text Available Atomic force microscopy (AFM has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image.

Biological processes for mitigation of greenhouse gases

Energy Technology Data Exchange (ETDEWEB)

Benemann, John R. [California Univ., Dept. of Plant and Microbial Biology, Berkeley, CA (United States)

1999-07-01

Biological processes driven by photosynthesis cycle through the atmosphere well over an order of magnitude more CO{sub 2} than is currently emitted from the combustion of fossils fuels. Already human activities control and appropriate almost half the primary photosynthetic productivity of the planet. Better management of natural and man-made ecosystems affords many opportunities for mitigation of greenhouse gases, through sink enhancements, source reduction and substitution of fossil fuels with biofuels. Biofuels can be recovered from most organic wastes, from agricultural and forestry residues, and from biomass produced solely for energy use. However, the currently low costs of fossil fuels limits the market for biofuels. Accounting for the greenhouse mitigation value of biofuels would significantly increase their contribution to world fuel suppliers, estimated to be currently equivalent to about 15% of fossil fuel usage. Another limiting factor in expanding the use of biofuels is the relatively low solar energy conversion efficiencies of photosynthesis. Currently well below 1% of solar energy is converted into biomass energy even by intensive agricultural or forestry systems, with peak conversion efficiencies about 2 to 3% for sugar cane or microalgae cultures. One approach to increase photosynthetic efficiencies, being developed at the University of California Berkeley, is to reduce the amount of light-gathering chlorophyll in microalgae and higher plants. This would reduce mutual shading and also increase photosynthetic efficiencies under full sunlight intensities. Estimates of the potential of photosynthetic greenhouse mitigation processes vary widely. However, even conservative estimates for biofuels substituting for fossil fuels project the potential to reduce a large fraction of current increases in atmospheric CO{sub 2} levels. Biofuels production will require integration with existing agronomic, forestry and animal husbandry systems, and improved

Effects of aerobic and anaerobic biological processes on leaching of heavy metals from soil amended with sewage sludge compost.

Science.gov (United States)

Fang, Wen; Wei, Yonghong; Liu, Jianguo; Kosson, David S; van der Sloot, Hans A; Zhang, Peng

2016-12-01

The risk from leaching of heavy metals is a major factor hindering land application of sewage sludge compost (SSC). Understanding the change in heavy metal leaching resulting from soil biological processes provides important information for assessing long-term behavior of heavy metals in the compost amended soil. In this paper, 180days aerobic incubation and 240days anaerobic incubation were conducted to investigate the effects of the aerobic and anaerobic biological processes on heavy metal leaching from soil amended with SSC, combined with chemical speciation modeling. Results showed that leaching concentrations of heavy metals at natural pH were similar before and after biological process. However, the major processes controlling heavy metals were influenced by the decrease of DOC with organic matter mineralization during biological processes. Mineralization of organic matter lowered the contribution of DOC-complexation to Ni and Zn leaching. Besides, the reducing condition produced by biological processes, particularly by the anaerobic biological process, resulted in the loss of sorption sites for As on Fe hydroxide, which increased the potential risk of As release at alkaline pH. Copyright © 2016 Elsevier Ltd. All rights reserved.

Process for the biological purification of waste water

DEFF Research Database (Denmark)

1992-01-01

Process for the biological purification of waste water by the activated sludge method, the waste water being mixed with recirculated sludge and being subjected to an anaerobic treatment, before the waste water thus treated is alternately subjected to anoxic and aerobic treatments and the waste...... water thus treated is led into a clarification zone for settling sludge, which sludge is recirculated in order to be mixed with the crude waste water. As a result, a simultaneous reduction of the content both of nitrogen and phosphorus of the waste water is achieved....

Removal of Refractory Organics from Biologically Treated Landfill Leachate by Microwave Discharge Electrodeless Lamp Assisted Fenton Process

Directory of Open Access Journals (Sweden)

Jiuyi Li

2015-01-01

Full Text Available Biologically treated leachate usually contains considerable amount of refractory organics and trace concentrations of xenobiotic pollutants. Removal of refractory organics from biologically treated landfill leachate by a novel microwave discharge electrodeless lamp (MDEL assisted Fenton process was investigated in the present study in comparison to conventional Fenton and ultraviolet Fenton processes. Conventional Fenton and ultraviolet Fenton processes could substantially remove up to 70% of the refractory organics in a membrane bioreactor treated leachate. MDEL assisted Fenton process achieved excellent removal performance of the refractory components, and the effluent chemical oxygen demand concentration was lower than 100 mg L−1. Most organic matters were transformed into smaller compounds with molecular weights less than 1000 Da. Ten different polycyclic aromatic hydrocarbons were detected in the biologically treated leachate, most of which were effectively removed by MDEL-Fenton treatment. MDEL-Fenton process provides powerful capability in degradation of refractory and xenobiotic organic pollutants in landfill leachate and could be adopted as a single-stage polishing process for biologically treated landfill leachate to meet the stringent discharge limit.

Unified Deep Learning Architecture for Modeling Biology Sequence.

Science.gov (United States)

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

2017-10-09

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

Removal of pharmaceuticals from wastewater by biological processes, hydrodynamic cavitation and UV treatment.

Science.gov (United States)

Zupanc, Mojca; Kosjek, Tina; Petkovšek, Martin; Dular, Matevž; Kompare, Boris; Širok, Brane; Blažeka, Željko; Heath, Ester

2013-07-01

To augment the removal of pharmaceuticals different conventional and alternative wastewater treatment processes and their combinations were investigated. We tested the efficiency of (1) two distinct laboratory scale biological processes: suspended activated sludge and attached-growth biomass, (2) a combined hydrodynamic cavitation-hydrogen peroxide process and (3) UV treatment. Five pharmaceuticals were chosen including ibuprofen, naproxen, ketoprofen, carbamazepine and diclofenac, and an active metabolite of the lipid regulating agent clofibric acid. Biological treatment efficiency was evaluated using lab-scale suspended activated sludge and moving bed biofilm flow-through reactors, which were operated under identical conditions in respect to hydraulic retention time, working volume, concentration of added pharmaceuticals and synthetic wastewater composition. The suspended activated sludge process showed poor and inconsistent removal of clofibric acid, carbamazepine and diclofenac, while ibuprofen, naproxen and ketoprofen yielded over 74% removal. Moving bed biofilm reactors were filled with two different types of carriers i.e. Kaldnes K1 and Mutag BioChip™ and resulted in higher removal efficiencies for ibuprofen and diclofenac. Augmentation and consistency in the removal of diclofenac were observed in reactors using Mutag BioChip™ carriers (85%±10%) compared to reactors using Kaldnes carriers and suspended activated sludge (74%±22% and 48%±19%, respectively). To enhance the removal of pharmaceuticals hydrodynamic cavitation with hydrogen peroxide process was evaluated and optimal conditions for removal were established regarding the duration of cavitation, amount of added hydrogen peroxide and initial pressure, all of which influence the efficiency of the process. Optimal parameters resulted in removal efficiencies between 3-70%. Coupling the attached-growth biomass biological treatment, hydrodynamic cavitation/hydrogen peroxide process and UV treatment

Applying the Nernst equation to simulate redox potential variations for biological nitrification and denitrification processes.

Science.gov (United States)

Chang, Cheng-Nan; Cheng, Hong-Bang; Chao, Allen C

2004-03-15

In this paper, various forms of Nernst equations have been developed based on the real stoichiometric relationship of biological nitrification and denitrification reactions. Instead of using the Nernst equation based on a one-to-one stoichiometric relation for the oxidizing and the reducing species, the basic Nernst equation is modified into slightly different forms. Each is suitable for simulating the redox potential (ORP) variation of a specific biological nitrification or denitrification process. Using the data published in the literature, the validity of these developed Nernst equations has been verified by close fits of the measured ORP data with the calculated ORP curve. The simulation results also indicate that if the biological process is simulated using an incorrect form of Nernst equation, the calculated ORP curve will not fit the measured data. Using these Nernst equations, the ORP value that corresponds to a predetermined degree of completion for the biochemical reaction can be calculated. Thus, these Nernst equations will enable a more efficient on-line control of the biological process.

Process of Argumentation in High School Biology Class: A Qualitative Analysis

Science.gov (United States)

Ramli, M.; Rakhmawati, E.; Hendarto, P.; Winarni

2017-02-01

Argumentation skill can be nurtured by designing a lesson in which students are provided with the opportunity to argue. This research aims to analyse argumentation process in biology class. The participants were students of three biology classes from different high schools in Surakarta Indonesia. One of the classroom was taught by a student teacher, and the rest were instructed by the assigned teachers. Through a classroom observation, oral activities were noted, audio-recorded and video-taped. Coding was done based on the existence of claiming-reasoning-evidence (CRE) process by McNeill and Krajcik. Data was analysed qualitatively focusing on the role of teachers to initiate questioning to support argumentation process. The lesson design of three were also analysed. The result shows that pedagogical skill of teachers to support argumentation process, such as skill to ask, answer, and respond to students’ question and statements need to be trained intensively. Most of the argumentation found were only claiming, without reasoning and evidence. Teachers have to change the routine of mostly posing open-ended questions to students, and giving directly a correct answer to students’ questions. Knowledge and skills to encourage student to follow inquiry-based learning have to be acquired by teachers.

Posttranslational modifications of desmin and their implication in biological processes and pathologies.

Science.gov (United States)

Winter, Daniel L; Paulin, Denise; Mericskay, Mathias; Li, Zhenlin

2014-01-01

Desmin, the muscle-specific intermediate filament, is involved in myofibrillar myopathies, dilated cardiomyopathy and muscle wasting. Desmin is the target of posttranslational modifications (PTMs) such as phosphorylation, ADP-ribosylation and ubiquitylation as well as nonenzymatic modifications such as glycation, oxidation and nitration. Several PTM target residues and their corresponding modifying enzymes have been discovered in human and nonhuman desmin. The major effect of phosphorylation and ADP-ribosylation is the disassembly of desmin filaments, while ubiquitylation of desmin leads to its degradation. The regulation of the desmin filament network by phosphorylation and ADP-ribosylation was found to be implicated in several major biological processes such as myogenesis, myoblast fusion, muscle contraction, muscle atrophy, cell division and possibly desmin interactions with its binding partners. Phosphorylation of desmin is also implicated in many forms of desmin-related myopathies (desminopathies). In this review, we summarize the findings on desmin PTMs and their implication in biological processes and pathologies, and discuss the current knowledge on the regulation of the desmin network by PTMs. We conclude that the desmin filament network can be seen as an intricate scaffold for muscle cell structure and biological processes and that its dynamics can be affected by PTMs. There are now precise tools to investigate PTMs and visualize cellular structures that have been underexploited in the study of desminopathies. Future studies should focus on these aspects.

Do two machine-learning based prognostic signatures for breast cancer capture the same biological processes?

Science.gov (United States)

Drier, Yotam; Domany, Eytan

2011-03-14

The fact that there is very little if any overlap between the genes of different prognostic signatures for early-discovery breast cancer is well documented. The reasons for this apparent discrepancy have been explained by the limits of simple machine-learning identification and ranking techniques, and the biological relevance and meaning of the prognostic gene lists was questioned. Subsequently, proponents of the prognostic gene lists claimed that different lists do capture similar underlying biological processes and pathways. The present study places under scrutiny the validity of this claim, for two important gene lists that are at the focus of current large-scale validation efforts. We performed careful enrichment analysis, controlling the effects of multiple testing in a manner which takes into account the nested dependent structure of gene ontologies. In contradiction to several previous publications, we find that the only biological process or pathway for which statistically significant concordance can be claimed is cell proliferation, a process whose relevance and prognostic value was well known long before gene expression profiling. We found that the claims reported by others, of wider concordance between the biological processes captured by the two prognostic signatures studied, were found either to be lacking statistical rigor or were in fact based on addressing some other question.

Do two machine-learning based prognostic signatures for breast cancer capture the same biological processes?

Directory of Open Access Journals (Sweden)

Yotam Drier

2011-03-01

Full Text Available The fact that there is very little if any overlap between the genes of different prognostic signatures for early-discovery breast cancer is well documented. The reasons for this apparent discrepancy have been explained by the limits of simple machine-learning identification and ranking techniques, and the biological relevance and meaning of the prognostic gene lists was questioned. Subsequently, proponents of the prognostic gene lists claimed that different lists do capture similar underlying biological processes and pathways. The present study places under scrutiny the validity of this claim, for two important gene lists that are at the focus of current large-scale validation efforts. We performed careful enrichment analysis, controlling the effects of multiple testing in a manner which takes into account the nested dependent structure of gene ontologies. In contradiction to several previous publications, we find that the only biological process or pathway for which statistically significant concordance can be claimed is cell proliferation, a process whose relevance and prognostic value was well known long before gene expression profiling. We found that the claims reported by others, of wider concordance between the biological processes captured by the two prognostic signatures studied, were found either to be lacking statistical rigor or were in fact based on addressing some other question.

Review on Physicochemical, Chemical, and Biological Processes for Pharmaceutical Wastewater

Science.gov (United States)

Li, Zhenchen; Yang, Ping

2018-02-01

Due to the needs of human life and health, pharmaceutical industry has made great progress in recent years, but it has also brought about severe environmental problems. The presence of pharmaceuticals in natural waters which might pose potential harm to the ecosystems and humans raised increasing concern worldwide. Pharmaceuticals cannot be effectively removed by conventional wastewater treatment plants (WWTPs) owing to the complex composition, high concentration of organic contaminants, high salinity and biological toxicity of pharmaceutical wastewater. Therefore, the development of efficient methods is needed to improve the removal effect of pharmaceuticals. This review provides an overview on three types of treatment technologies including physicochemical, chemical and biological processes and their advantages and disadvantages respectively. In addition, the future perspectives of pharmaceutical wastewater treatment are given.

The relativity of biological function.

Science.gov (United States)

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

2015-12-01

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

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

Science.gov (United States)

van Boxtel, Jeroen J A; Lu, Hongjing

2013-01-01

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

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

Directory of Open Access Journals (Sweden)

Jeroen J A Van Boxtel

2013-04-01

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

Wavelet data processing of micro-Raman spectra of biological samples

Science.gov (United States)

Camerlingo, C.; Zenone, F.; Gaeta, G. M.; Riccio, R.; Lepore, M.

2006-02-01

A wavelet multi-component decomposition algorithm is proposed for processing data from micro-Raman spectroscopy (μ-RS) of biological tissue. The μ-RS has been recently recognized as a promising tool for the biopsy test and in vivo diagnosis of degenerative human tissue pathologies, due to the high chemical and structural information contents of this spectroscopic technique. However, measurements of biological tissues are usually hampered by typically low-level signals and by the presence of noise and background components caused by light diffusion or fluorescence processes. In order to overcome these problems, a numerical method based on discrete wavelet transform is used for the analysis of data from μ-RS measurements performed in vitro on animal (pig and chicken) tissue samples and, in a preliminary form, on human skin and oral tissue biopsy from normal subjects. Visible light μ-RS was performed using a He-Ne laser and a monochromator with a liquid nitrogen cooled charge coupled device equipped with a grating of 1800 grooves mm-1. The validity of the proposed data procedure has been tested on the well-characterized Raman spectra of reference acetylsalicylic acid samples.

Describing long-range charge-separation processes with subsystem density-functional theory

Energy Technology Data Exchange (ETDEWEB)

Solovyeva, Alisa; Neugebauer, Johannes, E-mail: j.neugebauer@uni-muenster.de [Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Simulation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster (Germany); Pavanello, Michele, E-mail: m.pavanello@rutgers.edu [Department of Chemistry, Rutgers University, 73 Warren St., Newark, New Jersey 07102 (United States)

2014-04-28

Long-range charge-transfer processes in extended systems are difficult to describe with quantum chemical methods. In particular, cost-effective (non-hybrid) approximations within time-dependent density functional theory (DFT) are not applicable unless special precautions are taken. Here, we show that the efficient subsystem DFT can be employed as a constrained DFT variant to describe the energetics of long-range charge-separation processes. A formal analysis of the energy components in subsystem DFT for such excitation energies is presented, which demonstrates that both the distance dependence and the long-range limit are correctly described. In addition, electronic couplings for these processes as needed for rate constants in Marcus theory can be obtained from this method. It is shown that the electronic structure of charge-separated states constructed by a positively charged subsystem interacting with a negatively charged one is difficult to converge — charge leaking from the negative subsystem to the positive one can occur. This problem is related to the delocalization error in DFT and can be overcome with asymptotically correct exchange–correlation (XC) potentials or XC potentials including a sufficiently large amount of exact exchange. We also outline an approximate way to obtain charge-transfer couplings between locally excited and charge-separated states.

Describing long-range charge-separation processes with subsystem density-functional theory

International Nuclear Information System (INIS)

Solovyeva, Alisa; Neugebauer, Johannes; Pavanello, Michele

2014-01-01

Long-range charge-transfer processes in extended systems are difficult to describe with quantum chemical methods. In particular, cost-effective (non-hybrid) approximations within time-dependent density functional theory (DFT) are not applicable unless special precautions are taken. Here, we show that the efficient subsystem DFT can be employed as a constrained DFT variant to describe the energetics of long-range charge-separation processes. A formal analysis of the energy components in subsystem DFT for such excitation energies is presented, which demonstrates that both the distance dependence and the long-range limit are correctly described. In addition, electronic couplings for these processes as needed for rate constants in Marcus theory can be obtained from this method. It is shown that the electronic structure of charge-separated states constructed by a positively charged subsystem interacting with a negatively charged one is difficult to converge — charge leaking from the negative subsystem to the positive one can occur. This problem is related to the delocalization error in DFT and can be overcome with asymptotically correct exchange–correlation (XC) potentials or XC potentials including a sufficiently large amount of exact exchange. We also outline an approximate way to obtain charge-transfer couplings between locally excited and charge-separated states

Single amino acid substitution in important hemoglobinopathies does not disturb molecular function and biological process

Directory of Open Access Journals (Sweden)

Viroj Wiwanitkit

2008-06-01

Full Text Available Viroj WiwanitkitDepartment of Laboratory Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, ThailandAbstract: Hemoglobin is an important protein found in the red cells of many animals. In humans, the hemoglobin is mainly distributed in the red blood cell. Single amino acid substitution is the main pathogenesis of most hemoglobin disorders. Here, the author used a new gene ontology technology to predict the molecular function and biological process of four important hemoglobin disorders with single substitution. The four studied important abnormal hemoglobins (Hb with single substitution included Hb S, Hb E, Hb C, and Hb J-Baltimore. Using the GoFigure server, the molecular function and biological process in normal and abnormal hemoglobins was predicted. Compared with normal hemoglobin, all studied abnormal hemoglobins had the same function and biological process. This indicated that the overall function of oxygen transportation is not disturbed in the studied hemoglobin disorders. Clinical findings of oxygen depletion in abnormal hemoglobin should therefore be due to the other processes rather than genomics, proteomics, and expression levels.Keywords: hemoglobin, amino acid, substitution, function

Adoption: biological and social processes linked to adaptation.

Science.gov (United States)

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.

Development trend of radiation biology research-systems radiation biology

International Nuclear Information System (INIS)

Min Rui

2010-01-01

Radiation biology research has past 80 years. We have known much more about fundamentals, processes and results of biology effects induced by radiation and various factors that influence biology effects wide and deep, however many old and new scientific problems occurring in the field of radiation biology research remain to be illustrated. To explore and figure these scientific problems need systemic concept, methods and multi dimension view on the base of considerations of complexity of biology system, diversity of biology response, temporal and spatial process of biological effects during occurrence, and complex feed back network of biological regulations. (authors)

A Population Biology Perspective on the Stepwise Infection Process of the Bacterial Pathogen Pasteuria ramosa in Daphnia.

Science.gov (United States)

Ebert, Dieter; Duneau, David; Hall, Matthew D; Luijckx, Pepijn; Andras, Jason P; Du Pasquier, Louis; Ben-Ami, Frida

2016-01-01

The infection process of many diseases can be divided into series of steps, each one required to successfully complete the parasite's life and transmission cycle. This approach often reveals that the complex phenomenon of infection is composed of a series of more simple mechanisms. Here we demonstrate that a population biology approach, which takes into consideration the natural genetic and environmental variation at each step, can greatly aid our understanding of the evolutionary processes shaping disease traits. We focus in this review on the biology of the bacterial parasite Pasteuria ramosa and its aquatic crustacean host Daphnia, a model system for the evolutionary ecology of infectious disease. Our analysis reveals tremendous differences in the degree to which the environment, host genetics, parasite genetics and their interactions contribute to the expression of disease traits at each of seven different steps. This allows us to predict which steps may respond most readily to selection and which steps are evolutionarily constrained by an absence of variation. We show that the ability of Pasteuria to attach to the host's cuticle (attachment step) stands out as being strongly influenced by the interaction of host and parasite genotypes, but not by environmental factors, making it the prime candidate for coevolutionary interactions. Furthermore, the stepwise approach helps us understanding the evolution of resistance, virulence and host ranges. The population biological approach introduced here is a versatile tool that can be easily transferred to other systems of infectious disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nonequilibrium thermodynamics transport and rate processes in physical, chemical and biological systems

CERN Document Server

Demirel, Yasar

2014-01-01

Natural phenomena consist of simultaneously occurring transport processes and chemical reactions. These processes may interact with each other and may lead to self-organized structures, fluctuations, instabilities, and evolutionary systems. Nonequilibrium Thermodynamics, 3rd edition emphasizes the unifying role of thermodynamics in analyzing the natural phenomena. This third edition updates and expands on the first and second editions by focusing on the general balance equations for coupled processes of physical, chemical, and biological systems. The new edition contains a new chapte

Radiation biology for the non-biologist

International Nuclear Information System (INIS)

Myers, D.K.

1978-06-01

This colloquium introduces some of the general concepts used in cell biology and in the study of the effects of ionizing radiation on living organisms. The present research activities in radiation biology in the Biology Branch at the Chalk River Nuclear Laboratories cover a broad range of interests in the entire chain of events by which the initial radiation-induced changes in the living cell are translated into significant biological effects, including the eventual production of cancers and hereditary defects. The main theme of these research activities is an understanding of the mechanisms by which radiation damage to DNA (the carrier of hereditary information in all living organisms) can be actively repaired by the living cell. Advances in our understanding of these processes have broad implications for other areas of biology but also bear directly on the assessment of the biological hazards of ionizing radiation. The colloquium concludes with a brief discussion of the hazards of low-level radiation. (author)

Fixation and utilization of CO2 by biological and/or chemical processes

International Nuclear Information System (INIS)

Hiromichi, N.

1994-01-01

This paper presents the carbon dioxide fixation and utilisation by biological and/or chemical processes. It presents research objectives and program contents for the effective fixation of carbon dioxide by micro-organism and its hydrogenation. (TEC). 5 figs., 2 tabs

Howard Brenner's Legacy for Biological Transport Processes

Science.gov (United States)

Nitsche, Johannes

2014-11-01

This talk discusses the manner in which Howard Brenner's theoretical contributions have had, and long will have, strong and direct impact on the understanding of transport processes occurring in biological systems. His early work on low Reynolds number resistance/mobility coefficients of arbitrarily shaped particles, and particles near walls and in pores, is an essential component of models of hindered diffusion through many types of membranes and tissues, and convective transport in microfluidic diagnostic systems. His seminal contributions to macrotransport (coarse-graining, homogenization) theory presaged the growing discipline of multiscale modeling. For biological systems they represent the key to infusing diffusion models of a wide variety of tissues with a sound basis in their microscopic structure and properties, often over a hierarchy of scales. Both scientific currents are illustrated within the concrete context of diffusion models of drug/chemical diffusion through the skin. This area of theory, which is key to transdermal drug development and risk assessment of chemical exposure, has benefitted very directly from Brenner's contributions. In this as in other areas, Brenner's physicochemical insight, mathematical virtuosity, drive for fully justified analysis free of ad hoc assumptions, quest for generality, and impeccable exposition, have consistently elevated the level of theoretical understanding and presentation. We close with anecdotes showing how his personal qualities and warmth helped to impart high standards of rigor to generations of grateful research students. Authors are Johannes M. Nitsche, Ludwig C. Nitsche and Gerald B. Kasting.

Natural physical and biological processes compromise the long-term performance of compacted soil caps

International Nuclear Information System (INIS)

Smith, E.D.

1995-01-01

Compacted soil barriers are components of essentially all caps placed on closed waste disposal sites. The intended functions of soil barriers in waste facility caps include restricting infiltration of water and release of gases and vapors, either independently or in combination with synthetic membrane barriers, and protecting other manmade or natural barrier components. Review of the performance of installed soil barriers and of natural processes affecting their performance indicates that compacted soil caps may function effectively for relatively short periods (years to decades), but natural physical and biological processes can be expected to cause them to fail in the long term (decades to centuries). This paper addresses natural physical and biological processes that compromise the performance of compacted soil caps and suggests measures that may reduce the adverse consequences of these natural failure mechanisms

Efficient Long - Range Electron Transfer Processes in Polyfluorene – Perylene Diimide Blends

KAUST Repository

Isakova, Anna

2018-05-17

In bulk heterojunction donor-acceptor (D-A) blends, high photovoltaic yields require charge carrier separation to outcompete geminate recombination. Recently, evidence for long-range electron transfer mechanisms has been presented, avoiding strongly-bound interfacial charge transfer (CT) states. However, due to the lack of specific optical probes at the D-A interface, a detailed quantification of the long-range processes has not been feasible, until now. Here, we present a transient absorption study of long-range processes in a unique phase consisting of perylene diimide (PDI) crystals intercalated with polyfluorene (PFO), as widely used non-fullerene electron acceptor and donor, respectively. The intercalated PDI:PFO phase possesses specific well-separated spectral features for the excited states at the D-A interface. By use of femtosecond spectroscopy we reveal the excitation dynamics in this blend. PDI excitons undergo a clear symmetry-breaking charge separation in the PDI bulk, which occurs within several hundred femtoseconds, thus outcompeting excimer formation, known to limit charge separation yields when PDI is used as an acceptor. In contrast, PFO excitons are dissociated with very high yields in a one-step long-range process, enabled by large delocalization of the PFO exciton wavefunction. Moreover, both scenarios circumvent the formation of strongly-bound interfacial CT states and enable a targeted interfacial design for bulk heterojunction blends with near unity charge separation yields.

Efficient Long - Range Electron Transfer Processes in Polyfluorene – Perylene Diimide Blends

KAUST Repository

Isakova, Anna; Karuthedath, Safakath; Arnold, Thomas; Howse, Jonathan; Topham, Paul D.; Toolan, Daniel Thomas William; Laquai, Fré dé ric; Lü er, Larry

2018-01-01

In bulk heterojunction donor-acceptor (D-A) blends, high photovoltaic yields require charge carrier separation to outcompete geminate recombination. Recently, evidence for long-range electron transfer mechanisms has been presented, avoiding strongly-bound interfacial charge transfer (CT) states. However, due to the lack of specific optical probes at the D-A interface, a detailed quantification of the long-range processes has not been feasible, until now. Here, we present a transient absorption study of long-range processes in a unique phase consisting of perylene diimide (PDI) crystals intercalated with polyfluorene (PFO), as widely used non-fullerene electron acceptor and donor, respectively. The intercalated PDI:PFO phase possesses specific well-separated spectral features for the excited states at the D-A interface. By use of femtosecond spectroscopy we reveal the excitation dynamics in this blend. PDI excitons undergo a clear symmetry-breaking charge separation in the PDI bulk, which occurs within several hundred femtoseconds, thus outcompeting excimer formation, known to limit charge separation yields when PDI is used as an acceptor. In contrast, PFO excitons are dissociated with very high yields in a one-step long-range process, enabled by large delocalization of the PFO exciton wavefunction. Moreover, both scenarios circumvent the formation of strongly-bound interfacial CT states and enable a targeted interfacial design for bulk heterojunction blends with near unity charge separation yields.

Mixing and Processing of Complex Biological Fluids

National Research Council Canada - National Science Library

Liepmann, Dorian

2003-01-01

... of microfluidic control on the makeup and molecular structure of biological fluids. For this project, we focused on two critical fluids that are biologically significant and that are of critical importance to DoD...

A finite element simulation of biological conversion processes in landfills

International Nuclear Information System (INIS)

Robeck, M.; Ricken, T.; Widmann, R.

2011-01-01

Landfills are the most common way of waste disposal worldwide. Biological processes convert the organic material into an environmentally harmful landfill gas, which has an impact on the greenhouse effect. After the depositing of waste has been stopped, current conversion processes continue and emissions last for several decades and even up to 100 years and longer. A good prediction of these processes is of high importance for landfill operators as well as for authorities, but suitable models for a realistic description of landfill processes are rather poor. In order to take the strong coupled conversion processes into account, a constitutive three-dimensional model based on the multiphase Theory of Porous Media (TPM) has been developed at the University of Duisburg-Essen. The theoretical formulations are implemented in the finite element code FEAP. With the presented calculation concept we are able to simulate the coupled processes that occur in an actual landfill. The model's theoretical background and the results of the simulations as well as the meantime successfully performed simulation of a real landfill body will be shown in the following.

Controlled Carbon Source Addition to an Alternating Nitrification-Denitrification Wastewater Treatment Process Including Biological P Removal

DEFF Research Database (Denmark)

Isaacs, Steven Howard; Henze, Mogens

1995-01-01

The paper investigates the effect of adding an external carbon source on the rate of denitrification in an alternating activated sludge process including biological P removal. Two carbon sources were examined, acetate and hydrolysate derived from biologically hydrolyzed sludge. Preliminary batch ...

Mind the gap: non-biological processes contributing to soil CO2 efflux.

Science.gov (United States)

Rey, Ana

2015-05-01

Widespread recognition of the importance of soil CO2 efflux as a major source of CO2 to the atmosphere has led to active research. A large soil respiration database and recent reviews have compiled data, methods, and current challenges. This study highlights some deficiencies for a proper understanding of soil CO2 efflux focusing on processes of soil CO2 production and transport that have not received enough attention in the current soil respiration literature. It has mostly been assumed that soil CO2 efflux is the result of biological processes (i.e. soil respiration), but recent studies demonstrate that pedochemical and geological processes, such as geothermal and volcanic CO2 degassing, are potentially important in some areas. Besides the microbial decomposition of litter, solar radiation is responsible for photodegradation or photochemical degradation of litter. Diffusion is considered to be the main mechanism of CO2 transport in the soil, but changes in atmospheric pressure and thermal convection may also be important mechanisms driving soil CO2 efflux greater than diffusion under certain conditions. Lateral fluxes of carbon as dissolved organic and inorganic carbon occur and may cause an underestimation of soil CO2 efflux. Traditionally soil CO2 efflux has been measured with accumulation chambers assuming that the main transport mechanism is diffusion. New techniques are available such as improved automated chambers, CO2 concentration profiles and isotopic techniques that may help to elucidate the sources of carbon from soils. We need to develop specific and standardized methods for different CO2 sources to quantify this flux on a global scale. Biogeochemical models should include biological and non-biological CO2 production processes before we can predict the response of soil CO2 efflux to climate change. Improving our understanding of the processes involved in soil CO2 efflux should be a research priority given the importance of this flux in the global

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

Science.gov (United States)

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

2016-01-01

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

Investigation of the Nature of Metaconceptual Processes of Pre-Service Biology Teachers

Science.gov (United States)

Yuruk, Nejla; Selvi, Meryem; Yakisan, Mehmet

2017-01-01

Purpose of Study: The aim of this study is to investigate the nature of pre-service biology teachers' metaconceptual processes that were active as they participated in metaconceptual teaching activities. Methods: Several instructional activities, including poster drawing, concept mapping, group and class discussions, and journal writing, were…

Biological Potential in Serpentinizing Systems

Science.gov (United States)

Hoehler, Tori M.

2016-01-01

Generation of the microbial substrate hydrogen during serpentinization, the aqueous alteration of ultramafic rocks, has focused interest on the potential of serpentinizing systems to support biological communities or even the origin of life. However the process also generates considerable alkalinity, a challenge to life, and both pH and hydrogen concentrations vary widely across natural systems as a result of different host rock and fluid composition and differing physical and hydrogeologic conditions. Biological potential is expected to vary in concert. We examined the impact of such variability on the bioenergetics of an example metabolism, methanogenesis, using a cell-scale reactive transport model to compare rates of metabolic energy generation as a function of physicochemical environment. Potential rates vary over more than 5 orders of magnitude, including bioenergetically non-viable conditions, across the range of naturally occurring conditions. In parallel, we assayed rates of hydrogen metabolism in wells associated with the actively serpentinizing Coast Range Ophiolite, which includes conditions more alkaline and considerably less reducing than is typical of serpentinizing systems. Hydrogen metabolism is observed at pH approaching 12 but, consistent with the model predictions, biological methanogenesis is not observed.

Characteristic responses of biological and nanoscale systems in the terahertz frequency range

Energy Technology Data Exchange (ETDEWEB)

Angeluts, A A; Balakin, A V; Evdokimov, M G; Ozheredov, I A; Sapozhnikov, D A; Solyankin, P M; Shkurinov, A P [International Laser Center, M. V. Lomonosov Moscow State University, Moscow (Russian Federation); Esaulkov, M N; Nazarov, M M [Institute on Laser and Information Technologies, Russian Academy of Sciences, Shatura, Moscow Region (Russian Federation); Cherkasova, O P [Institute of Laser Physics, Siberian Branch, Russian Academy of Sciences, Novosibirsk (Russian Federation)

2014-07-31

This paper briefly examines methods for the generation of pulsed terahertz radiation and principles of pulsed terahertz spectroscopy, an advanced informative method for studies of complex biological and nanostructured systems. Some of its practical applications are described. Using a number of steroid hormones as examples, we demonstrate that terahertz spectroscopy in combination with molecular dynamics methods and computer simulation allows one to gain information about the structure of molecules in crystals. A 'terahertz colour vision' method is proposed for analysis of pulsed terahertz signals reflected from biological tissues and it is shown that this method can be effectively used to analyse the properties of biological tissues and for early skin cancer diagnosis. (laser biophotonics)

Finding biological process modifications in cancer tissues by mining gene expression correlations

Directory of Open Access Journals (Sweden)

Storari Sergio

2006-01-01

Full Text Available Abstract Background Through the use of DNA microarrays it is now possible to obtain quantitative measurements of the expression of thousands of genes from a biological sample. This technology yields a global view of gene expression that can be used in several ways. Functional insight into expression profiles is routinely obtained by using Gene Ontology terms associated to the cellular genes. In this paper, we deal with functional data mining from expression profiles, proposing a novel approach that studies the correlations between genes and their relations to Gene Ontology (GO. By using this "functional correlations comparison" we explore all possible pairs of genes identifying the affected biological processes by analyzing in a pair-wise manner gene expression patterns and linking correlated pairs with Gene Ontology terms. Results We apply here this "functional correlations comparison" approach to identify the existing correlations in hepatocarcinoma (161 microarray experiments and to reveal functional differences between normal liver and cancer tissues. The number of well-correlated pairs in each GO term highlights several differences in genetic interactions between cancer and normal tissues. We performed a bootstrap analysis in order to compute false detection rates (FDR and confidence limits. Conclusion Experimental results show the main advantage of the applied method: it both picks up general and specific GO terms (in particular it shows a fine resolution in the specific GO terms. The results obtained by this novel method are highly coherent with the ones proposed by other cancer biology studies. But additionally they highlight the most specific and interesting GO terms helping the biologist to focus his/her studies on the most relevant biological processes.

Modelling biological processes in WWTP; Modelado de procesos biologicos en las EDAR

Energy Technology Data Exchange (ETDEWEB)

Carpes, G.

2009-07-01

Biological technologies by active sludges are the most used in wastewater treatments. Multiple variants are affected in the characterization of this process, like wastewater treatment plant (WWTP) design, features and concentration of sludge, dissolved oxygen concentration and characteristics of the wastewater, including temperature and nutrients. Mathematical formula applied to WWTP modelling are presented to design its operation and to test the most important parameters, too. It is necessary to optimize the process in WWTP. (Author) 19 refs.

Chemical and Biological Defense: DOD Needs Consistent Policies and Clear Processes to Address the Survivability of Weapon Systems Against Chemical and Biological Threats

National Research Council Canada - National Science Library

2006-01-01

DOD, joint, and military service weapon system acquisition policies inconsistently address and do not establish a clear process for considering and testing system chemical and biological survivability...

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

Science.gov (United States)

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

2008-01-01

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

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

Science.gov (United States)

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

2009-01-01

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

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

Science.gov (United States)

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

2015-01-01

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

Quantum Processes and Dynamic Networks in Physical and Biological Systems.

Science.gov (United States)

Dudziak, Martin Joseph

Quantum theory since its earliest formulations in the Copenhagen Interpretation has been difficult to integrate with general relativity and with classical Newtonian physics. There has been traditionally a regard for quantum phenomena as being a limiting case for a natural order that is fundamentally classical except for microscopic extrema where quantum mechanics must be applied, more as a mathematical reconciliation rather than as a description and explanation. Macroscopic sciences including the study of biological neural networks, cellular energy transports and the broad field of non-linear and chaotic systems point to a quantum dimension extending across all scales of measurement and encompassing all of Nature as a fundamentally quantum universe. Theory and observation lead to a number of hypotheses all of which point to dynamic, evolving networks of fundamental or elementary processes as the underlying logico-physical structure (manifestation) in Nature and a strongly quantized dimension to macroscalar processes such as are found in biological, ecological and social systems. The fundamental thesis advanced and presented herein is that quantum phenomena may be the direct consequence of a universe built not from objects and substance but from interacting, interdependent processes collectively operating as sets and networks, giving rise to systems that on microcosmic or macroscopic scales function wholistically and organically, exhibiting non-locality and other non -classical phenomena. The argument is made that such effects as non-locality are not aberrations or departures from the norm but ordinary consequences of the process-network dynamics of Nature. Quantum processes are taken to be the fundamental action-events within Nature; rather than being the exception quantum theory is the rule. The argument is also presented that the study of quantum physics could benefit from the study of selective higher-scale complex systems, such as neural processes in the brain

Molecular comparison of cattle fever ticks from native and introduced ranges with insights into optimal search areas for classical biological control agents

Science.gov (United States)

Classical biological control using specialist parasitoids, predators and/or nematodes from the native ranges of cattle fever ticks could complement existing control strategies for this livestock pest in the transboundary region between Mexico and Texas. DNA fingerprinting tools were used to compare ...

A finite element simulation of biological conversion processes in landfills.

Science.gov (United States)

Robeck, M; Ricken, T; Widmann, R

2011-04-01

Landfills are the most common way of waste disposal worldwide. Biological processes convert the organic material into an environmentally harmful landfill gas, which has an impact on the greenhouse effect. After the depositing of waste has been stopped, current conversion processes continue and emissions last for several decades and even up to 100years and longer. A good prediction of these processes is of high importance for landfill operators as well as for authorities, but suitable models for a realistic description of landfill processes are rather poor. In order to take the strong coupled conversion processes into account, a constitutive three-dimensional model based on the multiphase Theory of Porous Media (TPM) has been developed at the University of Duisburg-Essen. The theoretical formulations are implemented in the finite element code FEAP. With the presented calculation concept we are able to simulate the coupled processes that occur in an actual landfill. The model's theoretical background and the results of the simulations as well as the meantime successfully performed simulation of a real landfill body will be shown in the following. Copyright © 2010 Elsevier Ltd. All rights reserved.

Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information

Directory of Open Access Journals (Sweden)

Lemke Ney

2009-09-01

Full Text Available Abstract Background The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for essential genes discovery are labor-intensive and time-consuming. Considering these experimental constraints, a computational approach capable of accurately predicting essential genes would be of great value. We therefore present here a machine learning-based computational approach relying on network topological features, cellular localization and biological process information for prediction of essential genes. Results We constructed a decision tree-based meta-classifier and trained it on datasets with individual and grouped attributes-network topological features, cellular compartments and biological processes-to generate various predictors of essential genes. We showed that the predictors with better performances are those generated by datasets with integrated attributes. Using the predictor with all attributes, i.e., network topological features, cellular compartments and biological processes, we obtained the best predictor of essential genes that was then used to classify yeast genes with unknown essentiality status. Finally, we generated decision trees by training the J48 algorithm on datasets with all network topological features, cellular localization and biological process information to discover cellular rules for essentiality. We found that the number of protein physical interactions, the nuclear localization of proteins and the number of regulating transcription factors are the most important factors determining gene essentiality. Conclusion We were able to demonstrate that network topological features, cellular localization and biological process information are reliable predictors of essential genes. Moreover, by constructing decision trees based on these data, we could discover cellular rules governing

Australian Biology Test Item Bank, Years 11 and 12. Volume II: Year 12.

Science.gov (United States)

Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

Australian Biology Test Item Bank, Years 11 and 12. Volume I: Year 11.

Science.gov (United States)

Brown, David W., Ed.; Sewell, Jeffrey J., Ed.

This document consists of test items which are applicable to biology courses throughout Australia (irrespective of course materials used); assess key concepts within course statement (for both core and optional studies); assess a wide range of cognitive processes; and are relevant to current biological concepts. These items are arranged under…

Thermal and biological gasification

Energy Technology Data Exchange (ETDEWEB)

Overend, R.P.; Rivard, C.J. [National Renewable Energy Lab., Golden, CO (United States)

1993-12-31

Gasification is being developed to enable a diverse range of biomass resources to meet modern secondary energy uses, especially in the electrical utility sector. Biological or anaerobic gasification in US landfills has resulted in the installation of almost 500 MW(e) of capacity and represents the largest scale application of gasification technology today. The development of integrated gasification combined cycle generation for coal technologies is being paralleled by bagasse and wood thermal gasification systems in Hawaii and Scandinavia, and will lead to significant deployment in the next decade as the current scale-up activities are commercialized. The advantages of highly reactive biomass over coal in the design of process units are being realized as new thermal gasifiers are being scaled up to produce medium-energy-content gas for conversion to synthetic natural gas and transportation fuels and to hydrogen for use in fuel cells. The advent of high solids anaerobic digestion reactors is leading to commercialization of controlled municipal solid waste biological gasification rather than landfill application. In both thermal and biological gasification, high rate process reactors are a necessary development for economic applications that address waste and residue management and the production and use of new crops for energy. The environmental contribution of biomass in reducing greenhouse gas emission will also be improved.

The mathematics and mechanics of biological growth

CERN Document Server

Goriely, Alain

2017-01-01

This monograph presents a general mechanical theory for biological growth. It provides both a conceptual and a technical foundation for the understanding and analysis of problems arising in biology and physiology. The theory and methods is illustrated on a wide range of examples and applications. A process of extreme complexity, growth plays a fundamental role in many biological processes and is considered to be the hallmark of life itself. Its description has been one of the fundamental problems of life sciences, but until recently, it has not attracted much attention from mathematicians, physicists, and engineers. The author herein presents the first major technical monograph on the problem of growth since D’Arcy Wentworth Thompson’s 1917 book On Growth and Form. The emphasis of the book is on the proper mathematical formulation of growth kinematics and mechanics. Accordingly, the discussion proceeds in order of complexity and the book is divided into five parts. First, a general introduction on the pro...

Laser apparatus and method for microscopic and spectroscopic analysis and processing of biological cells

Science.gov (United States)

Gourley, P.L.; Gourley, M.F.

1997-03-04

An apparatus and method are disclosed for microscopic and spectroscopic analysis and processing of biological cells. The apparatus comprises a laser having an analysis region within the laser cavity for containing one or more biological cells to be analyzed. The presence of a cell within the analysis region in superposition with an activated portion of a gain medium of the laser acts to encode information about the cell upon the laser beam, the cell information being recoverable by an analysis means that preferably includes an array photodetector such as a CCD camera and a spectrometer. The apparatus and method may be used to analyze biomedical cells including blood cells and the like, and may include processing means for manipulating, sorting, or eradicating cells after analysis. 20 figs.

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

Science.gov (United States)

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

2018-01-01

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

Biological desulfurisation

Energy Technology Data Exchange (ETDEWEB)

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

2001-03-01

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

Potential biological hazard of importance for HACCP plans in fresh fish processing

Directory of Open Access Journals (Sweden)

Baltić Milan Ž.

2009-01-01

Full Text Available The Hazard Analysis and Critical Control Point (HACCP system is scientifically based and focused on problem prevention in order to assure the produced food products are safe to consume. Prerequisite programs such as GMP (Good Manufacturing Practices, GHP (Good Hygienic Practices are an essential foundation for the development and implementation of successful HACCP plans. One of the preliminary tasks in the development of HACCP plan is to conduct a hazard analysis. The process of conducting a hazard analysis involves two stages. The first is hazard identification and the second stage is the HACCP team decision which potential hazards must be addressed in the HACCP plan. By definition, the HACCP concept covers all types of potential food safety hazards: biological, chemical and physical, whether they are naturally occurring in the food, contributed by the environment or generated by a mistake in the manufacturing process. In raw fish processing, potential significant biological hazards which are reasonably likely to cause illness of humans are parasites (Trematodae, Nematodae, Cestodae, bacteria (Salmonella, E. coli, Vibrio parahemolyticus, Vibrio vulnificus, Listeria monocytogenes, Clostridium botulinum, Staphyloccocus aureus, viruses (Norwalk virus, Entero virusesi, Hepatitis A, Rotovirus and bio-toxins. Upon completion of hazard analysis, any measure(s that are used to control the hazard(s should be described.

Innovative biological systems for anaerobic treatment of grain and food processing wastewaters

Energy Technology Data Exchange (ETDEWEB)

Sutton, P M

1986-09-01

The application of two innovative fixed film and suspended growth anaerobic biological systems to the treatment of grain and food processing wastewaters is discussed. A fluidized bed fixed film system and a suspended growth membrane system are described. The technical and economic factors dictating which system is selected for treatment of a specific industrial wastewater are discussed. Case history results from successful operation of full-scale, demonstration, and pilot-scale systems treating respectively, soy whey, cheese whey, and wheat flour processing wastewaters are presented.

Spies and Bloggers: New Synthetic Biology Tools to Understand Microbial Processes in Soils and Sediments

Science.gov (United States)

Masiello, C. A.; Silberg, J. J.; Cheng, H. Y.; Del Valle, I.; Fulk, E. M.; Gao, X.; Bennett, G. N.

2017-12-01

Microbes can be programmed through synthetic biology to report on their behavior, informing researchers when their environment has triggered changes in their gene expression (e.g. in response to shifts in O2 or H2O), or when they have participated in a specific step of an elemental cycle (e.g. denitrification). This use of synthetic biology has the potential to significantly improve our understanding of microbes' roles in elemental and water cycling, because it allows reporting on the environment from the perspective of a microbe, matching the measurement scale exactly to the scale that a microbe experiences. However, synthetic microbes have not yet seen wide use in soil and sediment laboratory experiments because synthetic organisms typically report by fluorescing, making their signals difficult to detect outside the petri dish. We are developing a new suite of microbial programs that report instead by releasing easily-detected gases, allowing the real-time, noninvasive monitoring of behaviors in sediments and soils. Microbial biosensors can, in theory, be programmed to detect dynamic processes that contribute to a wide range of geobiological processes, including C cycling (biofilm production, methanogenesis, and synthesis of extracellular enzymes that degrade organic matter), N cycling (expression of enzymes that underlie different steps of the N cycle) and potentially S cycling. We will provide an overview of the potential uses of gas-reporting biosensors in soil and sediment lab experiments, and will report the development of the systematics of these sensors. Successful development of gas biosensors for laboratory use will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise ratio; normalizing the gas reporter signal to cell population size, managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel.

Computer-Based Support of Decision Making Processes during Biological Incidents

Directory of Open Access Journals (Sweden)

Karel Antos

2010-04-01

Full Text Available The paper describes contextual analysis of a general system that should provide a computerized support of decision making processes related to response operations in case of a biological incident. This analysis is focused on information systems and information resources perspective and their integration using appropriate tools and technology. In the contextual design the basic modules of BioDSS system are suggested and further elaborated. The modules deal with incident description, scenarios development and recommendation of appropriate countermeasures. Proposals for further research are also included.

Continuous downstream processing for high value biological products: A Review.

Science.gov (United States)

Zydney, Andrew L

2016-03-01

There is growing interest in the possibility of developing truly continuous processes for the large-scale production of high value biological products. Continuous processing has the potential to provide significant reductions in cost and facility size while improving product quality and facilitating the design of flexible multi-product manufacturing facilities. This paper reviews the current state-of-the-art in separations technology suitable for continuous downstream bioprocessing, focusing on unit operations that would be most appropriate for the production of secreted proteins like monoclonal antibodies. This includes cell separation/recycle from the perfusion bioreactor, initial product recovery (capture), product purification (polishing), and formulation. Of particular importance are the available options, and alternatives, for continuous chromatographic separations. Although there are still significant challenges in developing integrated continuous bioprocesses, recent technological advances have provided process developers with a number of attractive options for development of truly continuous bioprocessing operations. © 2015 Wiley Periodicals, Inc.

Stochasticity in processes fundamentals and applications to chemistry and biology

CERN Document Server

Schuster, Peter

2016-01-01

This book has developed over the past fifteen years from a modern course on stochastic chemical kinetics for graduate students in physics, chemistry and biology. The first part presents a systematic collection of the mathematical background material needed to understand probability, statistics, and stochastic processes as a prerequisite for the increasingly challenging practical applications in chemistry and the life sciences examined in the second part. Recent advances in the development of new techniques and in the resolution of conventional experiments at nano-scales have been tremendous: today molecular spectroscopy can provide insights into processes down to scales at which current theories at the interface of physics, chemistry and the life sciences cannot be successful without a firm grasp of randomness and its sources. Routinely measured data is now sufficiently accurate to allow the direct recording of fluctuations. As a result, the sampling of data and the modeling of relevant processes are doomed t...

Influence of Technological Processes on Biologically Active Compounds of Produced Grapes Juices

Czech Academy of Sciences Publication Activity Database

Tříska, Jan; Balík, J.; Strohalm, J.; Novotná, P.; Vrchotová, Naděžda; Lefnerová, D.; Landfeld, A.; Híc, P.; Tománková, E.; Veverka, J.; Houška, M.

2016-01-01

Roč. 9, č. 3 (2016), s. 421-429 ISSN 1935-5130 R&D Projects: GA MŠk(CZ) LO1415; GA MZe QJ1210258; GA MZe QI91B094 Institutional support: RVO:67179843 Keywords : Grapevine juices * Thermomaceration * Biologically active compounds * Antioxidative capacity * Total polyphenols * Antimutagenic activity Subject RIV: GM - Food Processing Impact factor: 2.576, year: 2016

Biological removal of metal ions from aqueous process streams

International Nuclear Information System (INIS)

Shumate, S.E. II; Strandberg, G.W.; Parrott, J.R. Jr.

1978-01-01

Aqueous waste streams from nuclear fuel processing operations may contain trace quantities of heavy metals such as uranium. Conventional chemical and physical treatment may be ineffective or very expensive when uranium concentrations in the range of 10 to 100 g/m 3 must be reduced to 1 g/m 3 or less. The ability of some microorganisms to adsorb or complex dissolved heavy metals offers an alternative treatment method. Uranium uptake by Saccharomyces cerevisiae NRRL Y-2574 and a strain of Pseudomonas aeruginosa was examined to identify factors which might affect a process for the removal of uranium from wastewater streams. At uranium concentrations in the range of 10 to 500 g/m 3 , where the binding capacity of the biomass was not exceeded, temperature, pH, and initial uranium concentration were found to influence the rate of uranium uptake, but not the soluble uranium concentration at equilibrium. 6 figs

Charge equilibrium processes of energetic incident ions and their range

International Nuclear Information System (INIS)

Kawagoshi, Hiroshi; Karashima, Shosuke; Watanabe, Tsutomu.

1984-01-01

The charge state of energetic ions passing through a certain matter is varied by charge-exchange processes. A rate equation for charge fraction is given by using electron loss and capture cross sections in collision with a target atom under idealized condition. We solved the rate equation of the charge-exchange process of a single electron in a form of linear coupled differential equation. Our calcuiation for the range of ion were carried out for He, Ne and Ar ions passing through an atomic hydrogen gas target. We discuss the charge states of the projectile in relation to a local charge balance consituting a state of charge equilibrium in the target. (author)

Designing synthetic biology.

Science.gov (United States)

Agapakis, Christina M

2014-03-21

Synthetic biology is frequently defined as the application of engineering design principles to biology. Such principles are intended to streamline the practice of biological engineering, to shorten the time required to design, build, and test synthetic gene networks. This streamlining of iterative design cycles can facilitate the future construction of biological systems for a range of applications in the production of fuels, foods, materials, and medicines. The promise of these potential applications as well as the emphasis on design has prompted critical reflection on synthetic biology from design theorists and practicing designers from many fields, who can bring valuable perspectives to the discipline. While interdisciplinary connections between biologists and engineers have built synthetic biology via the science and the technology of biology, interdisciplinary collaboration with artists, designers, and social theorists can provide insight on the connections between technology and society. Such collaborations can open up new avenues and new principles for research and design, as well as shed new light on the challenging context-dependence-both biological and social-that face living technologies at many scales. This review is inspired by the session titled "Design and Synthetic Biology: Connecting People and Technology" at Synthetic Biology 6.0 and covers a range of literature on design practice in synthetic biology and beyond. Critical engagement with how design is used to shape the discipline opens up new possibilities for how we might design the future of synthetic biology.

Linear response in the nonequilibrium zero range process

International Nuclear Information System (INIS)

Maes, Christian; Salazar, Alberto

2014-01-01

We explore a number of explicit response formulæ around the boundary driven zero range process to changes in the exit and entrance rates. In such a nonequilibrium regime kinetic (and not only thermodynamic) aspects make a difference in the response. Apart from a number of formal approaches, we illustrate a general decomposition of the linear response into entropic and frenetic contributions, the latter being realized from changes in the dynamical activity at the boundaries. In particular in this way one obtains nonlinear modifications to the Green–Kubo relation. We end by bringing some general remarks about the situation where that nonequilibrium response remains given by the (equilibrium) Kubo formula such as for the density profile in the boundary driven Lorentz gas

Radiation biology using synchrotron radiation. In relation to radiation chemistry as an initial process

International Nuclear Information System (INIS)

Kobayashi, Katsumi

1995-01-01

Radiation biology using synchrotron radiation have been investigated, focusing on the mechanism of the formation of molecular damage. This paper introduces recent outcome of these studies. First, the process from imparted energy to the formation of molecular damage is outlined. The previous studies can be largely categorized as dealing with (1) biological effects of inner-shell ionization on elements composing the living body and (2) X-ray energy dependence of biological effects. Bromine and phosphorus are used as elements for the study of inner-cell ionization. In the study on lethal effects of monochromatic soft X-rays on the BrdUMP-incorporated yeast cells, Auger enhancement was found to occur. The first report on the effects of K-shell absorption of cellular phosphorus atoms has revealed that biological effects on cellular lethality and genetic changes was enhanced by 40%. Plasmid DNA and oligonucleotide have been used to study biological effects of vacuum ultraviolet rays to monochromatic soft X-ray, which makes it possible to study strand breaks. Because experimental production of energy required for the formation of double strand breaks has become possible, synchrotron radiation plays a very important role in radiation biological studies. Finally, future issues are presented. (N.K.)

A Case Study Documenting the Process by Which Biology Instructors Transition from Teacher-Centered to Learner-Centered Teaching.

Science.gov (United States)

Marbach-Ad, Gili; Hunt Rietschel, Carly

2016-01-01

In this study, we used a case study approach to obtain an in-depth understanding of the change process of two university instructors who were involved with redesigning a biology course. Given the hesitancy of many biology instructors to adopt evidence-based, learner-centered teaching methods, there is a critical need to understand how biology instructors transition from teacher-centered (i.e., lecture-based) instruction to teaching that focuses on the students. Using the innovation-decision model for change, we explored the motivation, decision-making, and reflective processes of the two instructors through two consecutive, large-enrollment biology course offerings. Our data reveal that the change process is somewhat unpredictable, requiring patience and persistence during inevitable challenges that arise for instructors and students. For example, the change process requires instructors to adopt a teacher-facilitator role as opposed to an expert role, to cover fewer course topics in greater depth, and to give students a degree of control over their own learning. Students must adjust to taking responsibility for their own learning, working collaboratively, and relinquishing the anonymity afforded by lecture-based teaching. We suggest implications for instructors wishing to change their teaching and administrators wishing to encourage adoption of learner-centered teaching at their institutions. © 2016 G. Marbach-Ad and C. H. Rietschel. 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).

Fiji: an open-source platform for biological-image analysis.

Science.gov (United States)

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

Microbiology and atmospheric processes: biological, physical and chemical characterization of aerosol particles

Directory of Open Access Journals (Sweden)

D. G. Georgakopoulos

2009-04-01

Full Text Available The interest in bioaerosols has traditionally been linked to health hazards for humans, animals and plants. However, several components of bioaerosols exhibit physical properties of great significance for cloud processes, such as ice nucleation and cloud condensation. To gain a better understanding of their influence on climate, it is therefore important to determine the composition, concentration, seasonal fluctuation, regional diversity and evolution of bioaerosols. In this paper, we will review briefly the existing techniques for detection, quantification, physical and chemical analysis of biological particles, attempting to bridge physical, chemical and biological methods for analysis of biological particles and integrate them with aerosol sampling techniques. We will also explore some emerging spectroscopy techniques for bulk and single-particle analysis that have potential for in-situ physical and chemical analysis. Lastly, we will outline open questions and further desired capabilities (e.g., in-situ, sensitive, both broad and selective, on-line, time-resolved, rapid, versatile, cost-effective techniques required prior to comprehensive understanding of chemical and physical characterization of bioaerosols.

Improving the effectiveness of detailed processing by dynamic control of processing with high sports range

Directory of Open Access Journals (Sweden)

Yu.V. Shapoval

2017-12-01

Full Text Available In this article the possibility of increasing the efficiency of the processing of parts with a diameter of up to 20 mm is analyzed, namely: vibration resistance of the cutting process at pinching due to cutting speed control in the processing, forecasting and selection of rotational frequencies, which ensure the stability of the processing system, controlling the dynamics of the process of displacement of the additional mass. The method of investigation of vibration processes during the sharpening is developed. As a result of the processing of experimental data, it was found that when an oscillatory motion is applied to the spindle rotation, the overall level of oscillation decreases, which is reflected on the quality of the treated surface. The choice of a previously known spindle rotation frequency range at which the lowest value of the oscillation amplitude of the instrument is observed in the radial direction to the detail part, allows you to increase the processing efficiency while maintaining the drawing requirements for roughness by increasing the spindle rotational speed. The combination of the node of the own forms of oscillation and the cutting zone, by dynamically controlling the fluctuations of the lathe armature due to the increase of the inertia characteristics of the machine and the reduction of the oscillation amplitude of the tool, can improve the accuracy of machining and roughness of the processed surface of the component at higher spindle speeds.

Determination of Biological Treatability Processes of Textile Wastewater and Implementation of a Fuzzy Logic Model

Directory of Open Access Journals (Sweden)

Harun Akif Kabuk

2015-01-01

Full Text Available This study investigated the biological treatability of textile wastewater. For this purpose, a membrane bioreactor (MBR was utilized for biological treatment after the ozonation process. Due to the refractory organic contents of textile wastewater that has a low biodegradability capacity, ozonation was implemented as an advanced oxidation process prior to the MBR system to increase the biodegradability of the wastewater. Textile wastewater, oxidized by ozonation, was fed to the MBR at different hydraulic retention times (HRT. During the process, color, chemical oxygen demand (COD, and biochemical oxygen demand (BOD removal efficiencies were monitored for 24-hour, 12-hour, 6-hour, and 3-hour retention times. Under these conditions, 94% color, 65% COD, and 55% BOD removal efficiencies were obtained in the MBR system. The experimental outputs were modeled with multiple linear regressions (MLR and fuzzy logic. MLR results suggested that color removal is more related to COD removal relative to BOD removal. A surface map of this issue was prepared with a fuzzy logic model. Furthermore, fuzzy logic was employed to the whole modeling of the biological system treatment. Determination coefficients for COD, BOD, and color removal efficiencies were 0.96, 0.97, and 0.92, respectively.

Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans.

Directory of Open Access Journals (Sweden)

Mei Zhan

2015-04-01

Full Text Available Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation. Increasingly, the capacity for high-throughput experimentation provided by new imaging modalities, contrast techniques, microscopy tools, microfluidics and computer controlled systems shifts the experimental bottleneck from the level of physical manipulation and raw data collection to automated recognition and data processing. Yet, despite their broad importance, image analysis solutions to address these needs have been narrowly tailored. Here, we present a generalizable formulation for autonomous identification of specific biological structures that is applicable for many problems. The process flow architecture we present here utilizes standard image processing techniques and the multi-tiered application of classification models such as support vector machines (SVM. These low-level functions are readily available in a large array of image processing software packages and programming languages. Our framework is thus both easy to implement at the modular level and provides specific high-level architecture to guide the solution of more complicated image-processing problems. We demonstrate the utility of the classification routine by developing two specific classifiers as a toolset for automation and cell identification in the model organism Caenorhabditis elegans. To serve a common need for automated high-resolution imaging and behavior applications in the C. elegans research community, we contribute a ready-to-use classifier for the identification of the head of the animal under bright field imaging. Furthermore, we extend our framework to address the pervasive problem of cell-specific identification under fluorescent imaging, which is critical for biological investigation in multicellular organisms or tissues. Using these examples as a

Automated Processing of Imaging Data through Multi-tiered Classification of Biological Structures Illustrated Using Caenorhabditis elegans.

Science.gov (United States)

Zhan, Mei; Crane, Matthew M; Entchev, Eugeni V; Caballero, Antonio; Fernandes de Abreu, Diana Andrea; Ch'ng, QueeLim; Lu, Hang

2015-04-01

Quantitative imaging has become a vital technique in biological discovery and clinical diagnostics; a plethora of tools have recently been developed to enable new and accelerated forms of biological investigation. Increasingly, the capacity for high-throughput experimentation provided by new imaging modalities, contrast techniques, microscopy tools, microfluidics and computer controlled systems shifts the experimental bottleneck from the level of physical manipulation and raw data collection to automated recognition and data processing. Yet, despite their broad importance, image analysis solutions to address these needs have been narrowly tailored. Here, we present a generalizable formulation for autonomous identification of specific biological structures that is applicable for many problems. The process flow architecture we present here utilizes standard image processing techniques and the multi-tiered application of classification models such as support vector machines (SVM). These low-level functions are readily available in a large array of image processing software packages and programming languages. Our framework is thus both easy to implement at the modular level and provides specific high-level architecture to guide the solution of more complicated image-processing problems. We demonstrate the utility of the classification routine by developing two specific classifiers as a toolset for automation and cell identification in the model organism Caenorhabditis elegans. To serve a common need for automated high-resolution imaging and behavior applications in the C. elegans research community, we contribute a ready-to-use classifier for the identification of the head of the animal under bright field imaging. Furthermore, we extend our framework to address the pervasive problem of cell-specific identification under fluorescent imaging, which is critical for biological investigation in multicellular organisms or tissues. Using these examples as a guide, we envision

On the analysis of complex biological supply chains: From Process Systems Engineering to Quantitative Systems Pharmacology.

Science.gov (United States)

Rao, Rohit T; Scherholz, Megerle L; Hartmanshenn, Clara; Bae, Seul-A; Androulakis, Ioannis P

2017-12-05

The use of models in biology has become particularly relevant as it enables investigators to develop a mechanistic framework for understanding the operating principles of living systems as well as in quantitatively predicting their response to both pathological perturbations and pharmacological interventions. This application has resulted in a synergistic convergence of systems biology and pharmacokinetic-pharmacodynamic modeling techniques that has led to the emergence of quantitative systems pharmacology (QSP). In this review, we discuss how the foundational principles of chemical process systems engineering inform the progressive development of more physiologically-based systems biology models.

Biotic and abiotic processes in eastside ecosystems: the effects of management on soil properties, processes, and productivity.

Science.gov (United States)

Alan E. Harvey; J. Michael Geist; Gerald L McDonald; Martin F. Jurgensen; Patrick H. Cochran; Darlene Zabowski; Robert T. Meurisse

1994-01-01

Productivity of forest and range land soils is based on a combination of diverse physical, chemical and biological properties. In ecosystems characteristic of eastside regions of Oregon and Washington, the productive zone is usually in the upper 1 or 2 m. Not only are the biological processes that drive both soil productivity and root development concentrated in...

A Case Study Documenting the Process by Which Biology Instructors Transition from Teacher-Centered to Learner-Centered Teaching

Science.gov (United States)

Marbach-Ad, Gili; Hunt Rietschel, Carly

2016-01-01

In this study, we used a case study approach to obtain an in-depth understanding of the change process of two university instructors who were involved with redesigning a biology course. Given the hesitancy of many biology instructors to adopt evidence-based, learner-centered teaching methods, there is a critical need to understand how biology instructors transition from teacher-centered (i.e., lecture-based) instruction to teaching that focuses on the students. Using the innovation-decision model for change, we explored the motivation, decision-making, and reflective processes of the two instructors through two consecutive, large-enrollment biology course offerings. Our data reveal that the change process is somewhat unpredictable, requiring patience and persistence during inevitable challenges that arise for instructors and students. For example, the change process requires instructors to adopt a teacher-facilitator role as opposed to an expert role, to cover fewer course topics in greater depth, and to give students a degree of control over their own learning. Students must adjust to taking responsibility for their own learning, working collaboratively, and relinquishing the anonymity afforded by lecture-based teaching. We suggest implications for instructors wishing to change their teaching and administrators wishing to encourage adoption of learner-centered teaching at their institutions. PMID:27856550

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

Science.gov (United States)

Melnikov, I. A.

2002-12-01

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

Profiling the biological activity of oxide nanomaterials with mechanistic models

NARCIS (Netherlands)

Burello, E.

2013-01-01

In this study we present three mechanistic models for profiling the potential biological and toxicological effects of oxide nanomaterials. The models attempt to describe the reactivity, protein adsorption and membrane adhesion processes of a large range of oxide materials and are based on properties

A short comparison of electron and proton transfer processes in biological systems

International Nuclear Information System (INIS)

Bertrand, Patrick

2005-01-01

The main differences between electron and proton transfers that take place in biological systems are examined. The relation between the distance dependence of the rate constant and the mass of the transferred particle is analyzed in detail. Differences between the two processes have important consequences at the experimental level, which are discussed. The various mechanisms that ensure the coupling between electron and proton transfers are briefly described

[Mechanisms of primary reception of electromagnetic waves of optical range].

Science.gov (United States)

Huliar, S O; Lymans'kyĭ, Iu P

2003-01-01

An existence of separate functional system of regulation of electromagnetic balance of organism has been substantiated and a working conception of light therapy has been formulated. As a basis, there is a possibility to use the acupuncture points for input of biologically necessary electromagnetic waves into the system of their conductors in a body that might be considered as a transport facility for energy of the polarized electromagnetic waves. Zones-recipients are organs having an electromagnetic disbalance due to excess of biologically inadequate radiation and being the targets for peroxide oxidation. Foremost, a body has the neurohormonal and immune regulatory systems. Electromagnetic stimulation or modification of functions of the zones-recipients determines the achievement of therapeutic and useful effects, and their combination with local reparative processes allows to attain a clinical goal. We represent own and literary experimental data about the development of physiological responses (analgesia) to BIOPTRON-light exposure on the acupuncture points or biologically active zones. We show the experimental facts in support of a hypothesis that a living organism can perceive an action of the electromagnetic fields of optical range not only via the visual system, but also through the off-nerve receptors (specific energy-sensitive proteins detecting critical changes of energy in cells and functioning as the "sensory" cell systems), as well as via the acupuncture points. It confirms an important role of the electromagnetic waves of optical range in providing normal vital functions of living organisms. A current approach to BIOPTRON light therapy (by polarized polychromatic coherent low energy light) consists in combined (local and system) exposure of the electromagnetic waves within the biologically necessary range.

Multi-level and hybrid modelling approaches for systems biology.

Science.gov (United States)

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

2017-01-01

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

Assessment of the Biological Treatability of Black Tea Processing ...

African Journals Online (AJOL)

The anaerobic degradability of tea beverage processing effluent was assessed using a stationary upflow anaerobic filter. The filter, with an active column of 1.2m height, inner diameter of 100 mm and filled with rock as the attachment medium was operated at room temperature ranging between 20-250C throughout the ...

Stochastic model of template-directed elongation processes in biology.

Science.gov (United States)

Schilstra, Maria J; Nehaniv, Chrystopher L

2010-10-01

We present a novel modular, stochastic model for biological template-based linear chain elongation processes. In this model, elongation complexes (ECs; DNA polymerase, RNA polymerase, or ribosomes associated with nascent chains) that span a finite number of template units step along the template, one after another, with semaphore constructs preventing overtaking. The central elongation module is readily extended with modules that represent initiation and termination processes. The model was used to explore the effect of EC span on motor velocity and dispersion, and the effect of initiation activator and repressor binding kinetics on the overall elongation dynamics. The results demonstrate that (1) motors that move smoothly are able to travel at a greater velocity and closer together than motors that move more erratically, and (2) the rate at which completed chains are released is proportional to the occupancy or vacancy of activator or repressor binding sites only when initiation or activator/repressor dissociation is slow in comparison with elongation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Mass fractionation processes of transition metal isotopes

Science.gov (United States)

Zhu, X. K.; Guo, Y.; Williams, R. J. P.; O'Nions, R. K.; Matthews, A.; Belshaw, N. S.; Canters, G. W.; de Waal, E. C.; Weser, U.; Burgess, B. K.; Salvato, B.

2002-06-01

Recent advances in mass spectrometry make it possible to utilise isotope variations of transition metals to address some important issues in solar system and biological sciences. Realisation of the potential offered by these new isotope systems however requires an adequate understanding of the factors controlling their isotope fractionation. Here we show the results of a broadly based study on copper and iron isotope fractionation during various inorganic and biological processes. These results demonstrate that: (1) naturally occurring inorganic processes can fractionate Fe isotope to a detectable level even at temperature ˜1000°C, which challenges the previous view that Fe isotope variations in natural system are unique biosignatures; (2) multiple-step equilibrium processes at low temperatures may cause large mass fractionation of transition metal isotopes even when the fractionation per single step is small; (3) oxidation-reduction is an importation controlling factor of isotope fractionation of transition metal elements with multiple valences, which opens a wide range of applications of these new isotope systems, ranging from metal-silicate fractionation in the solar system to uptake pathways of these elements in biological systems; (4) organisms incorporate lighter isotopes of transition metals preferentially, and transition metal isotope fractionation occurs stepwise along their pathways within biological systems during their uptake.

Synthetic Biology: Putting Synthesis into Biology

Science.gov (United States)

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

The ability to manipulate living organisms is at the heart of a range of emerging technologies that serve to address important and current problems in environment, energy, and health. However, with all its complexity and interconnectivity, biology has for many years been recalcitrant to engineering manipulations. The recent advances in synthesis, analysis, and modeling methods have finally provided the tools necessary to manipulate living systems in meaningful ways, and have led to the coining of a field named synthetic biology. The scope of synthetic biology is as complicated as life itself – encompassing many branches of science, and across many scales of application. New DNA synthesis and assembly techniques have made routine the customization of very large DNA molecules. This in turn has allowed the incorporation of multiple genes and pathways. By coupling these with techniques that allow for the modeling and design of protein functions, scientists have now gained the tools to create completely novel biological machineries. Even the ultimate biological machinery – a self-replicating organism – is being pursued at this moment. It is the purpose of this review to dissect and organize these various components of synthetic biology into a coherent picture. PMID:21064036

Scientific considerations on the improvement of the range of ...

African Journals Online (AJOL)

This article provides the results of the investigation of biological effectiveness and the development of the regulations on the use of new agents for the improvement and expansion of the range of herbicides for the protection of sunflower crops. Keywords: range of pesticides, herbicides, sunflower, weeds, biological ...

Biological treatment of fish processing wastewater: A case study from Sfax City (Southeastern Tunisia).

Science.gov (United States)

Jemli, Meryem; Karray, Fatma; Feki, Firas; Loukil, Slim; Mhiri, Najla; Aloui, Fathi; Sayadi, Sami

2015-04-01

The present work presents a study of the biological treatment of fish processing wastewater at salt concentration of 55 g/L. Wastewater was treated by both continuous stirred-tank reactor (CSTR) and membrane bioreactor (MBR) during 50 and 100 days, respectively. These biological processes involved salt-tolerant bacteria from natural hypersaline environments at different organic loading rates (OLRs). The phylogenetic analysis of the corresponding excised DGGE bands has demonstrated that the taxonomic affiliation of the most dominant species includes Halomonadaceae and Flavobacteriaceae families of the Proteobacteria (Gamma-proteobacteria class) and the Bacteroidetes phyla, respectively. The results of MBR were better than those of CSTR in the removal of total organic carbon with efficiencies from 97.9% to 98.6%. Nevertheless, salinity with increasing OLR aggravates fouling that requires more cleaning for a membrane in MBR while leads to deterioration of sludge settleability and effluent quality in CSTR. Copyright © 2015. Published by Elsevier B.V.

Are fish outside their usual ranges early indicators of climate-driven range shifts?

Science.gov (United States)

Fogarty, Hannah E; Burrows, Michael T; Pecl, Gretta T; Robinson, Lucy M; Poloczanska, Elvira S

2017-05-01

Shifts in species ranges are a global phenomenon, well known to occur in response to a changing climate. New species arriving in an area may become pest species, modify ecosystem structure, or represent challenges or opportunities for fisheries and recreation. Early detection of range shifts and prompt implementation of any appropriate management strategies is therefore crucial. This study investigates whether 'first sightings' of marine species outside their normal ranges could provide an early warning of impending climate-driven range shifts. We examine the relationships between first sightings and marine regions defined by patterns of local climate velocities (calculated on a 50-year timescale), while also considering the distribution of observational effort (i.e. number of sampling days recorded with biological observations in global databases). The marine trajectory regions include climate 'source' regions (areas lacking connections to warmer areas), 'corridor' regions (areas where moving isotherms converge), and 'sink' regions (areas where isotherms locally disappear). Additionally, we investigate the latitudinal band in which first sightings were recorded, and species' thermal affiliations. We found that first sightings are more likely to occur in climate sink and 'divergent' regions (areas where many rapid and diverging climate trajectories pass through) indicating a role of temperature in driving changes in marine species distributions. The majority of our fish first sightings appear to be tropical and subtropical species moving towards high latitudes, as would be expected in climate warming. Our results indicate that first sightings are likely related to longer-term climatic processes, and therefore have potential use to indicate likely climate-driven range shifts. The development of an approach to detect impending range shifts at an early stage will allow resource managers and researchers to better manage opportunities resulting from range

Signal processing for molecular and cellular biological physics: an emerging field.

Science.gov (United States)

Little, Max A; Jones, Nick S

2013-02-13

Recent advances in our ability to watch the molecular and cellular processes of life in action--such as atomic force microscopy, optical tweezers and Forster fluorescence resonance energy transfer--raise challenges for digital signal processing (DSP) of the resulting experimental data. This article explores the unique properties of such biophysical time series that set them apart from other signals, such as the prevalence of abrupt jumps and steps, multi-modal distributions and autocorrelated noise. It exposes the problems with classical linear DSP algorithms applied to this kind of data, and describes new nonlinear and non-Gaussian algorithms that are able to extract information that is of direct relevance to biological physicists. It is argued that these new methods applied in this context typify the nascent field of biophysical DSP. Practical experimental examples are supplied.

Synthetic Biology: Mapping the Scientific Landscape

Science.gov (United States)

Oldham, Paul; Hall, Stephen; Burton, Geoff

2012-01-01

This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves. PMID:22539946

Prospects for energy recovery during hydrothermal and biological processing of waste biomass.

Science.gov (United States)

Gerber Van Doren, Léda; Posmanik, Roy; Bicalho, Felipe A; Tester, Jefferson W; Sills, Deborah L

2017-02-01

Thermochemical and biological processes represent promising technologies for converting wet biomasses, such as animal manure, organic waste, or algae, to energy. To convert biomass to energy and bio-chemicals in an economical manner, internal energy recovery should be maximized to reduce the use of external heat and power. In this study, two conversion pathways that couple hydrothermal liquefaction with anaerobic digestion or catalytic hydrothermal gasification were compared. Each of these platforms is followed by two alternative processes for gas utilization: 1) combined heat and power; and 2) combustion in a boiler. Pinch analysis was applied to integrate thermal streams among unit processes and improve the overall system efficiency. A techno-economic analysis was conducted to compare the feasibility of the four modeled scenarios under different market conditions. Our results show that a systems approach designed to recover internal heat and power can reduce external energy demands and increase the overall process sustainability. Copyright © 2016 Elsevier Ltd. All rights reserved.

Investigation on thiosulfate-involved organics and nitrogen removal by a sulfur cycle-based biological wastewater treatment process.

Science.gov (United States)

Qian, Jin; Lu, Hui; Cui, Yanxiang; Wei, Li; Liu, Rulong; Chen, Guang-Hao

2015-02-01

Thiosulfate, as an intermediate of biological sulfate/sulfite reduction, can significantly improve nitrogen removal potential in a biological sulfur cycle-based process, namely the Sulfate reduction-Autotrophic denitrification-Nitrification Integrated (SANI(®)) process. However, the related thiosulfate bio-activities coupled with organics and nitrogen removal in wastewater treatment lacked detailed examinations and reports. In this study, S2O3(2-) transformation during biological SO4(2-)/SO3(2-) co-reduction coupled with organics removal as well as S2O3(2-) oxidation coupled with chemolithotrophic denitrification were extensively evaluated under different experimental conditions. Thiosulfate is produced from the co-reduction of sulfate and sulfite through biological pathway at an optimum pH of 7.5 for organics removal. And the produced S2O3(2-) may disproportionate to sulfide and sulfate during both biological S2O3(2-) reduction and oxidation most possibly carried out by Desulfovibrio-like species. Dosing the same amount of nitrate, pH was found to be the more direct factor influencing the denitritation activity than free nitrous acid (FNA) and the optimal pH for denitratation (7.0) and denitritation (8.0) activities were different. Spiking organics significantly improved both denitratation and denitritation activities while minimizing sulfide inhibition of NO3(-) reduction during thiosulfate-based denitrification. These findings in this study can improve the understanding of mechanisms of thiosulfate on organics and nitrogen removal in biological sulfur cycle-based wastewater treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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

Exploiting graphics processing units for computational biology and bioinformatics.

Science.gov (United States)

Payne, Joshua L; Sinnott-Armstrong, Nicholas A; Moore, Jason H

2010-09-01

Advances in the video gaming industry have led to the production of low-cost, high-performance graphics processing units (GPUs) that possess more memory bandwidth and computational capability than central processing units (CPUs), the standard workhorses of scientific computing. With the recent release of generalpurpose GPUs and NVIDIA's GPU programming language, CUDA, graphics engines are being adopted widely in scientific computing applications, particularly in the fields of computational biology and bioinformatics. The goal of this article is to concisely present an introduction to GPU hardware and programming, aimed at the computational biologist or bioinformaticist. To this end, we discuss the primary differences between GPU and CPU architecture, introduce the basics of the CUDA programming language, and discuss important CUDA programming practices, such as the proper use of coalesced reads, data types, and memory hierarchies. We highlight each of these topics in the context of computing the all-pairs distance between instances in a dataset, a common procedure in numerous disciplines of scientific computing. We conclude with a runtime analysis of the GPU and CPU implementations of the all-pairs distance calculation. We show our final GPU implementation to outperform the CPU implementation by a factor of 1700.

Advances in wastewater nitrogen removal by biological processes: state of the art review

Directory of Open Access Journals (Sweden)

Andrea G. Capodaglio

2016-04-01

Full Text Available The paper summarizes the state-of-the-art of the most recent advances in biological nitrogen removal, including process design criteria and technological innovations. With reference to the Modified Ludzck Ettinger (MLE process (pre-denitrification and nitrification in the activated sludge process, the most common nitrogen removal process used nowadays, a new design equation for the denitrification reactor based on specific denitrification rate (SDNR has been proposed. In addition, factors influencing SDNR (DO in the anoxic reactor; hydrodynamic behavior are analyzed, and technological solutions are proposed. Concerning technological advances, the paper presents a summary of various “deammonification” processes, better known by their patent names like ANAMMOX®, DEMON®, CANON®, ANITA® and others. These processes have already found applications in the treatment of high-strength wastewater such as digested sludge liquor and landfill leachate. Among other emerging denitrification technologies, consideration is given to the Membrane Biofilm Reactors (MBfRs that can be operated both in oxidation and reduction mode.

Photonics-based real-time ultra-high-range-resolution radar with broadband signal generation and processing.

Science.gov (United States)

Zhang, Fangzheng; Guo, Qingshui; Pan, Shilong

2017-10-23

Real-time and high-resolution target detection is highly desirable in modern radar applications. Electronic techniques have encountered grave difficulties in the development of such radars, which strictly rely on a large instantaneous bandwidth. In this article, a photonics-based real-time high-range-resolution radar is proposed with optical generation and processing of broadband linear frequency modulation (LFM) signals. A broadband LFM signal is generated in the transmitter by photonic frequency quadrupling, and the received echo is de-chirped to a low frequency signal by photonic frequency mixing. The system can operate at a high frequency and a large bandwidth while enabling real-time processing by low-speed analog-to-digital conversion and digital signal processing. A conceptual radar is established. Real-time processing of an 8-GHz LFM signal is achieved with a sampling rate of 500 MSa/s. Accurate distance measurement is implemented with a maximum error of 4 mm within a range of ~3.5 meters. Detection of two targets is demonstrated with a range-resolution as high as 1.875 cm. We believe the proposed radar architecture is a reliable solution to overcome the limitations of current radar on operation bandwidth and processing speed, and it is hopefully to be used in future radars for real-time and high-resolution target detection and imaging.

Prion potency in stem cells biology.

Science.gov (United States)

Lopes, Marilene H; Santos, Tiago G

2012-01-01

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

Thermostability of biological systems: fundamentals, challenges, and quantification.

Science.gov (United States)

He, Xiaoming

2011-01-01

This review examines the fundamentals and challenges in engineering/understanding the thermostability of biological systems over a wide temperature range (from the cryogenic to hyperthermic regimen). Applications of the bio-thermostability engineering to either destroy unwanted or stabilize useful biologicals for the treatment of diseases in modern medicine are first introduced. Studies on the biological responses to cryogenic and hyperthermic temperatures for the various applications are reviewed to understand the mechanism of thermal (both cryo and hyperthermic) injury and its quantification at the molecular, cellular and tissue/organ levels. Methods for quantifying the thermophysical processes of the various applications are then summarized accounting for the effect of blood perfusion, metabolism, water transport across cell plasma membrane, and phase transition (both equilibrium and non-equilibrium such as ice formation and glass transition) of water. The review concludes with a summary of the status quo and future perspectives in engineering the thermostability of biological systems.

A two-stage biological gas to liquid transfer process to convert carbon dioxide into bioplastic

KAUST Repository

Al Rowaihi, Israa; Kick, Benjamin; Grö tzinger, Stefan W.; Burger, Christian; Karan, Ram; Weuster-Botz, Dirk; Eppinger, Jö rg; Arold, Stefan T.

2018-01-01

The fermentation of carbon dioxide (CO2) with hydrogen (H2) uses available low-cost gases to synthesis acetic acid. Here, we present a two-stage biological process that allows the gas to liquid transfer (Bio-GTL) of CO2 into the biopolymer

Biological shielding design and qualification of concreting process for construction of electron beam irradiation facility

International Nuclear Information System (INIS)

Petwal, V.C.; Kumar, P.; Suresh, N.; Parchani, G.; Dwivedi, J.; Thakurta, A.C.

2011-01-01

A technology demonstration facility for irradiation of food and agricultural products is being set-up by RRCAT at Indore. The facility design is based on linear electron accelerator with maximum beam power of 10 kW and can be operated either in electron mode at 10 MeV or photon modes at 5/7.5 MeV. Biological shielding has been designed in accordance with NCRP 51 to achieve dose rate at all accessible points outside the irradiation vault less than the permissible limit of 0.1 mR/hr. In addition to radiation attenuation property, concrete must have satisfactory mechanical properties to meet the structural requirements. There are number of site specific variables which affect the structural, thermal and radiological properties of concrete, leading to considerable difference in actual values and design values. Hence it is essential to establish a suitable site and environmental specific process to cast the concrete and qualify the process by experimental measurement. For process qualification we have cast concrete test blocks of different thicknesses up to 3.25 m and evaluated the radiological and mechanical properties by radiometry, ultrasonic and mechanical tests. In this paper we describe the biological shielding design of the facility and analyse the results of tests carried out for qualification of the process. (author)

Dissecting Redox Biology Using Fluorescent Protein Sensors.

Science.gov (United States)

Schwarzländer, Markus; Dick, Tobias P; Meyer, Andreas J; Morgan, Bruce

2016-05-01

Fluorescent protein sensors have revitalized the field of redox biology by revolutionizing the study of redox processes in living cells and organisms. Within one decade, a set of fundamental new insights has been gained, driven by the rapid technical development of in vivo redox sensing. Redox-sensitive yellow and green fluorescent protein variants (rxYFP and roGFPs) have been the central players. Although widely used as an established standard tool, important questions remain surrounding their meaningful use in vivo. We review the growing range of thiol redox sensor variants and their application in different cells, tissues, and organisms. We highlight five key findings where in vivo sensing has been instrumental in changing our understanding of redox biology, critically assess the interpretation of in vivo redox data, and discuss technical and biological limitations of current redox sensors and sensing approaches. We explore how novel sensor variants may further add to the current momentum toward a novel mechanistic and integrated understanding of redox biology in vivo. Antioxid. Redox Signal. 24, 680-712.

Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology

OpenAIRE

Hazen, Terry C.

2008-01-01

Environmental biotechnology encompasses a wide range of characterization, monitoring and control for bioenergy and bioremediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment and potentially produce bioenergy fuels as we also cleanup the environment. Indeed, our ability to sequence an entire microbial genome in...

Design and Fabrication of Slotted Multimode Interference Devices for Chemical and Biological Sensing

Directory of Open Access Journals (Sweden)

M. Mayeh

2009-01-01

Full Text Available We present optical sensors based on slotted multimode interference waveguides. The sensor can be tuned to highest sensitivity in the refractive index ranges necessary to detect protein-based molecules or other water-soluble chemical or biological materials. The material of choice is low-loss silicon oxynitride (SiON which is highly stable to the reactivity with biological agents and processing chemicals. Sensors made with this technology are suited to high volume manufacturing.

Unambiguous range-Doppler LADAR processing using 2 giga-sample-per-second noise waveforms

International Nuclear Information System (INIS)

Cole, Z.; Roos, P.A.; Berg, T.; Kaylor, B.; Merkel, K.D.; Babbitt, W.R.; Reibel, R.R.

2007-01-01

We demonstrate sub-nanosecond range and unambiguous sub-50-Hz Doppler resolved laser radar (LADAR) measurements using spectral holographic processing in rare-earth ion doped crystals. The demonstration utilizes pseudo-random-noise 2 giga-sample-per-second baseband waveforms modulated onto an optical carrier

Unambiguous range-Doppler LADAR processing using 2 giga-sample-per-second noise waveforms

Energy Technology Data Exchange (ETDEWEB)

Cole, Z. [S2 Corporation, 2310 University Way 4-1, Bozeman, MT 59715 (United States)]. E-mail: cole@s2corporation.com; Roos, P.A. [Spectrum Lab, Montana State University, P.O. Box 173510, Bozeman, MT 59717 (United States); Berg, T. [S2 Corporation, 2310 University Way 4-1, Bozeman, MT 59715 (United States); Kaylor, B. [S2 Corporation, 2310 University Way 4-1, Bozeman, MT 59715 (United States); Merkel, K.D. [S2 Corporation, 2310 University Way 4-1, Bozeman, MT 59715 (United States); Babbitt, W.R. [Spectrum Lab, Montana State University, P.O. Box 173510, Bozeman, MT 59717 (United States); Reibel, R.R. [S2 Corporation, 2310 University Way 4-1, Bozeman, MT 59715 (United States)

2007-11-15

We demonstrate sub-nanosecond range and unambiguous sub-50-Hz Doppler resolved laser radar (LADAR) measurements using spectral holographic processing in rare-earth ion doped crystals. The demonstration utilizes pseudo-random-noise 2 giga-sample-per-second baseband waveforms modulated onto an optical carrier.

Using synthetic biology to make cells tomorrow's test tubes.

Science.gov (United States)

Garcia, Hernan G; Brewster, Robert C; Phillips, Rob

2016-04-18

The main tenet of physical biology is that biological phenomena can be subject to the same quantitative and predictive understanding that physics has afforded in the context of inanimate matter. However, the inherent complexity of many of these biological processes often leads to the derivation of complex theoretical descriptions containing a plethora of unknown parameters. Such complex descriptions pose a conceptual challenge to the establishment of a solid basis for predictive biology. In this article, we present various exciting examples of how synthetic biology can be used to simplify biological systems and distill these phenomena down to their essential features as a means to enable their theoretical description. Here, synthetic biology goes beyond previous efforts to engineer nature and becomes a tool to bend nature to understand it. We discuss various recent and classic experiments featuring applications of this synthetic approach to the elucidation of problems ranging from bacteriophage infection, to transcriptional regulation in bacteria and in developing embryos, to evolution. In all of these examples, synthetic biology provides the opportunity to turn cells into the equivalent of a test tube, where biological phenomena can be reconstituted and our theoretical understanding put to test with the same ease that these same phenomena can be studied in the in vitro setting.

Preliminary degradation process study of infectious biological waste in a 5 k W thermal plasma equipment

International Nuclear Information System (INIS)

Xochihua S M, M.C.

1997-01-01

This work is a preliminary study of infectious biological waste degradation process by thermal plasma and was made in Thermal Plasma Applications Laboratory of Environmental Studies Department of the National Institute of Nuclear Research (ININ). Infectious biological waste degradation process is realized by using samples such polyethylene, cotton, glass, etc., but the present study scope is to analyze polyethylene degradation process with mass and energy balances involved. Degradation method is realized as follow: a polyethylene sample is put in an appropriated crucible localized inside a pyrolysis reactor chamber, the plasma jet is projected to the sample, by the pyrolysis phenomena the sample is degraded into its constitutive particles: carbon and hydrogen. Air was utilized as a recombination gas in order to obtain the higher percent of CO 2 if amount of O 2 is greater in the recombination gas, the CO generation is reduced. The effluent gases of exhaust pyrolysis reactor through are passed through a heat exchanger to get cooled gases, the temperature water used is 15 Centigrade degrees. Finally the gases was tried into absorption tower with water as an absorbent fluid. Thermal plasma degradation process is a very promising technology, but is necessary to develop engineering process area to avail all advantages of thermal plasma. (Author)

Dyneins: structure, biology and disease

National Research Council Canada - National Science Library

King, Stephen M

2012-01-01

.... From bench to bedside, Dynein: Structure, Biology and Disease offers research on fundamental cellular processes to researchers and clinicians across developmental biology, cell biology, molecular biology, biophysics, biomedicine...

Combined oxidative and biological treatment of separated streams of tannery wastewater

Energy Technology Data Exchange (ETDEWEB)

Vidal, G.; Nieto, J. [Environmental Science Center EULA - Chile, Univ. of Concepcion, Concepcion (Chile); Mansilla, H.D. [Lab. of Renewable Resources, Univ. of Concepcion, Concepcion (Chile); Bornhardt, C. [Chemical Engineering Dept., Univ. of La Frontera, Temuco (Chile)

2003-07-01

Leather tanning effluents are a source of severe environmental impacts. In particular, the unhairing stage, belonging to the beamhouse processes, generates an alkaline wastewater with high concentrations of organic matter, sulphides, suspended solids, and salts, which shows significant toxicity. The objective of this work was to evaluate the biodegradation of this industrial wastewater by combined oxidative and biological treatments. An advanced oxidation process (AOP) with Fenton's reagent was used as batch pre-treatment. The relationships of H{sub 2}O{sub 2}/Fe{sup 2+} and H{sub 2}O{sub 2}/COD were 9 and 4, respectively, reaching an organic matter removal of about 90%. Subsequently, the oxidised beamhouse effluent was fed to an activated sludge system, at increasing organic load rates (OLR), in the range of 0.4 to 1.6 g COD/L.d. The biological organic matter removal of the pre-treated wastewater ranged between 35% and 60% for COD, and from 60% to 70% for BOD. Therefore, sequential AOP pretreatment and biological aerobic treatment increased the overall COD removal up to 96%, compared to 60% without pretreatment. Bioassays with D. magna and D. pulex showed that this kind of treatment achieves only a partial toxicity removal of the tannery effluent. (orig.)

Theoretical Biology and Medical Modelling: ensuring continued growth and future leadership.

Science.gov (United States)

Nishiura, Hiroshi; Rietman, Edward A; Wu, Rongling

2013-07-11

Theoretical biology encompasses a broad range of biological disciplines ranging from mathematical biology and biomathematics to philosophy of biology. Adopting a broad definition of "biology", Theoretical Biology and Medical Modelling, an open access journal, considers original research studies that focus on theoretical ideas and models associated with developments in biology and medicine.

Super-resolution and super-localization microscopy: A novel tool for imaging chemical and biological processes

Energy Technology Data Exchange (ETDEWEB)

Dong, Bin [Iowa State Univ., Ames, IA (United States)

2015-01-01

Optical microscopy imaging of single molecules and single particles is an essential method for studying fundamental biological and chemical processes at the molecular and nanometer scale. The best spatial resolution (~ λ/2) achievable in traditional optical microscopy is governed by the diffraction of light. However, single molecule-based super-localization and super-resolution microscopy imaging techniques have emerged in the past decade. Individual molecules can be localized with nanometer scale accuracy and precision for studying of biological and chemical processes.This work uncovered the heterogeneous properties of the pore structures. In this dissertation, the coupling of molecular transport and catalytic reaction at the single molecule and single particle level in multilayer mesoporous nanocatalysts was elucidated. Most previous studies dealt with these two important phenomena separately. A fluorogenic oxidation reaction of non-fluorescent amplex red to highly fluorescent resorufin was tested. The diffusion behavior of single resorufin molecules in aligned nanopores was studied using total internal reflection fluorescence microscopy (TIRFM).

Estimating monotonic rates from biological data using local linear regression.

Science.gov (United States)

Olito, Colin; White, Craig R; Marshall, Dustin J; Barneche, Diego R

2017-03-01

Accessing many fundamental questions in biology begins with empirical estimation of simple monotonic rates of underlying biological processes. Across a variety of disciplines, ranging from physiology to biogeochemistry, these rates are routinely estimated from non-linear and noisy time series data using linear regression and ad hoc manual truncation of non-linearities. Here, we introduce the R package LoLinR, a flexible toolkit to implement local linear regression techniques to objectively and reproducibly estimate monotonic biological rates from non-linear time series data, and demonstrate possible applications using metabolic rate data. LoLinR provides methods to easily and reliably estimate monotonic rates from time series data in a way that is statistically robust, facilitates reproducible research and is applicable to a wide variety of research disciplines in the biological sciences. © 2017. Published by The Company of Biologists Ltd.

The method validation step of biological dosimetry accreditation process

International Nuclear Information System (INIS)

Roy, L.; Voisin, P.A.; Guillou, A.C.; Busset, A.; Gregoire, E.; Buard, V.; Delbos, M.; Voisin, Ph.

2006-01-01

One of the missions of the Laboratory of Biological Dosimetry (L.D.B.) of the Institute for Radiation and Nuclear Safety (I.R.S.N.) is to assess the radiological dose after an accidental overexposure suspicion to ionising radiation, by using radio-induced changes of some biological parameters. The 'gold standard' is the yield of dicentrics observed in patients lymphocytes, and this yield is converted in dose using dose effect relationships. This method is complementary to clinical and physical dosimetry, for medical team in charge of the patients. To obtain a formal recognition of its operational activity, the laboratory decided three years ago, to require an accreditation, by following the recommendations of both 17025 General Requirements for the Competence of Testing and Calibration Laboratories and 19238 Performance criteria for service laboratories performing biological dosimetry by cyto-genetics. Diagnostics, risks analysis were realized to control the whole analysis process leading to documents writing. Purchases, personnel department, vocational training were also included in the quality system. Audits were very helpful to improve the quality system. One specificity of this technique is that it is not normalized therefore apart from quality management aspects, several technical points needed some validations. An inventory of potentially influent factors was carried out. To estimate their real effect on the yield of dicentrics, a Placket-Burman experimental design was conducted. The effect of seven parameters was tested: the BUdr (bromodeoxyuridine), PHA (phytohemagglutinin) and colcemid concentration, the culture duration, the incubator temperature, the blood volume and the medium volume. The chosen values were calculated according to the uncertainties on the way they were measured i.e. pipettes, thermometers, test tubes. None of the factors has a significant impact on the yield of dicentrics. Therefore the uncertainty linked to their use was considered as

The method validation step of biological dosimetry accreditation process

Energy Technology Data Exchange (ETDEWEB)

Roy, L.; Voisin, P.A.; Guillou, A.C.; Busset, A.; Gregoire, E.; Buard, V.; Delbos, M.; Voisin, Ph. [Institut de Radioprotection et de Surete Nucleaire, LDB, 92 - Fontenay aux Roses (France)

2006-07-01

One of the missions of the Laboratory of Biological Dosimetry (L.D.B.) of the Institute for Radiation and Nuclear Safety (I.R.S.N.) is to assess the radiological dose after an accidental overexposure suspicion to ionising radiation, by using radio-induced changes of some biological parameters. The 'gold standard' is the yield of dicentrics observed in patients lymphocytes, and this yield is converted in dose using dose effect relationships. This method is complementary to clinical and physical dosimetry, for medical team in charge of the patients. To obtain a formal recognition of its operational activity, the laboratory decided three years ago, to require an accreditation, by following the recommendations of both 17025 General Requirements for the Competence of Testing and Calibration Laboratories and 19238 Performance criteria for service laboratories performing biological dosimetry by cyto-genetics. Diagnostics, risks analysis were realized to control the whole analysis process leading to documents writing. Purchases, personnel department, vocational training were also included in the quality system. Audits were very helpful to improve the quality system. One specificity of this technique is that it is not normalized therefore apart from quality management aspects, several technical points needed some validations. An inventory of potentially influent factors was carried out. To estimate their real effect on the yield of dicentrics, a Placket-Burman experimental design was conducted. The effect of seven parameters was tested: the BUdr (bromodeoxyuridine), PHA (phytohemagglutinin) and colcemid concentration, the culture duration, the incubator temperature, the blood volume and the medium volume. The chosen values were calculated according to the uncertainties on the way they were measured i.e. pipettes, thermometers, test tubes. None of the factors has a significant impact on the yield of dicentrics. Therefore the uncertainty linked to their use was

Biological and Psychosocial Processes in the Development of Children’s Appetitive Traits: Insights from Developmental Theory and Research

Directory of Open Access Journals (Sweden)

Catherine G. Russell

2018-05-01

Full Text Available There has been increasing concern expressed about children’s food intakes and dietary patterns. These are closely linked to children’s appetitive traits (such as disinhibited eating and food fussiness/neophobia. Research has examined both biological and psychosocial correlates or predictors of these traits. There has been less focus on possible processes or mechanisms associated with children’s development of these traits and research that links biological and psychosocial factors. There is an absence of research that links biological and psychosocial factors. In the present article, we outline a model intended to facilitate theory and research on the development of appetitive traits. It is based on scholarship from developmental theory and research and incorporates biological factors such as genetic predispositions and temperament as well as psychosocial factors in terms of parent cognitions, feeding styles and feeding practices. Particular attention is directed to aspects such as emotional eating and feeding, self-regulation of energy intake, and non-shared family environments. We highlight the opportunity for longitudinal research that examines bidirectional, transactional and cascade processes and uses a developmental framework. The model provides a basis for connecting the biological foundations of appetitive traits to system-level analysis in the family. Knowledge generated through the application of the model should lead to more effective prevention and intervention initiatives.

Ordinary differential equations with applications in molecular biology.

Science.gov (United States)

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

. Ordinary differential equations are used to model biological processes on various levels ranging from DNA molecules or biosynthesis phospholipids on the cellular level.

Ecological and evolutionary processes at expanding range margins.

Science.gov (United States)

Thomas, C D; Bodsworth, E J; Wilson, R J; Simmons, A D; Davies, Z G; Musche, M; Conradt, L

2001-05-31

Many animals are regarded as relatively sedentary and specialized in marginal parts of their geographical distributions. They are expected to be slow at colonizing new habitats. Despite this, the cool margins of many species' distributions have expanded rapidly in association with recent climate warming. We examined four insect species that have expanded their geographical ranges in Britain over the past 20 years. Here we report that two butterfly species have increased the variety of habitat types that they can colonize, and that two bush cricket species show increased fractions of longer-winged (dispersive) individuals in recently founded populations. Both ecological and evolutionary processes are probably responsible for these changes. Increased habitat breadth and dispersal tendencies have resulted in about 3- to 15-fold increases in expansion rates, allowing these insects to cross habitat disjunctions that would have represented major or complete barriers to dispersal before the expansions started. The emergence of dispersive phenotypes will increase the speed at which species invade new environments, and probably underlies the responses of many species to both past and future climate change.

Simultaneous nitrogen and phosphorus removal in the sulfur cycle-associated Enhanced Biological Phosphorus Removal (EBPR) process.

Science.gov (United States)

Wu, Di; Ekama, George A; Wang, Hai-Guang; Wei, Li; Lu, Hui; Chui, Ho-Kwong; Liu, Wen-Tso; Brdjanovic, Damir; van Loosdrecht, Mark C M; Chen, Guang-Hao

2014-02-01

Hong Kong has practiced seawater toilet flushing since 1958, saving 750,000 m(3) of freshwater every day. A high sulfate-to-COD ratio (>1.25 mg SO4(2-)/mg COD) in the saline sewage resulting from this practice has enabled us to develop the Sulfate reduction, Autotrophic denitrification and Nitrification Integrated (SANI(®)) process with minimal sludge production and oxygen demand. Recently, the SANI(®) process has been expanded to include Enhanced Biological Phosphorus Removal (EBPR) in an alternating anaerobic/limited-oxygen (LOS-EBPR) aerobic sequencing batch reactor (SBR). This paper presents further development - an anaerobic/anoxic denitrifying sulfur cycle-associated EBPR, named as DS-EBPR, bioprocess in an alternating anaerobic/anoxic SBR for simultaneous removal of organics, nitrogen and phosphorus. The 211 day SBR operation confirmed the sulfur cycle-associated biological phosphorus uptake utilizing nitrate as electron acceptor. This new bioprocess cannot only reduce operation time but also enhance volumetric loading of SBR compared with the LOS-EBPR. The DS-EBPR process performed well at high temperatures of 30 °C and a high salinity of 20% seawater. A synergistic relationship may exist between sulfur cycle and biological phosphorus removal as the optimal ratio of P-release to SO4(2-)-reduction is close to 1.0 mg P/mg S. There were no conventional PAOs in the sludge. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dispensing processes impact apparent biological activity as determined by computational and statistical analyses.

Directory of Open Access Journals (Sweden)

Sean Ekins

Full Text Available Dispensing and dilution processes may profoundly influence estimates of biological activity of compounds. Published data show Ephrin type-B receptor 4 IC50 values obtained via tip-based serial dilution and dispensing versus acoustic dispensing with direct dilution differ by orders of magnitude with no correlation or ranking of datasets. We generated computational 3D pharmacophores based on data derived by both acoustic and tip-based transfer. The computed pharmacophores differ significantly depending upon dispensing and dilution methods. The acoustic dispensing-derived pharmacophore correctly identified active compounds in a subsequent test set where the tip-based method failed. Data from acoustic dispensing generates a pharmacophore containing two hydrophobic features, one hydrogen bond donor and one hydrogen bond acceptor. This is consistent with X-ray crystallography studies of ligand-protein interactions and automatically generated pharmacophores derived from this structural data. In contrast, the tip-based data suggest a pharmacophore with two hydrogen bond acceptors, one hydrogen bond donor and no hydrophobic features. This pharmacophore is inconsistent with the X-ray crystallographic studies and automatically generated pharmacophores. In short, traditional dispensing processes are another important source of error in high-throughput screening that impacts computational and statistical analyses. These findings have far-reaching implications in biological research.

Assessment of biological chromium among stainless steel and mild steel welders in relation to welding processes.

Science.gov (United States)

Edmé, J L; Shirali, P; Mereau, M; Sobaszek, A; Boulenguez, C; Diebold, F; Haguenoer, J M

1997-01-01

Air and biological monitoring were used for assessing external and internal chromium exposure among 116 stainless steel welders (SS welders) using manual metal arc (MMA), metal inert gas (MIG) and tungsten inert gas (TIG) welding processes (MMA: n = 57; MIG: n = 37; TIG: n = 22) and 30 mild steel welders (MS welders) using MMA and MIG welding processes (MMA: n = 14; MIG: n = 16). The levels of atmospheric total chromium were evaluated after personal air monitoring. The mean values for the different groups of SS welders were 201 micrograms/m3 (MMA) and 185 micrograms/m3 (MIG), 52 micrograms/m3 (TIG) and for MS welders 8.1 micrograms/m3 (MMA) and 7.3 micrograms/m3 (MIG). The curve of cumulative frequency distribution from biological monitoring among SS welders showed chromium geometric mean concentrations in whole blood of 3.6 micrograms/l (95th percentile = 19.9), in plasma of 3.3 micrograms/l (95th percentile = 21.0) and in urine samples of 6.2 micrograms/l (95th percentile = 58.0). Among MS welders, mean values in whole blood and plasma were rather more scattered (1.8 micrograms/l, 95th percentile = 9.3 and 1.3 micrograms/l, 95th percentile = 8.4, respectively) and in urine the value was 2.4 micrograms/l (95th percentile = 13.3). The analysis of variance of chromium concentrations in plasma previously showed a metal effect (F = 29.7, P process effect (F = 22.2, P process interaction (F = 1.3, P = 0.25). Concerning urinary chromium concentration, the analysis of variance also showed a metal effect (F = 30, P process effect (F = 72, P process interaction (F = 13.2, P = 0.0004). Throughout the study we noted any significant differences between smokers and non-smokers among welders. Taking in account the relationships between chromium concentrations in whole, plasma or urine and the different welding process. MMA-SS is definitely different from other processes because the biological values are clearly higher. These higher levels are due to the very significant

Monitoring Biological Modes in a Bioreactor Process by Computer Simulation

Directory of Open Access Journals (Sweden)

Samia Semcheddine

2015-12-01

Full Text Available This paper deals with the general framework of fermentation system modeling and monitoring, focusing on the fermentation of Escherichia coli. Our main objective is to develop an algorithm for the online detection of acetate production during the culture of recombinant proteins. The analysis the fermentation process shows that it behaves like a hybrid dynamic system with commutation (since it can be represented by 5 nonlinear models. We present a strategy of fault detection based on residual generation for detecting the different actual biological modes. The residual generation is based on nonlinear analytical redundancy relations. The simulation results show that the several modes that are occulted during the bacteria cultivation can be detected by residuals using a nonlinear dynamic model and a reduced instrumentation.

Principles for integrating reactive species into in vivo biological processes: Examples from exercise physiology.

Science.gov (United States)

Margaritelis, Nikos V; Cobley, James N; Paschalis, Vassilis; Veskoukis, Aristidis S; Theodorou, Anastasios A; Kyparos, Antonios; Nikolaidis, Michalis G

2016-04-01

The equivocal role of reactive species and redox signaling in exercise responses and adaptations is an example clearly showing the inadequacy of current redox biology research to shed light on fundamental biological processes in vivo. Part of the answer probably relies on the extreme complexity of the in vivo redox biology and the limitations of the currently applied methodological and experimental tools. We propose six fundamental principles that should be considered in future studies to mechanistically link reactive species production to exercise responses or adaptations: 1) identify and quantify the reactive species, 2) determine the potential signaling properties of the reactive species, 3) detect the sources of reactive species, 4) locate the domain modified and verify the (ir)reversibility of post-translational modifications, 5) establish causality between redox and physiological measurements, 6) use selective and targeted antioxidants. Fulfilling these principles requires an idealized human experimental setting, which is certainly a utopia. Thus, researchers should choose to satisfy those principles, which, based on scientific evidence, are most critical for their specific research question. Copyright © 2015 Elsevier Inc. All rights reserved.

Implied Movement in Static Images Reveals Biological Timing Processing

Directory of Open Access Journals (Sweden)

Francisco Carlos Nather

2015-08-01

Full Text Available Visual perception is adapted toward a better understanding of our own movements than those of non-conspecifics. The present study determined whether time perception is affected by pictures of different species by considering the evolutionary scale. Static (“S” and implied movement (“M” images of a dog, cheetah, chimpanzee, and man were presented to undergraduate students. S and M images of the same species were presented in random order or one after the other (S-M or M-S for two groups of participants. Movement, Velocity, and Arousal semantic scales were used to characterize some properties of the images. Implied movement affected time perception, in which M images were overestimated. The results are discussed in terms of visual motion perception related to biological timing processing that could be established early in terms of the adaptation of humankind to the environment.

Use of a cocktail of spin traps for fingerprinting large range of free radicals in biological systems.

Science.gov (United States)

Marchand, Valérie; Charlier, Nicolas; Verrax, Julien; Buc-Calderon, Pedro; Levêque, Philippe; Gallez, Bernard

2017-01-01

It is well established that the formation of radical species centered on various atoms is involved in the mechanism leading to the development of several diseases or to the appearance of deleterious effects of toxic molecules. The detection of free radical is possible using Electron Paramagnetic Resonance (EPR) spectroscopy and the spin trapping technique. The classical EPR spin-trapping technique can be considered as a "hypothesis-driven" approach because it requires an a priori assumption regarding the nature of the free radical in order to select the most appropriate spin-trap. We here describe a "data-driven" approach using EPR and a cocktail of spin-traps. The rationale for using this cocktail was that it would cover a wide range of biologically relevant free radicals and have a large range of hydrophilicity and lipophilicity in order to trap free radicals produced in different cellular compartments. As a proof-of-concept, we validated the ability of the system to measure a large variety of free radicals (O-, N-, C-, or S- centered) in well characterized conditions, and we illustrated the ability of the technique to unambiguously detect free radical production in cells exposed to chemicals known to be radical-mediated toxic agents.

Identification of Bacteria and Determination of Biological Indicators

Science.gov (United States)

Venkateswaran, Kasthuri; La Duc, Myron T.; Vaishampayan, Parag A.

2009-01-01

The ultimate goal of planetary protection research is to develop superior strategies for inactivating resistance bearing micro-organisms like Rummeli - bacillus stabekisii. By first identifying the particular physiologic pathway and/or structural component of the cell/spore that affords it such elevated tolerance, eradication regimes can then be designed to target these resistance-conferring moieties without jeopardizing the structural integrity of spacecraft hardware. Furthermore, hospitals and government agencies frequently use biological indicators to ensure the efficacy of a wide range of sterilization processes. The spores of Rummelibacillus stabekisii, which are far more resistant to many of such perturbations, could likely serve as a more significant biological indicator for potential survival than those being used currently.

Product/Process (P/P) Models For The Defense Waste Processing Facility (DWPF): Model Ranges And Validation Ranges For Future Processing

Energy Technology Data Exchange (ETDEWEB)

Jantzen, C. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Edwards, T. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

2015-09-25

Radioactive high level waste (HLW) at the Savannah River Site (SRS) has successfully been vitrified into borosilicate glass in the Defense Waste Processing Facility (DWPF) since 1996. Vitrification requires stringent product/process (P/P) constraints since the glass cannot be reworked once it is poured into ten foot tall by two foot diameter canisters. A unique “feed forward” statistical process control (SPC) was developed for this control rather than statistical quality control (SQC). In SPC, the feed composition to the DWPF melter is controlled prior to vitrification. In SQC, the glass product would be sampled after it is vitrified. Individual glass property-composition models form the basis for the “feed forward” SPC. The models transform constraints on the melt and glass properties into constraints on the feed composition going to the melter in order to guarantee, at the 95% confidence level, that the feed will be processable and that the durability of the resulting waste form will be acceptable to a geologic repository.

Novel opportunities for computational biology and sociology in drug discovery☆

Science.gov (United States)

Yao, Lixia; Evans, James A.; Rzhetsky, Andrey

2013-01-01

Current drug discovery is impossible without sophisticated modeling and computation. In this review we outline previous advances in computational biology and, by tracing the steps involved in pharmaceutical development, explore a range of novel, high-value opportunities for computational innovation in modeling the biological process of disease and the social process of drug discovery. These opportunities include text mining for new drug leads, modeling molecular pathways and predicting the efficacy of drug cocktails, analyzing genetic overlap between diseases and predicting alternative drug use. Computation can also be used to model research teams and innovative regions and to estimate the value of academy–industry links for scientific and human benefit. Attention to these opportunities could promise punctuated advance and will complement the well-established computational work on which drug discovery currently relies. PMID:20349528

Novel opportunities for computational biology and sociology in drug discovery

Science.gov (United States)

Yao, Lixia

2009-01-01

Drug discovery today is impossible without sophisticated modeling and computation. In this review we touch on previous advances in computational biology and by tracing the steps involved in pharmaceutical development, we explore a range of novel, high value opportunities for computational innovation in modeling the biological process of disease and the social process of drug discovery. These opportunities include text mining for new drug leads, modeling molecular pathways and predicting the efficacy of drug cocktails, analyzing genetic overlap between diseases and predicting alternative drug use. Computation can also be used to model research teams and innovative regions and to estimate the value of academy-industry ties for scientific and human benefit. Attention to these opportunities could promise punctuated advance, and will complement the well-established computational work on which drug discovery currently relies. PMID:19674801

Supporting cognition in systems biology analysis: findings on users' processes and design implications.

Science.gov (United States)

Mirel, Barbara

2009-02-13

Current usability studies of bioinformatics tools suggest that tools for exploratory analysis support some tasks related to finding relationships of interest but not the deep causal insights necessary for formulating plausible and credible hypotheses. To better understand design requirements for gaining these causal insights in systems biology analyses a longitudinal field study of 15 biomedical researchers was conducted. Researchers interacted with the same protein-protein interaction tools to discover possible disease mechanisms for further experimentation. Findings reveal patterns in scientists' exploratory and explanatory analysis and reveal that tools positively supported a number of well-structured query and analysis tasks. But for several of scientists' more complex, higher order ways of knowing and reasoning the tools did not offer adequate support. Results show that for a better fit with scientists' cognition for exploratory analysis systems biology tools need to better match scientists' processes for validating, for making a transition from classification to model-based reasoning, and for engaging in causal mental modelling. As the next great frontier in bioinformatics usability, tool designs for exploratory systems biology analysis need to move beyond the successes already achieved in supporting formulaic query and analysis tasks and now reduce current mismatches with several of scientists' higher order analytical practices. The implications of results for tool designs are discussed.

Process for paraffin isomerization of a distillate range hydrocarbon feedstock

Energy Technology Data Exchange (ETDEWEB)

Chen, N.Y.; Garwood, W.E.; McCullen, S.B.

1993-01-19

Various catalytic processes have been proposed to isomerize n-paraffins so as to lower the pour point of distillate range hydrocarbon feedstocks. However, many available feedstocks contain nitrogen impurities which tend to poison conventional paraffin isomerization catalysts. A process has been developed to obviate or alleviate this problem. According to the invention, the paraffin-containing feedstock is contacted with a crystalline aluminosilicate zeolite catalyst having pore openings defined by a ratio of sorption of n-hexane to o-xylene of over 3 vol % and the ability to crack 3-methylpentane in preference to 2,3 dimethylbutane under defined conditions. The zeolite catalyst includes a Group VIII metal and has a zeolite SiO[sub 2]/Al[sub 2]O[sub 3] ratio of at least 20:1. The contacting is carried out at 199-454 C and a pressure of 100-1,000 psig, preferably 250-600 psig. The group of medium pore zeolites which can be used in the process of the invention includes ZSM-22, ZSM-23, and ZSM-35. The Group VIII metals used in the catalyst are preferably selected from Pt, Pd, Ir, Os, Rh, and Ru and the metal is preferably incorporated into the zeolite by ion exchange up to a metal content of preferably 0.1-3 wt %. Experiments are described to illustrate the invention. 1 tab.

Remediation of a winery wastewater combining aerobic biological oxidation and electrochemical advanced oxidation processes.

Science.gov (United States)

Moreira, Francisca C; Boaventura, Rui A R; Brillas, Enric; Vilar, Vítor J P

2015-05-15

Apart from a high biodegradable fraction consisting of organic acids, sugars and alcohols, winery wastewaters exhibit a recalcitrant fraction containing high-molecular-weight compounds as polyphenols, tannins and lignins. In this context, a winery wastewater was firstly subjected to a biological oxidation to mineralize the biodegradable fraction and afterwards an electrochemical advanced oxidation process (EAOP) was applied in order to mineralize the refractory molecules or transform them into simpler ones that can be further biodegraded. The biological oxidation led to above 97% removals of dissolved organic carbon (DOC), chemical oxygen demand (COD) and 5-day biochemical oxygen demand (BOD5), but was inefficient on the degradation of a bioresistant fraction corresponding to 130 mg L(-1) of DOC, 380 mg O2 L(-1) of COD and 8.2 mg caffeic acid equivalent L(-1) of total dissolved polyphenols. Various EAOPs such as anodic oxidation with electrogenerated H2O2 (AO-H2O2), electro-Fenton (EF), UVA photoelectro-Fenton (PEF) and solar PEF (SPEF) were then applied to the recalcitrant effluent fraction using a 2.2 L lab-scale flow plant containing an electrochemical cell equipped with a boron-doped diamond (BDD) anode and a carbon-PTFE air-diffusion cathode and coupled to a photoreactor with compound parabolic collectors (CPCs). The influence of initial Fe(2+) concentration and current density on the PEF process was evaluated. The relative oxidative ability of EAOPs increased in the order AO-H2O2 < EF < PEF ≤ SPEF. The SPEF process using an initial Fe(2+) concentration of 35 mg L(-1), current density of 25 mA cm(-2), pH of 2.8 and 25 °C reached removals of 86% on DOC and 68% on COD after 240 min, regarding the biologically treated effluent, along with energy consumptions of 45 kWh (kg DOC)(-1) and 5.1 kWh m(-3). After this coupled treatment, color, odor, COD, BOD5, NH4(+), NO3(-) and SO4(2-) parameters complied with the legislation targets and, in addition, a total

Optimization of free ammonia concentration for nitrite accumulation in shortcut biological nitrogen removal process.

Science.gov (United States)

Chung, Jinwook; Shim, Hojae; Park, Seong-Jun; Kim, Seung-Jin; Bae, Wookeun

2006-03-01

A shortcut biological nitrogen removal (SBNR) utilizes the concept of a direct conversion of ammonium to nitrite and then to nitrogen gas. A successful SBNR requires accumulation of nitrite in the system and inhibition of the activity of nitrite oxidizers. A high concentration of free ammonia (FA) inhibits nitrite oxidizers, but unfortunately decreases the ammonium removal rate as well. Therefore, the optimal range of FA concentration is necessary not only to stabilize nitrite accumulation but also to achieve maximum ammonium removal. In order to derive such optimal FA concentrations, the specific substrate utilization rates of ammonium and nitrite oxidizers were measured. The optimal FA concentration range appeared to be 5-10 mg/L for the adapted sludge. The simulated results from the modified inhibition model expressed by FA and ammonium/nitrite concentrations were shown very similar to the experimental results.

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

Science.gov (United States)

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

1998-01-01

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

Design of fluidized-bed, biological denitrification systems

International Nuclear Information System (INIS)

Patton, B.D.; Hancher, C.W.; Pitt, W.W.; Walker, J.F.

1982-01-01

Many commercial processes yield nitrate-containing wastewaters that are being discharged to the environment because traditional recovery or disposal methods are economically unacceptable. The anticipated discharge limits (i.e., 10 to 20 g (NO 3 - )/m 3 ) being considered by many states will not allow continued release of these wastewaters. The new discharge standards can be met economically by use of the fluidizied-bed, biological denitrification process. Research and development studies were conducted with 0.05-, 0.10-, 0.20-, and 0.50-m-diam fluidized-bed bioreactor systems. Feed nitrate concentrations were in the 0 to 10,000 g (NO 3 - )/m 3 range. Using the data from these studies, rate expressions were developed for the destruction of nitrate as a function of nitrate concentration. Methods were also developed for sizing bioreactors and biomass control systems. The sizing methods for fluidized-bed denitrification systems are described, and support systems such as sampling and analysis, instrumentation and controls, utilities, and bacteria storage are discussed. Operation of the process is also briefly discussed to aid the designer. Using the methods presented in this report, fluidized-bed, biological denitrification systems can be designed to treat nitrate wastewater streams

MRI Proton Density Fat Fraction Is Robust Across the Biologically Plausible Range of Triglyceride Spectra in Adults With Nonalcoholic Steatohepatitis

Science.gov (United States)

Hong, Cheng William; Mamidipalli, Adrija; Hooker, Jonathan C.; Hamilton, Gavin; Wolfson, Tanya; Chen, Dennis H.; Dehkordy, Soudabeh Fazeli; Middleton, Michael S.; Reeder, Scott B.; Loomba, Rohit; Sirlin, Claude B.

2017-01-01

Background Proton density fat fraction (PDFF) estimation requires spectral modeling of the hepatic triglyceride (TG) signal. Deviations in the TG spectrum may occur, leading to bias in PDFF quantification. Purpose To investigate the effects of varying six-peak TG spectral models on PDFF estimation bias. Study Type Retrospective secondary analysis of prospectively acquired clinical research data. Population Forty-four adults with biopsy-confirmed nonalcoholic steatohepatitis. Field Strength/Sequence Confounder-corrected chemical-shift-encoded 3T MRI (using a 2D multiecho gradient-recalled echo technique with magnitude reconstruction) and MR spectroscopy. Assessment In each patient, 61 pairs of colocalized MRI-PDFF and MRS-PDFF values were estimated: one pair used the standard six-peak spectral model, the other 60 were six-peak variants calculated by adjusting spectral model parameters over their biologically plausible ranges. MRI-PDFF values calculated using each variant model and the standard model were compared, and the agreement between MRI-PDFF and MRS-PDFF was assessed. Statistical Tests MRS-PDFF and MRI-PDFF were summarized descriptively. Bland–Altman (BA) analyses were performed between PDFF values calculated using each variant model and the standard model. Linear regressions were performed between BA biases and mean PDFF values for each variant model, and between MRI-PDFF and MRS-PDFF. Results Using the standard model, mean MRS-PDFF of the study population was 17.9±8.0% (range: 4.1–34.3%). The difference between the highest and lowest mean variant MRI-PDFF values was 1.5%. Relative to the standard model, the model with the greatest absolute BA bias overestimated PDFF by 1.2%. Bias increased with increasing PDFF (P hepatic fat content, PDFF estimation is robust across the biologically plausible range of TG spectra. Although absolute estimation bias increased with higher PDFF, its magnitude was small and unlikely to be clinically meaningful. Level of

Growth performance of free-range village chickens fed dehydrated processed food waste

Directory of Open Access Journals (Sweden)

Hossein, S.

2015-06-01

Full Text Available The effect of dehydrated processed food waste (DPFW inclusion in the diets on the growth performance (feed intake, body weight gain, body weight change and feed conversion ratio of free-range village chickens was investigated. Food waste collected from 20 different restaurants of Universiti Putra Malaysia Serdang Selangor was processed into DPFW containing 89.3% dry matter, 16% crude protein, 7.1% crude fat, 3.7% crude fiber, 7.4% crude ash, 3.07% NaCl, 1.56% Ca, 0.87% phosphorous and 4053 kcal/kg GE. A total of of 180 village chickens of the Arabian breed were randomly allocated into four dietary treatments of 0 (control, 20, 40 and 60% DPFW for 5-9 week grower and 10-14 week finisher periods with three replicates (15 birds for each replicate. The results showed that the highest feed intake in grower and finisher phases was observed in the control group by 634.0 g and 2,722.1 g, respectively, while the lowest was in 60% DPFW with 586.3 g for grower and 2,542.6 g for finisher phases (P0.05. Body weight gain and body weight change declined linearly with increasing levels of DPFW of more than 20% in the village chicken diets during both grower and finisher rearing phases. FAR increased (P0.05. In conclusion it seems that the dehydrated processed food waste could substitute 20% of formulated feed in grower and finisher phases of free-range village chickens without any adverse effects on growth performance.

Improved elucidation of biological processes linked to diabetic nephropathy by single probe-based microarray data analysis.

Directory of Open Access Journals (Sweden)

Clemens D Cohen

Full Text Available BACKGROUND: Diabetic nephropathy (DN is a complex and chronic metabolic disease that evolves into a progressive fibrosing renal disorder. Effective transcriptomic profiling of slowly evolving disease processes such as DN can be problematic. The changes that occur are often subtle and can escape detection by conventional oligonucleotide DNA array analyses. METHODOLOGY/PRINCIPAL FINDINGS: We examined microdissected human renal tissue with or without DN using Affymetrix oligonucleotide microarrays (HG-U133A by standard Robust Multi-array Analysis (RMA. Subsequent gene ontology analysis by Database for Annotation, Visualization and Integrated Discovery (DAVID showed limited detection of biological processes previously identified as central mechanisms in the development of DN (e.g. inflammation and angiogenesis. This apparent lack of sensitivity may be associated with the gene-oriented averaging of oligonucleotide probe signals, as this includes signals from cross-hybridizing probes and gene annotation that is based on out of date genomic data. We then examined the same CEL file data using a different methodology to determine how well it could correlate transcriptomic data with observed biology. ChipInspector (CI is based on single probe analysis and de novo gene annotation that bypasses probe set definitions. Both methods, RMA and CI, used at default settings yielded comparable numbers of differentially regulated genes. However, when verified by RT-PCR, the single probe based analysis demonstrated reduced background noise with enhanced sensitivity and fewer false positives. CONCLUSIONS/SIGNIFICANCE: Using a single probe based analysis approach with de novo gene annotation allowed an improved representation of the biological processes linked to the development and progression of DN. The improved analysis was exemplified by the detection of Wnt signaling pathway activation in DN, a process not previously reported to be involved in this disease.

Development of biological treatment known as SBR process for supporting radiation treatment of industrial wastewater using electron beam

International Nuclear Information System (INIS)

Khomsaton Abu Bakar; Siti Aishah Hashim; Zulkafli Ghazali; Khairul Zaman Dahlan; Ismail Yaziz

2005-01-01

Electron beam irradiation of wastewater is capable of degrading stable non-biodegradable compound. However it requires high dose and in turn increase the cost of operation. A combination of irradiation and biological treatment is expected to overcome this problem. In this study, the treatment system will use a biological process known as Sequencing Batch Reactor (SBR). The SBR will be developed in a series and each series consist of reaction tank and clarifier tank. Filling and reaction step will occur in reaction tank while settling, decanting and idling step will ensue in the clarifier tank. The process is designed as such to enable rapid and simultaneous analysis on treated sample in order to achieve reliable results. (Author)

Systems Biology of the Fluxome

Directory of Open Access Journals (Sweden)

Miguel A. Aon

2015-07-01

Full Text Available The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. Systems biology-inspired computational methods for translating metabolomics data into fluxomics provide a direct functional, dynamic readout of metabolic networks. When combined with appropriate experimental design, these methods deliver insightful knowledge about cellular function under diverse conditions. The use of computational models accounting for detailed kinetics and regulatory mechanisms allow us to unravel the control and regulatory properties of the fluxome under steady and time-dependent behaviors. This approach extends the analysis of complex systems from description to prediction, including control of complex dynamic behavior ranging from biological rhythms to catastrophic lethal arrhythmias. The powerful quantitative metabolomics-fluxomics approach will help our ability to engineer unicellular and multicellular organisms evolve from trial-and-error to a more predictable process, and from cells to organ and organisms.

A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing.

Science.gov (United States)

Ahmad, Muneer; Jung, Low Tan; Bhuiyan, Al-Amin

2017-10-01

Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals. This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise. Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Π shaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40% to 125% as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms. This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary

Improving the reviewing process in Ecology and Evolutionary Biology

Directory of Open Access Journals (Sweden)

Grossman, G. D.

2014-06-01

Full Text Available I discuss current issues in reviewing and editorial practices in ecology and evolutionary biology and suggest possible solutions for current problems. The reviewing crisis is unlikely to change unless steps are taken by journals to provide greater inclusiveness and incentives to reviewers. In addition, both journals and institutions should reduce their emphasis on publication numbers (least publishable units and impact factors and focus instead on article synthesis and quality which will require longer publications. Academic and research institutions should consider reviewing manuscripts and editorial positions an important part of a researcher’s professional activities and reward them accordingly. Rewarding reviewers either monetarily or via other incentives such as free journal subscriptions may encourage participation in the reviewing process for both profit and non–profit journals. Reviewer performance will likely be improved by measures that increase inclusiveness, such as sending reviews and decision letters to reviewers. Journals may be able to evaluate the efficacy of their reviewing process by comparing citations of rejected but subsequently published papers with those published within the journal at similar times. Finally, constructive reviews: 1 identify important shortcomings and suggest solutions when possible, 2 distinguish trivial from non–trivial problems, and 3 include editor’s evaluations of the reviews including identification of trivial versus substantive comments (i.e., those that must be addressed.

The effect of sanitary landfill leachate aging on the biological treatment and assessment of photoelectrooxidation as a pre-treatment process

Energy Technology Data Exchange (ETDEWEB)

Müller, Gabriel Timm [Universidade Estadual do Rio Grande do Sul (UERGS), R. Gal. João Manoel, 50, CEP 90010-030 Porto Alegre, RS (Brazil); Giacobbo, Alexandre [Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Setor 4, Prédio 74, CEP 91501-970 Porto Alegre, RS (Brazil); Santos Chiaramonte, Edson Abel dos [Universidade Estadual do Rio Grande do Sul (UERGS), R. Gal. João Manoel, 50, CEP 90010-030 Porto Alegre, RS (Brazil); Rodrigues, Marco Antônio Siqueira [Universidade FEEVALE, ICET, RS 239, 2755, CEP 93352-000 Novo Hamburgo, RS (Brazil); Meneguzzi, Alvaro [Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Setor 4, Prédio 74, CEP 91501-970 Porto Alegre, RS (Brazil); Bernardes, Andréa Moura, E-mail: amb@ufrgs.br [Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500, Setor 4, Prédio 74, CEP 91501-970 Porto Alegre, RS (Brazil)

2015-02-15

Highlights: • Photoelectrooxidation (PEO) emerges as a new technology for leachate treatment. • Aging of sanitary landfills acts on leachate composition and biodegradability. • PEO is applied as leachate pretreatment before the biological processes. • PEO produced significant changes in the leachate matrix, easing biological process. - Abstract: The sanitary landfill leachate is a dark liquid, of highly variable composition, with recalcitrant features that hamper conventional biological treatment. The physical–chemical characteristics of the leachate along the landfill aging, as well as their effects on the efficiency of the conventional treatment, were evaluated at this paper. The feasibility of photoelectrooxidation process as an alternative technique for treatment of landfill leachates was also determined. Photoelectrooxidation experiments were conducted in a bench-scale reactor. Analysis of the raw leachate revealed many critical parameters demonstrating that the recalcitrance of leachate tends to increase with time, directly influencing the decline in efficiency of the conventional treatment currently employed. The effects of current density and lamp power were investigated. Using a 400 W power lamp and a current density of 31.5 mA cm{sup −2}, 53% and 61% efficiency for the removal of ammoniacal nitrogen and chemical oxygen demand were respectively achieved by applying photoelectrooxidation process. With the removal of these pollutants, downstream biological treatment should be improved. These results demonstrate that photoelectrooxidation is a feasible technique for the treatment of sanitary landfill leachate, even considering this effluent’s high resistance to treatment.

The effect of sanitary landfill leachate aging on the biological treatment and assessment of photoelectrooxidation as a pre-treatment process

International Nuclear Information System (INIS)

Müller, Gabriel Timm; Giacobbo, Alexandre; Santos Chiaramonte, Edson Abel dos; Rodrigues, Marco Antônio Siqueira; Meneguzzi, Alvaro; Bernardes, Andréa Moura

2015-01-01

Highlights: • Photoelectrooxidation (PEO) emerges as a new technology for leachate treatment. • Aging of sanitary landfills acts on leachate composition and biodegradability. • PEO is applied as leachate pretreatment before the biological processes. • PEO produced significant changes in the leachate matrix, easing biological process. - Abstract: The sanitary landfill leachate is a dark liquid, of highly variable composition, with recalcitrant features that hamper conventional biological treatment. The physical–chemical characteristics of the leachate along the landfill aging, as well as their effects on the efficiency of the conventional treatment, were evaluated at this paper. The feasibility of photoelectrooxidation process as an alternative technique for treatment of landfill leachates was also determined. Photoelectrooxidation experiments were conducted in a bench-scale reactor. Analysis of the raw leachate revealed many critical parameters demonstrating that the recalcitrance of leachate tends to increase with time, directly influencing the decline in efficiency of the conventional treatment currently employed. The effects of current density and lamp power were investigated. Using a 400 W power lamp and a current density of 31.5 mA cm −2 , 53% and 61% efficiency for the removal of ammoniacal nitrogen and chemical oxygen demand were respectively achieved by applying photoelectrooxidation process. With the removal of these pollutants, downstream biological treatment should be improved. These results demonstrate that photoelectrooxidation is a feasible technique for the treatment of sanitary landfill leachate, even considering this effluent’s high resistance to treatment

Biological treatment: Soil impacted with crude oil

International Nuclear Information System (INIS)

Gilbertson, N.; Severns, J.J.

1992-01-01

Biological land treatment proved to be a successful way to manage contamination at a California oil and gas production property. During the project, approximately 120,000 yards of contaminated soil was treated in the treatment plots to below the cleanup goals of 1,000 milligrams per kilograms (mg/kg) total petroleum hydrocarbons. In general, remaining hydrocarbon levels in treated soil were the 200 mg/kg total petroleum hydrocarbons range or lower. Cleanup goals were achieved in less than 2 months for each lift of soil treated. The treated soil was used as fill material in the excavation. No significant odor problems occurred during the project. Groundwater monitoring confirmed that no impact to groundwater occurred due to the biological land treatment process. Design of the treatment plan and regulatory requirements are also discussed

PREFACE: Nanobiology: from physics and engineering to biology

Science.gov (United States)

Nussinov, Ruth; Alemán, Carlos

2006-03-01

infancy. Yet, biology provides an enormous range of engaging and stimulating problems with many in vivo examples of intricate, complex, fascinating biological systems. Understanding, mimicking and controlling the devices which target these processes and which are constructed from these molecules is a tremendous challenge to the converging disciplines in nanobiology.

The yield, processing, and biological consequences of clustered DNA damage induced by ionizing radiation

International Nuclear Information System (INIS)

Shikazono, Naoya; Noguchi, Miho; Fujii, Kentaro; Urushibara, Ayumi; Yokoya, Akinari

2009-01-01

After living cells are exposed to ionizing radiation, a variety of chemical modifications of DNA are induced either directly by ionization of DNA or indirectly through interactions with water-derived radicals. The DNA lesions include single strand breaks (SSB), base lesions, sugar damage, and apurinic/apyrimidinic sites (AP sites). Clustered DNA damage, which is defined as two or more of such lesions within one to two helical turns of DNA induced by a single radiation track, is considered to be a unique feature of ionizing radiation. A double strand break (DSB) is a type of clustered DNA damage, in which single strand breaks are formed on opposite strands in close proximity. Formation and repair of DSBs have been studied in great detail over the years as they have been linked to important biological endpoints, such as cell death, loss of genetic material, chromosome aberration. Although non-DSB clustered DNA damage has received less attention, there is growing evidence of its biological significance. This review focuses on the current understanding of (1) the yield of non-DSB clustered damage induced by ionizing radiation (2) the processing, and (3) biological consequences of non-DSB clustered DNA damage. (author)

Mechanical-biological waste treatment and anaerobic processes. 59. information meeting, Neuwied, October 1999; Mechanisch-biologische Restabfallbehandlung und Anaerobverfahren. 59. Informationsgespraech in Neuwied im Oktober 1999

Energy Technology Data Exchange (ETDEWEB)

Hangen, H.O.; Euler, H.; Leonhardt, H.W. [comps.

1999-10-01

This proceedings volume discusses the specifications for and cost of mechanical-biological waste treatment, the optimisation of economic efficiency and pollutant emissons, the combination of mechanical-biological and thermal waste treatment processes, the value of mechanical-biological waste treatment, waste management concepts, process engineering and practical experience, and the eco-balance of the process. [German] Themen dieses Proceedingsbandes sind: Anforderungen und Kosten der mechanisch-biologischen Abfallbehandlung; Optimierung der Wirtschaftlichkeit und Emissionssituation; Kombination von mechanisch-biologischer und thermischer Muellbehandlung; Bewertung der mechanisch-biologischen Abfallbehandlung, Abfallwirtschaftskonzepte, Verfahrenstechnik und Betriebserfahrungen; Oekobilanz. (SR)

Biological treatment of inorganic ion contamination including radionuclides

Energy Technology Data Exchange (ETDEWEB)

Cherry, R S [Idaho National Engineering and Environmental Lab., Idaho Falls, ID (United States)

1997-12-01

Microorganisms and plants are capable of a broad range of activities useful in treating inorganic contaminants in soil, groundwater, and surface runoff water Among the advantages of biological processes for this purpose are relatively low costs (related to their mild conditions) and the practicality of letting them run unattended. This talk will review both kinds of treatment chemistry that can be done biologically as well as present data from INEEL projects on bioremediation of specific elements. Biological processes can either solubilize or immobilize metals and other ions depending on the need. Uranium ions are solubilized from soil by the local bioproduction of organic acids as chelating agents, allowing removal of this ion as part of an ex-situ treatment process. Further, the microbial production of sulfuric acid can be used to solubilize Cs contamination in concrete surfaces. More usual though is the need to control metal movement in soil or water. Various metals such as Se and Cd are taken up from soil by hyper-accumulating plants, where they can be harvested in concentrated form in the leaves and stems. Excess acidity and a broad variety of toxic metals in acid rock drainage, such as Hg, Cd, Zn and others, can be removed by the production of sulfide ion in an easily fielded biological reactor which may be useful on phosphate processing runoff water contaminated with naturally occuring radioactive materials. Soluble Co, Cu, and Cd can be treated by sorption onto immobilized algae. Inorganic ions can also be directly reduced by bacteria as part of treatment, for example the conversion of soluble selenate ion to insoluble elemental selenium and the conversion of highly toxic CR(VI) to the far less soluble and less toxic Cr(III).

Biological treatment of inorganic ion contamination including radionuclides

International Nuclear Information System (INIS)

Cherry, R.S.

1997-01-01

Microorganisms and plants are capable of a broad range of activities useful in treating inorganic contaminants in soil, groundwater, and surface runoff water Among the advantages of biological processes for this purpose are relatively low costs (related to their mild conditions) and the practicality of letting them run unattended. This talk will review both kinds of treatment chemistry that can be done biologically as well as present data from INEEL projects on bioremediation of specific elements. Biological processes can either solubilize or immobilize metals and other ions depending on the need. Uranium ions are solubilized from soil by the local bioproduction of organic acids as chelating agents, allowing removal of this ion as part of an ex-situ treatment process. Further, the microbial production of sulfuric acid can be used to solubilize Cs contamination in concrete surfaces. More usual though is the need to control metal movement in soil or water. Various metals such as Se and Cd are taken up from soil by hyper-accumulating plants, where they can be harvested in concentrated form in the leaves and stems. Excess acidity and a broad variety of toxic metals in acid rock drainage, such as Hg, Cd, Zn and others, can be removed by the production of sulfide ion in an easily fielded biological reactor which may be useful on phosphate processing runoff water contaminated with naturally occuring radioactive materials. Soluble Co, Cu, and Cd can be treated by sorption onto immobilized algae. Inorganic ions can also be directly reduced by bacteria as part of treatment, for example the conversion of soluble selenate ion to insoluble elemental selenium and the conversion of highly toxic CR(VI) to the far less soluble and less toxic Cr(III)

Multi-Gigahertz radar range processing of baseband and RF carrier modulated signals in Tm:YAG

International Nuclear Information System (INIS)

Merkel, K.D.; Krishna Mohan, R.; Cole, Z.; Chang, T.; Olson, A.; Babbitt, W.R.

2004-01-01

An optical device is described and demonstrated that uses a spatial-spectral holographic material to perform coherent signal processing operations on analog, high-bandwidth optical signals with large time-bandwidth-products. Signal processing is performed as the material records the coherent spectral interference (or cross-power spectrum) of modulated optical signals as a spatial-spectral population grating between electronic transition states. Multiple exposures of processing pulse sequences are integrated with increasing grating strength. The device, coined as the Spatial-Spectral Coherent Holographic Integrating Processor (or S 2 -CHIP), is described as currently envisioned for a broadband, mid-to-high pulse repetition frequency range-Doppler radar signal processing system. Experiments were performed in Tm:YAG (0.1 at% at 5 K) to demonstrate time delay variation, integration dynamics, and effects of coding as applied to a radar range processor. These demonstrations used baseband modulation with a 1 gigabit per second (GPBS) bit rate and code length of 512 bits (512 ns), where delays up to 1.0 μs were resolved with greater than a 40 dB peak to RMS sidelobe ratio after 800 processing shots. Multi-GHz processing was demonstrated using a bit rate of 2.5 GBPS (baseband modulation) and code length of 2048 bits (819.2 ns). Processing of double-sideband modulated signals on a radio frequency (RF) carrier was demonstrated, where 512 bit, 1.0 GBPS codes were modulated on a 1.75 GHz carrier and then modulated on the optical carrier

Structures linking physical and biological processes in headwater streams of the Maybeso watershed, Southeast Alaska

Science.gov (United States)

Mason D. Bryant; Takashi Gomi; Jack J. Piccolo

2007-01-01

We focus on headwater streams originating in the mountainous terrain of northern temperate rain forests. These streams rapidly descend from gradients greater than 20% to less than 5% in U-shaped glacial valleys. We use a set of studies on headwater streams in southeast Alaska to define headwater stream catchments, link physical and biological processes, and describe...

Improving the biological nitrogen removal process in pharmaceutical wastewater treatment plants: a case study.

Science.gov (United States)

Torrijos, M; Carrera, J; Lafuente, J

2004-04-01

The Biological Nitrogen Removal (BNR) process of some pharmaceutical wastewater treatment plants has important operational problems. This study shows that, in order to solve these problems, the design of industrial BNR processes should start by analysing three key parameters: the characteristics of the wastewater load, the determination of the maximum TKN removal rate and the detection of toxic or inhibitory compounds in the wastewater. A case study of this analysis in pharmaceutical wastewater is presented here. In this case, the conventional TKN analytical method does not make an accurate characterisation of the wastewater load because it measures a concentration of 100 mg TKN l(-1) whereas the real concentration, determined with a modified TKN analytical method, is 150-500 mg TKN l(-1). Also, the TKN removal of the treatment system is insufficient in some periods because it falls below legal requirements. This problem might be a consequence of the wrong characterisation of wastewater during the design process. The maximum TKN removal at 27 degrees C (24 mg N g VSS(-1) d(-1) or 197 mg N l(-1) d(-1)) was evaluated in a pilot-scale plant. This value is six times greater than the average NLR applied in the full-scale plant. Finally, some of the components of the wastewater, such as p-phenylenediamine, might have inhibitory or toxic effects on the biological process. P-phenylenediamine causes a large decrease in the nitrification rate. This effect was determined by respirometry. This methodology shows that the effect is mainly inhibitory with a contact time of 30 min and if the contact time is longer, 14 hours, a toxic effect is observed.

The Ansel Adams zone system: HDR capture and range compression by chemical processing

Science.gov (United States)

McCann, John J.

2010-02-01

We tend to think of digital imaging and the tools of PhotoshopTM as a new phenomenon in imaging. We are also familiar with multiple-exposure HDR techniques intended to capture a wider range of scene information, than conventional film photography. We know about tone-scale adjustments to make better pictures. We tend to think of everyday, consumer, silver-halide photography as a fixed window of scene capture with a limited, standard range of response. This description of photography is certainly true, between 1950 and 2000, for instant films and negatives processed at the drugstore. These systems had fixed dynamic range and fixed tone-scale response to light. All pixels in the film have the same response to light, so the same light exposure from different pixels was rendered as the same film density. Ansel Adams, along with Fred Archer, formulated the Zone System, staring in 1940. It was earlier than the trillions of consumer photos in the second half of the 20th century, yet it was much more sophisticated than today's digital techniques. This talk will describe the chemical mechanisms of the zone system in the parlance of digital image processing. It will describe the Zone System's chemical techniques for image synthesis. It also discusses dodging and burning techniques to fit the HDR scene into the LDR print. Although current HDR imaging shares some of the Zone System's achievements, it usually does not achieve all of them.

'TISUCROMA': A Software for Color Processing of Biological Tissue's Images

International Nuclear Information System (INIS)

Arista Romeu, Eduardo J.; La Rosa Vazquez, Jose Manuel de; Valor, Alma; Stolik, Suren

2016-01-01

In this work a software intended to plot and analyze digital image RGB histograms from normal and abnormal regions of biological tissue. The obtained RGB histograms from each zone can be used to show the image in only one color or the mixture of some of them. The Software was developed in Lab View to process the images in a laptop. Some medical application examples are shown. (Author)

State Estimation for a Biological Phosphorus Removal Process using an Asymptotic Observer

DEFF Research Database (Denmark)

Larose, Claude Alain; Jørgensen, Sten Bay

2001-01-01

This study investigated the use of an asymptotic observer for state estimation in a continuous biological phosphorus removal process. The estimated states are the concentration of heterotrophic, autotrophic, and phosphorus accumulating organisms, polyphosphate, glycogen and PHA. The reaction scheme...... if the convergence, driven by the dilution rate, was slow (from 15 to 60 days). The propagation of the measurement noise and a bias in the estimation of glycogen and PHA could be the result of the high condition number of one of the matrices used in the algorithm of the asymptotic observer for the aerated tanks....

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

Science.gov (United States)

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

2012-01-01

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

Personal Constructions of Biological Concepts – The Repertory Grid Approach

Directory of Open Access Journals (Sweden)

Thomas J. J. McCloughlin

2017-03-01

Full Text Available This work discusses repertory grid analysis as a tool for investigating the structures of students’ representations of biological concepts. Repertory grid analysis provides the researcher with a variety of techniques that are not associated with standard methods of concept mapping for investigating conceptual structures. It can provide valuable insights into the learning process, and can be used as a diagnostic tool in identifying problems that students have in understanding biological concepts. The biological concepts examined in this work are ‘natural kinds’: a technical class of concepts which ‘appear’ to have invisible ‘essences’ meaning carrying more perceptual weight than being perceptually similar. Because children give more weight to natural-kind membership when reasoning about traits, it would seem pertinent to apply such knowledge to deep-level research into how children reason in biology. The concept of natural kinds has a particular resonance with biology since biological kinds hold the distinction of being almost all natural kinds, such as when the same ‘stuff or thing’ takes many different forms. We have conducted a range of studies using a diversity of biological natural kinds, but in this paper, we wish to explore some of the theoretical underpinnings in more detail. To afford this exploration, we outline one case-study in a small group of secondary school students exploring the concept of ‘equine’ – that is, what is an equine? Five positive examples were chosen to engaged with by the students and one ‘outlier’ with which to compare the construction process. Recommendations are offered in applying this approach to biological education research.

Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.).

Science.gov (United States)

Bean, Dan W; Dalin, Peter; Dudley, Tom L

2012-07-01

In classical weed biological control, small collections of arthropods are made from one or a few sites in the native range of the target plant and are introduced to suppress the plant where it has become invasive, often across a wide geographic range. Ecological mismatches in the new range are likely, and success using the biocontrol agent may depend on postrelease evolution of beneficial life history traits. In this study, we measure the evolution of critical day length for diapause induction (day length at which 50% of the population enters dormancy), in a beetle (Diorhabda carinulata) introduced into North America from China to control an exotic shrub, Tamarix spp. Beetle populations were sampled from four sites in North America 7 years after introduction, and critical day length was shown to have declined, forming a cline over a latitudinal gradient At one field site, decreased critical day length was correlated with 16 additional days of reproductive activity, resulting in a closer match between beetle life history and the phenology of Tamarix. These findings indicate an enhanced efficacy and an increasingly wider range for D. carinulata in Tamarix control.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

Science.gov (United States)

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

TF-finder: A software package for identifying transcription factors involved in biological processes using microarray data and existing knowledge base

Directory of Open Access Journals (Sweden)

Cui Xiaoqi

2010-08-01

Full Text Available Abstract Background Identification of transcription factors (TFs involved in a biological process is the first step towards a better understanding of the underlying regulatory mechanisms. However, due to the involvement of a large number of genes and complicated interactions in a gene regulatory network (GRN, identification of the TFs involved in a biology process remains to be very challenging. In reality, the recognition of TFs for a given a biological process can be further complicated by the fact that most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation except for small conserved domains. This poses a significant challenge for identification of the exact TFs involved or ranking the importance of a set of TFs to a process of interest. Therefore, new methods for recognizing novel TFs are desperately needed. Although a plethora of methods have been developed to infer regulatory genes using microarray data, it is still rare to find the methods that use existing knowledge base in particular the validated genes known to be involved in a process to bait/guide discovery of novel TFs. Such methods can replace the sometimes-arbitrary process of selection of candidate genes for experimental validation and significantly advance our knowledge and understanding of the regulation of a process. Results We developed an automated software package called TF-finder for recognizing TFs involved in a biological process using microarray data and existing knowledge base. TF-finder contains two components, adaptive sparse canonical correlation analysis (ASCCA and enrichment test, for TF recognition. ASCCA uses positive target genes to bait TFS from gene expression data while enrichment test examines the presence of positive TFs in the outcomes from ASCCA. Using microarray data from salt and water stress experiments, we showed TF-finder is very efficient in recognizing

RARE EARTH ELEMENT IMPACTS ON BIOLOGICAL WASTEWATER TREATMENT

Energy Technology Data Exchange (ETDEWEB)

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

2016-09-01

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. We 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.

Synthesis of 1-indanones with a broad range of biological activity

Directory of Open Access Journals (Sweden)

Marika Turek

2017-03-01

Full Text Available This comprehensive review describes methods for the preparation of 1-indanones published in original and patent literature from 1926 to 2017. More than 100 synthetic methods utilizing carboxylic acids, esters, diesters, acid chlorides, ketones, alkynes, alcohols etc. as starting materials, have been performed. This review also covers the most important studies on the biological activity of 1-indanones and their derivatives which are potent antiviral, anti-inflammatory, analgesic, antimalarial, antibacterial and anticancer compounds. Moreover, they can be used in the treatment of neurodegenerative diseases and as effective insecticides, fungicides and herbicides.

The quest for a new modelling framework in mathematical biology. Comment on "On the interplay between mathematics and biology: Hallmarks towards a new systems biology" by N. Bellomo et al.

Science.gov (United States)

Eftimie, Raluca

2015-03-01

One of the main unsolved problems of modern physics is finding a "theory of everything" - a theory that can explain, with the help of mathematics, all physical aspects of the universe. While the laws of physics could explain some aspects of the biology of living systems (e.g., the phenomenological interpretation of movement of cells and animals), there are other aspects specific to biology that cannot be captured by physics models. For example, it is generally accepted that the evolution of a cell-based system is influenced by the activation state of cells (e.g., only activated and functional immune cells can fight diseases); on the other hand, the evolution of an animal-based system can be influenced by the psychological state (e.g., distress) of animals. Therefore, the last 10-20 years have seen also a quest for a "theory of everything"-approach extended to biology, with researchers trying to propose mathematical modelling frameworks that can explain various biological phenomena ranging from ecology to developmental biology and medicine [1,2,6]. The basic idea behind this approach can be found in a few reviews on ecology and cell biology [6,7,9-11], where researchers suggested that due to the parallel between the micro-scale dynamics and the emerging macro-scale phenomena in both cell biology and in ecology, many mathematical methods used for ecological processes could be adapted to cancer modelling [7,9] or to modelling in immunology [11]. However, this approach generally involved the use of different models to describe different biological aspects (e.g., models for cell and animal movement, models for competition between cells or animals, etc.).

The teach-learning process of high school students: a case of Educational Biology for teachers formation

OpenAIRE

Marisa Laporta Chudo; Maria Cecília Sonzogno

2007-01-01

Objective. To analyze the teach-learning process of high school students, in the scope of Educational Biology. To plan and to develop a methodology with lesson strategies that facilitate the learning. To analyze, in the students vision, the positive and negative points in the process. Method. A research was developed -- of which had participated students of the first semester of the Pedagogy of a high school private institution in São Paulo city -- of the type action-research, with increased ...

Quantum biological gravitational wave detectors

International Nuclear Information System (INIS)

Kopvillem, U.Kh.

1985-01-01

A possibility of producing biological detectors of gravitational waves is considered. High sensitivity of biological systems to outer effects can be ensured by existence of molecule subgroups in Dicke states. Existence of clusters in Dicke state-giant electric dipoles (GED) is supposed in the Froehlich theory. Comparison of biological and physical detectors shows that GED systems have unique properties for detection of gravitational waves if the reception range is narrow

Comparing biological and thermochemical processing of sugarcane bagasse: An energy balance perspective

International Nuclear Information System (INIS)

Leibbrandt, N.H.; Knoetze, J.H.; Goergens, J.F.

2011-01-01

The technical performance of lignocellulosic enzymatic hydrolysis and fermentation versus pyrolysis processes for sugarcane bagasse was evaluated, based on currently available technology. Process models were developed for bioethanol production from sugarcane bagasse using three different pretreatment methods, i.e. dilute acid, liquid hot water and steam explosion, at various solid concentrations. Two pyrolysis processes, namely fast pyrolysis and vacuum pyrolysis, were considered as alternatives to biological processing for the production of biofuels from sugarcane bagasse. For bioethanol production, a minimum of 30% solids in the pretreatment reactor was required to render the process energy self-sufficient, which led to a total process energy demand equivalent to roughly 40% of the feedstock higher heating value. Both vacuum pyrolysis and fast pyrolysis could be operated as energy self-sufficient if 45% of the produced char from fast pyrolysis is used to fuel the process. No char energy is required to fuel the vacuum pyrolysis process due to lower process energy demands (17% compared to 28% of the feedstock higher heating value). The process models indicated that effective process heat integration can result in a 10-15% increase in all process energy efficiencies. Process thermal efficiencies between 52 and 56% were obtained for bioethanol production at pretreatment solids at 30% and 50%, respectively, while the efficiencies were 70% for both pyrolysis processes. The liquid fuel energy efficiency of the best bioethanol process is 41%, while that of crude bio-oil production before upgrading is 67% and 56% via fast and vacuum pyrolysis, respectively. Efficiencies for pyrolysis processes are expected to decrease by up to 15% should upgrade to a transportation fuel of equivalent quality to bioethanol be taken into consideration. -- Highlights: → Liquid biofuels can be produced via lignocellulosic enzymatic hydrolysis and fermentation or pyrolysis. → A minimum of

Microgravity Fluids for Biology, Workshop

Science.gov (United States)

Griffin, DeVon; Kohl, Fred; Massa, Gioia D.; Motil, Brian; Parsons-Wingerter, Patricia; Quincy, Charles; Sato, Kevin; Singh, Bhim; Smith, Jeffrey D.; Wheeler, Raymond M.

2013-01-01

Microgravity Fluids for Biology represents an intersection of biology and fluid physics that present exciting research challenges to the Space Life and Physical Sciences Division. Solving and managing the transport processes and fluid mechanics in physiological and biological systems and processes are essential for future space exploration and colonization of space by humans. Adequate understanding of the underlying fluid physics and transport mechanisms will provide new, necessary insights and technologies for analyzing and designing biological systems critical to NASAs mission. To enable this mission, the fluid physics discipline needs to work to enhance the understanding of the influence of gravity on the scales and types of fluids (i.e., non-Newtonian) important to biology and life sciences. In turn, biomimetic, bio-inspired and synthetic biology applications based on physiology and biology can enrich the fluid mechanics and transport phenomena capabilities of the microgravity fluid physics community.

Network biology: Describing biological systems by complex networks. Comment on "Network science of biological systems at different scales: A review" by M. Gosak et al.

Science.gov (United States)

Jalili, Mahdi

2018-03-01

I enjoyed reading Gosak et al. review on analysing biological systems from network science perspective [1]. Network science, first started within Physics community, is now a mature multidisciplinary field of science with many applications ranging from Ecology to biology, medicine, social sciences, engineering and computer science. Gosak et al. discussed how biological systems can be modelled and described by complex network theory which is an important application of network science. Although there has been considerable progress in network biology over the past two decades, this is just the beginning and network science has a great deal to offer to biology and medical sciences.

A Range Ambiguity Suppression Processing Method for Spaceborne SAR with Up and Down Chirp Modulation.

Science.gov (United States)

Wen, Xuejiao; Qiu, Xiaolan; Han, Bing; Ding, Chibiao; Lei, Bin; Chen, Qi

2018-05-07

Range ambiguity is one of the factors which affect the SAR image quality. Alternately transmitting up and down chirp modulation pulses is one of the methods used to suppress the range ambiguity. However, the defocusing range ambiguous signal can still hold the stronger backscattering intensity than the mainlobe imaging area in some case, which has a severe impact on visual effects and subsequent applications. In this paper, a novel hybrid range ambiguity suppression method for up and down chirp modulation is proposed. The method can obtain the ambiguity area image and reduce the ambiguity signal power appropriately, by applying pulse compression using a contrary modulation rate and CFAR detecting method. The effectiveness and correctness of the approach is demonstrated by processing the archive images acquired by Chinese Gaofen-3 SAR sensor in full-polarization mode.

Comparative biology approaches for charged particle exposures and cancer development processes

Science.gov (United States)

Kronenberg, Amy; Gauny, Stacey; Kwoh, Ely; Sudo, Hiroko; Wiese, Claudia; Dan, Cristian; Turker, Mitchell

Comparative biology studies can provide useful information for the extrapolation of results be-tween cells in culture and the more complex environment of the tissue. In other circumstances, they provide a method to guide the interpretation of results obtained for cells from differ-ent species. We have considered several key cancer development processes following charged particle exposures using comparative biology approaches. Our particular emphases have been mutagenesis and genomic instability. Carcinogenesis requires the accumulation of mutations and most of htese mutations occur on autosomes. Two loci provide the greatest avenue for the consideration of charged particle-induced mutation involving autosomes: the TK1 locus in human cells and the APRT locus in mouse cells. Each locus can provide information on a wide variety of mutational changes, from small intragenic mutations through multilocus dele-tions and extensive tracts of mitotic recombination. In addition, the mouse model can provide a direct measurement of chromosome loss which cannot be accomplished in the human cell system. Another feature of the mouse APRT model is the ability to examine effects for cells exposed in vitro with those obtained for cells exposed in situ. We will provide a comparison of the results obtained for the TK1 locus following 1 GeV/amu Fe ion exposures to the human lymphoid cells with those obtained for the APRT locus for mouse kidney epithelial cells (in vitro or in situ). Substantial conservation of mechanisms is found amongst these three exposure scenarios, with some differences attributable to the specific conditions of exposure. A similar approach will be applied to the consideraiton of proton-induced autosomal mutations in the three model systems. A comparison of the results obtained for Fe ions vs. protons in each case will highlight LET-specificc differences in response. Another cancer development process that is receiving considerable interest is genomic instability. We

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

Science.gov (United States)

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

2016-03-01

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

Interactomes, manufacturomes and relational biology: analogies between systems biology and manufacturing systems

Science.gov (United States)

2011-01-01

Background We review and extend the work of Rosen and Casti who discuss category theory with regards to systems biology and manufacturing systems, respectively. Results We describe anticipatory systems, or long-range feed-forward chemical reaction chains, and compare them to open-loop manufacturing processes. We then close the loop by discussing metabolism-repair systems and describe the rationality of the self-referential equation f = f (f). This relationship is derived from some boundary conditions that, in molecular systems biology, can be stated as the cardinality of the following molecular sets must be about equal: metabolome, genome, proteome. We show that this conjecture is not likely correct so the problem of self-referential mappings for describing the boundary between living and nonliving systems remains an open question. We calculate a lower and upper bound for the number of edges in the molecular interaction network (the interactome) for two cellular organisms and for two manufacturomes for CMOS integrated circuit manufacturing. Conclusions We show that the relevant mapping relations may not be Abelian, and that these problems cannot yet be resolved because the interactomes and manufacturomes are incomplete. PMID:21689427

Biology technology, and innovation in high school curriculum

Directory of Open Access Journals (Sweden)

Antonio Carlos Rodrigues de Amorim

1998-01-01

Full Text Available Based on frameworks that propose the contextualization of science education centered in the science/technology/ society relationships, and on the belief that the teacher has a fundamental role on the curriculum innovation processes, this paper describes and analyses different elements of the pedagogical practice of teachers of the city of Campinas/SP, in the perspective of outlining an overview regarding the already existing biology and technology relationship. It focuses in a detailed way the conceptions of the relationships between biology and technology present in the instructional materials used or produced by teachers, describing and discussing the wide range spectrum of identified possibilities. It also emphasizes the approaches to biology and technology relationships identified by interviewing the teachers, being them similar or not to those found in the instructional materials. Indicators of the existence of a problematic theory and practice association, in which the theoretical elements (science are hierarchically superior to the practical elements (technology, were detected. This kind of association should constitute a focus of attention in the construction of innovative proposals for the biology curriculum, since science classroom discussions regarding technology – in their ethical, aesthetical, epistemological, and marketing aspects – represent an important path to dimension the biological knowledge in the capitalist contemporary society.

Integration of Principles of Systems Biology and Radiation Biology: Toward Development of in silico Models to Optimize IUdR-Mediated Radiosensitization of DNA Mismatch Repair Deficient (Damage Tolerant) Human Cancers

International Nuclear Information System (INIS)

Kinsella, Timothy J.; Gurkan-Cavusoglu, Evren; Du, Weinan; Loparo, Kenneth A.

2011-01-01

Over the last 7 years, we have focused our experimental and computational research efforts on improving our understanding of the biochemical, molecular, and cellular processing of iododeoxyuridine (IUdR) and ionizing radiation (IR) induced DNA base damage by DNA mismatch repair (MMR). These coordinated research efforts, sponsored by the National Cancer Institute Integrative Cancer Biology Program (ICBP), brought together system scientists with expertise in engineering, mathematics, and complex systems theory and translational cancer researchers with expertise in radiation biology. Our overall goal was to begin to develop computational models of IUdR- and/or IR-induced base damage processing by MMR that may provide new clinical strategies to optimize IUdR-mediated radiosensitization in MMR deficient (MMR − ) “damage tolerant” human cancers. Using multiple scales of experimental testing, ranging from purified protein systems to in vitro (cellular) and to in vivo (human tumor xenografts in athymic mice) models, we have begun to integrate and interpolate these experimental data with hybrid stochastic biochemical models of MMR damage processing and probabilistic cell cycle regulation models through a systems biology approach. In this article, we highlight the results and current status of our integration of radiation biology approaches and computational modeling to enhance IUdR-mediated radiosensitization in MMR − damage tolerant cancers.

The relative biological effectiveness of antiprotons

DEFF Research Database (Denmark)

Holzscheiter, Michael H.; Alsner, Jan; Bassler, Niels

2016-01-01

Background and purpose: Aside from the enhancement of physical dose deposited by antiprotons annihilating in tissue-like material compared to protons of the same range a further increase of biological effective dose has been demonstrated. This enhancement can be expressed in an increase of the re......Background and purpose: Aside from the enhancement of physical dose deposited by antiprotons annihilating in tissue-like material compared to protons of the same range a further increase of biological effective dose has been demonstrated. This enhancement can be expressed in an increase...... of the relative biological effectiveness (RBE) of antiprotons near the end of range. We have performed the first-ever direct measurement of the RBE of antiprotons both at rest and in flight. Materials and methods: Experimental data were generated on the RBE of an antiproton beam entering a tissue-like target...

Development of a computational system for management of risks in radiosterilization processes of biological tissues

International Nuclear Information System (INIS)

Montoya, Cynara Viterbo

2009-01-01

Risk management can be understood to be a systematic management which aims to identify record and control the risks of a process. Applying risk management becomes a complex activity, due to the variety of professionals involved. In order to execute risk management the following are requirements of paramount importance: the experience, discernment and judgment of a multidisciplinary team, guided by means of quality tools, so as to provide standardization in the process of investigating the cause and effects of risks and dynamism in obtaining the objective desired, i.e. the reduction and control of the risk. This work aims to develop a computational system of risk management (software) which makes it feasible to diagnose the risks of the processes of radiosterilization of biological tissues. The methodology adopted was action-research, according to which the researcher performs an active role in the establishment of the problems found, in the follow-up and in the evaluation of the actions taken owing to the problems. The scenario of this action-research was the Laboratory of Biological Tissues (LTB) in the Radiation Technology Center IPEN/CNEN-SP - Sao Paulo/Brazil. The software developed was executed in PHP and Flash/MySQL language, the server (hosting), the software is available on the Internet (www.vcrisk.com.br), which the user can access from anywhere by means of the login/access password previously sent by email to the team responsible for the tissue to be analyzed. The software presents friendly navigability whereby the user is directed step-by-step in the process of investigating the risk up to the means of reducing it. The software 'makes' the user comply with the term and present the effectiveness of the actions taken to reduce the risk. Applying this system provided the organization (LTB/CTR/IPEN) with dynamic communication, effective between the members of the multidisciplinary team: a) in decision-making; b) in lessons learned; c) in knowing the new risk

Methods to Enrich Exosomes from Conditioned Media and Biological Fluids.

Science.gov (United States)

Sharma, Shayna; Scholz-Romero, Katherin; Rice, Gregory E; Salomon, Carlos

2018-01-01

Exosomes are nano-vesicles which can transport a range of molecules including but not limited to proteins and miRNA. This ability of exosomes renders them useful in cellular communication often resulting in biological changes. They have several functions in facilitating normal biological processes such as immune responses and an involvement in pregnancy. However, they have also been linked to pathological conditions including cancer and pregnancy complications such as preeclampsia. An understanding for the role of exosomes in preeclampsia is based on the ability to purify and characterize exosomes. There have been several techniques proposed for the enrichment of exosomes such as ultracentrifugation, density gradient separation, and ultrafiltration although there is no widely accepted optimized technique. Here we describe a workflow for isolating exosomes from cell-conditioned media and biological fluids using a combination of centrifugation, buoyant density, and ultrafiltration approaches.

Biological fuel cells and their applications

OpenAIRE

Shukla, AK; Suresh, P; Berchmans, S; Rajendran, A

2004-01-01

One type of genuine fuel cell that does hold promise in the long-term is the biological fuel cell. Unlike conventional fuel cells, which employ hydrogen, ethanol and methanol as fuel, biological fuel cells use organic products produced by metabolic processes or use organic electron donors utilized in the growth processes as fuels for current generation. A distinctive feature of biological fuel cells is that the electrode reactions are controlled by biocatalysts, i.e. the biological redox-reac...

Biologically active compounds to develop bioelectronics and bio photonics

Science.gov (United States)

Mishra, Ashok Kumar; Tiwari, Satya Prakash

2018-05-01

Recent reports on biomaterials and biological systems at nano scale provide researchers with a fertile ground with regard to materials, enabling bioelectronics, bio sensing and new nanotechnologies that cover a wide range of applications. The signal transductions have been reported for many biological phenomenons and new field of biophysics namely Biosensors and Bioelectronics have been emerged out. The advances in the study of various aspects of bio molecules like electrical, optical, thermal etc has established the interesting area of research like biophotonics, nanobiotechnology, molecular solid, molecular liquids, bio instrumentation etc. The present study discusses the some aspects and applications of the bioprocess yields nanostructures that are nearly flawless in composition, stereo specific in structure, and flexible. Furthermore, these biomaterials are environment friendly because they are biodegradable in nature. Biological compounds are self assembled into complex nanostructures and behave like a system possessing long range hierarchical nanoscale order. In addition, chemical modification and genetic engineering can be used to modify bio materials to enhance a specific property. Various biomaterials have been reported which allow nanostructure control for nano photonic applications. The dielectric and conduction properties of the bio molecules have been the subject of many investigations. As a result, there exist a wealth of valuable information on the charge transport and rotational properties of many bio molecules. Amino acids and proteins, nucleic acids, lipids, cell and tissues have been characterized over a wide frequency spectrum ranging from a few hertz to Giga hertz. In certain cases, dielectric measurements have been exploited to probe the physical changes taking place in biologically important structures, for example, in lipid phase transition process in membrane. The phase transition in membrane may be analyzed by applying the theory for

Efficient high-throughput biological process characterization: Definitive screening design with the ambr250 bioreactor system.

Science.gov (United States)

Tai, Mitchell; Ly, Amanda; Leung, Inne; Nayar, Gautam

2015-01-01

The burgeoning pipeline for new biologic drugs has increased the need for high-throughput process characterization to efficiently use process development resources. Breakthroughs in highly automated and parallelized upstream process development have led to technologies such as the 250-mL automated mini bioreactor (ambr250™) system. Furthermore, developments in modern design of experiments (DoE) have promoted the use of definitive screening design (DSD) as an efficient method to combine factor screening and characterization. Here we utilize the 24-bioreactor ambr250™ system with 10-factor DSD to demonstrate a systematic experimental workflow to efficiently characterize an Escherichia coli (E. coli) fermentation process for recombinant protein production. The generated process model is further validated by laboratory-scale experiments and shows how the strategy is useful for quality by design (QbD) approaches to control strategies for late-stage characterization. © 2015 American Institute of Chemical Engineers.

Processing of biological waste. Ecological efficiency and potential; Behandlung von Bioabfaellen. Oekoeffizienz und Potenziale

Energy Technology Data Exchange (ETDEWEB)

Pitschke, Thorsten; Peche, Rene; Tronecker, Dieter; Kreibe, Siegfried [bifa Umweltinstitut GmbH, Augsburg (Germany)

2013-07-01

The sustainable usage of biological wastes has to be focused on the targets protection of resources and minimization of environmental impact. The only focus on the energy inventory is not sufficient. The following recommendations are summarized: separated bio-waste collection is usually more eco-efficient; the optimized bio-waste processing should be available according to the biodegradability; anaerobic degradation for biogas production and subsequent aerobic degradation of the fermentation product for compost can be combined; low-emission operational standards should be mandatory, innovation and investment should be promoted b reliable boundary conditions; ecological aspects should be equivalent to low-cost considerations; regulatory measures should be implemented for separated bio-waste collection and processing.

Intended process water management concept for the mechanical biological treatment of municipal solid waste

Institute of Scientific and Technical Information of China (English)

D. Weichgrebe; S. Maerker; T. Boning; H. Stegemann

2008-01-01

Accumulating operational experience in both aerobic and anaerobic mechanical biological waste treatment (MBT) makes it increasingly obvious that controlled water management would substantially reduce the cost of MBT and also enhance resource recovery of the organic and inorganic fraction. The MBT plant at Gescher, Germany, is used as an example in order to determine the quantity and composition of process water and leachates from intensive and subsequent rotting, pressing water from anaerobic digestion and scrubber water from acid exhaust air treatment, and hence prepare an MBT water balance. The potential of, requirements for and limits to internal process water reuse as well as the possibilities of resource recovery from scrubber water are also examined. Finally, an assimilated process water management concept with the purpose of an extensive reduction of wastewater quantity and freshwater demand is presented.

Towards Establishing Capacity for Biological Dosimetry at Ghana Atomic Energy Commission.

Science.gov (United States)

Achel, Daniel Gyingiri; Achoribo, Elom; Agbenyegah, Sandra; Adaboro, Rudolph M; Donkor, Shadrack; Adu-Bobi, Nana A K; Agyekum, Akwasi A; Akuamoa, Felicia; Tagoe, Samuel N; Kyei, Kofi A; Yarney, Joel; Serafin, Antonio; Akudugu, John M

2016-01-01

The aim of this study was not only to obtain basic technical prerequisites for the establishment of capacity of biological dosimetry at the Ghana Atomic Energy Commission (GAEC) but also to stimulate interest in biological dosimetry research in Ghana and Sub-Saharan Africa. Peripheral blood from four healthy donors was exposed to different doses (0-6 Gy) of gamma rays from a radiotherapy machine and lymphocytes were subsequently stimulated, cultured, and processed according to standard protocols for 48-50 h. Processed cells were analyzed for the frequencies of dicentric and centric ring chromosomes. Radiation dose delivered to the experimental model was verified using GafChromic® EBT films in parallel experiments. Basic technical prerequisites for the establishment of capacity of biological dosimetry in the GAEC have been realized and expertise in the dicentric chromosome assay consolidated. We successfully obtained preliminary cytogenetic data for a dose-response relationship of the irradiated blood lymphocytes. The data strongly indicate the existence of significant linear (α) and quadratic (β) components and are consistent with those published for the production of chromosome aberrations in comparable absorbed dose ranges.

Content-rich biological network constructed by mining PubMed abstracts

Directory of Open Access Journals (Sweden)

Sharp Burt M

2004-10-01

Full Text Available Abstract Background The integration of the rapidly expanding corpus of information about the genome, transcriptome, and proteome, engendered by powerful technological advances, such as microarrays, and the availability of genomic sequence from multiple species, challenges the grasp and comprehension of the scientific community. Despite the existence of text-mining methods that identify biological relationships based on the textual co-occurrence of gene/protein terms or similarities in abstract texts, knowledge of the underlying molecular connections on a large scale, which is prerequisite to understanding novel biological processes, lags far behind the accumulation of data. While computationally efficient, the co-occurrence-based approaches fail to characterize (e.g., inhibition or stimulation, directionality biological interactions. Programs with natural language processing (NLP capability have been created to address these limitations, however, they are in general not readily accessible to the public. Results We present a NLP-based text-mining approach, Chilibot, which constructs content-rich relationship networks among biological concepts, genes, proteins, or drugs. Amongst its features, suggestions for new hypotheses can be generated. Lastly, we provide evidence that the connectivity of molecular networks extracted from the biological literature follows the power-law distribution, indicating scale-free topologies consistent with the results of previous experimental analyses. Conclusions Chilibot distills scientific relationships from knowledge available throughout a wide range of biological domains and presents these in a content-rich graphical format, thus integrating general biomedical knowledge with the specialized knowledge and interests of the user. Chilibot http://www.chilibot.net can be accessed free of charge to academic users.

Fostering synergy between cell biology and systems biology.

Science.gov (United States)

Eddy, James A; Funk, Cory C; Price, Nathan D

2015-08-01

In the shared pursuit of elucidating detailed mechanisms of cell function, systems biology presents a natural complement to ongoing efforts in cell biology. Systems biology aims to characterize biological systems through integrated and quantitative modeling of cellular information. The process of model building and analysis provides value through synthesizing and cataloging information about cells and molecules, predicting mechanisms and identifying generalizable themes, generating hypotheses and guiding experimental design, and highlighting knowledge gaps and refining understanding. In turn, incorporating domain expertise and experimental data is crucial for building towards whole cell models. An iterative cycle of interaction between cell and systems biologists advances the goals of both fields and establishes a framework for mechanistic understanding of the genome-to-phenome relationship. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

From Biology to Quality (BQ)

DEFF Research Database (Denmark)

Nielsen, Michael Engelbrecht; Ingerslev, Hans-Christian

2011-01-01

“Quality is never an accident; it is always the result of high intention, sincere effort, intelligent direction and skilful execution; it represents the wise choice of many alternatives.” (William A. Foster) The quality of fish meat is dependent upon a wide range of biological and non-biological ...

Mathematical modeling of heat treatment processes conserving biological activity of plant bioresources

Science.gov (United States)

Rodionova, N. S.; Popov, E. S.; Pozhidaeva, E. A.; Pynzar, S. S.; Ryaskina, L. O.

2018-05-01

The aim of this study is to develop a mathematical model of the heat exchange process of LT-processing to estimate the dynamics of temperature field changes and optimize the regime parameters, due to the non-stationarity process, the physicochemical and thermophysical properties of food systems. The application of LT-processing, based on the use of low-temperature modes in thermal culinary processing of raw materials with preliminary vacuum packaging in a polymer heat- resistant film is a promising trend in the development of technics and technology in the catering field. LT-processing application of food raw materials guarantees the preservation of biologically active substances in food environments, which are characterized by a certain thermolability, as well as extend the shelf life and high consumer characteristics of food systems that are capillary-porous bodies. When performing the mathematical modeling of the LT-processing process, the packet of symbolic mathematics “Maple” was used, as well as the mathematical packet flexPDE that uses the finite element method for modeling objects with distributed parameters. The processing of experimental results was evaluated with the help of the developed software in the programming language Python 3.4. To calculate and optimize the parameters of the LT processing process of polycomponent food systems, the differential equation of non-stationary thermal conductivity was used, the solution of which makes it possible to identify the temperature change at any point of the solid at different moments. The present study specifies data on the thermophysical characteristics of the polycomponent food system based on plant raw materials, with the help of which the physico-mathematical model of the LT- processing process has been developed. The obtained mathematical model allows defining of the dynamics of the temperature field in different sections of the LT-processed polycomponent food systems on the basis of calculating the

Marine molecular biology: an emerging field of biological sciences.

Science.gov (United States)

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

2008-01-01

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

Biological Small Angle Scattering: Techniques, Strategies and Tips

Energy Technology Data Exchange (ETDEWEB)

Chaudhuri, Barnali [University at Buffalo (SUNY); Muñoz, Inés G. [Centro Nacional de Investigaciones Oncológicas Madrid, Madrid, Spain; Urban, Volker S. [ORNL; Qian, Shuo [ORNL

2017-12-01

This book provides a clear, comprehensible and up-to-date description of how Small Angle Scattering (SAS) can help structural biology researchers. SAS is an efficient technique that offers structural information on how biological macromolecules behave in solution. SAS provides distinct and complementary data for integrative structural biology approaches in combination with other widely used probes, such as X-ray crystallography, Nuclear magnetic resonance, Mass spectrometry and Cryo-electron Microscopy. The development of brilliant synchrotron small-angle X-ray scattering (SAXS) beam lines has increased the number of researchers interested in solution scattering. SAS is especially useful for studying conformational changes in proteins, highly flexible proteins, and intrinsically disordered proteins. Small-angle neutron scattering (SANS) with neutron contrast variation is ideally suited for studying multi-component assemblies as well as membrane proteins that are stabilized in surfactant micelles or vesicles. SAS is also used for studying dynamic processes of protein fibrillation in amyloid diseases, and pharmaceutical drug delivery. The combination with size-exclusion chromatography further increases the range of SAS applications.The book is written by leading experts in solution SAS methodologies. The principles and theoretical background of various SAS techniques are included, along with practical aspects that range from sample preparation to data presentation for publication. Topics covered include techniques for improving data quality and analysis, as well as different scientific applications of SAS. With abundant illustrations and practical tips, we hope the clear explanations of the principles and the reviews on the latest progresses will serve as a guide through all aspects of biological solution SAS.The scope of this book is particularly relevant for structural biology researchers who are new to SAS. Advanced users of the technique will find it helpful for

Diversity of Secondary Metabolites from Marine Bacillus Species: Chemistry and Biological Activity

Science.gov (United States)

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Islam, Mohammad Tofazzal

2013-01-01

Marine Bacillus species produce versatile secondary metabolites including lipopeptides, polypeptides, macrolactones, fatty acids, polyketides, and isocoumarins. These structurally diverse compounds exhibit a wide range of biological activities, such as antimicrobial, anticancer, and antialgal activities. Some marine Bacillus strains can detoxify heavy metals through reduction processes and have the ability to produce carotenoids. The present article reviews the chemistry and biological activities of secondary metabolites from marine isolates. Side by side, the potential for application of these novel natural products from marine Bacillus strains as drugs, pesticides, carotenoids, and tools for the bioremediation of heavy metal toxicity are also discussed. PMID:23941823

A Range Ambiguity Suppression Processing Method for Spaceborne SAR with Up and Down Chirp Modulation

Directory of Open Access Journals (Sweden)

Xuejiao Wen

2018-05-01

Full Text Available Range ambiguity is one of the factors which affect the SAR image quality. Alternately transmitting up and down chirp modulation pulses is one of the methods used to suppress the range ambiguity. However, the defocusing range ambiguous signal can still hold the stronger backscattering intensity than the mainlobe imaging area in some case, which has a severe impact on visual effects and subsequent applications. In this paper, a novel hybrid range ambiguity suppression method for up and down chirp modulation is proposed. The method can obtain the ambiguity area image and reduce the ambiguity signal power appropriately, by applying pulse compression using a contrary modulation rate and CFAR detecting method. The effectiveness and correctness of the approach is demonstrated by processing the archive images acquired by Chinese Gaofen-3 SAR sensor in full-polarization mode.

Range expansion drives dispersal evolution in an equatorial three-species symbiosis.

Science.gov (United States)

Léotard, Guillaume; Debout, Gabriel; Dalecky, Ambroise; Guillot, Sylvain; Gaume, Laurence; McKey, Doyle; Kjellberg, Finn

2009-01-01

Recurrent climatic oscillations have produced dramatic changes in species distributions. This process has been proposed to be a major evolutionary force, shaping many life history traits of species, and to govern global patterns of biodiversity at different scales. During range expansions selection may favor the evolution of higher dispersal, and symbiotic interactions may be affected. It has been argued that a weakness of climate fluctuation-driven range dynamics at equatorial latitudes has facilitated the persistence there of more specialized species and interactions. However, how much the biology and ecology of species is changed by range dynamics has seldom been investigated, particularly in equatorial regions. We studied a three-species symbiosis endemic to coastal equatorial rainforests in Cameroon, where the impact of range dynamics is supposed to be limited, comprised of two species-specific obligate mutualists--an ant-plant and its protective ant--and a species-specific ant parasite of this mutualism. We combined analyses of within-species genetic diversity and of phenotypic variation in a transect at the southern range limit of this ant-plant system. All three species present congruent genetic signatures of recent gradual southward expansion, a result compatible with available regional paleoclimatic data. As predicted, this expansion has been accompanied by the evolution of more dispersive traits in the two ant species. In contrast, we detected no evidence of change in lifetime reproductive strategy in the tree, nor in its investment in food resources provided to its symbiotic ants. Despite the decreasing investment in protective workers and the increasing investment in dispersing females by both the mutualistic and the parasitic ant species, there was no evidence of destabilization of the symbiosis at the colonization front. To our knowledge, we provide here the first evidence at equatorial latitudes that biological traits associated with dispersal are

Integrated omics in systems biology: The new frontier for environmental biotechnology, ecology, and evolution

OpenAIRE

Hazen, Terry C.

2006-01-01

Environmental biotechnology encompasses a wide range of characterization, monitoring and control or remediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment. Indeed, our ability to sequence an entire microbial genome in just a few hours is leading to similar breakthroughs in characterizing proteomes, metabolome...

An introduction to continuous-time stochastic processes theory, models, and applications to finance, biology, and medicine

CERN Document Server

Capasso, Vincenzo

2015-01-01

This textbook, now in its third edition, offers a rigorous and self-contained introduction to the theory of continuous-time stochastic processes, stochastic integrals, and stochastic differential equations. Expertly balancing theory and applications, the work features concrete examples of modeling real-world problems from biology, medicine, industrial applications, finance, and insurance using stochastic methods. No previous knowledge of stochastic processes is required. Key topics include: * Markov processes * Stochastic differential equations * Arbitrage-free markets and financial derivatives * Insurance risk * Population dynamics, and epidemics * Agent-based models New to the Third Edition: * Infinitely divisible distributions * Random measures * Levy processes * Fractional Brownian motion * Ergodic theory * Karhunen-Loeve expansion * Additional applications * Additional  exercises * Smoluchowski  approximation of  Langevin systems An Introduction to Continuous-Time Stochastic Processes, Third Editio...

Applications of Free Electron Lasers in Biology and Medicine

International Nuclear Information System (INIS)

Pelka, J.B.; Tybor, K.R.; Nietubyc, R.; Wrochna, G.

2010-01-01

The advent of free electron lasers opens up new opportunities to probe the dynamics of ultrafast processes and the structure of matter with unprecedented spatial and temporal resolution. New methods inaccessible with other known types of radiation sources can be developed, resulting in a breakthrough in deep understanding the fundamentals of life as well as in numerous medical and biological applications. In the present work the properties of free electron laser radiation that make the sources excellent for probing biological matter at an arbitrary wavelength, in a wide range of intensities and pulse durations are briefly discussed. A number of biophysical and biomedical applications of the new sources, currently considered among the most promising in the field, are presented. (author)

Biology of Healthy Aging and Longevity.

Science.gov (United States)

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

Anaerobic-aerobic biological treatment of a mixture of cheese whey and dairy manure

Energy Technology Data Exchange (ETDEWEB)

Lo, K.V.; Liao, P.H.

1989-01-01

The integrated anaerobic-aerobic biological treatment system consisted of an anaerobic rotating biological reactor and an aerobic sequencing batch reactor. Three sequencing batch reactors were used in the aerobic process. A mixture of cheese whey and dairy manure was successfully digested in an anaerobic rotating biological contactor which served as a first step in the waste treatment process. The methane production rate, which is dependent on the organic loading rate, ranged between 1.43 and 3.74 litres methane per litre reactor per day. As the organic loading rate increased, total methane production also increased. In the anaerobic digestion step, over 46% of chemical oxygen demand was removed. The potential pollutants were further destroyed by the aerobic treatment. More than 93% of the remaining chemical oxygen demand was removed in the sequencing batch reactors operated at 22/sup 0/C. The treatment efficiency was lower for the aerobic reactor operated at a lower temperature (10/sup 0/C). (author).

Stochastic Methods in Biology

CERN Document Server

Kallianpur, Gopinath; Hida, Takeyuki

1987-01-01

The use of probabilistic methods in the biological sciences has been so well established by now that mathematical biology is regarded by many as a distinct dis­ cipline with its own repertoire of techniques. The purpose of the Workshop on sto­ chastic methods in biology held at Nagoya University during the week of July 8-12, 1985, was to enable biologists and probabilists from Japan and the U. S. to discuss the latest developments in their respective fields and to exchange ideas on the ap­ plicability of the more recent developments in stochastic process theory to problems in biology. Eighteen papers were presented at the Workshop and have been grouped under the following headings: I. Population genetics (five papers) II. Measure valued diffusion processes related to population genetics (three papers) III. Neurophysiology (two papers) IV. Fluctuation in living cells (two papers) V. Mathematical methods related to other problems in biology, epidemiology, population dynamics, etc. (six papers) An important f...

Evaluation of the processing of dry biological ferment for gamma radiation

International Nuclear Information System (INIS)

Sabundjian, Ingrid Traete

2007-01-01

The developed work had with objectives to demonstrate if it had alteration in the growth of UFC in plate and in the viability of yeasts and total bacteria when dry biological ferment was dealt with by different doses to gamma radiation and under different times storage, to determine the D10 dose for total bacteria and yeasts in this product and to analyzed the processing of this product it promoted some benefit without causing unfeasibility of exactly. The different samples of dry biological ferment had been irradiated at IPEN in a Gammacell - 220 source at 0.5; 1; 2 and 3 kGy doses (dose rate of 3.51 kGy/h). This procedure referring samples to each dose of radiation had been after destined to the microbiological analysis and the test of viability while excessively the samples had been stored the ambient temperature (23 degree C). The increase of the dose of radiation caused a reduction in the counting of yeasts growth, of total bacteria growth and also in the frequency of viable yeast cells, demonstrated by FDA-EB fluorescent method. Beyond of radiation the storage time also it influenced in counting reduction of total bacteria and reduction of frequency of viable cells. According with the analysis of simple linear regression, the dose of radiation necessary to eliminate 90% of the yeast population was between 1.10 and 2.23 kGy and for the bacterial population varied between 2.31 and 2.95 kGy. These results demonstrated clearly the negative points of the application of ionizing radiation in dry biological ferment; therefore the interval of D10 found for total bacteria is superior to found for yeasts. Being thus, the use of this resource for the improvement of the product quality becomes impracticable, since to reduce significantly the bacterial population necessarily we have that to diminish the population of yeasts. With yeasts reduction of we will go significantly to modify the quality and the viability of product. (author)

Birth/birth-death processes and their computable transition probabilities with biological applications.

Science.gov (United States)

Ho, Lam Si Tung; Xu, Jason; Crawford, Forrest W; Minin, Vladimir N; Suchard, Marc A

2018-03-01

Birth-death processes track the size of a univariate population, but many biological systems involve interaction between populations, necessitating models for two or more populations simultaneously. A lack of efficient methods for evaluating finite-time transition probabilities of bivariate processes, however, has restricted statistical inference in these models. Researchers rely on computationally expensive methods such as matrix exponentiation or Monte Carlo approximation, restricting likelihood-based inference to small systems, or indirect methods such as approximate Bayesian computation. In this paper, we introduce the birth/birth-death process, a tractable bivariate extension of the birth-death process, where rates are allowed to be nonlinear. We develop an efficient algorithm to calculate its transition probabilities using a continued fraction representation of their Laplace transforms. Next, we identify several exemplary models arising in molecular epidemiology, macro-parasite evolution, and infectious disease modeling that fall within this class, and demonstrate advantages of our proposed method over existing approaches to inference in these models. Notably, the ubiquitous stochastic susceptible-infectious-removed (SIR) model falls within this class, and we emphasize that computable transition probabilities newly enable direct inference of parameters in the SIR model. We also propose a very fast method for approximating the transition probabilities under the SIR model via a novel branching process simplification, and compare it to the continued fraction representation method with application to the 17th century plague in Eyam. Although the two methods produce similar maximum a posteriori estimates, the branching process approximation fails to capture the correlation structure in the joint posterior distribution.

Removal of dimethyl sulfide by the combination of non-thermal plasma and biological process.

Science.gov (United States)

Wei, Z S; Li, H Q; He, J C; Ye, Q H; Huang, Q R; Luo, Y W

2013-10-01

A bench scale system integrated with a non-thermal plasma (NTP) and a biotricking filtration (BTF) unit for the treatment of gases containing dimethyl sulfide (DMS) was investigated. DMS removal efficiency in the integrated system was up to 96%. Bacterial communities in the BTF were assessed by PCR-DGGE, which play the dominant role in the biological processes of metabolism, sulfur oxidation, sulfate-reducing and carbon oxidation. The addition of ozone from NTP made microbial community in BTF more complicated and active for DMS removal. The NTP oxidize DMS to simple compounds such as methanol and carbonyl sulfide; the intermediate organic products and DMS are further oxidized to sulfate, carbon dioxide, water vapors by biological degradation. These results show that NTP-BTF is achievable and open new possibilities for applying the integrated with NTP and BTF to odour gas treatment. Copyright © 2013 The Authors. Published by Elsevier Ltd.. All rights reserved.

Carbon footprint of aerobic biological treatment of winery wastewater.

Science.gov (United States)

Rosso, D; Bolzonella, D

2009-01-01

The carbon associated with wastewater and its treatment accounts for approximately 6% of the global carbon balance. Within the wastewater treatment industry, winery wastewater has a minor contribution, although it can have a major impact on wine-producing regions. Typically, winery wastewater is treated by biological processes, such as the activated sludge process. Biomass produced during treatment is usually disposed of directly, i.e. without digestion or other anaerobic processes. We applied our previously published model for carbon-footprint calculation to the areas worldwide producing yearly more than 10(6) m(3) of wine (i.e., France, Italy, Spain, California, Argentina, Australia, China, and South Africa). Datasets on wine production from the Food and Agriculture Organisation were processed and wastewater flow rates calculated with assumptions based on our previous experience. Results show that the wine production, hence the calculated wastewater flow, is reported as fairly constant in the period 2005-2007. Nevertheless, treatment process efficiency and energy-conservation may play a significant role on the overall carbon-footprint. We performed a sensitivity analysis on the efficiency of the aeration process (alphaSOTE per unit depth, or alphaSOTE/Z) in the biological treatment operations and showed significant margin for improvement. Our results show that the carbon-footprint reduction via aeration efficiency improvement is in the range of 8.1 to 12.3%.

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

Science.gov (United States)

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

2016-06-17

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

Roles of extracellular polymeric substances in enhanced biological phosphorus removal process.

Science.gov (United States)

Li, Wen-Wei; Zhang, Hai-Ling; Sheng, Guo-Ping; Yu, Han-Qing

2015-12-01

Enhanced biological phosphorus removal (EBPR) process is known to mainly rely on the ability of phosphorus-accumulating organisms to take up, transform and store excess amount of phosphorus (P) inside the cells. However, recent studies have revealed considerable accumulation of P also in the extracellular polymeric substances (EPS) of sludge, implying a non-negligible role of EPS in P removal by EBPR sludge. However, the contribution of EPS to P uptake and the forms of accumulated extracellular P vary substantially in different studies, and the underlying mechanism of P transformation and transportation in EPS remains poorly understood. This review provides a new recognition into the P removal process in EBPR system by incorporating the role of EPS. It overviews on the characteristics of P accumulation in EPS, explores the mechanism of P transformation and transportation in EBPR sludge and EPS, summarizes the main influential factors for the P-accumulation properties of EPS, and discusses the remaining knowledge gaps and needed future efforts that may lead to better understanding and use of such an EPS role for maximizing P recovery from wastewater. Copyright © 2015 Elsevier Ltd. All rights reserved.

Biological treatment processes for PCB contaminated soil at a site in Newfoundland

International Nuclear Information System (INIS)

Punt, M.; Cooper, D.; Velicogna, D.; Mohn, W.; Reimer, K.; Parsons, D.; Patel, T.; Daugulis, A.

2002-01-01

SAIC Canada is conducting a study under the direction of a joint research and development contract between Public Works and Government Services Canada and Environment Canada to examine the biological options for treating PCB contaminated soil found at a containment cell at a former U.S. Military Base near Stephenville, Newfoundland. In particular, the study examines the feasibility of using indigenous microbes for the degradation of PCBs. The first phase of the study involved the testing of the microbes in a bioreactor. The second phase, currently underway, involves a complete evaluation of possible microbes for PCB degradation. It also involves further study into the biological process options for the site. Suitable indigenous and non-indigenous microbes for PCB dechlorination and biphenyl degradation are being identified and evaluated. In addition, the effectiveness and economics of microbial treatment in a conventional bioreactor is being evaluated. The conventional bioreactor used in this study is the two-phase partitioning bioreactor (TPPB) using a biopile process. Results thus far will be used to help Public Works and Government Services Canada to choose the most appropriate remedial technology. Preliminary results suggest that the use of soil classification could reduce the volume of soil requiring treatment. The soil in the containment cell contains microorganisms that could grow in isolation on biphenyl, naphthalene and potentially Aroclor 1254. Isolated native microbes were inoculated in the TPPB for growth. The TPPB was also run successfully under anaerobic conditions. Future work will involve lab-scale evaluation of microbes for PCB dechlorination and biphenyl degradation using both indigenous and non-indigenous microbes. The next phase of study may also involve field-scale demonstration of treatment methods. 2 refs., 3 tabs., 5 figs

Control of the biological process through continuous measurement of the sludge age. Experiences in the WWTP Molina de Segura (Murcia, Spain)

International Nuclear Information System (INIS)

Marques, F.; Pradas, P.; Lardin, C.; Simon, P.

2010-01-01

This paper reports the results obtained when a sludge age based control is incorporated in the biological process of a wastewater treatment plant (WWTP). Greater stability of the biological process is achieved when this control is implemented in WWTP of Molina de Segura. In particular biodiversity has increased and it has been possible to reduce and stabilize the secondary sludge production. An improvement of the sludge decantation and a reduction of the specific volumetric load of secondary clarifiers have also been observed. finally, costs have been reduced dur to the decrease of cationic polyelectrolyte consumption. (Author) 16 refs.

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

Science.gov (United States)

2014-01-01

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

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

Directory of Open Access Journals (Sweden)

Bardia Yousefi

2014-01-01

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

Biological treatment process for removing petroleum hydrocarbons from oil field produced waters

Energy Technology Data Exchange (ETDEWEB)

Tellez, G.; Khandan, N.

1995-12-31

The feasibility of removing petroleum hydrocarbons from oil fields produced waters using biological treatment was evaluated under laboratory and field conditions. Based on previous laboratory studies, a field-scale prototype system was designed and operated over a period of four months. Two different sources of produced waters were tested in this field study under various continuous flow rates ranging from 375 1/D to 1,800 1/D. One source of produced water was an open storage pit; the other, a closed storage tank. The TDS concentrations of these sources exceeded 50,000 mg/l; total n-alkanes exceeded 100 mg/l; total petroleum hydrocarbons exceeded 125 mg/l; and total BTEX exceeded 3 mg/l. Removals of total n-alkanes, total petroleum hydrocarbons, and BTEX remained consistently high over 99%. During these tests, the energy costs averaged $0.20/bbl at 12 bbl/D.

The JCSG high-throughput structural biology pipeline

International Nuclear Information System (INIS)

Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wooley, John; Wüthrich, Kurt; Wilson, Ian A.

2010-01-01

The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years and has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe. The Joint Center for Structural Genomics high-throughput structural biology pipeline has delivered more than 1000 structures to the community over the past ten years. The JCSG has made a significant contribution to the overall goal of the NIH Protein Structure Initiative (PSI) of expanding structural coverage of the protein universe, as well as making substantial inroads into structural coverage of an entire organism. Targets are processed through an extensive combination of bioinformatics and biophysical analyses to efficiently characterize and optimize each target prior to selection for structure determination. The pipeline uses parallel processing methods at almost every step in the process and can adapt to a wide range of protein targets from bacterial to human. The construction, expansion and optimization of the JCSG gene-to-structure pipeline over the years have resulted in many technological and methodological advances and developments. The vast number of targets and the enormous amounts of associated data processed through the multiple stages of the experimental pipeline required the development of variety of valuable resources that, wherever feasible, have been converted to free-access web-based tools and applications

Group processing in an undergraduate biology course for preservice teachers: Experiences and attitudes

Science.gov (United States)

Schellenberger, Lauren Brownback

Group processing is a key principle of cooperative learning in which small groups discuss their strengths and weaknesses and set group goals or norms. However, group processing has not been well-studied at the post-secondary level or from a qualitative or mixed methods perspective. This mixed methods study uses a phenomenological framework to examine the experience of group processing for students in an undergraduate biology course for preservice teachers. The effect of group processing on students' attitudes toward future group work and group processing is also examined. Additionally, this research investigated preservice teachers' plans for incorporating group processing into future lessons. Students primarily experienced group processing as a time to reflect on past performance. Also, students experienced group processing as a time to increase communication among group members and become motivated for future group assignments. Three factors directly influenced students' experiences with group processing: (1) previous experience with group work, (2) instructor interaction, and (3) gender. Survey data indicated that group processing had a slight positive effect on students' attitudes toward future group work and group processing. Participants who were interviewed felt that group processing was an important part of group work and that it had increased their group's effectiveness as well as their ability to work effectively with other people. Participants held positive views on group work prior to engaging in group processing, and group processing did not alter their atittude toward group work. Preservice teachers who were interviewed planned to use group work and a modified group processing protocol in their future classrooms. They also felt that group processing had prepared them for their future professions by modeling effective collaboration and group skills. Based on this research, a new model for group processing has been created which includes extensive

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

Science.gov (United States)

Diaz Acosta, B.

2011-01-01

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

Brain oscillatory subsequent memory effects differ in power and long-range synchronization between semantic and survival processing.

Science.gov (United States)

Fellner, Marie-Christin; Bäuml, Karl-Heinz T; Hanslmayr, Simon

2013-10-01

Memory crucially depends on the way information is processed during encoding. Differences in processes during encoding not only lead to differences in memory performance but also rely on different brain networks. Although these assumptions are corroborated by several previous fMRI and ERP studies, little is known about how brain oscillations dissociate between different memory encoding tasks. The present study therefore compared encoding related brain oscillatory activity elicited by two very efficient encoding tasks: a typical deep semantic item feature judgment task and a more elaborative survival encoding task. Subjects were asked to judge words either for survival relevance or for animacy, as indicated by a cue presented prior to the item. This allowed dissociating pre-item activity from item-related activity for both tasks. Replicating prior studies, survival processing led to higher recognition performance than semantic processing. Successful encoding in the semantic condition was reflected by a strong decrease in alpha and beta power, whereas successful encoding in the survival condition was related to increased alpha and beta long-range phase synchrony. Moreover, a pre-item subsequent memory effect in theta power was found which did not vary with encoding condition. These results show that measures of local synchrony (power) and global long range-synchrony (phase synchronization) dissociate between memory encoding processes. Whereas semantic encoding was reflected in decreases in local synchrony, increases in global long range synchrony were related to elaborative survival encoding, presumably reflecting the involvement of a more widespread cortical network in this task. Copyright © 2013 Elsevier Inc. All rights reserved.

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

International Nuclear Information System (INIS)

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.

2007-01-01

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

Effect of residual H2O2 from advanced oxidation processes on subsequent biological water treatmen : A laboratory batch study

NARCIS (Netherlands)

Wang, F.; van Halem, D.; Liu, G.; Lekkerkerker-Teunissen, K.; van der Hoek, J.P.

2017-01-01

H2O2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H2O2 residuals influence sand systems with an emphasis on

Homonuclear long-range correlation spectra from HMBC experiments by covariance processing.

Science.gov (United States)

Schoefberger, Wolfgang; Smrecki, Vilko; Vikić-Topić, Drazen; Müller, Norbert

2007-07-01

We present a new application of covariance nuclear magnetic resonance processing based on 1H--13C-HMBC experiments which provides an effective way for establishing indirect 1H--1H and 13C--13C nuclear spin connectivity at natural isotope abundance. The method, which identifies correlated spin networks in terms of covariance between one-dimensional traces from a single decoupled HMBC experiment, derives 13C--13C as well as 1H--1H spin connectivity maps from the two-dimensional frequency domain heteronuclear long-range correlation data matrix. The potential and limitations of this novel covariance NMR application are demonstrated on two compounds: eugenyl-beta-D-glucopyranoside and an emodin-derivative. Copyright (c) 2007 John Wiley & Sons, Ltd.

The Importance of Biological Databases in Biological Discovery.

Science.gov (United States)

Baxevanis, Andreas D; Bateman, Alex

2015-06-19

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

Design of the RFID for Storage of Biological Information

Directory of Open Access Journals (Sweden)

Sang-Hee Son

2009-02-01

Full Text Available Recent advances in RFID (radio frequency identification technology promises to create a wireless circuitry capable of interfacing with biological systems for acquisition, identification and processing of biological data based on radio frequency interaction. Thus, the RFID tag can be attached not only to consumer products and form part of the supply chain, but also to animals, plants and in particular human body. This paper describes the strategy for the design of a novel RFID tag, which stores vital biological information such as body temperature and blood pressure and heartbeat in accordance with the EPC global Class-1 standard. Biological data is obtained from a sensor technology that is based on resistance deviation-to-pulse width converter. The integrated chip consists of an analog front end, command interpreter, collision avoidance block, data storage, sensors, and interface circuitry. The system is capable of supporting heartbeats in the range of 40~200 beats per a minute and blood pressure 0~300mmHg. The proposed system employs collision free algorithm that supports access to single tag within a multiple tag environment. The approach facilitates intelligent management of patients in hospitals as part of an integrated healthcare management system.

Computer modeling in developmental biology: growing today, essential tomorrow.

Science.gov (United States)

Sharpe, James

2017-12-01

D'Arcy Thompson was a true pioneer, applying mathematical concepts and analyses to the question of morphogenesis over 100 years ago. The centenary of his famous book, On Growth and Form , is therefore a great occasion on which to review the types of computer modeling now being pursued to understand the development of organs and organisms. Here, I present some of the latest modeling projects in the field, covering a wide range of developmental biology concepts, from molecular patterning to tissue morphogenesis. Rather than classifying them according to scientific question, or scale of problem, I focus instead on the different ways that modeling contributes to the scientific process and discuss the likely future of modeling in developmental biology. © 2017. Published by The Company of Biologists Ltd.

Exemplary Programs in Secondary School Biology.

Science.gov (United States)

McComas, William F.; Penick, John E.

1989-01-01

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

Resonant long-range interactions between polar macromolecules

International Nuclear Information System (INIS)

Preto, Jordane; Pettini, Marco

2013-01-01

Motivated by its prospective biological relevance, the issue of resonant long-range interactions between two molecules displaying oscillating dipole moments is reinvestigated within the framework of classical electrodynamics. In particular, our findings shed new light on Fröhlich's theory of selective long-range interactions between biomolecules. First, terms of a very long-range kind – which have never been reported so far – are found in the interaction potential, due to field retardation. Second, at variance with a long-standing belief, it is shown that sizable resonant long-range interactions may exist only if the interacting system is out of thermal equilibrium.

Biological flue gas desulfurization

Energy Technology Data Exchange (ETDEWEB)

Buisman, C.J.N.; Dijkman, H.; Wijte, G.; Prins, W.L.; Verbraak, P.; Hartog, H.A.J. den [Paper B.V. Blak (Netherlands)

1995-08-01

A new biological flue gas desulfurization process (BIO-FGD) producing sulphur as a by-product was invented by Paques BV and Hoogens Technical Services in 1993. Sulphur dioxide is absorbed from flue gas using a combination of a sodium based scrubber and two biological reactors, an anaerobic and an aerobic biological reactor. The article describes the process and its evaluation in a pilot plant at 2 MW scale, designed to remove 6 kg/hr SO{sub 2} of the 2 million m{sup 3}/hr of flue gas produced at the 600 MW coal fired power station Amer-8 situated in Geertruidenberg in the south of the Netherlands. Research so far has proved the process works successfully and at low cost. A second pilot plant due to start-up in May 1995 will provide data on scale up and further information on sulphur recovery. 5 refs., 5 figs.

Long-Range Reduced Predictive Information Transfers of Autistic Youths in EEG Sensor-Space During Face Processing.

Science.gov (United States)

Khadem, Ali; Hossein-Zadeh, Gholam-Ali; Khorrami, Anahita

2016-03-01

The majority of previous functional/effective connectivity studies conducted on the autistic patients converged to the underconnectivity theory of ASD: "long-range underconnectivity and sometimes short-rang overconnectivity". However, to the best of our knowledge the total (linear and nonlinear) predictive information transfers (PITs) of autistic patients have not been investigated yet. Also, EEG data have rarely been used for exploring the information processing deficits in autistic subjects. This study is aimed at comparing the total (linear and nonlinear) PITs of autistic and typically developing healthy youths during human face processing by using EEG data. The ERPs of 12 autistic youths and 19 age-matched healthy control (HC) subjects were recorded while they were watching upright and inverted human face images. The PITs among EEG channels were quantified using two measures separately: transfer entropy with self-prediction optimality (TESPO), and modified transfer entropy with self-prediction optimality (MTESPO). Afterwards, the directed differential connectivity graphs (dDCGs) were constructed to characterize the significant changes in the estimated PITs of autistic subjects compared with HC ones. By using both TESPO and MTESPO, long-range reduction of PITs of ASD group during face processing was revealed (particularly from frontal channels to right temporal channels). Also, it seemed the orientation of face images (upright or upside down) did not modulate the binary pattern of PIT-based dDCGs, significantly. Moreover, compared with TESPO, the results of MTESPO were more compatible with the underconnectivity theory of ASD in the sense that MTESPO showed no long-range increase in PIT. It is also noteworthy that to the best of our knowledge it is the first time that a version of MTE is applied for patients (here ASD) and it is also its first use for EEG data analysis.

Biological variation of cystatin C

DEFF Research Database (Denmark)

Reinhard, Mark; Erlandsen, Erland; Randers, Else

2009-01-01

Introduction: Cystatin C has been investigated as a marker of the glomerular filtration rate. However, previous studies have reported conflicting results concerning the biological variation of cystatin C. The aim of the present study was to evaluate the biological variation of cystatin C...... in comparison to creatinine. Methods: Eight weekly morning blood samples were taken from twenty healthy volunteers (13 females, 7 males) aged 25-61 years. Mean creatinine clearance was 99.7 ml/min/1.73 m2 (range 61.8-139.5) and mean body mass index 23.9 kg/m2 (range 20.3-28.7). A total of 155 samples were...

Dependence of radiocaesium biological half-life in freshwater fish on water potassium concentration and temperature

International Nuclear Information System (INIS)

Carreiro, M.C.V.; Corisco, J.A.G.

1998-01-01

Short-term experiments (35-49 days) showed that the rate of cesium elimination from fish increases with increasing potassium concentration in water (the biological half-life decreases); this, however, is only true of the potassium concentration range of 0.35 to 3.5 ppm, whereas higher potassium concentrations do not seem to affect the elimination rate. Decrease in water temperature within the 20 degC to 5 degC range slows down the cesium elimination process. (P.A.)

BioCore Guide: A Tool for Interpreting the Core Concepts of Vision and Change for Biology Majors

Science.gov (United States)

Freeman, Scott; Wenderoth, Mary Pat; Crowe, Alison J.

2014-01-01

Vision and Change in Undergraduate Biology Education outlined five core concepts intended to guide undergraduate biology education: 1) evolution; 2) structure and function; 3) information flow, exchange, and storage; 4) pathways and transformations of energy and matter; and 5) systems. We have taken these general recommendations and created a Vision and Change BioCore Guide—a set of general principles and specific statements that expand upon the core concepts, creating a framework that biology departments can use to align with the goals of Vision and Change. We used a grassroots approach to generate the BioCore Guide, beginning with faculty ideas as the basis for an iterative process that incorporated feedback from more than 240 biologists and biology educators at a diverse range of academic institutions throughout the United States. The final validation step in this process demonstrated strong national consensus, with more than 90% of respondents agreeing with the importance and scientific accuracy of the statements. It is our hope that the BioCore Guide will serve as an agent of change for biology departments as we move toward transforming undergraduate biology education. PMID:26086653

Assessing the application of advanced oxidation processes, and their combination with biological treatment, to effluents from pulp and paper industry.

Science.gov (United States)

Merayo, Noemí; Hermosilla, Daphne; Blanco, Laura; Cortijo, Luis; Blanco, Angeles

2013-11-15

The closure of water circuits within pulp and paper mills has resulted in a higher contamination load of the final mill effluent, which must consequently be further treated in many cases to meet the standards imposed by the legislation in force. Different treatment strategies based on advanced oxidation processes (ozonation and TiO2-photocatalysis), and their combination with biological treatment (MBR), are herein assessed for effluents of a recycled paper mill and a kraft pulp mill. Ozone treatment achieved the highest efficiency of all. The consumption of 2.4 g O3 L(-1) resulted in about a 60% COD reduction treating the effluent from the kraft pulp mill at an initial pH=7; although it only reached about a 35% COD removal for the effluent of the recycled paper mill. Otherwise, photocatalysis achieved about a 20-30% reduction of the COD for both type of effluents. In addition, the effluent from the recycled paper mill showed a higher biodegradability, so combinations of these AOPs with biological treatment were tested. As a result, photocatalysis did not report any significant COD reduction improvement whether being performed as pre- or post-treatment of the biological process; whereas the use of ozonation as post-biological treatment enhanced COD removal a further 10%, summing up a total 90% reduction of the COD for the combined treatment, as well as it also supposed an increase of the presence of volatile fatty acids, which might ultimately enable the resultant wastewater to be recirculated back to further biological treatment. Copyright © 2013 Elsevier B.V. All rights reserved.

Theoretical considerations concerning the effect of relativistic velocities on the rate of biological processes.

Science.gov (United States)

Heneine, I F

1997-06-01

Theoretical considerations were advanced on the reaction rate of biological systems in a rocket accelerated at fractional levels of the velocity of light. The values of mass increase in reacting molecules and length contraction of space under these relativistic velocities attained by the hypothetical rocket were inserted in equations of the absolute reaction rate theory. The equations employed were for the frequency of collisions, and for the internal kinetic energy of molecular reactions. Results of both sets of equations indicated that reduction of reaction rates were correlated to the mass increase. This would imply a general slowing of all chemical, biochemical and biological processes taking place. A human would suffer a related decrease in metabolic rate. Contrary to what is generally accepted, the biological aging of the space traveler under velocities bearable by humans, namely under 0.50c, would follow a pace very similar to that of an observer remaining in the resting frame of reference. With increased increments of the velocity, the space traveler would display a more intense lowering of the metabolic rate, with signs and symptoms comparable to body core hypothermia. Metabolic rates at insufficient levels to maintain the vital functions would be attained at 0.70c and higher, leading swiftly to coma and death. The presence of an endocrine dysfunction such as hypothyroidism or obesity in the space traveler would aggravate the signs and symptoms. Space travel at efficient velocities would be unbearable for a warm-blooded animal.

Evaluation of Fenton Oxidation Process Coupled with Biological Treatment for the Removal of Reactive Black 5 from Aqueous Solution

Directory of Open Access Journals (Sweden)

Pegah Bahmani

2013-06-01

Full Text Available Biodegradation of azo dyes is difficult due to their complex structures and low BOD to COD ratios. In the present study, the efficiency of using Fenton’s reagent (H2O2 + Fe2+ as a pretreatment process to enhance microbial transformation of reactive black 5 (RB5 in an aqueous system was evaluated. The RB5 with an initial concentration of 250 mg/L was decolorized up to 90% in 60 h by using a bacterial consortium. Fenton’s reagent at a Fe2+ concentration of 0.5 mM and H2O2 concentration of 2.9 mM (molar ratio, 1:5.8 was most effective for decolorization at pH = 3.0. The extent of RB5 removal by the combined Fenton–biotreatment was about 2 times higher than that of biotreatment alone. The production of some aromatic amines intermediates implied partial mineralization of the RB5 in Fenton treatment alone; in addition, decreasing of GC-MS peaks suggested that dearomatization occurred in Fenton-biological process. Fenton pretreatment seems to be a cost–effective option for the biotreatment of azo dyes, due mainly to the lower doses of chemicals, lower sludge generation, and saving of time. Our results demonstrated positive effects of inoculating bacterial consortium which was capable of dye biodegradation with a Fenton’s pretreatment step as well as the benefits of low time required for the biological process. In addition, the potential of field performance of Fenton-biological process because of using bacterial consortium is an other positive effect of it.

Processing biological literature with customizable Web services supporting interoperable formats.

Science.gov (United States)

Rak, Rafal; Batista-Navarro, Riza Theresa; Carter, Jacob; Rowley, Andrew; Ananiadou, Sophia

2014-01-01

Web services have become a popular means of interconnecting solutions for processing a body of scientific literature. This has fuelled research on high-level data exchange formats suitable for a given domain and ensuring the interoperability of Web services. In this article, we focus on the biological domain and consider four interoperability formats, BioC, BioNLP, XMI and RDF, that represent domain-specific and generic representations and include well-established as well as emerging specifications. We use the formats in the context of customizable Web services created in our Web-based, text-mining workbench Argo that features an ever-growing library of elementary analytics and capabilities to build and deploy Web services straight from a convenient graphical user interface. We demonstrate a 2-fold customization of Web services: by building task-specific processing pipelines from a repository of available analytics, and by configuring services to accept and produce a combination of input and output data interchange formats. We provide qualitative evaluation of the formats as well as quantitative evaluation of automatic analytics. The latter was carried out as part of our participation in the fourth edition of the BioCreative challenge. Our analytics built into Web services for recognizing biochemical concepts in BioC collections achieved the highest combined scores out of 10 participating teams. Database URL: http://argo.nactem.ac.uk. © The Author(s) 2014. Published by Oxford University Press.

Full Monte Carlo-Based Biologic Treatment Plan Optimization System for Intensity Modulated Carbon Ion Therapy on Graphics Processing Unit.

Science.gov (United States)

Qin, Nan; Shen, Chenyang; Tsai, Min-Yu; Pinto, Marco; Tian, Zhen; Dedes, Georgios; Pompos, Arnold; Jiang, Steve B; Parodi, Katia; Jia, Xun

2018-01-01

One of the major benefits of carbon ion therapy is enhanced biological effectiveness at the Bragg peak region. For intensity modulated carbon ion therapy (IMCT), it is desirable to use Monte Carlo (MC) methods to compute the properties of each pencil beam spot for treatment planning, because of their accuracy in modeling physics processes and estimating biological effects. We previously developed goCMC, a graphics processing unit (GPU)-oriented MC engine for carbon ion therapy. The purpose of the present study was to build a biological treatment plan optimization system using goCMC. The repair-misrepair-fixation model was implemented to compute the spatial distribution of linear-quadratic model parameters for each spot. A treatment plan optimization module was developed to minimize the difference between the prescribed and actual biological effect. We used a gradient-based algorithm to solve the optimization problem. The system was embedded in the Varian Eclipse treatment planning system under a client-server architecture to achieve a user-friendly planning environment. We tested the system with a 1-dimensional homogeneous water case and 3 3-dimensional patient cases. Our system generated treatment plans with biological spread-out Bragg peaks covering the targeted regions and sparing critical structures. Using 4 NVidia GTX 1080 GPUs, the total computation time, including spot simulation, optimization, and final dose calculation, was 0.6 hour for the prostate case (8282 spots), 0.2 hour for the pancreas case (3795 spots), and 0.3 hour for the brain case (6724 spots). The computation time was dominated by MC spot simulation. We built a biological treatment plan optimization system for IMCT that performs simulations using a fast MC engine, goCMC. To the best of our knowledge, this is the first time that full MC-based IMCT inverse planning has been achieved in a clinically viable time frame. Copyright © 2017 Elsevier Inc. All rights reserved.

Scaffolded biology.

Science.gov (United States)

Minelli, Alessandro

2016-09-01

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

Alpha process with biological elimination of nitrogen. Application of mathematical models; Proceso alpha con eliminacion biologica de nitrogeno. Aplicacion de modelos matematicos

Energy Technology Data Exchange (ETDEWEB)

Rodriguez, J. C.; Lopez-Carrasco, M. D.; Cortacans, J. A.; Larrea, L.; Larrea, A.

1999-07-01

This article illustrates the advantages of a step feed process for the biological elimination of nitrogen by presenting the experiments carried out by INFILCO at a pilot plant in San Sebastian. This arrangement, also known as the alpha (alternative phase step feed) process, reduces the volume of the biological reactor, eliminates the need for internal recycling and optimised the consumption of the organic matter used for denitrication. This article also demonstrates the possibility of employing a mathematical model as a tool in assessing, designing and operating full scale treatment plants for typically urban sewage. (Author) 6 refs.

Towards physical principles of biological evolution

Science.gov (United States)

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

2018-03-01

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

Order of current variance and diffusivity in the rate one totally asymmetric zero range process

NARCIS (Netherlands)

Balázs, M.; Komjáthy, J.

2008-01-01

We prove that the variance of the current across a characteristic is of order t 2/3 in a stationary constant rate totally asymmetric zero range process, and that the diffusivity has order t 1/3. This is a step towards proving universality of this scaling behavior in the class of one-dimensional

Real-time processing for full-range Fourier-domain optical-coherence tomography with zero-filling interpolation using multiple graphic processing units.

Science.gov (United States)

Watanabe, Yuuki; Maeno, Seiya; Aoshima, Kenji; Hasegawa, Haruyuki; Koseki, Hitoshi

2010-09-01

The real-time display of full-range, 2048?axial pixelx1024?lateral pixel, Fourier-domain optical-coherence tomography (FD-OCT) images is demonstrated. The required speed was achieved by using dual graphic processing units (GPUs) with many stream processors to realize highly parallel processing. We used a zero-filling technique, including a forward Fourier transform, a zero padding to increase the axial data-array size to 8192, an inverse-Fourier transform back to the spectral domain, a linear interpolation from wavelength to wavenumber, a lateral Hilbert transform to obtain the complex spectrum, a Fourier transform to obtain the axial profiles, and a log scaling. The data-transfer time of the frame grabber was 15.73?ms, and the processing time, which includes the data transfer between the GPU memory and the host computer, was 14.75?ms, for a total time shorter than the 36.70?ms frame-interval time using a line-scan CCD camera operated at 27.9?kHz. That is, our OCT system achieved a processed-image display rate of 27.23 frames/s.

Self-Organized Biological Dynamics and Nonlinear Control

Science.gov (United States)

Walleczek, Jan

2006-04-01

The frontiers and challenges of biodynamics research Jan Walleczek; Part I. Nonlinear Dynamics in Biology and Response to Stimuli: 1. External signals and internal oscillation dynamics - principal aspects and response of stimulated rhythmic processes Friedemann Kaiser; 2. Nonlinear dynamics in biochemical and biophysical systems: from enzyme kinetics to epilepsy Raima Larter, Robert Worth and Brent Speelman; 3. Fractal mechanisms in neural control: human heartbeat and gait dynamics in health and disease Chung-Kang Peng, Jeffrey M. Hausdorff and Ary L. Goldberger; 4. Self-organising dynamics in human coordination and perception Mingzhou Ding, Yanqing Chen, J. A. Scott Kelso and Betty Tuller; 5. Signal processing in biochemical reaction networks Adam P. Arkin; Part II. Nonlinear Sensitivity of Biological Systems to Electromagnetic Stimuli: 6. Electrical signal detection and noise in systems with long-range coherence Paul C. Gailey; 7. Oscillatory signals in migrating neutrophils: effects of time-varying chemical and electrical fields Howard R. Petty; 8. Enzyme kinetics and nonlinear biochemical amplification in response to static and oscillating magnetic fields Jan Walleczek and Clemens F. Eichwald; 9. Magnetic field sensitivity in the hippocampus Stefan Engström, Suzanne Bawin and W. Ross Adey; Part III. Stochastic Noise-Induced Dynamics and Transport in Biological Systems: 10. Stochastic resonance: looking forward Frank Moss; 11. Stochastic resonance and small-amplitude signal transduction in voltage-gated ion channels Sergey M. Bezrukov and Igor Vodyanoy; 12. Ratchets, rectifiers and demons: the constructive role of noise in free energy and signal transduction R. Dean Astumian; 13. Cellular transduction of periodic and stochastic energy signals by electroconformational coupling Tian Y. Tsong; Part IV. Nonlinear Control of Biological and Other Excitable Systems: 14. Controlling chaos in dynamical systems Kenneth Showalter; 15. Electromagnetic fields and biological

Electro-induced reactions of biologically important molecules

International Nuclear Information System (INIS)

Kocisek, J.

2010-01-01

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

Catechol-Based Hydrogel for Chemical Information Processing

Directory of Open Access Journals (Sweden)

Eunkyoung Kim

2017-07-01

Full Text Available Catechols offer diverse properties and are used in biology to perform various functions that range from adhesion (e.g., mussel proteins to neurotransmission (e.g., dopamine, and mimicking the capabilities of biological catechols have yielded important new materials (e.g., polydopamine. It is well known that catechols are also redox-active and we have observed that biomimetic catechol-modified chitosan films are redox-active and possess interesting molecular electronic properties. In particular, these films can accept, store and donate electrons, and thus offer redox-capacitor capabilities. We are enlisting these capabilities to bridge communication between biology and electronics. Specifically, we are investigating an interactive redox-probing approach to access redox-based chemical information and convert this information into an electrical modality that facilitates analysis by methods from signal processing. In this review, we describe the broad vision and then cite recent examples in which the catechol–chitosan redox-capacitor can assist in accessing and understanding chemical information. Further, this redox-capacitor can be coupled with synthetic biology to enhance the power of chemical information processing. Potentially, the progress with this biomimetic catechol–chitosan film may even help in understanding how biology uses the redox properties of catechols for redox signaling.

Culture, Urbanism and Changing Human Biology.

Science.gov (United States)

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.

Crowdsourcing and curation: perspectives from biology and natural language processing.

Science.gov (United States)

Hirschman, Lynette; Fort, Karën; Boué, Stéphanie; Kyrpides, Nikos; Islamaj Doğan, Rezarta; Cohen, Kevin Bretonnel

2016-01-01

Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging 'the crowd'; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9-11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.Database URL: http://www.mitre.org/publications/technical-papers/crowdsourcing-and-curation-perspectives. © The Author(s) 2016. Published by Oxford University Press.

Microbiology and atmospheric processes: chemical interactions of primary biological aerosols

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L. Deguillaume

2008-07-01

Full Text Available This paper discusses the influence of primary biological aerosols (PBA on atmospheric chemistry and vice versa through microbiological and chemical properties and processes. Several studies have shown that PBA represent a significant fraction of air particulate matter and hence affect the microstructure and water uptake of aerosol particles. Moreover, airborne micro-organisms, namely fungal spores and bacteria, can transform chemical constituents of the atmosphere by metabolic activity. Recent studies have emphasized the viability of bacteria and metabolic degradation of organic substances in cloud water. On the other hand, the viability and metabolic activity of airborne micro-organisms depend strongly on physical and chemical atmospheric parameters such as temperature, pressure, radiation, pH value and nutrient concentrations. In spite of recent advances, however, our knowledge of the microbiological and chemical interactions of PBA in the atmosphere is rather limited. Further targeted investigations combining laboratory experiments, field measurements, and modelling studies will be required to characterize the chemical feedbacks, microbiological activities at the air/snow/water interface supplied to the atmosphere.

Quantum biological information theory

CERN Document Server

Djordjevic, Ivan B

2016-01-01

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

Synthetic biology and occupational risk.

Science.gov (United States)

Howard, John; Murashov, Vladimir; Schulte, Paul

2017-03-01

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

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

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

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

Quality transformation of dissolved organic carbon during water transit through lakes: contrasting controls by photochemical and biological processes

Science.gov (United States)

Berggren, Martin; Klaus, Marcus; Panneer Selvam, Balathandayuthabani; Ström, Lena; Laudon, Hjalmar; Jansson, Mats; Karlsson, Jan

2018-01-01

Dissolved organic carbon (DOC) may be removed, transformed, or added during water transit through lakes, resulting in changes in DOC composition and pigmentation (color). However, the process-based understanding of these changes is incomplete, especially for headwater lakes. We hypothesized that because heterotrophic bacteria preferentially consume noncolored DOC, while photochemical processing removes colored fractions, the overall changes in DOC color upon water passage through a lake depend on the relative importance of these two processes, accordingly. To test this hypothesis we combined laboratory experiments with field studies in nine boreal lakes, assessing both the relative importance of different DOC decay processes (biological or photochemical) and the loss of color during water transit time (WTT) through the lakes. We found that influence from photo-decay dominated changes in DOC quality in the epilimnia of relatively clear headwater lakes, resulting in systematic and selective net losses of colored DOC. However, in highly pigmented brown-water lakes (absorbance at 420 nm > 7 m-1) biological processes dominated, and there was no systematic relationship between color loss and WTT. Moreover, in situ data and dark experiments supported our hypothesis on the selective microbial removal of nonpigmented DOC, mainly of low molecular weight, leading to persistent water color in these highly colored lakes. Our study shows that brown headwater lakes may not conform to the commonly reported pattern of the selective removal of colored constituents in freshwaters, as DOC can show a sustained degree of pigmentation upon transit through these lakes.

The relative contributions of biological and abiotic processes to carbon dynamics in subarctic sea ice

DEFF Research Database (Denmark)

Søgaard, Dorte Haubjerg; Thomas, David; Rysgaard, Søren

2013-01-01

Knowledge on the relative effects of biological activity and precipitation/dissolution of calcium carbonate (CaCO3) in influencing the air-ice CO2 exchange in sea-ice-covered season is currently lacking. Furthermore, the spatial and temporal occurrence of CaCO3 and other biogeochemical parameters...... in sea ice are still not well described. Here we investigated autotrophic and heterotrophic activity as well as the precipitation/dissolution of CaCO3 in subarctic sea ice in South West Greenland. Integrated over the entire ice season (71 days), the sea ice was net autotrophic with a net carbon fixation...... and CaCO3 precipitation. The net biological production could only explain 4 % of this sea-ice-driven CO2 uptake. Abiotic processes contributed to an air-sea CO2 uptake of 1.5 mmol m(-2) sea ice day(-1), and dissolution of CaCO3 increased the air-sea CO2 uptake by 36 % compared to a theoretical estimate...

Real-time image processing of TOF range images using a reconfigurable processor system

Science.gov (United States)

Hussmann, S.; Knoll, F.; Edeler, T.

2011-07-01

During the last years, Time-of-Flight sensors achieved a significant impact onto research fields in machine vision. In comparison to stereo vision system and laser range scanners they combine the advantages of active sensors providing accurate distance measurements and camera-based systems recording a 2D matrix at a high frame rate. Moreover low cost 3D imaging has the potential to open a wide field of additional applications and solutions in markets like consumer electronics, multimedia, digital photography, robotics and medical technologies. This paper focuses on the currently implemented 4-phase-shift algorithm in this type of sensors. The most time critical operation of the phase-shift algorithm is the arctangent function. In this paper a novel hardware implementation of the arctangent function using a reconfigurable processor system is presented and benchmarked against the state-of-the-art CORDIC arctangent algorithm. Experimental results show that the proposed algorithm is well suited for real-time processing of the range images of TOF cameras.

Opportunities in plant synthetic biology.

Science.gov (United States)

Cook, Charis; Martin, Lisa; Bastow, Ruth

2014-05-01

Synthetic biology is an emerging field uniting scientists from all disciplines with the aim of designing or re-designing biological processes. Initially, synthetic biology breakthroughs came from microbiology, chemistry, physics, computer science, materials science, mathematics, and engineering disciplines. A transition to multicellular systems is the next logical step for synthetic biologists and plants will provide an ideal platform for this new phase of research. This meeting report highlights some of the exciting plant synthetic biology projects, and tools and resources, presented and discussed at the 2013 GARNet workshop on plant synthetic biology.

Complete Host Range Testing on Common Reed with Potential Biological Control Agents and Investigation into Biological Control for Flowering Rush

Science.gov (United States)

2016-07-01

CR-16-5 v Preface This report was prepared by Drs. Patrick Häfliger and Hariet Hinz, Centre for Agriculture and Bioscience International (CABI...through Cornell University, the Washington Department of Agriculture , the Washington Department of Ecology, the Washington Department of Natural...capacity during biological invasion in an aquatic plant Butomus umbellatus (Butomaceae). American Journal of Botany 92:495–502. Dieckmann, L. 1983

Metabolomics: Definitions and Significance in Systems Biology.

Science.gov (United States)

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

2017-01-01

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

Open Water Processes of the San Francisco Estuary: From Physical Forcing to Biological Responses

Directory of Open Access Journals (Sweden)

Wim Kimmerer

2004-02-01

Full Text Available This paper reviews the current state of knowledge of the open waters of the San Francisco Estuary. This estuary is well known for the extent to which it has been altered through loss of wetlands, changes in hydrography, and the introduction of chemical and biological contaminants. It is also one of the most studied estuaries in the world, with much of the recent research effort aimed at supporting restoration efforts. In this review I emphasize the conceptual foundations for our current understanding of estuarine dynamics, particularly those aspects relevant to restoration. Several themes run throughout this paper. First is the critical role physical dynamics play in setting the stage for chemical and biological responses. Physical forcing by the tides and by variation in freshwater input combine to control the movement of the salinity field, and to establish stratification, mixing, and dilution patterns throughout the estuary. Many aspects of estuarine dynamics respond to interannual variation in freshwater flow; in particular, abundance of several estuarine-dependent species of fish and shrimp varies positively with flow, although the mechanisms behind these relationships are largely unknown. The second theme is the importance of time scales in determining the degree of interaction between dynamic processes. Physical effects tend to dominate when they operate at shorter time scales than biological processes; when the two time scales are similar, important interactions can arise between physical and biological variability. These interactions can be seen, for example, in the response of phytoplankton blooms, with characteristic time scales of days, to stratification events occurring during neap tides. The third theme is the key role of introduced species in all estuarine habitats; particularly noteworthy are introduced waterweeds and fishes in the tidal freshwater reaches of the estuary, and introduced clams there and in brackish water. The

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

Directory of Open Access Journals (Sweden)

Ayse Pinar Saygin

2010-10-01

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

Biological treatment of sludge digester liquids.

Science.gov (United States)

van Loosdrecht, M C M; Salem, S

2006-01-01

Nitrogen removal in side stream processes offers a good potential for upgrading wastewater treatment plants (WWTPs) that need to meet stricter effluent standards. Removing nutrients from these internal process flows significantly reduces the N-load to the main treatment plant. These internal flows mainly result from the sludge processing and have a high temperature and a high concentration of ammonia. Therefore, the required reactor volumes as well as the required aerobic SRT are small. Generally, biological treatment processes are more economical and preferred over physical-chemical processes. Recently, several biological treatment processes have been introduced for sludge water treatment. These processes are available now on the activated sludge market (e.g. SHARON, ANAMMOX and BABE processes). The technologies differ in concept and in the limitations guiding the application of these processes for upgrading WWTPs. This paper reviews and compares different biological alternatives for nitrogen removal in side streams. The limitations for selecting a technology from the available ones in the activated sludge market are noted and analysed. It is stressed that the choice for a certain process is based on more aspects than pure process engineering arguments.

The value of mechanistic biophysical information for systems-level understanding of complex biological processes such as cytokinesis.

Science.gov (United States)

Pollard, Thomas D

2014-12-02

This review illustrates the value of quantitative information including concentrations, kinetic constants and equilibrium constants in modeling and simulating complex biological processes. Although much has been learned about some biological systems without these parameter values, they greatly strengthen mechanistic accounts of dynamical systems. The analysis of muscle contraction is a classic example of the value of combining an inventory of the molecules, atomic structures of the molecules, kinetic constants for the reactions, reconstitutions with purified proteins and theoretical modeling to account for the contraction of whole muscles. A similar strategy is now being used to understand the mechanism of cytokinesis using fission yeast as a favorable model system. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Image processing pipeline for segmentation and material classification based on multispectral high dynamic range polarimetric images.

Science.gov (United States)

Martínez-Domingo, Miguel Ángel; Valero, Eva M; Hernández-Andrés, Javier; Tominaga, Shoji; Horiuchi, Takahiko; Hirai, Keita

2017-11-27

We propose a method for the capture of high dynamic range (HDR), multispectral (MS), polarimetric (Pol) images of indoor scenes using a liquid crystal tunable filter (LCTF). We have included the adaptive exposure estimation (AEE) method to fully automatize the capturing process. We also propose a pre-processing method which can be applied for the registration of HDR images after they are already built as the result of combining different low dynamic range (LDR) images. This method is applied to ensure a correct alignment of the different polarization HDR images for each spectral band. We have focused our efforts in two main applications: object segmentation and classification into metal and dielectric classes. We have simplified the segmentation using mean shift combined with cluster averaging and region merging techniques. We compare the performance of our segmentation with that of Ncut and Watershed methods. For the classification task, we propose to use information not only in the highlight regions but also in their surrounding area, extracted from the degree of linear polarization (DoLP) maps. We present experimental results which proof that the proposed image processing pipeline outperforms previous techniques developed specifically for MSHDRPol image cubes.

Range expansion drives dispersal evolution in an equatorial three-species symbiosis.

Directory of Open Access Journals (Sweden)

Guillaume Léotard

Full Text Available Recurrent climatic oscillations have produced dramatic changes in species distributions. This process has been proposed to be a major evolutionary force, shaping many life history traits of species, and to govern global patterns of biodiversity at different scales. During range expansions selection may favor the evolution of higher dispersal, and symbiotic interactions may be affected. It has been argued that a weakness of climate fluctuation-driven range dynamics at equatorial latitudes has facilitated the persistence there of more specialized species and interactions. However, how much the biology and ecology of species is changed by range dynamics has seldom been investigated, particularly in equatorial regions.We studied a three-species symbiosis endemic to coastal equatorial rainforests in Cameroon, where the impact of range dynamics is supposed to be limited, comprised of two species-specific obligate mutualists--an ant-plant and its protective ant--and a species-specific ant parasite of this mutualism. We combined analyses of within-species genetic diversity and of phenotypic variation in a transect at the southern range limit of this ant-plant system. All three species present congruent genetic signatures of recent gradual southward expansion, a result compatible with available regional paleoclimatic data. As predicted, this expansion has been accompanied by the evolution of more dispersive traits in the two ant species. In contrast, we detected no evidence of change in lifetime reproductive strategy in the tree, nor in its investment in food resources provided to its symbiotic ants.Despite the decreasing investment in protective workers and the increasing investment in dispersing females by both the mutualistic and the parasitic ant species, there was no evidence of destabilization of the symbiosis at the colonization front. To our knowledge, we provide here the first evidence at equatorial latitudes that biological traits associated

AN ADVANCED OXIDATION PROCESS : FENTON PROCESS

Directory of Open Access Journals (Sweden)

Engin GÜRTEKİN

2008-03-01

Full Text Available Biological wastewater treatment is not effective treatment method if raw wastewater contains toxic and refractory organics. Advanced oxidation processes are applied before or after biological treatment for the detoxification and reclamation of this kind of wastewaters. The advanced oxidation processes are based on the formation of powerful hydroxyl radicals. Among advanced oxidation processes Fenton process is one of the most promising methods. Because application of Fenton process is simple and cost effective and also reaction occurs in a short time period. Fenton process is applied for many different proposes. In this study, Fenton process was evaluated as an advanced oxidation process in wastewater treatment.

On the selection and validation of biological treatment processes. The GDF experience; Le choix et la validation des procedes de traitement biologique. L`experience de GDF

Energy Technology Data Exchange (ETDEWEB)

Druelle, V [Gaz de France (GDF), 75 - Paris (France)

1997-12-31

The biological treatment process was selected by Gaz de France (GDF), the French national gas utility, for the de-pollution of an old gas works where the main pollutants are coal tars containing polycyclic aromatic hydrocarbons. Microorganism-based biological treatment techniques may involve bio-reactors, static ground knolls (where oxygen is brought through drains) and dynamic knolls (where oxygenation is carried out by turning up the soil). Issues on sampling, sorting, process testing, site preparation, process control, etc. are reviewed

On the selection and validation of biological treatment processes. The GDF experience; Le choix et la validation des procedes de traitement biologique. L`experience de GDF

Energy Technology Data Exchange (ETDEWEB)

Druelle, V. [Gaz de France (GDF), 75 - Paris (France)

1996-12-31

The biological treatment process was selected by Gaz de France (GDF), the French national gas utility, for the de-pollution of an old gas works where the main pollutants are coal tars containing polycyclic aromatic hydrocarbons. Microorganism-based biological treatment techniques may involve bio-reactors, static ground knolls (where oxygen is brought through drains) and dynamic knolls (where oxygenation is carried out by turning up the soil). Issues on sampling, sorting, process testing, site preparation, process control, etc. are reviewed

An improved method to quantitate mature plant microRNA in biological matrices using periodate treatment and internal control

Science.gov (United States)

MicroRNAs (miRNAs) ubiquitously exist in microorganisms, plants and animals, and appear to modulate a wide range of critical biological processes. However, no definitive conclusion has been reached regarding the uptake of exogenous dietary small RNAs into mammalian circulation and organs and cross-k...

Discovering biological progression underlying microarray samples.

Directory of Open Access Journals (Sweden)

Peng Qiu

2011-04-01

Full Text Available In biological systems that undergo processes such as differentiation, a clear concept of progression exists. We present a novel computational approach, called Sample Progression Discovery (SPD, to discover patterns of biological progression underlying microarray gene expression data. SPD assumes that individual samples of a microarray dataset are related by an unknown biological process (i.e., differentiation, development, cell cycle, disease progression, and that each sample represents one unknown point along the progression of that process. SPD aims to organize the samples in a manner that reveals the underlying progression and to simultaneously identify subsets of genes that are responsible for that progression. We demonstrate the performance of SPD on a variety of microarray datasets that were generated by sampling a biological process at different points along its progression, without providing SPD any information of the underlying process. When applied to a cell cycle time series microarray dataset, SPD was not provided any prior knowledge of samples' time order or of which genes are cell-cycle regulated, yet SPD recovered the correct time order and identified many genes that have been associated with the cell cycle. When applied to B-cell differentiation data, SPD recovered the correct order of stages of normal B-cell differentiation and the linkage between preB-ALL tumor cells with their cell origin preB. When applied to mouse embryonic stem cell differentiation data, SPD uncovered a landscape of ESC differentiation into various lineages and genes that represent both generic and lineage specific processes. When applied to a prostate cancer microarray dataset, SPD identified gene modules that reflect a progression consistent with disease stages. SPD may be best viewed as a novel tool for synthesizing biological hypotheses because it provides a likely biological progression underlying a microarray dataset and, perhaps more importantly, the

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.

Science.gov (United States)

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.

Application of magnetic iron oxide nanoparticles in stabilization process of biological molecules

Directory of Open Access Journals (Sweden)

Mohammad Hossien Salmani

2017-07-01

Conclusion: Co-precipitation method is an easy way to prepare magnetic nanoparticles of iron with a large surface and small particle size, which increases the ability of these particles to act as a suitable carrier for enzyme stabilization. Adequate modification of the surface of these nanoparticles enhances their ability to bind to biological molecules. The immobilized protein or enzyme on magnetic nanoparticles are more stable against structural changes, temperature and pH in comparison with un-stabilized structures, and it is widely used in various sciences, including protein isolation and purification, pharmaceutical science, and food analysis. Stabilization based on the covalent bonds and physical absorption is nonspecific, which greatly limits their functionality. The process of stabilization through bio-mediums provide a new method to overcome the selectivity problem.

Biological AMS at Uppsala University: Status report

International Nuclear Information System (INIS)

Salehpour, Mehran; Forsgard, Niklas; Possnert, Goeran

2010-01-01

In January 2007 a new research program was initiated at Uppsala University focusing on the biological applications of AMS. We have used a 5 MV Pelletron Tandem accelerator to study biological samples. With Microdosing applications in mind, a variety of measurements have been performed on human blood, plasma and urine that have been labeled with a 14 C-labeled pharmaceutical drug covering a concentration range, spanning 3 orders of magnitude. Furthermore, by studying small sample amounts and low concentrations, we have demonstrated sensitivity in the hundred zeptomole range for a small pharmaceutical substance in human blood. Another application of interest, based on the enhanced 14 C activity from the cold war bomb-peak, is dating of DNA molecules providing fundamental data for the regenerative medicine and stem cell research community. We show data on a sensitive carrier method for measuring the isotopic ratio of small biological sample in the few μgC range.

Biological processes for concentrating trace elements from uranium mine waters. Technical completion report

International Nuclear Information System (INIS)

Brierley, C.L.; Brierley, J.A.

1981-12-01

Waste water from uranium mines in the Ambrosia Lake district near Grants, New Mexico, USA, contains uranium, selenium, radium and molybdenum. The Kerr-McGee Corporation has a novel treatment process for waters from two mines to reduce the concentrations of the trace contaminants. Particulates are settled by ponding, and the waters are passed through an ion exchange resin to remove uranium; barium chloride is added to precipitate sulfate and radium from the mine waters. The mine waters are subsequently passed through three consecutive algae ponds prior to discharge. Water, sediment and biological samples were collected over a 4-year period and analyzed to assess the role of biological agents in removal of inorganic trace contaminants from the mine waters. Some of the conclusions derived from this study are: (1) The concentrations of soluble uranium, selenium and molybdenum were not diminished in the mine waters by passage through the series of impoundments which constituted the mine water treatment facility. Uranium concentrations were reduced but this was due to passage of the water through an ion exchange column. (2) The particulate concentrations of the mine water were reduced at least ten-fold by passage of the waters through the impoundments. (3) The sediments were anoxic and enriched in uranium, molybdenum and selenium. The deposition of particulates and the formation of insoluble compounds were proposed as mechanisms for sediment enrichment. (4) The predominant algae of the treatment ponds were the filamentous Spirogyra and Oscillatoria, and the benthic alga, Chara. (5) Adsorptive processes resulted in the accumulation of metals in the algae cells. (6) Stimulation of sulfate reduction by the bacteria resulted in retention of molybdenum, selenium, and uranium in sediments. 1 figure, 16 tables

Mammalian synthetic biology for studying the cell.

Science.gov (United States)

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

2017-01-02

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

Utilization of the cyanobacteria Anabaena sp CH1 in biological carbon dioxide mitigation processes

Energy Technology Data Exchange (ETDEWEB)

Chiang, C.L.; Lee, C.M.; Chen, P.C. [Hungkuang University, Taichung (Taiwan)

2011-05-15

Before switching totally to alternative fuel stage, CO{sub 2} mitigation process has considered a transitional strategy for combustion of fossil fuels inevitably. In comparison to other CO{sub 2} mitigation options, such as oceanic or geologic injection, the biological photosynthetic process would present a far superior and sustainable solution under both environmental and social considerations. The utilization of the cyanobacteria Anabaena sp. CH1 in carbon dioxide mitigation processes is analyzed in our research. It was found that an original developed photobioreactor with internal light source exhibits high light utilization. Anabaena sp. CH1 demonstrates excellent CO{sub 2} tolerance even at 15% CO{sub 2} level. This enables flue gas from power plant to be directly introduced to Anabaena sp. CH1 culture. Double light intensity and increased 47% CO{sub 2} bubble retention time could enhance CO{sub 2} removal efficiencies by 79% and 67%, respectively. A maximum CO{sub 2} fixation rate of 1.01 g CO{sub 2} L{sup -1} day{sup -1} was measured experimentally.

Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum.

Directory of Open Access Journals (Sweden)

Miriam Grace

2015-11-01

Full Text Available Spatiotemporal patterns often emerge from local interactions in a self-organizing fashion. In biology, the resulting patterns are also subject to the influence of the systematic differences between the system's constituents (biological variability. This regulation of spatiotemporal patterns by biological variability is the topic of our review. We discuss several examples of correlations between cell properties and the self-organized spatiotemporal patterns, together with their relevance for biology. Our guiding, illustrative example will be spiral waves of cAMP in a colony of Dictyostelium discoideum cells. Analogous processes take place in diverse situations (such as cardiac tissue, where spiral waves occur in potentially fatal ventricular fibrillation so a deeper understanding of this additional layer of self-organized pattern formation would be beneficial to a wide range of applications. One of the most striking differences between pattern-forming systems in physics or chemistry and those in biology is the potential importance of variability. In the former, system components are essentially identical with random fluctuations determining the details of the self-organization process and the resulting patterns. In biology, due to variability, the properties of potentially very few cells can have a driving influence on the resulting asymptotic collective state of the colony. Variability is one means of implementing a few-element control on the collective mode. Regulatory architectures, parameters of signaling cascades, and properties of structure formation processes can be "reverse-engineered" from observed spatiotemporal patterns, as different types of regulation and forms of interactions between the constituents can lead to markedly different correlations. The power of this biology-inspired view of pattern formation lies in building a bridge between two scales: the patterns as a collective state of a very large number of cells on the one hand

Biological reduction of nitrates in wastewaters from nuclear processing using a fluidized-bed bioreactor

International Nuclear Information System (INIS)

Pitt, W.W.; Hancher, C.W.; Patton, B.D.

1981-01-01

There are a number of nitrate-containing wastewater sources, as concentrated as 30 wt.% NO 3 - and as large as 2000 m 3 /day, in the nuclear fuel cycle. The biological reduction of nitrate in wastewater to gaseous nitrogen, accompanied by the oxidation of a nutrient carbon source to gaseous carbon dioxide, is an ecologically sound and cost-effective method of treating wastewaters containing nitrates. These nitrate-containing wastewater sources can be successfully biologically denitrified to meet discharge standards in the range of 10 to 20 gN(NO 3 - )/m 3 by the use of a fluidized-bed bioreactor. The denitrification bacteria are a mixed culture derived from garden soil; the major strain is Pseudomonas. In the fluidized-bed bioreactor the bacteria are allowed to attach to 0.25- to 0.50-mm-diam coal fluidization particles, which are then fluidized by the upward flow of influent wastewater. Maintaining the bacteria-to-coal weight ratio at approximately 1:10 results in a bioreactor bacteria loading of greater than 20,000 g/m 3 . This paper describes the results of a biodenitrification R and D program based on the use of fluidized bioreactors capable of operating at nitrate levels up to 7000 g/m 3 and achieving denitrification rates as high as 80 g N(NO 3 - ) per day per liter of empty bioreactor volume. 4 figures, 7 tables

Impact of some herbicides on the biomass activity in biological treatment plants and biodegradability enhancement by a photo-Fenton process.

Science.gov (United States)

Benzaquén, T B; Benzzo, M T; Isla, M A; Alfano, O M

2013-01-01

In recent years, the use of agrochemicals has increased because they are essential for profitable agricultural production. Herbicides are heavily demanded compounds and among these, the most marketed are 2,4-D, atrazine and acetochlor. They have characteristics that can cause problems to humans and the environment. Therefore, it is necessary to design systems that can reduce these compounds to harmless molecules. This work aims at evaluating the possibility of incorporating these herbicides into degradable effluents in a biological treatment system, without reducing its efficiency. For this purpose, studies of organic matter degradability in the presence of these agrochemicals were performed. A synthetic effluent based on glucose and mineral salts was inoculated with microorganisms. Glucose consumption and biomass concentration were assessed. Subsequently, preliminary studies were performed to test the viability of degradation of the most harmful compound with an advanced oxidation process (AOP). The results showed that the incorporation of these herbicides into degradable effluents in a biological treatment system has a negative impact on microorganisms. Therefore, the application of an AOP, such as the Fenton or photo-Fenton processes, prior to a biological treatment was found to degrade these substances to simpler and less toxic molecules.

Quantum Mechanics predicts evolutionary biology.

Science.gov (United States)

Torday, J S

2018-07-01

Nowhere are the shortcomings of conventional descriptive biology more evident than in the literature on Quantum Biology. In the on-going effort to apply Quantum Mechanics to evolutionary biology, merging Quantum Mechanics with the fundamentals of evolution as the First Principles of Physiology-namely negentropy, chemiosmosis and homeostasis-offers an authentic opportunity to understand how and why physics constitutes the basic principles of biology. Negentropy and chemiosmosis confer determinism on the unicell, whereas homeostasis constitutes Free Will because it offers a probabilistic range of physiologic set points. Similarly, on this basis several principles of Quantum Mechanics also apply directly to biology. The Pauli Exclusion Principle is both deterministic and probabilistic, whereas non-localization and the Heisenberg Uncertainty Principle are both probabilistic, providing the long-sought after ontologic and causal continuum from physics to biology and evolution as the holistic integration recognized as consciousness for the first time. Copyright © 2018 Elsevier Ltd. All rights reserved.

Epidemic processes in complex networks

OpenAIRE

Pastor Satorras, Romualdo; Castellano, Claudio; Van Mieghem, Piet; Vespignani, Alessandro

2015-01-01

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and sociotechnical systems. The complex properties of real-world networks have a profound impact on the behavior of equilibrium and nonequilibrium phenomena occurring in various systems, and the study of epidemic spreading is central to our understanding of the unfolding of dynamical processes in complex networks. The t...

Biological impact of preschool music classes on processing speech in noise.

Science.gov (United States)

Strait, Dana L; Parbery-Clark, Alexandra; O'Connell, Samantha; Kraus, Nina

2013-10-01

Musicians have increased resilience to the effects of noise on speech perception and its neural underpinnings. We do not know, however, how early in life these enhancements arise. We compared auditory brainstem responses to speech in noise in 32 preschool children, half of whom were engaged in music training. Thirteen children returned for testing one year later, permitting the first longitudinal assessment of subcortical auditory function with music training. Results indicate emerging neural enhancements in musically trained preschoolers for processing speech in noise. Longitudinal outcomes reveal that children enrolled in music classes experience further increased neural resilience to background noise following one year of continued training compared to nonmusician peers. Together, these data reveal enhanced development of neural mechanisms undergirding speech-in-noise perception in preschoolers undergoing music training and may indicate a biological impact of music training on auditory function during early childhood. Copyright © 2013 Elsevier Ltd. All rights reserved.

A practical approach for exploration and modeling of the design space of a bacterial vaccine cultivation process.

Science.gov (United States)

Streefland, M; Van Herpen, P F G; Van de Waterbeemd, B; Van der Pol, L A; Beuvery, E C; Tramper, J; Martens, D E; Toft, M

2009-10-15

A licensed pharmaceutical process is required to be executed within the validated ranges throughout the lifetime of product manufacturing. Changes to the process, especially for processes involving biological products, usually require the manufacturer to demonstrate that the safety and efficacy of the product remains unchanged by new or additional clinical testing. Recent changes in the regulations for pharmaceutical processing allow broader ranges of process settings to be submitted for regulatory approval, the so-called process design space, which means that a manufacturer can optimize his process within the submitted ranges after the product has entered the market, which allows flexible processes. In this article, the applicability of this concept of the process design space is investigated for the cultivation process step for a vaccine against whooping cough disease. An experimental design (DoE) is applied to investigate the ranges of critical process parameters that still result in a product that meets specifications. The on-line process data, including near infrared spectroscopy, are used to build a descriptive model of the processes used in the experimental design. Finally, the data of all processes are integrated in a multivariate batch monitoring model that represents the investigated process design space. This article demonstrates how the general principles of PAT and process design space can be applied for an undefined biological product such as a whole cell vaccine. The approach chosen for model development described here, allows on line monitoring and control of cultivation batches in order to assure in real time that a process is running within the process design space.

The application of membrane technology for reuse of process water and minimisation of waste water in a textile washing range

NARCIS (Netherlands)

van t Hul, J.P.; Racz, I.G.; Reith, T.

1997-01-01

Recycling of process streams and reduction of waste disposal using membrane technology in a continuous textile washing process after dyeing with reactive dyes have been investigated theoretically. A mathematical process model of a conventional open-width washing range has been extended by membrane

Antibiotic abatement in different advanced oxidation processes coupled with a biological sequencing batch biofilm reactor

International Nuclear Information System (INIS)

Esplugas, M.; Gonzalez, O.; Benito, J.; Sans, C.

2009-01-01

During the last decade, the lack of fresh water is becoming a major concern. Recently, the present of recalcitrant products such as pharmaceuticals has caused a special interest due to their undefined environmental impact. Among these antibiotics are one of the numerous recalcitrant pollutants present in surface waters that might not be completely removed in the biological stage of sewage treatment plants because of their antibacterial nature. Advanced Oxidation Processes (AOPs) have proved to be highly efficient for the degradation of most organic pollutants in wastewaters. (Author)

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

Science.gov (United States)

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.

Physics and biology

International Nuclear Information System (INIS)

Frauenfelder, H.

1988-01-01

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

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

Science.gov (United States)

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.

High-density native-range species affects the invasive plant Chromolaena odorata more strongly than species from its invasive range.

Science.gov (United States)

Zheng, Yulong; Liao, Zhiyong

2017-11-22

Invasive plant species often form dense mono-dominant stands in areas they have invaded, while having only sparse distribution in their native ranges, and the reasons behind this phenomenon are a key point of research in invasive species biology. Differences in species composition between native and invasive ranges may contribute to the difference in distribution status. In this study, we found that the high-density condition had a more negative effect on C. odorata than the low-density condition when co-grown with neighbor plants from its native range in Mexico, while this pattern was not in evidence when it was grown with neighbors from its invasive range in China. Different competitive ability and coevolutionary history with C. odorata between native-range neighbors and invasive-range neighbors may lead to the inconsistent patterns.

PSL Chemical Biology Symposia First 2016 Edition: When Chemistry and Biology Share the Language of Discovery.

Science.gov (United States)

Gautier, Arnaud; Rodriguez, Raphaël

2017-05-18

Chemical biology, the science of understanding biological processes at the molecular level, has grown exponentially with the development of chemical strategies to manipulate and quantify biology with unprecedented precision. Recent advances presented at the Université Paris Sciences et Lettres symposium are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Basis of the biological decomposition of xenobiotica

International Nuclear Information System (INIS)

Mueller, R. von

1993-01-01

The ability of micro-organisms to decompose different molecules and to use them as a source of carbon, nitrogen, sulphur or energy is the basis for all biological processes for cleaning up contaminated soil. Therefore, the knowledge of these decomposition processes is an important precondition for judging which contamination can be treated biologically at all and which materials can be decomposed biologically. The decomposition schemes of the most important harmful material classes (aliphatic, aromatic and chlorinated hydrocarbons) are introduced and the consequences which arise for the practical application in biological cleaning up of contaminated soils are discussed. (orig.) [de

Mechanical Biological Treatment

DEFF Research Database (Denmark)

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

2011-01-01

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

Composting of the solid fraction of digestate derived from pig slurry: Biological processes and compost properties

Energy Technology Data Exchange (ETDEWEB)

Tambone, Fulvia, E-mail: fulvia.tambone@unimi.it; Terruzzi, Laura; Scaglia, Barbara; Adani, Fabrizio

2015-01-15

Highlights: • Anaerobic digestion leads to the production of a biologically stable digestate. • Solid–liquid separation produces a solid fraction having high fertilizer value. • Composting process shows low biological activity due to high biological stability of digestate. • Solid digestate fraction can be composted in a short time or used directly as organic fertilizer. - Abstract: The aim of this paper was to assess the characteristics of the solid fractions (SF) obtained by mechanical separation of digestate, their compostability and compost quality. To do so, the SF of digestates obtained from anaerobic digestion of pig slurry, energy crops and agro-industrial residues were sampled in five plants located in Northern Italy. Results obtained indicated that anaerobic digestion by itself promoted the high biological stability of biomasses with a Potential Dynamic Respiration Index (PDRI) close to 1000 mgO{sub 2} kg V S{sup −1} h{sup −1}. Subsequent composting of digestates, with an added bulking agent, did not give remarkably different results, and led only to a slight modification of the characteristics of the initial non-composted mixtures; the composts obtained fully respected the legal limits for high quality compost. Chemical studies of organic matter composition of the biomasses by using CP MAS {sup 13}C NMR, indicated that the compost was composed of a high relative content of O-alkyl-C (71.47% of total C) (cellulose and hemicelluloses) and a low alkyl-C (12.42%) (i.e. volatile fatty acids, steroid-like molecules, aliphatic biopolymers and proteins)

Composting of the solid fraction of digestate derived from pig slurry: Biological processes and compost properties

International Nuclear Information System (INIS)

Tambone, Fulvia; Terruzzi, Laura; Scaglia, Barbara; Adani, Fabrizio

2015-01-01

Highlights: • Anaerobic digestion leads to the production of a biologically stable digestate. • Solid–liquid separation produces a solid fraction having high fertilizer value. • Composting process shows low biological activity due to high biological stability of digestate. • Solid digestate fraction can be composted in a short time or used directly as organic fertilizer. - Abstract: The aim of this paper was to assess the characteristics of the solid fractions (SF) obtained by mechanical separation of digestate, their compostability and compost quality. To do so, the SF of digestates obtained from anaerobic digestion of pig slurry, energy crops and agro-industrial residues were sampled in five plants located in Northern Italy. Results obtained indicated that anaerobic digestion by itself promoted the high biological stability of biomasses with a Potential Dynamic Respiration Index (PDRI) close to 1000 mgO 2 kg V S −1 h −1 . Subsequent composting of digestates, with an added bulking agent, did not give remarkably different results, and led only to a slight modification of the characteristics of the initial non-composted mixtures; the composts obtained fully respected the legal limits for high quality compost. Chemical studies of organic matter composition of the biomasses by using CP MAS 13 C NMR, indicated that the compost was composed of a high relative content of O-alkyl-C (71.47% of total C) (cellulose and hemicelluloses) and a low alkyl-C (12.42%) (i.e. volatile fatty acids, steroid-like molecules, aliphatic biopolymers and proteins)

Paradigms for biologically inspired design

DEFF Research Database (Denmark)

Lenau, T. A.; Metzea, A.-L.; Hesselberg, T.

2018-01-01

engineering, medical engineering, nanotechnology, photonics,environmental protection and agriculture. However, a major obstacle for the wider use of biologically inspired design isthe knowledge barrier that exist between the application engineers that have insight into how to design suitable productsand......Biologically inspired design is attracting increasing interest since it offers access to a huge biological repository of wellproven design principles that can be used for developing new and innovative products. Biological phenomena can inspireproduct innovation in as diverse areas as mechanical...... the biologists with detailed knowledge and experience in understanding how biological organisms function in theirenvironment. The biologically inspired design process can therefore be approached using different design paradigmsdepending on the dominant opportunities, challenges and knowledge characteristics...

Enhanced Biological Phosphorus Removal: Metabolic Insights and Salinity Effects

OpenAIRE

Welles, L.

2015-01-01

Enhanced biological phosphorus removal (EBPR) is a biological process for efficient phosphate removal from wastewaters through intracellular storage of polyphosphate by polyphosphate-accumulating organisms (PAO) and subsequent removal of PAO from the system through wastage of sludge. In comparison to physical and chemical phosphorus removal processes, the biological process has several advantages such as high removal efficiency, low cost, and no chemical sludge production, but disturbances an...

Development of a LC-MS/MS Method for the Simultaneous Detection of Tricarboxylic Acid Cycle Intermediates in a Range of Biological Matrices

Directory of Open Access Journals (Sweden)

Omar Al Kadhi

2017-01-01

Full Text Available It is now well-established that perturbations in the tricarboxylic acid (TCA cycle play an important role in the metabolic transformation occurring in cancer including that of the prostate. A method for simultaneous qualitative and quantitative analysis of TCA cycle intermediates in body fluids, tissues, and cultured cell lines of human origin was developed using a common C18 reversed-phase column by LC-MS/MS technique. This LC-MS/MS method for profiling TCA cycle intermediates offers significant advantages including simple and fast preparation of a wide range of human biological samples. The analytical method was validated according to the guideline of the Royal Society of Chemistry Analytical Methods Committee. The limits of detection were below 60 nM for most of the TCA intermediates with the exception of lactic and fumaric acids. The calibration curves of all TCA analytes showed linearity with correlation coefficients r2>0.9998. Recoveries were >95% for all TCA analytes. This method was established taking into consideration problems and limitations of existing techniques. We envisage that its application to different biological matrices will facilitate deeper understanding of the metabolic changes in the TCA cycle from in vitro, ex vivo, and in vivo studies.

Weapons of Mass Destruction Technology Evaluation and Training Range

Energy Technology Data Exchange (ETDEWEB)

Kevin Larry Young

2009-05-01

The Idaho National Laboratory (INL) has a long history for providing technology evaluation and training for military and other federal level Weapons of Mass Destruction (WMD) response agencies. Currently there are many federal organizations and commercial companies developing technologies related to detecting, assessing, mitigating and protecting against hazards associated with a WMD event. Unfortunately, very few locations exist within the United States where WMD response technologies are realistically field tested and evaluated using real chemical, biological, radiological, nuclear and explosive materials. This is particularly true with biological and radiological hazards. Related to this lack of adequate WMD, multi-hazard technology testing capability is the shortage of locations where WMD response teams can train using actual chemical, biological, and radiological material or highly realistic simulates. In response to these technology evaluation and training needs, the INL has assembled a consortium of subject matter experts from existing programs and identified dedicated resources for the purpose of establishing an all-hazards, WMD technology evaluation and training range. The author describes the challenges associated with creating the all-hazards WMD technology evaluation and training range and lists the technical, logistical and financial benefits of an all-hazards technology evaluation and training range. Current resources and capabilities for conducting all-hazard technology evaluation and training at the INL are identified. Existing technology evaluation and training programs at the INL related to radiological, biological and chemical hazards are highlighted, including successes and lessons learned. Finally, remaining gaps in WMD technology evaluation and training capabilities are identified along with recommendations for closing those gaps.

Novel MBR_based main stream biological nutrient removal process: high performance and microbial community.

Science.gov (United States)

Zhang, Chuanyi; Xu, Xinhai; Zhao, Kuixia; Tang, Lianggang; Zou, Siqi; Yuan, Limei

2018-02-01

For municipal wastewater treatment, main stream biological nutrient removal (BNR) process is becoming more and more important. This lab-scale study, novel MBR_based BNR processes (named A 2 N-MBR and A 2 NO-MBR) were built. Comparison of the COD removal, results obtained demonstrated that COD removal efficiencies were almost the same in three processes, with effluent concentration all bellowed 30 mg L -1 . However, the two-sludge systems (A 2 N-MBR and A 2 NO-MBR) had an obvious advantage over the A 2 /O for denitrification and phosphorus removal, with the average TP removal rates of 91.20, 98.05% and TN removal rates of 73.00, 79.49%, respectively, higher than that of 86.45 and 61.60% in A 2 /O process. Illumina Miseq sequencing revealed that Candidatus_Accumulibacter, which is capable of using nitrate as an electron acceptor for phosphorus and nitrogen removal simultaneously, was the dominant phylum in both A 2 N-MBR and A 2 NO-MBR process, accounting for 28.74 and 23.98%, respectively. Distinguishingly, major organism groups related to nitrogen and phosphorus removal in A 2 /O system were Anaerolineaceae_uncultured, Saprospiraceae_uncultured and Thauera, with proportions of 11.31, 8.56 and 5.00%, respectively. Hence, the diversity of dominant PAOs group was likely responsible for the difference in nitrogen and phosphorus removal in the three processes.

A Biological Perspective on the Meaning of Time

Science.gov (United States)

Rothschild, Lynn J.

2014-01-01

We have become impatient waiting for a web page to load, but the first member of our species evolved about 150,000 years ago - a geological instant as brief and as transitory as a text message. The shortest generation time of a bacterium is a sprint at under ten minutes, whereas a 200-year old whale, turtle or tree is not unknown. Life is a phenomenon that integrates processes ranging from the near instantaneous reactions of photosynthesis to the more stately pace of evolution. Here I will elucidate these processes with radically different time scales that go to creating and maintaining the diversity of life on earth, the clocks that nature uses to time them, and how modern biology is being used to alter the natural time scales.

Introductory Biology Labs... They Just Aren't Sexy Enough!

Science.gov (United States)

Cotner, Sehoya; Gallup, Gordon G., Jr.

2011-01-01

The typical introductory biology curriculum includes the nature of science, evolution and genetics. Laboratory activities are designed to engage students in typical subject areas ranging from cell biology and physiology, to ecology and evolution. There are few, if any, laboratory classes exploring the biology and evolution of human sexual…

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

Science.gov (United States)

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

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

Atmospheric plasma processes for environmental applications

OpenAIRE

Shapoval, Volodymyr

2012-01-01

Plasma chemistry is a rapidly growing field which covers applications ranging from technological processing of materials, including biological tissues, to environmental remediation and energy production. The so called atmospheric plasma, produced by electric corona or dielectric barrier discharges in a gas at atmospheric pressure, is particularly attractive for the low costs and ease of operation and maintenance involved. The high concentrations of energetic and chemically active species (e.g...

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

Complicated systems cannot survive the rigors of a chaotic environment, without balancing mechanisms that sense, decide upon and counteract the exerted disturbances. Especially so with living organisms, forced by competition to incredible complexities, escalating also their self-controlling plight. Therefore, they compute. Can we harness biological mechanisms to create artificial computing systems? Biology offers several levels of design abstraction: molecular machines, cells, organisms... ranging from the more easily-defined to the more inherently complex. At the bottom of this stack we find the nucleic acids, RNA and DNA, with their digital structure and relatively precise interactions. They are central enablers of designing artificial biological systems, in the confluence of engineering and biology, that we call Synthetic biology. In the first part, let us follow their trail towards an overview of building computing machines with molecules -- and in the second part, take the case study of iGEM Greece 201...

Optimization of electrocoagulation process to treat biologically pretreated bagasse effluent

Directory of Open Access Journals (Sweden)

Thirugnanasambandham K.

2014-01-01

Full Text Available The main objective of the present study was to investigate the efficiency of electrocoagulation process as a post-treatment to treat biologically pretreated bagasse effluent using iron electrodes. The removal of chemical oxygen demand (COD and total suspended solids (TSS were studied under different operating conditions such as amount of dilution, initial pH, applied current and electrolyte dose by using response surface methodology (RSM coupled with four-factor three-level Box-Behnken experimental design (BBD. The experimental results were analyzed by Pareto analysis of variance (ANOVA and second order polynomial mathematical models were developed with high correlation of efficiency (R2 for COD, TSS removal and electrical energy consumption (EEC. The individual and combined effect of variables on responses was studied using three dimensional response surface plots. Under the optimum operating conditions, such as amount of dilution at 30 %, initial pH of 6.5, applied current of 8 mA cm-2 and electrolyte dose of 740 mg l-1 shows the higher removal efficiency of COD (98 % and TSS (93 % with EEC of 2.40 Wh, which were confirmed by validation experiments.

High-speed AFM for Studying Dynamic Biomolecular Processes

Science.gov (United States)

Ando, Toshio

2008-03-01

Biological molecules show their vital activities only in aqueous solutions. It had been one of dreams in biological sciences to directly observe biological macromolecules (protein, DNA) at work under a physiological condition because such observation is straightforward to understanding their dynamic behaviors and functional mechanisms. Optical microscopy has no sufficient spatial resolution and electron microscopy is not applicable to in-liquid samples. Atomic force microscopy (AFM) can visualize molecules in liquids at high resolution but its imaging rate was too low to capture dynamic biological processes. This slow imaging rate is because AFM employs mechanical probes (cantilevers) and mechanical scanners to detect the sample height at each pixel. It is quite difficult to quickly move a mechanical device of macroscopic size with sub-nanometer accuracy without producing unwanted vibrations. It is also difficult to maintain the delicate contact between a probe tip and fragile samples. Two key techniques are required to realize high-speed AFM for biological research; fast feedback control to maintain a weak tip-sample interaction force and a technique to suppress mechanical vibrations of the scanner. Various efforts have been carried out in the past decade to materialize high-speed AFM. The current high-speed AFM can capture images on video at 30-60 frames/s for a scan range of 250nm and 100 scan lines, without significantly disturbing week biomolecular interaction. Our recent studies demonstrated that this new microscope can reveal biomolecular processes such as myosin V walking along actin tracks and association/dissociation dynamics of chaperonin GroEL-GroES that occurs in a negatively cooperative manner. The capacity of nanometer-scale visualization of dynamic processes in liquids will innovate on biological research. In addition, it will open a new way to study dynamic chemical/physical processes of various phenomena that occur at the liquid-solid interfaces.

Physical models of biological information and adaptation.

Science.gov (United States)

Stuart, C I

1985-04-07

The bio-informational equivalence asserts that biological processes reduce to processes of information transfer. In this paper, that equivalence is treated as a metaphor with deeply anthropomorphic content of a sort that resists constitutive-analytical definition, including formulation within mathematical theories of information. It is argued that continuance of the metaphor, as a quasi-theoretical perspective in biology, must entail a methodological dislocation between biological and physical science. It is proposed that a general class of functions, drawn from classical physics, can serve to eliminate the anthropomorphism. Further considerations indicate that the concept of biological adaptation is central to the general applicability of the informational idea in biology; a non-anthropomorphic treatment of adaptive phenomena is suggested in terms of variational principles.

Computer Models and Automata Theory in Biology and Medicine

CERN Document Server

Baianu, I C

2004-01-01

The applications of computers to biological and biomedical problem solving goes back to the very beginnings of computer science, automata theory [1], and mathematical biology [2]. With the advent of more versatile and powerful computers, biological and biomedical applications of computers have proliferated so rapidly that it would be virtually impossible to compile a comprehensive review of all developments in this field. Limitations of computer simulations in biology have also come under close scrutiny, and claims have been made that biological systems have limited information processing power [3]. Such general conjectures do not, however, deter biologists and biomedical researchers from developing new computer applications in biology and medicine. Microprocessors are being widely employed in biological laboratories both for automatic data acquisition/processing and modeling; one particular area, which is of great biomedical interest, involves fast digital image processing and is already established for rout...

Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications.

Science.gov (United States)

Hage, David S

2017-06-01

The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically related binding agent, are 2 methods that can be used to study these interactions. This review presents various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples. © 2016 American Association for Clinical Chemistry.

Tritium biological effects and perspective of the biological study

International Nuclear Information System (INIS)

Komatsu, Kenshi

1998-01-01

Since tritium is an emitter of weak β-rays (5.7keV) and is able to bind to DNA, i.e., the most important genome component, the biological effects should be expected to be more profound than that of X-rays and γ-rays. When carcinogenesis, genetical effects and the detriments for fetus and embryo were used as a biological endpoint, most of tritium RBE (relative biological effectiveness) ranged from 1 to 2. The tritium risk in man could be calculated from these RBEs and γ-ray risk for human exposure, which are obtained mainly from the data on Atomic Bomb survivors. However, the exposure modality from environmental tritium should be a chronic irradiation with ultra low dose rate or a fractionated irradiation. We must estimate the tritium effect in man based on biological experiments alone, due to lack of such epidemiological data. Low dose rate experiment should be always accompanied by the statistical problem of data, since their biological effects are fairy low, and they should involve a possible repair system, such as adaptive response (or hormesis effect) and 'Kada effect' observed in bacteria. Here we discuss future works for the tritium assessment in man, such as (1) developing a high radiation sensitive assay system with rodent hybrid cells containing a single human chromosome and also (2) study on mammal DNA repair at molecular levels using a radiosensitive hereditary disease, Nijmegen Breakage Syndrome. (author)

Resolving the range ambiguity in OFDR using digital signal processing

International Nuclear Information System (INIS)

Riesen, Nicolas; Lam, Timothy T-Y; Chow, Jong H

2014-01-01

A digitally range-gated variant of optical frequency domain reflectometry is demonstrated which overcomes the beat note ambiguity when sensing beyond a single frequency sweep. The range-gating is achieved using a spread spectrum technique involving time-stamping of the optical signal using high-frequency pseudorandom phase modulation. The reflections from different sections of fiber can then be isolated in the time domain by digitally inverting the phase modulation using appropriately-delayed copies of the pseudorandom noise code. Since the technique overcomes the range ambiguity in OFDR, it permits high sweep repetition rates without sacrificing range, thus allowing for high-bandwidth sensing over long lengths of fiber. This is demonstrated for the case of quasi-distributed sensing. (paper)

Simulation and optimization of a coking wastewater biological treatment process by activated sludge models (ASM).

Science.gov (United States)

Wu, Xiaohui; Yang, Yang; Wu, Gaoming; Mao, Juan; Zhou, Tao

2016-01-01

Applications of activated sludge models (ASM) in simulating industrial biological wastewater treatment plants (WWTPs) are still difficult due to refractory and complex components in influents as well as diversity in activated sludges. In this study, an ASM3 modeling study was conducted to simulate and optimize a practical coking wastewater treatment plant (CWTP). First, respirometric characterizations of the coking wastewater and CWTP biomasses were conducted to determine the specific kinetic and stoichiometric model parameters for the consecutive aeration-anoxic-aeration (O-A/O) biological process. All ASM3 parameters have been further estimated and calibrated, through cross validation by the model dynamic simulation procedure. Consequently, an ASM3 model was successfully established to accurately simulate the CWTP performances in removing COD and NH4-N. An optimized CWTP operation condition could be proposed reducing the operation cost from 6.2 to 5.5 €/m(3) wastewater. This study is expected to provide a useful reference for mathematic simulations of practical industrial WWTPs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Excited states in biological systems

International Nuclear Information System (INIS)

Cilento, G.; Zinner, K.; Bechara, E.J.H.; Duran, N.; Baptista, R.C. de; Shimizu, Y.; Augusto, O.; Faljoni-Alario, A.; Vidigal, C.C.C.; Oliveira, O.M.M.F.; Haun, M.

1979-01-01

Some aspects of bioluminescence related to bioenergetics are discussed: 1. chemical generation of excited species, by means of two general processes: electron transference and cyclic - and linear peroxide cleavage; 2. biological systems capable of generating excited states and 3. biological functions of these states, specially the non-emissive ones (tripletes). The production and the role of non-emissive excited states in biological systems are analysed, the main purpose of the study being the search for non-emissive states. Experiences carried out in biological systems are described; results and conclusions are given. (M.A.) [pt

Processing of acceleration and dive data on-board satellite relay tags to investigate diving and foraging behaviour in free-ranging marine predators.

Science.gov (United States)

Cox, Sam L; Orgeret, Florian; Gesta, Mathieu; Rodde, Charles; Heizer, Isaac; Weimerskirch, Henri; Guinet, Christophe

2018-01-01

Biologging technologies are changing the way in which the marine environment is observed and monitored. However, because device retrieval is typically required to access the high-resolution data they collect, their use is generally restricted to those animals that predictably return to land. Data abstraction and transmission techniques aim to address this, although currently these are limited in scope and do not incorporate, for example, acceleration measurements which can quantify animal behaviours and movement patterns over fine-scales.In this study, we present a new method for the collection, abstraction and transmission of accelerometer data from free-ranging marine predators via the Argos satellite system. We test run the technique on 20 juvenile southern elephant seals Mirounga leonina from the Kerguelen Islands during their first months at sea following weaning. Using retrieved archival data from nine individuals that returned to the colony, we compare and validate abstracted transmissions against outputs from established accelerometer processing procedures.Abstracted transmissions included estimates, across five segments of a dive profile, of time spent in prey catch attempt (PrCA) behaviours, swimming effort and pitch. These were then summarised and compared to archival outputs across three dive phases: descent, bottom and ascent. Correlations between the two datasets were variable but generally good (dependent on dive phase, marginal R 2 values of between .45 and .6 to >.9) and consistent between individuals. Transmitted estimates of PrCA behaviours and swimming effort were positively biased to those from archival processing.Data from this study represent some of the first remotely transmitted quantifications from accelerometers. The methods presented and analysed can be used to provide novel insight towards the behaviours and movements of free-ranging marine predators, such as juvenile southern elephant seals, from whom logger retrieval is challenging

Perception of biological motion in visual agnosia

Directory of Open Access Journals (Sweden)

Elisabeth eHuberle

2012-08-01

Full Text Available Over the past twenty-five years, visual processing has been discussed in the context of the dual stream hypothesis consisting of a ventral (‘what' and a dorsal ('where' visual information processing pathway. Patients with brain damage of the ventral pathway typically present with signs of visual agnosia, the inability to identify and discriminate objects by visual exploration, but show normal perception of motion perception. A dissociation between the perception of biological motion and non-biological motion has been suggested: Perception of biological motion might be impaired when 'non-biological' motion perception is intact and vice versa. The impact of object recognition on the perception of biological motion remains unclear. We thus investigated this question in a patient with severe visual agnosia, who showed normal perception of non-biological motion. The data suggested that the patient's perception of biological motion remained largely intact. However, when tested with objects constructed of coherently moving dots (‘Shape-from-Motion’, recognition was severely impaired. The results are discussed in the context of possible mechanisms of biological motion perception.

Structural biology data archiving: where we are and what lies ahead.

Science.gov (United States)

Kleywegt, Gerard J; Velankar, Sameer; Patwardhan, Ardan

2018-05-10

For almost 50 years, structural biology has endeavoured to conserve and share its experimental data and their interpretations (usually, atomistic models) through global public archives such as the Protein Data Bank (PDB), Electron Microscopy Data Bank (EMDB) and Biologic Magnetic Resonance Bank (BMRB). These archives are treasure troves of freely accessible data that document our quest for molecular or atomic understanding of biological function and processes in health and disease. They have prepared the field to tackle new archiving challenges as more and more (combinations of) techniques are being utilised to elucidate structure at ever increasing length scales. Furthermore, the field has made substantial efforts to develop validation methods that help users to assess the reliability of structures and to identify the most appropriate data for their needs. In this Review, we present an overview of public data archives in structural biology and discuss the importance of validation for users and producers of structural data. Finally, we sketch our efforts to integrate structural data with bioimaging data and with other sources of biological data. This will make relevant structural information available and more easily discoverable for a wide range of scientists. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Site remediation using biological processes

International Nuclear Information System (INIS)

Lei, J.; Sansregret, J.L.; Cyr, B.; Pouliot, Y.

1995-01-01

The main process used in the bioremediation of contaminated sites is the microbial degradation and mineralization of pollutants. The bioengineering processes developed and applied by the company to optimize the microbial degradation are described and full scale case studies are reviewed. In each case, the site characteristics (type of contaminants, nature of soil, geographic location, etc.) and the results obtained are presented. The selected projects cover different bioremediation techniques (biopile, bioventing and air sparging), different contaminants (PAH, PCP, hydrocarbons) and different types of industrial sites (former gas work plant, petroleum depot, refinery, etc.)

Synthetic biology, inspired by synthetic chemistry.

Science.gov (United States)

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

2012-07-16

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

Geographical ranges in macroecology: Processes, patterns and implications

DEFF Research Database (Denmark)

Borregaard, Michael Krabbe

, are distributed over the entire Earth. Species’ ranges are one of the basic units of the science of macroecology, which deals with patterns in the distribution of life on Earth. An example of such patterns is the large geographic variation in species richness between areas. These patterns are closely linked...... for this relationship. In going through the mechanisms, I distinguish between ‘structural’ causes, such as differences between the niches of species; and ‘dynamic’ causes, such as dispersal of individuals among populations. A central conclusion is that both of these types of mechanisms contribute to creating...... group includes a popularly written book chapter, where the causes and consequences of the spatial distribution of organisms are introduced more generally. The second group consists of several papers investigating the link between ranges and richness patterns. Variation in species richness is probably...

Modeling of long-range memory processes with inverse cubic distributions by the nonlinear stochastic differential equations

Science.gov (United States)

Kaulakys, B.; Alaburda, M.; Ruseckas, J.

2016-05-01

A well-known fact in the financial markets is the so-called ‘inverse cubic law’ of the cumulative distributions of the long-range memory fluctuations of market indicators such as a number of events of trades, trading volume and the logarithmic price change. We propose the nonlinear stochastic differential equation (SDE) giving both the power-law behavior of the power spectral density and the long-range dependent inverse cubic law of the cumulative distribution. This is achieved using the suggestion that when the market evolves from calm to violent behavior there is a decrease of the delay time of multiplicative feedback of the system in comparison to the driving noise correlation time. This results in a transition from the Itô to the Stratonovich sense of the SDE and yields a long-range memory process.

Nutritional Systems Biology

DEFF Research Database (Denmark)

Jensen, Kasper

and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...