WorldWideScience

Sample records for underlying biological bases

  1. Biologically Based Methods for Pest Management in Agriculture under Changing Climates: Challenges and Future Directions

    Directory of Open Access Journals (Sweden)

    Casper Nyamukondiwa

    2012-11-01

    Full Text Available The current changes in global climatic regimes present a significant societal challenge, affecting in all likelihood insect physiology, biochemistry, biogeography and population dynamics. With the increasing resistance of many insect pest species to chemical insecticides and an increasing organic food market, pest control strategies are slowly shifting towards more sustainable, ecologically sound and economically viable options. Biologically based pest management strategies present such opportunities through predation or parasitism of pests and plant direct or indirect defense mechanisms that can all be important components of sustainable integrated pest management programs. Inevitably, the efficacy of biological control systems is highly dependent on natural enemy-prey interactions, which will likely be modified by changing climates. Therefore, knowledge of how insect pests and their natural enemies respond to climate variation is of fundamental importance in understanding biological insect pest management under global climate change. Here, we discuss biological control, its challenges under climate change scenarios and how increased global temperatures will require adaptive management strategies to cope with changing status of insects and their natural enemies.

  2. Biologically Based Methods for Pest Management in Agriculture under Changing Climates: Challenges and Future Directions.

    Science.gov (United States)

    Chidawanyika, Frank; Mudavanhu, Pride; Nyamukondiwa, Casper

    2012-11-09

    The current changes in global climatic regimes present a significant societal challenge, affecting in all likelihood insect physiology, biochemistry, biogeography and population dynamics. With the increasing resistance of many insect pest species to chemical insecticides and an increasing organic food market, pest control strategies are slowly shifting towards more sustainable, ecologically sound and economically viable options. Biologically based pest management strategies present such opportunities through predation or parasitism of pests and plant direct or indirect defense mechanisms that can all be important components of sustainable integrated pest management programs. Inevitably, the efficacy of biological control systems is highly dependent on natural enemy-prey interactions, which will likely be modified by changing climates. Therefore, knowledge of how insect pests and their natural enemies respond to climate variation is of fundamental importance in understanding biological insect pest management under global climate change. Here, we discuss biological control, its challenges under climate change scenarios and how increased global temperatures will require adaptive management strategies to cope with changing status of insects and their natural enemies.

  3. Biologically Based Methods for Pest Management in Agriculture under Changing Climates: Challenges and Future Directions

    OpenAIRE

    Chidawanyika, Frank; Mudavanhu, Pride; Nyamukondiwa, Casper

    2012-01-01

    The current changes in global climatic regimes present a significant societal challenge, affecting in all likelihood insect physiology, biochemistry, biogeography and population dynamics. With the increasing resistance of many insect pest species to chemical insecticides and an increasing organic food market, pest control strategies are slowly shifting towards more sustainable, ecologically sound and economically viable options. Biologically based pest management strategies present such oppor...

  4. 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

  5. Biological degradation of chernozems under irrigation

    Directory of Open Access Journals (Sweden)

    Oksana Naydyonova

    2014-12-01

    Full Text Available We studied the changes in the state of microbial cenosis of Ukraine’s chernozems under irrigation. Considerable part of Ukraine’s chernozems is located in the areas where humidification is insufficient and unstable. Irrigation is a soil-reclamation measure for chernozems of Ukrainian Forest-steppe and Steppe which enables getting the assured yield, especially vegetable and fodder crops. At the same time, irrigation is a powerful anthropogenic factor that affects the soil, causes a significant transformation of many of its properties and regimes including biological ones. Often these changes are negative. The purpose of our investigation was to identify changes in the state of microbial cenoses of chernozem soils under irrigation which depend on such factors as the quality of irrigation water, the duration and intensity of irrigation, the initial properties of soil, the structure of crop rotation, usage of fertilizing systems and agroameliorative techniques. We identified direction and evaluated a degree of changes in biological properties of chernozems under influence of irrigation in different agro-irrigational and soil-climatic conditions. In the long-term stationary field experiments we identified the following biological indices of irrigated soils and their non-irrigated analogues: a number of microorganisms which belong to main ecological-trophic groups, activity of soil enzymes (dehydrogenase, invertase, phenol oxidase, soil phytotoxic activity, cellulose destroying capacity of soil, indices of oligotrophy and mineralization, summary biological index (SBI and index of biological degradation (BDI. Results of researches showed that irrigation unbalanced the soil ecosystem and stipulated the forming of microbial cenosis with new parameters. Long-term intensive irrigation of typical chernozem (Kharkiv Region with fresh water under condition of 4-fields vegetable crop rotation led to the degradation changes of its microbial cenosis such as

  6. Biological denitrification process based on the Fe(0)-carbon micro-electrolysis for simultaneous ammonia and nitrate removal from low organic carbon water under a microaerobic condition.

    Science.gov (United States)

    Deng, Shihai; Li, Desheng; Yang, Xue; Xing, Wei; Li, Jinlong; Zhang, Qi

    2016-11-01

    A combined process between micro-electrolysis and biological denitrification (MEBD) using iron scraps and an activated carbon-based micro-electrolysis carrier was developed for nitrogen removal under a microaerobic condition. The process provided NH4(+)-N and total nitrogen (TN) removal efficiencies of 92.6% and 95.3%, respectively, and TN removal rate of 0.373±0.11kgN/(m(3)d) at corresponding DO of 1.0±0.1mg/L and HRT of 3h, and the optimal pH of 7.6-8.4. High-throughput sequencing analysis verified that dominant classes belonged to β-, α-, and γ-Proteobacteria, and Nitrospira. The dominant genera Hydrogenophaga and Sphaerotilus significantly increased during the operation, covering 13.2% and 6.1% in biofilms attached to the carrier in the middle of the reactor, respectively. Autotrophic denitrification contributed to >80% of the TN removal. The developed MEBD achieved efficient simultaneous nitrification and autotrophic denitrification, presenting significant potential for application in practical low organic carbon water treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  7. The Biological Bases of Conformity

    Directory of Open Access Journals (Sweden)

    Thomas Joshau Henry Morgan

    2012-06-01

    Full Text Available Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favour adaptive learning strategies that facilitate effective use of social information in decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behaviour in nonhuman animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history and ontogeny of conformity and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behaviour conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subject’s behaviour is the result of both social and asocial influences, the resultant behaviour may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for

  8. The Biological Bases of Conformity

    Science.gov (United States)

    Morgan, T. J. H.; Laland, K. N.

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects’ behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning. PMID:22712006

  9. The biological bases of conformity.

    Science.gov (United States)

    Morgan, T J H; Laland, K N

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects' behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning.

  10. Biological clockwork underlying adaptive rhythmic movements

    Science.gov (United States)

    Iwasaki, Tetsuya; Chen, Jun; Friesen, W. Otto

    2014-01-01

    Owing to the complexity of neuronal circuits, precise mathematical descriptions of brain functions remain an elusive ambition. A more modest focus of many neuroscientists, central pattern generators, are more tractable neuronal circuits specialized to generate rhythmic movements, including locomotion. The relative simplicity and well-defined motor functions of these circuits provide an opportunity for uncovering fundamental principles of neuronal information processing. Here we present the culmination of mathematical analysis that captures the adaptive behaviors emerging from interactions between a central pattern generator, the body, and the physical environment during locomotion. The biologically realistic model describes the undulatory motions of swimming leeches with quantitative accuracy and, without further parameter tuning, predicts the sweeping changes in oscillation patterns of leeches undulating in air or swimming in high-viscosity fluid. The study demonstrates that central pattern generators are capable of adapting oscillations to the environment through sensory feedback, but without guidance from the brain. PMID:24395788

  11. Silk-polypyrrole biocompatible actuator performance under biologically relevant conditions

    Science.gov (United States)

    Hagler, Jo'elen; Peterson, Ben; Murphy, Amanda; Leger, Janelle

    Biocompatible actuators that are capable of controlled movement and can function under biologically relevant conditions are of significant interest in biomedical fields. Previously, we have demonstrated that a composite material of silk biopolymer and the conducting polymer polypyrrole (PPy) can be formed into a bilayer device that can bend under applied voltage. Further, these silk-PPy composites can generate forces comparable to human muscle (>0.1 MPa) making them ideal candidates for interfacing with biological tissues. Here silk-PPy composite films are tested for performance under biologically relevant conditions including exposure to a complex protein serum and biologically relevant temperatures. Free-end bending actuation performance, current response, force generation and, mass degradation were investigated . Preliminary results show that when exposed to proteins and biologically relevant temperatures, these silk-PPy composites show minimal degradation and are able to generate forces and conduct currents comparable to devices tested under standard conditions. NSF.

  12. Genetically-Based Biologic Technologies. Biology and Human Welfare.

    Science.gov (United States)

    Mayer, William V.; McInerney, Joseph D.

    The purpose of this six-part booklet is to review the current status of genetically-based biologic technologies and to suggest how information about these technologies can be inserted into existing educational programs. Topic areas included in the six parts are: (1) genetically-based technologies in the curriculum; (2) genetic technologies…

  13. Biology of Triatoma sherlocki (Hemiptera: Reduviidae) Under Laboratory Conditions: Biological Cycle and Resistance to Starvation.

    Science.gov (United States)

    Lima-Neiva, Vanessa; Gonçalves, Teresa C M; Bastos, Leonardo S; Gumiel, Marcia; Correia, Nathália C; Silva, Catia C; Almeida, Carlos E; Costa, Jane

    2017-07-01

    Triatoma sherlocki Papa, Jurberg, Carcavallo, Cerqueira & Barata was described in 2002, based on specimens caught in the wild in the municipality of Gentio do Ouro, Bahia, Brazil. In 2009, nymphs and adults were detected inside homes and sylvatic specimens were positive for Trypanosoma cruzi (Chagas). No information on the bionomics of T. sherlocki exists, although such data are considered essential to estimate its vector and colonization potential in domestic environments. Herein, the biological cycle of T. sherlocki was studied based on 123 eggs, with nymphs and adults fed on Mus musculus (Linnaeus). Nymphal development time phases, number of meals consumed, and stage-specific mortality rates were analyzed. Survival time under starvation conditions was measured between ecdysis and death among 50 nymphs (first to fifth instar) and 50 male and female adults. The median development time from egg to adult was 621.0 (CI: 489-656) d. The number of meals consumed ranged from 1 to 20 for nymphs of the first to fifth instar. The fifth instar showed the greatest resistance to starvation, with a mean of 156.5 d. The high number of meals consumed by T. sherlocki favored infection with and transmission of T. cruzi. The full development of this species under laboratory conditions with a low mortality rate indicates that this vector presents biological characteristics that may contribute to its adaptation to artificial human ecotopes. Its high resistance to starvation emphasizes the importance of entomological surveillance for this species. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  14. Biological factors underlying regularity and chaos in aquatic ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Biosciences; Volume 26; Issue 1. Biological factors underlying regularity and chaos in aquatic ecosystems: Simple models of complex dynamics. A B Medvinsky S V Petrovskii D A Tikhonov I A Tikhonova G R Ivanitsky E Venturino H Malchow. Articles Volume 26 Issue 1 March 2001 pp 77-108 ...

  15. Biological phosphorus uptake under anoxic and aerobic conditions

    DEFF Research Database (Denmark)

    Kerrn-Jespersen, Jens Peter; Henze, Mogens

    1993-01-01

    Biological phosphorus removal was investigated under anoxic and aerobic conditions. Tests were made to establish whether phosphorus accumulating bacteria can take up phosphate under anoxic conditions and thus utilise nitrate as oxidant. Furthermore, it was tested how the amount of organic matter...... taken up by the phosphorus accumulating bacteria during the anaerobic phase affects the total denitrification rate, as well as the rate at which the phosphorus accumulating bacteria take up phosphate under anoxic conditions. The tests were conducted as batch experiments in 21. reactors with activated...... conditions. There was a linear relationship between the amount of acetate taken up in the anaerobic phase, the denitrification rate and the phosphorus uptake rate....

  16. Changes in the species composition of the rhizosphere and phyllosphere of sugar beet under the impact of biological preparations based on endophytic bacteria and their metabolites

    Science.gov (United States)

    Pusenkova, L. I.; Il'yasova, E. Yu.; Lastochkina, O. V.; Maksimov, I. V.; Leonova, S. A.

    2016-10-01

    The species structure of the mycobiota in the rhizosphere and phyllosphere of sugar beet in ontogenesis was studied. The treatment of the plants with biopreparations based on endophytic bacteria and their metabolites (Phytosporin-M, Vitaplan, and Albit) were shown to create conditions for the colonization of the plant rhizosphere and phyllosphere by bacteria-antagonists displacing phytopathogenic microorganisms and stimulating plant growth, which induces the transformation of the microbial cenosis.

  17. Nanomaterials modulate stem cell differentiation: biological interaction and underlying mechanisms.

    Science.gov (United States)

    Wei, Min; Li, Song; Le, Weidong

    2017-10-25

    Stem cells are unspecialized cells that have the potential for self-renewal and differentiation into more specialized cell types. The chemical and physical properties of surrounding microenvironment contribute to the growth and differentiation of stem cells and consequently play crucial roles in the regulation of stem cells' fate. Nanomaterials hold great promise in biological and biomedical fields owing to their unique properties, such as controllable particle size, facile synthesis, large surface-to-volume ratio, tunable surface chemistry, and biocompatibility. Over the recent years, accumulating evidence has shown that nanomaterials can facilitate stem cell proliferation and differentiation, and great effort is undertaken to explore their possible modulating manners and mechanisms on stem cell differentiation. In present review, we summarize recent progress in the regulating potential of various nanomaterials on stem cell differentiation and discuss the possible cell uptake, biological interaction and underlying mechanisms.

  18. Biological bases of human musicality.

    Science.gov (United States)

    Perrone-Capano, Carla; Volpicelli, Floriana; di Porzio, Umberto

    2017-04-01

    Music is a universal language, present in all human societies. It pervades the lives of most human beings and can recall memories and feelings of the past, can exert positive effects on our mood, can be strongly evocative and ignite intense emotions, and can establish or strengthen social bonds. In this review, we summarize the research and recent progress on the origins and neural substrates of human musicality as well as the changes in brain plasticity elicited by listening or performing music. Indeed, music improves performance in a number of cognitive tasks and may have beneficial effects on diseased brains. The emerging picture begins to unravel how and why particular brain circuits are affected by music. Numerous studies show that music affects emotions and mood, as it is strongly associated with the brain's reward system. We can therefore assume that an in-depth study of the relationship between music and the brain may help to shed light on how the mind works and how the emotions arise and may improve the methods of music-based rehabilitation for people with neurological disorders. However, many facets of the mind-music connection still remain to be explored and enlightened.

  19. Biological Treatment of Solvent-Based Paint

    Science.gov (United States)

    2011-01-01

    COVERED (From - To) Mar 2005- Mar 2010 4. TITLE AND SUBTITLE Biological Treatment of Solvent-Based Paint 5a. CONTRACT NUMBER WP 200520 5b...GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Torres, Tom; Hoffard, Theresa 5d. PROJECT NUMBER WP 200520 Lagerquist, Jenny 5e. TASK...nonhazardous and can be landfarmed, composted , or captured in a filter press and landfilled. Most industrial biological treatment systems will also require

  20. Biology of Dermacentor marginatus (Acari: Ixodidae under laboratory conditions

    Directory of Open Access Journals (Sweden)

    Mohammad Mehdi Darvishi

    2014-02-01

    Full Text Available Objective: To investigate and survey the biology of Dermacentor marginatus (D. marginatus under laboratory conditions. Methods: In this investigation, D. marginatus adult ticks were collected from sheep in Semnan province. Then various developmental stages of D. marginatus including larvae, nymphs and adult males and females under laboratory condition were bred and their biology was scrutinized. Results: The requisite time to complete the life cycle of D. marginatus under controlled laboratory conditions for larvae (26 °C, 75% relative humidity and nymph (26 °C, 95% relative humidity moulting, was on average 92 d (range 75-104 d, including preoviposition and egg incubation (22.5 d, larvae incubation (20.5 d, nymphal stage (28 d along with male maturation (21 d. The index of conversion efficiency and the index of reproduction efficiency in females were 0.397 and 8.300, respectively. Conclusions: Although in this investigation, there was no meaningful correlation between preoviposition period and the weight of female ticks which were laid successfully. The significant linear relationship was fully observed between the weight of engorged female of D. marginatus and the number of eggs laid. The mean of preoviposition period from 5.4 d in autumn to 34.2 d in spring increased. The minimum weight of ticks with laying capacity was 69 mg and lighter ticks (21 mg either did not lay or if they did their eggs did not hatch.

  1. Instance-Based Generative Biological Shape Modeling.

    Science.gov (United States)

    Peng, Tao; Wang, Wei; Rohde, Gustavo K; Murphy, Robert F

    2009-01-01

    Biological shape modeling is an essential task that is required for systems biology efforts to simulate complex cell behaviors. Statistical learning methods have been used to build generative shape models based on reconstructive shape parameters extracted from microscope image collections. However, such parametric modeling approaches are usually limited to simple shapes and easily-modeled parameter distributions. Moreover, to maximize the reconstruction accuracy, significant effort is required to design models for specific datasets or patterns. We have therefore developed an instance-based approach to model biological shapes within a shape space built upon diffeomorphic measurement. We also designed a recursive interpolation algorithm to probabilistically synthesize new shape instances using the shape space model and the original instances. The method is quite generalizable and therefore can be applied to most nuclear, cell and protein object shapes, in both 2D and 3D.

  2. Agent-based modelling in synthetic biology.

    Science.gov (United States)

    Gorochowski, Thomas E

    2016-11-30

    Biological systems exhibit complex behaviours that emerge at many different levels of organization. These span the regulation of gene expression within single cells to the use of quorum sensing to co-ordinate the action of entire bacterial colonies. Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours. However, in many cases, it is not understood how individual cells should be programmed to ensure the emergence of a required collective behaviour. Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules. In this article, I review the use of agent-based models in synthetic biology, outline the available computational tools, and provide details on recently engineered biological systems that are amenable to this approach. I further highlight the challenges facing this methodology and some of the potential future directions. © 2016 The Author(s).

  3. Knowledge base and functionality of concepts of some Filipino biology teachers in five biology topics

    Science.gov (United States)

    Barquilla, Manuel B.

    2018-01-01

    This mixed research, is a snapshot of some Filipino Biology teachers' knowledge structure and how their concepts of the five topics in Biology (Photosynthesis, Cellular Respiration, human reproductive system, Mendelian genetics and NonMendelian genetics) functions and develops inside a biology classroom. The study focuses on the six biology teachers and a total of 222 students in their respective classes. Of the Six (6) teachers, three (3) are under the Science curriculum and the other three (3) are under regular curriculum in both public and private schools in Iligan city and Lanao del Norte, Philippines. The study utilized classroom discourses, concept maps, interpretative case-study method, bracketing method, and concept analysis for qualitative part; the quantitative part uses a nonparametric statistical tool, Kendall's tau Coefficient for determining relationship and congruency while measures of central tendencies and dispersion (mean, and standard deviation) for concept maps scores interpretation. Knowledge Base of Biology teachers were evaluated by experts in field of specialization having a doctorate program (e.g. PhD in Genetics) and PhD Biology candidates. The data collection entailed seven (7) months immersion: one (1) month for preliminary phase for the researcher to gain teachers' and students' confidence and the succeeding six (6) months for main observation and data collection. The evaluation of teachers' knowledge base by experts indicated that teachers' knowledge of (65%) is lower than the minimum (75%) recommended by ABD-el-Khalick and Boujaoude (1997). Thus, the experts believe that content knowledge of the teachers is hardly adequate for their teaching assignment. Moreover, the teachers in this study do not systematically use reallife situation to apply the concepts they teach. They can identify concepts too abstract for their student; however, they seldom use innovative ways to bring the discussion to their students' level of readiness and

  4. Construction of a Linux based chemical and biological information system.

    Science.gov (United States)

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  5. Foundational concepts and underlying theories for majors in "biochemistry and molecular biology".

    Science.gov (United States)

    Tansey, John T; Baird, Teaster; Cox, Michael M; Fox, Kristin M; Knight, Jennifer; Sears, Duane; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3) foundational skills that undergraduate majors in biochemistry and molecular biology must understand to complete their major coursework. Using information gained from these workshops, as well as from the ASBMB accreditation working group and the NSF Vision and Change report, the Core Concepts working group has developed a consensus list of learning outcomes and objectives based on five foundational concepts (evolution, matter and energy transformation, homeostasis, information flow, and macromolecular structure and function) that represent the expected conceptual knowledge base for undergraduate degrees in biochemistry and molecular biology. This consensus will aid biochemistry and molecular biology educators in the development of assessment tools for the new ASBMB recommended curriculum. © 2013 by The International Union of Biochemistry and Molecular Biology.

  6. Biological-based and physical-based optimization for biological evaluation of prostate patient's plans

    Science.gov (United States)

    Sukhikh, E.; Sheino, I.; Vertinsky, A.

    2017-09-01

    Modern modalities of radiation treatment therapy allow irradiation of the tumor to high dose values and irradiation of organs at risk (OARs) to low dose values at the same time. In this paper we study optimal radiation treatment plans made in Monaco system. The first aim of this study was to evaluate dosimetric features of Monaco treatment planning system using biological versus dose-based cost functions for the OARs and irradiation targets (namely tumors) when the full potential of built-in biological cost functions is utilized. The second aim was to develop criteria for the evaluation of radiation dosimetry plans for patients based on the macroscopic radiobiological criteria - TCP/NTCP. In the framework of the study four dosimetric plans were created utilizing the full extent of biological and physical cost functions using dose calculation-based treatment planning for IMRT Step-and-Shoot delivery of stereotactic body radiation therapy (SBRT) in prostate case (5 fractions per 7 Gy).

  7. Introductory Biology Textbooks Under-Represent Scientific Process

    Directory of Open Access Journals (Sweden)

    Dara B. Duncan

    2011-08-01

    Full Text Available Attrition of undergraduates from Biology majors is a long-standing problem. Introductory courses that fail to engage students or spark their curiosity by emphasizing the open-ended and creative nature of biological investigation and discovery could contribute to student detachment from the field. Our hypothesis was that introductory biology books devote relatively few figures to illustration of the design and interpretation of experiments or field studies, thereby de-emphasizing the scientific process.To investigate this possibility, we examined figures in six Introductory Biology textbooks published in 2008. On average, multistep scientific investigations were presented in fewer than 5% of the hundreds of figures in each book. Devoting such a small percentage of figures to the processes by which discoveries are made discourages an emphasis on scientific thinking. We suggest that by increasing significantly the illustration of scientific investigations, textbooks could support undergraduates’ early interest in biology, stimulate the development of design and analytical skills, and inspire some students to participate in investigations of their own.

  8. Strategic considerations under the Biologics Price Competition and Innovation Act.

    Science.gov (United States)

    Marquardt, John L; Auten, Stephen R

    2013-08-01

    The Biologics Price Competition and Innovation Act provides a pathway for regulatory approval of generic drugs and the associated patent challenge. This article reviews strategic considerations during the patent litigation and injunction phases. Considerations during the initial patent litigation phase include when and whether to exchange a paragraph k application and the listing and exchange of patent information during the volley phase.

  9. Clinical oncology based upon radiation biology

    International Nuclear Information System (INIS)

    Hirata, Hideki

    2016-01-01

    This paper discussed the biological effects of radiation as physical energy, especially those of X-ray as electromagnetic radiation, by associating the position of clinical oncology with classical radiation cell biology as well as recent molecular biology. First, it described the physical and biological effects of radiation, cell death due to radiation and recovery, radiation effects at tissue level, and location information and dosage information in the radiotherapy of cancer. It also described the territories unresolved through radiation biology, such as low-dose high-sensitivity, bystander effects, etc. (A.O.)

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

    Davies, Robin; Hodge, Terrell; Enyedi, Alexander

    2010-01-01

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

  12. Brillouin Spectroscopy Data Base for Biological Threats

    National Research Council Canada - National Science Library

    Rubel, Glenn

    2003-01-01

    .... Brillouin scattering from DNA, ovalbumen, the Bacillus spores globigii and thuringiensis were measured to determine the feasibility of biological material discrimination using Brillouin scattering...

  13. Viral immune evasion strategies and the underlying cell biology.

    Science.gov (United States)

    Lorenzo, M E; Ploegh, H L; Tirabassi, R S

    2001-02-01

    Evasion of the immune system by viruses is a well-studied field. It remains a challenge to understand how these viral tactics affect pathogenesis and the viral lifecycle. At the same time, the study of viral proteins involved in immune evasion has helped us to better understand a number of cellular processes at the molecular level. Here we review recent data on different viral tactics for immune evasion and highlight what these viral interventions might teach us about cell biology. Copyright 2001 Academic Press.

  14. Network-Based Models in Molecular Biology

    Science.gov (United States)

    Beyer, Andreas

    Biological systems are characterized by a large number of diverse interactions. Interaction maps have been used to abstract those interactions at all biological scales ranging from food webs at the ecosystem level down to protein interaction networks at the molecular scale.

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

    Science.gov (United States)

    Ewing, Tracy S.

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

  16. Complex systems of biological interest stability under ionising radiations

    International Nuclear Information System (INIS)

    Maclot, Sylvain

    2014-01-01

    This PhD work presents the study of stability of molecular systems of biological interest in the gas phase after interaction with ionising radiations. The use of ionising radiation can probe the physical chemistry of complex systems at the molecular scale and thus consider their intrinsic properties. Beyond the fundamental aspect, this work is part of the overall understanding of radiation effects on living organisms and in particular the use of ionizing radiation in radiotherapy. Specifically, this study focused on the use of low-energy multiply charged ions (tens of keV) provided by the GANIL (Caen), which includes most of the experiments presented. In addition, experiments using VUV photons were also conducted at synchrotron ELETTRA (Trieste, Italy). The bio-molecular systems studied are amino acids and nucleic acid constituents. Using an experimental crossed beams device allows interaction between biomolecules and ionising radiation leads mainly to the ionization and fragmentation of the system. The study of its relaxation dynamics is by time-of-flight mass spectrometry coupled to a coincidences measurements method. It is shown that an approach combining experiment and theory allows a detailed study of the fragmentation dynamics of complex systems. The results indicate that fragmentation is generally governed by the Coulomb repulsion but the intramolecular rearrangements involve specific relaxation mechanisms. (author) [fr

  17. Understanding the basic biology underlying the flavor world of children

    Directory of Open Access Journals (Sweden)

    Julie A. MENNELLA, Alison K. VENTURA

    2010-12-01

    Full Text Available Health organizations worldwide recommend that adults and children minimize intakes of excess energy and salty, sweet, and fatty foods (all of which are highly preferred tastes and eat diets richer in whole grains, low- and non- fat dairy products, legumes, fish, lean meat, fruits, and vegetables (many of which taste bitter. Despite such recommendations and the well-established benefits of these foods to human health, adults are not complying, nor are their children. A primary reason for this difficulty is the remarkably potent rewarding properties of the tastes and flavors of foods high in sweetness, saltiness, and fatness. While we cannot easily change children’s basic ingrained biology of liking sweets and avoiding bitterness, we can modulate their flavor preferences by providing early exposure, starting in utero, to a wide variety of flavors within healthy foods, such as fruits, vegetables, and whole grains. Because the flavors of foods mothers eat during pregnancy and lactation also flavor amniotic fluid and breast milk and become preferred by infants, pregnant and lactating women should widen their food choices to include as many flavorful and healthy foods as possible. These experiences, combined with repeated exposure to nutritious foods and flavor variety during the weaning period and beyond, should maximize the chances that children will select and enjoy a healthier diet [Current Zoology 56 (6: 834–841, 2010].

  18. Towards biologically conformal radiation therapy (BCRT): Selective IMRT dose escalation under the guidance of spatial biology distribution

    International Nuclear Information System (INIS)

    Yang Yong; Xing Lei

    2005-01-01

    It is well known that the spatial biology distribution (e.g., clonogen density, radiosensitivity, tumor proliferation rate, functional importance) in most tumors and sensitive structures is heterogeneous. Recent progress in biological imaging is making the mapping of this distribution increasingly possible. The purpose of this work is to establish a theoretical framework to quantitatively incorporate the spatial biology data into intensity modulated radiation therapy (IMRT) inverse planning. In order to implement this, we first derive a general formula for determining the desired dose to each tumor voxel for a known biology distribution of the tumor based on a linear-quadratic model. The desired target dose distribution is then used as the prescription for inverse planning. An objective function with the voxel-dependent prescription is constructed with incorporation of the nonuniform dose prescription. The functional unit density distribution in a sensitive structure is also considered phenomenologically when constructing the objective function. Two cases with different hypothetical biology distributions are used to illustrate the new inverse planning formalism. For comparison, treatments with a few uniform dose prescriptions and a simultaneous integrated boost are also planned. The biological indices, tumor control probability (TCP) and normal tissue complication probability (NTCP), are calculated for both types of plans and the superiority of the proposed technique over the conventional dose escalation scheme is demonstrated. Our calculations revealed that it is technically feasible to produce deliberately nonuniform dose distributions with consideration of biological information. Compared with the conventional dose escalation schemes, the new technique is capable of generating biologically conformal IMRT plans that significantly improve the TCP while reducing or keeping the NTCPs at their current levels. Biologically conformal radiation therapy (BCRT

  19. Biologically Driven Differences in Decomposition Dynamics Under Changing Ecosystems (Invited)

    Science.gov (United States)

    Grandy, S.

    2010-12-01

    Predicting the effects of environmental changes on soil organic matter dynamics remains difficult. Here I explore the possibility that differences in decomposition and soil organic matter dynamics are due in part to links between litter decomposition processes, changes in litter chemistry, and variation in decomposer communities. I explored these relationships under three types of ecosystem changes: 1) N enrichment of forest ecosystems; 2) elevated atmospheric carbon dioxide concentrations in forest ecosystems; and 3) agricultural land-use intensification. My overarching hypothesis was that litter mass loss and litter chemistry would vary under different environmental conditions, and those differences would correlate with ecosystem-specific variations in decomposer community structure and function. In three separate field experiments, I found strong evidence that decomposer communities influenced the chemistry of decomposing litter. In a related laboratory study I found that the presence of the oribatid mite Scheloribates moestus Banks (Acari: Oribatida) can substantially change litter decomposition dynamics and the molecular chemistry of decomposing litter. Most current conceptual models estimate changes in litter chemistry over the course of decomposition from initial litter chemistry and the extent of mass loss. These models suggest consistent and predictable changes in the chemical structure of organic matter during decomposition and do not explicitly consider the potential effects of variations in decomposer community structure on decomposition. In contrast, my results show that differences in decomposer communities lead to changes in litter chemistry during decomposition. Accurately predicting management effects on litter chemistry. and thus also soil organic matter dynamics, through time may require accounting for the degree to which variations in decomposer community composition influence organic matter chemistry.

  20. Biologically based multistage modeling of radiation effects

    Energy Technology Data Exchange (ETDEWEB)

    William Hazelton; Suresh Moolgavkar; E. Georg Luebeck

    2005-08-30

    This past year we have made substantial progress in modeling the contribution of homeostatic regulation to low-dose radiation effects and carcinogenesis. We have worked to refine and apply our multistage carcinogenesis models to explicitly incorporate cell cycle states, simple and complex damage, checkpoint delay, slow and fast repair, differentiation, and apoptosis to study the effects of low-dose ionizing radiation in mouse intestinal crypts, as well as in other tissues. We have one paper accepted for publication in ''Advances in Space Research'', and another manuscript in preparation describing this work. I also wrote a chapter describing our combined cell-cycle and multistage carcinogenesis model that will be published in a book on stochastic carcinogenesis models edited by Wei-Yuan Tan. In addition, we organized and held a workshop on ''Biologically Based Modeling of Human Health Effects of Low dose Ionizing Radiation'', July 28-29, 2005 at Fred Hutchinson Cancer Research Center in Seattle, Washington. We had over 20 participants, including Mary Helen Barcellos-Hoff as keynote speaker, talks by most of the low-dose modelers in the DOE low-dose program, experimentalists including Les Redpath (and Mary Helen), Noelle Metting from DOE, and Tony Brooks. It appears that homeostatic regulation may be central to understanding low-dose radiation phenomena. The primary effects of ionizing radiation (IR) are cell killing, delayed cell cycling, and induction of mutations. However, homeostatic regulation causes cells that are killed or damaged by IR to eventually be replaced. Cells with an initiating mutation may have a replacement advantage, leading to clonal expansion of these initiated cells. Thus we have focused particularly on modeling effects that disturb homeostatic regulation as early steps in the carcinogenic process. There are two primary considerations that support our focus on homeostatic regulation. First, a number of

  1. Reconstruction of biological networks based on life science data integration

    Directory of Open Access Journals (Sweden)

    Kormeier Benjamin

    2010-06-01

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

  2. Biological Based Risk Assessment for Space Exploration

    Science.gov (United States)

    Cucinotta, Francis A.

    2011-01-01

    Exposures from galactic cosmic rays (GCR) - made up of high-energy protons and high-energy and charge (HZE) nuclei, and solar particle events (SPEs) - comprised largely of low- to medium-energy protons are the primary health concern for astronauts for long-term space missions. Experimental studies have shown that HZE nuclei produce both qualitative and quantitative differences in biological effects compared to terrestrial radiation, making risk assessments for cancer and degenerative risks, such as central nervous system effects and heart disease, highly uncertain. The goal for space radiation protection at NASA is to be able to reduce the uncertainties in risk assessments for Mars exploration to be small enough to ensure acceptable levels of risks are not exceeded and to adequately assess the efficacy of mitigation measures such as shielding or biological countermeasures. We review the recent BEIR VII and UNSCEAR-2006 models of cancer risks and their uncertainties. These models are shown to have an inherent 2-fold uncertainty as defined by ratio of the 95% percent confidence level to the mean projection, even before radiation quality is considered. In order to overcome the uncertainties in these models, new approaches to risk assessment are warranted. We consider new computational biology approaches to modeling cancer risks. A basic program of research that includes stochastic descriptions of the physics and chemistry of radiation tracks and biochemistry of metabolic pathways, to emerging biological understanding of cellular and tissue modifications leading to cancer is described.

  3. Function-Based Algorithms for Biological Sequences

    Science.gov (United States)

    Mohanty, Pragyan Sheela P.

    2015-01-01

    Two problems at two different abstraction levels of computational biology are studied. At the molecular level, efficient pattern matching algorithms in DNA sequences are presented. For gene order data, an efficient data structure is presented capable of storing all gene re-orderings in a systematic manner. A common characteristic of presented…

  4. [Conceptual bases of biological safety. Part 1].

    Science.gov (United States)

    Onishchenko, G G; Smolenskiĭ, V Iu; Ezhlova, E B; Demina, Iu V; Toporkov, V P; Toprokov, A V; Liapin, M N; Kutyrev, V V

    2013-01-01

    Up to date there is a narrow and broad interpretation of the term biological safety (BS) the world over. In the narrow sense it is defined as availability of international regulations applied to diagnostic, manufacturing, or experimental works with pathogenic biological agents (PBA) in accordance with specified levels of biological hazard and BS. In a broader context it has no national, conceptual, terminological or defying basis. Therewith, establishment of this framework has become the core issue of the study. Investigations have revealed that BS should conceptually cover the whole sphere of sanitary-and-epidemiological welfare as well as related fields such as veterinary-sanitary, phytosanitary provision, ecological safety, environmental conditions (occupational, socio-economic and geopolitical infrastructures, ecological system), and be exercised to prevent and control emergency situations (ES) of biological character. It is demonstrated that this type of ES differs from ES in the sphere of public health care of international concern which is formalized in IHR (2005), in the way that it is characterized by high socio-economic and geopolitical significance of the negative influence on human vital activities, comparable with national and international security hazard. Elaborated is the conceptual, terminological and defying toolkit of the BS broad interpretation (27 terms).

  5. Spectroscopic analysis of biologically synthesized silver nanoparticles under clinorotation

    Science.gov (United States)

    Jagtap, Sagar; Vidyasagar, Pandit; Ghemud, Vipul; Dixit, Jyotsana

    Nanoparticles are one of the hot topics of research due to their size dependent optical, electrical and magnetic properties & their anti-bacterial and anti-fungal nature. Synthesis of nano particles can be done by various physical and chemical methods. However, Biosynthesis of nanoparticles is environment friendly, can take place around room temperature, and require little intervention or input of energy. In the present study, the synthesis of silver nanoparticles (AgNPs) using bacteria and the effect of clinorotation on rate of synthesis is discussed. The freshly grown bacterial isolate was inoculated in to 250-ml Erlenmeyer flask containing 50 ml sterile nutrient broth (LB). The cultured flasks were incubated in a shaker at 120 rpm for 24 h at 370C. Culture was centrifuged at 10,000 rpm for 10 min. The supernatant was used for carrying extracellular production of silver nanoparticles by mixing it with 5mM AgNO3 solution. The above solution was clinorotated at 2 rpm for 24 h. The synthesis was carried out at 60oC. Visual observation was conducted periodically to check for the nanoparticles formation in normal gravity as well as under clinorotation. UV-visible spectroscopic analysis showed that rate of synthesis was faster in case of clinorotated sample than control. Further, the results of FTIR and XRD characterization will be discussed.

  6. Respirator Filter Efficiency Testing Against Particulate and Biological Aerosols Under Moderate to High Flow Rates

    National Research Council Canada - National Science Library

    Richardson, Aaron W; Eshbaugh, Jonathan P; Hofacre, Kent C; Gardner, Paul D

    2006-01-01

    ...) and biological test aerosols under breather flow rates associated with high work rates. The inert test challenges consisted of solid and oil aerosols having nominal diameters ranging from 0.02...

  7. Biological Control Outcomes Using the Generalist Aphid Predator Aphidoletes aphidimyza under Multi-Prey Conditions

    Directory of Open Access Journals (Sweden)

    Sarah E. Jandricic

    2016-12-01

    Full Text Available The aphidophagous midge Aphidoletes aphidimyza (Diptera: Cecidomyiidae is used in biological control programs against aphids in many crops. Short-term trials with this natural enemy demonstrated that that females prefer to oviposit among aphids colonizing the new growth of plants, leading to differential attack rates for aphid species that differ in their within-plant distributions. Thus, we hypothesized that biological control efficacy could be compromised when more than one aphid species is present. We further hypothesized that control outcomes may be different at different crop stages if aphid species shift their preferred feeding locations. Here, we used greenhouse trials to determine biological control outcomes using A. aphidimyza under multi-prey conditions and at different crop stages. At all plant stages, aphid species had a significant effect on the number of predator eggs laid. More eggs were found on M. persicae versus A. solani-infested plants, since M. persicae consistently colonized plant meristems across plant growth stages. This translated to higher numbers of predatory larvae on M. periscae-infested plants in two out of our three experiments, and more consistent control of this pest (78%–95% control across all stages of plant growth. In contrast, control of A. solani was inconsistent in the presence of M. persicae, with 36%–80% control achieved. An additional experiment demonstrated control of A. solani by A. aphidimyza was significantly greater in the absence of M. persicae than in its presence. Our study illustrates that suitability of a natural enemy for pest control may change over a crop cycle as the position of prey on the plant changes, and that prey preference based on within-plant prey location can negatively influence biological control programs in systems with pest complexes. Careful monitoring of the less-preferred pest and its relative position on the plant is suggested.

  8. PENERAPAN BLENDED-PROBLEM BASED LEARNING DALAM PEMBELAJARAN BIOLOGI

    Directory of Open Access Journals (Sweden)

    Samuel Agus Triyanto

    2016-07-01

    Biologi abad 21 merupakan integrasi dan mengintegrasikan kembali sub disiplin ilmu biologi, serta integrasi biologi dengan disiplin ilmu lain untuk mengatasi permasalahan sosial. Penelitian ini bertujuan untuk mengetahui penerapan Blended-Problem Based Learning, aktivitas belajar, dan respon siswa dalam pembelajaran biologi. Penelitian ini merupakan penelitian survei dengan pendekatan deskriptif kualitatif. Data hasil penelitian menunjukkan bahwa aktivitas positif siswa dalam pembelajaran memuaskan, sedangkan respon siswa baik terhadap pembelajaran. Berdasarkan hasil penelitian, disimpulkan bahwa Blended-Problem Based Learning dapat diterapkan dan diterima sebagai model dalam pembelajaran.

  9. Biological treatment of refinery spent caustics under halo-alkaline conditions

    NARCIS (Netherlands)

    Graaff, de M.; Bijmans, M.F.M.; Abbas, B.; Euverink, G.J.W.; Muyzer, G.; Janssen, A.J.H.

    2011-01-01

    The present research demonstrates the biological treatment of refinery sulfidic spent caustics in a continuously fed system under halo-alkaline conditions (i.e. pH 9.5; Na(+)= 0.8M). Experiments were performed in identical gas-lift bioreactors operated under aerobic conditions (80-90% saturation) at

  10. Language Based Techniques for Systems Biology

    DEFF Research Database (Denmark)

    Pilegaard, Henrik

    Process calculus is the common denominator for a class of compact, idealised, domain-specific formalisms normally associated with the study of reactive concurrent systems within Computer Science. With the rise of the interactioncentred science of Systems Biology a number of bio-inspired process......), is context insensitive, while the other, a poly-variant analysis (2CFA), is context-sensitive. These analyses compute safe approximations to the set of spatial configurations that are reachable according to a given model. This is useful in the qualitative study of cellular self-organisation and, e.......g., the effects of receptor defects or drug delivery mechanisms. The property of sequential realisability. which is closely related to the function of biochemical pathways, is addressed by a variant of traditional Data Flow Analysis (DFA). This so-called ‘Pathway Analysis’ computes safe approximations to the set...

  11. Ontology- and graph-based similarity assessment in biological networks.

    Science.gov (United States)

    Wang, Haiying; Zheng, Huiru; Azuaje, Francisco

    2010-10-15

    A standard systems-based approach to biomarker and drug target discovery consists of placing putative biomarkers in the context of a network of biological interactions, followed by different 'guilt-by-association' analyses. The latter is typically done based on network structural features. Here, an alternative analysis approach in which the networks are analyzed on a 'semantic similarity' space is reported. Such information is extracted from ontology-based functional annotations. We present SimTrek, a Cytoscape plugin for ontology-based similarity assessment in biological networks. http://rosalind.infj.ulst.ac.uk/SimTrek.html francisco.azuaje@crp-sante.lu Supplementary data are available at Bioinformatics online.

  12. A literature-based similarity metric for biological processes

    Directory of Open Access Journals (Sweden)

    Chagoyen Monica

    2006-07-01

    Full Text Available Abstract Background Recent analyses in systems biology pursue the discovery of functional modules within the cell. Recognition of such modules requires the integrative analysis of genome-wide experimental data together with available functional schemes. In this line, methods to bridge the gap between the abstract definitions of cellular processes in current schemes and the interlinked nature of biological networks are required. Results This work explores the use of the scientific literature to establish potential relationships among cellular processes. To this end we haveused a document based similarity method to compute pair-wise similarities of the biological processes described in the Gene Ontology (GO. The method has been applied to the biological processes annotated for the Saccharomyces cerevisiae genome. We compared our results with similarities obtained with two ontology-based metrics, as well as with gene product annotation relationships. We show that the literature-based metric conserves most direct ontological relationships, while reveals biologically sounded similarities that are not obtained using ontology-based metrics and/or genome annotation. Conclusion The scientific literature is a valuable source of information from which to compute similarities among biological processes. The associations discovered by literature analysis are a valuable complement to those encoded in existing functional schemes, and those that arise by genome annotation. These similarities can be used to conveniently map the interlinked structure of cellular processes in a particular organism.

  13. Mitral valve replacement in patients under 65 years of age: mechanical or biological valves?

    Science.gov (United States)

    Reineke, David C; Heinisch, Paul Philipp; Winkler, Bernhard; Englberger, Lars; Carrel, Thierry P

    2015-03-01

    There is controversy regarding the optimal choice of prosthetic valves in patients less than 65 years of age requiring mitral valve replacement (MVR). Recently, trends for valve replacement are moving towards biological prosthesis also in younger patients, which is justified by the fact that a later valve-in-valve procedure is feasible in the case of degeneration of the tissue valve. This strategy is increasingly recommended in aortic valve surgery but is questionable for MVR. The purpose of this review is to evaluate current guidelines and analyse evidence for biological MVR in patients under 65 years. There are differences between guidelines of the American Heart Association and those of the European Society of Cardiology concerning the choice of prostheses in patients undergoing MVR. Although the European Society of Cardiology recommends a mechanical mitral valve in patients under 65 years of age, the American Heart Association does not provide detailed advice for these patients. Mitral valve replacement with biological valves in patients under 65 years is associated with higher rates of reoperation due to structural valve deterioration. In addition, several studies showed a decreased survival after biological MVR. Evidence for biological MVR in patients less than 65 years without comorbidities or contraindication for oral anticoagulation does not exist. Recommendations for patients less than 65 years of age should not be blurred by current 'en-vogue' methods for promising but not yet proven valve-in-valve strategies.

  14. Access and benefit sharing (ABS) under the convention on biological diversity (CBD): implications for microbial biological control

    Science.gov (United States)

    Researchers and implementers of biological control are confronted with a variety of scientific, regulatory and administrative challenges to their biological control programs. One developing challenge will arise from the implementation of provisions of the Convention on Biological Diversity (CBD) co...

  15. Foundational Concepts and Underlying Theories for Majors in "Biochemistry and Molecular Biology"

    Science.gov (United States)

    Tansey, John T.; Baird, Teaster, Jr.; Cox, Michael M.; Fox, Kristin M.; Knight, Jennifer; Sears, Duane; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members and science educators from around the country that focused on identifying: 1) core principles of biochemistry and molecular biology, 2) essential concepts and underlying theories from physics, chemistry, and mathematics, and 3)…

  16. Evaluation of a commercial biologically based IMRT treatment planning system

    International Nuclear Information System (INIS)

    Semenenko, Vladimir A.; Reitz, Bodo; Day, Ellen; Qi, X. Sharon; Miften, Moyed; Li, X. Allen

    2008-01-01

    A new inverse treatment planning system (TPS) for external beam radiation therapy with high energy photons is commercially available that utilizes both dose-volume-based cost functions and a selection of cost functions which are based on biological models. The purpose of this work is to evaluate quality of intensity-modulated radiation therapy (IMRT) plans resulting from the use of biological cost functions in comparison to plans designed using a traditional TPS employing dose-volume-based optimization. Treatment planning was performed independently at two institutions. For six cancer patients, including head and neck (one case from each institution), prostate, brain, liver, and rectal cases, segmental multileaf collimator IMRT plans were designed using biological cost functions and compared with clinically used dose-based plans for the same patients. Dose-volume histograms and dosimetric indices, such as minimum, maximum, and mean dose, were extracted and compared between the two types of treatment plans. Comparisons of the generalized equivalent uniform dose (EUD), a previously proposed plan quality index (fEUD), target conformity and heterogeneity indices, and the number of segments and monitor units were also performed. The most prominent feature of the biologically based plans was better sparing of organs at risk (OARs). When all plans from both institutions were combined, the biologically based plans resulted in smaller EUD values for 26 out of 33 OARs by an average of 5.6 Gy (range 0.24 to 15 Gy). Owing to more efficient beam segmentation and leaf sequencing tools implemented in the biologically based TPS compared to the dose-based TPS, an estimated treatment delivery time was shorter in most (five out of six) cases with some plans showing up to 50% reduction. The biologically based plans were generally characterized by a smaller conformity index, but greater heterogeneity index compared to the dose-based plans. Overall, compared to plans based on dose

  17. "Omics" of High Altitude Biology: A Urinary Metabolomics Biomarker Study of Rats Under Hypobaric Hypoxia.

    Science.gov (United States)

    Koundal, Sunil; Gandhi, Sonia; Kaur, Tanzeer; Mazumder, Avik; Khushu, Subash

    2015-12-01

    High altitude medicine is an emerging subspecialty that has crosscutting relevance for 21(st) century science and society: from sports medicine and aerospace industry to urban and rural communities living in high altitude. Recreational travel to high altitude has also become increasingly popular. Rarely has the biology of high altitude biology been studied using systems sciences and omics high-throughput technologies. In the present study, 1H-NMR-based metabolomics, along with multivariate analyses, were employed in a preclinical rat model to characterize the urinary metabolome under hypobaric hypoxia stress. Rats were exposed to simulated altitude of 6700 m above the sea level. The urine samples were collected from pre- and post-exposure (1, 3, 7, and 14 days) of hypobaric hypoxia. Metabolomics urinalysis showed alterations in TCA cycle metabolites (citrate, α-ketoglutarate), cell membrane metabolism (choline), gut micro-flora metabolism (hippurate, phenylacetylglycine), and others (N-acetyl glutamate, creatine, taurine) in response to hypobaric hypoxia. Taurine, a potential biomarker of hepatic function, was elevated after 3 days of hypobaric hypoxia, which indicates altered liver functioning. Liver histopathology confirmed the damage to tissue architecture due to hypobaric hypoxia. The metabolic pathway analysis identified taurine metabolism and TCA as important pathways that might have contributed to hypobaric hypoxia-induced pathophysiology. This study demonstrates the use of metabolomics as a promising tool for discovery and understanding of novel biochemical responses to hypobaric hypoxia exposure, providing new insight in the field of high altitude medicine and the attendant health problems that occur in response to high altitude. The findings reported here also have potential relevance for sports medicine and aviation sciences.

  18. Study Under AC Stimulation on Excitement Properties of Weighted Small-World Biological Neural Networks with Side-Restrain Mechanism

    International Nuclear Information System (INIS)

    Yuan Wujie; Luo Xiaoshu; Jiang Pinqun

    2007-01-01

    In this paper, we propose a new model of weighted small-world biological neural networks based on biophysical Hodgkin-Huxley neurons with side-restrain mechanism. Then we study excitement properties of the model under alternating current (AC) stimulation. The study shows that the excitement properties in the networks are preferably consistent with the behavior properties of a brain nervous system under different AC stimuli, such as refractory period and the brain neural excitement response induced by different intensities of noise and coupling. The results of the study have reference worthiness for the brain nerve electrophysiology and epistemological science.

  19. Biological information systems: Evolution as cognition-based information management.

    Science.gov (United States)

    Miller, William B

    2018-05-01

    An alternative biological synthesis is presented that conceptualizes evolutionary biology as an epiphenomenon of integrated self-referential information management. Since all biological information has inherent ambiguity, the systematic assessment of information is required by living organisms to maintain self-identity and homeostatic equipoise in confrontation with environmental challenges. Through their self-referential attachment to information space, cells are the cornerstone of biological action. That individualized assessment of information space permits self-referential, self-organizing niche construction. That deployment of information and its subsequent selection enacted the dominant stable unicellular informational architectures whose biological expressions are the prokaryotic, archaeal, and eukaryotic unicellular forms. Multicellularity represents the collective appraisal of equivocal environmental information through a shared information space. This concerted action can be viewed as systematized information management to improve information quality for the maintenance of preferred homeostatic boundaries among the varied participants. When reiterated in successive scales, this same collaborative exchange of information yields macroscopic organisms as obligatory multicellular holobionts. Cognition-Based Evolution (CBE) upholds that assessment of information precedes biological action, and the deployment of information through integrative self-referential niche construction and natural cellular engineering antecedes selection. Therefore, evolutionary biology can be framed as a complex reciprocating interactome that consists of the assessment, communication, deployment and management of information by self-referential organisms at multiple scales in continuous confrontation with environmental stresses. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Histological image classification using biologically interpretable shape-based features

    International Nuclear Information System (INIS)

    Kothari, Sonal; Phan, John H; Young, Andrew N; Wang, May D

    2013-01-01

    Automatic cancer diagnostic systems based on histological image classification are important for improving therapeutic decisions. Previous studies propose textural and morphological features for such systems. These features capture patterns in histological images that are useful for both cancer grading and subtyping. However, because many of these features lack a clear biological interpretation, pathologists may be reluctant to adopt these features for clinical diagnosis. We examine the utility of biologically interpretable shape-based features for classification of histological renal tumor images. Using Fourier shape descriptors, we extract shape-based features that capture the distribution of stain-enhanced cellular and tissue structures in each image and evaluate these features using a multi-class prediction model. We compare the predictive performance of the shape-based diagnostic model to that of traditional models, i.e., using textural, morphological and topological features. The shape-based model, with an average accuracy of 77%, outperforms or complements traditional models. We identify the most informative shapes for each renal tumor subtype from the top-selected features. Results suggest that these shapes are not only accurate diagnostic features, but also correlate with known biological characteristics of renal tumors. Shape-based analysis of histological renal tumor images accurately classifies disease subtypes and reveals biologically insightful discriminatory features. This method for shape-based analysis can be extended to other histological datasets to aid pathologists in diagnostic and therapeutic decisions

  1. Global stability analysis and robust design of multi-time-scale biological networks under parametric uncertainties.

    Science.gov (United States)

    Meyer-Baese, Anke; Koshkouei, Ali J; Emmett, Mark R; Goodall, David P

    2009-01-01

    Biological networks are prone to internal parametric fluctuations and external noises. Robustness represents a crucial property of these networks, which militates the effects of internal fluctuations and external noises. In this paper biological networks are formulated as coupled nonlinear differential systems operating at different time-scales under vanishing perturbations. In contrast to previous work viewing biological parametric uncertain systems as perturbations to a known nominal linear system, the perturbed biological system is modeled as nonlinear perturbations to a known nonlinear idealized system and is represented by two time-scales (subsystems). In addition, conditions for the existence of a global uniform attractor of the perturbed biological system are presented. By using an appropriate Lyapunov function for the coupled system, a maximal upper bound for the fast time-scale associated with the fast state is derived. The proposed robust system design principles are potentially applicable to robust biosynthetic network design. Finally, two examples of two important biological networks, a neural network and a gene regulatory network, are presented to illustrate the applicability of the developed theoretical framework.

  2. A Color-Opponency Based Biological Model for Color Constancy

    Directory of Open Access Journals (Sweden)

    Yongjie Li

    2011-05-01

    Full Text Available Color constancy is the ability of the human visual system to adaptively correct color-biased scenes under different illuminants. Most of the existing color constancy models are nonphysiologically plausible. Among the limited biological models, the great majority is Retinex and its variations, and only two or three models directly simulate the feature of color-opponency, but only of the very earliest stages of visual pathway, i.e., the single-opponent mechanisms involved at the levels of retinal ganglion cells and lateral geniculate nucleus (LGN neurons. Considering the extensive physiological evidences supporting that both the single-opponent cells in retina and LGN and the double-opponent neurons in primary visual cortex (V1 are the building blocks for color constancy, in this study we construct a color-opponency based color constancy model by simulating the opponent fashions of both the single-opponent and double-opponent cells in a forward manner. As for the spatial structure of the receptive fields (RF, both the classical RF (CRF center and the nonclassical RF (nCRF surround are taken into account for all the cells. The proposed model was tested on several typical image databases commonly used for performance evaluation of color constancy methods, and exciting results were achieved.

  3. Sustainable production of biologically active molecules of marine based origin.

    Science.gov (United States)

    Murray, Patrick M; Moane, Siobhan; Collins, Catherine; Beletskaya, Tanya; Thomas, Olivier P; Duarte, Alysson W F; Nobre, Fernando S; Owoyemi, Ifeloju O; Pagnocca, Fernando C; Sette, L D; McHugh, Edward; Causse, Eric; Pérez-López, Paula; Feijoo, Gumersindo; Moreira, Ma T; Rubiolo, Juan; Leirós, Marta; Botana, Luis M; Pinteus, Susete; Alves, Celso; Horta, André; Pedrosa, Rui; Jeffryes, Clayton; Agathos, Spiros N; Allewaert, Celine; Verween, Annick; Vyverman, Wim; Laptev, Ivan; Sineoky, Sergei; Bisio, Angela; Manconi, Renata; Ledda, Fabio; Marchi, Mario; Pronzato, Roberto; Walsh, Daniel J

    2013-09-25

    The marine environment offers both economic and scientific potential which are relatively untapped from a biotechnological point of view. These environments whilst harsh are ironically fragile and dependent on a harmonious life form balance. Exploitation of natural resources by exhaustive wild harvesting has obvious negative environmental consequences. From a European industry perspective marine organisms are a largely underutilised resource. This is not due to lack of interest but due to a lack of choice the industry faces for cost competitive, sustainable and environmentally conscientious product alternatives. Knowledge of the biotechnological potential of marine organisms together with the development of sustainable systems for their cultivation, processing and utilisation are essential. In 2010, the European Commission recognised this need and funded a collaborative RTD/SME project under the Framework 7-Knowledge Based Bio-Economy (KBBE) Theme 2 Programme 'Sustainable culture of marine microorganisms, algae and/or invertebrates for high value added products'. The scope of that project entitled 'Sustainable Production of Biologically Active Molecules of Marine Based Origin' (BAMMBO) is outlined. Although the Union is a global leader in many technologies, it faces increasing competition from traditional rivals and emerging economies alike and must therefore improve its innovation performance. For this reason innovation is placed at the heart of a European Horizon 2020 Strategy wherein the challenge is to connect economic performance to eco performance. This article provides a synopsis of the research activities of the BAMMBO project as they fit within the wider scope of sustainable environmentally conscientious marine resource exploitation for high-value biomolecules. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Essential concepts and underlying theories from physics, chemistry, and mathematics for "biochemistry and molecular biology" majors.

    Science.gov (United States)

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry, and Mathematics that all Biochemistry or Molecular Biology majors must understand to complete their major coursework. The allied fields working group created a survey to validate foundational concepts from Physics, Chemistry, and Mathematics identified from participant feedback at various workshops. One-hundred twenty participants responded to the survey and 68% of the respondents answered yes to the question: "We have identified the following as the core concepts and underlying theories from Physics, Chemistry, and Mathematics that Biochemistry majors or Molecular Biology majors need to understand after they complete their major courses: 1) mechanical concepts from Physics, 2) energy and thermodynamic concepts from Physics, 3) critical concepts of structure from chemistry, 4) critical concepts of reactions from Chemistry, and 5) essential Mathematics. In your opinion, is the above list complete?" Respondents also delineated subcategories they felt should be included in these broad categories. From the results of the survey and this analysis the allied fields working group constructed a consensus list of allied fields concepts, which will help inform Biochemistry and Molecular Biology educators when considering the ASBMB recommended curriculum for Biochemistry or Molecular Biology majors and in the development of appropriate assessment tools to gauge student understanding of how these concepts relate to biochemistry and molecular biology. © 2013 by The International Union of Biochemistry and Molecular Biology.

  5. Biological Impact of Music and Software-Based Auditory Training

    Science.gov (United States)

    Kraus, Nina

    2012-01-01

    Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals--both young and old--encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in…

  6. A Project-Based Biologically-Inspired Robotics Module

    Science.gov (United States)

    Crowder, R. M.; Zauner, K.-P.

    2013-01-01

    The design of any robotic system requires input from engineers from a variety of technical fields. This paper describes a project-based module, "Biologically-Inspired Robotics," that is offered to Electronics and Computer Science students at the University of Southampton, U.K. The overall objective of the module is for student groups to…

  7. Expanding Kenya's protected areas under the Convention on Biological Diversity to maximize coverage of plant diversity.

    Science.gov (United States)

    Scherer, Laura; Curran, Michael; Alvarez, Miguel

    2017-04-01

    Biodiversity is highly valuable and critically threatened by anthropogenic degradation of the natural environment. In response, governments have pledged enhanced protected-area coverage, which requires scarce biological data to identify conservation priorities. To assist this effort, we mapped conservation priorities in Kenya based on maximizing alpha (species richness) and beta diversity (species turnover) of plant communities while minimizing economic costs. We used plant-cover percentages from vegetation surveys of over 2000 plots to build separate models for each type of diversity. Opportunity and management costs were based on literature data and interviews with conservation organizations. Species richness was predicted to be highest in a belt from Lake Turkana through Mount Kenya and in a belt parallel to the coast, and species turnover was predicted to be highest in western Kenya and along the coast. Our results suggest the expanding reserve network should focus on the coast and northeastern provinces of Kenya, where new biological surveys would also fill biological data gaps. Meeting the Convention on Biological Diversity target of 17% terrestrial coverage by 2020 would increase representation of Kenya's plant communities by 75%. However, this would require about 50 times more funds than Kenya has received thus far from the Global Environment Facility. © 2016 Society for Conservation Biology.

  8. AIEgen-Based Fluorescent Nanomaterials: Fabrication and Biological Applications

    Directory of Open Access Journals (Sweden)

    Hui Gao

    2018-02-01

    Full Text Available In recent years, luminogens with the feature of aggregation-induced emission (AIEgen have emerged as advanced luminescent materials for fluorescent nanomaterial preparation. AIEgen-based nanomaterials show enhanced fluorescence efficiency and superior photostability, which thusly offer unique advantages in biological applications. In this review, we will summarize the fabrication methods of AIEgen-based nanomaterials and their applications in in vitro/in vivo imaging, cell tracing, photodynamic therapy and drug delivery, focusing on the recent progress.

  9. Biological impact of music and software-based auditory training

    OpenAIRE

    Kraus, Nina

    2012-01-01

    Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals – both young and old – encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in noisy environments and reading, pointing to an intersection between hearing and cognition. Musical experience, amplification, and software-based ...

  10. Biological Bases for Radiation Adaptive Responses in the Lung

    Energy Technology Data Exchange (ETDEWEB)

    Scott, Bobby R. [Lovelace Biomedical and Environmental Research Inst., Albuquerque, NM (United States); Lin, Yong [Lovelace Biomedical and Environmental Research Inst., Albuquerque, NM (United States); Wilder, Julie [Lovelace Biomedical and Environmental Research Inst., Albuquerque, NM (United States); Belinsky, Steven [Lovelace Biomedical and Environmental Research Inst., Albuquerque, NM (United States)

    2015-03-01

    Our main research objective was to determine the biological bases for low-dose, radiation-induced adaptive responses in the lung, and use the knowledge gained to produce an improved risk model for radiation-induced lung cancer that accounts for activated natural protection, genetic influences, and the role of epigenetic regulation (epiregulation). Currently, low-dose radiation risk assessment is based on the linear-no-threshold hypothesis, which now is known to be unsupported by a large volume of data.

  11. Synthetic biology for microbial production of lipid-based biofuels.

    Science.gov (United States)

    d'Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel; Keasling, Jay D

    2015-12-01

    The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing. Published by Elsevier Ltd.

  12. Synthesis, characterization and biological evaluation of tryptamine based benzamide derivatives.

    Science.gov (United States)

    Aftab, Kiran; Aslam, Kinza; Kousar, Shazia; Nadeem, Muhammad Jawad Ul Hasan

    2016-03-01

    Benzamides and tryptamine are biologically significant compounds, therefore, various benzamide analogous of tryptamine have been efficiently synthesized using tryptamine and different benzoyl chlorides, in order to find new biologically active compounds. The resulting products were then characterized by melting point determination, calculation of Rf values and LC-MS techniques. At last, structure activity relationship (SAR) of the synthesized compounds was evaluated against two microbial strains; Bacillus subtilis and Aspergillus niger. All the five prepared products have shown high yield, sharp characterization and significant resistance against the growth of tested microorganism, providing a new range of tryptamine based benzamide derivatives having significant antimicrobial activities.

  13. Synthetic biology for microbial production of lipid-based biofuels

    Energy Technology Data Exchange (ETDEWEB)

    d' Espaux, L; Mendez-Perez, D; Li, R; Keasling, JD

    2015-10-23

    The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here in this paper we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. Lastly, we further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing.

  14. Prototype Biology-Based Radiation Risk Module Project

    Science.gov (United States)

    Terrier, Douglas; Clayton, Ronald G.; Patel, Zarana; Hu, Shaowen; Huff, Janice

    2015-01-01

    Biological effects of space radiation and risk mitigation are strategic knowledge gaps for the Evolvable Mars Campaign. The current epidemiology-based NASA Space Cancer Risk (NSCR) model contains large uncertainties (HAT #6.5a) due to lack of information on the radiobiology of galactic cosmic rays (GCR) and lack of human data. The use of experimental models that most accurately replicate the response of human tissues is critical for precision in risk projections. Our proposed study will compare DNA damage, histological, and cell kinetic parameters after irradiation in normal 2D human cells versus 3D tissue models, and it will use a multi-scale computational model (CHASTE) to investigate various biological processes that may contribute to carcinogenesis, including radiation-induced cellular signaling pathways. This cross-disciplinary work, with biological validation of an evolvable mathematical computational model, will help reduce uncertainties within NSCR and aid risk mitigation for radiation-induced carcinogenesis.

  15. The potential of standards-based agriculture biology as an alternative to traditional biology in California

    Science.gov (United States)

    Sellu, George Sahr

    schools. Thoron & Meyer (2011) suggested that research into the contribution of integrated science courses toward higher test scores yielded mixed results. This finding may have been due in part to the fact that integrated science courses only incorporate select topics into agriculture education courses. In California, however, agriculture educators have developed standards-based courses such as Agriculture Biology (AgBio) that cover the same content standards as core traditional courses such as traditional biology. Students in both AgBio and traditional biology take the same standardized biology test. This is the first time there has been an opportunity for a fair comparison and a uniform metric for an agriscience course such as AgBio to be directly compared to traditional biology. This study will examine whether there are differences between AgBio and traditional biology with regard to standardized test scores in biology. Furthermore, the study examines differences in perception between teachers and students regarding teaching and learning activities associated with higher achievement in science. The findings of the study could provide a basis for presenting AgBio as a potential alternative to traditional biology. The findings of this study suggest that there are no differences between AgBio and traditional biology students with regard to standardized biology test scores. Additionally, the findings indicate that co-curricular activities in AgBio could contribute higher student achievement in biology. However, further research is required to identify specific activities in AgBio that contribute to higher achievement in science.

  16. Stochastic noncooperative and cooperative evolutionary game strategies of a population of biological networks under natural selection.

    Science.gov (United States)

    Chen, Bor-Sen; Yeh, Chin-Hsun

    2017-12-01

    We review current static and dynamic evolutionary game strategies of biological networks and discuss the lack of random genetic variations and stochastic environmental disturbances in these models. To include these factors, a population of evolving biological networks is modeled as a nonlinear stochastic biological system with Poisson-driven genetic variations and random environmental fluctuations (stimuli). To gain insight into the evolutionary game theory of stochastic biological networks under natural selection, the phenotypic robustness and network evolvability of noncooperative and cooperative evolutionary game strategies are discussed from a stochastic Nash game perspective. The noncooperative strategy can be transformed into an equivalent multi-objective optimization problem and is shown to display significantly improved network robustness to tolerate genetic variations and buffer environmental disturbances, maintaining phenotypic traits for longer than the cooperative strategy. However, the noncooperative case requires greater effort and more compromises between partly conflicting players. Global linearization is used to simplify the problem of solving nonlinear stochastic evolutionary games. Finally, a simple stochastic evolutionary model of a metabolic pathway is simulated to illustrate the procedure of solving for two evolutionary game strategies and to confirm and compare their respective characteristics in the evolutionary process. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Effects of transgenic Bt cotton on soil fertility and biology under field conditions in subtropical inceptisol.

    Science.gov (United States)

    Singh, Raman Jeet; Ahlawat, I P S; Singh, Surender

    2013-01-01

    Although there is large-scale adoption of Bt cotton by the farmers because of immediate financial gain, there is concern that Bt crops release Bt toxins into the soil environment which reduces soil chemical and biological activities. However, the majorities of such studies were mainly performed under pot experiments, relatively little research has examined the direct and indirect effects of associated cover crop of peanut with fertilization by combined application of organic and inorganic sources of nitrogen under field conditions. We compared soil chemical and biological parameters of Bt cotton with pure crop of peanut to arrive on a valid conclusion. Significantly higher dehydrogenase enzyme activity and KMnO(4)-N content of soil were observed in Bt cotton with cover crop of peanut over pure Bt cotton followed by pure peanut at all the crop growth stages. However, higher microbial population was maintained by pure peanut over intercropped Bt cotton, but these differences were related to the presence of high amount of KMnO(4)-N content of soil. By growing cover crop of peanut between Bt cotton rows, bacteria, fungi, and actinomycetes population increased by 60%, 14%, and 10%, respectively, over Bt cotton alone. Bt cotton fertilized by combined application of urea and farm yard manure (FYM) maintained higher dehydrogenase enzyme activity, KMnO(4)-N content of soil and microbial population over urea alone. Significant positive correlations were observed for dry matter accumulation, dehydrogenase enzyme activity, KMnO(4)-N content, and microbial population of soil of Bt cotton, which indicates no harmful effects of Bt cotton on soil biological parameters and associated cover crop. Our results suggest that inclusion of cover crop of peanut and FYM in Bt cotton enhanced soil chemical and biological parameters which can mask any negative effect of the Bt toxin on microbial activity and thus on enzymatic activities.

  18. Competency-based reforms of the undergraduate biology curriculum: integrating the physical and biological sciences.

    Science.gov (United States)

    Thompson, Katerina V; Chmielewski, Jean; Gaines, Michael S; Hrycyna, Christine A; LaCourse, William R

    2013-06-01

    The National Experiment in Undergraduate Science Education project funded by the Howard Hughes Medical Institute is a direct response to the Scientific Foundations for Future Physicians report, which urged a shift in premedical student preparation from a narrow list of specific course work to a more flexible curriculum that helps students develop broad scientific competencies. A consortium of four universities is working to create, pilot, and assess modular, competency-based curricular units that require students to use higher-order cognitive skills and reason across traditional disciplinary boundaries. Purdue University; the University of Maryland, Baltimore County; and the University of Miami are each developing modules and case studies that integrate the biological, chemical, physical, and mathematical sciences. The University of Maryland, College Park, is leading the effort to create an introductory physics for life sciences course that is reformed in both content and pedagogy. This course has prerequisites of biology, chemistry, and calculus, allowing students to apply strategies from the physical sciences to solving authentic biological problems. A comprehensive assessment plan is examining students' conceptual knowledge of physics, their attitudes toward interdisciplinary approaches, and the development of specific scientific competencies. Teaching modules developed during this initial phase will be tested on multiple partner campuses in preparation for eventual broad dissemination.

  19. What is infidelity? Perceptions based on biological sex and personality

    OpenAIRE

    Thornton, Victoria; Nagurney, Alexander

    2011-01-01

    Victoria Thornton, Alexander NagurneyTexas State University – San Marcos, San Marcos, Texas, USAAbstract: The study examines perceptions of infidelity, paying particular attention to how these perceptions differ based on biological sex and personality traits, specifically agency and communion and their unmitigated counterparts. The study utilizes a sample of 125 male and 233 female college students. In addition to the personality measures, participants completed a 19-item checklist ...

  20. A Biologically Based Chemo-Sensing UAV for Humanitarian Demining

    Directory of Open Access Journals (Sweden)

    Paul F.M.J. Verschure

    2008-11-01

    Full Text Available Antipersonnel mines, weapons of cheap manufacture but lethal effect, have a high impact on the population even decades after the conflicts have finished. Here we investigate the use of a chemo-sensing Unmanned Aerial Vehicle (cUAV for demining tasks. We developed a blimp based UAV that is equipped with a broadly tuned metal-thin oxide chemo-sensor. A number of chemical mapping strategies were investigated including two biologically based localization strategies derived from the moth chemical search that can optimize the efficiency of the detection and localization of explosives and therefore be used in the demining process. Additionally, we developed a control layer that allows for both fully autonomous and manual controlled flight, as well as for the scheduling of a fleet of cUAVs. Our results confirm the feasibility of this technology for demining in real-world scenarios and give further support to a biologically based approach where the understanding of biological systems is used to solve difficult engineering problems.

  1. A Biologically Based Chemo-Sensing UAV for Humanitarian Demining

    Directory of Open Access Journals (Sweden)

    Sergi Bermúdez i Badia

    2007-06-01

    Full Text Available Antipersonnel mines, weapons of cheap manufacture but lethal effect, have a high impact on the population even decades after the conflicts have finished. Here we investigate the use of a chemo-sensing Unmanned Aerial Vehicle (cUAV for demining tasks. We developed a blimp based UAV that is equipped with a broadly tuned metal-thin oxide chemo-sensor. A number of chemical mapping strategies were investigated including two biologically based localization strategies derived from the moth chemical search that can optimize the efficiency of the detection and localization of explosives and therefore be used in the demining process. Additionally, we developed a control layer that allows for both fully autonomous and manual controlled flight, as well as for the scheduling of a fleet of cUAVs. Our results confirm the feasibility of this technology for demining in real-world scenarios and give further support to a biologically based approach where the understanding of biological systems is used to solve difficult engineering problems.

  2. Margin based ontology sparse vector learning algorithm and applied in biology science.

    Science.gov (United States)

    Gao, Wei; Qudair Baig, Abdul; Ali, Haidar; Sajjad, Wasim; Reza Farahani, Mohammad

    2017-01-01

    In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and application in biology. In this paper, using knowledge of marginal likelihood and marginal distribution, the optimized strategy of marginal based ontology sparse vector learning algorithm is presented. Finally, the new algorithm is applied to gene ontology and plant ontology to verify its efficiency.

  3. Number size distribution measurements of biological aerosols under contrasting environments and seasons from southern tropical India

    Science.gov (United States)

    Valsan, Aswathy; Cv, Biju; Krishna, Ravi; Huffman, Alex; Poschl, Ulrich; Gunthe, Sachin

    2016-04-01

    Biological aerosols constitute a wide range of dead and alive biological materials and structures that are suspended in the atmosphere. They play an important role in the atmospheric physical, chemical and biological processes and health of living being by spread of diseases among humans, plants, and, animals. The atmospheric abundance, sources, physical properties of PBAPs as compared to non-biological aerosols, however, is poorly characterized. Though omnipresent, their concentration and composition exhibit large spatial and temporal variations depending up on their sources, land-use, and local meteorology. The Indian tropical region, which constitutes approximately 18% of the world's total population exhibits vast geographical extend and experiences a distinctive meteorological phenomenon by means of Indian Summer Monsoon (IMS). Thus, the sources, properties and characteristics of biological aerosols are also expected to have significant variations over the Indian subcontinent depending upon the location and seasons. Here we present the number concentration and size distribution of Fluorescent Biological Aerosol Particles (FBAP) from two contrasting locations in Southern tropical India measured during contrasting seasons using Ultra Violet Aerodynamic Particle Sizer (UV-APS). Measurements were carried out at a pristine high altitude continental site, Munnar (10.09 N, 77.06 E; 1605 m asl) during two contrasting seasons, South-West Monsoon (June-August, 2014) and winter (Jan - Feb, 2015) and in Chennai, a coastal urban area, during July - November 2015. FBAP concentrations at both the locations showed large variability with higher concentrations occurring at Chennai. Apart from regional variations, the FBAP concentrations also exhibited variations over two different seasons under the same environmental condition. In Munnar the FBAP concentration increased by a factor of four from South-West Monsoon to winter season. The average size distribution of FBAP at both

  4. Biological iron oxidation by Gallionella spp. in drinking water production under fully aerated conditions.

    Science.gov (United States)

    de Vet, W W J M; Dinkla, I J T; Rietveld, L C; van Loosdrecht, M C M

    2011-11-01

    Iron oxidation under neutral conditions (pH 6.5-8) may be a homo- or heterogeneous chemically- or a biologically-mediated process. The chemical oxidation is supposed to outpace the biological process under slightly alkaline conditions (pH 7-8). The iron oxidation kinetics and growth of Gallionella spp. - obligatory chemolithotrophic iron oxidizers - were assessed in natural, organic carbon-containing water, in continuous lab-scale reactors and full-scale groundwater trickling filters in the Netherlands. From Gallionella cell numbers determined by qPCR, balances were made for all systems. The homogeneous chemical iron oxidation occurred in accordance with the literature, but was retarded by a low water temperature (13 °C). The contribution of the heterogeneous chemical oxidation was, despite the presence of freshly formed iron oxyhydroxides, much lower than in previous studies in ultrapure water. This could be caused by the adsorption of natural organic matter (NOM) on the iron oxide surfaces. In the oxygen-saturated natural water with a pH ranging from 6.5 to 7.7, Gallionella spp. grew uninhibited and biological iron oxidation was an important, and probably the dominant, process. Gallionella growth was not even inhibited in a full-scale filter after plate aeration. From this we conclude that Gallionella spp. can grow under neutral pH and fully aerated conditions when the chemical iron oxidation is retarded by low water temperature and inhibition of the autocatalytic iron oxidation. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. N-Cadherin Maintains the Healthy Biology of Nucleus Pulposus Cells under High-Magnitude Compression.

    Science.gov (United States)

    Wang, Zhenyu; Leng, Jiali; Zhao, Yuguang; Yu, Dehai; Xu, Feng; Song, Qingxu; Qu, Zhigang; Zhuang, Xinming; Liu, Yi

    2017-01-01

    Mechanical load can regulate disc nucleus pulposus (NP) biology in terms of cell viability, matrix homeostasis and cell phenotype. N-cadherin (N-CDH) is a molecular marker of NP cells. This study investigated the role of N-CDH in maintaining NP cell phenotype, NP matrix synthesis and NP cell viability under high-magnitude compression. Rat NP cells seeded on scaffolds were perfusion-cultured using a self-developed perfusion bioreactor for 5 days. NP cell biology in terms of cell apoptosis, matrix biosynthesis and cell phenotype was studied after the cells were subjected to different compressive magnitudes (low- and high-magnitudes: 2% and 20% compressive deformation, respectively). Non-loaded NP cells were used as controls. Lentivirus-mediated N-CDH overexpression was used to further investigate the role of N-CDH under high-magnitude compression. The 20% deformation compression condition significantly decreased N-CDH expression compared with the 2% deformation compression and control conditions. Meanwhile, 20% deformation compression increased the number of apoptotic NP cells, up-regulated the expression of Bax and cleaved-caspase-3 and down-regulated the expression of Bcl-2, matrix macromolecules (aggrecan and collagen II) and NP cell markers (glypican-3, CAXII and keratin-19) compared with 2% deformation compression. Additionally, N-CDH overexpression attenuated the effects of 20% deformation compression on NP cell biology in relation to the designated parameters. N-CDH helps to restore the cell viability, matrix biosynthesis and cellular phenotype of NP cells under high-magnitude compression. © 2017 The Author(s). Published by S. Karger AG, Basel.

  6. N-Cadherin Maintains the Healthy Biology of Nucleus Pulposus Cells under High-Magnitude Compression

    Directory of Open Access Journals (Sweden)

    Zhenyu Wang

    2017-10-01

    Full Text Available Background/Aims: Mechanical load can regulate disc nucleus pulposus (NP biology in terms of cell viability, matrix homeostasis and cell phenotype. N-cadherin (N-CDH is a molecular marker of NP cells. This study investigated the role of N-CDH in maintaining NP cell phenotype, NP matrix synthesis and NP cell viability under high-magnitude compression. Methods: Rat NP cells seeded on scaffolds were perfusion-cultured using a self-developed perfusion bioreactor for 5 days. NP cell biology in terms of cell apoptosis, matrix biosynthesis and cell phenotype was studied after the cells were subjected to different compressive magnitudes (low- and high-magnitudes: 2% and 20% compressive deformation, respectively. Non-loaded NP cells were used as controls. Lentivirus-mediated N-CDH overexpression was used to further investigate the role of N-CDH under high-magnitude compression. Results: The 20% deformation compression condition significantly decreased N-CDH expression compared with the 2% deformation compression and control conditions. Meanwhile, 20% deformation compression increased the number of apoptotic NP cells, up-regulated the expression of Bax and cleaved-caspase-3 and down-regulated the expression of Bcl-2, matrix macromolecules (aggrecan and collagen II and NP cell markers (glypican-3, CAXII and keratin-19 compared with 2% deformation compression. Additionally, N-CDH overexpression attenuated the effects of 20% deformation compression on NP cell biology in relation to the designated parameters. Conclusion: N-CDH helps to restore the cell viability, matrix biosynthesis and cellular phenotype of NP cells under high-magnitude compression.

  7. MORPHOMETRIC CHARACTERISTIC OF RATS LIVER UNDER PRE-SLAUGHTER STRESS AND USAGE OF BIOLOGICALLY ACTIVE SUBSTANCES

    Directory of Open Access Journals (Sweden)

    Grabovskyi S. S.

    2015-04-01

    Full Text Available We have studied morphometric parameters of rats’ liver under stress conditions using the biologically active substances of plant and animal origin: spleen, Echinacea and Chinese lemon extracts, sprouted grain. Aerosol introduction of spleen extract to the rats feed for five days before slaughter was caused to liver morphological state moderate deviation, indicating the antistressors properties of polyamines contained in this extract. The results of model experiment on rats can be used in research of farm animals for correction of pre-slaughter stress influence and getting the receiving of quality industrial production.

  8. Evaluation of biological attributes of soil type latossol under agroecological production

    Directory of Open Access Journals (Sweden)

    Marisol Rivero Herrada

    2016-10-01

    Full Text Available Biological soil attributes have shown to be good indicators of soil changes as a result of the management function. The aim of this study was to evaluate the effect of using cover crops, as well as planting and tillage systems on the biological attributes of a yellowish red latosol soil. Soil samples were taken at 0 to 0.10 m depth, seven days before the bean harvest. Microbial biomass carbon and nitrogen, basal soil respiration, metabolic ratio and total enzyme activity were evaluated in this study. The best agroecological management was achieved under the association of the ground cover with millet and in direct seeding because they showed higher soil microbial biomass carbon and nitrogen content and lower metabolic quotient, being pork bean the best plant coverage. All biological soil attributes were sensitive to the tillage system, which showed the best results of the total enzyme activity and of the soil metabolic quotient which resulted to be the most efficient.

  9. Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations.

    Science.gov (United States)

    Nagarajan, Karthiga; Loh, Kai-Chee

    2014-08-01

    Species-specific enumeration of mixed community is invaluable as it facilitates a better understanding of the significance of the individual strains, their interactions, and the underlying mechanisms of community dynamics. Mixed microbial community has been characterized by microbiological, biochemical, or molecular biology-based methods. While microbiological and biochemical techniques do not provide adequate quantitative information of the members of the consortia and require additional techniques for a more comprehensive analysis, molecular biology-based methods analyze the microbial consortium based on specific DNA sequences and do not require isolation and culturing of bacteria for quantitative analysis. These methods outshine conventional culture-based techniques in terms of better sensitivity, reproducibility, and reliability. Quantitative molecular biology methods have been classified as PCR-based and probe hybridization methods. The PCR-based methods includes quantitative real-time PCR and terminal restriction fragment length polymorphism, while fluorescent in situ hybridization and DNA microarrays fall under probe hybridization methods. The workflow, the quantification methods, and their potential applications are discussed in this review by highlighting their advantages and possible limitations.

  10. Biological impact of music and software-based auditory training

    Science.gov (United States)

    Kraus, Nina

    2012-01-01

    Auditory-based communication skills are developed at a young age and are maintained throughout our lives. However, some individuals – both young and old – encounter difficulties in achieving or maintaining communication proficiency. Biological signals arising from hearing sounds relate to real-life communication skills such as listening to speech in noisy environments and reading, pointing to an intersection between hearing and cognition. Musical experience, amplification, and software-based training can improve these biological signals. These findings of biological plasticity, in a variety of subject populations, relate to attention and auditory memory, and represent an integrated auditory system influenced by both sensation and cognition. Learning outcomes The reader will (1) understand that the auditory system is malleable to experience and training, (2) learn the ingredients necessary for auditory learning to successfully be applied to communication, (3) learn that the auditory brainstem response to complex sounds (cABR) is a window into the integrated auditory system, and (4) see examples of how cABR can be used to track the outcome of experience and training. PMID:22789822

  11. Biology-based combined-modality radiotherapy: workshop report

    International Nuclear Information System (INIS)

    Mason, Kathryn A.; Komaki, Ritsuko; Cox, James D.; Milas, Luka

    2001-01-01

    Purpose: The purpose of this workshop summary is to provide an overview of preclinical and clinical data on combined-modality radiotherapy. Methods and Materials: The 8th Annual Radiation Workshop at Round Top was held April 13-16, 2000 at the International Festival Institute (Round Top, TX). Results: Presentations by 30 speakers (from Germany, Netherlands, Australia, England, and France along with U.S. participants and M. D. Anderson Cancer Center faculty) formed the framework for discussions on the current status and future perspectives of biology-based combined-modality radiotherapy. Conclusion: Cellular and molecular pathways available for radiation modification by chemical and biologic agents are numerous, providing new opportunities for translational research in radiation oncology and for more effective combined-modality treatment of cancer

  12. Custom AFM for X-ray beamlines: in situ biological investigations under physiological conditions

    International Nuclear Information System (INIS)

    Gumí-Audenis, B.; Carlà, F.; Vitorino, M. V.; Panzarella, A.; Porcar, L.; Boilot, M.; Guerber, S.; Bernard, P.; Rodrigues, M. S.; Sanz, F.; Giannotti, M. I.; Costa, L.

    2015-01-01

    The performance of a custom atomic force microscope for grazing-incidence X-ray experiments on hydrated soft and biological samples is presented. A fast atomic force microscope (AFM) has been developed that can be installed as a sample holder for grazing-incidence X-ray experiments at solid/gas or solid/liquid interfaces. It allows a wide range of possible investigations, including soft and biological samples under physiological conditions (hydrated specimens). The structural information obtained using the X-rays is combined with the data gathered with the AFM (morphology and mechanical properties), providing a unique characterization of the specimen and its dynamics in situ during an experiment. In this work, lipid monolayers and bilayers in air or liquid environment have been investigated by means of AFM, both with imaging and force spectroscopy, and X-ray reflectivity. In addition, this combination allows the radiation damage induced by the beam on the sample to be studied, as has been observed on DOPC and DPPC supported lipid bilayers under physiological conditions

  13. Custom AFM for X-ray beamlines: in situ biological investigations under physiological conditions

    Energy Technology Data Exchange (ETDEWEB)

    Gumí-Audenis, B. [ESRF, The European Synchrotron, Grenoble (France); Institute for Bioengineering of Catalonia (IBEC), Barcelona (Spain); Physical Chemistry Department, Universitat de Barcelona, Barcelona (Spain); Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid (Spain); Carlà, F. [ESRF, The European Synchrotron, Grenoble (France); Vitorino, M. V. [University of Lisboa, Falculty of Science, Biosystems and Integrative Sciences Institute - BIOISI, Lisbon (Portugal); Panzarella, A. [ESRF, The European Synchrotron, Grenoble (France); Porcar, L. [Institut Laue-Langevin, Grenoble (France); Boilot, M. [ORTEC, Marseille (France); Guerber, S. [CEA, LETI Grenoble (France); Bernard, P. [ESRF, The European Synchrotron, Grenoble (France); Rodrigues, M. S. [University of Lisboa, Falculty of Science, Biosystems and Integrative Sciences Institute - BIOISI, Lisbon (Portugal); Sanz, F.; Giannotti, M. I. [Institute for Bioengineering of Catalonia (IBEC), Barcelona (Spain); Physical Chemistry Department, Universitat de Barcelona, Barcelona (Spain); Networking Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid (Spain); Costa, L., E-mail: luca.costa@esrf.fr [ESRF, The European Synchrotron, Grenoble (France)

    2015-09-30

    The performance of a custom atomic force microscope for grazing-incidence X-ray experiments on hydrated soft and biological samples is presented. A fast atomic force microscope (AFM) has been developed that can be installed as a sample holder for grazing-incidence X-ray experiments at solid/gas or solid/liquid interfaces. It allows a wide range of possible investigations, including soft and biological samples under physiological conditions (hydrated specimens). The structural information obtained using the X-rays is combined with the data gathered with the AFM (morphology and mechanical properties), providing a unique characterization of the specimen and its dynamics in situ during an experiment. In this work, lipid monolayers and bilayers in air or liquid environment have been investigated by means of AFM, both with imaging and force spectroscopy, and X-ray reflectivity. In addition, this combination allows the radiation damage induced by the beam on the sample to be studied, as has been observed on DOPC and DPPC supported lipid bilayers under physiological conditions.

  14. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  15. Using Nonlinear Stochastic Evolutionary Game Strategy to Model an Evolutionary Biological Network of Organ Carcinogenesis Under a Natural Selection Scheme.

    Science.gov (United States)

    Chen, Bor-Sen; Tsai, Kun-Wei; Li, Cheng-Wei

    2015-01-01

    -associated cell network takes 54.5 years from a normal state to stage I cancer, 1.5 years from stage I to stage II cancer, and 2.5 years from stage II to stage III cancer, with a reasonable match for the statistical result of the average age of lung cancer. These results suggest that a robust negative feedback scheme, based on a stochastic evolutionary game strategy, plays a critical role in an evolutionary biological network of carcinogenesis under a natural selection scheme.

  16. Identification of key processes underlying cancer phenotypes using biologic pathway analysis.

    Directory of Open Access Journals (Sweden)

    Sol Efroni

    2007-05-01

    Full Text Available Cancer is recognized to be a family of gene-based diseases whose causes are to be found in disruptions of basic biologic processes. An increasingly deep catalogue of canonical networks details the specific molecular interaction of genes and their products. However, mapping of disease phenotypes to alterations of these networks of interactions is accomplished indirectly and non-systematically. Here we objectively identify pathways associated with malignancy, staging, and outcome in cancer through application of an analytic approach that systematically evaluates differences in the activity and consistency of interactions within canonical biologic processes. Using large collections of publicly accessible genome-wide gene expression, we identify small, common sets of pathways - Trka Receptor, Apoptosis response to DNA Damage, Ceramide, Telomerase, CD40L and Calcineurin - whose differences robustly distinguish diverse tumor types from corresponding normal samples, predict tumor grade, and distinguish phenotypes such as estrogen receptor status and p53 mutation state. Pathways identified through this analysis perform as well or better than phenotypes used in the original studies in predicting cancer outcome. This approach provides a means to use genome-wide characterizations to map key biological processes to important clinical features in disease.

  17. Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms.

    Directory of Open Access Journals (Sweden)

    Daniel Z Grunspan

    Full Text Available Women who start college in one of the natural or physical sciences leave in greater proportions than their male peers. The reasons for this difference are complex, and one possible contributing factor is the social environment women experience in the classroom. Using social network analysis, we explore how gender influences the confidence that college-level biology students have in each other's mastery of biology. Results reveal that males are more likely than females to be named by peers as being knowledgeable about the course content. This effect increases as the term progresses, and persists even after controlling for class performance and outspokenness. The bias in nominations is specifically due to males over-nominating their male peers relative to their performance. The over-nomination of male peers is commensurate with an overestimation of male grades by 0.57 points on a 4 point grade scale, indicating a strong male bias among males when assessing their classmates. Females, in contrast, nominated equitably based on student performance rather than gender, suggesting they lacked gender biases in filling out these surveys. These trends persist across eleven surveys taken in three different iterations of the same Biology course. In every class, the most renowned students are always male. This favoring of males by peers could influence student self-confidence, and thus persistence in this STEM discipline.

  18. Males Under-Estimate Academic Performance of Their Female Peers in Undergraduate Biology Classrooms.

    Science.gov (United States)

    Grunspan, Daniel Z; Eddy, Sarah L; Brownell, Sara E; Wiggins, Benjamin L; Crowe, Alison J; Goodreau, Steven M

    2016-01-01

    Women who start college in one of the natural or physical sciences leave in greater proportions than their male peers. The reasons for this difference are complex, and one possible contributing factor is the social environment women experience in the classroom. Using social network analysis, we explore how gender influences the confidence that college-level biology students have in each other's mastery of biology. Results reveal that males are more likely than females to be named by peers as being knowledgeable about the course content. This effect increases as the term progresses, and persists even after controlling for class performance and outspokenness. The bias in nominations is specifically due to males over-nominating their male peers relative to their performance. The over-nomination of male peers is commensurate with an overestimation of male grades by 0.57 points on a 4 point grade scale, indicating a strong male bias among males when assessing their classmates. Females, in contrast, nominated equitably based on student performance rather than gender, suggesting they lacked gender biases in filling out these surveys. These trends persist across eleven surveys taken in three different iterations of the same Biology course. In every class, the most renowned students are always male. This favoring of males by peers could influence student self-confidence, and thus persistence in this STEM discipline.

  19. The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

    Science.gov (United States)

    Chen, Bor-Sen; Ho, Shih-Ju

    2014-01-01

    In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to

  20. Learning Cell Biology as a Team: A Project-Based Approach to Upper-Division Cell Biology

    Science.gov (United States)

    Wright, Robin; Boggs, James

    2002-01-01

    To help students develop successful strategies for learning how to learn and communicate complex information in cell biology, we developed a quarter-long cell biology class based on team projects. Each team researches a particular human disease and presents information about the cellular structure or process affected by the disease, the cellular…

  1. Biology

    Indian Academy of Sciences (India)

    I am particularly happy that the Academy is bringing out this document by Professor M S. Valiathan on Ayurvedic Biology. It is an effort to place before the scientific community, especially that of India, the unique scientific opportunities that arise out of viewing Ayurveda from the perspective of contemporary science, its tools ...

  2. Heavy-ion radiobiology: new approaches to delineate mechanisms underlying enhanced biological effectiveness

    Science.gov (United States)

    Blakely, E. A.; Kronenberg, A.; Chatterjee, A. (Principal Investigator)

    1998-01-01

    Shortly after the discovery of polonium and radium by Marie Curie and her husband and colleague, Pierre Curie, it was learned that exposure to these alpha-particle emitters produced deleterious biological effects. The mechanisms underlying the increased biological effectiveness of densely ionizing radiations, including alpha particles, neutrons and highly energetic heavy charged particles, remain an active area of investigation. In this paper, we review recent advances in several areas of the radiobiology of these densely ionizing radiations, also known as heavy ions. Advances are described in the areas of DNA damage and repair, chromosome aberrations, mutagenesis, neoplastic transformation in vitro, genomic instability, normal tissue radiobiology and carcinogenesis in vivo. We focus on technical innovations, including novel applications of pulsed-field gel electrophoresis, fluorescence in situ hybridization (FISH), linkage analysis, and studies of gene expression and protein expression. We also highlight the use of new cellular and animal systems, including those with defined DNA repair deficiencies, as well as epithelial cell model systems to assess neoplastic transformation both in vitro and in vivo. The studies reviewed herein have had a substantial impact on our understanding of the genotoxic effects of heavy ions as well as their distinct effects on tissue homeostasis. The use of these radiations in cancer therapy is also discussed. The use of both heavy-ion and proton therapy is on the upswing in several centers around the world, due to their unique energy deposition characteristics that enhance the therapeutic effect and help reduce damage to normal tissue.

  3. Application of Biologically-Based Lumping To Investigate the ...

    Science.gov (United States)

    People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. However, investigators have often considered complex mixtures as one lumped entity. Valuable information can be obtained from these experiments, though this simplification provides little insight into the impact of a mixture's chemical composition on toxicologically-relevant metabolic interactions that may occur among its constituents. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically-based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate performance of our PBPK model. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course kinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for the 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 non-target chemicals. Application of this biologic

  4. Dynamics of intracellular polymers in enhanced biological phosphorus removal processes under different organic carbon concentrations.

    Science.gov (United States)

    Xing, Lizhen; Ren, Li; Tang, Bo; Wu, Guangxue; Guan, Yuntao

    2013-01-01

    Enhanced biological phosphorus removal (EBPR) may deteriorate or fail during low organic carbon loading periods. Polyphosphate accumulating organisms (PAOs) in EBPR were acclimated under both high and low organic carbon conditions, and then dynamics of polymers in typical cycles, anaerobic conditions with excess organic carbons, and endogenous respiration conditions were examined. After long-term acclimation, it was found that organic loading rates did not affect the yield of PAOs and the applied low organic carbon concentrations were advantageous for the enrichment of PAOs. A low influent organic carbon concentration induced a high production of extracellular carbohydrate. During both anaerobic and aerobic endogenous respirations, when glycogen decreased to around 80 ± 10 mg C per gram of volatile suspended solids, PAOs began to utilize polyphosphate significantly. Regressed by the first-order reaction model, glycogen possessed the highest degradation rate and then was followed by polyphosphate, while biomass decay had the lowest degradation rate.

  5. Biological control of white mold by Trichoderma harzianum in common bean under field conditions

    Directory of Open Access Journals (Sweden)

    Daniel Diego Costa Carvalho

    2015-12-01

    Full Text Available Abstract: The objective of this work was to evaluate Trichoderma harzianum isolates for biological control of white mold in common bean (Phaseolus vulgaris. Five isolates were evaluated for biocontrol of white mold in 'Perola' common bean under field conditions, in the 2009 and 2010 crop seasons. A commercial isolate (1306 and a control treatment were included. Foliar applications at 2x109 conidia mL-1 were performed at 42 and 52 days after sowing (DAS, in 2009, and at 52 DAS in 2010. The CEN287, CEN316, and 1306 isolates decreased the number of Sclerotinia sclerotiorum apothecia per square meter in comparison to the control, in both crop seasons. CEN287, CEN316, and 1306 decreased white mold severity during the experimental period, when compared to the control.

  6. Model-based Prognostics under Limited Sensing

    Data.gov (United States)

    National Aeronautics and Space Administration — Prognostics is crucial to providing reliable condition-based maintenance decisions. To obtain accurate predictions of component life, a variety of sensors are often...

  7. N deposition as a threat to the World's protected areas under the Convention on Biological Diversity

    International Nuclear Information System (INIS)

    Bleeker, A.; Hicks, W.K.; Dentener, F.; Galloway, J.; Erisman, J.W.

    2011-01-01

    This paper combines the world's protected areas (PAs) under the Convention on Biological Diversity (CBD), common classification systems of ecosystem conservation status, and current knowledge on ecosystem responses to nitrogen (N) deposition to determine areas most at risk. The results show that 40% (approx. 11% of total area) of PAs currently receive >10 kg N/ha/yr with projections for 2030 indicating that this situation is not expected to change. Furthermore, 950 PAs are projected to receive >30 kg N/ha/yr by 2030 (approx. twice the 2000 number), of which 62 (approx. 11,300 km 2 ) are also Biodiversity Hotspots and G200 ecoregions; with forest and grassland ecosystems in Asia particularly at risk. Many of these sites are known to be sensitive to N deposition effects, both in terms of biodiversity changes and ecosystem services they provide. Urgent assessment of high risk areas identified in this study is recommended to inform the conservation efforts of the CBD. - Highlights: → Significant areas of the Protected Areas Programme under the CBD will likely be under threat of high N deposition levels by the year 2030.→ Approx. 950 PAs are projected to receive N deposition levels of more than 30 kg N/ha/yr by 2030.→ 62 of these sites are also Biodiversity Hotspots and G200 ecoregions, where forest and grassland ecosystems in Asia will be particularly at risk.→ Many of these sites are known to be sensitive to N deposition effects, both in terms of biodiversity changes and ecosystem services they provide → Urgent assessment of high risk areas identified in this study is recommended to inform the conservation efforts of the CBD. - Significant areas of the UNEP Protected Areas Programme under the CBD receive high N deposition rates that are likely to increase in the future, especially in Asia, and may pose a significant threat to biodiversity.

  8. 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.

  9. 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.

  10. Population-based health funding under attack

    African Journals Online (AJOL)

    A 'static, outdated and in- flexible' population-based funding formula for public health is putting huge pres- sure on well-run and well- equipped hospitals in the Western Cape,. KwaZulu-Natal and Gauteng as people from other provinces migrate there in their tens of thousands to seek a better life. The frustrated heads of ...

  11. Simulation on scattering features of biological tissue based on generated refractive-index model

    International Nuclear Information System (INIS)

    Wang Baoyong; Ding Zhihua

    2011-01-01

    Important information on morphology of biological tissue can be deduced from elastic scattering spectra, and their analyses are based on the known refractive-index model of tissue. In this paper, a new numerical refractive-index model is put forward, and its scattering properties are intensively studied. Spectral decomposition [1] is a widely used method to generate random medium in geology, but it is never used in biology. Biological tissue is different from geology in the sense of random medium. Autocorrelation function describe almost all of features in geology, but biological tissue is not as random as geology, its structure is regular in the sense of fractal geometry [2] , and fractal dimension can be used to describe its regularity under random. Firstly scattering theories of this fractal media are reviewed. Secondly the detailed generation process of refractive-index is presented. Finally the scattering features are simulated in FDTD (Finite Difference Time Domain) Solutions software. From the simulation results, we find that autocorrelation length and fractal dimension controls scattering feature of biological tissue.

  12. Simulation on scattering features of biological tissue based on generated refractive-index model

    Energy Technology Data Exchange (ETDEWEB)

    Wang Baoyong; Ding Zhihua, E-mail: zh_ding@zju.edu.cn [State Key Lab of Modern Optical Instrumentation, Zhejiang University 38 Zheda Rd., Hangzhou 310027 (China)

    2011-01-01

    Important information on morphology of biological tissue can be deduced from elastic scattering spectra, and their analyses are based on the known refractive-index model of tissue. In this paper, a new numerical refractive-index model is put forward, and its scattering properties are intensively studied. Spectral decomposition{sup [1]} is a widely used method to generate random medium in geology, but it is never used in biology. Biological tissue is different from geology in the sense of random medium. Autocorrelation function describe almost all of features in geology, but biological tissue is not as random as geology, its structure is regular in the sense of fractal geometry{sup [2]}, and fractal dimension can be used to describe its regularity under random. Firstly scattering theories of this fractal media are reviewed. Secondly the detailed generation process of refractive-index is presented. Finally the scattering features are simulated in FDTD (Finite Difference Time Domain) Solutions software. From the simulation results, we find that autocorrelation length and fractal dimension controls scattering feature of biological tissue.

  13. Source-sink interaction: a century old concept under the light of modern molecular systems biology.

    Science.gov (United States)

    Chang, Tian-Gen; Zhu, Xin-Guang; Raines, Christine

    2017-07-20

    Many approaches to engineer source strength have been proposed to enhance crop yield potential. However, a well-co-ordinated source-sink relationship is required finally to realize the promised increase in crop yield potential in the farmer's field. Source-sink interaction has been intensively studied for decades, and a vast amount of knowledge about the interaction in different crops and under different environments has been accumulated. In this review, we first introduce the basic concepts of source, sink and their interactions, then summarize current understanding of how source and sink can be manipulated through both environmental control and genetic manipulations. We show that the source-sink interaction underlies the diverse responses of crops to the same perturbations and argue that development of a molecular systems model of source-sink interaction is required towards a rational manipulation of the source-sink relationship for increased yield. We finally discuss both bottom-up and top-down routes to develop such a model and emphasize that a community effort is needed for development of this model. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  14. IBPRO - A Novel Short-Duration Teaching Course in Advanced Physics and Biology Underlying Cancer Radiotherapy.

    Science.gov (United States)

    Joiner, Michael C; Tracey, Monica W; Kacin, Sara E; Burmeister, Jay W

    2017-06-01

    This article provides a summary and status report of the ongoing advanced education program IBPRO - Integrated course in Biology and Physics of Radiation Oncology. IBPRO is a five-year program funded by NCI. It addresses the recognized deficiency in the number of mentors available who have the required knowledge and skill to provide the teaching and training that is required for future radiation oncologists and researchers in radiation sciences. Each year, IBPRO brings together 50 attendees typically at assistant professor level and upwards, who are already qualified/certified radiation oncologists, medical physicists or biologists. These attendees receive keynote lectures and activities based on active learning strategies, merging together the clinical, biological and physics underpinnings of radiation oncology, at the forefront of the field. This experience is aimed at increasing collaborations, raising the level and amount of basic and applied research undertaken in radiation oncology, and enabling attendees to confidently become involved in the future teaching and training of researchers and radiation oncologists.

  15. What is infidelity? Perceptions based on biological sex and personality

    Science.gov (United States)

    Thornton, Victoria; Nagurney, Alexander

    2011-01-01

    The study examines perceptions of infidelity, paying particular attention to how these perceptions differ based on biological sex and personality traits, specifically agency and communion and their unmitigated counterparts. The study utilizes a sample of 125 male and 233 female college students. In addition to the personality measures, participants completed a 19-item checklist that assessed their perceptions of specific items that could potentially be construed as infidelity. It was hypothesized that females would construe more items as infidelity than would males. It was also predicted that unmitigated communion and communion would be positively correlated with these perceptions and that unmitigated agency would be negatively correlated with these perceptions. No correlation was predicted between agency and infidelity. All hypotheses were supported. Implications and suggestions for future research are discussed. PMID:22114535

  16. What is infidelity? Perceptions based on biological sex and personality

    Directory of Open Access Journals (Sweden)

    Thornton V

    2011-05-01

    Full Text Available Victoria Thornton, Alexander NagurneyTexas State University – San Marcos, San Marcos, Texas, USAAbstract: The study examines perceptions of infidelity, paying particular attention to how these perceptions differ based on biological sex and personality traits, specifically agency and communion and their unmitigated counterparts. The study utilizes a sample of 125 male and 233 female college students. In addition to the personality measures, participants completed a 19-item checklist that assessed their perceptions of specific items that could potentially be construed as infidelity. It was hypothesized that females would construe more items as infidelity than would males. It was also predicted that unmitigated communion and communion would be positively correlated with these perceptions and that unmitigated agency would be negatively correlated with these perceptions. No correlation was predicted between agency and infidelity. All hypotheses were supported. Implications and suggestions for future research are discussed.Keywords: infidelity, communion, agency, questionnaire, relationship

  17. What is infidelity? Perceptions based on biological sex and personality.

    Science.gov (United States)

    Thornton, Victoria; Nagurney, Alexander

    2011-01-01

    The study examines perceptions of infidelity, paying particular attention to how these perceptions differ based on biological sex and personality traits, specifically agency and communion and their unmitigated counterparts. The study utilizes a sample of 125 male and 233 female college students. In addition to the personality measures, participants completed a 19-item checklist that assessed their perceptions of specific items that could potentially be construed as infidelity. It was hypothesized that females would construe more items as infidelity than would males. It was also predicted that unmitigated communion and communion would be positively correlated with these perceptions and that unmitigated agency would be negatively correlated with these perceptions. No correlation was predicted between agency and infidelity. All hypotheses were supported. Implications and suggestions for future research are discussed.

  18. Synthetic biology in cell-based cancer immunotherapy.

    Science.gov (United States)

    Chakravarti, Deboki; Wong, Wilson W

    2015-08-01

    The adoptive transfer of genetically engineered T cells with cancer-targeting receptors has shown tremendous promise for eradicating tumors in clinical trials. This form of cellular immunotherapy presents a unique opportunity to incorporate advanced systems and synthetic biology approaches to create cancer therapeutics with novel functions. We first review the development of synthetic receptors, switches, and circuits to control the location, duration, and strength of T cell activity against tumors. In addition, we discuss the cellular engineering and genome editing of host cells (or the chassis) to improve the efficacy of cell-based cancer therapeutics, and to reduce the time and cost of manufacturing. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Competing for phosphors under changing redox conditions: biological versus geochemical sinks

    Science.gov (United States)

    Gross, A.; Pett-Ridge, J.; Silver, W. L.

    2016-12-01

    Competing for phosphorus under changing redox conditions: biological versus geochemical sinksAvner Gross1, Jennifer Pett-Ridge2 and Whendee L Silver1 University of California Berkeley, Department of Environmental Science, Policy, & Management, Berkeley, CA, USA. Lawrence Livermore National Laboratory, Physical and Life Science Directorate, Livermore, CA, USA. The cycling of phosphorous (P) in highly weathered, humid tropical forest soils is tightly regulated by P sorption dynamics to the surfaces of Fe(III) (hydr)oxides and root and microbial demands for P. Periods of anoxic soil conditions, which are common in humid environments, induce the reduction of Fe (III) to Fe (II) and may release sorbed P into the soil solution. The microbial demand for P is influenced by the C and nutrient composition of their available substrates. Therefore, we hypothesize that soil redox conditions and substrate quality and availability will control the partitioning of P between microbial biomass and the soil mineral phase. The aim of this study was to examine how fluctuations in soil redox conditions and changes in microbial P demand affect the fate of new P that enters the soil solution. To achieve this aim we conducted a series of soil incubation experiments using a wet tropical soil from Puerto Rico (where redox conditions and P availability naturally oscillate) with a single pulse of phosphate (PO4), altering both the microbial activity and redox conditions. To follow the fate the added P, the added phosphate was labeled with 18O. As the exchange of oxygen between phosphate and water only occurs during biological processes, P-18O labeling can be used as an indicator of microbial use. To quantify sizes of the microbial and mineral P pools we used traditional chemical extractions in the bulk scale. We used NanoSIMS isotopic imaging to map the distribution of P-16O and P-18O and co-localization with Fe minerals at the nano scale. Our results show that the amount of the added P fixed

  20. Nutrient Recovery of Plant Leachates Under Thermal, Biological, and Photocatalytic Pretreatments

    Science.gov (United States)

    Wong, Les

    2015-01-01

    Nutrient recovery has always been a problem for long distance and long-term space missions. To allow humans to man these missions, a steady source of oxygen, water, and food are necessary for survival beyond Earth's atmosphere. Plants are currently an area of interest since they are capable of providing all three resources for life sustainability. We are currently interested in nutrient recovery for future plant growth and simple aqueous leachate extractions can recover some of the nutrients. However, leaching plants also removes water-soluble organic plant wastes, which inhibits plant growth if not separated properly. To combat the issues with waste and maximize nutrient recovery, we are attempting to pre-treat the plant matter using biological, thermal, and photocatalytic methods before subjecting the solution with variable-strength acid digestion. For the biological method, the inoculums: mixed heterotrophic/nitrifying bioreactor effluent and Trichoderma vessei are used in an attempt to liberate more nutrients from the plant matter. For the thermal method, plants are subjected to varying temperatures at different retention times to determine nutrient recovery. Lastly, the photocatalytic method utilizes TiO (sub 2)'s oxidizing abilities under specific pHs and retention times to reduce organic wastes and improve nutrient gains. A final acid digestion serves to liberate nutrients even further in order to maximize recovery. So far, we have tested ideal acid digestion variables for practicality and performance in our experiments. We found that a low retention time of 10 minutes and a high acid concentration of 0.1 and 1 mole HCl were the most effective at nutrient recovery. For space travel purposes, 0.1 mole currently looks like a viable acid digestion to use since it is relatively effective and sustainable from a mass and energy balance if acid recovery can be performed on waste brines. Biological pretreatments do not look to be too effective and the thermal and

  1. Suitability of Commercial Transport Media for Biological Pathogens under Nonideal Conditions

    Directory of Open Access Journals (Sweden)

    Kyle Hubbard

    2011-01-01

    Full Text Available There is extensive data to support the use of commercial transport media as a stabilizer for known clinical samples; however, there is little information to support their use outside of controlled conditions specified by the manufacturer. Furthermore, there is no data to determine the suitability of said media for biological pathogens, specifically those of interest to the US military. This study evaluates commercial off-the-shelf (COTS transport media based on sample recovery, viability, and quality of nucleic acids and peptides for nonpathogenic strains of Bacillus anthracis, Yersinia pestis, and Venezuelan equine encephalitis virus, in addition to ricin toxin. Samples were stored in COTS, PBST, or no media at various temperatures over an extended test period. The results demonstrate that COTS media, although sufficient for the preservation of nucleic acid and proteinaceous material, are not capable of maintaining an accurate representation of biothreat agents at the time of collection.

  2. Patient Preference for Dosing Frequency Based on Prior Biologic Experience.

    Science.gov (United States)

    Zhang, Mingliang; Carter, Chureen; Olson, William H; Johnson, Michael P; Brennem, Susan K; Lee, Seina; Farahi, Kamyar

    2017-03-01

    There is limited research exploring patient preferences regarding dosing frequency of biologic treatment of psoriasis. Patients with moderate-to-severe plaque psoriasis identified in a healthcare claims database completed a survey regarding experience with psoriasis treatments and preferred dosing frequency. Survey questions regarding preferences were posed in two ways: (1) by likelihood of choosing once per week or 2 weeks, or 12 weeks; and (2) by choosing one option among once every 1-2 or 3-4 weeks or 1-2 or 2-3 months. Data were analyzed by prior biologic history (biologic-experienced vs biologic-naïve, and with one or two specific biologics). Overall, 426 patients completed the survey: 163 biologic-naïve patients and 263 biologic-experienced patients (159 had some experience with etanercept, 105 with adalimumab, and 49 with ustekinumab). Among patients who indicated experience with one or two biologics, data were available for 219 (30 with three biologics and 14 did not specify which biologic experience). The majority of biologic-naïve (68.8%) and overall biologic-experienced (69.4%) patients indicated that they were very likely to choose the least frequent dosing option of once every 12 weeks (Table 1). In contrast, fewer biologic-naïve (9.1% and 16.7%) and biologic-experienced (22.5% and 25.3%) patients indicated that they were very likely to choose the 1-week and 2-week dosing interval options, respectively. In each cohort grouped by experience with specific biologics, among those with no experience with ustekinumab, the most chosen option was 1-2 weeks. The most frequently chosen option was every 2-3 months, among patients with any experience with ustekinumab, regardless of their experience with other biologics. The least frequent dosing interval was preferred among biologic naïve patients and patients who had any experience with ustekinumab. Dosing interval may influence the shared decision-making process for psoriasis treatment with biologics. J

  3. Systematically biological prioritizing remediation sites based on datasets of biological investigations and heavy metals in soil

    Science.gov (United States)

    Lin, Wei-Chih; Lin, Yu-Pin; Anthony, Johnathen

    2015-04-01

    Heavy metal pollution has adverse effects on not only the focal invertebrate species of this study, such as reduction in pupa weight and increased larval mortality, but also on the higher trophic level organisms which feed on them, either directly or indirectly, through the process of biomagnification. Despite this, few studies regarding remediation prioritization take species distribution or biological conservation priorities into consideration. This study develops a novel approach for delineating sites which are both contaminated by any of 5 readily bioaccumulated heavy metal soil contaminants and are of high ecological importance for the highly mobile, low trophic level focal species. The conservation priority of each site was based on the projected distributions of 6 moth species simulated via the presence-only maximum entropy species distribution model followed by the subsequent application of a systematic conservation tool. In order to increase the number of available samples, we also integrated crowd-sourced data with professionally-collected data via a novel optimization procedure based on a simulated annealing algorithm. This integration procedure was important since while crowd-sourced data can drastically increase the number of data samples available to ecologists, still the quality or reliability of crowd-sourced data can be called into question, adding yet another source of uncertainty in projecting species distributions. The optimization method screens crowd-sourced data in terms of the environmental variables which correspond to professionally-collected data. The sample distribution data was derived from two different sources, including the EnjoyMoths project in Taiwan (crowd-sourced data) and the Global Biodiversity Information Facility (GBIF) ?eld data (professional data). The distributions of heavy metal concentrations were generated via 1000 iterations of a geostatistical co-simulation approach. The uncertainties in distributions of the heavy

  4. Soil Physical Characteristics and Biological Indicators of Soil Quality Under Different Biodegradable Mulches

    Science.gov (United States)

    Schaeffer, S. M.; Flury, M.; Sintim, H.; Bandopadhyay, S.; Ghimire, S.; Bary, A.; DeBruyn, J.

    2015-12-01

    Application of conventional polyethylene (PE) mulch in crop production offers benefits of increased water use efficiency, weed control, management of certain plant diseases, and maintenance of a micro-climate conducive for plant growth. These factors improve crop yield and quality, but PE must be retrieved and safely disposed of after usage. Substituting PE with biodegradable plastic mulches (BDM) would alleviate disposal needs, and is potentially a more sustainable practice. However, knowledge of potential impacts of BDMs on agricultural soil ecosystems is needed to evaluate sustainability. We (a) monitored soil moisture and temperature dynamics, and (b) assessed soil quality upon usage of different mulches, with pie pumpkin (Cucurbita pepo) as the test crop. Experimental field trials are ongoing at two sites, one at Northwestern Washington Research and Extension Center, Mount Vernon, WA, and the other at East Tennessee Research and Education Center, Knoxville, TN. The treatments constitute four different commercial BDM products, one experimental BDM; no mulch and PE served as the controls. Soil quality parameters being examined include: organic matter content, aggregate stability, water infiltration rate, CO2 flux, pH, and extracellular enzyme activity. In addition, lysimeters were installed to examine the soil water and heat flow dynamics. We present baseline and the first field season results from this study. Mulch cover appeared to moderate soil temperatures, but biodegradable mulches also appeared to lose water more quickly than PE. All mulch types, with the exception of cellulose, reduced the diurnal fluctuations in soil temperature at 10cm depth from 1 to 4ºC. However, volumetric water content ranged from 0.10 to 0.22 m3 m-3 under the five biodegradable mulches compared to 0.22 to 0.28 m3 m-3 under conventional PE. Results from the study will be useful for management practices by providing knowledge on how different mulches impact soil physical and

  5. Biological Detection System Technologies Technology and Industrial Base Study. A Primer on Biological Detection Technologies

    National Research Council Canada - National Science Library

    2001-01-01

    .... and Canadian military personnel. In light of these concerns both defense departments have increased efforts to develop and field biological agent detection systems to help protect their military forces and fixed assets...

  6. Interferometric laser detection of nanomechanical perturbations in biological media under ablation conditions

    International Nuclear Information System (INIS)

    Morales-Bonilla, S; Torres-Torres, C; Urriolagoitia-Sosa, G; Hernandez-Gomez, L H; Urriolagoitia-Calderon, G

    2011-01-01

    This article has to do with the development of a reliable and sensitive non-invasive laser technique for assessing damage of structures and systems involved in laser ablation processes. The optical response of a Michelson Interferometer in combination with a Measuring Reflectance System has been analyzed in order to identify the stability of the mechanical properties of the sample, the physical perturbations associated with the systems and the environment where the target is contained. This test includes the use of a cyan laser system with 10 mW at 488 nm wavelength as optical source. We found out that with the inclusion of an optical feedback in a sensing system it is possible to determine the modification of the physical properties exhibited by a biological medium under sharp ablation conditions with a high accuracy degree. The results reported in this research have potential applications related to the amount of light intensity that can be tolerated by human tissue. A wide array of disciplines, such as medicine, mechanical industry and optical instrumentation can benefit from this ultrafast optical feedback for controlling high intensity laser signals. Collateral damage of tissue around the laser irradiated zones can be reduced by using intelligent lasers systems with ultra-short temporal response.

  7. Interferometric laser detection of nanomechanical perturbations in biological media under ablation conditions

    Science.gov (United States)

    Morales-Bonilla, S.; Torres-Torres, C.; Urriolagoitia-Sosa, G.; Hernández-Gómez, L. H.; Urriolagoitia-Calderón, G.

    2011-07-01

    This article has to do with the development of a reliable and sensitive non-invasive laser technique for assessing damage of structures and systems involved in laser ablation processes. The optical response of a Michelson Interferometer in combination with a Measuring Reflectance System has been analyzed in order to identify the stability of the mechanical properties of the sample, the physical perturbations associated with the systems and the environment where the target is contained. This test includes the use of a cyan laser system with 10 mW at 488 nm wavelength as optical source. We found out that with the inclusion of an optical feedback in a sensing system it is possible to determine the modification of the physical properties exhibited by a biological medium under sharp ablation conditions with a high accuracy degree. The results reported in this research have potential applications related to the amount of light intensity that can be tolerated by human tissue. A wide array of disciplines, such as medicine, mechanical industry and optical instrumentation can benefit from this ultrafast optical feedback for controlling high intensity laser signals. Collateral damage of tissue around the laser irradiated zones can be reduced by using intelligent lasers systems with ultra-short temporal response.

  8. Why the long face? The importance of vertical image structure for biological "barcodes" underlying face recognition.

    Science.gov (United States)

    Spence, Morgan L; Storrs, Katherine R; Arnold, Derek H

    2014-07-29

    Humans are experts at face recognition. The mechanisms underlying this complex capacity are not fully understood. Recently, it has been proposed that face recognition is supported by a coarse-scale analysis of visual information contained in horizontal bands of contrast distributed along the vertical image axis-a biological facial "barcode" (Dakin & Watt, 2009). A critical prediction of the facial barcode hypothesis is that the distribution of image contrast along the vertical axis will be more important for face recognition than image distributions along the horizontal axis. Using a novel paradigm involving dynamic image distortions, a series of experiments are presented examining famous face recognition impairments from selectively disrupting image distributions along the vertical or horizontal image axes. Results show that disrupting the image distribution along the vertical image axis is more disruptive for recognition than matched distortions along the horizontal axis. Consistent with the facial barcode hypothesis, these results suggest that human face recognition relies disproportionately on appropriately scaled distributions of image contrast along the vertical image axis. © 2014 ARVO.

  9. Facilitating problem based learning in an online biology laboratory course

    Science.gov (United States)

    Wesolowski, Meredith C.

    Online instruction offers many benefits to underserved populations in higher education, particularly increased access. However, incorporation of preferred pedagogical methods, particularly those involving student collaboration, can be more difficult to facilitate in online courses due to geographic separation. In the area of laboratory science education, there is a strong argument for use of constructivist, collaborative pedagogy to promote many facets of student learning. This EPP describes the process used to develop two problem based learning (PBL) laboratory activities based on recommendations found in the literature, their incorporation into an online biology laboratory science course (BIO101) and their impact on student achievement and critical thinking skills. Data analysis revealed a high level of achievement within the study semester. In addition, use of synchronous group discussions as part of the PBL framework resulted in a broad range of discussions reflective of successful problem solving interactions described in the literature. Together, these suggest a observed benefit from incorporation of PBL in this online course. In addition, specific areas for modification were identified as potential future improvements.

  10. Effect of Biological and Chemical Fertilizers on Oil, Seed Yield and some Agronomic Traits of Safflower under Different Irrigation Regimes

    Directory of Open Access Journals (Sweden)

    Hamidreza Fanaei

    2017-03-01

    Full Text Available Introduction Safflower Carthamus tinctorius L. is a tolerant plant to water deficit due to long roots and capability for high water absorption from soil deeper parts. Safflower can growth successfully in regions with low soil fertility and temperature. Behdani and Mosavifar (2011 reported that drought stress affect on yield by reducing yield components and agronomic traits. Biofertilizer during a biological process chanced the nutrients from unusable to usable form for plants in soils (Aseretal, 2008. Mirzakhani et al. (2008 found that inoculation of seed with free-living bacterium azotobacter and a symbiotic fungus productive mycorrhiza addition to increasing oil and seed cause increasing resistance against two factors of unfavorable environmental and to improve quality of product. In order to study the effect of biological and chemical fertilizers on oil, seed yield and some of agronomic traits of Safflower under irrigation of different regimes an experimental design was conducted. Materials and methods In order to study the effect of biological and chemical fertilizers on oil, seed yield and some of agronomic traits of safflower under irrigation of different regimes an experiment was carried out split plot based on randomized complete block design (RCBD with three replications in experimental farm of payame-Noor university of Zabol during 2012-2013 growing season. Irrigation regime in three levels include: I1 (control irrigation in all growth stages, I2 stop irrigation from sowing to flowering (irrigation in growth stages flowering, and seed filling, I3 irrigation in growth stages rosset, stem elongation, heading and stop irrigation in flowering, and seed filling were as main plots and fertilizer resources in five levels included: F1 non application chemical fertilizer (control, F2 pure application chemical fertilizer (NPK 99, 44 and 123 kg.ha-1 respectively, F3 Nitroxin application (2 L.ha-1 F4 Azotobacter application (2 L.ha-1 and F5

  11. Effect of Biological and Chemical Fertilizers on Oil, Seed Yield and some Agronomic Traits of Safflower under Different Irrigation Regimes

    Directory of Open Access Journals (Sweden)

    Hamidreza Fanaei

    2017-08-01

    Full Text Available Introduction Safflower Carthamus tinctorius L. is a tolerant plant to water deficit due to long roots and capability for high water absorption from soil deeper parts. Safflower can growth successfully in regions with low soil fertility and temperature. Behdani and Mosavifar (2011 reported that drought stress affect on yield by reducing yield components and agronomic traits. Biofertilizer during a biological process chanced the nutrients from unusable to usable form for plants in soils (Aseretal, 2008. Mirzakhani et al. (2008 found that inoculation of seed with free-living bacterium azotobacter and a symbiotic fungus productive mycorrhiza addition to increasing oil and seed cause increasing resistance against two factors of unfavorable environmental and to improve quality of product. In order to study the effect of biological and chemical fertilizers on oil, seed yield and some of agronomic traits of Safflower under irrigation of different regimes an experimental design was conducted. Materials and methods In order to study the effect of biological and chemical fertilizers on oil, seed yield and some of agronomic traits of safflower under irrigation of different regimes an experiment was carried out split plot based on randomized complete block design (RCBD with three replications in experimental farm of payame-Noor university of Zabol during 2012-2013 growing season. Irrigation regime in three levels include: I1 (control irrigation in all growth stages, I2 stop irrigation from sowing to flowering (irrigation in growth stages flowering, and seed filling, I3 irrigation in growth stages rosset, stem elongation, heading and stop irrigation in flowering, and seed filling were as main plots and fertilizer resources in five levels included: F1 non application chemical fertilizer (control, F2 pure application chemical fertilizer (NPK 99, 44 and 123 kg.ha-1 respectively, F3 Nitroxin application (2 L.ha-1 F4 Azotobacter application (2 L.ha-1 and F5

  12. The Implementation of Research-based Learning on Biology Seminar Course in Biology Education Study Program of FKIP UMRAH

    Science.gov (United States)

    Amelia, T.

    2018-04-01

    Biology Seminar is a course in Biology Education Study Program of Faculty of Teacher Training and Education University of Maritim Raja Ali Haji (FKIP UMRAH) that requires students to have the ability to apply scientific attitudes, perform scientific writing and undertake scientific publications on a small scale. One of the learning strategies that can drive the achievement of learning outcomes in this course is Research-Based Learning. Research-Based Learning principles are considered in accordance with learning outcomes in Biology Seminar courses and generally in accordance with the purpose of higher education. On this basis, this article which is derived from a qualitative research aims at describing Research-based Learning on Biology Seminar course. Based on a case study research, it was known that Research-Based Learning on Biology Seminar courses is applied through: designing learning activities around contemporary research issues; teaching research methods, techniques and skills explicitly within program; drawing on personal research in designing and teaching courses; building small-scale research activities into undergraduate assignment; and infusing teaching with the values of researchers.

  13. Margin based ontology sparse vector learning algorithm and applied in biology science

    Directory of Open Access Journals (Sweden)

    Wei Gao

    2017-01-01

    Full Text Available In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and application in biology. In this paper, using knowledge of marginal likelihood and marginal distribution, the optimized strategy of marginal based ontology sparse vector learning algorithm is presented. Finally, the new algorithm is applied to gene ontology and plant ontology to verify its efficiency.

  14. In Situ Denitrification and Biological Nitrogen Fixation Under Enhanced Atmospheric Reactive Nitrogen Deposition in UK Peatlands

    Science.gov (United States)

    Ullah, Sami; Saiz Val, Ernesto; Sgouridis, Fotis; Peichl, Matthias; Nilsson, Mats

    2017-04-01

    Dinitrogen (N2) and nitrous oxide (N2O) losses due to denitrification and biological N2 fixation (BNF) are the most uncertain components of the nitrogen (N) cycle in peatlands under enhanced atmospheric reactive nitrogen (Nr) deposition. This uncertainty hampers our ability to assess the contribution of denitrification to the removal of biologically fixed and/or atmospherically deposited Nr in peatlands. This uncertainty emanates from the difficulty in measuring in situ soil N2 and N2O production and consumption in peatlands. In situ denitrification and its contribution to total N2O flux was measured monthly between April 2013 and October 2014 in peatlands in two UK catchments. An adapted 15N-Gas Flux method1 with low level addition of 15N tracer (0.03 ± 0.005 kg 15N ha-1) was used to measure denitrification and its contribution to net N2O production (DN2O/TN2O). BNF was measured in situ through incubation of selected sphagnum species under 15N2 gas tracer. Denitrification2 varied temporally and averaged 8 kg N-N2 ha-1 y-1. The contribution of denitrification was about 48% to total N2O flux3 of 0.05 kg N ha-1 y-1. Soil moisture, temperature, ecosystem respiration, pH and mineral N content mainly regulated the flux of N2 and N2O. Preliminary results showed suppression of BNF, which was 1.8 to 7 times lower in peatland mosses exposed to ˜15 to 20 kg N ha-1 y-1 Nr deposition in the UK than in peatland mosses in northern Sweden with background Nr deposition. Overall, the contribution of denitrification to Nr removal in the selected peatlands was ˜50% of the annual Nr deposition rates, making these ecosystems vulnerable to chronic N saturation. These results point to a need for a more comprehensive annual BNF measurement to more accurately account for total Nr input into peatlands and its atmospheric loss due to denitrification. References Sgouridis F, Stott A & Ullah S, 2016. Application of the 15N-Gas Flux method for measuring in situ N2 and N2O fluxes due to

  15. Vision-based judgment of tomato maturity under growth conditions ...

    African Journals Online (AJOL)

    Vision-based judgment of tomato maturity under growth conditions. X Wang, H Mao, X Han, J Yin. Abstract. To determine the picking time of tomato and design the control strategy for the harvesting robot, the judgment of tomato maturity under natural conditions is required. Tomato samples were collected based on the fruit ...

  16. Organization of a radioisotope based molecular biology laboratory

    International Nuclear Information System (INIS)

    2006-12-01

    Polymerase chain reaction (PCR) has revolutionized the application of molecular techniques to medicine. Together with other molecular biology techniques it is being increasingly applied to human health for identifying prognostic markers and drug resistant profiles, developing diagnostic tests and genotyping systems and for treatment follow-up of certain diseases in developed countries. Developing Member States have expressed their need to also benefit from the dissemination of molecular advances. The use of radioisotopes, as a step in the detection process or for increased sensitivity and specificity is well established, making it ideally suitable for technology transfer. Many molecular based projects using isotopes for detecting and studying micro organisms, hereditary and neoplastic diseases are received for approval every year. In keeping with the IAEA's programme, several training activities and seminars have been organized to enhance the capabilities of developing Member States to employ in vitro nuclear medicine technologies for managing their important health problems and for undertaking related basic and clinical research. The background material for this publication was collected at training activities and from feedback received from participants at research and coordination meetings. In addition, a consultants' meeting was held in June 2004 to compile the first draft of this report. Previous IAEA TECDOCS, namely IAEA-TECDOC-748 and IAEA-TECDOC-1001, focused on molecular techniques and their application to medicine while the present publication provides information on organization of the laboratory, quality assurance and radio-safety. The technology has specific requirements of the way the laboratory is organized (e.g. for avoiding contamination and false positives in PCR) and of quality assurance in order to provide accurate information to decision makers. In addition while users of the technology accept the scientific rationale of using radio

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

    Directory of Open Access Journals (Sweden)

    Nisar A. Bhat

    2017-09-01

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

  18. The Biology and some Population Parameters of the Grasshopper, Ronderosia bergi, Under Laboratory Conditions

    Science.gov (United States)

    Mariottini, Yanina; de Wysiecki, Maria Laura; Lange, Carlos

    2010-01-01

    Some biological and population parameters of Ronderosia bergi (Stål) (Orthoptera: Acrididae: Melanoplinae) were estimated by monitoring five cohorts of the first generation (F1) of individuals born in captivity from grasshoppers collected in the South of Misiones province, northeastern Argentina, and held under controlled conditions (30° C, 14:10 L:D, 40% RH). The mean embryonic development time was 40.6 ± 1.7 days. Five nymphal instars were recorded. Total duration of nymphal development was 30.8 ± 0.54 days. The mean lifespan of cohorts was 22.6 ± 0.7 weeks. The number of egg-pods per female was 7.6 ± 1.44, and the amount of eggs per egg-pod was 16.45 ± 0.85. Mean fecundity was 125 ± 5.83 eggs per female with an oviposition rate of 1.55 ± 0.57 eggs/female/day. Survivorship curves showed that mortality was concentrated in the final weeks of adulthood, and the life expectancy curve decreased accordingly. The population parameters estimated gave the following values: the net rate of reproduction (R0) was 46.75 ± 11.2, generation time (T) was 18.87 ± 1.67 weeks, duplication time (D) was 3.31 ± 0.34, the intrinsic rate of population growth (rm) was 0.21 ± 0.021 and the finite rate of population increase (λ) was 1.24 ± 0.026. The reproductive values (Vx) indicated that the largest contribution of females to the subsequent generation was between weeks 15 and 25. PMID:20673116

  19. THE STUDY OF THE BIOLOGICAL PROPERTIES OF PROBIOTIC LACTOBACILLUS SPP. STRAINS UNDER AEROBIC AND MICROAEROPHILIC CULTIVATION CONDITIONS

    Directory of Open Access Journals (Sweden)

    Babych E.M.

    2014-01-01

    Full Text Available The biological properties (growth characteristics, adhesive activity and sensitivity to antimicrobial of probiotic Lactobacillus strains were studied under different gas composition of incubation atmosphere. It was found that the number of viable lactobacilli cells in the one dose of investigated probiotic preparations was lower than it was claimed by the manufacturer. Gas composition of incubation atmosphere affects cell viability of probiotic strains. The number of colony forming units of lactobacilli under microaerophilic conditions increased in 1,19-1,33 times as compared with aerobic conditions. It was proved that adhesive activity of probiotic Lactobacillus strains and sensitivity to 2th, 3th, 4th generations of cephalosporins (cefuroxime, cefotaxime, cefepime and tetracyclines (doxycycline also increased under microaerophilic conditions. The changes of the biological properties of lactobacilli under different cultivation conditions require further study for optimization of correction of dysbiotic disorders.

  20. Acute toxicity and chemical evaluation of coking wastewater under biological and advanced physicochemical treatment processes.

    Science.gov (United States)

    Dehua, Ma; Cong, Liu; Xiaobiao, Zhu; Rui, Liu; Lujun, Chen

    2016-09-01

    This study investigated the changes of toxic compounds in coking wastewater with biological treatment (anaerobic reactor, anoxic reactor and aerobic-membrane bioreactor, A1/A2/O-MBR) and advanced physicochemical treatment (Fenton oxidation and activated carbon adsorption) stages. As the biological treatment stages preceding, the inhibition effect of coking wastewater on the luminescence of Vibrio qinghaiensis sp. Nov. Q67 decreased. Toxic units (TU) of coking wastewater were removed by A1/A2/O-MBR treatment process, however approximately 30 % TU remained in the biologically treated effluent. There is a tendency that fewer and fewer residual organic compounds could exert equal acute toxicity during the biological treatment stages. Activated carbon adsorption further removed toxic pollutants of biologically treated effluent but the Fenton effluent increased acute toxicity. The composition of coking wastewater during the treatment was evaluated using the three-dimensional fluorescence spectra, gas chromatography-mass spectrometry (GC-MS). The organic compounds with high polarity were the main cause of acute toxicity in the coking wastewater. Aromatic protein-like matters in the coking wastewater with low biodegradability and high toxicity contributed mostly to the remaining acute toxicity of the biologically treated effluents. Chlorine generated from the oxidation process was responsible for the acute toxicity increase after Fenton oxidation. Therefore, the incorporation of appropriate advanced physicochemical treatment process, e.g., activated carbon adsorption, should be implemented following biological treatment processes to meet the stricter discharge standards and be safer to the environment.

  1. 78 FR 74218 - Imposition of Additional Sanctions on Syria Under the Chemical and Biological Weapons Control and...

    Science.gov (United States)

    2013-12-10

    ... DEPARTMENT OF STATE [Public Notice 8545] Imposition of Additional Sanctions on Syria Under the... determination was made that the Government of Syria used chemical weapons in violation of international law or... sanctions against the Government of Syria. Section 307(b) of the Chemical and Biological Weapons Control and...

  2. Physical, chemical, and biological properties of soil under soybean cultivation and at an adjacent rainforest in Amazonia

    Science.gov (United States)

    T.P. Beldini; R.C. Oliveira Junior; Michael Keller; P.B. de Camargo; P.M. Crill; A. Damasceno da Silva; D. Bentes dos Santos; D. Rocha de Oliveira

    2015-01-01

    Land-use change in the Amazon basin has occurred at an accelerated pace during the last decade, and it is important that the effects induced by these changes on soil properties are better understood. This study investigated the chemical, physical, and biological properties of soil in a field under cultivation of soy and rice, and at an adjacent primary rain forest....

  3. Some problems of biological effects under the combined action of nitrogen oxides, their metabolites and radiation

    International Nuclear Information System (INIS)

    Malenchenko, A.F.

    1985-01-01

    The progress of power engineering envisages the intensive construction of nuclear-energy plants, where an organic or nuclear fuel is used. Nowadays the concept of nuclear-energy plant with the coolant based on dissociating N 2 O 4 is being developed. A great deal of radioactive and chemical products escapes into surroundings as the result of the power plants being in service. Their action on organisms is performed simultaneously, that could have an essential effect on the quantitative and qualitative regularities of response. The estimation of the combined effect of nitrogen oxides, sodium nitrite and nitrate and radiation has been carried out on the base of the investigation into methemoglobin formation, genetic effects and the pathomorphological changes in lungs. The formation of methemoglobin has been studied on rats in 1, 3, 7 and 15 days after the single total irradiation of 300 and 700 R doses at the gamma-installation (UGU-420) using a radioactive 60 Co. Methemoglobin was determined in the interval of 15-180 min after NaNO 2 administration in the dosage of 7.0 mg per 100 g body weight. The irradiation essentially affects the process of methemoglobin formation and its reduction. The methemoglobin content in the blood of radiation exposed animals exceeds the value, that could be expected to obtain by summing up its concentration under the separate effects of nitrite and irradiation. The genetic effects of sodium nitrite and nitrate and X-radiation have been studied on the Drosophila. The one-day flies were exposed to the radiation dose of 1500 R in the medium with the sodium nitrite or nitrate contents of 0.1 or 1.0 g/l, respectively. The combined action estimated through the frequency of the dominant lethal mutation, recessive coupled with a lethal mutation sex, viability and fecundity definitely differs from the expected summing values of the separate effect indices of radiation and toxic factors. The morpho- and functional changes in the rat lungs (the

  4. A Study of the Literature on Lab-Based Instruction in Biology

    Science.gov (United States)

    Puttick, Gillian; Drayton, Brian; Cohen, Eliza

    2015-01-01

    We analyzed the practitioner literature on lab-based instruction in biology in "The American Biology Teacher" between 2007 and 2012. We investigated what laboratory learning looks like in biology classrooms, what topics are addressed, what instructional methods and activities are described, and what is being learned about student…

  5. Challenges and Opportunities for Learning Biology in Distance-Based Settings

    Science.gov (United States)

    Hallyburton, Chad L.; Lunsford, Eddie

    2013-01-01

    The history of learning biology through distance education is documented. A review of terminology and unique problems associated with biology instruction is presented. Using published research and their own teaching experience, the authors present recommendations and best practices for managing biology in distance-based formats. They offer ideas…

  6. The biological bases of the dose-effect relationship

    International Nuclear Information System (INIS)

    Lafuma, J.

    2001-01-01

    In radiation protection, the recent data in epidemiology, in animal experimentation and on the base researches are no more compatible with a linear dose-effect relationship without threshold and do not account for the radiological risks at low doses. The cancers should be accelerated by radiations as any pathology linked to the ageing and for which threshold exit. Relative to the genetic risk it is known today that the natural exposure that lasts for several generations has not lead excess of hereditary illness as it was to be feared in 1959 for several countries. Considering that for populations the exposure levels induced by human activities have already been, under these ones of average natural exposures the genetic risk can be negligible and it is the somatic risk alone, with its thresholds that has to be into account. (N.C.)

  7. Regio-controlled hydrogen-deuterium exchange of biologically important indoles under uv irradiation

    International Nuclear Information System (INIS)

    Saito, Isao; Muramatsu, Shigeru; Sugiyama, Hiroshi; Yamamoto, Akihiro; Matsuura, Teruo

    1985-01-01

    Photochemical hydrogen-deuterium exchange reaction of biologically important indoles is reported. The regioselectivity of the photodeuteration was found to be controlled by the ammonium group of the side chain. (author)

  8. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

    Directory of Open Access Journals (Sweden)

    Christopher Y Park

    Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

  9. Biological nitrogen fixation in mung bean under stress environment (acid soils)

    International Nuclear Information System (INIS)

    Rosales, C.M.; Grafia, A.O.; Rivera, F.G.

    1996-01-01

    Our previous studies in biological nitrogen fixation by different mung bean varieties showed the 15 N isotope dilution technique proved to be useful and reliable im measuring the amount of N 2 fixed. These studies were done in nearly neutral soil pH. But since acid soils in the Philippines are widely distributed which comprises about 56 percent of the total land area of the country, this prompted us to conduct studies in this kind of soil to help the farmers in the hilly lands and marginal lands. A preliminary pot experiment was first conducted to determine what are limiting factors/elements in mung bean production in an acid soil. Field experiment followed to verify and implement our results. It was conducted at the National Research Center, Bureau of Soils and Water Management (BSWM), Cuyambay, Tanay, Rizal, 73 kms. northeast of Manila to determine the N 2 fixation and yield performance of 3 mung bean varieties grown under stress environment (acid soils) using isotope dilution technique. PAEC (Philippine Atomic Energy Agency) 3 mung bean variety responded better to phosphorous (P) application compared with neither NIAB 92 or M79-25-106. From a mean seed yield of only 50 kg/ha without lime and P, PAEC 3 further increased its yield to 523 kg/ha with the application of both P and lime. The dry matter yields of three mung bean varieties responded well with P application than lime. Without lime or P, the dry matter yield was only 287 kg/ha. The addition increased the dry matter yield to 533 kg/ha. Both P and lime added dry matter yield further increased to 1359 kg/ha. N 2 fixation increased slightly with the application of lime. With both lime and phosphorous, N 2 fixation increased further. M79-25-106 fixed the highest amount of nitrogen (23.56 kg/ha) while PAEC 3 and NIAB 92 fixed only about 18.8 and 18.67 kg/ha respectively. (author)

  10. High rate of serious infection in juvenile idiopathic arthritis patients under biologic therapy in a real-life setting.

    Science.gov (United States)

    Brunelli, Juliana Barbosa; Schmidt, Ana Renata; Sallum, Adriana Maluf Elias; Goldenstein-Schainberg, Claudia; Bonfá, Eloisa; Silva, Clovis A; Aikawa, Nádia Emi

    2018-03-01

    To assess the rate of serious and/or opportunistic infections in juvenile idiopathic arthritis (JIA) patients from a single tertiary center under biologic therapy and to identify possible risk factors associated to these complications. A total of 107 JIA patients followed at the biologic therapy center of our tertiary university hospital using a standardized electronic database protocol including demographic data, clinical and laboratorial findings and treatment at baseline and at the moment of infection. Opportunistic infections included tuberculosis, herpes zoster and systemic mycosis. A total of 398 patient-yrs(py) were included. The median time of biologic exposure was 3.0 years (0.15-11.5). We observed 35 serious/opportunistic infectious events in 27 (25%) patients: 31(88.6%) were serious infections and four (11.4%) opportunistic infections. Serious/opportunistic infections rates were 10.6/100py for ETN, 10.9/100py for ADA, 2.6/100py for ABA and 14.8/100py for TCZ. Comparison of 27 patients with and 80 without infection showed a higher frequency of systemic-onset JIA, lower age at biologic therapy initiation and a history of previous serious infection (p biologic therapy in a real-life setting. Systemic-onset JIA, lower age at biologic therapy start and history of previous serious infections were important risk factors for these complications. Also, higher rates of severe infections comparing to the former studies was possibly due to elevated MTX doses in our patients.

  11. Expansion of biological pathways based on evolutionary inference.

    Science.gov (United States)

    Li, Yang; Calvo, Sarah E; Gutman, Roee; Liu, Jun S; Mootha, Vamsi K

    2014-07-03

    The availability of diverse genomes makes it possible to predict gene function based on shared evolutionary history. This approach can be challenging, however, for pathways whose components do not exhibit a shared history but rather consist of distinct "evolutionary modules." We introduce a computational algorithm, clustering by inferred models of evolution (CLIME), which inputs a eukaryotic species tree, homology matrix, and pathway (gene set) of interest. CLIME partitions the gene set into disjoint evolutionary modules, simultaneously learning the number of modules and a tree-based evolutionary history that defines each module. CLIME then expands each module by scanning the genome for new components that likely arose under the inferred evolutionary model. Application of CLIME to ∼1,000 annotated human pathways and to the proteomes of yeast, red algae, and malaria reveals unanticipated evolutionary modularity and coevolving components. CLIME is freely available and should become increasingly powerful with the growing wealth of eukaryotic genomes. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Integrative network analysis highlights biological processes underlying GLP-1 stimulated insulin secretion: A DIRECT study.

    Directory of Open Access Journals (Sweden)

    Valborg Gudmundsdottir

    Full Text Available Glucagon-like peptide 1 (GLP-1 stimulated insulin secretion has a considerable heritable component as estimated from twin studies, yet few genetic variants influencing this phenotype have been identified. We performed the first genome-wide association study (GWAS of GLP-1 stimulated insulin secretion in non-diabetic individuals from the Netherlands Twin register (n = 126. This GWAS was enhanced using a tissue-specific protein-protein interaction network approach. We identified a beta-cell protein-protein interaction module that was significantly enriched for low gene scores based on the GWAS P-values and found support at the network level in an independent cohort from Tübingen, Germany (n = 100. Additionally, a polygenic risk score based on SNPs prioritized from the network was associated (P < 0.05 with glucose-stimulated insulin secretion phenotypes in up to 5,318 individuals in MAGIC cohorts. The network contains both known and novel genes in the context of insulin secretion and is enriched for members of the focal adhesion, extracellular-matrix receptor interaction, actin cytoskeleton regulation, Rap1 and PI3K-Akt signaling pathways. Adipose tissue is, like the beta-cell, one of the target tissues of GLP-1 and we thus hypothesized that similar networks might be functional in both tissues. In order to verify peripheral effects of GLP-1 stimulation, we compared the transcriptome profiling of ob/ob mice treated with liraglutide, a clinically used GLP-1 receptor agonist, versus baseline controls. Some of the upstream regulators of differentially expressed genes in the white adipose tissue of ob/ob mice were also detected in the human beta-cell network of genes associated with GLP-1 stimulated insulin secretion. The findings provide biological insight into the mechanisms through which the effects of GLP-1 may be modulated and highlight a potential role of the beta-cell expressed genes RYR2, GDI2, KIAA0232, COL4A1 and COL4A2 in GLP-1 stimulated

  13. How accelerated biological aging can affect solar reflective polymeric based building materials

    Science.gov (United States)

    Ferrari, C.; Santunione, G.; Libbra, A.; Muscio, A.; Sgarbi, E.

    2017-11-01

    Among the main issues concerning building materials, in particular outdoor ones, one can identify the colonization by microorganisms referred to as biological aggression. This can affect not only the aesthetical aspect but also the thermal performance of solar reflective materials. In order to improve the reliability of tests aimed to assess the resistance to biological aggression and contextually reduce the test duration, an accelerated test method has been developed. It is based on a lab reproducible setup where specific and controlled environmental and boundary conditions are imposed to accelerate as much as possible biological growth on building materials. Due to their widespread use, polymeric materials have been selected for the present analysis, in the aim of reaching an advanced bio-aged level in a relatively short time (8 weeks or less) and at the same time comparatively evaluate different materials under a given set of ageing conditions. Surface properties before, during and after ageing have been investigated by surface, microstructural and chemical analyses, as well as by examination of time progressive images to assess bacterial and algal growth rate.

  14. Neural sensitivity to statistical regularities as a fundamental biological process that underlies auditory learning: the role of musical practice.

    Science.gov (United States)

    François, Clément; Schön, Daniele

    2014-02-01

    There is increasing evidence that humans and other nonhuman mammals are sensitive to the statistical structure of auditory input. Indeed, neural sensitivity to statistical regularities seems to be a fundamental biological property underlying auditory learning. In the case of speech, statistical regularities play a crucial role in the acquisition of several linguistic features, from phonotactic to more complex rules such as morphosyntactic rules. Interestingly, a similar sensitivity has been shown with non-speech streams: sequences of sounds changing in frequency or timbre can be segmented on the sole basis of conditional probabilities between adjacent sounds. We recently ran a set of cross-sectional and longitudinal experiments showing that merging music and speech information in song facilitates stream segmentation and, further, that musical practice enhances sensitivity to statistical regularities in speech at both neural and behavioral levels. Based on recent findings showing the involvement of a fronto-temporal network in speech segmentation, we defend the idea that enhanced auditory learning observed in musicians originates via at least three distinct pathways: enhanced low-level auditory processing, enhanced phono-articulatory mapping via the left Inferior Frontal Gyrus and Pre-Motor cortex and increased functional connectivity within the audio-motor network. Finally, we discuss how these data predict a beneficial use of music for optimizing speech acquisition in both normal and impaired populations. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. Biological armors under impact—effect of keratin coating, and synthetic bio-inspired analogues

    International Nuclear Information System (INIS)

    Achrai, B; Wagner, H D; Bar-On, B

    2015-01-01

    A number of biological armors, such as turtle shells, consist of a strong exoskeleton covered with a thin keratin coating. The mechanical role upon impact of this keratin coating has surprisingly not been investigated thus far. Low-velocity impact tests on the turtle shell reveal a unique toughening phenomenon attributed to the thin covering keratin layer, the presence of which noticeably improves the fracture energy and shell integrity. Synthetic substrate/coating analogues were subsequently prepared and exhibit an impact behavior similar to the biological ones. The results of the present study may improve our understanding, and even future designs, of impact-tolerant structures. (paper)

  16. Fuzzy method of recognition of high molecular substances in evidence-based biology

    Science.gov (United States)

    Olevskyi, V. I.; Smetanin, V. T.; Olevska, Yu. B.

    2017-10-01

    Nowadays modern requirements to achieving reliable results along with high quality of researches put mathematical analysis methods of results at the forefront. Because of this, evidence-based methods of processing experimental data have become increasingly popular in the biological sciences and medicine. Their basis is meta-analysis, a method of quantitative generalization of a large number of randomized trails contributing to a same special problem, which are often contradictory and performed by different authors. It allows identifying the most important trends and quantitative indicators of the data, verification of advanced hypotheses and discovering new effects in the population genotype. The existing methods of recognizing high molecular substances by gel electrophoresis of proteins under denaturing conditions are based on approximate methods for comparing the contrast of electrophoregrams with a standard solution of known substances. We propose a fuzzy method for modeling experimental data to increase the accuracy and validity of the findings of the detection of new proteins.

  17. Assessing the Soil Physiological Potential Using Pedo-Biological Diagnosis Under Minimum-Tillage System and Mineral Fertilization

    Directory of Open Access Journals (Sweden)

    Lazar Bireescu

    2014-11-01

    Full Text Available The main objective of sustainable agriculture is the protection of environment and natural vegetal and soil resources. Accordingly, the objective of this research was to assess the impact of technological systems by minimum tillage on soil biological activity, using the Pedo-Biological Diagnosis of Soil Resources. Our research was conducted on haplic chernozem from Experimental Station of UASVM of Iasi, Romania, during the seasonal dynamic, to the soybean crop, on unfertilized and fertilized agrofond, using moderate mineral doses (N80P80 as average of 2009–2010 period, under minimum tillage (2x disk, paraplow, chisel compared to conventional (plugging at 20 cm and 30 cm. In the case of soil works with chisel and paraplow without return of furrow, the Pedo-Biological Diagnosis highlights an increase of soil physiological potential, in the both variants (unfertilized and fertilized, unlike the method of alternating the depth of plugging that proved to be ineffective.

  18. Biological and physical factors controlling aggregate stability under different climatic conditions in Southern Spain.

    Science.gov (United States)

    Ángel Gabarrón-Galeote, Miguel; Damián Ruiz-Sinoga, Jose; Francisco Martinez-Murillo, Juan; Lavee, Hanoch

    2013-04-01

    Soil aggregation is a key factor determining the soil structure. The presence of stable aggregates is essential to maintain a good soil structure, that in turn plays an important role in sustaining agricultural productivity and preserving environmental quality. A wide range of physical and biological soil components are involved in the aggregate formation and stabilization, namely clay mineral content; the quantity and quality of organic matter, that can be derived from plants, fungal hyphae, microorganism and soil animals; and the soil water content. Climatic conditions, through their effect on soil water content, vegetation cover and organic matter content, are supposed to affect soil aggregation. Thus the main objective of this research is to analyse the effect of organic matter, clay content and soil water content on aggregate stability along a climatic transect in Southern Spain. This study was conducted in four catchments along a pluviometric gradient in the South of Spain (rainfall depth decreases from west to east from more than 1000 mm year-1 to less than 300 mm year-1) and was based on a methodology approximating the climatic gradient in Mediterranean conditions. The selected sites shared similar conditions of geology, topography and soil use, which allowed making comparisons among them and relating the differences to the pluviometric conditions. In February 2007, 250 disturbed and undisturbed samples from the first 5cm of the soil were collected along the transect. We measured the aggregate stability, organic matter, clay content and bulk density of every sample. In the field we measured rainfall, air temperature, relative humidity, wind speed, wind direction, solar radiation, potential evapotranspiration, soil water content, vegetation cover and presence of litter. Our results suggest that aggregate stability is a property determined by a great number of highly variable factors, which can make extremely difficult to predict its behavior taking in

  19. Systems Biology based studies on anti-inflammatory compounds

    NARCIS (Netherlands)

    Verhoeckx, Kitty Catharina Maria

    2005-01-01

    The introduction of the ‘omics’ techniques (transcriptomics, proteomics, and metabolomics) and systems biology, has caused fundamental changes in the drug discovery process and many other fields in the life science area. In this thesis we explored the possibilities to apply these holistic

  20. Using biological effects tools to define Good Environmental Status under the Marine Strategy Framework Directive

    NARCIS (Netherlands)

    Lyons, B.P.; Thain, J.E.; Hylland, K.; Davis, I.; Vethaak, A.D.

    2010-01-01

    The use of biological effects tools offer enormous potential to meet the challenges outlined by the European Union Marine Strategy Framework Directive (MSFD) whereby Member States are required to develop a robust set of tools for defining 11 qualitative descriptors of Good Environmental Status

  1. Inhibition of a biological sulfide oxidation under haloalkaline conditions by thiols and diorgano polysulfanes

    NARCIS (Netherlands)

    Roman, Pawel; Lipińska, Joanna; Bijmans, Martijn F.M.; Sorokin, Dimitry Y.; Keesman, Karel J.; Janssen, Albert J.H.

    2016-01-01

    A novel approach has been developed for the simultaneous description of reaction kinetics to describe the formation of polysulfide and sulfate anions from the biological oxidation of hydrogen sulfide (H2S) using a quick, sulfide-dependent respiration test. Next to H2S,

  2. Essential Concepts and Underlying Theories from Physics, Chemistry, and Mathematics for "Biochemistry and Molecular Biology" Majors

    Science.gov (United States)

    Wright, Ann; Provost, Joseph; Roecklein-Canfield, Jennifer A.; Bell, Ellis

    2013-01-01

    Over the past two years, through an NSF RCN UBE grant, the ASBMB has held regional workshops for faculty members from around the country. The workshops have focused on developing lists of Core Principles or Foundational Concepts in Biochemistry and Molecular Biology, a list of foundational skills, and foundational concepts from Physics, Chemistry,…

  3. Nutrient cycling and soil biology in row crop systems under intensive tillage

    Science.gov (United States)

    Recent interest in management of the soil biological component to improve soil health requires a better understanding on how management practices (e.g., tillage) and environmental conditions influence soil organisms. Intensive tillage often results in reduced organic matter content in the surface so...

  4. Elevated temperature altered photosynthetic products in wheat seedlings and organic compounds and biological activity in rhizopshere soil under cadmium stress.

    Science.gov (United States)

    Jia, Xia; Zhao, YongHua; Wang, WenKe; He, Yunhua

    2015-09-23

    The objective of this study was to investigate the effects of slightly elevated atmospheric temperature in the spring on photosynthetic products in wheat seedlings and on organic compounds and biological activity in rhizosphere soil under cadmium (Cd) stress. Elevated temperature was associated with increased soluble sugars, reducing sugars, starch, and total sugars, and with decreased amino acids in wheat seedlings under Cd stress. Elevated temperature improved total soluble sugars, free amino acids, soluble phenolic acids, and organic acids in rhizosphere soil under Cd stress. The activity of amylase, phenol oxidase, invertase, β-glucosidase, and l-asparaginase in rhizosphere soil was significantly improved by elevated temperature under Cd stress; while cellulase, neutral phosphatase, and urease activity significantly decreased. Elevated temperature significantly improved bacteria, fungi, actinomycetes, and total microorganisms abundance and fluorescein diacetate activity under Cd stress. In conclusion, slightly elevated atmospheric temperature in the spring improved the carbohydrate levels in wheat seedlings and organic compounds and biological activity in rhizosphere soil under Cd stress in the short term. In addition, elevated atmospheric temperature in the spring stimulated available Cd by affecting pH, DOC, phenolic acids, and organic acids in rhizosphere soil, which resulted in the improvement of the Cd uptake by wheat seedlings.

  5. Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations

    Directory of Open Access Journals (Sweden)

    Kleessen Sabrina

    2012-03-01

    Full Text Available Abstract Background Flux balance analysis (FBA together with its extension, dynamic FBA, have proven instrumental for analyzing the robustness and dynamics of metabolic networks by employing only the stoichiometry of the included reactions coupled with adequately chosen objective function. In addition, under the assumption of minimization of metabolic adjustment, dynamic FBA has recently been employed to analyze the transition between metabolic states. Results Here, we propose a suite of novel methods for analyzing the dynamics of (internally perturbed metabolic networks and for quantifying their robustness with limited knowledge of kinetic parameters. Following the biochemically meaningful premise that metabolite concentrations exhibit smooth temporal changes, the proposed methods rely on minimizing the significant fluctuations of metabolic profiles to predict the time-resolved metabolic state, characterized by both fluxes and concentrations. By conducting a comparative analysis with a kinetic model of the Calvin-Benson cycle and a model of plant carbohydrate metabolism, we demonstrate that the principle of regulatory on/off minimization coupled with dynamic FBA can accurately predict the changes in metabolic states. Conclusions Our methods outperform the existing dynamic FBA-based modeling alternatives, and could help in revealing the mechanisms for maintaining robustness of dynamic processes in metabolic networks over time.

  6. Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments.

    Science.gov (United States)

    Kudoh, Hiroshi

    2016-04-01

    Phenology refers to the study of seasonal schedules of organisms. Molecular phenology is defined here as the study of the seasonal patterns of organisms captured by molecular biology techniques. The history of molecular phenology is reviewed briefly in relation to advances in the quantification technology of gene expression. High-resolution molecular phenology (HMP) data have enabled us to study phenology with an approach of in natura systems biology. I review recent analyses of FLOWERING LOCUS C (FLC), a temperature-responsive repressor of flowering, along the six steps in the typical flow of in natura systems biology. The extensive studies of the regulation of FLC have made this example a successful case in which a comprehensive understanding of gene functions has been progressing. The FLC-mediated long-term memory of past temperatures creates time lags with other seasonal signals, such as photoperiod and short-term temperature. Major signals that control flowering time have a phase lag between them under natural conditions, and hypothetical phase lag calendars are proposed as mechanisms of season detection in plants. Transcriptomic HMP brings a novel strategy to the study of molecular phenology, because it provides a comprehensive representation of plant functions. I discuss future perspectives of molecular phenology from the standpoints of molecular biology, evolutionary biology and ecology. © 2015 The Author. New Phytologist © 2015 New Phytologist Trust.

  7. Biologically constrained optimization based cell membrane segmentation in C. elegans embryos.

    Science.gov (United States)

    Azuma, Yusuke; Onami, Shuichi

    2017-06-19

    Recent advances in bioimaging and automated analysis methods have enabled the large-scale systematic analysis of cellular dynamics during the embryonic development of Caenorhabditis elegans. Most of these analyses have focused on cell lineage tracing rather than cell shape dynamics. Cell shape analysis requires cell membrane segmentation, which is challenging because of insufficient resolution and image quality. This problem is currently solved by complicated segmentation methods requiring laborious and time consuming parameter adjustments. Our new framework BCOMS (Biologically Constrained Optimization based cell Membrane Segmentation) automates the extraction of the cell shape of C. elegans embryos. Both the segmentation and evaluation processes are automated. To automate the evaluation, we solve an optimization problem under biological constraints. The performance of BCOMS was validated against a manually created ground truth of the 24-cell stage embryo. The average deviation of 25 cell shape features was 5.6%. The deviation was mainly caused by membranes parallel to the focal planes, which either contact the surfaces of adjacent cells or make no contact with other cells. Because segmentation of these membranes was difficult even by manual inspection, the automated segmentation was sufficiently accurate for cell shape analysis. As the number of manually created ground truths is necessarily limited, we compared the segmentation results between two adjacent time points. Across all cells and all cell cycles, the average deviation of the 25 cell shape features was 4.3%, smaller than that between the automated segmentation result and ground truth. BCOMS automated the accurate extraction of cell shapes in developing C. elegans embryos. By replacing image processing parameters with easily adjustable biological constraints, BCOMS provides a user-friendly framework. The framework is also applicable to other model organisms. Creating the biological constraints is a

  8. Zirconia based ceramics, some clinical and biological aspects: Review

    Directory of Open Access Journals (Sweden)

    Ossama Saleh Abd El-Ghany

    2016-12-01

    Full Text Available Improved material strength, enhanced esthethic and high biocompatibility give Zirconia ceramic a great possibility to be used for a wide range of promising clinical applications. This review presents the different types of zirconia materials available for dental application, the effect of machining procedures on these materials, the esthetic of zirconia ceramics and bonding of the veneering ceramics in addition to the biologic properties of these new materials.

  9. [Biological properties of lateritic red soil and their relationships with soil fertility in Southern China under different land use types].

    Science.gov (United States)

    Zhang, Jing; Gao, Yun-Hua; Zhang, Chi; Zhou, Bo; Li, Jing-Juan; Yang, Xiao-Xue; Xu, Huan; Dai, Jun

    2013-12-01

    Taking the lateritic red soil on a typical slopeland in Southern China as test object, this paper studied the soil microbial properties, enzyme activities, and their relationships with soil fertility under four land use types (newly cultivated dryland, shrub land, Eucalyptus land, and orchard). There existed significant differences in the soil biological properties under different land use types, among which, orchard soil had the highest microbial quantity and enzyme activities, newly cultivated dryland soil had the fastest soil respiration rate, the fewest soil microorganism quantity, and the lowest enzyme activities, whereas shrub land and woodland soils had the biological properties ranged between newly cultivated dryland and orchard soils, and there was a high similarity in the biological properties between shrub land and woodland soils. Under different land use types, the soil microbial quantity and enzyme activities were positively correlated with soil organic carbon and most of the soil nutrients. It was suggested the soils with high soil organic matter content and high fertility level were beneficial to the soil microbial growth and enzyme activities.

  10. Deaf, Hard-of-Hearing, and Hearing Signing Undergraduates' Attitudes toward Science in Inquiry-Based Biology Laboratory Classes.

    Science.gov (United States)

    Gormally, Cara

    2017-01-01

    For science learning to be successful, students must develop attitudes toward support future engagement with challenging social issues related to science. This is especially important for increasing participation of students from underrepresented populations. This study investigated how participation in inquiry-based biology laboratory classes affected students' attitudes toward science, focusing on deaf, hard-of-hearing, and hearing signing students in bilingual learning environments (i.e., taught in American Sign Language and English). Analysis of reflection assignments and interviews revealed that the majority of students developed positive attitudes toward science and scientific attitudes after participating in inquiry-based biology laboratory classes. Attitudinal growth appears to be driven by student value of laboratory activities, repeated direct engagement with scientific inquiry, and peer collaboration. Students perceived that hands-on experimentation involving peer collaboration and a positive, welcoming learning environment were key features of inquiry-based laboratories, affording attitudinal growth. Students who did not perceive biology as useful for their majors, careers, or lives did not develop positive attitudes. Students highlighted the importance of the climate of the learning environment for encouraging student contribution and noted both the benefits and pitfalls of teamwork. Informed by students' characterizations of their learning experiences, recommendations are made for inquiry-based learning in college biology. © 2017 C. Gormally. CBE—Life Sciences Education © 2017 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).

  11. Identifying the underlying causes of biological instability in a full-scale drinking water supply system.

    Science.gov (United States)

    Nescerecka, Alina; Juhna, Talis; Hammes, Frederik

    2018-05-15

    Changes in bacterial concentration and composition in drinking water during distribution are often attributed to biological (in)stability. Here we assessed temporal biological stability in a full-scale distribution network (DN) supplied with different types of source water: treated and chlorinated surface water and chlorinated groundwater produced at three water treatment plants (WTP). Monitoring was performed weekly during 12 months in two locations in the DN. Flow cytometric total and intact cell concentration (ICC) measurements showed considerable seasonal fluctuations, which were different for two locations. ICC varied between 0.1-3.75 × 10 5  cells mL -1 and 0.69-4.37 × 10 5  cells mL -1 at two locations respectively, with ICC increases attributed to temperature-dependent bacterial growth during distribution. Chlorinated water from the different WTP was further analysed with a modified growth potential method, identifying primary and secondary growth limiting compounds. It was observed that bacterial growth in the surface water sample after chlorination was primarily inhibited by phosphorus limitation and secondly by organic carbon limitation, while carbon was limiting in the chlorinated groundwater samples. However, the ratio of available nutrients changed during distribution, and together with disinfection residual decay, this resulted in higher bacterial growth potential detected in the DN than at the WTP. In this study, bacterial growth was found to be higher (i) at higher water temperatures, (ii) in samples with lower chlorine residuals and (iii) in samples with less nutrient (carbon, phosphorus, nitrogen, iron) limitation, while this was significantly different between the samples of different origin. Thus drinking water microbiological quality and biological stability could change during different seasons, and the extent of these changes depends on water temperature, the water source and treatment. Furthermore, differences in primary

  12. Quality of life of patients with rheumatoid arthritis under biological therapy

    Directory of Open Access Journals (Sweden)

    Amanda Figueiredo Barbosa Azevedo

    2015-04-01

    Full Text Available Summary Objective: assessing health-related quality of life (HRQL in patients with rheumatoid arthritis (RA, before and after treatment with biological therapy. Methods: a longitudinal study, conducted from November 2010 to September 2011, with implementation of the instruments HAQ II (health assessment questionnaire and SF-36 (medical outcomes short-from health survey. Barlett test, Anova, Friedman and paired t-test were performed for multiple extracts. Results: 30 patients were evaluated, mean age of 47.6 (SD: 12.25 years and prevalence of females (90%. The mean score of HAQ II before treatment was 1.97, with significant reduction of up to 1.23 after six months of biological therapy (p<0.01. Most of the SF-36 domains showed significant improvement after six months of treatment (p<0.01, highlighting the social aspects, pain, physical functioning, emotional issues, vitality and physical aspects. Conclusion: the use of biologic therapy in patients with RA refractory to standard therapies proved to be an important pharmacological strategy for improving HRQL.

  13. Biologically-based mechanistic models of radiation-related carcinogenesis applied to epidemiological data.

    Science.gov (United States)

    Rühm, Werner; Eidemüller, Markus; Kaiser, Jan Christian

    2017-10-01

    Biologically-based mechanistic models that are used in combining current understanding of human carcinogenesis with epidemiological studies were reviewed. Assessment was made of how well they fit the data, whether they account for non-linear radiobiological low-dose effects, and whether they suggest any implications for the dose response at low doses and dose rates. However, the present paper does not make an attempt to provide a complete review of the existing literature on biologically-based models and their application to epidemiological data. In most studies the two-stage clonal expansion (TSCE) model of carcinogenesis was used. The model provided robust estimates of identifiable parameters and radiation risk. While relatively simple, it is flexible, so that more stages can easily be added, and tests made of various types of radiation action. In general, the model performed similarly or better than descriptive excess absolute and excess relative risk models, in terms of quality of fit and number of parameters. Only very rarely the shape of dose-response predicted by the models was investigated. For some tumors, when more detailed biological information was known, additional pathways were included in the model. The future development of these models will benefit from growing knowledge on carcinogenesis processes, and in particular from use of biobank tissue samples and advances in omics technologies. Their use appears a promising approach to investigate the radiation risk at low doses and low dose rates. However, the uncertainties involved are still considerable, and the models provide only a simplified description of the underlying complexity of carcinogenesis. Current assumptions in radiation protection including the linear-non-threshold (LNT) model are not in contradiction to what is presently known on the process of cancer development.

  14. From Raw Data to Biological Discoveries: A Computational Analysis Pipeline for Mass Spectrometry-Based Proteomics

    Science.gov (United States)

    Lavallée-Adam, Mathieu; Park, Sung Kyu Robin; Martínez-Bartolomé, Salvador; He, Lin; Yates, John R.

    2015-11-01

    In the last two decades, computational tools for mass spectrometry-based proteomics data analysis have evolved from a few stand-alone software solutions serving specific goals, such as the identification of amino acid sequences based on mass spectrometry spectra, to large-scale complex pipelines integrating multiple computer programs to solve a collection of problems. This software evolution has been mostly driven by the appearance of novel technologies that allowed the community to tackle complex biological problems, such as the identification of proteins that are differentially expressed in two samples under different conditions. The achievement of such objectives requires a large suite of programs to analyze the intricate mass spectrometry data. Our laboratory addresses complex proteomics questions by producing and using algorithms and software packages. Our current computational pipeline includes, among other things, tools for mass spectrometry raw data processing, peptide and protein identification and quantification, post-translational modification analysis, and protein functional enrichment analysis. In this paper, we describe a suite of software packages we have developed to process mass spectrometry-based proteomics data and we highlight some of the new features of previously published programs as well as tools currently under development.

  15. PDBlocal: A web-based tool for local inspection of biological macromolecular 3D structures

    Directory of Open Access Journals (Sweden)

    Pan Wang

    2018-03-01

    Full Text Available Functional research on biological macromolecules must focus on specific local regions. PDBlocal is a web-based tool developed to overcome the limitations of traditional molecular visualization tools for three-dimensional (3D inspection of local regions. PDBlocal provides an intuitive and easy-to-manipulate web page interface and some new useful functions. It can keep local regions flashing, display sequence text that is dynamically consistent with the 3D structure in local appearance under multiple local manipulations, use two scenes to help users inspect the same local region with different statuses, list all historical manipulation statuses with a tree structure, allow users to annotate regions of interest, and save all historical statuses and other data to a web server for future research. PDBlocal has met expectations and shown satisfactory performance for both expert and novice users. This tool is available at http://labsystem.scuec.edu.cn/pdblocal/.

  16. Event-based text mining for biology and functional genomics.

    Science.gov (United States)

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. © The Author 2014. Published by Oxford University Press.

  17. Event-based text mining for biology and functional genomics

    Science.gov (United States)

    Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B.

    2015-01-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research. PMID:24907365

  18. Measuring enzyme activities under standardized in vivo-like conditions for Systems Biology

    NARCIS (Netherlands)

    van Eunen, K.; Bouwman, J.; Daran-Lapujade, P.A.L.; Postmus, J.; Canelas, A.; Mensonides, F.I.C.; Orij, R.; Tuzun, I.; van der Brink, J.; Smits, G.J.; van Gulik, W.M.; Brul, S.; Heijnen, J.J.; de Winde, J.H.; Teixeira de Mattos, M.J.; Kettner, C.; Nielsen, J.; Westerhoff, H.V.; Bakker, B.M.

    2010-01-01

    Realistic quantitative models require data from many laboratories. Therefore, standardization of experimental systems and assay conditions is crucial. Moreover, standards should be representative of the in vivo conditions. However, most often, enzyme-kinetic parameters are measured under assay

  19. Measuring enzyme activities under standardized in vivo-like conditions for systems biology

    NARCIS (Netherlands)

    van Eunen, Karen; Bouwman, Jildau; Daran-Lapujade, Pascale; Postmus, Jarne; Canelas, Andre B.; Mensonides, Femke I. C.; Orij, Rick; Tuzun, Isil; van den Brink, Joost; Smits, Gertien J.; van Gulik, Walter M.; Brul, Stanley; de Winde, Johannes H.; de Mattos, M. J. Teixeira; Kettner, Carsten; Nielsen, Jens; Westerhoff, Hans V.; Bakker, Barbara M.; Heijnen, J.J.

    Realistic quantitative models require data from many laboratories. Therefore, standardization of experimental systems and assay conditions is crucial. Moreover, standards should be representative of the in vivo conditions. However, most often, enzyme-kinetic parameters are measured under assay

  20. Opto-mechanical coupling in interfaces under static and propagative conditions and its biological implications.

    Science.gov (United States)

    Shrivastava, Shamit; Schneider, Matthias F

    2013-01-01

    Fluorescent dyes are vital for studying static and dynamic patterns and pattern formation in cell biology. Emission properties of the dyes incorporated in a biological interface are known to be sensitive to their local environment. We report that the fluorescence intensity of dye molecules embedded in lipid interfaces is indeed a thermodynamic observable of the system. Opto-mechanical coupling of lipid-dye system was measured as a function of the thermodynamic state of the interface. The corresponding state diagrams quantify the thermodynamic coupling between intensity I and lateral pressure π. We further demonstrate that the coupling is conserved upon varying the temperature T. Notably, the observed opto-mechanical coupling is not limited to equilibrium conditions, but also holds for propagating pressure pulses. The non-equilibrium data show, that fluorescence is especially sensitive to dynamic changes in state such as the LE-LC phase transition. We conclude that variations in the thermodynamic state (here π and T, in general pH, membrane potential V, etc also) of lipid membranes are capable of controlling fluorescence intensity. Therefore, interfacial thermodynamic state diagrams of I should be obtained for a proper interpretation of intensity data.

  1. Opto-mechanical coupling in interfaces under static and propagative conditions and its biological implications.

    Directory of Open Access Journals (Sweden)

    Shamit Shrivastava

    Full Text Available Fluorescent dyes are vital for studying static and dynamic patterns and pattern formation in cell biology. Emission properties of the dyes incorporated in a biological interface are known to be sensitive to their local environment. We report that the fluorescence intensity of dye molecules embedded in lipid interfaces is indeed a thermodynamic observable of the system. Opto-mechanical coupling of lipid-dye system was measured as a function of the thermodynamic state of the interface. The corresponding state diagrams quantify the thermodynamic coupling between intensity I and lateral pressure π. We further demonstrate that the coupling is conserved upon varying the temperature T. Notably, the observed opto-mechanical coupling is not limited to equilibrium conditions, but also holds for propagating pressure pulses. The non-equilibrium data show, that fluorescence is especially sensitive to dynamic changes in state such as the LE-LC phase transition. We conclude that variations in the thermodynamic state (here π and T, in general pH, membrane potential V, etc also of lipid membranes are capable of controlling fluorescence intensity. Therefore, interfacial thermodynamic state diagrams of I should be obtained for a proper interpretation of intensity data.

  2. Fibromyalgia and chronic fatigue: the underlying biology and related theoretical issues.

    Science.gov (United States)

    Romano, Graziella F; Tomassi, Simona; Russell, Alice; Mondelli, Valeria; Pariante, Carmine M

    2015-01-01

    There is an increasing interest in understanding the biological mechanism underpinning fibromyalgia (FM) and chronic fatigue syndrome (CFS). Despite the presence of mixed findings in this area, a few biological systems have been consistently involved, and the increasing number of studies in the field is encouraging. This chapter will focus on inflammatory and oxidative stress pathways and on the neuroendocrine system, which have been more commonly examined. Chronic inflammation, together with raised levels of oxidative stress and mitochondrial dysfunction, has been increasingly associated with the manifestation of symptoms such as pain, fatigue, impaired memory, and depression, which largely characterise at least some patients suffering from CFS and FM. Furthermore, the presence of blunted hypothalamic-pituitary-adrenal axis activity, with reduced cortisol secretion both at baseline and in response to stimulation tests, suggests a role for the hypothalamic-pituitary-adrenal axis and cortisol in the pathogenesis of these syndromes. However, to what extent these systems' abnormalities could be considered as primary or secondary factors causing FM and CFS has yet to be clarified. © 2015 S. Karger AG, Basel.

  3. [Rome: capital of an empire under the banner of political biology (1936-1942)].

    Science.gov (United States)

    Vallejo, Gustavo

    2012-01-01

    This paper analyzes the symbolic conformation of Rome and Romanism as important factors in the affirmation of the power of fascism, especially after the proclamation of the Empire in 1936. Within this framework, it explores the role of science in legitimizing the direct correlation of this symbolic universe with a praxis that exalted racial superiority inherited from Ancient Rome. It investigates the links between the eugenic discourse and the exercise of power behind the "biology policy", including fascist organicism and racism. In fact, Rome was the essence of an empire that was reborn after fifteen centuries and, between its historical legacy and the new scenarios created by fascism for disciplining the population, Romanism had to condense all of the merits of the race, encouraging military conquests and promoting responsibility for maintaining racial purity and avoiding "unwanted miscegenation" with conquered peoples. The idea of Romanism also encouraged a continuation of the persecution of Jews started in Germany. Hence, science ratified a widespread idea of the Romanization as a crusade to impose a force, exaggerated on racial grounds, which integrated confidence in environmental factors with a crude biological determinism.

  4. Physiological and Molecular Changes in Various Biological Organisms Cultured under Simulated Microgravity Conditions

    Science.gov (United States)

    Udave, Ceasar

    2017-01-01

    Microgravity is one of the most import factors in space flight where its impact on living biological organisms is concerned. Many different ailments have been reported in astronauts such as spaceflight related osteopenia, cardiovascular concerns, and loss of eye sight. In order to understand why µg causes these issues we must understand what is happening at the most basic of biological structures, the cell. The work done in this report is a culmination of contributions made to a much larger project. The project seeks to understand how cellular physiology is changing in SMG conditions and use this knowledge to feed into a follow-up study on the genetic changes that are seen in SMG environments. Cells were imaged using confocal microscopy after 20hrs and 48hrs in a 3D clinostat called the Gravite. Lengths, widths, heights, and total cell areas were measured using an image analysis software package ImageJ. There were significant differences in lengths and widths of cell nuclei, and total area of cell coverage. The report then discusses some of the problems with the testing apparatus and how 3D printing technology may be used to create better sample holders for the 3D clinostat.

  5. Dysfunctional Hematopoietic Stem Cell Biology: Underlying Mechanisms and Potential Therapeutic Strategies

    Directory of Open Access Journals (Sweden)

    Anja Geiselhart

    2012-01-01

    Full Text Available Fanconi anemia (FA is the most common inherited bone marrow failure syndrome. FA patients suffer to varying degrees from a heterogeneous range of developmental defects and, in addition, have an increased likelihood of developing cancer. Almost all FA patients develop a severe, progressive bone marrow failure syndrome, which impacts upon the production of all hematopoietic lineages and, hence, is thought to be driven by a defect at the level of the hematopoietic stem cell (HSC. This hypothesis would also correlate with the very high incidence of MDS and AML that is observed in FA patients. In this paper, we discuss the evidence that supports the role of dysfunctional HSC biology in driving the etiology of the disease. Furthermore, we consider the different model systems currently available to study the biology of cells defective in the FA signaling pathway and how they are informative in terms of identifying the physiologic mediators of HSC depletion and dissecting their putative mechanism of action. Finally, we ask whether the insights gained using such disease models can be translated into potential novel therapeutic strategies for the treatment of the hematologic disorders in FA patients.

  6. Biological parameters of Amblyomma coelebs Neumann, 1906 (Acari: Ixodidae under experimental conditions

    Directory of Open Access Journals (Sweden)

    André de Abreu Rangel Aguirre

    2018-02-01

    Full Text Available Abstract One generation of Amblyomma coelebs life cycle under experimental conditions was evaluated. Ten tick pairs were allowed to feed on rabbits under laboratory conditions (LC, resulting six engorged females with a mean weight of 1,403.9 mg. Two females were maintained in a forest reserve under natural conditions (NC, and four were maintained in incubators (LC. The engorgement period lasted 10.33 days. Pre-oviposition periods were 10.75 (NC and 22 days (LC. The mean egg-mass weight was 514.76 mg, and the blood meal conversion index was 36.67% (LC. Incubation period under NC and LC were 91 and 56.33 days and hatching rates were 50% and 28.33%, respectively. Larval engorgement period ranged from 4 to 10 days, with average weight of 1.1 mg. Engorged larvae were incubated under NC and LC, with a premolt period of 27 to 36 days and molting rate of 7.1% and 28.7%, respectively. Nymphal engorgement period ranged from 5 to 7 days, with a mean weight of 18.8 mg and a recovery rate of 54.54%. In LC, the ecdysis mean period was 24.5 days, and molting rate was 44.44%, resulting in 24 adult A. coelebs. Our results show a life cycle of 187.45 (NC and 149 (LC days.

  7. Biologically-based signal processing system applied to noise removal for signal extraction

    Science.gov (United States)

    Fu, Chi Yung; Petrich, Loren I.

    2004-07-13

    The method and system described herein use a biologically-based signal processing system for noise removal for signal extraction. A wavelet transform may be used in conjunction with a neural network to imitate a biological system. The neural network may be trained using ideal data derived from physical principles or noiseless signals to determine to remove noise from the signal.

  8. Problem-based learning through field investigation: Boosting questioning skill, biological literacy, and academic achievement

    Science.gov (United States)

    Suwono, Hadi; Wibowo, Agung

    2018-01-01

    Biology learning emphasizes problem-based learning as a learning strategy to develop students ability in identifying and solving problems in the surrounding environment. Problem identification skills are closely correlated with questioning skills. By holding this skill, students tend to deliver a procedural question instead of the descriptive one. Problem-based learning through field investigation is an instruction model which directly exposes the students to problems or phenomena that occur in the environment, and then the students design the field investigation activities to solve these problems. The purpose of this research was to describe the improvement of undergraduate biology students on questioning skills, biological literacy, and academic achievement through problem-based learning through field investigation (PBFI) compared with the lecture-based instruction (LBI). This research was a time series quasi-experimental design. The research was conducted on August - December 2015 and involved 26 undergraduate biology students at the State University of Malang on the Freshwater Ecology course. The data were collected during the learning with LBI and PBFI, in which questioning skills, biological literacy, and academic achievement were collected 3 times in each learning model. The data showed that the procedural correlative and causal types of questions are produced by the students to guide them in conducting investigations and problem-solving in PBFI. The biological literacy and academic achievement of the students at PBFI are significantly higher than those at LBI. The results show that PBFI increases the questioning skill, biological literacy, and the academic achievement of undergraduate biology students.

  9. Lack of Evolution Acceptance Inhibits Students' Negotiation of Biology-Based Socioscientific Issues

    Science.gov (United States)

    Fowler, S. R.; Zeidler, D. L.

    2016-01-01

    The purpose of this study was to explore science content used during college students' negotiation of biology-based socioscientific issues (SSI) and examine how it related to students' conceptual understanding and acceptance of biological evolution. The Socioscientific Issues Questionnaire (SSI-Q) was developed to measure depth of evolutionary…

  10. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

    Science.gov (United States)

    Liu, Fang; Jenssen, Tor-Kristian; Trimarchi, Jeff; Punzo, Claudio; Cepko, Connie L; Ohno-Machado, Lucila; Hovig, Eivind; Kuo, Winston Patrick

    2007-06-07

    High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies. As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing). The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery. Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive alternatives for measuring gene expression, and currently, both are important tools for transcriptome profiling.

  11. Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates

    Directory of Open Access Journals (Sweden)

    Cepko Connie L

    2007-06-01

    Full Text Available Abstract Background High-throughput systems for gene expression profiling have been developed and have matured rapidly through the past decade. Broadly, these can be divided into two categories: hybridization-based and sequencing-based approaches. With data from different technologies being accumulated, concerns and challenges are raised about the level of agreement across technologies. As part of an ongoing large-scale cross-platform data comparison framework, we report here a comparison based on identical samples between one-dye DNA microarray platforms and MPSS (Massively Parallel Signature Sequencing. Results The DNA microarray platforms generally provided highly correlated data, while moderate correlations between microarrays and MPSS were obtained. Disagreements between the two types of technologies can be attributed to limitations inherent to both technologies. The variation found between pooled biological replicates underlines the importance of exercising caution in identification of differential expression, especially for the purposes of biomarker discovery. Conclusion Based on different principles, hybridization-based and sequencing-based technologies should be considered complementary to each other, rather than competitive alternatives for measuring gene expression, and currently, both are important tools for transcriptome profiling.

  12. Improving Secondary School Students' Achievement and Retention in Biology Through Video-based Multimedia Instruction

    Directory of Open Access Journals (Sweden)

    Amosa Isiaka Gambari, PhD

    2014-08-01

    Full Text Available The study examined the effects of video-based multimedia instruction on secondary school students' achievement and retention in biology. In Nigeria, 120 students (60 boys and 60 girls were randomly selected from four secondary schools assigned either into one of three experimental groups: Animation + Narration; Animation + On-screen Text; Animation + Narration + On-screen Text or a control group. The pretest, posttest experimental, and control group design was adopted. A 50-item multiple-choice objective test termed Biology Achievement Test (BAT was used for collecting data. The validated BAT was tested for reliability using Kuder Richardson (KR20, which yielded 0.89. T-test, analysis of covariance (ANCOVA, and Scheffe’s post-hoc analysis were used in determining the significant differences among the four groups. The results showed that there was no statistically significant difference among the experimental groups. Generally, students under multimedia instruction performed better than their colleagues in the conventional teaching method. However, students in conventional teaching method had better retention than other groups.

  13. BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

    Directory of Open Access Journals (Sweden)

    Thomas E Gorochowski

    Full Text Available Large-scale collective behaviors such as synchronization and coordination spontaneously arise in many bacterial populations. With systems biology attempting to understand these phenomena, and synthetic biology opening up the possibility of engineering them for our own benefit, there is growing interest in how bacterial populations are best modeled. Here we introduce BSim, a highly flexible agent-based computational tool for analyzing the relationships between single-cell dynamics and population level features. BSim includes reference implementations of many bacterial traits to enable the quick development of new models partially built from existing ones. Unlike existing modeling tools, BSim fully considers spatial aspects of a model allowing for the description of intricate micro-scale structures, enabling the modeling of bacterial behavior in more realistic three-dimensional, complex environments. The new opportunities that BSim opens are illustrated through several diverse examples covering: spatial multicellular computing, modeling complex environments, population dynamics of the lac operon, and the synchronization of genetic oscillators. BSim is open source software that is freely available from http://bsim-bccs.sf.net and distributed under the Open Source Initiative (OSI recognized MIT license. Developer documentation and a wide range of example simulations are also available from the website. BSim requires Java version 1.6 or higher.

  14. Defining the biological bases of individual differences in musicality

    NARCIS (Netherlands)

    Gingras, B.; Honing, H.; Peretz, I.; Trainor, L.J.; Fisher, S.E.

    2015-01-01

    Advances in molecular technologies make it possible to pinpoint genomic factors associated with complex human traits. For cognition and behaviour, identification of underlying genes provides new entry points for deciphering the key neurobiological pathways. In the past decade, the search for genetic

  15. Spinocerebellar ataxia: miRNAs expose biological pathways underlying pervasive Purkinje cell degeneration.

    Science.gov (United States)

    van der Stijl, Rogier; Withoff, Sebo; Verbeek, Dineke S

    2017-12-01

    Recent work has demonstrated the importance of miRNAs in the pathogenesis of various brain disorders including the neurodegenerative disorder spinocerebellar ataxia (SCA). This review focuses on the role of miRNAs in the shared pathogenesis of the different SCA types. We examine the novel findings of a recent cell-type-specific RNA-sequencing study in mouse brain and discuss how the identification of Purkinje-cell-enriched miRNAs highlights biological pathways that expose the mechanisms behind pervasive Purkinje cell degeneration in SCA. These key pathways are likely to contain targets for therapeutic development and represent potential candidate genes for genetically unsolved SCAs. Copyright © 2017 Elsevier Inc. All rights reserved.

  16. Design, synthesis and biological evaluation of Arylpiperazine-based ...

    Indian Academy of Sciences (India)

    years, several piperazine-based molecules have been reported to possess strong apoptotic activity on cancer- ous cells.21 28 Piperazine based small amides such as. AK301 (I), have been stated to induce mitotic arrest and to increase ligand-dependent apoptosis in HT29 human colon cancer cells (ED50: 115nM).21 Also,.

  17. Coupling of solar-assisted advanced oxidative and biological treatment for degradation of agro-residue-based soda bleaching effluent.

    Science.gov (United States)

    Dhir, Amit; Prakash, Nagaraja Tejo; Sud, Dhiraj

    2012-11-01

    This study evaluates the effect of integrated solar-assisted advanced oxidation process (AOP) and biological treatment on the extent of degradation of effluents from chlorination (C) and first alkaline extraction (E(1)) stages of soda pulp bleaching in agro-residue-based pulp and paper mill. Biodegradation of the effluents was attempted in suspended mode using activated sludge from the functional pulp and paper industry effluent treatment plant acclimatized to effluents in question. The photocatalytic treatment was employed using zinc oxide (ZnO) in slurry mode for decontamination of effluents in a batch manner and the degradation was evaluated in terms of reduction in chemical oxygen demand. The biological treatment (24 h) of C and E(1) effluent resulted in 30 and 57 % of degradation, respectively. Solar-induced AOP of C and E(1) effluents resulted in 53 and 43 % degradation under optimized conditions (2.5 g L(-1) ZnO at pH 8.0) after 6 h of exposure. For C effluent, a short duration of solar/ZnO (1 h) prior to biological treatment reduced the time required at biological step from 24 to 12 h for almost same extent (92 %) of degradation. However, sequential biological treatment (24 h) followed by solar/ZnO (2 h) resulted in 85.5 % degradation. In contrast, in the case of E(1) effluent, sequential biological (24 h)-solar/ZnO (2 h) system effectively degrades effluent to 95.4 % as compared to 84.8 % degradation achieved in solar/ZnO (2 h)-biological treatment (24 h) system. In the present study, the sequencing of photocatalysis with the biological treatment is observably efficient and technically viable process for the complete mineralization of the effluents.

  18. Fair value versus historical cost-based valuation for biological assets: predictability of financial information

    Directory of Open Access Journals (Sweden)

    Josep M. Argilés

    2011-08-01

    This paper performs an empirical study with a sample of Spanish farms valuing biological assets at HC and a sample applying FV, finding no significant differences between both valuation methods to assess future cash flows. However, most tests reveal more predictive power of future earnings under fair valuation of biological assets, which is not explained by differences in volatility of earnings and profitability. The study also evidences the existence of flawed HC accounting practices for biological assets in agriculture, which suggests scarce information content of this valuation method in the predominant small business units existing in the agricultural sector in advanced Western countries.

  19. ACTIVITY OF LICHENS UNDER THE INFLUENCE OF SNOW AND ICE (18th Symposium on Polar Biology)

    OpenAIRE

    Ludger, KAPPEN; Burkhard, SCHROETER

    1997-01-01

    A major aim of our investigations is to explain the adaptation of vegetation to the peculiar environmental conditions in polar regions. Our concept describes the main limiting and favorable factors influencing photosynthetic production of cryptogams, mainly lichens. Snow and ice-usually stress factors to the activity of plants-can be effectively used by lichens because of their poikilohydrous nature. Light, the basic driving force for photosynthetic activity, may be deleterious under certain ...

  20. Biological evaluation of silver nanoparticles incorporated into chitosan-based membranes

    NARCIS (Netherlands)

    Shao, J.; Yu, N.; Kolwijck, E.; Wang, B.; Tan, K.W.; Jansen, J.A.; Walboomers, X.F.; Yang, F.

    2017-01-01

    AIM: To evaluate the antibacterial potential and biological performance of silver nanoparticles in chitosan-based membranes. MATERIALS & METHODS: Electrospun chitosan/poly(ethylene oxide) membranes with different amounts of silver nanoparticles were evaluated for antibacterial properties and

  1. Robotic, MEMS-based Multi Utility Sample Preparation Instrument for ISS Biological Workstation, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will develop a multi-functional, automated sample preparation instrument for biological wet-lab workstations on the ISS. The instrument is based on a...

  2. Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

    Directory of Open Access Journals (Sweden)

    Manzini Giovanni

    2007-07-01

    Full Text Available Abstract Background Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic studies since they do not scale well with data set size and they seem to be confined only to genomic and proteomic sequences. Therefore, alignment-free similarity measures are actively pursued. Among those, USM (Universal Similarity Metric has gained prominence. It is based on the deep theory of Kolmogorov Complexity and universality is its most novel striking feature. Since it can only be approximated via data compression, USM is a methodology rather than a formula quantifying the similarity of two strings. Three approximations of USM are available, namely UCD (Universal Compression Dissimilarity, NCD (Normalized Compression Dissimilarity and CD (Compression Dissimilarity. Their applicability and robustness is tested on various data sets yielding a first massive quantitative estimate that the USM methodology and its approximations are of value. Despite the rich theory developed around USM, its experimental assessment has limitations: only a few data compressors have been tested in conjunction with USM and mostly at a qualitative level, no comparison among UCD, NCD and CD is available and no comparison of USM with existing methods, both based on alignments and not, seems to be available. Results We experimentally test the USM methodology by using 25 compressors, all three of its known approximations and six data sets of relevance to Molecular Biology. This offers the first systematic and quantitative experimental assessment of this methodology, that naturally complements the many theoretical and the preliminary experimental results available. Moreover, we compare the USM methodology both with methods based on alignments and not. We may group our experiments into two sets. The first one, performed via ROC

  3. Biological properties of Majnnthemum bifolium (L. F. W. Schm. polycormones under various ecological conditions

    Directory of Open Access Journals (Sweden)

    Bożena Czarnecka

    2014-01-01

    Full Text Available Majanthemum bifolium (L. F. W. Schm. populations exhibit a two-level organisation. Individuals in the biological sense (polycormones consists of a number of basic units-above-ground shoots joined by durable rhizomes. The role of the individual in the population and plant community depends on its age, size and individual area which is the exponent of the number and biomass of the produced organs. It is considered that there exist both intra- and interpopulation differences in the number of above-ground shoots and length of rhizomes as well as in the structure of the developmental phases and age states of the above- and underground parts of the polycormones. In all populations the greater part of the biomass falls to underground organs. A more favourable ratio of shoot biomass to that of rhizomes is, however, found in the polycormones of Dentario glandulosae-Fagetum and Carici elongatae-Alnetum where the presence of nitrogen in nitrate form was disclosed. With increase of participation of young age classes of shoots more of the total biomass falls to the above-ground parts.

  4. Biology of Anicla infecta (Ochsenheimer, 1816 (Lepidoptera, Noctuidae, Noctuinae, under laboratory conditions

    Directory of Open Access Journals (Sweden)

    J. A. TESTON

    Full Text Available Larvae of Anicla infecta (Ochsenheimer, 1816 (Noctuidae feed upon many grasses and may be harmful to cereals and fodder of economic importance. This study was developed aiming to contribute to knowledge of the biology of this species. The rearing was done in an environmental chamber with the following settings: temperature of 25 ± 1ºC; relative humidity of 70% ± 10%, and photoperiod of L14: D10. The larvae fed on ryegrass, Lolium multiflorum Lam. The results express the mean and standard error for the length of every stage in days. For each stage we observed the following time of development: egg 3.2 ± 0.09; larvae 18.7 ± 0.07; pre-pupae 3.3 ± 0.04; pupae 12.6 ± 0.14; and adult longevity was 12.1 ± 1.03. Also the pre-egg-laying period was 4.4 ± 0.59; the egg-laying period was 8.1 ± 0.84; and the post-egg-laying period was 0.3 ± 0.14. The mean number of egg-laying cycles per female was 6.7 ± 0.73; that of eggs per cycle was 77.5 ± 4.37; and total eggs per female was 521.4 ± 47.36.

  5. Biology and predatory potential of coccinella septempunctata linn. on schizaphis graminum aphid under controlled conditions

    International Nuclear Information System (INIS)

    Rauf, M.; Gillani, W.A.; Haq, E.U.; Khan, J.; Ali, A.

    2013-01-01

    The biology and predatory potential of Coccinella septempunctata (Linn.) were studied on aphid, Schizaphis graminum (Rondani) at three constant temperatures 20+-1 degree C, 25+-1 degree C and 30+-1 degree C in Insectary-Bio Control Laboratories, National Agricultural Research Centre (NARC), Islamabad. The results revealed that incubation period of C. septempunctata was 5.12, 3.62 and 3.20 days with 75.6%, 82.0% and 71.2% hatchability, respectively. The larval durations were 29.5, 15.9 and 8.1 days with predatory potential of 573.7, 575.0 and 667.8 aphids per larvae. The results indicated that with increasing temperature, develop-mental duration decreases significantly. The pupal developmental duration was 14.0, 9.2 and 5.2 days, respectively which are significantly different from each other. The adult male and female longevity were 44.7, 37.7, 30.0 and 60.3, 58.9 and 43.7 days. Fecundity rate of females were 123.5, 251.5 and 293.2 eggs per female, respectively. This indicates that adult male and female developmental duration, female fecundity rate were significantly different from each other at three constant temperatures. Maximum female and male predatory potential was 3262.8 and 2571.7 aphids at 25 +-1 degree C while minimum was 2276.8 and 1890.6 aphids, respectively. (author)

  6. Quantum Biology

    Directory of Open Access Journals (Sweden)

    Alessandro Sergi

    2009-06-01

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

  7. Biology Based Lung Cancer Model for Chronic Low Radon Exposures

    International Nuclear Information System (INIS)

    Truta-Popa, Lucia-Adina; Hofmann, Werner; Fakir, Hatim; Cosma, Constantin

    2008-01-01

    Low dose effects of alpha particles at the tissue level are characterized by the interaction of single alpha particles, affecting only a small fraction of the cells within that tissue. Alpha particle intersections of bronchial target cells during a given exposure period were simulated by an initiation-promotion model, formulated in terms of cellular hits within the cycle time of the cell (dose-rate) and then integrated over the whole exposure period (dose). For a given average number of cellular hits during the lifetime of bronchial cells, the actual number of single and multiple hits was selected from a Poisson distribution. While oncogenic transformation is interpreted as the primary initiation step, stimulated mitosis by killing adjacent cells is assumed to be the primary radiological promotion event. Analytical initiation and promotion functions were derived from experimental in vitro data on oncogenic transformation and cellular survival.To investigate the shape of the lung cancer risk function at chronic, low level exposures in more detail, additional biological factors describing the tissue response and operating specifically at low doses were incorporated into the initiation-promotion model. These mechanisms modifying the initial response at the cellular level were: adaptive response, genomic instability, induction of apoptosis by surrounding cells, and detrimental as well as protective bystander mechanisms. To quantify the effects of these mechanisms as functions of dose, analytical functions were derived from the experimental evidence presently available. Predictions of lung cancer risk, including these mechanisms, exhibit a distinct sublinear dose-response relationship at low exposures, particularly for very low exposure rates

  8. Elevated atmospheric CO2 affected photosynthetic products in wheat seedlings and biological activity in rhizosphere soil under cadmium stress.

    Science.gov (United States)

    Jia, Xia; Liu, Tuo; Zhao, Yonghua; He, Yunhua; Yang, Mingyan

    2016-01-01

    The objective of this study was to investigate the effects of elevated CO2 (700 ± 23 μmol mol(-1)) on photosynthetic products in wheat seedlings and on organic compounds and biological activity in rhizosphere soil under cadmium (Cd) stress. Elevated CO2 was associated with decreased quantities of reducing sugars, starch, and soluble amino acids, and with increased quantities of soluble sugars, total sugars, and soluble proteins in wheat seedlings under Cd stress. The contents of total soluble sugars, total free amino acids, total soluble phenolic acids, and total organic acids in the rhizosphere soil under Cd stress were improved by elevated CO2. Compared to Cd stress alone, the activity of amylase, phenol oxidase, urease, L-asparaginase, β-glucosidase, neutral phosphatase, and fluorescein diacetate increased under elevated CO2 in combination with Cd stress; only cellulase activity decreased. Bacterial abundance in rhizosphere soil was stimulated by elevated CO2 at low Cd concentrations (1.31-5.31 mg Cd kg(-1) dry soil). Actinomycetes, total microbial abundance, and fungi decreased under the combined conditions at 5.31-10.31 mg Cd kg(-1) dry soil. In conclusion, increased production of soluble sugars, total sugars, and proteins in wheat seedlings under elevated CO2 + Cd stress led to greater quantities of organic compounds in the rhizosphere soil relative to seedlings grown under Cd stress only. Elevated CO2 concentrations could moderate the effects of heavy metal pollution on enzyme activity and microorganism abundance in rhizosphere soils, thus improving soil fertility and the microecological rhizosphere environment of wheat under Cd stress.

  9. Drawing-to-learn: a framework for using drawings to promote model-based reasoning in biology.

    Science.gov (United States)

    Quillin, Kim; Thomas, Stephen

    2015-03-02

    The drawing of visual representations is important for learners and scientists alike, such as the drawing of models to enable visual model-based reasoning. Yet few biology instructors recognize drawing as a teachable science process skill, as reflected by its absence in the Vision and Change report's Modeling and Simulation core competency. Further, the diffuse research on drawing can be difficult to access, synthesize, and apply to classroom practice. We have created a framework of drawing-to-learn that defines drawing, categorizes the reasons for using drawing in the biology classroom, and outlines a number of interventions that can help instructors create an environment conducive to student drawing in general and visual model-based reasoning in particular. The suggested interventions are organized to address elements of affect, visual literacy, and visual model-based reasoning, with specific examples cited for each. Further, a Blooming tool for drawing exercises is provided, as are suggestions to help instructors address possible barriers to implementing and assessing drawing-to-learn in the classroom. Overall, the goal of the framework is to increase the visibility of drawing as a skill in biology and to promote the research and implementation of best practices. © 2015 K. Quillin and S. Thomas. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  10. Mood disorders and biological rhythms in young adults: A large population-based study.

    Science.gov (United States)

    Mondin, Thaíse Campos; Cardoso, Taiane de Azevedo; Souza, Luciano Dias de Mattos; Jansen, Karen; da Silva Magalhães, Pedro Vieira; Kapczinski, Flávio; da Silva, Ricardo Azevedo

    2017-01-01

    It is known that sleep disturbance has been considered a trait-marker of mood disorders. However, the role of disruptions in biological rhythms, such as eating, activity, and social patterns, needs to be better understood. To assess the differences in biological rhythms in subjects with bipolar disorder, major depressive disorder, and healthy controls. We also tested the association between disruptions of biological rhythms and circadian preferences. A cross-sectional, population-based study with a representative sample of 1023 young adults. Bipolar disorder and depression were diagnosed using The Mini International Neuropsychiatric Interview - PLUS and DSM Structured Clinical Interview. Self-reported biological rhythms and circadian preference were assessed using the Biological Rhythm Interview of Assessment in Neuropsychiatry (BRIAN). Bipolar disorders and depression subjects presented higher rates of disruption in biological rhythms when compared to healthy controls even after adjusting for sex, socioeconomic status, alcohol, tobacco, illicit drug use, anxiety disorder and psychotropic medication use. Euthymic subjects showed higher biological rhythm disruption when compared to controls. Higher disruption in biological rhythms was observed in subjects with evening preferences. Higher disruption in biological rhythms occurs in individuals with depression and bipolar disorder even on periods of euthymia. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Biology of Triatoma carcavalloi Jurberg, Rocha & Lent, 1998 under laboratory conditions.

    Science.gov (United States)

    Cardozo-de-Almeida, Margareth; Neves, Simone Caldas Teves; Almeida, Carlos Eduardo de; Lima, Nathanielly Rocha Casado de; Oliveira, Maria Luiza Ribeiro de; Santos-Mallet, Jacenir Reis dos; Gonçalves, Teresa Cristina Monte

    2014-01-01

    Triatoma carcavalloi is a wild species that is found in sympatry with Triatoma rubrovaria and Triatoma circummaculata, which are vectors of Trypanosoma cruzi currently found in rural areas of Rio Grande do Sul, Brazil. Fertility was assessed and to determine the incubation period, the eggs were observed until hatching. The first meal was offered to 1st stage nymphs. The intermolt period was also determined. The number of blood meals was quantified at each nymphal stage and the resistance to fasting as the period between ecdysis and death. Mortality was assessed and longevity was determined by recording the time that elapsed from molting to the adult stage and until death. The developmental cycle was assessed by recording the length in days of each stage from molting to adult hood. The average incubation period was 22.7 days. The average first meal occurred 3.1 days after hatching. The 5th stage nymph to adult intermolting period was the longest at 193.4 days. The average number of feedings during nymphal development was 13.4. The resistance to fasting assay indicated that the 3rd, 4th and 5th stage nymphs presented higher resistance than did adults. The highest mortality rate was observed in the 3rd stage nymphs (22.2%). The average length of adult survival was 25.6 weeks, and the average total life cycle lasted 503.4 days. This study is the first report on the biology of T. carcavalloi that fed on mice. The presented findings expand the bionomic knowledge of these species.

  12. NK cell-based cancer immunotherapy: from basic biology to clinical application.

    Science.gov (United States)

    Li, Yang; Yin, Jie; Li, Ting; Huang, Shan; Yan, Han; Leavenworth, JianMei; Wang, Xi

    2015-12-01

    Natural killer (NK) cells, which recognize and kill target cells independent of antigen specificity and major histocompatibility complex (MHC) matching, play pivotal roles in immune defence against tumors. However, tumor cells often acquire the ability to escape NK cell-mediated immune surveillance. Thus, understanding mechanisms underlying regulation of NK cell phenotype and function within the tumor environment is instrumental for designing new approaches to improve the current cell-based immunotherapy. In this review, we elaborate the main biological features and molecular mechanisms of NK cells that pertain to regulation of NK cell-mediated anti-tumor activity. We further overview current clinical approaches regarding NK cell-based cancer therapy, including cytokine infusion, adoptive transfer of autologous or allogeneic NK cells, applications of chimeric antigen receptor (CAR)-expressing NK cells and adoptive transfer of memory-like NK cells. With these promising clinical outcomes and fuller understanding the basic questions raised in this review, we foresee that NK cell-based approaches may hold great potential for future cancer immunotherapy.

  13. 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.

  14. Bernstein approximations in glasso-based estimation of biological networks

    NARCIS (Netherlands)

    Purutcuoglu, Vilda; Agraz, Melih; Wit, Ernst

    The Gaussian graphical model (GGM) is one of the common dynamic modelling approaches in the construction of gene networks. In inference of this modelling the interaction between genes can be detected mainly via graphical lasso (glasso) or coordinate descent-based approaches. Although these methods

  15. Radiations from GSM Base Stations and its Biological Effects

    African Journals Online (AJOL)

    Michael Horsfall

    0.05) higher than the RF radiations (59mV/m) in the control stations where no base stations were located within 300m radius. Comparison of these values to the International. Commission on Non-Ionizing Radiation Protection. (ICNIRP) guideline ...

  16. Promoting Conceptual Coherence Within Context-Based Biology Education

    NARCIS (Netherlands)

    Ummels, Micha H J; Kamp, Marcel J A; De Kroon, Hans; Boersma, Kerst Th

    2015-01-01

    In secondary science education, the learning and teaching of coherent conceptual understanding are often problematic. Context-based education has been proposed as a partial solution to this problem. This study aims to gain insight into the development of conceptual coherence and how context-embedded

  17. A DNA-Based Encryption Method Based on Two Biological Axioms of DNA Chip and Polymerase Chain Reaction (PCR) Amplification Techniques.

    Science.gov (United States)

    Zhang, Yunpeng; Wang, Zhiwen; Wang, Zhenzhen; Liu, Xin; Yuan, Xiaojing

    2017-09-27

    Researchers have gained a deeper understanding of DNA-based encryption and its effectiveness in enhancing information security in recent years. However, there are many theoretical and technical issues about DNA-based encryption that need to be addressed before it can be effectively used in the field of security. Currently, the most popular DNA-based encryption schemes are based on traditional cryptography and the integration of existing DNA technology. These schemes are not completely based on DNA computing and biotechnology. Herein, as inspired by nature, encryption based on DNA has been developed, which is, in turn, based on two fundamental biological axioms about DNA sequencing: 1) DNA sequencing is difficult under the conditions of not knowing the correct sequencing primers and probes, and 2) without knowing the correct probe, it is difficult to decipher precisely and sequence the information of unknown and mixed DNA/peptide nucleic acid (PNA) probes, which only differ in nucleotide sequence, arranged on DNA chips (microarrays). In essence, when creating DNA-based encryption by means of biological technologies, such as DNA chips and polymerase chain reaction (PCR) amplification, the encryption method discussed herein cannot be decrypted, unless the DNA/PNA probe or PCR amplification is known. The biological analysis, mathematical analysis, and simulation results demonstrate the feasibility of the method, which provides much stronger security and reliability than that of traditional encryption methods. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism

    Science.gov (United States)

    Zielinski, Daniel C.; Jamshidi, Neema; Corbett, Austin J.; Bordbar, Aarash; Thomas, Alex; Palsson, Bernhard O.

    2017-01-01

    Malignant transformation is often accompanied by significant metabolic changes. To identify drivers underlying these changes, we calculated metabolic flux states for the NCI60 cell line collection and correlated the variance between metabolic states of these lines with their other properties. The analysis revealed a remarkably consistent structure underlying high flux metabolism. The three primary uptake pathways, glucose, glutamine and serine, are each characterized by three features: (1) metabolite uptake sufficient for the stoichiometric requirement to sustain observed growth, (2) overflow metabolism, which scales with excess nutrient uptake over the basal growth requirement, and (3) redox production, which also scales with nutrient uptake but greatly exceeds the requirement for growth. We discovered that resistance to chemotherapeutic drugs in these lines broadly correlates with the amount of glucose uptake. These results support an interpretation of the Warburg effect and glutamine addiction as features of a growth state that provides resistance to metabolic stress through excess redox and energy production. Furthermore, overflow metabolism observed may indicate that mitochondrial catabolic capacity is a key constraint setting an upper limit on the rate of cofactor production possible. These results provide a greater context within which the metabolic alterations in cancer can be understood.

  19. Treatment of the azo dye direct blue 2 in a biological aerated filter under anaerobic/aerobic conditions.

    Science.gov (United States)

    González-Martínez, S; Piña-Mondragón, S; González-Barceló, O

    2010-01-01

    The main objective of this research was to determine the feasibility to treat the azo dye direct blue 2 together with municipal wastewater in a biological aerated filter (BAF) using lava stones as support of the microorganisms and under combined anaerobic/aerobic conditions. A 3 m high pilot biological aerated filter was fed with municipal wastewater and, after several weeks, the azo dye direct blue 2 was added to the wastewater to reach a final concentration of 50 mg/L (34 mgCOD/L). Under continuous operation, two strategies were tested: Alternating aeration (12 h anaerobic and 12 h aerobic) and combined aeration (the lower part of the filter anaerobic and the upper part aerobic). The results indicate that municipal wastewater acted as a good electron donor resulting in satisfactory COD and dye removal rates. Better dye removal (61%) was obtained with combined aeration than with alternating aeration (45%). After beginning the azo dye addition, the COD removal rates decreased from 87 to 81% for both alternating and combined aeration procedures. The average ammonia nitrogen removal, without the addition of the dye, was 73% and increased to 90% shortly after beginning the dye addition, then it decreased to 81% during the combined aeration period. Excellent nitrification was observed in the upper aerobic part of the filter. For the combined aeration phase, the conditions change from anaerobic to aerobic does not seem to affect the behavior of the COD and TSS curves.

  20. Biological control of broad-leaved dock infestation in wheat using plant antagonistic bacteria under field conditions.

    Science.gov (United States)

    Abbas, Tasawar; Zahir, Zahir Ahmad; Naveed, Muhammad; Aslam, Zubair

    2017-06-01

    Conventional weed management systems have produced many harmful effects on weed ecology, human health and environment. Biological control of invasive weeds may be helpful to minimize these harmful effects and economic losses incurred to crops by weeds. In our earlier studies, plant antagonistic bacteria were obtained after screening a large number of rhizobacteria for production of phytotoxic substances and effects on wheat and its associated weeds under laboratory conditions. In this study, five efficient strains inhibitory to broad-leaved dock and non-inhibitory to wheat were selected and applied to broad-leaved dock co-seeded with wheat both in pot trial and chronically infested field trial. Effects of plant antagonistic bacteria on the weed and infested wheat were studied at tillering, booting and harvesting stage of wheat. The applied strains significantly inhibited the germination and growth of the weed to variable extent. Similarly, variable recovery in losses of grain and straw yield of infested wheat from 11.6 to 68 and 13 to 72.6% was obtained in pot trial while from 17.3 to 62.9 and 22.4 to 71.3% was obtained in field trial, respectively. Effects of plant antagonistic bacteria were also evident from the improvement in physiology and nutrient contents of infested wheat. This study suggests the use of these plant antagonistic bacteria to biologically control infestation of broad-leaved dock in wheat under field conditions.

  1. Separable mechanisms underlying global feature-based attention.

    Science.gov (United States)

    Bondarenko, Rowena; Boehler, Carsten N; Stoppel, Christian M; Heinze, Hans-Jochen; Schoenfeld, Mircea A; Hopf, Jens-Max

    2012-10-31

    Feature-based attention is known to operate in a spatially global manner, in that the selection of attended features is not bound to the spatial focus of attention. Here we used electromagnetic recordings in human observers to characterize the spatiotemporal signature of such global selection of an orientation feature. Observers performed a simple orientation-discrimination task while ignoring task-irrelevant orientation probes outside the focus of attention. We observed that global feature-based selection, indexed by the brain response to unattended orientation probes, is composed of separable functional components. One such component reflects global selection based on the similarity of the probe with task-relevant orientation values ("template matching"), which is followed by a component reflecting selection based on the similarity of the probe with the orientation value under discrimination in the focus of attention ("discrimination matching"). Importantly, template matching occurs at ∼150 ms after stimulus onset, ∼80 ms before the onset of discrimination matching. Moreover, source activity underlying template matching and discrimination matching was found to originate from ventral extrastriate cortex, with the former being generated in more anterolateral and the latter in more posteromedial parts, suggesting template matching to occur in visual cortex higher up in the visual processing hierarchy than discrimination matching. We take these observations to indicate that the population-level signature of global feature-based selection reflects a sequence of hierarchically ordered operations in extrastriate visual cortex, in which the selection based on task relevance has temporal priority over the selection based on the sensory similarity between input representations.

  2. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops--A Proteomic Perspective.

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-09-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

  3. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    Science.gov (United States)

    Kosová, Klára; Vítámvás, Pavel; Urban, Milan Oldřich; Klíma, Miroslav; Roy, Amitava; Prášil, Ilja Tom

    2015-01-01

    Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum), durum wheat (Triticum durum), barley (Hordeum vulgare), maize (Zea mays); leguminous plants: alfalfa (Medicago sativa), soybean (Glycine max), common bean (Phaseolus vulgaris), pea (Pisum sativum); oilseed rape (Brassica napus); potato (Solanum tuberosum); tobacco (Nicotiana tabaccum); tomato (Lycopersicon esculentum); and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals) are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton) are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed. PMID:26340626

  4. Biological Networks Underlying Abiotic Stress Tolerance in Temperate Crops—A Proteomic Perspective

    Directory of Open Access Journals (Sweden)

    Klára Kosová

    2015-09-01

    Full Text Available Abiotic stress factors, especially low temperatures, drought, and salinity, represent the major constraints limiting agricultural production in temperate climate. Under the conditions of global climate change, the risk of damaging effects of abiotic stresses on crop production increases. Plant stress response represents an active process aimed at an establishment of novel homeostasis under altered environmental conditions. Proteins play a crucial role in plant stress response since they are directly involved in shaping the final phenotype. In the review, results of proteomic studies focused on stress response of major crops grown in temperate climate including cereals: common wheat (Triticum aestivum, durum wheat (Triticum durum, barley (Hordeum vulgare, maize (Zea mays; leguminous plants: alfalfa (Medicago sativa, soybean (Glycine max, common bean (Phaseolus vulgaris, pea (Pisum sativum; oilseed rape (Brassica napus; potato (Solanum tuberosum; tobacco (Nicotiana tabaccum; tomato (Lycopersicon esculentum; and others, to a wide range of abiotic stresses (cold, drought, salinity, heat, imbalances in mineral nutrition and heavy metals are summarized. The dynamics of changes in various protein functional groups including signaling and regulatory proteins, transcription factors, proteins involved in protein metabolism, amino acid metabolism, metabolism of several stress-related compounds, proteins with chaperone and protective functions as well as structural proteins (cell wall components, cytoskeleton are briefly overviewed. Attention is paid to the differences found between differentially tolerant genotypes. In addition, proteomic studies aimed at proteomic investigation of multiple stress factors are discussed. In conclusion, contribution of proteomic studies to understanding the complexity of crop response to abiotic stresses as well as possibilities to identify and utilize protein markers in crop breeding processes are discussed.

  5. Inquiry-based Science Instruction in High School Biology Courses: A Multiple Case Study

    Science.gov (United States)

    Aso, Eze

    A lack of research exists about how secondary school science teachers use inquiry-based instruction to improve student learning. The purpose of this qualitative study was to explore how science teachers used inquiry-based instruction to improve student learning in high school biology courses. The conceptual framework was based on Banchi and Bell's model of increasing levels of complexity for inquiry-based instruction. A multiple case study research design was conducted of biology programs at 3 high schools in an urban school district in the northeastern region of the United States. Participants included 2 biology teachers from each of the 3 high schools. Data were collected from individual interviews with biology teachers, observations of lessons in biology, and documents related to state standards, assessments, and professional development. The first level of data analysis involved coding and categorizing the interview and observation data. A content analysis was used for the documents. The second level of data analysis involved examining data across all sources and all cases for themes and discrepancies. According to study findings, biology teachers used confirmation, structure, and guided inquiry to improve student learning. However, they found open inquiry challenging and frustrating to implement because professional development about scaffolding of instruction over time was needed, and students' reading and writing skills needed to improve. This study contributes to positive social change by providing educators and researchers with a deeper understanding about how to scaffold levels of inquiry-based science instruction in order to help students become scientifically literate citizens.

  6. RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation

    International Nuclear Information System (INIS)

    Dawid, Alexandre; Cayrol, Bastien; Isambert, Hervé

    2009-01-01

    Among all biopolymers, ribonucleic acids or RNA have unique functional versatility, which led to the early suggestion that RNA alone (or a closely related biopolymer) might have once sustained a primitive form of life based on a single type of biopolymer. This has been supported by the demonstration of processive RNA-based replication and the discovery of 'riboswitches' or RNA switches, which directly sense their metabolic environment. In this paper, we further explore the plausibility of this 'RNA world' scenario and show, through synthetic molecular design guided by advanced RNA simulations, that RNA can also perform elementary regulation tasks on its own. We demonstrate that RNA synthetic regulatory modules directly inspired from bacterial transcription attenuators can efficiently activate or repress the expression of other RNA by merely controlling their folding paths 'on the fly' during transcription through simple RNA–RNA antisense interaction. Factors, such as NTP concentration and RNA synthesis rate, affecting the efficiency of this kinetic regulation mechanism are also studied and discussed in the light of evolutionary constraints. Overall, this suggests that direct coupling among synthesis, folding and regulation of RNAs may have enabled the early emergence of autonomous RNA-based regulation networks in absence of both DNA and protein partners

  7. RNA synthetic biology inspired from bacteria: construction of transcription attenuators under antisense regulation.

    Science.gov (United States)

    Dawid, Alexandre; Cayrol, Bastien; Isambert, Hervé

    2009-07-01

    Among all biopolymers, ribonucleic acids or RNA have unique functional versatility, which led to the early suggestion that RNA alone (or a closely related biopolymer) might have once sustained a primitive form of life based on a single type of biopolymer. This has been supported by the demonstration of processive RNA-based replication and the discovery of 'riboswitches' or RNA switches, which directly sense their metabolic environment. In this paper, we further explore the plausibility of this 'RNA world' scenario and show, through synthetic molecular design guided by advanced RNA simulations, that RNA can also perform elementary regulation tasks on its own. We demonstrate that RNA synthetic regulatory modules directly inspired from bacterial transcription attenuators can efficiently activate or repress the expression of other RNA by merely controlling their folding paths 'on the fly' during transcription through simple RNA-RNA antisense interaction. Factors, such as NTP concentration and RNA synthesis rate, affecting the efficiency of this kinetic regulation mechanism are also studied and discussed in the light of evolutionary constraints. Overall, this suggests that direct coupling among synthesis, folding and regulation of RNAs may have enabled the early emergence of autonomous RNA-based regulation networks in absence of both DNA and protein partners.

  8. Defining the biological bases of individual differences in musicality.

    Science.gov (United States)

    Gingras, Bruno; Honing, Henkjan; Peretz, Isabelle; Trainor, Laurel J; Fisher, Simon E

    2015-03-19

    Advances in molecular technologies make it possible to pinpoint genomic factors associated with complex human traits. For cognition and behaviour, identification of underlying genes provides new entry points for deciphering the key neurobiological pathways. In the past decade, the search for genetic correlates of musicality has gained traction. Reports have documented familial clustering for different extremes of ability, including amusia and absolute pitch (AP), with twin studies demonstrating high heritability for some music-related skills, such as pitch perception. Certain chromosomal regions have been linked to AP and musical aptitude, while individual candidate genes have been investigated in relation to aptitude and creativity. Most recently, researchers in this field started performing genome-wide association scans. Thus far, studies have been hampered by relatively small sample sizes and limitations in defining components of musicality, including an emphasis on skills that can only be assessed in trained musicians. With opportunities to administer standardized aptitude tests online, systematic large-scale assessment of musical abilities is now feasible, an important step towards high-powered genome-wide screens. Here, we offer a synthesis of existing literatures and outline concrete suggestions for the development of comprehensive operational tools for the analysis of musical phenotypes. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  9. Synthesize of biological active substances on base carbom oxides

    Directory of Open Access Journals (Sweden)

    Kh. Suerbaev

    2012-03-01

    Full Text Available New effective method of obtaining of drugs on basice hydroxybenzoic acids and esters of isovaleric acid (drug substances «Ethylic ether of α-bromisovaleric acid», «Salycilic acid», «p-Hydroxybenzoic acid» and drugs «Validolum», «Korvalolum», «p-Aminosalycilic acid» had been worked out. The methods based on catalytical isobutylene hydroalkoxycarbonylation reaction with carbon monoxide and alcohols and phenol carboxylation reaction with alkaline salts of ethylcarbonic acid, easily obtained from carbon dioxide.

  10. Pulse Equivalent Area Based Orientation of a Class of Under-Actuated System under Constraints

    Directory of Open Access Journals (Sweden)

    ATIF ALI

    2017-07-01

    Full Text Available A PEA (Pulse Equivalent Area approach for orientation control of an under actuated pointing device is proposed. The presented work is a sequel to the earlier work done by the authors for the orientation control of the drill machine. The desired orientation is realized through control pulses during specific roll instants. These pulses are generated through single pair of electromagnets mounted on the housing of the pointing device. Due to practical limitation of the system, there is an additional constraint on the actuating signal. The amplitude of the actuating signal is fixed and the Pulse width or duration of the pulse can vary. A discrete equivalent model of pointing device is also developed. A novel approach based on PEA is developed since the exact solution of discrete equivalent model under constraints was not possible. The simulations are included to compare proposed technique with the existing technique developed for similar systems. The performance is also shown under both nominal and parameter variations through Monte Carlo simulations

  11. Are biological effects of space radiation really altered under the microgravity environment?

    Science.gov (United States)

    Yatagai, Fumio; Ishioka, Noriaki

    2014-10-01

    Two major factors of space environment are space radiation and microgravity. It is generally considered that a high level of ionizing radiation (IR) in space has an influence on living organisms including humans; therefore, the possible alteration of space-radiation influences by the microgravity environment is of great concern. In fact, examination of such a possibility has been extensively conducted since the early days of space experiments, suggesting a possible synergistic effect of radiation and microgravity in some experiments but a negative observation in others. Because these complicated results remain not well understood, we propose a solution to this problem. Gene expression analysis is one of the solutions to the problem. In fact, gene expression may be changed by microgravity, and further modification may be possible through IR. This result could reveal an interactive effect of both factors on the cellular responses, which could in turn reveal whether the human-health abnormalities expected under the microgravity environment can be altered by space radiation. We believe that this is a new aspect in the study of the interactive effect of radiation and microgravity. However, further improvements in space experimental technologies are required for future studies.

  12. Biological diversity of yeasts in the gastrointestinal tract of weaned piglets kept under different farm conditions.

    Science.gov (United States)

    Urubschurov, Vladimir; Janczyk, Pawel; Pieper, Robert; Souffrant, Wolfgang B

    2008-12-01

    The study was conducted to determine yeasts present in the gastrointestinal tract (GIT) of piglets kept under experimental farm (EF) and commercial farm (CF) conditions. Ninety five German Landrace full- and half-sibling piglets were sacrificed at 39 days of age. Sixty eight piglets were weaned at 28th day of life, when they were offered one diet ad libitum. Twenty seven piglets remained unweaned by their dams. None of the piglets received any creep feed before weaning. Digesta samples were collected from 1/3 distal small intestine (SI), caecum and proximal colon. One hundred seventy three colonies of isolated yeasts were characterized by sequence analysis of the PCR-amplified D1/D2 domain of the 26S rRNA gene with following alignment of the recovered sequences to GenBank entries. From the 17 phylotypes found, isolates most closely related to Galactomyces geotrichum, Kazachstania slooffiae and Candida catenulata dominated in the GIT of CF piglets. Kazachstania slooffiae and Candida glabrata dominated in GIT of EF piglets. Sørenson and Morisita-Horn similarity indices between farms were low (0.44 and 0.54 respectively) and the Simpson diversity index was higher for EF (7.58) than for CF (4.34). The study brings new data on yeasts composition in the pig GIT and shows differences in yeasts biodiversity between farms operated at different hygiene conditions.

  13. Comparative systems biology between human and animal models based on next-generation sequencing methods.

    Science.gov (United States)

    Zhao, Yu-Qi; Li, Gong-Hua; Huang, Jing-Fei

    2013-04-01

    Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.

  14. Aqueous biological graphene based formulations for ink-jet printing

    Directory of Open Access Journals (Sweden)

    Dybowska-Sarapuk Łucja

    2016-06-01

    Full Text Available The aim of the study was to produce heterophasic graphene nanoplatelets based formulation designed for ink-jet printing and biomedical applications. The compositions should meet two conditions: should be cytocompatible and have the rheological properties that allow to apply it with ink-jet printing technique. In view of the above conditions, the selection of suspensions components, such as binder, solvent and surfactants was performed. In the first stage of the research the homogeneity of the dispersion of nanoplatelets and their sedimentation behaviour in diverse solutions were tested. Subsequently, the cytotoxicity of each ink on human mesenchymal stem cells was examined using the Alamar Blue Test. At the same time the rheology of the resulting suspensions was tested. As a result of these tests the best ink composition was elaborated: water, polyethylene glycol, graphene nanoplatelets and the surfactant from DuPont company.

  15. Influence of tillage practices on soil biologically active organic matter content over a growing season under semiarid Mediterranean climate

    Directory of Open Access Journals (Sweden)

    D. Martín-Lammerding

    2013-02-01

    Full Text Available In semiarid areas, traditional, intensive tillage has led to the depletion of soil organic matter, which has resulted in reduced soil fertility. The aim of the present work was to evaluate the effects of different soil management systems, practised over 12 years, on soil organic carbon (SOC, nitrogen (SN and biologically active organic matter (particulate organic matter [POM]; potentially mineralisable nitrogen [PMN]; microbial biomass [MB]. A Mediterranean Alfisol, located in central Spain, was managed using combinations of conventional tillage (CT, minimum tillage (MT or no-tillage (NT, plus a cropping background of either continuous wheat (WW or a fallow/wheat/pea/barley rotation (FW. Soil was sampled at two depths on four occasions during 2006-2007. The results showed the sampling date and the cropping background to significantly affect the SOC (p<0.0057 and p<0.0001 respectively. Tillage practice, however, had no effect on SOC or SN. The C-and N-POM contents were significantly influenced by the date, tillage and rotation. These variables were significantly higher under NT than CT and under WW than FW. The PMN was influenced by date, tillage and rotation, while C-MB was significantly affected by tillage (p< 0.0063, but not by rotation. The NT plots accumulated 66% C-POM, 60% N-POM, 39% PMN and 84% C-MB more than the CT plots. After more than 12 years, the benefits of conservation practices were found in the considered soil properties, mainly under no tillage. In order to obtain a consistent data set to predict soil biological status, it is necessary further study over time.

  16. 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.

  17. Enhancing Higher Order Thinking Skills In A Marine Biology Class Through Problem-Based Learning

    Directory of Open Access Journals (Sweden)

    Richard M. Magsino

    2014-10-01

    Full Text Available The purpose of this research was to examine students' perspectives of their learning in marine biology in the collaborative group context of Problem-based Learning (PBL. Students’ higher order thinking skills (HOTS using PBL involves the development of their logical thinking and reasoning abilities which stimulates their curiosity and associative thinking. This study aimed to investigate how critical thinking skills, particularly analysis, synthesis and evaluation were enhanced in a marine biology class through PBL. Qualitative research approach was used to examine student responses in a questionnaire involving 10 open-ended questions that target students’ HOTS on a problem presented in a marine biology class for BS Biology students. Using axial coding as a qualitative data analysis technique by which grounded theory can be performed, the study was able to determine how students manifest their higher reasoning abilities when confronted with a marine biology situation. Results show student responses yielding affirmative remarks on the 10 questions intended to know their level of analysis (e.g., analyzing, classifying, inferring, discriminating and relating or connecting, synthesis (e.g., synthesizing and collaborating, and evaluation (e.g., comparing, criticizing, and convincing of information from the presented marine biology problem. Consequently, students were able to effectively design experiments to address the presented issue through problem-based learning. Results of the study show that PBL is an efficient instructional strategy embedded within a conventional curriculum used to develop or enhance critical thinking in marine biology.

  18. Bacteriophage-based synthetic biology for the study of infectious diseases

    Science.gov (United States)

    Lu, Timothy K.

    2014-01-01

    Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the microbiome. PMID:24997401

  19. Chemical and biological properties of phosphorus-fertilized soil under legume and grass cover (Cerrado region, Brazil

    Directory of Open Access Journals (Sweden)

    Marcelo Fernando Pereira Souza

    2013-12-01

    Full Text Available The use of cover crops has been suggested as an effective method to maintain and/or increase the organic matter content, while maintaining and/or enhancing the soil physical, chemical and biological properties. The fertility of Cerrado soils is low and, consequently, phosphorus levels as well. Phosphorus is required at every metabolic stage of the plant, as it plays a role in the processes of protein and energy synthesis and influences the photosynthetic process. This study evaluated the influence of cover crops and phosphorus rates on soil chemical and biological properties after two consecutive years of common bean. The study analyzed an Oxisol in Selvíria (Mato Grosso do Sul, Brazil, in a randomized block, split plot design, in a total of 24 treatments with three replications. The plot treatments consisted of cover crops (millet, pigeon pea, crotalaria, velvet bean, millet + pigeon pea, millet + crotalaria, and millet + velvet bean and one plot was left fallow. The subplots were represented by phosphorus rates applied as monoammonium phosphate (0, 60 and 90 kg ha-1 P2O5. In August 2011, the soil chemical properties were evaluated (pH, organic matter, phosphorus, potential acidity, cation exchange capacity, and base saturation as well as biological variables (carbon of released CO2, microbial carbon, metabolic quotient and microbial quotient. After two years of cover crops in rotation with common bean, the cover crop biomass had not altered the soil chemical properties and barely influenced the microbial activity. The biomass production of millet and crotalaria (monoculture or intercropped was highest. The biological variables were sensitive and responded to increasing phosphorus rates with increases in microbial carbon and reduction of the metabolic quotient.

  20. Image processing strategies based on saliency segmentation for object recognition under simulated prosthetic vision.

    Science.gov (United States)

    Li, Heng; Su, Xiaofan; Wang, Jing; Kan, Han; Han, Tingting; Zeng, Yajie; Chai, Xinyu

    2018-01-01

    Current retinal prostheses can only generate low-resolution visual percepts constituted of limited phosphenes which are elicited by an electrode array and with uncontrollable color and restricted grayscale. Under this visual perception, prosthetic recipients can just complete some simple visual tasks, but more complex tasks like face identification/object recognition are extremely difficult. Therefore, it is necessary to investigate and apply image processing strategies for optimizing the visual perception of the recipients. This study focuses on recognition of the object of interest employing simulated prosthetic vision. We used a saliency segmentation method based on a biologically plausible graph-based visual saliency model and a grabCut-based self-adaptive-iterative optimization framework to automatically extract foreground objects. Based on this, two image processing strategies, Addition of Separate Pixelization and Background Pixel Shrink, were further utilized to enhance the extracted foreground objects. i) The results showed by verification of psychophysical experiments that under simulated prosthetic vision, both strategies had marked advantages over Direct Pixelization in terms of recognition accuracy and efficiency. ii) We also found that recognition performance under two strategies was tied to the segmentation results and was affected positively by the paired-interrelated objects in the scene. The use of the saliency segmentation method and image processing strategies can automatically extract and enhance foreground objects, and significantly improve object recognition performance towards recipients implanted a high-density implant. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Synthesis, structural, spectroscopic and biological studies of Schiff base complexes

    Science.gov (United States)

    Diab, M. A.; El-Sonbati, A. Z.; Shoair, A. F.; Eldesoky, A. M.; El-Far, N. M.

    2017-08-01

    Schiff base ligand 4-((pyridin-2- yl)methyleneamino)-1,2-dihydro-2,3-dimethyl-1-phenylpyrazol-5-one (PDMP) and its complexes were prepared and characterized on the basis of elemental analysis, IR, mass spectra and thermogravimetric analysis. All results confirm that the complexes have 1:1 (M: PMDP) stoichiometric formula [M(PMDP)Cl2H2O ] (M = Cu(II), Co(II), Ni(II) and Mn(II)), [Cd(PMDP)Cl2] and the ligand behaves as a bi/tridentate forming five-membered chelating ring towards the metal ions, bonding through azomethine nitrogen/exocyclic carbonyl oxygen, azomethine pyridine nitrogen and exocyclic carbonyl oxygen. The shift in the band positions of the groups involved in coordination has been utilized to estimate the metal-nitrogen and/or oxygen bond lengths. The complexes of Co(II), Ni(II) and Cu(II) are paramagnetic and the magnetic as well as spectral data suggest octahedral geometry, whereas the Cd(II) complex is tetrahedral. The XRD studies show that both the ligand and its metal complexes (1 and 3) show polycrystalline with crystal structure. Molecular docking was used to predict the binding between PMDP ligand and the receptors. The corrosion inhibition of mild steel in 2 M HCl solution by PDMP was explored utilizing potentiodynamic polarization, electrochemical impedance spectroscopy (EIS) and (EFM) electrochemical frequency modulation method. Potentiodynamic polarization demonstrated that PDMP compound is mixed-type inhibitor. EIS spectra exhibit one capacitive loop and confirm the protective ability. The percentage of inhibition efficiency was found to increase with increasing the inhibitor concentration.

  2. The Design of a Molecular Assembly Line Based on Biological Molecules

    Science.gov (United States)

    2003-06-01

    the biological molecules polyketide synthase and kinesin, and in some embodiments, may employ biomolecules like DNA as components of the system. The...and will demonstrate how one can construct a purely synthetic analogue of a polyketide synthase . 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF...scaffold in programmed assembly and molecular electronics. It is based on the principles of the biological molecules polyketide synthase and kinesin, and in

  3. From menarche to menopause: exploring the underlying biology of depression in women experiencing hormonal changes.

    Science.gov (United States)

    Deecher, Darlene; Andree, Terrance H; Sloan, Diane; Schechter, Lee E

    2008-01-01

    Epidemiologic data consistently report an elevated prevalence of major depressive disorder (MDD) in women. This increase begins during adolescence and continues through the menopausal transition. Population-based clinical studies report an increase in the incidence of MDD during perimenopause compared to either the premenopausal or postmenopausal period. Evidence suggests that fluctuations and decline of hormonal levels are correlated with this observed increase in risk for MDD. A strong predictor of depression in the perimenopausal period is a previous history of MDD. However, recent studies revealed an increased risk of new onset depression in perimenopausal women without a history of MDD. Additionally, recent reports have indicated that the presence of vasomotor symptoms may be associated with an increased the risk for MDD. The objective of this paper is to review evidence that would support our hypothesis that neurotransmitter systems are affected by changes in hormonal status over the course of a woman's life, leading to increase vulnerability to perimenopausal depression. Relevant data from nonclinical experiments will be discussed in the context of observed clinical evidence of the risk for MDD before, during, and after the menopausal transition. A testable hypothesis will be proposed to advance our understanding of hormonal effects on mood.

  4. The constitutional protection of trade secrets and patents under the Biologics Price Competition and Innovation Act of 2009.

    Science.gov (United States)

    Epstein, Richard A

    2011-01-01

    The Biologics Price Competition and Innovation Act of 2009 ("Biosimilars Act") is for the field of pharmaceutical products the single most important legislative development since passage of the Drug Price Competition and Patent Term Restoration Act of 1984 ("Hatch-Waxman Act"), on which portions of the Biosimilars Act are clearly patterned. Congress revised section 351 of the Public Health Service Act (PHSA) to create a pathway for FDA approval of "biosimilar" biological products. Each biosimilar applicant is required to cite in its application a "reference product" that was approved on the basis of a full application containing testing data and manufacturing information, which is owned and was submitted by another company and much of which constitutes trade secret information subject to constitutional protection. Because the Biosimilars Act authorizes biosimilar applicants to cite these previously approved applications, the implementation of the new legislative scheme raises critical issues under the Fifth Amendment of the Constitution, pursuant to which private property--trade secrets included--may not be taken for public use, without "just compensation." FDA must confront those issues as it implements the scheme set out in the Biosimilars Act. This article will discuss these issues, after providing a brief overview of the Biosimilars Act and a more detailed examination of the law of trade secrets.

  5. Spatio-temporal thermal kinetics of in situ MWCNT heating in biological tissues under NIR laser irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Picou, Laura; McMann, Casey; Boldor, Dorin [Department of Biological and Agricultural Engineering, Louisiana State University Agricultural Center, 149 E B Doran Building, Baton Rouge, LA 70803-4505 (United States); Elzer, Philip H; Enright, Frederick M [Department of Veterinary Sciences, Louisiana State University Agricultural Center, 111 Dalrymple Building, Baton Rouge, LA 70803 (United States); Biris, Alexandru S, E-mail: DBoldor@agcenter.lsu.edu [Nanotechnology Center, University of Arkansas-Little Rock, 2801 South University Avenue, ETAS 151, Little Rock, AR 72204-1099 (United States)

    2010-10-29

    Carbon nanotubes have many potential applications in life sciences and engineering as they have very high absorbance in the near-infrared (NIR) spectrum, while biological tissues do not. The purpose of this study was to determine the effect of 1064 nm NIR laser power levels on the spatial temperature distribution and the temperature kinetics in mammalian tissue at both macroscopic and microscopic scales. The model tissue was the 'flat' of a chicken wing (the section containing the radius and ulna), which was injected under the skin in the subcutaneous layer of tissue. Specimens were exposed to laser radiation and an infrared thermography system was used to measure and record the temperature distributions in the specimens at both the macroscopic and microscopic scales. Experimental results concluded that power levels of 1536 mW easily achieved hyperthermic temperatures with localized values as high as 172.7 deg. C.

  6. Chemical Composition and Biological Activity of Essential Oils of Origanum vulgare L. subsp. vulgare L. under Different Growth Conditions

    Directory of Open Access Journals (Sweden)

    Enrica De Falco

    2013-12-01

    Full Text Available This research was aimed at investigating the essential oil production, chemical composition and biological activity of a crop of pink flowered oregano (Origanum vulgare L. subsp. vulgare L. under different spatial distribution of the plants (single and binate rows. This plant factor was shown to affect its growth, soil covering, fresh biomass, essential oil amount and composition. In particular, the essential oil percentage was higher for the binate row treatment at the full bloom. The chemical composition of the oils obtained by hydrodistillation was fully characterized by GC and GC-MS. The oil from plants grown in single rows was rich in sabinene, while plants grown in double rows were richer in ocimenes. The essential oils showed antimicrobial action, mainly against Gram-positive pathogens and particularly Bacillus cereus and B. subtilis.

  7. Biological carbon fixation: A study of Isochrysis sp. growth under actual coal-fired power plant's flue gas

    International Nuclear Information System (INIS)

    Yahya, Liyana; Chik, Muhammad Nazry; Pang, Mohd Asyraf Mohd Azmir

    2013-01-01

    Preliminary study on the growth of marine microalgae Isochrysis sp. was carried out using actual flue gas from a coal-fired power station. The species was cultured using a 2×10-L customized bubble column photobioreactor skid under specified culture conditions. With an initial culture density of 0.459 Abs (optical density at 560 nm wavelength), the species was found able to survive – observed by increases in optical densities, number of cells and weights – in the presence of actual coal-fired flue gas containing on average 4.08 % O 2 , 200.21 mg/m 3 SO 2 , 212.29 mg/m 3 NO x , 4.73 % CO 2 and 50.72 mg/m 3 CO. Results thus add value to the potential and capability of microalgae, especially for Isochrysis sp., to be the biological carbon fixer in neutralizing carbon emissions from power plants.

  8. Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations

    KAUST Repository

    Smaili, Fatima Zohra

    2018-01-31

    We propose the Onto2Vec method, an approach to learn feature vectors for biological entities based on their annotations to biomedical ontologies. Our method can be applied to a wide range of bioinformatics research problems such as similarity-based prediction of interactions between proteins, classification of interaction types using supervised learning, or clustering.

  9. Comparison and analysis of biological agent category lists based on biosafety and biodefense.

    Directory of Open Access Journals (Sweden)

    Deqiao Tian

    Full Text Available Biological agents pose a serious threat to human health, economic development, social stability and even national security. The classification of biological agents is a basic requirement for both biosafety and biodefense. We compared and analyzed the Biological Agent Laboratory Biosafety Category list and the defining criteria according to the World Health Organization (WHO, the National Institutes of Health (NIH, the European Union (EU and China. We also compared and analyzed the Biological Agent Biodefense Category list and the defining criteria according to the Centers for Disease Control and Prevention (CDC of the United States, the EU and Russia. The results show some inconsistencies among or between the two types of category lists and criteria. We suggest that the classification of biological agents based on laboratory biosafety should reduce the number of inconsistencies and contradictions. Developing countries should also produce lists of biological agents to direct their development of biodefense capabilities.To develop a suitable biological agent list should also strengthen international collaboration and cooperation.

  10. Evaluation of Parallel Authentic Research-Based Courses in Human Biology on Student Experiences at Stanford University and the University of Gothenburg

    Science.gov (United States)

    Lindh, Jacob; Annerstedt, Claes; Besier, Thor; Matheson, Gordon O.; Rydmark, Martin

    2016-01-01

    Under a previous grant (2005-08), researchers and teachers at Stanford University (SU) and the University of Gothenburg (GU) co-designed a ten-week interdisciplinary, research-based laboratory course in human biology to be taught online to undergraduate students. Essentials in the subject were taught during the first four weeks of this course.…

  11. A LabVIEW-based electrical bioimpedance spectroscopic data interpreter (LEBISDI) for biological tissue impedance analysis and equivalent circuit modelling

    KAUST Repository

    Bera, Tushar Kanti

    2016-12-05

    Under an alternating electrical signal, biological tissues produce a complex electrical bioimpedance that is a function of tissue composition and applied signal frequencies. By studying the bioimpedance spectra of biological tissues over a wide range of frequencies, we can noninvasively probe the physiological properties of these tissues to detect possible pathological conditions. Electrical impedance spectroscopy (EIS) can provide the spectra that are needed to calculate impedance parameters within a wide range of frequencies. Before impedance parameters can be calculated and tissue information extracted, impedance spectra should be processed and analyzed by a dedicated software program. National Instruments (NI) Inc. offers LabVIEW, a fast, portable, robust, user-friendly platform for designing dataanalyzing software. We developed a LabVIEW-based electrical bioimpedance spectroscopic data interpreter (LEBISDI) to analyze the electrical impedance spectra for tissue characterization in medical, biomedical and biological applications. Here, we test, calibrate and evaluate the performance of LEBISDI on the impedance data obtained from simulation studies as well as the practical EIS experimentations conducted on electronic circuit element combinations and the biological tissue samples. We analyze the Nyquist plots obtained from the EIS measurements and compare the equivalent circuit parameters calculated by LEBISDI with the corresponding original circuit parameters to assess the accuracy of the program developed. Calibration studies show that LEBISDI not only interpreted the simulated and circuitelement data accurately, but also successfully interpreted tissues impedance data and estimated the capacitive and resistive components produced by the compositions biological cells. Finally, LEBISDI efficiently calculated and analyzed variation in bioimpedance parameters of different tissue compositions, health and temperatures. LEBISDI can also be used for human tissue

  12. Permutation based decision making under fuzzy environment using Tabu search

    Directory of Open Access Journals (Sweden)

    Mahdi Bashiri

    2012-04-01

    Full Text Available One of the techniques, which are used for Multiple Criteria Decision Making (MCDM is the permutation. In the classical form of permutation, it is assumed that weights and decision matrix components are crisp. However, when group decision making is under consideration and decision makers could not agree on a crisp value for weights and decision matrix components, fuzzy numbers should be used. In this article, the fuzzy permutation technique for MCDM problems has been explained. The main deficiency of permutation is its big computational time, so a Tabu Search (TS based algorithm has been proposed to reduce the computational time. A numerical example has illustrated the proposed approach clearly. Then, some benchmark instances extracted from literature are solved by proposed TS. The analyses of the results show the proper performance of the proposed method.

  13. Defining a Research Agenda to Address the Converging Epidemics of Tuberculosis and Diabetes: Part 2: Underlying Biologic Mechanisms.

    Science.gov (United States)

    Ronacher, Katharina; van Crevel, Reinout; Critchley, Julia A; Bremer, Andrew A; Schlesinger, Larry S; Kapur, Anil; Basaraba, Randall; Kornfeld, Hardy; Restrepo, Blanca I

    2017-07-01

    There is growing interest in the re-emerging interaction between type 2 diabetes (DM) and TB, but the underlying biologic mechanisms are poorly understood despite their possible implications in clinical management. Experts in epidemiologic, public health, basic science, and clinical studies recently convened and identified research priorities for elucidating the underlying mechanisms for the co-occurrence of TB and DM. We identified gaps in current knowledge of altered immunity in patients with DM during TB, where most studies suggest an underperforming innate immunity, but exaggerated adaptive immunity to Mycobacterium tuberculosis. Various molecular mechanisms and pathways may underlie these observations in the DM host. These include signaling induced by excess advanced glycation end products and their receptor, higher levels of reactive oxidative species and oxidative stress, epigenetic changes due to chronic hyperglycemia, altered nuclear receptors, and/or differences in cell metabolism (immunometabolism). Studies in humans at different stages of DM (no DM, pre-DM, and DM) or TB (latent or active TB) should be complemented with findings in animal models, which provide the unique opportunity to study early events in the host-pathogen interaction. Such studies could also help identify biomarkers that will complement clinical studies in order to tailor the prevention of TB-DM, or to avoid the adverse TB treatment outcomes that are more likely in these patients. Such studies will also inform new approaches to host-directed therapies. Copyright © 2017 American College of Chest Physicians. All rights reserved.

  14. Switching profiles in a population-based cohort of rheumatoid arthritis receiving biologic therapy: results from the KOBIO registry.

    Science.gov (United States)

    Park, Dong-Jin; Choi, Sung Jae; Shin, Kichul; Kim, Hyoun-Ah; Park, Yong-Beom; Kang, Seong Wook; Kwok, Seung-Ki; Kim, Seong-Kyu; Nam, Eon Jeong; Sung, Yoon-Kyoung; Lee, Jaejoon; Lee, Chang Hoon; Jeon, Chan Hong; Lee, Shin-Seok

    2017-05-01

    Despite improved quality of care for rheumatoid arthritis (RA) patients, many still experience treatment failure with a biologic agent and eventually switch to another biologic agent. We investigated patterns of biologic treatment and reasons for switching biologics in patients with RA. Patients with RA who had started on a biologic agent or had switched to another biologic agent were identified from the prospective observational Korean nationwide Biologics (KOBIO) registry. The KOBIO registry contained 1184 patients with RA at the time of initiation or switching of biologic agents. Patients were categorized according to the chronological order of the introduction of biologic agents, and reasons for switching biologics were also evaluated. Of the 1184 patients with RA, 801 started with their first biologic agent, 228 were first-time switchers, and 89 were second-time or more switchers. Second-time or more switchers had lower rheumatoid factor and anti-CCP positivity, and higher disease activity scores at the time of enrollment than the other groups. Among these patients, tocilizumab was the most commonly prescribed biologic agent, followed by adalimumab and etanercept. The most common reason for switching biologics was inefficacy, followed by adverse events, including infusion reactions, infections, and skin eruptions. Furthermore, the proportion of inefficacy, as a reason for switching, was significantly higher with respect to switching between biologics with different mechanisms of action than between biologics with similar mechanisms. In this registry, we showed diverse prescribing patterns and differing baseline profiles based on the chronological order of biologic agents.

  15. Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production

    Energy Technology Data Exchange (ETDEWEB)

    Papoutsakis, Elefterios [Univ. of Delaware, Newark, DE (United States)

    2015-04-30

    This is the final project report for project "Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production" for the funding period of 9/1/12 to 2/28/2015 (three years with a 6-month no-cost extension) OVERVIEW AND PROJECT GOALS The bottleneck of achieving higher rates and titers of toxic metabolites (such as solvents and carboxylic acids that can used as biofuels or biofuel precursors) can be overcome by engineering the stress response system. Thus, understanding and modeling the response of cells to toxic metabolites is a problem of great fundamental and practical significance. In this project, our goal is to dissect at the molecular systems level and build models (conceptual and quantitative) for the stress response of C. acetobutylicum (Cac) to its two toxic metabolites: butanol (BuOH) and butyrate (BA). Transcriptional (RNAseq and microarray based), proteomic and fluxomic data and their analysis are key requirements for this goal. Transcriptional data from mid-exponential cultures of Cac under 4 different levels of BuOH and BA stress was obtained using both microarrays (Papoutsakis group) and deep sequencing (RNAseq; Meyers and Papoutsakis groups). These two sets of data do not only serve to validate each other, but are also used for identification of stress-induced changes in transcript levels, small regulatory RNAs, & in transcriptional start sites. Quantitative proteomic data (Lee group), collected using the iTRAQ technology, are essential for understanding of protein levels and turnover under stress and the various protein-protein interactions that orchestrate the stress response. Metabolic flux changes (Antoniewicz group) of core pathways, which provide important information on the re-allocation of energy and carbon resources under metabolite stress, were examined using 13C-labelled chemicals. Omics data are integrated at different levels and scales. At the metabolic-pathway level, omics data are integrated into a 2nd generation genome

  16. A Bayesian spatial model for neuroimaging data based on biologically informed basis functions.

    Science.gov (United States)

    Huertas, Ismael; Oldehinkel, Marianne; van Oort, Erik S B; Garcia-Solis, David; Mir, Pablo; Beckmann, Christian F; Marquand, Andre F

    2017-11-01

    The dominant approach to neuroimaging data analysis employs the voxel as the unit of computation. While convenient, voxels lack biological meaning and their size is arbitrarily determined by the resolution of the image. Here, we propose a multivariate spatial model in which neuroimaging data are characterised as a linearly weighted combination of multiscale basis functions which map onto underlying brain nuclei or networks or nuclei. In this model, the elementary building blocks are derived to reflect the functional anatomy of the brain during the resting state. This model is estimated using a Bayesian framework which accurately quantifies uncertainty and automatically finds the most accurate and parsimonious combination of basis functions describing the data. We demonstrate the utility of this framework by predicting quantitative SPECT images of striatal dopamine function and we compare a variety of basis sets including generic isotropic functions, anatomical representations of the striatum derived from structural MRI, and two different soft functional parcellations of the striatum derived from resting-state fMRI (rfMRI). We found that a combination of ∼50 multiscale functional basis functions accurately represented the striatal dopamine activity, and that functional basis functions derived from an advanced parcellation technique known as Instantaneous Connectivity Parcellation (ICP) provided the most parsimonious models of dopamine function. Importantly, functional basis functions derived from resting fMRI were more accurate than both structural and generic basis sets in representing dopamine function in the striatum for a fixed model order. We demonstrate the translational validity of our framework by constructing classification models for discriminating parkinsonian disorders and their subtypes. Here, we show that ICP approach is the only basis set that performs well across all comparisons and performs better overall than the classical voxel-based approach

  17. Inferring Broad Regulatory Biology from Time Course Data: Have We Reached an Upper Bound under Constraints Typical of In Vivo Studies?

    Directory of Open Access Journals (Sweden)

    Saurabh Vashishtha

    Full Text Available There is a growing appreciation for the network biology that regulates the coordinated expression of molecular and cellular markers however questions persist regarding the identifiability of these networks. Here we explore some of the issues relevant to recovering directed regulatory networks from time course data collected under experimental constraints typical of in vivo studies. NetSim simulations of sparsely connected biological networks were used to evaluate two simple feature selection techniques used in the construction of linear Ordinary Differential Equation (ODE models, namely truncation of terms versus latent vector projection. Performance was compared with ODE-based Time Series Network Identification (TSNI integral, and the information-theoretic Time-Delay ARACNE (TD-ARACNE. Projection-based techniques and TSNI integral outperformed truncation-based selection and TD-ARACNE on aggregate networks with edge densities of 10-30%, i.e. transcription factor, protein-protein cliques and immune signaling networks. All were more robust to noise than truncation-based feature selection. Performance was comparable on the in silico 10-node DREAM 3 network, a 5-node Yeast synthetic network designed for In vivo Reverse-engineering and Modeling Assessment (IRMA and a 9-node human HeLa cell cycle network of similar size and edge density. Performance was more sensitive to the number of time courses than to sample frequency and extrapolated better to larger networks by grouping experiments. In all cases performance declined rapidly in larger networks with lower edge density. Limited recovery and high false positive rates obtained overall bring into question our ability to generate informative time course data rather than the design of any particular reverse engineering algorithm.

  18. Internal modelling under Risk-Based Capital (RBC) framework

    Science.gov (United States)

    Ling, Ang Siew; Hin, Pooi Ah

    2015-12-01

    Very often the methods for the internal modelling under the Risk-Based Capital framework make use of the data which are in the form of run-off triangle. The present research will instead extract from a group of n customers, the historical data for the sum insured si of the i-th customer together with the amount paid yij and the amount aij reported but not yet paid in the j-th development year for j = 1, 2, 3, 4, 5, 6. We model the future value (yij+1, aij+1) to be dependent on the present year value (yij, aij) and the sum insured si via a conditional distribution which is derived from a multivariate power-normal mixture distribution. For a group of given customers with different original purchase dates, the distribution of the aggregate claims liabilities may be obtained from the proposed model. The prediction interval based on the distribution for the aggregate claim liabilities is found to have good ability of covering the observed aggregate claim liabilities.

  19. Evolutionary Connectionism: Algorithmic Principles Underlying the Evolution of Biological Organisation in Evo-Devo, Evo-Eco and Evolutionary Transitions.

    Science.gov (United States)

    Watson, Richard A; Mills, Rob; Buckley, C L; Kouvaris, Kostas; Jackson, Adam; Powers, Simon T; Cox, Chris; Tudge, Simon; Davies, Adam; Kounios, Loizos; Power, Daniel

    2016-01-01

    The mechanisms of variation, selection and inheritance, on which evolution by natural selection depends, are not fixed over evolutionary time. Current evolutionary biology is increasingly focussed on understanding how the evolution of developmental organisations modifies the distribution of phenotypic variation, the evolution of ecological relationships modifies the selective environment, and the evolution of reproductive relationships modifies the heritability of the evolutionary unit. The major transitions in evolution, in particular, involve radical changes in developmental, ecological and reproductive organisations that instantiate variation, selection and inheritance at a higher level of biological organisation. However, current evolutionary theory is poorly equipped to describe how these organisations change over evolutionary time and especially how that results in adaptive complexes at successive scales of organisation (the key problem is that evolution is self-referential, i.e. the products of evolution change the parameters of the evolutionary process). Here we first reinterpret the central open questions in these domains from a perspective that emphasises the common underlying themes. We then synthesise the findings from a developing body of work that is building a new theoretical approach to these questions by converting well-understood theory and results from models of cognitive learning. Specifically, connectionist models of memory and learning demonstrate how simple incremental mechanisms, adjusting the relationships between individually-simple components, can produce organisations that exhibit complex system-level behaviours and improve the adaptive capabilities of the system. We use the term "evolutionary connectionism" to recognise that, by functionally equivalent processes, natural selection acting on the relationships within and between evolutionary entities can result in organisations that produce complex system-level behaviours in evolutionary

  20. NMR-based metabolomics of water-buffalo milk after conventional or biological feeding

    Directory of Open Access Journals (Sweden)

    Pierluigi Mazzei

    2018-02-01

    Full Text Available Abstract Background Biological farming in dairy production is often advocated as one of the most virtuous solutions to the environmental problems of conventional farming while improving the sustainability of production and cattle welfare. However, it is still under debate whether the conversion from conventional to biological farming has an influence on milk composition. In addition, the possible frauds related to biological dairy products call for analytical tools enabling the authentication of products quality and consumers protection. The aim of this work was to determine the composition of milk produced by water-buffaloes and to identify the specific metabolic profiles discriminating a biological from a conventional feeding diet. Methods Liquid-state 1H, 13C, and 31P nuclear magnetic resonance (NMR spectroscopies were used to study milk samples which were supplied during a 2-year-long experimentation by a single dairy farm and sampled from conventionally and biologically fed buffaloes (CFM and BFM, respectively. For each milk sample, we obtained NMR spectra of both raw milk and milk cream fractions comprising neutral lipids and phospholipids. Results The elaboration of multinuclear spectroscopic NMR results by the principal component analysis (PCA enabled the identification of diagnostic differences in the milk composition between CFM and BFM samples. In particular, BFM were characterized by larger content of unsaturated lipids and phosphatidylcholine. Our findings confirmed that the conversion from a conventional to biological feeding regime influenced the buffalo milk composition, with possible implications for sensorial and nutritional properties of dairy products. Finally, the analytical methodology of NMR spectroscopy shown here may be considered as a useful tool to assess the quality and the authenticity of biological milk.

  1. Effect of Corm Density on Yield and Qualitative Traits of Saffron (Crocus sativus L. under Different Urea and Biological Fertilizers in Shahr-e-Rey Region

    Directory of Open Access Journals (Sweden)

    Alireza pazoki

    2017-07-01

    Full Text Available To study the effect of corm density on yield and qualitative traits of saffron (Crocus sativus L. under different biological and chemical nitrogen fertilizers, a factorial experiment based on completely randomized block design with 3 replications was done in 2014 at Shahr-e-Rey region (Ghomi Abad. The experimental factors were: corm density in 3 levels (60, 120 and 180 corm per square meter and biological and chemical nitrogen fertilizers in 4 levels (without fertilizer application, 150 kg.ha-1 of Urea, 5 L.ha-1 of Nitroxin and 75 kg.ha-1 of Urea +5 L.ha-1 of Nitroxin. The results indicated that the corm density affects number of daughter corm, fresh daughter corm weight, corm diameter, dry stigma and style weight, dry and fresh flower weight significantly. Mean comparisons also indicated that by increasing corm density from 6o to 180, saffron dry yield of saffron improved by 2.7 fold. However, increasing corm density reduced corm diameter, fresh corm daughter weight and their numbers per square meter. It can be concluded that nitroxin as an organic fertilizer, increases vegetative traits and saffron dry yield (stigma + style weight to 2.08 kg.ha-1 and highly improves in qualitative traits like Safranal, Picrocrocin, and Crocin. It can be also said that combined use of nitroxin and urea would be an alternative method to reduce application of urea.

  2. Teaching statistics in biology: using inquiry-based learning to strengthen understanding of statistical analysis in biology laboratory courses.

    Science.gov (United States)

    Metz, Anneke M

    2008-01-01

    There is an increasing need for students in the biological sciences to build a strong foundation in quantitative approaches to data analyses. Although most science, engineering, and math field majors are required to take at least one statistics course, statistical analysis is poorly integrated into undergraduate biology course work, particularly at the lower-division level. Elements of statistics were incorporated into an introductory biology course, including a review of statistics concepts and opportunity for students to perform statistical analysis in a biological context. Learning gains were measured with an 11-item statistics learning survey instrument developed for the course. Students showed a statistically significant 25% (p biology. Students improved their scores on the survey after completing introductory biology, even if they had previously completed an introductory statistics course (9%, improvement p biology showed no loss of their statistics knowledge as measured by this instrument, suggesting that the use of statistics in biology course work may aid long-term retention of statistics knowledge. No statistically significant differences in learning were detected between male and female students in the study.

  3. Margin based ontology sparse vector learning algorithm and applied in biology science

    OpenAIRE

    Gao, Wei; Qudair Baig, Abdul; Ali, Haidar; Sajjad, Wasim; Reza Farahani, Mohammad

    2016-01-01

    In biology field, the ontology application relates to a large amount of genetic information and chemical information of molecular structure, which makes knowledge of ontology concepts convey much information. Therefore, in mathematical notation, the dimension of vector which corresponds to the ontology concept is often very large, and thus improves the higher requirements of ontology algorithm. Under this background, we consider the designing of ontology sparse vector algorithm and applicatio...

  4. Agent-based re-engineering of ErbB signaling: a modeling pipeline for integrative systems biology.

    Science.gov (United States)

    Das, Arya A; Ajayakumar Darsana, T; Jacob, Elizabeth

    2017-03-01

    Experiments in systems biology are generally supported by a computational model which quantitatively estimates the parameters of the system by finding the best fit to the experiment. Mathematical models have proved to be successful in reverse engineering the system. The data generated is interpreted to understand the dynamics of the underlying phenomena. The question we have sought to answer is that - is it possible to use an agent-based approach to re-engineer a biological process, making use of the available knowledge from experimental and modelling efforts? Can the bottom-up approach benefit from the top-down exercise so as to create an integrated modelling formalism for systems biology? We propose a modelling pipeline that learns from the data given by reverse engineering, and uses it for re-engineering the system, to carry out in-silico experiments. A mathematical model that quantitatively predicts co-expression of EGFR-HER2 receptors in activation and trafficking has been taken for this study. The pipeline architecture takes cues from the population model that gives the rates of biochemical reactions, to formulate knowledge-based rules for the particle model. Agent-based simulations using these rules, support the existing facts on EGFR-HER2 dynamics. We conclude that, re-engineering models, built using the results of reverse engineering, opens up the possibility of harnessing the power pack of data which now lies scattered in literature. Virtual experiments could then become more realistic when empowered with the findings of empirical cell biology and modelling studies. Implemented on the Agent Modelling Framework developed in-house. C ++ code templates available in Supplementary material . liz.csir@gmail.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  5. Biological standards for the Knowledge-Based BioEconomy: What is at stake.

    Science.gov (United States)

    de Lorenzo, Víctor; Schmidt, Markus

    2018-01-25

    The contribution of life sciences to the Knowledge-Based Bioeconomy (KBBE) asks for the transition of contemporary, gene-based biotechnology from being a trial-and-error endeavour to becoming an authentic branch of engineering. One requisite to this end is the need for standards to measure and represent accurately biological functions, along with languages for data description and exchange. However, the inherent complexity of biological systems and the lack of quantitative tradition in the field have largely curbed this enterprise. Fortunately, the onset of systems and synthetic biology has emphasized the need for standards not only to manage omics data, but also to increase reproducibility and provide the means of engineering living systems in earnest. Some domains of biotechnology can be easily standardized (e.g. physical composition of DNA sequences, tools for genome editing, languages to encode workflows), while others might be standardized with some dedicated research (e.g. biological metrology, operative systems for bio-programming cells) and finally others will require a considerable effort, e.g. defining the rules that allow functional composition of biological activities. Despite difficulties, these are worthy attempts, as the history of technology shows that those who set/adopt standards gain a competitive advantage over those who do not. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Electrochemical sensor and biosensor platforms based on advanced nanomaterials for biological and biomedical applications.

    Science.gov (United States)

    Maduraiveeran, Govindhan; Sasidharan, Manickam; Ganesan, Vellaichamy

    2018-04-30

    Introduction of novel functional nanomaterials and analytical technologies signify a foremost possibility for the advance of electrochemical sensor and biosensor platforms/devices for a broad series of applications including biological, biomedical, biotechnological, clinical and medical diagnostics, environmental and health monitoring, and food industries. The design of sensitive and selective electrochemical biological sensor platforms are accomplished conceivably by offering new surface modifications, microfabrication techniques, and diverse nanomaterials with unique properties for in vivo and in vitro medical analysis via relating a sensibly planned electrode/solution interface. The advantageous attributes such as low-cost, miniaturization, energy efficient, easy fabrication, online monitoring, and the simultaneous sensing capability are the driving force towards continued growth of electrochemical biosensing platforms, which have fascinated the interdisciplinary research arenas spanning chemistry, material science, biological science, and medical industries. The electrochemical biosensor platforms have potential applications in the early-stage detection and diagnosis of disease as stout and tunable diagnostic and therapeutic systems. The key aim of this review is to emphasize the newest development in the design of sensing and biosensing platforms based on functional nanomaterials for biological and biomedical applications. High sensitivity and selectivity, fast response, and excellent durability in biological media are all critical aspects which will also be wisely addressed. Potential applications of electrochemical sensor and biosensor platforms based on advanced functional nanomaterials for neuroscience diagnostics, clinical, point-of-care diagnostics and medical industries are also concisely presented. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Flush of CO2 as a biologically based tool to predict nitrogen mineralization from soil

    Science.gov (United States)

    A biologically based tool to improve nitrogen (N) management in cereal crops is currently lacking from soil testing programs, but very much needed to optimize N fertilizer inputs to be able apply enough N fertilizer to achieve high production and avoid excess application that is damaging to the envi...

  8. MCT-based SWIR hyperspectral imaging system for evaluation of biological samples

    Science.gov (United States)

    Hyperspectral imaging has been shown to be a powerful tool for nondestructive evaluation of biological samples. We recently developed a new line-scan-based shortwave infrared (SWIR) hyperspectral imaging system. Critical sensing components of the system include a SWIR spectrograph, an MCT (HgCdTe) a...

  9. A Journal-Club-Based Class that Promotes Active and Cooperative Learning of Biology

    Science.gov (United States)

    Kitazono, Ana A.

    2010-01-01

    A journal-club-based class has been developed to promote active and cooperative learning and expose seniors in biochemistry and cellular molecular biology to recent research in the field. Besides giving oral presentations, students also write three papers: one discussing an article of their own choosing and two, discussing articles presented by…

  10. Extended Problem-Based Learning Improves Scientific Communication in Senior Biology Students

    Science.gov (United States)

    Kolber, Benedict J.

    2011-01-01

    This article describes a model of extended problem-based learning that instructed upper-level undergraduate students to focus on a single biological problem while improving their critical thinking, presentation, and scientific-writing skills. This course was developed in response to students' requests for formal training in oral presentation…

  11. Biofilm growth of Chlorella sorokiniana in a rotating biological contactor based photobioreactor

    NARCIS (Netherlands)

    Blanken, W.M.; Janssen, M.G.J.; Cuaresma, M.; Libor, Z.; Bhaiji, T.; Wijffels, R.H.

    2014-01-01

    Microalgae biofilms could be used as a production platform for microalgae biomass. In this study, a photobioreactor design based on a rotating biological contactor (RBC) was used as a production platform for microalgae biomass cultivated in biofilm. In the photobioreactor, referred to as Algadisk,

  12. Preparing Biology Teachers to Teach Evolution in a Project-Based Approach

    Science.gov (United States)

    Cook, Kristin; Buck, Gayle; Park Rogers, Meredith

    2012-01-01

    This study investigates a project-based learning (PBL) approach to teaching evolution to inform efforts in teacher preparation. Data analysis of a secondary biology educator teaching evolution through a PBL approach illuminated: (1) active student voice, which allowed students to reflect on their positioning on evolution and consider multiple…

  13. Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology

    Science.gov (United States)

    Shin, Jonghyeon; Caschera, Filippo; Murray, Richard M.; Noireaux, Vincent

    2013-01-01

    Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.1 This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology.2,3 To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems.4,5 The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.6 Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted.7 The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters.6,8 Accompanying mathematical models are available.9,10 The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard." PMID:24084388

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

    Science.gov (United States)

    Ziegler, Brittany Ann

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

  15. GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology

    Directory of Open Access Journals (Sweden)

    Adrien Basso-Blandin

    2012-11-01

    Full Text Available In this article, we propose a domain specific language, GUBS (Genomic Unified Behavior Specification, dedicated to the behavioral specification of synthetic biological devices, viewed as discrete open dynamical systems. GUBS is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system. The semantics of the language accounts the existence of some hidden non-specified actions possibly altering the behavior of the programmed device. The compilation framework follows a scheme similar to automatic theorem proving, aiming at improving synthetic biological design safety.

  16. Synthesis, Physical Characterization and Biological Activity of Some Schiff Base Complexes

    Directory of Open Access Journals (Sweden)

    R. Rajavel

    2008-01-01

    Full Text Available Structural modification of organic molecule has considerable biological relevance. Further, coordination of a biomolecules to the metal ions significantly alters the effectiveness of the biomolecules. In view of the antimicrobial activity ligand [bis-(2-aminobenzaldehyde] malonoyl dihydrazone], metal complexes with Cu(II, Ni(II, Zn(II and oxovanadium(IV have been synthesized and found to be potential antimicrobial agents. An attempt is also made to correlate the biological activities with geometry of the complexes. The complexes have been characterized by elemental analysis, molar conductance, spectra and cyclicvoltammetric measurements. The structural assessment of the complexes has been carried out based on electronic, infrared and molar conductivity values.

  17. Carbon exchange in biological soil crust communities under differential temperatures and soil water contents: implications for global change

    Science.gov (United States)

    Grote, Edmund E.; Belnap, Jayne; Housman, David C.; Sparks, Jed P.

    2010-01-01

    Biological soil crusts (biocrusts) are an integral part of the soil system in arid regions worldwide, stabilizing soil surfaces, aiding vascular plant establishment, and are significant sources of ecosystem nitrogen and carbon. Hydration and temperature primarily control ecosystem CO2 flux in these systems. Using constructed mesocosms for incubations under controlled laboratory conditions, we examined the effect of temperature (5-35 1C) and water content (WC, 20-100%) on CO2 exchange in light cyanobacterially dominated) and dark cyanobacteria/lichen and moss dominated) biocrusts of the cool Colorado Plateau Desert in Utah and the hot Chihuahuan Desert in New Mexico. In light crusts from both Utah and New Mexico, net photosynthesis was highest at temperatures 430 1C. Net photosynthesis in light crusts from Utah was relatively insensitive to changes in soil moisture. In contrast, light crusts from New Mexico tended to exhibit higher rates of net photosynthesis at higher soil moisture. Dark crusts originating from both sites exhibited the greatest net photosynthesis at intermediate soil water content (40-60%). Declines in net photosynthesis were observed in dark crusts with crusts from Utah showing declines at temperatures 425 1C and those originating from New Mexico showing declines at temperatures 435 1C. Maximum net photosynthesis in all crust types from all locations were strongly influenced by offsets in the optimal temperature and water content for gross photosynthesis compared with dark respiration. Gross photosynthesis tended to be maximized at some intermediate value of temperature and water content and dark respiration tended to increase linearly. The results of this study suggest biocrusts are capable of CO2 exchange under a wide range of conditions. However, significant changes in the magnitude of this exchange should be expected for the temperature and precipitation changes suggested by current climate models.

  18. Molecular Bases Underlying the Hepatoprotective Effects of Coffee

    Directory of Open Access Journals (Sweden)

    Federico Salomone

    2017-01-01

    Full Text Available Coffee is the most consumed beverage worldwide. Epidemiological studies with prospective cohorts showed that coffee intake is associated with reduced cardiovascular and all-cause mortality independently of caffeine content. Cohort and case-control studies reported an inverse association between coffee consumption and the degree of liver fibrosis as well as the development of liver cancer. Furthermore, the beneficial effects of coffee have been recently confirmed by large meta-analyses. In the last two decades, various in vitro and in vivo studies evaluated the molecular determinants for the hepatoprotective effects of coffee. In the present article, we aimed to critically review experimental evidence regarding the active components and the molecular bases underlying the beneficial role of coffee against chronic liver diseases. Almost all studies highlighted the beneficial effects of this beverage against liver fibrosis with the most solid results indicating a pivot role for both caffeine and chlorogenic acids. In particular, in experimental models of fibrosis, caffeine was shown to inhibit hepatic stellate cell activation by blocking adenosine receptors, and emerging evidence indicated that caffeine may also favorably impact angiogenesis and hepatic hemodynamics. On the other side, chlorogenic acids, potent phenolic antioxidants, suppress liver fibrogenesis and carcinogenesis by reducing oxidative stress and counteract steatogenesis through the modulation of glucose and lipid homeostasis in the liver. Overall, these molecular insights may have translational significance and suggest that coffee components need clinical evaluation.

  19. Dryland biological soil crust cyanobacteria show unexpected decreases in abundance under long-term elevated CO2

    Science.gov (United States)

    Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris M.; Belnap, Jayne; Evans, R. David; Kuske, Cheryl R.

    2012-01-01

    Biological soil crusts (biocrusts) cover soil surfaces in many drylands globally. The impacts of 10 years of elevated atmospheric CO2 on the cyanobacteria in biocrusts of an arid shrubland were examined at a large manipulated experiment in Nevada, USA. Cyanobacteria-specific quantitative PCR surveys of cyanobacteria small-subunit (SSU) rRNA genes suggested a reduction in biocrust cyanobacterial biomass in the elevated CO2 treatment relative to the ambient controls. Additionally, SSU rRNA gene libraries and shotgun metagenomes showed reduced representation of cyanobacteria in the total microbial community. Taxonomic composition of the cyanobacteria was similar under ambient and elevated CO2 conditions, indicating the decline was manifest across multiple cyanobacterial lineages. Recruitment of cyanobacteria sequences from replicate shotgun metagenomes to cyanobacterial genomes representing major biocrust orders also suggested decreased abundance of cyanobacteria sequences across the majority of genomes tested. Functional assignment of cyanobacteria-related shotgun metagenome sequences indicated that four subsystem categories, three related to oxidative stress, were differentially abundant in relation to the elevated CO2 treatment. Taken together, these results suggest that elevated CO2 affected a generalized decrease in cyanobacteria in the biocrusts and may have favoured cyanobacteria with altered gene inventories for coping with oxidative stress.

  20. Physical, chemical, and biological properties of soil under soybean cultivation and at an adjacent rainforest in Amazonia

    Directory of Open Access Journals (Sweden)

    Troy Patrick Beldini

    2015-11-01

    Full Text Available Land-use change in the Amazon basin has occurred at an accelerated pace during the last decade, and it is important that the effects induced by these changes on soil properties are better understood. This study investigated the chemical, physical, and biological properties of soil in a field under cultivation of soy and rice, and at an adjacent primary rain forest. Increases in soil bulk density, exchangeable cations and pH were observed in the soy field soil. In the primary forest, soil microbial biomass and basal respiration rates were higher, and the microbial community was metabolically more efficient. The sum of basal respiration across the A, AB and BA horizons on a mass per area basis ranged from 7.31 to 10.05 Mg CO2-C ha-1yr-1, thus yielding estimates for total soil respiration between 9.6 and 15.5 Mg CO2-C ha-1yr-1 across sites and seasons. These estimates are in good agreement with literature values for Amazonian ecosystems. The estimates of heterotrophic respiration made in this study help to further constrain the estimates of autotrophic soil respiration and will be useful for monitoring the effects of future land-use in Amazonian ecosystems.

  1. Biological Select Agents and Toxins: Risk-Based Assessment Management and Oversight.

    Energy Technology Data Exchange (ETDEWEB)

    Burnett, LouAnn Crawford; Brodsky, Benjamin H.

    2016-12-01

    Sandia National Laboratories' International Biological and Chemical Threat Reduction (SNL/IBCTR) conducted, on behalf of the Federal Select Agent Program (FSAP), a review of risk assessment in modern select agent laboratories. This review and analysis consisted of literature review, interviews of FSAP staff, entities regulated by FSAP, and deliberations of an expert panel. Additionally, SNL/IBCTR reviewed oversight mechanisms used by industries, US agencies, and other countries for high-consequence risks (e.g, nuclear, chemical, or biological materials, aviation, off-shore drilling, etc.) to determine if alternate oversight mechanisms existed that might be applicable to FSAP oversight of biological select agents and toxins. This report contains five findings, based on these reviews and analyses, with recommendations and suggested actions for FSAP to consider.

  2. Evaluation and modeling of HIV based on communication theory in biological systems.

    Science.gov (United States)

    Dong, Miaowu; Li, Wenrong; Xu, Xi

    2016-12-01

    Some forms of communication are used in biological systems such as HIV transmission in human beings. In this paper, we plan to get a unique insight into biological communication systems generally through the analogy between HIV infection and electrical communication system. The model established in this paper can be used to test and simulate various communication systems since it provides researchers with an opportunity. We interpret biological communication systems by using telecommunications exemplification from a layered communication protocol developed before and use the model to indicate HIV spreading. We also implement a simulation of HIV infection based on the layered communication protocol to predict the development of this disease and the results prove the validity of the model. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Systems Biology-Based Platforms to Accelerate Research of Emerging Infectious Diseases.

    Science.gov (United States)

    Oh, Soo Jin; Choi, Young Ki; Shin, Ok Sarah

    2018-03-01

    Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. © Copyright: Yonsei University College of Medicine 2018.

  4. Microdosimetric study on influence of low energy photons on relative biological effectiveness under therapeutic conditions using 6 MV linac

    International Nuclear Information System (INIS)

    Okamoto, Hiroyuki; Kohno, Toshiyuki; Kanai, Tatsuaki; Kase, Yuki; Matsumoto, Yoshitaka; Furusawa, Yoshiya; Fujita, Yukio; Saitoh, Hidetoshi; Itami, Jun

    2011-01-01

    Purpose: Microdosimetry has been developed for the evaluation of radiation quality, and single-event dose-mean lineal energy y D is well-used to represent the radiation quality. In this study, the changes of the relative biological effectiveness (RBE) values under the therapeutic conditions using a 6 MV linac were investigated with a microdosimetric method. Methods: The y D values under the various irradiation conditions for x-rays from a 6 MV linac were measured with a tissue-equivalent proportional counter (TEPC) at an extremely low dose rate of a few tens of μGy/min by decreasing the gun grid voltage of the linac. According to the microdosimetric kinetic model (MK model), the RBE MK values for cell killing of the human salivary gland (HSG) tumor cells can be derived if the y D values are obtained from TEPC measurements. The Monte Carlo code GEANT4 was also used to calculate the photon energy distributions and to investigate the changes of the y D values under the various conditions. Results: The changes of the y D values were less than approximately 10% when the field size and the depth in a phantom varied. However, in the measurements perpendicular to a central beam axis, large changes were observed between the y D values inside the field and those outside the field. The maximum increase of approximately 50% in the y D value outside the field was obtained compared with those inside the field. The GEANT4 calculations showed that there existed a large relative number of low energy photons outside of the field as compared with inside of the field. The percentages of the photon fluences below 200 keV outside the field were approximately 40% against approximately 8% inside the field. By using the MK model, the field size and the depth dependence of the RBE MK values were less than approximately 2% inside the field. However, the RBE MK values outside the field were 6.6% higher than those inside the field. Conclusions: The increase of the RBE MK values by 6

  5. An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks

    Science.gov (United States)

    2014-01-01

    Background Motif mining has always been a hot research topic in bioinformatics. Most of current research on biological networks focuses on exact motif mining. However, due to the inevitable experimental error and noisy data, biological network data represented as the probability model could better reflect the authenticity and biological significance, therefore, it is more biological meaningful to discover probability motif in uncertain biological networks. One of the key steps in probability motif mining is frequent pattern discovery which is usually based on the possible world model having a relatively high computational complexity. Methods In this paper, we present a novel method for detecting frequent probability patterns based on circuit simulation in the uncertain biological networks. First, the partition based efficient search is applied to the non-tree like subgraph mining where the probability of occurrence in random networks is small. Then, an algorithm of probability isomorphic based on circuit simulation is proposed. The probability isomorphic combines the analysis of circuit topology structure with related physical properties of voltage in order to evaluate the probability isomorphism between probability subgraphs. The circuit simulation based probability isomorphic can avoid using traditional possible world model. Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters. Results The experiment results on data sets of the Protein-Protein Interaction (PPI) networks and the transcriptional regulatory networks of E. coli and S. cerevisiae show that the proposed method can efficiently discover the frequent probability subgraphs. The discovered subgraphs in our study contain all probability motifs reported in the experiments published in other related papers. Conclusions The algorithm of probability graph isomorphism

  6. Biological soil crust formation under artificial vegetation effect and its properties in the Mugetan sandy land, northeastern Qinghai-Tibet Plateau

    Science.gov (United States)

    Li, Y. F.; Li, Z. W.; Jia, Y. H.; Zhang, K.

    2016-08-01

    Mugetan sandy land is an inland desertification area of about 2,065 km2 in the northeastern Qinghai-Tibet Plateau. In the ecological restoration region of the Mugetan sandy land, different crusts have formed under the action of vegetation in three types of sandy soil (i.e. semi-fixed sand dune, fixed sand dune and ancient fixed aeolian sandy soil). The surface sand particle distribution, mineral component and vegetation composition of moving sand dunes and three types of sandy soil were studied in 2010-2014 to analyze the biological crust formation properties in the Mugetan sandy land and the effects of artificial vegetation. Results from this study revealed that artificial vegetation increases the clay content and encourages the development of biological curst. The fine particles (i.e. clay and humus) of the surface layer of the sand dunes increased more than 15% ten years after the artificial vegetation planting, and further increased up to 20% after one hundred years. The interaction of clay, humus, and other fine particles formed the soil aggregate structure. Meanwhile, under the vegetation effect from the microbes, algae, and moss, the sand particles stuck together and a biological crust formed. The interconnection of the partial crusts caused the sand dunes to gradually be fixed as a whole. Maintaining the integrity of the biological crust plays a vital role in fixing the sand under the crust. The precipitation and temperature conditions in the Mugetan sandy land could satisfy the demand of biological crust formation and development. If rational vegetation measures are adopted in the region with moving sand dunes, the lichen-moss-algae biological curst will form after ten years, but it still takes more time for the sand dunes to reach the nutrient enrichment state. If the biological curst is partly broken due to human activities, reasonable closure and restoration measures can shorten the restoration time of the biological crust.

  7. BODIPY-based azamacrocyclic ensemble for selective fluorescence detection and quantification of homocysteine in biological applications.

    Science.gov (United States)

    Li, Zan; Geng, Zhi-Rong; Zhang, Cui; Wang, Xiao-Bo; Wang, Zhi-Lin

    2015-10-15

    Considering the significant role of plasma homocysteine in physiological processes, two ensembles (F465-Cu(2+) and F508-Cu(2+)) were constructed based on a BODIPY (4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene) scaffold conjugated with an azamacrocyclic (1,4,7-triazacyclononane and 1,4,7,10-tetraazacyclododecane) Cu(2+) complex. The results of this effort demonstrated that the F465-Cu(2+) ensemble could be employed to detect homocysteine in the presence of other biologically relevant species, including cysteine and glutathione, under physiological conditions with high selectivity and sensitivity in the turn-on fluorescence mode, while the F508-Cu(2+) ensemble showed no fluorescence responses toward biothiols. A possible mechanism for this homocysteine-specific specificity involving the formation of a homocysteine-induced six-membered ring sandwich structure was proposed and confirmed for the first time by time-dependent fluorescence spectra, ESI-MS and EPR. The detection limit of homocysteine in deproteinized human serum was calculated to be 241.4 nM with a linear range of 0-90.0 μM and the detection limit of F465 for Cu(2+) is 74.7 nM with a linear range of 0-6.0 μM (F508, 80.2 nM, 0-7.0 μM). We have demonstrated the application of the F465-Cu(2+) ensemble for detecting homocysteine in human serum and monitoring the activity of cystathionine β-synthase in vitro. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Supporting High School Student Accomplishment of Biology Content Using Interactive Computer-Based Curricular Case Studies

    Science.gov (United States)

    Oliver, Joseph Steve; Hodges, Georgia W.; Moore, James N.; Cohen, Allan; Jang, Yoonsun; Brown, Scott A.; Kwon, Kyung A.; Jeong, Sophia; Raven, Sara P.; Jurkiewicz, Melissa; Robertson, Tom P.

    2017-11-01

    Research into the efficacy of modules featuring dynamic visualizations, case studies, and interactive learning environments is reported here. This quasi-experimental 2-year study examined the implementation of three interactive computer-based instructional modules within a curricular unit covering cellular biology concepts in an introductory high school biology course. The modules featured dynamic visualizations and focused on three processes that underlie much of cellular biology: diffusion, osmosis, and filtration. Pre-tests and post-tests were used to assess knowledge growth across the unit. A mixture Rasch model analysis of the post-test data revealed two groups of students. In both years of the study, a large proportion of the students were classified as low-achieving based on their pre-test scores. The use of the modules in the Cell Unit in year 2 was associated with a much larger proportion of the students having transitioned to the high-achieving group than in year 1. In year 2, the same teachers taught the same concepts as year 1 but incorporated the interactive computer-based modules into the cell biology unit of the curriculum. In year 2, 67% of students initially classified as low-achieving were classified as high-achieving at the end of the unit. Examination of responses to assessments embedded within the modules as well as post-test items linked transition to the high-achieving group with correct responses to items that both referenced the visualization and the contextualization of that visualization within the module. This study points to the importance of dynamic visualization within contextualized case studies as a means to support student knowledge acquisition in biology.

  9. YAGM: a web tool for mining associated genes in yeast based on diverse biological associations.

    Science.gov (United States)

    Wu, Wei-Sheng; Wang, Chung-Ching; Jhou, Meng-Jhun; Wang, Yu-Cheng

    2015-01-01

    Investigating association between genes can be used in understanding the relations of genes in biological processes. STRING and GeneMANIA are two well-known web tools which can provide a list of associated genes of a query gene based on diverse biological associations such as co-expression, co-localization, co-citation and so on. However, the transcriptional regulation association and mutant phenotype association have not been used in these two web tools. Since the comprehensive transcription factor (TF)-gene binding data, TF-gene regulation data and mutant phenotype data are available in yeast, we developed a web tool called YAGM (Yeast Associated Genes Miner) which constructed the transcriptional regulation association, mutant phenotype association and five commonly used biological associations to mine a list of associated genes of a query yeast gene. In YAGM, we collected seven kinds of datasets including TF-gene binding (TFB) data, TF-gene regulation (TFR) data, mutant phenotype (MP) data, functional annotation (FA) data, physical interaction (PI) data, genetic interaction (GI) data, and literature evidence (LE) data. Then by using the hypergeometric test to calculate the association scores of all gene pairs in yeast, we constructed seven biological associations including two transcriptional regulation associations (TFB association and TFR association), MP association, FA association, PI association, GI association, and LE association. Moreover, the expression profile association from SPELL database was also included in YAGM. When using YAGM, users can input a query gene and choose any possible subsets of the eight biological associations, then a list of associated genes of the query gene will be returned based on the chosen biological associations. In this study, we presented the YAGM which provides eight biological associations for mining associated genes of a query gene in yeast. Among the eight biological associations constructed in YAGM, three (TFB

  10. Versatile micropipette technology based on deep reactive ion etching and anodic bonding for biological applications

    International Nuclear Information System (INIS)

    Lopez-Martinez, M J; Campo, E M; Esteve, J; Plaza, J A; Caballero, D; Errachid, A; Fernandez, E

    2009-01-01

    A novel, versatile and robust technology to manufacture transparent micropipettes, suitable for biological applications, is presented here. Up to three deep reactive ion etchings have been included in the manufacturing process, providing highly controlled geometry of reservoirs, connection cavities and inlet ports. Etching processes have been used for the definition of chip and reservoir and for nozzle release. Additionally, special design considerations have been developed to facilitate micro-to-macro fluidic connections. Implementation of anodic bonding to seal a glass substrate to the fluidic structure etched on Si, allowed observation of the flow inside the reservoir. Flow tests have been conducted by filling channels with different fluids. Flow was observed under an optical microscope, both during capillary filling and also during pumping. Dispensing has been demonstrated by functionalizing the surface of an AFM cantilever. Mechanical tests performed by piercing live mouse cells with FIB-sharpened micropipettes suggest the design is sturdy for biological piercing applications

  11. Analysis of carbon based materials under fusion relevant thermal loads

    International Nuclear Information System (INIS)

    Compan, Jeremie Saint-Helene

    2008-01-01

    Carbon based materials (CBMs) are used in fusion devices as plasma facing materials for decades. They have been selected due to the inherent advantages of carbon for fusion applications. The main ones are its low atomic number and the fact that it does not melt but sublimate (above 3000 C) under the planned working conditions. In addition, graphitic materials retain their mechanical properties at elevated temperatures and their thermal shock resistance is one of the highest, making them suitable for thermal management purpose during long or extremely short heat pulses. Nuclear grade fine grain graphite was the prime form of CBM which was set as a standard but when it comes to large fusion devices created nowadays, thermo-mechanical constraints created during transient heat loads (few GW.m-2 can be deposited in few ms) are so high that carbon/carbon composites (so-called Carbon Fiber Composites (CFCs)) have to be utilized. CFCs can achieve superior thermal conductivity as well as mechanical properties than fine grain graphite. However, all the thermo-mechanical properties of CFCs are highly dependent on the loading direction as a consequence of the graphite structure. In this work, the background on the anisotropy of the graphitic structures but also on the production of fine grain graphite and CFCs is highlighted, showing the major principles which are relevant for the further understanding of the study. Nine advanced CBMs were then compared in terms of microstructure and thermo-mechanical properties. Among them, two fine grain graphites were considered as useful reference materials to allow comparing advantages reached by the developed CFCs. The presented microstructural investigation methods permitted to make statements which can be applied for CFCs presenting similarities in terms of fiber architecture. Determination of the volumetric percentage of the major sub-units of CFCs, i.e. laminates, felt layers or needled fiber groups, lead to a better understanding on

  12. The underlying biological mechanisms of biocompatibility differences between bare and TiN-coated NiTi alloys.

    Science.gov (United States)

    Lifeng, Zhao; Yan, Hong; Dayun, Yang; Xiaoying, Lü; Tingfei, Xi; Deyuan, Zhang; Ying, Hong; Jinfeng, Yuan

    2011-04-01

    TiN coating has been demonstrated to improve the biocompatibility of bare NiTi alloys; however, essential biocompatibility differences between NiTi alloys before and after TiN coating are not known so far. In this study, to explore the underlying biological mechanisms of biocompatibility differences between them, the changes of bare and TiN-coated NiTi alloys in surface chemical composition, morphology, hydrophilicity, Ni ions release, cytotoxicity, apoptosis, and gene expression profiles were compared using energy-dispersive spectroscopy, scanning electron microscopy, contact angle, surface energy, Ni ions release analysis, the methylthiazoltetrazolium (MTT) method, flow cytometry and microarray methods, respectively. Pathways binding to networks and real-time polymerase chain reaction (PCR) were employed to analyze and validate the microarray data, respectively. It was found that, compared with the bare NiTi alloys, TiN coating significantly decreased Ni ions content on the surfaces of the NiTi alloys and reduced the release of Ni ions from the alloys, attenuated the inhibition of Ni ions to the expression of genes associated with anti-inflammatory, and also suppressed the promotion of Ni ions to the expression of apoptosis-related genes. Moreover, TiN coating distinctly improved the hydrophilicity and uniformity of the surfaces of the NiTi alloys, and contributed to the expression of genes participating in cell adhesion and other physiological activities. These results indicate that the TiN-coated NiTi alloys will help overcome the shortcomings of NiTi alloys used in clinical application currently, and can be expected to be a replacement of biomaterials for a medical device field.

  13. The underlying biological mechanisms of biocompatibility differences between bare and TiN-coated NiTi alloys

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Lifeng; Hong Yan; Yang Dayun; Lue Xiaoying [State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 (China); Xi Tingfei [Shenzhen Research Institute, Peking University, Shenzhen, 518055 (China); Deyuan, Zhang [R and D Center of Lifetech Scientific (Shenzhen) Co., Ltd, Shenzhen, 518057 (China); Hong Ying [Department of Gynecology and Obstetrics, Nanjing Drum-Tower Hospital, Nanjing, 210096 (China); Yuan Jinfeng, E-mail: luxy@seu.edu.cn [Department of Gynecology and Obstetrics, Xuanwu Hospital, Nanjing, 210096 (China)

    2011-04-15

    TiN coating has been demonstrated to improve the biocompatibility of bare NiTi alloys; however, essential biocompatibility differences between NiTi alloys before and after TiN coating are not known so far. In this study, to explore the underlying biological mechanisms of biocompatibility differences between them, the changes of bare and TiN-coated NiTi alloys in surface chemical composition, morphology, hydrophilicity, Ni ions release, cytotoxicity, apoptosis, and gene expression profiles were compared using energy-dispersive spectroscopy, scanning electron microscopy, contact angle, surface energy, Ni ions release analysis, the methylthiazoltetrazolium (MTT) method, flow cytometry and microarray methods, respectively. Pathways binding to networks and real-time polymerase chain reaction (PCR) were employed to analyze and validate the microarray data, respectively. It was found that, compared with the bare NiTi alloys, TiN coating significantly decreased Ni ions content on the surfaces of the NiTi alloys and reduced the release of Ni ions from the alloys, attenuated the inhibition of Ni ions to the expression of genes associated with anti-inflammatory, and also suppressed the promotion of Ni ions to the expression of apoptosis-related genes. Moreover, TiN coating distinctly improved the hydrophilicity and uniformity of the surfaces of the NiTi alloys, and contributed to the expression of genes participating in cell adhesion and other physiological activities. These results indicate that the TiN-coated NiTi alloys will help overcome the shortcomings of NiTi alloys used in clinical application currently, and can be expected to be a replacement of biomaterials for a medical device field.

  14. Aber-OWL: a framework for ontology-based data access in biology

    KAUST Repository

    Hoehndorf, Robert

    2015-01-28

    Background: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning. Results: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net. Conclusions: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

  15. The ability of biologically based wastewater treatment systems to remove emerging organic contaminants--a review.

    Science.gov (United States)

    Garcia-Rodríguez, Aida; Matamoros, Víctor; Fontàs, Clàudia; Salvadó, Victòria

    2014-10-01

    Biologically based wastewater treatment systems are considered a sustainable, cost-effective alternative to conventional wastewater treatment systems. These systems have been used and studied for the treatment of urban sewage from small communities, and recently, it has been reported that they can also effectively remove emerging organic contaminants (EOCs). EOCs are a new group of unregulated contaminants which include pharmaceutical and personal care products, some pesticides, veterinary products, and industrial compounds among others that are thought to have long-term adverse effects on human health and ecosystems. This review is focused on reporting the ability of biologically based wastewater treatment systems to remove EOCs and the main elimination mechanisms and degradation processes (i.e., biodegradation, photodegradation, phytoremediation, and sorption) taking place in constructed wetlands, ponds, and Daphnia and fungal reactors.

  16. Enhancement of COPD biological networks using a web-based collaboration interface [v2; ref status: indexed, http://f1000r.es/5ew

    Directory of Open Access Journals (Sweden)

    The sbv IMPROVER project team (in alphabetical order

    2015-05-01

    Full Text Available The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website (https://bionet.sbvimprover.com/ and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD

  17. MSD-MAP: A Network-Based Systems Biology Platform for Predicting Disease-Metabolite Links.

    Science.gov (United States)

    Wathieu, Henri; Issa, Naiem T; Mohandoss, Manisha; Byers, Stephen W; Dakshanamurthy, Sivanesan

    2017-01-01

    Cancer-associated metabolites result from cell-wide mechanisms of dysregulation. The field of metabolomics has sought to identify these aberrant metabolites as disease biomarkers, clues to understanding disease mechanisms, or even as therapeutic agents. This study was undertaken to reliably predict metabolites associated with colorectal, esophageal, and prostate cancers. Metabolite and disease biological action networks were compared in a computational platform called MSD-MAP (Multi Scale Disease-Metabolite Association Platform). Using differential gene expression analysis with patient-based RNAseq data from The Cancer Genome Atlas, genes up- or down-regulated in cancer compared to normal tissue were identified. Relational databases were used to map biological entities including pathways, functions, and interacting proteins, to those differential disease genes. Similar relational maps were built for metabolites, stemming from known and in silico predicted metabolite-protein associations. The hypergeometric test was used to find statistically significant relationships between disease and metabolite biological signatures at each tier, and metabolites were assessed for multi-scale association with each cancer. Metabolite networks were also directly associated with various other diseases using a disease functional perturbation database. Our platform recapitulated metabolite-disease links that have been empirically verified in the scientific literature, with network-based mapping of jointly-associated biological activity also matching known disease mechanisms. This was true for colorectal, esophageal, and prostate cancers, using metabolite action networks stemming from both predicted and known functional protein associations. By employing systems biology concepts, MSD-MAP reliably predicted known cancermetabolite links, and may serve as a predictive tool to streamline conventional metabolomic profiling methodologies. Copyright© Bentham Science Publishers; For any

  18. [Impact of biologically important anions on reactive oxygen species formation in water under the effect of non-ionizing physical agents].

    Science.gov (United States)

    Gudkov, S V; Ivanov, V E; Karp, O É; Chernikov, A V; Belosludtsev, K N; Bobylev, A G; Astashev, M E; Gapeev, A B; Bruskov, V I

    2014-01-01

    The influence of biologically relevant anions (succinate, acetate, citrate, chloride, bicarbonate, hydroorthophosphate, dihydroorthophosphate, nitrite, nitrate) on the formation of hydrogen peroxide and hydroxyl radicals in water was studied under the effect of non-ionizing radiation: heat, laser light with a wavelength of 632.8 nm, corresponding to the maximum absorption of molecular oxygen, and electromagnetic radiation of extremely high frequencies. It has been established that various anions may both inhibit the formation of reactive oxygen species and increase it. Bicarbonate and sulfate anions included in the biological fluids' and medicinal mineral waters have significant, but opposite effects on reactive oxygen species production. Different molecular mechanisms of reactive oxygen species formation are considered under the action of the investigated physical factors involving these anions, which may influence the biological processes by signal-regulatory manner and provide a healing effect in physical therapy.

  19. Intelligence-based anti-doping from an equine biological passport.

    Science.gov (United States)

    Cawley, Adam T; Keledjian, John

    2017-09-01

    The move towards personalized medicine derived from individually focused clinical chemistry measurements has been translated by the human anti-doping movement over the past decade into developing the athlete biological passport. There is considerable potential for animal sports to adapt this model to facilitate an intelligence-based anti-doping system. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  20. Effectiveness of Biology-Based Methods for Inhibiting Orthodontic Tooth Movement. A Systematic Review.

    Science.gov (United States)

    Cadenas de Llano-Pérula, M; Yañez-Vico, R M; Solano-Reina, E; Palma-Fernandez, J C; Iglesias-Linares, A

    Several experimental studies in the literature have tested different biology-based methods for inhibiting or decreasing orthodontic tooth movement (OTM) in humans. This systematic review investigated the effects of these interventions on the rate of tooth movement. Electronic [MedLine; SCOPUS; Cochrane Library; OpenGrey;Web of Science] and manual searches were conducted up to January 26th, 2016 in order to identify publications of clinical trials that compared the decreasing or inhibiting effects of different biology-based methods over OTM in humans. A primary outcome (rate of OTM deceleration/inhibition) and a number of secondary outcomes were examined (clinical applicability, orthodontic force used, possible side effects). Two reviewers selected the studies complying with the eligibility criteria (PICO format) and assessed risk of bias [Cochrane Collaboration's tool]. Data collection and analysis were performed following the Cochrane recommendations. From the initial electronic search, 3726 articles were retrieved and 5 studies were finally included. Two types of biology-based techniques used to reduce the rate of OTM in humans were described: pharmacological and low-level laser therapy. In the first group, human Relaxin was compared to a placebo and administered orally. It was described as having no effect on the inhibition of OTM in humans after 32 days, while the drug tenoxicam, injected locally, inhibited the rate of OTM by up to 10% in humans after 42 days. In the second group, no statistically significant differences were reported, compared to placebo, for the rate of inhibition of OTM in humans after 90 days of observation when a 860 nm continuous wave GaAlA slow-level laser was used. The currently available data do not allow us to draw definitive conclusions about the use of various pharmacological substances and biology-based therapies in humans able to inhibit or decrease the OTM rate. There is an urgent need for more sound well-designed randomized

  1. Do biological-based strategies hold promise to biofouling control in MBRs?

    KAUST Repository

    Malaeb, Lilian

    2013-10-01

    Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of

  2. Do biological-based strategies hold promise to biofouling control in MBRs?

    Science.gov (United States)

    Malaeb, Lilian; Le-Clech, Pierre; Vrouwenvelder, Johannes S; Ayoub, George M; Saikaly, Pascal E

    2013-10-01

    Biofouling in membrane bioreactors (MBRs) remains a primary challenge for their wider application, despite the growing acceptance of MBRs worldwide. Research studies on membrane fouling are extensive in the literature, with more than 200 publications on MBR fouling in the last 3 years; yet, improvements in practice on biofouling control and management have been remarkably slow. Commonly applied cleaning methods are only partially effective and membrane replacement often becomes frequent. The reason for the slow advancement in successful control of biofouling is largely attributed to the complex interactions of involved biological compounds and the lack of representative-for-practice experimental approaches to evaluate potential effective control strategies. Biofouling is driven by microorganisms and their associated extra-cellular polymeric substances (EPS) and microbial products. Microorganisms and their products convene together to form matrices that are commonly treated as a black box in conventional control approaches. Biological-based antifouling strategies seem to be a promising constituent of an effective integrated control approach since they target the essence of biofouling problems. However, biological-based strategies are in their developmental phase and several questions should be addressed to set a roadmap for translating existing and new information into sustainable and effective control techniques. This paper investigates membrane biofouling in MBRs from the microbiological perspective to evaluate the potential of biological-based strategies in offering viable control alternatives. Limitations of available control methods highlight the importance of an integrated anti-fouling approach including biological strategies. Successful development of these strategies requires detailed characterization of microorganisms and EPS through the proper selection of analytical tools and assembly of results. Existing microbiological/EPS studies reveal a number of

  3. A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

    Science.gov (United States)

    Jafari, Mohieddin; Ansari-Pour, Naser; Azimzadeh, Sadegh; Mirzaie, Mehdi

    It is nearly half a century past the age of the introduction of the Central Dogma (CD) of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

  4. Pore Pressure Under A Gravity Based Structure Under The Influence Of Waves

    DEFF Research Database (Denmark)

    Christensen, Erik Damgaard; Carstensen, Stefan; Madsen, Mikael Thyge

    2017-01-01

    based foundation. This leads typically to very conservative designs in order to accommodate the uncertainties in the procedure. The experiments shall lead to better prediction models based on for instance CFD model’s with the direct calculation of pressure variations in the seabed and any erosion...

  5. Improving creative thinking skills and scientific attitude through inquiry-based learning in basic biology lecture toward student of biology education

    Directory of Open Access Journals (Sweden)

    Bayu Sandika

    2018-03-01

    Full Text Available Inquiry-based learning is one of the learning methods which can provide an active and authentic scientific learning process in order students are able to improve the creative thinking skills and scientific attitude. This study aims at improving creative thinking skills and scientific attitude through inquiry-based learning in basic biology lecture toward students of biology education at the Institut Agama Islam Negeri (IAIN Jember, Indonesia. This study is included in a descriptive quantitative research. The research focused on the topic of cell transport which was taught toward 25 students of Biology 2 class from 2017 academic year of Biology Education Department at the IAIN Jember. The learning process was conducted in two meetings in November 2017. The enhancement of students' creative thinking skills was determined by one group pre-test and post-test research design using test instrument meanwhile the scientific attitude focused on curiosity and objectivity were observed using the non-test instrument. Research result showed that students' creative thinking skills enhanced highly and students' scientific attitude improved excellently through inquiry-based learning in basic biology lecture.

  6. Vicus: Exploiting local structures to improve network-based analysis of biological data.

    Directory of Open Access Journals (Sweden)

    Bo Wang

    2017-10-01

    Full Text Available Biological networks entail important topological features and patterns critical to understanding interactions within complicated biological systems. Despite a great progress in understanding their structure, much more can be done to improve our inference and network analysis. Spectral methods play a key role in many network-based applications. Fundamental to spectral methods is the Laplacian, a matrix that captures the global structure of the network. Unfortunately, the Laplacian does not take into account intricacies of the network's local structure and is sensitive to noise in the network. These two properties are fundamental to biological networks and cannot be ignored. We propose an alternative matrix Vicus. The Vicus matrix captures the local neighborhood structure of the network and thus is more effective at modeling biological interactions. We demonstrate the advantages of Vicus in the context of spectral methods by extensive empirical benchmarking on tasks such as single cell dimensionality reduction, protein module discovery and ranking genes for cancer subtyping. Our experiments show that using Vicus, spectral methods result in more accurate and robust performance in all of these tasks.

  7. Vicus: Exploiting local structures to improve network-based analysis of biological data.

    Science.gov (United States)

    Wang, Bo; Huang, Lin; Zhu, Yuke; Kundaje, Anshul; Batzoglou, Serafim; Goldenberg, Anna

    2017-10-01

    Biological networks entail important topological features and patterns critical to understanding interactions within complicated biological systems. Despite a great progress in understanding their structure, much more can be done to improve our inference and network analysis. Spectral methods play a key role in many network-based applications. Fundamental to spectral methods is the Laplacian, a matrix that captures the global structure of the network. Unfortunately, the Laplacian does not take into account intricacies of the network's local structure and is sensitive to noise in the network. These two properties are fundamental to biological networks and cannot be ignored. We propose an alternative matrix Vicus. The Vicus matrix captures the local neighborhood structure of the network and thus is more effective at modeling biological interactions. We demonstrate the advantages of Vicus in the context of spectral methods by extensive empirical benchmarking on tasks such as single cell dimensionality reduction, protein module discovery and ranking genes for cancer subtyping. Our experiments show that using Vicus, spectral methods result in more accurate and robust performance in all of these tasks.

  8. Automated numerical simulation of biological pattern formation based on visual feedback simulation framework.

    Science.gov (United States)

    Sun, Mingzhu; Xu, Hui; Zeng, Xingjuan; Zhao, Xin

    2017-01-01

    There are various fantastic biological phenomena in biological pattern formation. Mathematical modeling using reaction-diffusion partial differential equation systems is employed to study the mechanism of pattern formation. However, model parameter selection is both difficult and time consuming. In this paper, a visual feedback simulation framework is proposed to calculate the parameters of a mathematical model automatically based on the basic principle of feedback control. In the simulation framework, the simulation results are visualized, and the image features are extracted as the system feedback. Then, the unknown model parameters are obtained by comparing the image features of the simulation image and the target biological pattern. Considering two typical applications, the visual feedback simulation framework is applied to fulfill pattern formation simulations for vascular mesenchymal cells and lung development. In the simulation framework, the spot, stripe, labyrinthine patterns of vascular mesenchymal cells, the normal branching pattern and the branching pattern lacking side branching for lung branching are obtained in a finite number of iterations. The simulation results indicate that it is easy to achieve the simulation targets, especially when the simulation patterns are sensitive to the model parameters. Moreover, this simulation framework can expand to other types of biological pattern formation.

  9. Synthesis and biological activity evaluation of hydrazone derivatives based on a Tröger's base skeleton

    Czech Academy of Sciences Publication Activity Database

    Kaplánek, R.; Havlík, M.; Dolenský, B.; Rak, J.; Džubák, P.; Konečný, P.; Hajdúch, M.; Králová, Jarmila; Král, V.

    2015-01-01

    Roč. 23, č. 7 (2015), s. 1651-1659 ISSN 0968-0896 R&D Projects: GA ČR(CZ) GAP303/11/1291 Grant - others:GA MŠk(CZ) EE2.3.30.0060; GA MŠk(CZ) LO1304 Program:EE; LD Institutional support: RVO:68378050 Keywords : Anticancer agents * Cancer treatment * Complexation studies * Hydrazone * Troger's base Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.923, year: 2015

  10. Ultrasensitive Hybridization-Based ELISA Method for the Determination of Phosphorodiamidate Morpholino Oligonucleotides in Biological samples.

    Science.gov (United States)

    Burki, Umar; Straub, Volker

    2017-01-01

    Determining the concentration of oligonucleotide in biological samples such as tissue lysate and serum is essential for determining the biodistribution and pharmacokinetic profile, respectively. ELISA-based assays have shown far greater sensitivities compared to other methods such as HPLC and LC/MS. Here, we describe a novel ultrasensitive hybridization-based ELISA method for quantitating morpholino oligonucleotides in mouse tissue lysate and serum samples. The assay has a linear detection range of 5-250 pM (R2 > 0.99).

  11. Transients and cooperative action of β-carotine, vitamine E and vitamine C in biological systems in vitro under irradiation

    International Nuclear Information System (INIS)

    Getof, N.; Platzer, I.; Winkelbauer, C.

    1998-01-01

    Complete text of publication follows. In the scope of clinical studies in the USA it has been established that β-carotine (β car) and vitamine A (vit A; retinol) give rise to lung cancer and cardiovascular diseases on humans. The consumption of vitamine E (vit E) and β-carotine provokes lung cancer and other types of tumors on male smokers. This effect increases even significantly by a simultaneous consumption of alcohol. In contrary to these results there are other scientists, who did not observe any increase of the rate of lung cancer or other tumors by the consumption of β-car or vit E. Based on these contradictory statements experiments following two pathways were performed: Pulse radiolysis studies on radical cations and radical anions of β-car and vit E Investigations on baeteria (E. coli AB 1157) and cell cultures (SCC VII): their survival was studied as a function of the absorbed dose in the abscence and in the presence of the above mentioned vitamines and vitamine C (vit C). From our extensive studies we obtain following conclusions: - Metabolic changes in normal cells could probably be initiated by the radical cation of β-carotine (β-car '+) resulting from the action of β-car as an antioxidant. - Vitamine E can repair β-car '+ by electron transfer, forming the radical cation of vit E (vit E '+), whose biological action is yet unknown. - Vitamine C (ascorbate) is able to repair both, the β-caz'+ and the vit E'+ by electron transfer (cascade electron transfer), resulting in ascorbate radical, which can disproportionate to vit C and dehydroascorbic acid (DHA). The last one can be converted again enzymatically into ascorbic acid

  12. Fractional Calculus-Based Modeling of Electromagnetic Field Propagation in Arbitrary Biological Tissue

    Directory of Open Access Journals (Sweden)

    Pietro Bia

    2016-01-01

    Full Text Available The interaction of electromagnetic fields and biological tissues has become a topic of increasing interest for new research activities in bioelectrics, a new interdisciplinary field combining knowledge of electromagnetic theory, modeling, and simulations, physics, material science, cell biology, and medicine. In particular, the feasibility of pulsed electromagnetic fields in RF and mm-wave frequency range has been investigated with the objective to discover new noninvasive techniques in healthcare. The aim of this contribution is to illustrate a novel Finite-Difference Time-Domain (FDTD scheme for simulating electromagnetic pulse propagation in arbitrary dispersive biological media. The proposed method is based on the fractional calculus theory and a general series expansion of the permittivity function. The spatial dispersion effects are taken into account, too. The resulting formulation is explicit, it has a second-order accuracy, and the need for additional storage variables is minimal. The comparison between simulation results and those evaluated by using an analytical method based on the Fourier transformation demonstrates the accuracy and effectiveness of the developed FDTD model. Five numerical examples showing the plane wave propagation in a variety of dispersive media are examined.

  13. Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

    Science.gov (United States)

    Lan, Haidong; Chan, Yuandong; Xu, Kai; Schmidt, Bertil; Peng, Shaoliang; Liu, Weiguo

    2016-07-19

    Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data parallelism, thread-level coarse-grained parallelism, and vector-level fine-grained parallelism. Furthermore, we re-organize the sequence datasets and use Xeon Phi shuffle operations to improve I/O efficiency. Evaluations show that our method achieves a peak overall performance up to 220 GCUPS for scanning real protein sequence databanks on a single node consisting of two Intel E5-2620 CPUs and two Intel Xeon Phi 7110P cards. It also exhibits good scalability in terms of sequence length and size, and number of compute nodes for both database scanning and multiple sequence alignment. Furthermore, the achieved performance is highly competitive in comparison to optimized Xeon Phi and GPU implementations. Our implementation is available at https://github.com/turbo0628/LSDBS-mpi .

  14. Students Mental Representation of Biology Diagrams/Pictures Conventions Based on Formation of Causal Network

    Science.gov (United States)

    Sampurno, A. W.; Rahmat, A.; Diana, S.

    2017-09-01

    Diagrams/pictures conventions is one form of visual media that often used to assist students in understanding the biological concepts. The effectiveness of use diagrams/pictures in biology learning at school level has also been mostly reported. This study examines the ability of high school students in reading diagrams/pictures biological convention which is described by Mental Representation based on formation of causal networks. The study involved 30 students 11th grade MIA senior high school Banten Indonesia who are studying the excretory system. MR data obtained by Instrument worksheet, developed based on CNET-protocol, in which there are diagrams/drawings of nephron structure and urinary mechanism. Three patterns formed MR, namely Markov chain, feedback control with a single measurement, and repeated feedback control with multiple measurement. The third pattern is the most dominating pattern, differences in the pattern of MR reveal the difference in how and from which point the students begin to uncover important information contained in the diagram to establish a causal networks. Further analysis shows that a difference in the pattern of MR relate to how complex the students process the information contained in the diagrams/pictures.

  15. Challenges of diatom-based biological monitoring and assessment of streams in developing countries.

    Science.gov (United States)

    Bere, Taurai

    2016-03-01

    Stream biomonitoring tools are largely lacking for many developing countries, resulting in adoption of tools developed from other countries/regions. In many instances, however, the applicability of adopted tools to the new system has not been explicitly evaluated. The objective of this study was to test the applicability of foreign diatom-based water quality assessment indices to streams in Zimbabwe, with the view to highlight challenges being faced in diatom-based biological monitoring in this developing country. The study evaluated the relationship between measured water quality variables and diatom index scores and observed some degree of concordance between water quality variables and diatom index scores emphasising the importance of diatom indices in characterisation and monitoring of stream ecological conditions in developing countries. However, ecological requirements of some diatom species need to be clarified and incorporated in a diatom-based water quality assessment protocol unique to these regions. Resources should be channelled towards tackling challenges associated with diatom-based biological monitoring, principally taxonomic studies, training of skilled labour and acquiring and maintaining the necessary infrastructure. Meanwhile, simpler coarse taxonomy-based rapid bioassessment protocol, which is less time and resource consuming and requires less specialised manpower, can be developed for the country.

  16. A technique for measuring oxygen saturation in biological tissues based on diffuse optical spectroscopy

    Science.gov (United States)

    Kleshnin, Mikhail; Orlova, Anna; Kirillin, Mikhail; Golubiatnikov, German; Turchin, Ilya

    2017-07-01

    A new approach to optical measuring blood oxygen saturation was developed and implemented. This technique is based on an original three-stage algorithm for reconstructing the relative concentration of biological chromophores (hemoglobin, water, lipids) from the measured spectra of diffusely scattered light at different distances from the probing radiation source. The numerical experiments and approbation of the proposed technique on a biological phantom have shown the high reconstruction accuracy and the possibility of correct calculation of hemoglobin oxygenation in the presence of additive noise and calibration errors. The obtained results of animal studies have agreed with the previously published results of other research groups and demonstrated the possibility to apply the developed technique to monitor oxygen saturation in tumor tissue.

  17. Optical Antenna-Based Fluorescence Correlation Spectroscopy to Probe the Nanoscale Dynamics of Biological Membranes.

    Science.gov (United States)

    Winkler, Pamina M; Regmi, Raju; Flauraud, Valentin; Brugger, Jürgen; Rigneault, Hervé; Wenger, Jérôme; García-Parajo, María F

    2018-01-04

    The plasma membrane of living cells is compartmentalized at multiple spatial scales ranging from the nano- to the mesoscale. This nonrandom organization is crucial for a large number of cellular functions. At the nanoscale, cell membranes organize into dynamic nanoassemblies enriched by cholesterol, sphingolipids, and certain types of proteins. Investigating these nanoassemblies known as lipid rafts is of paramount interest in fundamental cell biology. However, this goal requires simultaneous nanometer spatial precision and microsecond temporal resolution, which is beyond the reach of common microscopes. Optical antennas based on metallic nanostructures efficiently enhance and confine light into nanometer dimensions, breaching the diffraction limit of light. In this Perspective, we discuss recent progress combining optical antennas with fluorescence correlation spectroscopy (FCS) to monitor microsecond dynamics at nanoscale spatial dimensions. These new developments offer numerous opportunities to investigate lipid and protein dynamics in both mimetic and native biological membranes.

  18. A Biologically-Based Alternative Water Processor for Long Duration Space Missions

    Science.gov (United States)

    Barta, Daniel J.; Pickering, Karen D.; Meyer, Caitlin; Pensinger, Stuart; Vega, Leticia; Flynn, Michael; Jackson, Andrew; Wheeler, Raymond

    2015-01-01

    A wastewater recovery system has been developed that combines novel biological and physicochemical components for recycling wastewater on long duration space missions. Functionally, this Alternative Water Processor (AWP) would replace the Urine Processing Assembly on the International Space Station and reduce or eliminate the need for the multifiltration beds of the Water Processing Assembly (WPA). At its center are two unique game changing technologies: 1) a biological water processor (BWP) to mineralize organic forms of carbon and nitrogen and 2) an advanced membrane processor (Forward Osmosis Secondary Treatment) for removal of solids and inorganic ions. The AWP is designed for recycling larger quantities of wastewater from multiple sources expected during future exploration missions, including urine, hygiene (hand wash, shower, oral and shave) and laundry. The BWP utilizes a single-stage membrane-aerated biological reactor for simultaneous nitrification and denitrification. The Forward Osmosis Secondary Treatment (FOST) system uses a combination of forward osmosis (FO) and reverse osmosis (RO), is resistant to biofouling and can easily tolerate wastewaters high in non-volatile organics and solids associated with shower and/or hand washing. The BWP was operated continuously for over 300 days. After startup, the mature biological system averaged 85% organic carbon removal and 44% nitrogen removal, close to maximum based on available carbon. The FOST has averaged 93% water recovery, with a maximum of 98%. If the wastewater is slighty acidified, ammonia rejection is optimal. This paper will provide a description of the technology and summarize results from ground-based testing using real wastewater.

  19. Organisation of biological research carried out in the United States by the A.E.C. or under her contract (1960)

    International Nuclear Information System (INIS)

    Pellerin, J.

    1960-01-01

    This report is based on information gathered in the course of a trip to the United States, in November and December 1958 which consisted chiefly of visits to the main biological and medical research laboratories and discussions with the heads of these establishments. A description is given of the general organisation of the Atomic Energy Commission's Division of Biology and Medicine, and of the distribution of responsibility for radiation protection work and for biological, medical and agricultural research amongst the various Services attached to it; this is followed by a more detailed account of the activities carried on in this field at the great national laboratories. Finally, the systems of collaboration set up with external research organisations in the form of research contracts are examined, together with the substantial help provided by the A.E.C. for biological, medical and agricultural research in general, owing to a systematic policy of subsidising the distribution of radioisotopes for this purpose. (author) [fr

  20. Content-based music recommendation using underlying music preference structure

    OpenAIRE

    Soleymani M.; Aljanaki A.; Wiering F.; Veltkamp R.C.

    2015-01-01

    The cold start problem for new users or items is a great challenge for recommender systems. New items can be positioned within the existing items using a similarity metric to estimate their ratings. However, the calculation of similarity varies by domain and available resources. In this paper, we propose a content-based music recommender system which is based on a set of attributes derived from psychological studies of music preference. These five attributes, namely, Mellow, Unpretentious, So...

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

    Directory of Open Access Journals (Sweden)

    Dale L. Beach

    2015-08-01

    Full Text Available Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic “parts,” students construct a “reporter plasmid” expressing a reporter gene (GFP controlled by a hybrid promoter regulated by the lac-repressor protein (lacI. In combination with a “sensor plasmid,” the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey and end (post-survey of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05 for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses. Editor's Note:The ASM advocates that students must successfully demonstrate the ability to explain and practice safe

  2. Biological-based optimization and volumetric modulated arc therapy delivery for stereotactic body radiation therapy

    International Nuclear Information System (INIS)

    Diot, Quentin; Kavanagh, Brian; Timmerman, Robert; Miften, Moyed

    2012-01-01

    Purpose: To describe biological-based optimization and Monte Carlo (MC) dose calculation-based treatment planning for volumetric modulated arc therapy (VMAT) delivery of stereotactic body radiation therapy (SBRT) in lung, liver, and prostate patients. Methods: Optimization strategies and VMAT planning parameters using a biological-based optimization MC planning system were analyzed for 24 SBRT patients. Patients received a median dose of 45 Gy [range, 34-54 Gy] for lung tumors in 1-5 fxs and a median dose of 52 Gy [range, 48-60 Gy] for liver tumors in 3-6 fxs. Prostate patients received a fractional dose of 10 Gy in 5 fxs. Biological-cost functions were used for plan optimization, and its dosimetric quality was evaluated using the conformity index (CI), the conformation number (CN), the ratio of the volume receiving 50% of the prescription dose over the planning target volume (Rx/PTV50). The quality and efficiency of the delivery were assessed according to measured quality assurance (QA) passing rates and delivery times. For each disease site, one patient was replanned using physical cost function and compared to the corresponding biological plan. Results: Median CI, CN, and Rx/PTV50 for all 24 patients were 1.13 (1.02-1.28), 0.79 (0.70-0.88), and 5.3 (3.1-10.8), respectively. The median delivery rate for all patients was 410 MU/min with a maximum possible rate of 480 MU/min (85%). Median QA passing rate was 96.7%, and it did not significantly vary with the tumor site. Conclusions: VMAT delivery of SBRT plans optimized using biological-motivated cost-functions result in highly conformal dose distributions. Plans offer shorter treatment-time benefits and provide efficient dose delivery without compromising the plan conformity for tumors in the prostate, lung, and liver, thereby improving patient comfort and clinical throughput. The short delivery times minimize the risk of patient setup and intrafraction motion errors often associated with long SBRT treatment

  3. Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

    Directory of Open Access Journals (Sweden)

    de los Reyes Benildo G

    2008-04-01

    Full Text Available Abstract Background Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths and depths, while databases contain biological information based on established facts or published data. Integrating these complementary datasets helps infer a mutually consistent transcriptional regulatory network (TRN with strong similarity to the structure of the underlying genetic regulatory modules. Decomposing the TRN into a small set of recurring regulatory patterns, called network motifs (NM, facilitates the inference. Identifying NMs defined by specific transcription factors (TF establishes the framework structure of a TRN and allows the inference of TF-target gene relationship. This paper introduces a computational framework for utilizing data from multiple sources to infer TF-target gene relationships on the basis of NMs. The data include time course gene expression profiles, genome-wide location analysis data, binding sequence data, and gene ontology (GO information. Results The proposed computational framework was tested using gene expression data associated with cell cycle progression in yeast. Among 800 cell cycle related genes, 85 were identified as candidate TFs and classified into four previously defined NMs. The NMs for a subset of TFs are obtained from literature. Support vector machine (SVM classifiers were used to estimate NMs for the remaining TFs. The potential downstream target genes for the TFs were clustered into 34 biologically significant groups. The relationships between TFs and potential target gene clusters were examined by training recurrent neural networks whose topologies mimic the NMs to which the TFs are classified. The identified relationships between TFs and gene clusters were evaluated using the following biological validation and statistical analyses: (1 Gene set enrichment

  4. Data mining and biological sample exportation from South Africa: A new wave of bioexploitation under the guise of clinical care?

    Science.gov (United States)

    Staunton, Ciara; Moodley, Keymanthri

    2016-01-07

    Discovery Health, one of the leading healthcare funders in South Africa (SA), will offer genetic testing to its members for USD250 (approximately ZAR3 400) per test from 2016. On the surface, this appears to be innovative and futuristic. However, a deeper look at this announcement reveals considerable problems in the exportation of biological samples and data out of SA, and brings into sharp focus the lack of protection in place for potential donors. In return for a reduced-cost genetic test, which will nevertheless be billed to a member's savings plan, data from the patient's results, and probably the sample itself, will be sent to the USA for storage, research purposes and possible commercial use, with no further benefit for the patient. This development has demonstrated the need for more stringent protection of the movement of biological samples and data out of SA, particularly with reference to consenting procedures, material transfer agreements, and the export of biological data themselves.

  5. WE-B-304-02: Treatment Planning Evaluation and Optimization Should Be Biologically and Not Dose/volume Based

    International Nuclear Information System (INIS)

    Deasy, J.

    2015-01-01

    The ultimate goal of radiotherapy treatment planning is to find a treatment that will yield a high tumor control probability (TCP) with an acceptable normal tissue complication probability (NTCP). Yet most treatment planning today is not based upon optimization of TCPs and NTCPs, but rather upon meeting physical dose and volume constraints defined by the planner. It has been suggested that treatment planning evaluation and optimization would be more effective if they were biologically and not dose/volume based, and this is the claim debated in this month’s Point/Counterpoint. After a brief overview of biologically and DVH based treatment planning by the Moderator Colin Orton, Joseph Deasy (for biological planning) and Charles Mayo (against biological planning) will begin the debate. Some of the arguments in support of biological planning include: this will result in more effective dose distributions for many patients DVH-based measures of plan quality are known to have little predictive value there is little evidence that either D95 or D98 of the PTV is a good predictor of tumor control sufficient validated outcome prediction models are now becoming available and should be used to drive planning and optimization Some of the arguments against biological planning include: several decades of experience with DVH-based planning should not be discarded we do not know enough about the reliability and errors associated with biological models the radiotherapy community in general has little direct experience with side by side comparisons of DVH vs biological metrics and outcomes it is unlikely that a clinician would accept extremely cold regions in a CTV or hot regions in a PTV, despite having acceptable TCP values Learning Objectives: To understand dose/volume based treatment planning and its potential limitations To understand biological metrics such as EUD, TCP, and NTCP To understand biologically based treatment planning and its potential limitations

  6. Convex reformulation of biologically-based multi-criteria intensity-modulated radiation therapy optimization including fractionation effects.

    Science.gov (United States)

    Hoffmann, Aswin L; den Hertog, Dick; Siem, Alex Y D; Kaanders, Johannes H A M; Huizenga, Henk

    2008-11-21

    Finding fluence maps for intensity-modulated radiation therapy (IMRT) can be formulated as a multi-criteria optimization problem for which Pareto optimal treatment plans exist. To account for the dose-per-fraction effect of fractionated IMRT, it is desirable to exploit radiobiological treatment plan evaluation criteria based on the linear-quadratic (LQ) cell survival model as a means to balance the radiation benefits and risks in terms of biologic response. Unfortunately, the LQ-model-based radiobiological criteria are nonconvex functions, which make the optimization problem hard to solve. We apply the framework proposed by Romeijn et al (2004 Phys. Med. Biol. 49 1991-2013) to find transformations of LQ-model-based radiobiological functions and establish conditions under which transformed functions result in equivalent convex criteria that do not change the set of Pareto optimal treatment plans. The functions analysed are: the LQ-Poisson-based model for tumour control probability (TCP) with and without inter-patient heterogeneity in radiation sensitivity, the LQ-Poisson-based relative seriality s-model for normal tissue complication probability (NTCP), the equivalent uniform dose (EUD) under the LQ-Poisson model and the fractionation-corrected Probit-based model for NTCP according to Lyman, Kutcher and Burman. These functions differ from those analysed before in that they cannot be decomposed into elementary EUD or generalized-EUD functions. In addition, we show that applying increasing and concave transformations to the convexified functions is beneficial for the piecewise approximation of the Pareto efficient frontier.

  7. Foreword to 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', a special issue in Honour of Fumio Arisaka's 70th birthday.

    Science.gov (United States)

    Hall, Damien; Takagi, Junichi; Nakamura, Haruki

    2018-03-02

    This issue of Biophysical Reviews, titled 'Multiscale structural biology: biophysical principles and mechanisms underlying the action of bio-nanomachines', is a collection of articles dedicated in honour of Professor Fumio Arisaka's 70th birthday. Initially, working in the fields of haemocyanin and actin filament assembly, Fumio went on to publish important work on the elucidation of structural and functional aspects of T4 phage biology. As his career has transitioned levels of complexity from proteins (hemocyanin) to large protein complexes (actin) to even more massive bio-nanomachinery (phage), it is fitting that the subject of this special issue is similarly reflective of his multiscale approach to structural biology. This festschrift contains articles spanning biophysical structure and function from the bio-molecular through to the bio-nanomachine level.

  8. Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology

    Science.gov (United States)

    Hucka, M.

    2015-09-01

    In common with many fields, including astronomy, a vast number of software tools for computational modeling and simulation are available today in systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Despite working with different software tools, researchers want to disseminate their work widely as well as reuse and extend the models of other researchers. This situation led in the year 2000 to an effort to create a tool-independent, machine-readable file format for representing models: SBML, the Systems Biology Markup Language. SBML has since become the de facto standard for its purpose. Its success and general approach has inspired and influenced other community-oriented standardization efforts in systems biology. Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize successful community-based standards. I draw on personal experiences from the development of SBML and summarize some of the lessons learned, in the hope that this may be useful to other groups seeking to develop open standards in a community-oriented fashion.

  9. Societal Risk Evaluation Scheme (SRES: Scenario-Based Multi-Criteria Evaluation of Synthetic Biology Applications.

    Directory of Open Access Journals (Sweden)

    Christopher L Cummings

    Full Text Available Synthetic biology (SB applies engineering principles to biology for the construction of novel biological systems designed for useful purposes. From an oversight perspective, SB products come with significant uncertainty. Yet there is a need to anticipate and prepare for SB applications before deployment. This study develops a Societal Risk Evaluation Scheme (SRES in order to advance methods for anticipatory governance of emerging technologies such as SB. The SRES is based upon societal risk factors that were identified as important through a policy Delphi study. These factors range from those associated with traditional risk assessment, such as health and environmental consequences, to broader features of risk such as those associated with reversibility, manageability, anticipated levels of public concern, and uncertainty. A multi-disciplinary panel with diverse perspectives and affiliations assessed four case studies of SB using the SRES. Rankings of the SRES components are compared within and across the case studies. From these comparisons, we found levels of controllability and familiarity associated with the cases to be important for overall SRES rankings. From a theoretical standpoint, this study illustrates the applicability of the psychometric paradigm to evaluating SB cases. In addition, our paper describes how the SRES can be incorporated into anticipatory governance models as a screening tool to prioritize research, information collection, and dialogue in the face of the limited capacity of governance systems. To our knowledge, this is the first study to elicit data on specific cases of SB with the goal of developing theory and tools for risk governance.

  10. Nation-Based Occurrence and Endogenous Biological Reduction of Mycotoxins in Medicinal Herbs and Spices

    Directory of Open Access Journals (Sweden)

    Kee Hun Do

    2015-10-01

    Full Text Available Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. Moreover, the health benefits of spices have been extensively recognized in recent studies. However, inevitable contaminants, including mycotoxins, in medicinal herbs and spices can cause serious problems for humans in spite of their health benefits. Along with the different nation-based occurrences of mycotoxins, the ultimate exposure and toxicities can be diversely influenced by the endogenous food components in different commodities of the medicinal herbs and spices. The phytochemicals in these food stuffs can influence mold growth, mycotoxin production and biological action of the mycotoxins in exposed crops, as well as in animal and human bodies. The present review focuses on the occurrence of mycotoxins in medicinal herbs and spices and the biological interaction between mold, mycotoxin and herbal components. These networks will provide insights into the methods of mycotoxin reduction and toxicological risk assessment of mycotoxin-contaminated medicinal food components in the environment and biological organisms.

  11. Nation-Based Occurrence and Endogenous Biological Reduction of Mycotoxins in Medicinal Herbs and Spices.

    Science.gov (United States)

    Do, Kee Hun; An, Tae Jin; Oh, Sang-Keun; Moon, Yuseok

    2015-10-14

    Medicinal herbs have been increasingly used for therapeutic purposes against a diverse range of human diseases worldwide. Moreover, the health benefits of spices have been extensively recognized in recent studies. However, inevitable contaminants, including mycotoxins, in medicinal herbs and spices can cause serious problems for humans in spite of their health benefits. Along with the different nation-based occurrences of mycotoxins, the ultimate exposure and toxicities can be diversely influenced by the endogenous food components in different commodities of the medicinal herbs and spices. The phytochemicals in these food stuffs can influence mold growth, mycotoxin production and biological action of the mycotoxins in exposed crops, as well as in animal and human bodies. The present review focuses on the occurrence of mycotoxins in medicinal herbs and spices and the biological interaction between mold, mycotoxin and herbal components. These networks will provide insights into the methods of mycotoxin reduction and toxicological risk assessment of mycotoxin-contaminated medicinal food components in the environment and biological organisms.

  12. A neurosemantic theory of concrete noun representation based on the underlying brain codes.

    Directory of Open Access Journals (Sweden)

    Marcel Adam Just

    Full Text Available This article describes the discovery of a set of biologically-driven semantic dimensions underlying the neural representation of concrete nouns, and then demonstrates how a resulting theory of noun representation can be used to identify simple thoughts through their fMRI patterns. We use factor analysis of fMRI brain imaging data to reveal the biological representation of individual concrete nouns like apple, in the absence of any pictorial stimuli. From this analysis emerge three main semantic factors underpinning the neural representation of nouns naming physical objects, which we label manipulation, shelter, and eating. Each factor is neurally represented in 3-4 different brain locations that correspond to a cortical network that co-activates in non-linguistic tasks, such as tool use pantomime for the manipulation factor. Several converging methods, such as the use of behavioral ratings of word meaning and text corpus characteristics, provide independent evidence of the centrality of these factors to the representations. The factors are then used with machine learning classifier techniques to show that the fMRI-measured brain representation of an individual concrete noun like apple can be identified with good accuracy from among 60 candidate words, using only the fMRI activity in the 16 locations associated with these factors. To further demonstrate the generativity of the proposed account, a theory-based model is developed to predict the brain activation patterns for words to which the algorithm has not been previously exposed. The methods, findings, and theory constitute a new approach of using brain activity for understanding how object concepts are represented in the mind.

  13. Needs Assessment to Development of Biology Textbook for High School Class X-Based the Local Wisdom of Timor

    Science.gov (United States)

    Ardan, Andam S.; Ardi, M.; Hala, Yusminah; Supu, Amiruddin; Dirawan, Gufran D.

    2015-01-01

    This research aims to analyze the needs of the development of the X grade Biology textbook of Senior High School based on the local wisdom of Timor. The subject is a Senior High School Biology curriculum. Classes are taught at Senior High School X SMA in Kupang Regency in the academic years 2012/2013. Object of research includes: (1) core…

  14. Shaping scientific attitude of biology education students through research-based teaching

    Science.gov (United States)

    Firdaus, Darmadi

    2017-08-01

    Scientific attitude is need of today's society for peaceful and meaningful living of every person in a multicultural world. A case study was conducted at the Faculty of Teacher Training and Education, University of Riau, Pekanbaru in order to describe the scientific attitude that shaped by research-based teaching (RBT). Eighteen students of English for Biology bilingual program were selected from 88 regular students as a subject of the study. RBT designed consists of 9 steps: 1) field observations, 2) developing research proposals, 3) research proposal seminar, 4) field data collecting, 5) data analyzing & ilustrating, 6) writing research papers, 7) preparing power point slides, 8) creating a scientific poster, 9) seminar & poster session. Data were collected by using check list observation instuments during 14 weeks (course sessions), then analyzed by using descriptive-quantitative method. The results showed that RBT were able to shape critical-mindedness, suspended judgement, respect for evidence, honesty, objectivity, and questioning attitude as well as tolerance of uncertainty. These attitudes which shaped were varies according to every steps of learning activities. It's seems that the preparation of scientific posters and research seminar quite good in shaping the critical-mindedness, suspended judgment, respect for evidence, honesty, objectivity, and questioning attitude, as well as tolerance of uncertainty. In conclusion, the application of research-based teaching through the English for Biology courses could shape the students scientific attitudes. However, the consistency of the appearance of a scientific attitude in every stage of Biology-based RBT learning process need more intensive and critical assessment.

  15. A Mistake Based Approach Probing Students' Under- standing of PV ...

    Indian Academy of Sciences (India)

    lic forum results in a paradigm of learning called the 'mis- take based approach'. This approach is a subset ... necting the science with the math – there are so many equations floating around, but which one to use for which ..... In conjunction with the traditional approach of teaching subject- wise/chapter-wise, this approach ...

  16. Optimizing block-based maintenance under random machine usage

    NARCIS (Netherlands)

    de Jonge, Bram; Jakobsons, Edgars

    Existing studies on maintenance optimization generally assume that machines are either used continuously, or that times until failure do not depend on the actual usage. In practice, however, these assumptions are often not realistic. In this paper, we consider block-based maintenance optimization

  17. Under-resourced speech recognition based on the speech manifold

    CSIR Research Space (South Africa)

    Sahraeian, R

    2015-09-01

    Full Text Available other typical spectral-based features, and therefore exploiting out-of-language data in this feature space is beneficial. They demonstrate the positive effect of ISA in the frame work of multilingual DNN systems where Flemish and Afrikaans are used...

  18. Tandem base-free synthesis of -hydroxy sulphides under ...

    Indian Academy of Sciences (India)

    The important features of this methodology are base-free, odourless, high yield, reasonably rapid reaction rate, simple workup, high regioselectivity, costeffective and no requirement of transition metal catalysts. It is noteworthy that ring-opening reaction of 1,2-diphenyldiselane with 2-(phenoxymethyl)oxirane are also ...

  19. Human Pluripotent Stem Cell Based Developmental Toxicity Assays for Chemical Safety Screening and Systems Biology Data Generation.

    Science.gov (United States)

    Shinde, Vaibhav; Klima, Stefanie; Sureshkumar, Perumal Srinivasan; Meganathan, Kesavan; Jagtap, Smita; Rempel, Eugen; Rahnenführer, Jörg; Hengstler, Jan Georg; Waldmann, Tanja; Hescheler, Jürgen; Leist, Marcel; Sachinidis, Agapios

    2015-06-17

    Efficient protocols to differentiate human pluripotent stem cells to various tissues in combination with -omics technologies opened up new horizons for in vitro toxicity testing of potential drugs. To provide a solid scientific basis for such assays, it will be important to gain quantitative information on the time course of development and on the underlying regulatory mechanisms by systems biology approaches. Two assays have therefore been tuned here for these requirements. In the UKK test system, human embryonic stem cells (hESC) (or other pluripotent cells) are left to spontaneously differentiate for 14 days in embryoid bodies, to allow generation of cells of all three germ layers. This system recapitulates key steps of early human embryonic development, and it can predict human-specific early embryonic toxicity/teratogenicity, if cells are exposed to chemicals during differentiation. The UKN1 test system is based on hESC differentiating to a population of neuroectodermal progenitor (NEP) cells for 6 days. This system recapitulates early neural development and predicts early developmental neurotoxicity and epigenetic changes triggered by chemicals. Both systems, in combination with transcriptome microarray studies, are suitable for identifying toxicity biomarkers. Moreover, they may be used in combination to generate input data for systems biology analysis. These test systems have advantages over the traditional toxicological studies requiring large amounts of animals. The test systems may contribute to a reduction of the costs for drug development and chemical safety evaluation. Their combination sheds light especially on compounds that may influence neurodevelopment specifically.

  20. Mathematical Modeling of Column-Base Connections under Monotonic Loading

    Directory of Open Access Journals (Sweden)

    Gholamreza Abdollahzadeh

    2014-12-01

    Full Text Available Some considerable damage to steel structures during the Hyogo-ken Nanbu Earthquake occurred. Among them, many exposed-type column bases failed in several consistent patterns, such as brittle base plate fracture, excessive bolt elongation, unexpected early bolt failure, and inferior construction work, etc. The lessons from these phenomena led to the need for improved understanding of column base behavior. Joint behavior must be modeled when analyzing semi-rigid frames, which is associated with a mathematical model of the moment–rotation curve. The most accurate model uses continuous nonlinear functions. This article presents three areas of steel joint research: (1 analysis methods of semi-rigid joints; (2 prediction methods for the mechanical behavior of joints; (3 mathematical representations of the moment–rotation curve. In the current study, a new exponential model to depict the moment–rotation relationship of column base connection is proposed. The proposed nonlinear model represents an approach to the prediction of M–θ curves, taking into account the possible failure modes and the deformation characteristics of the connection elements. The new model has three physical parameters, along with two curve-fitted factors. These physical parameters are generated from dimensional details of the connection, as well as the material properties. The M–θ curves obtained by the model are compared with published connection tests and 3D FEM research. The proposed mathematical model adequately comes close to characterizing M–θ behavior through the full range of loading/rotations. As a result, modeling of column base connections using the proposed mathematical model can give crucial beforehand information, and overcome the disadvantages of time consuming workmanship and cost of experimental studies.

  1. Application of Biologically Based Lumping To Investigate the Toxicokinetic Interactions of a Complex Gasoline Mixture.

    Science.gov (United States)

    Jasper, Micah N; Martin, Sheppard A; Oshiro, Wendy M; Ford, Jermaine; Bushnell, Philip J; El-Masri, Hisham

    2016-03-15

    People are often exposed to complex mixtures of environmental chemicals such as gasoline, tobacco smoke, water contaminants, or food additives. We developed an approach that applies chemical lumping methods to complex mixtures, in this case gasoline, based on biologically relevant parameters used in physiologically based pharmacokinetic (PBPK) modeling. Inhalation exposures were performed with rats to evaluate the performance of our PBPK model and chemical lumping method. There were 109 chemicals identified and quantified in the vapor in the chamber. The time-course toxicokinetic profiles of 10 target chemicals were also determined from blood samples collected during and following the in vivo experiments. A general PBPK model was used to compare the experimental data to the simulated values of blood concentration for 10 target chemicals with various numbers of lumps, iteratively increasing from 0 to 99. Large reductions in simulation error were gained by incorporating enzymatic chemical interactions, in comparison to simulating the individual chemicals separately. The error was further reduced by lumping the 99 nontarget chemicals. The same biologically based lumping approach can be used to simplify any complex mixture with tens, hundreds, or thousands of constituents.

  2. Carbon Nanomaterials Based Electrochemical Sensors/Biosensors for the Sensitive Detection of Pharmaceutical and Biological Compounds.

    Science.gov (United States)

    Adhikari, Bal-Ram; Govindhan, Maduraiveeran; Chen, Aicheng

    2015-09-04

    Electrochemical sensors and biosensors have attracted considerable attention for the sensitive detection of a variety of biological and pharmaceutical compounds. Since the discovery of carbon-based nanomaterials, including carbon nanotubes, C60 and graphene, they have garnered tremendous interest for their potential in the design of high-performance electrochemical sensor platforms due to their exceptional thermal, mechanical, electronic, and catalytic properties. Carbon nanomaterial-based electrochemical sensors have been employed for the detection of various analytes with rapid electron transfer kinetics. This feature article focuses on the recent design and use of carbon nanomaterials, primarily single-walled carbon nanotubes (SWCNTs), reduced graphene oxide (rGO), SWCNTs-rGO, Au nanoparticle-rGO nanocomposites, and buckypaper as sensing materials for the electrochemical detection of some representative biological and pharmaceutical compounds such as methylglyoxal, acetaminophen, valacyclovir, β-nicotinamide adenine dinucleotide hydrate (NADH), and glucose. Furthermore, the electrochemical performance of SWCNTs, rGO, and SWCNT-rGO for the detection of acetaminophen and valacyclovir was comparatively studied, revealing that SWCNT-rGO nanocomposites possess excellent electrocatalytic activity in comparison to individual SWCNT and rGO platforms. The sensitive, reliable and rapid analysis of critical disease biomarkers and globally emerging pharmaceutical compounds at carbon nanomaterials based electrochemical sensor platforms may enable an extensive range of applications in preemptive medical diagnostics.

  3. Carbon Nanomaterials Based Electrochemical Sensors/Biosensors for the Sensitive Detection of Pharmaceutical and Biological Compounds

    Directory of Open Access Journals (Sweden)

    Bal-Ram Adhikari

    2015-09-01

    Full Text Available Electrochemical sensors and biosensors have attracted considerable attention for the sensitive detection of a variety of biological and pharmaceutical compounds. Since the discovery of carbon-based nanomaterials, including carbon nanotubes, C60 and graphene, they have garnered tremendous interest for their potential in the design of high-performance electrochemical sensor platforms due to their exceptional thermal, mechanical, electronic, and catalytic properties. Carbon nanomaterial-based electrochemical sensors have been employed for the detection of various analytes with rapid electron transfer kinetics. This feature article focuses on the recent design and use of carbon nanomaterials, primarily single-walled carbon nanotubes (SWCNTs, reduced graphene oxide (rGO, SWCNTs-rGO, Au nanoparticle-rGO nanocomposites, and buckypaper as sensing materials for the electrochemical detection of some representative biological and pharmaceutical compounds such as methylglyoxal, acetaminophen, valacyclovir, β-nicotinamide adenine dinucleotide hydrate (NADH, and glucose. Furthermore, the electrochemical performance of SWCNTs, rGO, and SWCNT-rGO for the detection of acetaminophen and valacyclovir was comparatively studied, revealing that SWCNT-rGO nanocomposites possess excellent electrocatalytic activity in comparison to individual SWCNT and rGO platforms. The sensitive, reliable and rapid analysis of critical disease biomarkers and globally emerging pharmaceutical compounds at carbon nanomaterials based electrochemical sensor platforms may enable an extensive range of applications in preemptive medical diagnostics.

  4. Inquiry-based laboratory investigations and student performance on standardized tests in biological science

    Science.gov (United States)

    Patke, Usha

    Achievement data from the 3rd International Mathematics and Sciences Study and Program for International Student Assessment in science have indicated that Black students from economically disadvantaged families underachieve at alarming rates in comparison to White and economically advantaged peer groups. The study site was a predominately Black, urban school district experiencing underachievement. The purpose of this correlational study was to examine the relationship between students' use of inquiry-based laboratory investigations and their performance on the Biology End of Course Test, as well as to examine the relationship while partialling out the effects of student gender. Constructivist theory formed the theoretical foundation of the study. Students' perceived levels of experience with inquiry-based laboratory investigations were measured using the Laboratory Program Variable Inventory (LPVI) survey. LPVI scores of 256 students were correlated with test scores and were examined by student gender. The Pearson correlation coefficient revealed a small direct correlation between students' experience in inquiry-based laboratory investigation classes and standardized test scores on the Biology EOCT. A partial correlational analysis indicated that the correlation remained after controlling for gender. This study may prompt a change from teacher-centered to student-centered pedagogy at the local site in order to increase academic achievement for all students. The results of this study may also influence administrators and policy makers to initiate local, state, or nationwide curricular development. A change in curriculum may promote social change as students become more competent, and more able, to succeed in life beyond secondary school.

  5. Optical monitoring of surface anchoring changes for nematic liquid crystal based chemical and biological sensors

    Science.gov (United States)

    Zou, Yang

    In this dissertation, optically monitoring the surface anchoring changes of liquid crystal (LC) due to the chemical or biological bindings is presented. The deformation of LC director with different anchoring energies is simulated using Finite Element Method and continuum theory of nematic LC. The optical properties of the LC film are simulated using the Finite Difference Time Domain method. First, the interference color method was used to monitor the anchoring change. The calculated and experimental interference colors of liquid crystal films due to the optical retardation of two orthogonal electromagnetic components at different surface anchoring conditions and applied voltages are studied. The calculated colors were converted into sRGB parameters so that the corresponding colors can be displayed on a color computer monitor and printed out on a color printer. A gold micro-structure was fabricated and used to control the optical retardation. Polarizing micrographs were collected and compared with the calculated colors. Second, the influence of a bias voltage on the surface-driven orientational transition of liquid crystals resulted from the weakening anchoring and anchoring transition is analyzed theoretically and experimentally. The same interdigitated Au micro-structure was used in the nematic LC based chemical and biological sensors. With a suitable bias electric field, the process of the weakening anchoring energy and the uniform surface-driven orientational transition due to targeted molecules binding to a functionalized surface were observed optically. Finally, measurement of optical transmission was used to monitor the anchoring change. Polarizing micrographs were collected and compared with simulated textures. Experimental and simulation results both demonstrate the optical method can effectively monitor the surface anchoring change due to the presence of targeted analytes. These results show that these optical techniques are suitable for LC based sensing

  6. Performance based investigations of structural systems under fire

    DEFF Research Database (Denmark)

    Gentili, Filippo; Crosti, Chiara; Giuliani, Luisa

    2010-01-01

    Prescriptive measures and procedures developed over the past here are mostly aimed at preventing structural failures of single elements for the time required for the evacuation. The response to fire and fire effects of the structural system as a whole remains often unknown and the survival of the...... structures are presented and discussed, with particular attention to methodological aspects. The effects of different assumptions in the modeling and in the definition of the collapse are highlighted, as critical aspects of a performance-based investigation....... these kinds of events, the mitigation of possible collapse induced by fire should be achieved. In this respect, a performance-based investigation of the structure aimed at highlight fire effects and fire-induced collapse mechanisms becomes of interest. In the paper collapse mechanisms of some simple...

  7. Optical image encryption based on interference under convergent random illumination

    International Nuclear Information System (INIS)

    Kumar, Pramod; Joseph, Joby; Singh, Kehar

    2010-01-01

    In an optical image encryption system based on the interference principle, two pure phase masks are designed analytically to hide an image. These two masks are illuminated with a plane wavefront to retrieve the original image in the form of an interference pattern at the decryption plane. Replacement of the plane wavefront with convergent random illumination in the proposed scheme leads to an improvement in the security of interference based encryption. The proposed encryption scheme retains the simplicity of an interference based method, as the two pure masks are generated with an analytical method without any iterative algorithm. In addition to the free-space propagation distance and the two pure phase masks, the convergence distance and the randomized lens phase function are two new encryption parameters to enhance the system security. The robustness of this scheme against occlusion of the random phase mask of the randomized lens phase function is investigated. The feasibility of the proposed scheme is demonstrated with numerical simulation results

  8. Optical image encryption based on interference under convergent random illumination

    Science.gov (United States)

    Kumar, Pramod; Joseph, Joby; Singh, Kehar

    2010-09-01

    In an optical image encryption system based on the interference principle, two pure phase masks are designed analytically to hide an image. These two masks are illuminated with a plane wavefront to retrieve the original image in the form of an interference pattern at the decryption plane. Replacement of the plane wavefront with convergent random illumination in the proposed scheme leads to an improvement in the security of interference based encryption. The proposed encryption scheme retains the simplicity of an interference based method, as the two pure masks are generated with an analytical method without any iterative algorithm. In addition to the free-space propagation distance and the two pure phase masks, the convergence distance and the randomized lens phase function are two new encryption parameters to enhance the system security. The robustness of this scheme against occlusion of the random phase mask of the randomized lens phase function is investigated. The feasibility of the proposed scheme is demonstrated with numerical simulation results.

  9. Z-scores-based methods and their application to biological monitoring: an example in professional soccer players.

    Science.gov (United States)

    Saulière, Guillaume; Dedecker, Jérôme; Marquet, Laurie-Anne; Rochcongar, Pierre; Toussaint, Jean-Francois; Berthelot, Geoffroy

    2017-11-15

    The clinical and biological follow-up of individuals, such as the biological passport for athletes, is typically based on the individual and longitudinal monitoring of hematological or urine markers. These follow-ups aim to identify abnormal behavior by comparing the individual's biological samples to an established baseline. These comparisons may be done via different ways, but each of them requires an appropriate extra population to compute the significance levels, which is a non-trivial issue. Moreover, it is not necessarily relevant to compare the measures of a biomarker of a professional athlete to that of a reference population (even restricted to other athletes), and a reasonable alternative is to detect the abnormal values by considering only the other measurements of the same athlete. Here we propose a simple adaptive statistic based on maxima of Z-scores that does not rely on the use of an extra population. We show that, in the Gaussian framework, it is a practical and relevant method for detecting abnormal values in a series of observations from the same individual. The distribution of this statistic does not depend on the individual parameters under the null hypothesis, and its quantiles can be computed using Monte Carlo simulations. The proposed method is tested on the 3-year follow-up of ferritin, serum iron, erythrocytes, hemoglobin, and hematocrit markers in 2577 elite male soccer players. For instance, if we consider the abnormal values for the hematocrit at a 5% level, we found that 5.57% of the selected cohort had at least one abnormal value (which is not significantly different from the expected false-discovery rate). The approach is a starting point for more elaborate models that would produce a refined individual baseline. The method can be extended to the Gaussian linear model, in order to include additional variables such as the age or exposure to altitude. The method could also be applied to other domains, such as the clinical patient

  10. The Effect of Chemical, Biological and Organic Nutritional Treatments on Sunflowers Yield and Yield Components under the Influence of Water Deficit Stress

    Directory of Open Access Journals (Sweden)

    fatemeh soleymani

    2016-07-01

    Full Text Available Introduction To achieve the higher economic yield of crop plants, supplying enough nutrients to plants is very important. Moreover, nutrient uptakes by plants is influenced by the soil water contents. However, nowadays chemical fertilizer application is important agronomic factor that has significant effects on growth and quantity and quality of final yield, but traditional nutrient management and excessive use of chemical fertilizers may cause the environmental problems such as contamination of soil and water resources, low quality of agricultural products and reduction of soil fertility. These factors have drawn attention to health and ecological sustainable farming systems (Sharma, 2002. In this context, usage of organic and biological products for plant nutrition is considered as one of the solutions to achieve the goals of sustainable agriculture. Materials and methods To evaluate the effect of various feeding systems on yield and yield components of sunflower (Helianthus annuus L. under the influence of water deficit stress, a split-plot experiment based on randomized complete block design with three replications, was carried out in the Agricultural Faculty of Bu-Ali Sina University during the growing season of 2013-2014. Main plots consisted of two irrigation levels: optimum irrigation and deficit irrigation stress (irrigation after 60 and 120 mm evaporation from evaporation pan, class A, respectively and sub-plots included of nine nutrition systems: 1- no bio or chemical fertilizer application, 2- 100% of the recommended chemical fertilizer , 3- vermicompost, 4- phospho nitro kara, 5- vermicompost+ phospho nitro kara, 6- vermicompost+ ½ chemical fertilizer, 7- phospho nitro kara+ ½ chemical fertilizer, 8- vermicompost+ phospho nitro kara+ ½ chemical fertilizer, 9- ½ proposed chemical fertilizer. Phospho-nitro-kara which contains phosphate solubilizing and nitrogen fixing bacteria (Bacillus coagulans, azotobactr chroocuccum and

  11. Lyapunov Based Estimation of Flight Stability Boundary under Icing Conditions

    Directory of Open Access Journals (Sweden)

    Binbin Pei

    2017-01-01

    Full Text Available Current fight boundary of the envelope protection in icing conditions is usually defined by the critical values of state parameters; however, such method does not take the interrelationship of each parameter and the effect of the external disturbance into consideration. This paper proposes constructing the stability boundary of the aircraft in icing conditions through analyzing the region of attraction (ROA around the equilibrium point. Nonlinear icing effect model is proposed according to existing wind tunnel test results. On this basis, the iced polynomial short period model can be deduced further to obtain the stability boundary under icing conditions using ROA analysis. Simulation results for a series of icing severity demonstrate that, regardless of the icing severity, the boundary of the calculated ROA can be treated as an estimation of the stability boundary around an equilibrium point. The proposed methodology is believed to be a promising way for ROA analysis and stability boundary construction of the aircraft in icing conditions, and it will provide theoretical support for multiple boundary protection of icing tolerant flight.

  12. Biologically Based Methods for Control of Fumonisin-Producing Fusarium Species and Reduction of the Fumonisins

    Science.gov (United States)

    Alberts, Johanna F.; van Zyl, Willem H.; Gelderblom, Wentzel C. A.

    2016-01-01

    Infection by the fumonisin-producing Fusarium spp. and subsequent fumonisin contamination of maize adversely affect international trade and economy with deleterious effects on human and animal health. In developed countries high standards of the major food suppliers and retailers are upheld and regulatory controls deter the importation and local marketing of fumonisin-contaminated food products. In developing countries regulatory measures are either lacking or poorly enforced, due to food insecurity, resulting in an increased mycotoxin exposure. The lack and poor accessibility of effective and environmentally safe control methods have led to an increased interest in practical and biological alternatives to reduce fumonisin intake. These include the application of natural resources, including plants, microbial cultures, genetic material thereof, or clay minerals pre- and post-harvest. Pre-harvest approaches include breeding for resistant maize cultivars, introduction of biocontrol microorganisms, application of phenolic plant extracts, and expression of antifungal proteins and fumonisin degrading enzymes in transgenic maize cultivars. Post-harvest approaches include the removal of fumonisins by natural clay adsorbents and enzymatic degradation of fumonisins through decarboxylation and deamination by recombinant carboxylesterase and aminotransferase enzymes. Although, the knowledge base on biological control methods has expanded, only a limited number of authorized decontamination products and methods are commercially available. As many studies detailed the use of natural compounds in vitro, concepts in reducing fumonisin contamination should be developed further for application in planta and in the field pre-harvest, post-harvest, and during storage and food-processing. In developed countries an integrated approach, involving good agricultural management practices, hazard analysis and critical control point (HACCP) production, and storage management, together with

  13. Biologically Based Methods for Control of Fumonisin-producing Fusarium species and Reduction of the Fumonisins

    Directory of Open Access Journals (Sweden)

    Johanna Francina Alberts

    2016-04-01

    Full Text Available Infection by the fumonisin-producing Fusarium spp. and subsequent fumonisin contamination of maize adversely affect international trade and economy with deleterious effects on human and animal health. In developed countries high standards of the major food suppliers and retailers are upheld and regulatory controls deter the importation and local marketing of fumonisin-contaminated food products. In developing countries regulatory measures are either lacking or poorly enforced, due to food insecurity, resulting in an increased mycotoxin exposure. The lack and poor accessibility of effective and environmentally safe control methods have led to an increased interest in practical and biological alternatives to reduce fumonisin intake. These include the application of natural resources, including plants, microbial cultures, genetic material thereof or clay minerals pre- and postharvest. Pre-harvest approaches include breeding for resistant maize cultivars, introduction of biocontrol microorganisms, application of phenolic plant extracts, and expression of antifungal proteins and fumonisin degrading enzymes in transgenic maize cultivars. Postharvest approaches include the removal of fumonisins by natural clay adsorbents and enzymatic degradation of fumonisins through decarboxylation and deamination by recombinant carboxylesterase and aminotransferase enzymes. Although the knowledge base on biological control methods has expanded, only a limited number of authorized decontamination products and methods are commercially available. As many studies detailed the use of natural compounds in vitro, concepts in reducing fumonisin contamination should be developed further for application in planta and in the field pre-harvest, postharvest, and during storage and food-processing. In developed countries an integrated approach, involving good agricultural management practices, hazard analysis and critical control point (HACCP production and storage management

  14. Biologically Based Methods for Control of Fumonisin-Producing Fusarium Species and Reduction of the Fumonisins.

    Science.gov (United States)

    Alberts, Johanna F; van Zyl, Willem H; Gelderblom, Wentzel C A

    2016-01-01

    Infection by the fumonisin-producing Fusarium spp. and subsequent fumonisin contamination of maize adversely affect international trade and economy with deleterious effects on human and animal health. In developed countries high standards of the major food suppliers and retailers are upheld and regulatory controls deter the importation and local marketing of fumonisin-contaminated food products. In developing countries regulatory measures are either lacking or poorly enforced, due to food insecurity, resulting in an increased mycotoxin exposure. The lack and poor accessibility of effective and environmentally safe control methods have led to an increased interest in practical and biological alternatives to reduce fumonisin intake. These include the application of natural resources, including plants, microbial cultures, genetic material thereof, or clay minerals pre- and post-harvest. Pre-harvest approaches include breeding for resistant maize cultivars, introduction of biocontrol microorganisms, application of phenolic plant extracts, and expression of antifungal proteins and fumonisin degrading enzymes in transgenic maize cultivars. Post-harvest approaches include the removal of fumonisins by natural clay adsorbents and enzymatic degradation of fumonisins through decarboxylation and deamination by recombinant carboxylesterase and aminotransferase enzymes. Although, the knowledge base on biological control methods has expanded, only a limited number of authorized decontamination products and methods are commercially available. As many studies detailed the use of natural compounds in vitro, concepts in reducing fumonisin contamination should be developed further for application in planta and in the field pre-harvest, post-harvest, and during storage and food-processing. In developed countries an integrated approach, involving good agricultural management practices, hazard analysis and critical control point (HACCP) production, and storage management, together with

  15. Learning Systems Biology: Conceptual Considerations toward a Web-Based Learning Platform

    Science.gov (United States)

    Emmert-Streib, Frank; Dehmer, Matthias; Lyardet, Fernando

    2013-01-01

    Within recent years, there is an increasing need to train students, from biology and beyond, in quantitative methods that are relevant to cope with data-driven biology. Systems Biology is such a field that places a particular focus on the functional aspect of biology and molecular interacting processes. This paper deals with the conceptual design…

  16. Ligand-based virtual screening under partial shape constraints

    Science.gov (United States)

    von Behren, Mathias M.; Rarey, Matthias

    2017-04-01

    Ligand-based virtual screening has proven to be a viable technology during the search for new lead structures in drug discovery. Despite the rapidly increasing number of published methods, meaningful shape matching as well as ligand and target flexibility still remain open challenges. In this work, we analyze the influence of knowledge-based sterical constraints on the performance of the recently published ligand-based virtual screening method mRAISE. We introduce the concept of partial shape matching enabling a more differentiated view on chemical structure. The new method is integrated into the LBVS tool mRAISE providing multiple options for such constraints. The applied constraints can either be derived automatically from a protein-ligand complex structure or by manual selection of ligand atoms. In this way, the descriptor directly encodes the fit of a ligand into the binding site. Furthermore, the conservation of close contacts between the binding site surface and the query ligand can be enforced. We validated our new method on the DUD and DUD-E datasets. Although the statistical performance remains on the same level, detailed analysis reveal that for certain and especially very flexible targets a significant improvement can be achieved. This is further highlighted looking at the quality of calculated molecular alignments using the recently introduced mRAISE dataset. The new partial shape constraints improved the overall quality of molecular alignments especially for difficult targets with highly flexible or different sized molecules. The software tool mRAISE is freely available on Linux operating systems for evaluation purposes and academic use (see http://www.zbh.uni-hamburg.de/raise).

  17. Biological – chemical regeneration of desulphurization sorbents based on zinc ferrite

    Directory of Open Access Journals (Sweden)

    Šepelák Vladimír

    2002-03-01

    Full Text Available One of the main sources of air pollution is the combustion of fuels by various thermal and power plants, transport facilities, and metallurgical plants. Main components of industrial gases that pollute air are carbon oxides, nitrogen oxides, sulphur oxides and hydrogen sulphide. Sulphur has received a more attention than any other contaminant, because the sulphur released into the atmosphere in the form of sulphur dioxide or hydrogen sulphide is a precursor of the “acid rain” formation. To meet environmental emission regulations, sulphur and other contaminant species released during the gasification of coal must be removed from the fuel gas stream. The removal of contaminat at high temperatures is referred to as hot-gas cleanup in general and hot-gas desulphurization in particular when sulphur species are the primary contaminants to be remove. In recent years, zinc ferrite is the leading candidate for hot-gas desulphurization, capable of removing sulphur-containing species from coal gas at gasifier exit temperatures. It can also be of being regenerated for a continuous use. The conventional methods of the regeneration of sulphurized sorbents are based on oxidizing pyrolysis of sulphides or on the pressure leaching of sulphides in the water environment at high temperatures. The first results of the experiments using the biological-chemical leaching, as a new way of regeneration of sulphurized sorbent based on zinc ferrite, are presented in this paper. The results show that the biological-chemical leaching leads to the removal of sulphides layers (á-ZnS, â-ZnS from the surface of the sorbent at room temperature. The biological-chemical leaching process results in the increase of the active surface area of the regenerated sorbent.

  18. The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development

    Directory of Open Access Journals (Sweden)

    Amy L. Chang

    2016-05-01

    Full Text Available The American Society for Microbiology (ASM established its ASM-NSF (National Science Foundation Biology Scholars Program (BSP to promote undergraduate education reform by 1 supporting biologists to implement evidence-based teaching practices, 2 engaging life science professional societies to facilitate biologists’ leadership in scholarly teaching within the discipline, and 3 participating in a teaching community that fosters disciplinary-level science, technology, engineering, and mathematics (STEM reform. Since 2005, the program has utilized year-long residency training to provide a continuum of learning and practice centered on principles from the scholarship of teaching and learning (SoTL to more than 270 participants (“scholars” from biology and multiple other disciplines. Additionally, the program has recruited 11 life science professional societies to support faculty development in SoTL and discipline-based education research (DBER. To identify the BSP’s long-term outcomes and impacts, ASM engaged an external evaluator to conduct a study of the program’s 2010­–2014 scholars (n = 127 and society partners. The study methods included online surveys, focus groups, participant observation, and analysis of various documents. Study participants indicate that the program achieved its proposed goals relative to scholarship, professional society impact, leadership, community, and faculty professional development. Although participants also identified barriers that hindered elements of their BSP participation, findings suggest that the program was essential to their development as faculty and provides evidence of the BSP as a model for other societies seeking to advance undergraduate science education reform. The BSP is the longest-standing faculty development program sponsored by a collective group of life science societies. This collaboration promotes success across a fragmented system of more than 80 societies representing the life

  19. The ASM-NSF Biology Scholars Program: An Evidence-Based Model for Faculty Development.

    Science.gov (United States)

    Chang, Amy L; Pribbenow, Christine M

    2016-05-01

    The American Society for Microbiology (ASM) established its ASM-NSF (National Science Foundation) Biology Scholars Program (BSP) to promote undergraduate education reform by 1) supporting biologists to implement evidence-based teaching practices, 2) engaging life science professional societies to facilitate biologists' leadership in scholarly teaching within the discipline, and 3) participating in a teaching community that fosters disciplinary-level science, technology, engineering, and mathematics (STEM) reform. Since 2005, the program has utilized year-long residency training to provide a continuum of learning and practice centered on principles from the scholarship of teaching and learning (SoTL) to more than 270 participants ("scholars") from biology and multiple other disciplines. Additionally, the program has recruited 11 life science professional societies to support faculty development in SoTL and discipline-based education research (DBER). To identify the BSP's long-term outcomes and impacts, ASM engaged an external evaluator to conduct a study of the program's 2010-2014 scholars (n = 127) and society partners. The study methods included online surveys, focus groups, participant observation, and analysis of various documents. Study participants indicate that the program achieved its proposed goals relative to scholarship, professional society impact, leadership, community, and faculty professional development. Although participants also identified barriers that hindered elements of their BSP participation, findings suggest that the program was essential to their development as faculty and provides evidence of the BSP as a model for other societies seeking to advance undergraduate science education reform. The BSP is the longest-standing faculty development program sponsored by a collective group of life science societies. This collaboration promotes success across a fragmented system of more than 80 societies representing the life sciences and helps

  20. A substrate dependent biological containment systems for Pseudomonas putida based on the Escherichia coli gef gene

    DEFF Research Database (Denmark)

    Jensen, Lars Bogø; Ramos, J. L.; Kaneva, Z.

    1993-01-01

    A model substrate-dependent suicide system to biologically contain Pseudomonas putida KT2440 is reported. The system consists of two elements. One element carries a fusion between a synthetic lac promoter (PA1-04/03) and the gef gene, which encodes a killing function. This element is contained...... within a transposaseless mini-Tn5 transposon so that it can be integrated at random locations on the Pseudomonas chromosome. The second element, harbored by plasmid pCC102, is designed to control the first and bears a fusion between the promoter of the P. putida TOL plasmid-encoded meta-cleavage pathway...... operon (Pm) and the lacI gene, encoding the Lac repressor, plus xylS2, coding for a positive regulator of Pm. In liquid culture under optimal growth conditions and in sterile and nonsterile soil microcosms, P. putida KT2440 (pWWO) bearing the containment system behaves as designed. In the presence...

  1. Nonlinear Resonance Analysis of Slender Portal Frames under Base Excitation

    Directory of Open Access Journals (Sweden)

    Luis Fernando Paullo Muñoz

    2017-01-01

    Full Text Available The dynamic nonlinear response and stability of slender structures in the main resonance regions are a topic of importance in structural analysis. In complex problems, the determination of the response in the frequency domain indirectly obtained through analyses in time domain can lead to huge computational effort in large systems. In nonlinear cases, the response in the frequency domain becomes even more cumbersome because of the possibility of multiple solutions for certain forcing frequencies. Those solutions can be stable and unstable, in particular saddle-node bifurcation at the turning points along the resonance curves. In this work, an incremental technique for direct calculation of the nonlinear response in frequency domain of plane frames subjected to base excitation is proposed. The transformation of equations of motion to the frequency domain is made through the harmonic balance method in conjunction with the Galerkin method. The resulting system of nonlinear equations in terms of the modal amplitudes and forcing frequency is solved by the Newton-Raphson method together with an arc-length procedure to obtain the nonlinear resonance curves. Suitable examples are presented, and the influence of the frame geometric parameters and base motion on the nonlinear resonance curves is investigated.

  2. Resilience Analysis of Countries under Disasters Based on Multisource Data.

    Science.gov (United States)

    Zhang, Nan; Huang, Hong

    2018-01-01

    Disasters occur almost daily in the world. Because emergencies frequently have no precedent, are highly uncertain, and can be very destructive, improving a country's resilience is an efficient way to reduce risk. In this article, we collected more than 20,000 historical data points from disasters from 207 countries to enable us to calculate the severity of disasters and the danger they pose to countries. In addition, 6 primary indices (disaster, personal attribute, infrastructure, economics, education, and occupation) including 38 secondary influencing factors are considered in analyzing the resilience of countries. Using these data, we obtained the danger, expected number of deaths, and resilience of all 207 countries. We found that a country covering a large area is more likely to have a low resilience score. Through sensitivity analysis of all secondary indices, we found that population density, frequency of disasters, and GDP are the three most critical factors affecting resilience. Based on broad-spectrum resilience analysis of the different continents, Oceania and South America have the highest resilience, while Asia has the lowest. Over the past 50 years, the resilience of many countries has been improved sharply, especially in developing countries. Based on our results, we analyze the comprehensive resilience and provide some optimal suggestions to efficiently improve resilience. © 2017 Society for Risk Analysis.

  3. Biological Phosphorus Release and Uptake Under Alternating Anaerobic and Anoxic Conditions In a Fixed-Film Reactor

    DEFF Research Database (Denmark)

    Kerrn-Jespersen, Jens Peter; Henze, Mogens; Strube, Rune

    1994-01-01

    Biological phosphorus removal was investigated in a fixed-film reactor with alternating anaerobic and anoxic conditions. The tests showed that biological phosphorus removal can be obtained in a fixed-film reactor with nitrate as oxidising agent. In the anaerobic period, 0.52 mg of PO4-P...... was released per mg of acetate taken up on an average. In the anoxic period, 2.0 mg of PO4-P was taken up per mg of NO3-N reduced on an average. The relationship between potassium released and phosphate released in the anaerobic phase was determined to be 0.37 mg K/mg P, while the relationship between...

  4. Effcacy of different biological control agents against major postharvest pathogens of grapes under room temperature storage conditions

    OpenAIRE

    Ramu SENTHIL; Kuppusamy PRABAKAR; Lingan RAJENDRAN; Gandhi KARTHIKEYAN

    2011-01-01

    Grapes were treated post harvest with a variety of biological agents to determine their effcacy in reducing yield loss. The agents Pseudomonas, Bacillus, Trichoderma and yeast isolates were individually screened against a number of postharvest pathogens including Aspergillus carbonarius, Penicillum expansum, and Fusarium moniliforme. B. subtilis strains EPC-8 and EPCO-16 showed high mycelial growth suppression of A. carbonarius and P. expansum  in vitro. The fungal antagonist Trichoder...

  5. Integrated Ecological River Health Assessments, Based on Water Chemistry, Physical Habitat Quality and Biological Integrity

    Directory of Open Access Journals (Sweden)

    Ji Yoon Kim

    2015-11-01

    Full Text Available This study evaluated integrative river ecosystem health using stressor-based models of physical habitat health, chemical water health, and biological health of fish and identified multiple-stressor indicators influencing the ecosystem health. Integrated health responses (IHRs, based on star-plot approach, were calculated from qualitative habitat evaluation index (QHEI, nutrient pollution index (NPI, and index of biological integrity (IBI in four different longitudinal regions (Groups I–IV. For the calculations of IHRs values, multi-metric QHEI, NPI, and IBI models were developed and their criteria for the diagnosis of the health were determined. The longitudinal patterns of the river were analyzed by a self-organizing map (SOM model and the key major stressors in the river were identified by principal component analysis (PCA. Our model scores of integrated health responses (IHRs suggested that mid-stream and downstream regions were impaired, and the key stressors were closely associated with nutrient enrichment (N and P and organic matter pollutions from domestic wastewater disposal plants and urban sewage. This modeling approach of IHRs may be used as an effective tool for evaluations of integrative ecological river health..

  6. A genome-based approach for the study of erythroid biology and disease.

    Science.gov (United States)

    Miller, Jeffery L

    2004-01-01

    The human genome contains all elements of the erythroid transcriptome with the exception of those genes encoded in mitochondrial DNA. The concept of a "genome-based" approach for the study of erythroid biology and disease was envisioned in the mid-1990s as a logical offshoot of efforts to map the human genome. Although a completed human genome map was not expected until 2005 [Science 279 (1998) 23], the idea of creating a robust and retrievable description of erythroid gene activity was both encouraged and supported on the NIDDK Bethesda campus of the National Institutes of Health. The 5-10-year goals were organized into three parts. The initial project goal involved the collection of sequence data derived from mRNA expressed in developmentally staged erythroblasts. Those cells were isolated prospectively by flow cytometry monitoring of CD71 and glycophorin A expression patterns. Next, the sequence data was organized into a database and integrated with related information available in the public domain. The paramount goal of the project continues to be clinical application. As discussed in this paper, progress already made in each of these areas suggests that genome-based approaches will greatly facilitate future studies of erythroid biology and disease.

  7. Proteomics-Based Analysis of Protein Complexes in Pluripotent Stem Cells and Cancer Biology.

    Science.gov (United States)

    Sudhir, Putty-Reddy; Chen, Chung-Hsuan

    2016-03-22

    A protein complex consists of two or more proteins that are linked together through protein-protein interactions. The proteins show stable/transient and direct/indirect interactions within the protein complex or between the protein complexes. Protein complexes are involved in regulation of most of the cellular processes and molecular functions. The delineation of protein complexes is important to expand our knowledge on proteins functional roles in physiological and pathological conditions. The genetic yeast-2-hybrid method has been extensively used to characterize protein-protein interactions. Alternatively, a biochemical-based affinity purification coupled with mass spectrometry (AP-MS) approach has been widely used to characterize the protein complexes. In the AP-MS method, a protein complex of a target protein of interest is purified using a specific antibody or an affinity tag (e.g., DYKDDDDK peptide (FLAG) and polyhistidine (His)) and is subsequently analyzed by means of MS. Tandem affinity purification, a two-step purification system, coupled with MS has been widely used mainly to reduce the contaminants. We review here a general principle for AP-MS-based characterization of protein complexes and we explore several protein complexes identified in pluripotent stem cell biology and cancer biology as examples.

  8. Ruminant Metabolic Systems Biology: Reconstruction and Integration of Transcriptome Dynamics Underlying Functional Responses of Tissues to Nutrition and Physiological Statea

    Science.gov (United States)

    Bionaz, Massimo; Loor, Juan J.

    2012-01-01

    High-throughput ‘omics’ data analysis via bioinformatics is one key component of the systems biology approach. The systems approach is particularly well-suited for the study of the interactions between nutrition and physiological state with tissue metabolism and functions during key life stages of organisms such as the transition from pregnancy to lactation in mammals, ie, the peripartal period. In modern dairy cows with an unprecedented genetic potential for milk synthesis, the nature of the physiologic and metabolic adaptations during the peripartal period is multifaceted and involves key tissues such as liver, adipose, and mammary. In order to understand such adaptation, we have reviewed several works performed in our and other labs. In addition, we have used a novel bioinformatics approach, Dynamic Impact Approach (DIA), in combination with partly previously published data to help interpret longitudinal biological adaptations of bovine liver, adipose, and mammary tissue to lactation using transcriptomics datasets. Use of DIA with transcriptomic data from those tissues during normal physiological adaptations and in animals fed different levels of energy prepartum allowed visualization and integration of most-impacted metabolic pathways around the time of parturition. The DIA is a suitable tool for applying the integrative systems biology approach. The ultimate goal is to visualize the complexity of the systems at study and uncover key molecular players involved in the tissue’s adaptations to physiological state or nutrition. PMID:22807626

  9. Fair Value Versus Historical Cost-Based Valuation for Biological Assets: Predictability of Financial Information

    Directory of Open Access Journals (Sweden)

    Josep M. Argilés

    2011-12-01

    Full Text Available There is an intense debate on the convenience of moving from historical cost (HC toward the fair value (FV principle. The debate and academic research is usually concerned with financial instruments, but the IAS 41 requirement of fair valuation for biological assets brings it into the agricultural domain.This paper performs an empirical study with a sample of Spanish farms valuing biological assets at HC and a sample applying FV, finding no significant differences between both valuation methods to assess future cash flows. However, most tests reveal more predictive power of future earnings under fair valuation of biological assets, which is not explained by differences in volatility of earnings and profitability. The study also evidences the existence of flawed HC accounting practices for biological assets in agriculture, which suggests scarce information content of this valuation method in the predominant small business units existing in the agricultural sector in advanced Western countries.La evolución de la contabilidad desde el coste histórico (CH hacia el valor razonable (VR ha suscitado debates y controversias, tanto en el ámbito profesional, como en el académico. Si bien el debate y los estudios se han referido principalmente a los instrumentos financieros, el requerimiento de la NIC41 de valorar los activos biológicos al VR ha ampliado el debate a la contabilidad agrícola.Este trabajo realiza un estudio empírico mediante una muestra de explotaciones agrícolas españolas que valoran sus activos biológicos al CH y otra que valoran al VR, para comparar el poder predictivo de ambos criterios de valoración. No se encuentran diferencias significativas entre ambos criterios para la predicción de los futuros flujos de tesorería. No obstante, la mayor parte de los tests realizados revelan un mayor poder predictivo de los futuros resultados contables bajo el valor razonable, que no se explica en función de diferencias en la

  10. Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization.

    Science.gov (United States)

    Tambong, James T; Xu, Renlin; Bromfield, Eden S P

    2017-04-01

    The bacterial strain 2-92T, isolated from a field plot under long-term (>40 years) mineral fertilization, exhibited in vitro antagonistic properties against fungal pathogens. A polyphasic approach was undertaken to verify its taxonomic status. Strain 2-92T was Gram-reaction-negative, aerobic, non-spore-forming, motile by one or more flagella, and oxidase-, catalase- and urease-positive. The optimal growth temperature of strain 2-92T was 30 °C. 16S rRNA gene sequence analysis demonstrated that the strain is related to species of the genus Pseudomonas. Phylogenetic analysis of six housekeeping genes (dnaA, gyrB, recA, recF, rpoB and rpoD) revealed that strain 2-92T clustered as a distinct and well separated lineage with Pseudomonassimiae as the most closely related species. Polar lipid and fatty acid compositions corroborated the taxonomic position of strain 2-92T in the genus Pseudomonas. Phenotypic characteristics from carbon utilization tests could be used to differentiate strain 2-92T from closely related species of the genus Pseudomonas. DNA-DNA hybridization values (wet laboratory and genome-based) and average nucleotide identity data confirmed that this strain represents a novel species. On the basis of phenotypic and genotypic characteristics, it is concluded that this strain represents a separate novel species for which the name Pseudomonas canadensis sp. nov. is proposed, with type strain 2-92T (=LMG 28499T=DOAB 798T). The DNA G+C content is 60.30 mol%.

  11. Mesenchymal Stem Cells as a Biological Drug for Heart Disease: Where Are We With Cardiac Cell-Based Therapy?

    Science.gov (United States)

    Sanina, Cristina; Hare, Joshua M

    2015-07-17

    Cell-based treatment represents a new generation in the evolution of biological therapeutics. A prototypic cell-based therapy, the mesenchymal stem cell, has successfully entered phase III pivotal trials for heart failure, signifying adequate enabling safety and efficacy data from phase I and II trials. Successful phase III trials can lead to approval of a new biological therapy for regenerative medicine. © 2015 American Heart Association, Inc.

  12. Inquiry-based training improves teaching effectiveness of biology teaching assistants

    Science.gov (United States)

    Hughes, P. William; Ellefson, Michelle R.

    2013-01-01

    Graduate teaching assistants (GTAs) are used extensively as undergraduate science lab instructors at universities, yet they often have having minimal instructional training and little is known about effective training methods. This blind randomized control trial study assessed the impact of two training regimens on GTA teaching effectiveness. GTAs teaching undergraduate biology labs (n = 52) completed five hours of training in either inquiry-based learning pedagogy or general instructional “best practices”. GTA teaching effectiveness was evaluated using: (1) a nine-factor student evaluation of educational quality; (2) a six-factor questionnaire for student learning; and (3) course grades. Ratings from both GTAs and undergraduates indicated that indicated that the inquiry-based learning pedagogy training has a positive effect on GTA teaching effectiveness. PMID:24147138

  13. Inquiry-based training improves teaching effectiveness of biology teaching assistants.

    Science.gov (United States)

    Hughes, P William; Ellefson, Michelle R

    2013-01-01

    Graduate teaching assistants (GTAs) are used extensively as undergraduate science lab instructors at universities, yet they often have having minimal instructional training and little is known about effective training methods. This blind randomized control trial study assessed the impact of two training regimens on GTA teaching effectiveness. GTAs teaching undergraduate biology labs (n = 52) completed five hours of training in either inquiry-based learning pedagogy or general instructional "best practices". GTA teaching effectiveness was evaluated using: (1) a nine-factor student evaluation of educational quality; (2) a six-factor questionnaire for student learning; and (3) course grades. Ratings from both GTAs and undergraduates indicated that indicated that the inquiry-based learning pedagogy training has a positive effect on GTA teaching effectiveness.

  14. Inquiry-based training improves teaching effectiveness of biology teaching assistants.

    Directory of Open Access Journals (Sweden)

    P William Hughes

    Full Text Available Graduate teaching assistants (GTAs are used extensively as undergraduate science lab instructors at universities, yet they often have having minimal instructional training and little is known about effective training methods. This blind randomized control trial study assessed the impact of two training regimens on GTA teaching effectiveness. GTAs teaching undergraduate biology labs (n = 52 completed five hours of training in either inquiry-based learning pedagogy or general instructional "best practices". GTA teaching effectiveness was evaluated using: (1 a nine-factor student evaluation of educational quality; (2 a six-factor questionnaire for student learning; and (3 course grades. Ratings from both GTAs and undergraduates indicated that indicated that the inquiry-based learning pedagogy training has a positive effect on GTA teaching effectiveness.

  15. Phases stability of shape memory alloys Cu based under irradiation

    International Nuclear Information System (INIS)

    Zelaya, Maria Eugenia

    2006-01-01

    The effects of irradiation on the relative phase stability of phases related by a martensitic transformation in copper based shape memory alloys were studied in this work.Different kind of particles and energies were employed in the irradiation experiments.The first kind of irradiation was performed with 2,6 MeV electrons, the second one with 170 keV and 300 keV Cu ions and the third one with swift heavy ions (Kr, Xe, Au) with energies between 200 and 600 MeV.Stabilization of the 18 R martensite in Cu-Zn-Al-Ni induced by electron irradiation was studied.The results were compared to those of the stabilization induced by quenching and ageing in the same alloy, and the ones obtained by irradiation in 18 R-Cu-Zn-Al alloys.The effects of Cu irradiation over b phase were analyzed with several electron microscopy techniques including: scanning electron microscopy (S E M), high resolution electron microscopy (H R E M), micro diffraction and X-ray energy dispersive spectroscopy (E D S). Structural changes in Cu-Zn-Al b phase into a closed packed structure were induced by Cu ion implantation.The closed packed structures depend on the irradiation fluence.Based on these results, the interface between these structures (closed packed and b) and the stability of disordered phases were analyzed. It was also compared the evolution of long range order in the Cu-Zn-Al and in the Cu-Zn-Al-Ni b phase as a function of fluence.The evolution of the g phase was also compared. Both results were discussed in terms of the mobility of irradiation induced point defects.Finally, the effects induced by swift heavy ions in b phase and 18 R martensite were studied. The results of the irradiation in b phase were qualitatively similar to those produced by irradiation with lower energies. On the contrary, nano metric defects were found in the irradiated 18 R martensite.These defects were characterized by H R E M.The characteristic contrast of the defects was associated to a local change in the

  16. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets

    Science.gov (United States)

    Li, Yang; Liu, Jun S.; Mootha, Vamsi K.

    2017-01-01

    In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression. CLIC accepts as input a pathway consisting of two or more genes. It then uses a Bayesian partition model to simultaneously partition the input gene set into coherent co-expressed modules (CEMs), while assigning the posterior probability for each dataset in support of each CEM. CLIC then expands each CEM by scanning the transcriptome for additional co-expressed genes, quantified by an integrated log-likelihood ratio (LLR) score weighted for each dataset. As a byproduct, CLIC automatically learns the conditions (datasets) within which a CEM is operative. We implemented CLIC using a compendium of 1774 mouse microarray datasets (28628 microarrays) or 1887 human microarray datasets (45158 microarrays). CLIC analysis reveals that of 910 canonical biological pathways, 30% consist of strongly co-expressed gene modules for which new members are predicted. For example, CLIC predicts a functional connection between protein C7orf55 (FMC1) and the mitochondrial ATP synthase complex that we have experimentally validated. CLIC is freely available at www.gene-clic.org. We anticipate that CLIC will be valuable both for revealing new components of biological pathways as well as the conditions in which they are active. PMID:28719601

  17. CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets.

    Directory of Open Access Journals (Sweden)

    Yang Li

    2017-07-01

    Full Text Available In recent years, there has been a huge rise in the number of publicly available transcriptional profiling datasets. These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways. Such analyses can be very challenging, however, since biological pathways are modular and may exhibit co-expression only in specific contexts. To overcome these challenges we introduce CLIC, CLustering by Inferred Co-expression. CLIC accepts as input a pathway consisting of two or more genes. It then uses a Bayesian partition model to simultaneously partition the input gene set into coherent co-expressed modules (CEMs, while assigning the posterior probability for each dataset in support of each CEM. CLIC then expands each CEM by scanning the transcriptome for additional co-expressed genes, quantified by an integrated log-likelihood ratio (LLR score weighted for each dataset. As a byproduct, CLIC automatically learns the conditions (datasets within which a CEM is operative. We implemented CLIC using a compendium of 1774 mouse microarray datasets (28628 microarrays or 1887 human microarray datasets (45158 microarrays. CLIC analysis reveals that of 910 canonical biological pathways, 30% consist of strongly co-expressed gene modules for which new members are predicted. For example, CLIC predicts a functional connection between protein C7orf55 (FMC1 and the mitochondrial ATP synthase complex that we have experimentally validated. CLIC is freely available at www.gene-clic.org. We anticipate that CLIC will be valuable both for revealing new components of biological pathways as well as the conditions in which they are active.

  18. Physical, chemical and biological studies of gelatin/chitosan based transdermal fims with embedded silver nanoparticles

    Directory of Open Access Journals (Sweden)

    Sneha Paul

    2015-12-01

    Full Text Available Objective: To study the physical, chemical and biological properties of composite chitosangelatin transdermal film along with silver nanoparticles as binding agent and determine the compatibility of the prepared amalgamation towards wound management. Methods: Transdermal film preparations were done by solvent casting method containing different concentrations of biological synthesized silver nanoparticles. The films were characterized by using scanning electron microscope for their morphology and the determination of silver metal was done by using inductively coupled plasma atomic emission spectroscopy. Then a quantity of silver nanoparticles was further proceeded by physiochemical parameters (weight, thickness, temperature, solubility, absorption, tensile strength, in vitro drug release and skin permeation and biological parameters studies (anti-microbial, cytotoxicity and reactive oxygen species. Results: The film prepared by utilizing 2 g of gelatin and 0.5 g of chitosan exhibited better results. The physiochemical parameters studies revealed higher concentration of silver nanoparticles would give better results. In vitro drug release studies through dialysis and skin permeation showed the release of drug versus time (h. These films had shown excellent inhibition against Streptococcus and Escherichia coli species. Cytotoxicity study by MTT indicated the mild toxicity existed as the concentration of silver nanoparticles increased. Reactive oxygen species generation studies of transdermal film by using 2'7'-dichlorofluorescein diacetate assay demonstrated that the fluorescent cells were found in the higher concentration, which indicated cell damage (reactive oxygen species generated. Conclusions: Based on these observations, in vitro performances against various characteristics of transdermal film, would be utilized as a distinct dressing material and patches accessible in market.

  19. A Novel Robot System Integrating Biological and Mechanical Intelligence Based on Dissociated Neural Network-Controlled Closed-Loop Environment.

    Science.gov (United States)

    Li, Yongcheng; Sun, Rong; Wang, Yuechao; Li, Hongyi; Zheng, Xiongfei

    2016-01-01

    We propose the architecture of a novel robot system merging biological and artificial intelligence based on a neural controller connected to an external agent. We initially built a framework that connected the dissociated neural network to a mobile robot system to implement a realistic vehicle. The mobile robot system characterized by a camera and two-wheeled robot was designed to execute the target-searching task. We modified a software architecture and developed a home-made stimulation generator to build a bi-directional connection between the biological and the artificial components via simple binomial coding/decoding schemes. In this paper, we utilized a specific hierarchical dissociated neural network for the first time as the neural controller. Based on our work, neural cultures were successfully employed to control an artificial agent resulting in high performance. Surprisingly, under the tetanus stimulus training, the robot performed better and better with the increasement of training cycle because of the short-term plasticity of neural network (a kind of reinforced learning). Comparing to the work previously reported, we adopted an effective experimental proposal (i.e. increasing the training cycle) to make sure of the occurrence of the short-term plasticity, and preliminarily demonstrated that the improvement of the robot's performance could be caused independently by the plasticity development of dissociated neural network. This new framework may provide some possible solutions for the learning abilities of intelligent robots by the engineering application of the plasticity processing of neural networks, also for the development of theoretical inspiration for the next generation neuro-prostheses on the basis of the bi-directional exchange of information within the hierarchical neural networks.

  20. A Novel Robot System Integrating Biological and Mechanical Intelligence Based on Dissociated Neural Network-Controlled Closed-Loop Environment.

    Directory of Open Access Journals (Sweden)

    Yongcheng Li

    Full Text Available We propose the architecture of a novel robot system merging biological and artificial intelligence based on a neural controller connected to an external agent. We initially built a framework that connected the dissociated neural network to a mobile robot system to implement a realistic vehicle. The mobile robot system characterized by a camera and two-wheeled robot was designed to execute the target-searching task. We modified a software architecture and developed a home-made stimulation generator to build a bi-directional connection between the biological and the artificial components via simple binomial coding/decoding schemes. In this paper, we utilized a specific hierarchical dissociated neural network for the first time as the neural controller. Based on our work, neural cultures were successfully employed to control an artificial agent resulting in high performance. Surprisingly, under the tetanus stimulus training, the robot performed better and better with the increasement of training cycle because of the short-term plasticity of neural network (a kind of reinforced learning. Comparing to the work previously reported, we adopted an effective experimental proposal (i.e. increasing the training cycle to make sure of the occurrence of the short-term plasticity, and preliminarily demonstrated that the improvement of the robot's performance could be caused independently by the plasticity development of dissociated neural network. This new framework may provide some possible solutions for the learning abilities of intelligent robots by the engineering application of the plasticity processing of neural networks, also for the development of theoretical inspiration for the next generation neuro-prostheses on the basis of the bi-directional exchange of information within the hierarchical neural networks.

  1. Alfven Waves Underlying Ionospheric Destabilization: Ground-Based Observations

    Science.gov (United States)

    Hirsch, Michael

    During geomagnetic storms, terawatts of power in the million mile-per-hour solar wind pierce the Earth's magnetosphere. Geomagnetic storms and substorms create transverse magnetic waves known as Alfven waves. In the auroral acceleration region, Alfven waves accelerate electrons up to one-tenth the speed of light via wave-particle interactions. These inertial Alfven wave (IAW) accelerated electrons are imbued with sub-100 meter structure perpendicular to geomagnetic field B. The IAW electric field parallel to B accelerates electrons up to about 10 keV along B. The IAW dispersion relation quantifies the precipitating electron striation observed with high-speed cameras as spatiotemporally dynamic fine structured aurora. A network of tightly synchronized tomographic auroral observatories using model based iterative reconstruction (MBIR) techniques were developed in this dissertation. The TRANSCAR electron penetration model creates a basis set of monoenergetic electron beam eigenprofiles of auroral volume emission rate for the given location and ionospheric conditions. Each eigenprofile consists of nearly 200 broadband line spectra modulated by atmospheric attenuation, bandstop filter and imager quantum efficiency. The L-BFGS-B minimization routine combined with sub-pixel registered electron multiplying CCD video stream at order 10 ms cadence yields estimates of electron differential number flux at the top of the ionosphere. Our automatic data curation algorithm reduces one terabyte/camera/day into accurate MBIR-processed estimates of IAW-driven electron precipitation microstructure. This computer vision structured auroral discrimination algorithm was developed using a multiscale dual-camera system observing a 175 km and 14 km swath of sky simultaneously. This collective behavior algorithm exploits the "swarm" behavior of aurora, detectable even as video SNR approaches zero. A modified version of the algorithm is applied to topside ionospheric radar at Mars and

  2. Effects of Web Based Inquiry Science Environment on Cognitive Outcomes in Biological Science in Correlation to Emotional Intelligence

    Science.gov (United States)

    Manoj, T. I.; Devanathan, S.

    2010-01-01

    This research study is the report of an experiment conducted to find out the effects of web based inquiry science environment on cognitive outcomes in Biological science in correlation to Emotional intelligence. Web based inquiry science environment (WISE) provides a platform for creating inquiry-based science projects for students to work…

  3. Testing Silica Fume-Based Concrete Composites under Chemical and Microbiological Sulfate Attacks

    Directory of Open Access Journals (Sweden)

    Adriana Estokova

    2016-04-01

    Full Text Available Current design practices based on descriptive approaches to concrete specification may not be appropriate for the management of aggressive environments. In this study, the durability of cement-based materials with and without the addition of silica fume, subjected to conditions that leach calcium and silicon, were investigated. Chemical corrosion was simulated by employing various H2SO4 and MgSO4 solutions, and biological corrosion was simulated using Acidithiobacillus sp. bacterial inoculation, leading to disrupted and damaged surfaces; the samples’ mass changes were studied following both chemical and biological attacks. Different leaching trends were observed via X-ray fluorescence when comparing chemical with biological leaching. Lower leaching rates were found for concrete samples fortified with silica fume than those without silica fume. X-ray diffraction and scanning electron microscopy confirmed a massive sulfate precipitate formation on the concrete surface due to bacterial exposure.

  4. Genome-Based Characterization of Biological Processes That Differentiate Closely Related Bacteria.

    Science.gov (United States)

    Palmer, Marike; Steenkamp, Emma T; Coetzee, Martin P A; Blom, Jochen; Venter, Stephanus N

    2018-01-01

    Bacteriologists have strived toward attaining a natural classification system based on evolutionary relationships for nearly 100 years. In the early twentieth century it was accepted that a phylogeny-based system would be the most appropriate, but in the absence of molecular data, this approach proved exceedingly difficult. Subsequent technical advances and the increasing availability of genome sequencing have allowed for the generation of robust phylogenies at all taxonomic levels. In this study, we explored the possibility of linking biological characters to higher-level taxonomic groups in bacteria by making use of whole genome sequence information. For this purpose, we specifically targeted the genus Pantoea and its four main lineages. The shared gene sets were determined for Pantoea , the four lineages within the genus, as well as its sister-genus Tatumella . This was followed by functional characterization of the gene sets using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In comparison to Tatumella , various traits involved in nutrient cycling were identified within Pantoea , providing evidence for increased efficacy in recycling of metabolites within the genus. Additionally, a number of traits associated with pathogenicity were identified within species often associated with opportunistic infections, with some support for adaptation toward overcoming host defenses. Some traits were also only conserved within specific lineages, potentially acquired in an ancestor to the lineage and subsequently maintained. It was also observed that the species isolated from the most diverse sources were generally the most versatile in their carbon metabolism. By investigating evolution, based on the more variable genomic regions, it may be possible to detect biologically relevant differences associated with the course of evolution and speciation.

  5. Bridging cancer biology and the patients' needs with nanotechnology-based approaches.

    Science.gov (United States)

    Fonseca, Nuno A; Gregório, Ana C; Valério-Fernandes, Angela; Simões, Sérgio; Moreira, João N

    2014-06-01

    Cancer remains as stressful condition and a leading cause of death in the western world. Actual cornerstone treatments of cancer disease rest as an elusive alternative, offering limited efficacy with extensive secondary effects as a result of severe cytotoxic effects in healthy tissues. The advent of nanotechnology brought the promise to revolutionize many fields including oncology, proposing advanced systems for cancer treatment. Drug delivery systems rest among the most successful examples of nanotechnology. Throughout time they have been able to evolve as a function of an increased understanding from cancer biology and the tumor microenvironment. Marketing of Doxil® unleashed a remarkable impulse in the development of drug delivery systems. Since then, several nanocarriers have been introduced, with aspirations to overrule previous technologies, demonstrating increased therapeutic efficacy besides decreased toxicity. Spatial and temporal targeting to cancer cells has been explored, as well as the use of drug combinations co-encapsulated in the same particle as a mean to take advantage of synergistic interactions in vivo. Importantly, targeted delivery of siRNA for gene silencing therapy has made its way to the clinic for a "first in man" trial using lipid-polymeric-based particles. Focusing in state-of-the-art technology, this review will provide an insightful vision on nanotechnology-based strategies for cancer treatment, approaching them from a tumor biology-driven perspective, since their early EPR-based dawn to the ones that have truly the potential to address unmet medical needs in the field of oncology, upon targeting key cell subpopulations from the tumor microenvironment. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. 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.

  7. RiceGeneThresher: a web-based application for mining genes underlying QTL in rice genome.

    Science.gov (United States)

    Thongjuea, Supat; Ruanjaichon, Vinitchan; Bruskiewich, Richard; Vanavichit, Apichart

    2009-01-01

    RiceGeneThresher is a public online resource for mining genes underlying genome regions of interest or quantitative trait loci (QTL) in rice genome. It is a compendium of rice genomic resources consisting of genetic markers, genome annotation, expressed sequence tags (ESTs), protein domains, gene ontology, plant stress-responsive genes, metabolic pathways and prediction of protein-protein interactions. RiceGeneThresher system integrates these diverse data sources and provides powerful web-based applications, and flexible tools for delivering customized set of biological data on rice. Its system supports whole-genome gene mining for QTL by querying using DNA marker intervals or genomic loci. RiceGeneThresher provides biologically supported evidences that are essential for targeting groups or networks of genes involved in controlling traits underlying QTL. Users can use it to discover and to assign the most promising candidate genes in preparation for the further gene function validation analysis. The web-based application is freely available at http://rice.kps.ku.ac.th.

  8. A hybrid biology course: Implications of merging Internet-enhanced and campus-based instructional modes

    Science.gov (United States)

    Clark, Sharron Ann

    This is possibly the first study of a hybrid online biology course where WebCT internet-enhanced modes of instruction replaced conventional face-to-face (F2F) lecture materials, merging with collaborative inquiry-based on-campus laboratory instructional modes. Although not a true experiment, the design of this study included three independent cohorts, a pretest and three posttests, as described by Gay and Airasian (2000). This study reported differences in age, gender, number of prior online courses and pretest scores. Over time, persistence, achievement and computer self-efficacy differed in one hybrid online section (N = 31) and two F2F cohorts (N = 29 and 30). One F2F cohort used written test materials and the other used intranet-delivered materials to examine possible differences in groups using electronic assessment modes. In this study, community college students self-selecting into online hybrid and traditional versions of the same biology course did not have the same number of prior online courses, achievement or persistence rates as those self-selecting into F2F sections of the same course with the same laboratories and instructor. This study includes twenty pretest items selected from Instructor's Manual and Test Item File to Accompany: Inquiry into Life, 9th Edition (Schrock, 2000). This study produced 63 tables, 13 figures and 173 references.

  9. Pulp development, repair, and regeneration: challenges of the transition from traditional dentistry to biologically based therapies.

    Science.gov (United States)

    Schmalz, Gottfried; Smith, Anthony J

    2014-04-01

    The traditional concept of replacing diseased tooth/pulp tissues by inert materials (restoration) is being challenged by recent advances in pulp biology leading to regenerative strategies aiming at the generation of new vital tissue. New tissue formation in the pulp chamber can be observed after adequate infection control and the formation of a blood clot. However, differentiation of true odontoblasts is still more speculative, and the approach is largely limited to immature teeth with open apices. A more systematic approach may be provided by the adoption of the tissue engineering concepts of using matrices, suitable (stem) cells, and signaling molecules to direct tissue events. With these tools, pulplike constructs have already been generated in experimental animals. However, a number of challenges still remain for clinical translation of pulp regeneration (eg, the cell source [resident vs nonresident stem cells, the latter associated with cell-free approaches], mechanisms of odontoblast differentiation, the pulp environment, the role of infection and inflammation, dentin pretreatment to release fossilized signaling molecules from dentin, and the provision of suitable matrices). Transition as a process, defined by moving from one form of "normal" to another, is based not only on the progress of science but also on achieving change to established treatment concepts in daily practice. However, it is clear that the significant recent achievements in pulp biology are providing an exciting platform from which clinical translation of dental pulp regeneration can advance. Copyright © 2014. Published by Elsevier Inc.

  10. New, simple theory-based, accurate polarization microscope for birefringence imaging of biological cells

    Science.gov (United States)

    Shin, In Hee; Shin, Sang-Mo; Kim, Dug Young

    2010-01-01

    We propose a new, simple theory-based, accurate polarization microscope for birefringence imaging of cytoskeletal structures of biological cells. The new theory lets us calculate very easily the phase retardation and the orientation of the principal axis of a particular area of a biological living cell in media by simply measuring the intensity variation of a pixel of a CCD camera while rotating a single polarizer. Just from the measured intensity maxima and minima, the amount of phase retardation δ between the fast and the slow axis of the sample area is obtained with an accuracy of 5.010+/-0.798×10-3 rad. The orientation of the principal axis is calculated from the angle of the polarizer for the intensity maximum. We have compared our microscopes with two previously reported polarization microscopes for birefringence imaging of cytoskeletal structures and demonstrated the utility of our microscope with the phase retardation and orientation images of weakly invasive MCF7 and highly invasive MDA MB 231 human breast cancer cells as an example.

  11. Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

    Science.gov (United States)

    Brohée, Sylvain; Barriot, Roland; Moreau, Yves

    2010-09-01

    In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

  12. Cancer stem cells in hepatocellular carcinoma: Therapeutic implications based on stem cell biology.

    Science.gov (United States)

    Chiba, Tetsuhiro; Iwama, Atsushi; Yokosuka, Osamu

    2016-01-01

    Hepatocellular carcinoma (HCC) is the sixth most common cancer and the third most frequent cause of cancer-related death worldwide. Despite advances in its diagnosis and treatment, the prognosis of patients with advanced HCC remains unfavorable. Recent advances in stem cell biology and associated technologies have enabled the identification of minor components of tumorigenic cells, termed cancer stem cells (CSC) or tumor-initiating cells, in cancers such as HCC. Furthermore, because CSC play a central role in tumor development, metastasis and recurrence, they are considered to be a therapeutic target in cancer treatment. Hepatic CSC have been successfully identified using functional and cell surface markers. The analysis of purified hepatic CSC has revealed the molecular machinery and signaling pathways involved in their maintenance. In addition, epigenetic transcriptional regulation has been shown to be important in the development and maintenance of CSC. Although inhibitors of CSC show promise as CSC-targeting drugs, novel therapeutic approaches for the eradication of CSC are yet to be established. In this review, we describe recent progress in hepatic CSC research and provide a perspective on the available therapeutic approaches based on stem cell biology. © 2015 The Japan Society of Hepatology.

  13. A phenomenological biological dose model for proton therapy based on linear energy transfer spectra.

    Science.gov (United States)

    Rørvik, Eivind; Thörnqvist, Sara; Stokkevåg, Camilla H; Dahle, Tordis J; Fjaera, Lars Fredrik; Ytre-Hauge, Kristian S

    2017-06-01

    The relative biological effectiveness (RBE) of protons varies with the radiation quality, quantified by the linear energy transfer (LET). Most phenomenological models employ a linear dependency of the dose-averaged LET (LET d ) to calculate the biological dose. However, several experiments have indicated a possible non-linear trend. Our aim was to investigate if biological dose models including non-linear LET dependencies should be considered, by introducing a LET spectrum based dose model. The RBE-LET relationship was investigated by fitting of polynomials from 1st to 5th degree to a database of 85 data points from aerobic in vitro experiments. We included both unweighted and weighted regression, the latter taking into account experimental uncertainties. Statistical testing was performed to decide whether higher degree polynomials provided better fits to the data as compared to lower degrees. The newly developed models were compared to three published LET d based models for a simulated spread out Bragg peak (SOBP) scenario. The statistical analysis of the weighted regression analysis favored a non-linear RBE-LET relationship, with the quartic polynomial found to best represent the experimental data (P = 0.010). The results of the unweighted regression analysis were on the borderline of statistical significance for non-linear functions (P = 0.053), and with the current database a linear dependency could not be rejected. For the SOBP scenario, the weighted non-linear model estimated a similar mean RBE value (1.14) compared to the three established models (1.13-1.17). The unweighted model calculated a considerably higher RBE value (1.22). The analysis indicated that non-linear models could give a better representation of the RBE-LET relationship. However, this is not decisive, as inclusion of the experimental uncertainties in the regression analysis had a significant impact on the determination and ranking of the models. As differences between the models were

  14. Effcacy of different biological control agents against major postharvest pathogens of grapes under room temperature storage conditions

    Directory of Open Access Journals (Sweden)

    Ramu SENTHIL

    2011-05-01

    Full Text Available Normal 0 14 false false false IT ZH-TW X-NONE MicrosoftInternetExplorer4 Grapes were treated post harvest with a variety of biological agents to determine their effcacy in reducing yield loss. The agents Pseudomonas, Bacillus, Trichoderma and yeast isolates were individually screened against a number of postharvest pathogens including Aspergillus carbonarius, Penicillum expansum, and Fusarium moniliforme. B. subtilis strains EPC-8 and EPCO-16 showed high mycelial growth suppression of A. carbonarius and P. expansum  in vitro. The fungal antagonist Trichoderma viride strain (Tv Tvm was the most effective, inhibiting mycelial growth by 88.8 per cent. The biological control agents were tested in pre, post and combined inoculation studies against postharvest pathogens of grapes.  In the pre inoculation, B. subtilis (EPC-8 reduced the disease incidence of A. carbonarius causing rot, T. harzianum (Th Co was effective against P. expansum, and T. viride (Tv Tvm was effective against F. moniliforme. The same trend of effectiveness was also found in the post-inoculation and combined inoculation tests.

  15. Reality-based practice under pressure improves handgun shooting performance of police officers.

    NARCIS (Netherlands)

    Oudejans, R.R.D.

    2008-01-01

    The current study examined whether reality-based practice under pressure may help in preventing degradation of handgun shooting performance under pressure for police officers. Using a pre-post-test design, one group of nine police officers practised handgun shooting under pressure evoked by an

  16. The biological effectiveness of targeted radionuclide therapy based on a whole-body pharmacokinetic model

    Science.gov (United States)

    Grudzinski, Joseph J; Tomé, Wolfgang; Weichert, Jamey P; Jeraj, Robert

    2013-01-01

    Biologically effective dose (BED) may be more of a relevant quantity than absorbed dose for establishing tumour response relationships. By taking into account the dose rate and tissue-specific parameters such as repair and radiosensitivity, it is possible to compare the relative biological effects of different targeted radionuclide therapy (TRT) agents. The aim of this work was to develop an analytical tumour BED calculation for TRT that could predict a relative biological effect based on normal body and tumour pharmacokinetics. This work represents a step in the direction of establishing relative pharmacokinetic criteria of when the BED formalism is more applicable than absorbed dose for TRT. A previously established pharmacokinetic (PK) model for TRT was used and adapted into the BED formalism. An analytical equation for the protraction factor, which incorporates dose rate and repair rate, was derived. Dose rates within the normal body and tumour were related to the slopes of their time–activity curves which were determined by the ratios of their respective PK parameters. The relationships between the tumour influx-to-efflux ratio (k34:k43), central compartment efflux-to-influx ratio (k12:k21), central elimination (kel), and tumour repair rate (μ), and tumour BED were investigated. As the k34:k43 ratio increases and the k12:k21 ratio decreases, the difference between tumour BED and D increases. In contrast, as the k34:k43 ratios decrease and the k12:k21 ratios increase, the tumour BED approaches D. At large k34:k43 ratios, the difference between tumour BED and D increases to a maximum as kel increases. At small k34:k43 ratios, the tumour BED approaches D at very small kel. At small μ and small k34:k43 ratios, the tumour BED approaches D. For large k34:k43 ratios, large μ values cause tumour BED to approach D. This work represents a step in the direction of establishing relative PK criteria of when the BED formalism is more applicable than absorbed dose for

  17. Dynamic neuronal ensembles: Issues in representing structure change in object-oriented, biologically-based brain models

    Energy Technology Data Exchange (ETDEWEB)

    Vahie, S.; Zeigler, B.P.; Cho, H. [Univ. of Arizona, Tucson, AZ (United States)

    1996-12-31

    This paper describes the structure of dynamic neuronal ensembles (DNEs). DNEs represent a new paradigm for learning, based on biological neural networks that use variable structures. We present a computational neural element that demonstrates biological neuron functionality such as neurotransmitter feedback absolute refractory period and multiple output potentials. More specifically, we will develop a network of neural elements that have the ability to dynamically strengthen, weaken, add and remove interconnections. We demonstrate that the DNE is capable of performing dynamic modifications to neuron connections and exhibiting biological neuron functionality. In addition to its applications for learning, DNEs provide an excellent environment for testing and analysis of biological neural systems. An example of habituation and hyper-sensitization in biological systems, using a neural circuit from a snail is presented and discussed. This paper provides an insight into the DNE paradigm using models developed and simulated in DEVS.

  18. Steady state visual evoked potential (SSVEP based brain-computer interface (BCI performance under different perturbations.

    Directory of Open Access Journals (Sweden)

    Zafer İşcan

    Full Text Available Brain-computer interface (BCI paradigms are usually tested when environmental and biological artifacts are intentionally avoided. In this study, we deliberately introduced different perturbations in order to test the robustness of a steady state visual evoked potential (SSVEP based BCI. Specifically we investigated to what extent a drop in performance is related to the degraded quality of EEG signals or rather due to increased cognitive load. In the online tasks, subjects focused on one of the four circles and gave feedback on the correctness of the classification under four conditions randomized across subjects: Control (no perturbation, Speaking (counting loudly and repeatedly from one to ten, Thinking (mentally counting repeatedly from one to ten, and Listening (listening to verbal counting from one to ten. Decision tree, Naïve Bayes and K-Nearest Neighbor classifiers were used to evaluate the classification performance using features generated by canonical correlation analysis. During the online condition, Speaking and Thinking decreased moderately the mean classification accuracy compared to Control condition whereas there was no significant difference between Listening and Control conditions across subjects. The performances were sensitive to the classification method and to the perturbation conditions. We have not observed significant artifacts in EEG during perturbations in the frequency range of interest except in theta band. Therefore we concluded that the drop in the performance is likely to have a cognitive origin. During the Listening condition relative alpha power in a broad area including central and temporal regions primarily over the left hemisphere correlated negatively with the performance thus most likely indicating active suppression of the distracting presentation of the playback. This is the first study that systematically evaluates the effects of natural artifacts (i.e. mental, verbal and audio perturbations on SSVEP-based

  19. Steady state visual evoked potential (SSVEP) based brain-computer interface (BCI) performance under different perturbations.

    Science.gov (United States)

    İşcan, Zafer; Nikulin, Vadim V

    2018-01-01

    Brain-computer interface (BCI) paradigms are usually tested when environmental and biological artifacts are intentionally avoided. In this study, we deliberately introduced different perturbations in order to test the robustness of a steady state visual evoked potential (SSVEP) based BCI. Specifically we investigated to what extent a drop in performance is related to the degraded quality of EEG signals or rather due to increased cognitive load. In the online tasks, subjects focused on one of the four circles and gave feedback on the correctness of the classification under four conditions randomized across subjects: Control (no perturbation), Speaking (counting loudly and repeatedly from one to ten), Thinking (mentally counting repeatedly from one to ten), and Listening (listening to verbal counting from one to ten). Decision tree, Naïve Bayes and K-Nearest Neighbor classifiers were used to evaluate the classification performance using features generated by canonical correlation analysis. During the online condition, Speaking and Thinking decreased moderately the mean classification accuracy compared to Control condition whereas there was no significant difference between Listening and Control conditions across subjects. The performances were sensitive to the classification method and to the perturbation conditions. We have not observed significant artifacts in EEG during perturbations in the frequency range of interest except in theta band. Therefore we concluded that the drop in the performance is likely to have a cognitive origin. During the Listening condition relative alpha power in a broad area including central and temporal regions primarily over the left hemisphere correlated negatively with the performance thus most likely indicating active suppression of the distracting presentation of the playback. This is the first study that systematically evaluates the effects of natural artifacts (i.e. mental, verbal and audio perturbations) on SSVEP-based BCIs. The

  20. Synthesis, characterization and biological assay of Salicylaldehyde Schiff base Cu(II) complexes and their precursors

    Science.gov (United States)

    Iftikhar, Bushra; Javed, Kanwal; Khan, Muhammad Saif Ullah; Akhter, Zareen; Mirza, Bushra; Mckee, Vickie

    2018-03-01

    Three new Schiff base ligands were synthesized by the reaction of Salicylaldehyde with semi-aromatic diamines, prepared by the reduction of corresponding dinitro-compounds, and were further used for the formation of complexes with Cu(II) metal ion. The structural features of the synthesized compounds were confirmed by their physical properties and infrared, electronic and NMR spectroscopic techniques. The studies revealed that the synthesized Schiff bases existed as tetradentate ligands and bonded to the metal ion through the phenolic oxygen and azomethine nitrogen. One of the dinitro precursors was also analyzed by single crystal X-ray crystallography, which showed that it crystallizes in monoclinic system with space group P2/n. The thermal behavior of the Cu(II) complexes was determined by thermogravimetric analysis (TGA) and kinetic parameters were evaluated from the data. Schiff base ligands, their precursors and metal complexes were also screened for antibacterial, antifungal, antitumor, Brine shrimp lethality, DPPH free radical scavenging and DNA damage assays. The results of these analyses indicated the substantial potential of the synthesized Schiff bases, their precursors and Cu(II) complexes in biological field as future drugs.

  1. Synthesis, characterization and biological behavior of some Schiff's and Mannich base derivatives of Lamotrigine

    Directory of Open Access Journals (Sweden)

    A.A. Kulkarni

    2017-02-01

    Full Text Available A series of various Schiff's and Mannich base derivatives (N1–2 & ND1–6 of Lamotrigine with isatin and substituted isatin were synthesized to get more potent anticonvulsant agents. The starting material for the synthesis of various new Schiff's and Mannich base derivatives was isatin (1H-indole- 2, 3-dione which in turn was prepared from substituted isonitrosoacetanilide using aniline. Lamotrigine reacts with isatin & substituted isatin gave Schiff's bases (N1–2 which on reaction with various secondary amines (dimethylamine, diethylamine, morpholine produced Mannich bases (ND1–6. The structures of newly synthesized compounds were characterized by using TLC, UV, FT-IR, 1HNMR and studied for their anticonvulsant activity. Anticonvulsant activity of all the derivatives was evaluated by MES method using phenobarbitone sodium & Lamotrigine as standard drugs and % reduction of time spent by animals in extension, flexion, clonus, and stupor phase were noted. Compounds ND-4 and ND-6 showed significant anticonvulsant activity when compared with that of standard drugs. The remaining all compounds show moderate activity. Biological activity data of the synthesized derivatives revealed that, the synthesized derivatives are good anticonvulsant agents as compared to Lamotrigine.

  2. Review for carrageenan-based pharmaceutical biomaterials: favourable physical features versus adverse biological effects.

    Science.gov (United States)

    Liu, Jingjing; Zhan, Xiudan; Wan, Jianbo; Wang, Yitao; Wang, Chunming

    2015-05-05

    Carrageenan (CRG) is a family of natural polysaccharides derived from seaweeds and has widely been used as food additives. In the past decade, owing to its attractive physicochemical properties, CRG has been developed into versatile biomaterials vehicles for drug delivery. Nevertheless, studies also emerged to reveal its adverse effects on the biological system. In this review, we critically appraise the latest literature (two thirds since 2008) on the development of CRG-based pharmaceutical vehicles and the perspective of using CRG for broader biomedical applications. We focus on how current strategies exploit the unique gelling mechanisms, strong water absorption and abundant functional groups of the three major CRG varieties. Notably, CRG-based matrices are demonstrated to increase drug loading and drug solubility, enabling release of orally administrated drugs in zero-order or in a significantly prolonged period. Other amazing features, such as pH-sensitivity and adhesive property, of CRG-based formulations are also introduced. Finally, we discuss the adverse influence of CRG on the human body and then suggest some future directions for the development of CRG-based biomaterials for broader applications in biomedicine. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Priority Queue Based Reactive Buffer Management Policy for Delay Tolerant Network under City Based Environments

    Science.gov (United States)

    Ngadi, Asri; Rashid, Sulma; Habib, Hafiz Adnan

    2018-01-01

    Delay Tolerant Network (DTN) multi-copy routing protocols are privileged to create and transmit multiple copies of each message that causes congestion and some messages are dropped. This process is known as reactive drop because messages were dropped re-actively to overcome buffer overflows. The existing reactive buffer management policies apply a single metric to drop source, relay and destine messages. Hereby, selection to drop a message is dubious because each message as source, relay or destine may have consumed dissimilar magnitude of network resources. Similarly, DTN has included time to live (ttl) parameter which defines lifetime of message. Hence, when ttl expires then message is automatically destroyed from relay nodes. However, time-to-live (ttl) is not applicable on messages reached at their destinations. Moreover, nodes keep replicating messages till ttl expires even-though large number of messages has already been dispersed. In this paper, we have proposed Priority Queue Based Reactive Buffer Management Policy (PQB-R) for DTN under City Based Environments. The PQB-R classifies buffered messages into source, relay and destine queues. Moreover, separate drop metric has been applied on individual queue. The experiment results prove that proposed PQB-R has reduced number of messages transmissions, message drop and increases delivery ratio. PMID:29438438

  4. Priority Queue Based Reactive Buffer Management Policy for Delay Tolerant Network under City Based Environments.

    Directory of Open Access Journals (Sweden)

    Qaisar Ayub

    Full Text Available Delay Tolerant Network (DTN multi-copy routing protocols are privileged to create and transmit multiple copies of each message that causes congestion and some messages are dropped. This process is known as reactive drop because messages were dropped re-actively to overcome buffer overflows. The existing reactive buffer management policies apply a single metric to drop source, relay and destine messages. Hereby, selection to drop a message is dubious because each message as source, relay or destine may have consumed dissimilar magnitude of network resources. Similarly, DTN has included time to live (ttl parameter which defines lifetime of message. Hence, when ttl expires then message is automatically destroyed from relay nodes. However, time-to-live (ttl is not applicable on messages reached at their destinations. Moreover, nodes keep replicating messages till ttl expires even-though large number of messages has already been dispersed. In this paper, we have proposed Priority Queue Based Reactive Buffer Management Policy (PQB-R for DTN under City Based Environments. The PQB-R classifies buffered messages into source, relay and destine queues. Moreover, separate drop metric has been applied on individual queue. The experiment results prove that proposed PQB-R has reduced number of messages transmissions, message drop and increases delivery ratio.

  5. Biological Course-Based Undergraduate Research Experiences: An Examination of an Introductory Level Implementation

    Science.gov (United States)

    Knoth, Kenneth Charles

    Course-based undergraduate research experiences (CUREs) provide authentic research benefits to an entire laboratory course population. CURE experiences are proposed to enhance research skills, critical thinking, productivity, and retention in science. CURE curriculum developers face numerous obstacles, such as the logistics and time commitment involved in bringing a CURE to larger student populations. In addition, an ideal CURE topic requires affordable resources, lab techniques that can be quickly mastered, time for multiple iterations within one semester, and the opportunity to generate new data. This study identifies some of the CURE activities that lead to proposed participant outcomes. Introductory Biology I CURE lab students at Southern Illinois University Edwardsville completed research related to the process of converting storage lipids in microalgae into biodiesel. Data collected from CURE and traditional lab student participants indicate increased CURE student reports of project ownership, scientific self-efficacy, identification as a scientist, and sense of belonging to a science community. Study limitations and unanticipated benefits are discussed.

  6. Fractional Calculus Based FDTD Modeling of Layered Biological Media Exposure to Wideband Electromagnetic Pulses

    Directory of Open Access Journals (Sweden)

    Luciano Mescia

    2017-11-01

    Full Text Available Electromagnetic fields are involved in several therapeutic and diagnostic applications such as hyperthermia and electroporation. For these applications, pulsed electric fields (PEFs and transient phenomena are playing a key role for understanding the biological response due to the exposure to non-ionizing wideband pulses. To this end, the PEF propagation in the six-layered planar structure modeling the human head has been studied. The electromagnetic field and the specific absorption rate (SAR have been calculated through an accurate finite-difference time-domain (FDTD dispersive modeling based on the fractional derivative operator. The temperature rise inside the tissues due to the electromagnetic field exposure has been evaluated using both the non-thermoregulated and thermoregulated Gagge’s two-node models. Moreover, additional parametric studies have been carried out with the aim to investigate the thermal response by changing the amplitude and duration of the electric pulses.

  7. Surface plasmon resonance based sensing of different chemical and biological samples using admittance loci method

    Science.gov (United States)

    Brahmachari, Kaushik; Ghosh, Sharmila; Ray, Mina

    2013-06-01

    The admittance loci method plays an important role in the design of multilayer thin film structures. In this paper, admittance loci method has been explored theoretically for sensing of various chemical and biological samples based on surface plasmon resonance (SPR) phenomenon. A dielectric multilayer structure consisting of a Boro silicate glass (BSG) substrate, calcium fluoride (CaF2) and zirconium dioxide (ZrO2) along with different dielectric layers has been investigated. Moreover, admittance loci as well as SPR curves of metal-dielectric multilayer structure consisting of the BSG substrate, gold metal film and various dielectric samples has been simulated in MATLAB environment. To validate the proposed simulation results, calibration curves have also been provided.

  8. Perceptron-like computation based on biologically-inspired neurons with heterosynaptic mechanisms

    Science.gov (United States)

    Kaluza, Pablo; Urdapilleta, Eugenio

    2014-10-01

    Perceptrons are one of the fundamental paradigms in artificial neural networks and a key processing scheme in supervised classification tasks. However, the algorithm they provide is given in terms of unrealistically simple processing units and connections and therefore, its implementation in real neural networks is hard to be fulfilled. In this work, we present a neural circuit able to perform perceptron's computation based on realistic models of neurons and synapses. The model uses Wang-Buzsáki neurons with coupling provided by axodendritic and axoaxonic synapses (heterosynapsis). The main characteristics of the feedforward perceptron operation are conserved, which allows to combine both approaches: whereas the classical artificial system can be used to learn a particular problem, its solution can be directly implemented in this neural circuit. As a result, we propose a biologically-inspired system able to work appropriately in a wide range of frequencies and system parameters, while keeping robust to noise and error.

  9. VisBOL: Web-Based Tools for Synthetic Biology Design Visualization.

    Science.gov (United States)

    McLaughlin, James Alastair; Pocock, Matthew; Mısırlı, Göksel; Madsen, Curtis; Wipat, Anil

    2016-08-19

    VisBOL is a Web-based application that allows the rendering of genetic circuit designs, enabling synthetic biologists to visually convey designs in SBOL visual format. VisBOL designs can be exported to formats including PNG and SVG images to be embedded in Web pages, presentations and publications. The VisBOL tool enables the automated generation of visualizations from designs specified using the Synthetic Biology Open Language (SBOL) version 2.0, as well as a range of well-known bioinformatics formats including GenBank and Pigeoncad notation. VisBOL is provided both as a user accessible Web site and as an open-source (BSD) JavaScript library that can be used to embed diagrams within other content and software.

  10. Energy-based control for a biologically inspired hexapod robot with rolling locomotion

    Directory of Open Access Journals (Sweden)

    Takuma Nemoto

    2015-04-01

    Full Text Available This paper presents an approach to control rolling locomotion on the level ground with a biologically inspired hexapod robot. For controlling rolling locomotion, a controller which can compensate energy loss with rolling locomotion of the hexapod robot is designed based on its dynamic model. The dynamic model describes the rolling locomotion which is limited to planar one by an assumption that the hexapod robot does not fall down while rolling and influences due to collision and contact with the ground, and it is applied for computing the mechanical energy of the hexapod robot and a plant for a numerical simulation. The numerical simulation of the rolling locomotion on the level ground verifies the effectiveness of the proposed controller. The simulation results show that the hexapod robot can perform the rolling locomotion with the proposed controller. In conclusion, it is shown that the proposed control approach is effective in achieving the rolling locomotion on the level ground.

  11. A View of the Therapy for Bell's Palsy Based on Molecular Biological Analyses of Facial Muscles.

    Science.gov (United States)

    Moriyama, Hiroshi; Mitsukawa, Nobuyuki; Itoh, Masahiro; Otsuka, Naruhito

    2017-12-01

    Details regarding the molecular biological features of Bell's palsy have not been widely reported in textbooks. We genetically analyzed facial muscles and clarified these points. We performed genetic analysis of facial muscle specimens from Japanese patients with severe (House-Brackmann facial nerve grading system V) and moderate (House-Brackmann facial nerve grading system III) dysfunction due to Bell's palsy. Microarray analysis of gene expression was performed using specimens from the healthy and affected sides, and gene expression was compared. Changes in gene expression were defined as an affected side/healthy side ratio of >1.5 or Bell's palsy changes with the degree of facial nerve palsy. Especially, muscle, neuron, and energy category genes tended to fluctuate with the degree of facial nerve palsy. It is expected that this study will aid in the development of new treatments and diagnostic/prognostic markers based on the severity of facial nerve palsy.

  12. The Development of Environment based Textbook in Biology Course at Tribhuwana Tunggadewi University

    Directory of Open Access Journals (Sweden)

    Nugroho Aji Prasetiyo

    2017-03-01

    Full Text Available Environmental issues are rooted in human behavior is often found in everyday life, one contributing factor was not maximal the environment learning outcomes in the education. The purpose of this study is to develop environment based textbook in Biology course suited to the needs and character of college students. The development model used in this research and development are modified Thiagarajan et al model consists of three stages: define, design, and develop. The technique of collecting data using questionnaires validation for experts, and small-scale trials. The result of the development of textbooks showing the average results of the validation and testing is in the category with a good fit for use in accordance with the table eligibility criteria and product revision level.

  13. Differentiation of Xanthomonas spp. Causing Bacterial Spot in Bulgaria Based on Biolog System

    Directory of Open Access Journals (Sweden)

    Mariya Stoyanova

    2014-01-01

    Full Text Available During the last 20 years, the causative agents of bacterial spot of tomato and pepper have been subjected to many studies and reclassifications. According to the current data, the species are four (X. euvesicatoria, X. vesicatoria, X. gardneri, and X. perforans and cause similar symptoms in plants but possess different phenotypic properties. This work provides the full metabolic characteristics obtained by Biolog system of bacterial spot’s xanthomonads based on a large selection of strains from different vegetable-producing regions of Bulgaria with accent on their major differentiating properties which could be used for species differentiation by metabolic profiles. The results are compared to the data available in the literature in order to clarify the strong features of each species and distinguish the variable ones. Simple characteristics like amylase activity and utilization of cis-aconitate cannot serve alone for differentiation.

  14. Supplemental control of lepidopterous pests on Bt transgenic sweet corn with biologically-based spray treatments.

    Science.gov (United States)

    Farrar, Robert R; Shepard, B Merle; Shapiro, Martin; Hassell, Richard L; Schaffer, Mark L; Smith, Chad M

    2009-01-01

    Biologically-based spray treatments, including nucleopolyhedroviruses, neem, and spinosad, were evaluated as supplemental controls for the fall armyworm, Spodoptera frugiperda (J. E. Smith), and corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), on transgenic sweet corn, Zea mays (L.) (Poales: Poaceae), expressing a Cry1Ab toxin from Bacillus thuringiensis Berliner (Bacillales: Bacillaceae) (Bt). Overall, transgenic corn supported lower densities of both pests than did nontransgenic corn. Control of the fall armyworm was improved in both whorl-stage and tassel-stage corn by the use of either a nucleopolyhedrovirus or neem, but the greatest improvement was seen with spinosad. Only spinosad consistently reduced damage to ears, which was caused by both pest species. In general, efficacy of the spray materials did not differ greatly between transgenic and nontransgenic corn.

  15. Biology Procedural Knowledge at Eleventh Grade of Senior High School in West Lampung Based on Curriculum

    Science.gov (United States)

    Sari, T. M.; Paidi; Mercuriani, I. S.

    2018-03-01

    This study was aim to determine Biology procedural knowledge of senior high school in West Lampung based on curriculum at 11th grade in even semester. This research was descriptive research. The population was all students of senior high school in West Lampung. The sampling technique in this research used purposive sampling technique, so the researcher obtained 3 schools using K13 and 3 schools using KTSP. Data collecting technique used instrument test. Data analysis technique used U-Mann Whitney test. The result showed that p=0.028 (p<0.05), so there was significant differences between school using K13 and KTSP. The procedural knowledge of schools which using K13 is higher than school which using KTSP, with the mean score K13=4.35 and KTSP=4.00

  16. Effect of Chemical and Biological Phosphorus on Antioxidant Enzymes Activity and Some Biochemical Traits of Spring Safflower (Carthamus tinctorius L. under Water Deficit Stress Conditions

    Directory of Open Access Journals (Sweden)

    S. Heshmati

    2016-05-01

    Full Text Available To study the effects of biological and chemical phosphorus on antioxidant enzyme activity in safflower under water deficit conditions, an experiment was conducted in 2012 at the Research Field of the Faculty of Agriculture, Shahed University, Tehran, Iran. The experimental design was a split-factorial with three replicates. The main factor was the three levels of irrigation treatment: full irrigation (irrigation up to 50% soil moisture depletion relative to field capacity, water stress in the vegetative and flowering stages (irrigation up to 75% soil moisture depletion relative to field capacity. The sub-factor was the six treatments resulting from three levels of phosphate chemical fertilizer (0, 50, and 100 kg ha-1 Triple Super Phosphate, each at two levels of Barvar-2 bio-fertilizer (with and without inoculation with Barvar-2. According to the results of our experiment, antioxidant enzyme activity is affected by high levels of chemical phosphorus when there is no inoculation with biofertilizer (Barvar 2 under water stress in the vegetative and flowering stages. The results showed that inoculation with Barvar 2 in the absence of added chemical phosphorus increases the catalase activity and soluble protein concentration under drought stress in the vegetative and flowering stages. Also, using chemical phosphorus followed by Barvar 2 led to increase in the polyphenol oxidase activity and superoxide dismutase activity under these conditions. Inoculation with Barvar 2 in the absence of added chemical phosphorus significantly decreased the amount of malondialdehyde under stress condition at the flowering stage. It was demonstrated that inoculation with a biological fertilizer (Barvar 2 followed by application of a chemical phosphorus fertilizer under drought conditions could decrease the detrimental effects of drought stress on spring safflower.

  17. BClass: A Bayesian Approach Based on Mixture Models for Clustering and Classification of Heterogeneous Biological Data

    Directory of Open Access Journals (Sweden)

    Arturo Medrano-Soto

    2004-12-01

    Full Text Available Based on mixture models, we present a Bayesian method (called BClass to classify biological entities (e.g. genes when variables of quite heterogeneous nature are analyzed. Various statistical distributions are used to model the continuous/categorical data commonly produced by genetic experiments and large-scale genomic projects. We calculate the posterior probability of each entry to belong to each element (group in the mixture. In this way, an original set of heterogeneous variables is transformed into a set of purely homogeneous characteristics represented by the probabilities of each entry to belong to the groups. The number of groups in the analysis is controlled dynamically by rendering the groups as 'alive' and 'dormant' depending upon the number of entities classified within them. Using standard Metropolis-Hastings and Gibbs sampling algorithms, we constructed a sampler to approximate posterior moments and grouping probabilities. Since this method does not require the definition of similarity measures, it is especially suitable for data mining and knowledge discovery in biological databases. We applied BClass to classify genes in RegulonDB, a database specialized in information about the transcriptional regulation of gene expression in the bacterium Escherichia coli. The classification obtained is consistent with current knowledge and allowed prediction of missing values for a number of genes. BClass is object-oriented and fully programmed in Lisp-Stat. The output grouping probabilities are analyzed and interpreted using graphical (dynamically linked plots and query-based approaches. We discuss the advantages of using Lisp-Stat as a programming language as well as the problems we faced when the data volume increased exponentially due to the ever-growing number of genomic projects.

  18. Ni-Cr based dental alloys; Ni release, corrosion and biological evaluation.

    Science.gov (United States)

    Reclaru, L; Unger, R E; Kirkpatrick, C J; Susz, C; Eschler, P-Y; Zuercher, M-H; Antoniac, I; Lüthy, H

    2012-08-01

    In the last years the dental alloy market has undergone dramatic changes for reasons of economy and biocompatibility. Nickel based alloys have become widely used substitute for the much more expensive precious metal alloys. In Europe the prevalence of nickel allergy is 10-15% for female adults and 1-3% for male adults. Despite the restrictions imposed by the EU for the protection of the general population in contact dermatitis, the use of Ni-Cr dental alloys is on the increase. Some questions have to be faced regarding the safety risk of nickel contained in dental alloys. We have collected based on many EU markets, 8 Ni-Cr dental alloys. Microstructure characterization, corrosion resistance (generalized, crevice and pitting) in saliva and the quantities of cations released in particular nickel and CrVI have been evaluated. We have applied non parametric classification tests (Kendall rank correlation) for all chemical results. Also cytotoxicity tests and an evaluation specific to TNF-alpha have been conducted. According to the obtained results, it was found that their behavior to corrosion was weak but that nickel release was high. The quantities of nickel released are higher than the limits imposed in the EU concerning contact with the skin or piercing. Surprisingly the biological tests did not show any cytotoxic effect on Hela and L929 cells or any change in TNF-alpha expression in monocytic cells. The alloys did not show any proinflammatory response in endothelial cells as demonstrated by the absence of ICAM-1 induction. We note therefore that there is really no direct relationship between the in vitro biological evaluation tests and the physico-chemical characterization of these dental alloys. Clinical and epidemiological studies are required to clarify these aspects. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Biological transformation of anthracene in soil by Pleurotus ostreatus under solid-state fermentation conditions using wheat bran and compost

    International Nuclear Information System (INIS)

    Vargas, M C; Rodriguez, R; Sanchez, F; Ramirez, N

    2001-01-01

    Pleurotus ostreatus was grown in a soil mixture contaminated with anthracene, wheat bran and compost, in varying combinations. Assays with added bacteria and reinoculation of the fungus were also included. The results indicated that in many of the combinations, most of the anthracene was removed at the earliest sample time, 15 days. The most effective combination was spiked (anthracene-added) soil, fungus and compost and the addition of acclimated bacteria to this mixture inhibited anthracene removal. Analyses of extract by high-pressure liquid chromatography HPLC indicated that - anthraquinone, was the major metabolite formed. The results of this study indicate that solid-state fermentation of anthracene-contaminated soils using P. ostreatus in combination with wheat bran and compost additives can produce an accelerated rate of biological removal of anthracene from the soil

  20. The timing of biological carbon sequestration and carbon abatement in the energy sector under optimal strategies against climate risks

    International Nuclear Information System (INIS)

    Gitz, V.; Hourcade, J.Ch.; Ciais, Ph.

    2005-10-01

    This paper addresses the timing of the use of biological carbon sequestration and its capacity to alleviate the carbon constraint on the energy sector. We constructed a stochastic optimal control model balancing the costs of fossil emission abatement, the opportunity costs of lands allocated to afforestation, and the costs of uncertain climate damages. We show that a minor part of the sequestration potential should start immediately as a 'brake', slowing down both the rate of growth of concentrations and the rate of abatement in the energy sector. thus increasing the option value of the emission trajectories. But, most of the potential is put in reserve to be used as a 'safety valve' after the resolution of uncertainty, if a higher and faster decarbonization is required: sequestration cuts off the peaks of costs of fossil abatement and postpones the pivoting of the energy system by up to two decades. (authors)

  1. Ni-Cr based dental alloys; Ni release, corrosion and biological evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Reclaru, L., E-mail: lucien.reclaru@pxgroup.com [PX Holding S.A., Dep R and D Corrosion and Biocompatibility Group, Bd. des Eplatures 42, CH-2304 La Chaux-de-Fonds (Switzerland); Unger, R.E.; Kirkpatrick, C.J. [Institute for Pathology, REPAIR Lab, University Medical Center, Johannes Gutenberg University Mainz, Langenbeckstr.1, D-55101 Mainz (Germany); Susz, C.; Eschler, P.-Y.; Zuercher, M.-H. [PX Holding S.A., Dep R and D Corrosion and Biocompatibility Group, Bd. des Eplatures 42, CH-2304 La Chaux-de-Fonds (Switzerland); Antoniac, I. [Materials Science and Engineering Faculty, Politehnica of Bucharest, 060042 Bucharest (Romania); Luethy, H. [Institute of Dental Materials Science and Technology, University of Basel, Hebelstrasse 3, CH-4056 Basel (Switzerland)

    2012-08-01

    In the last years the dental alloy market has undergone dramatic changes for reasons of economy and biocompatibility. Nickel based alloys have become widely used substitute for the much more expensive precious metal alloys. In Europe the prevalence of nickel allergy is 10-15% for female adults and 1-3% for male adults. Despite the restrictions imposed by the EU for the protection of the general population in contact dermatitis, the use of Ni-Cr dental alloys is on the increase. Some questions have to be faced regarding the safety risk of nickel contained in dental alloys. We have collected based on many EU markets, 8 Ni-Cr dental alloys. Microstructure characterization, corrosion resistance (generalized, crevice and pitting) in saliva and the quantities of cations released in particular nickel and CrVI have been evaluated. We have applied non parametric classification tests (Kendall rank correlation) for all chemical results. Also cytotoxicity tests and an evaluation specific to TNF-alpha have been conducted. According to the obtained results, it was found that their behavior to corrosion was weak but that nickel release was high. The quantities of nickel released are higher than the limits imposed in the EU concerning contact with the skin or piercing. Surprisingly the biological tests did not show any cytotoxic effect on Hela and L929 cells or any change in TNF-alpha expression in monocytic cells. The alloys did not show any proinflammatory response in endothelial cells as demonstrated by the absence of ICAM-1 induction. We note therefore that there is really no direct relationship between the in vitro biological evaluation tests and the physico-chemical characterization of these dental alloys. Clinical and epidemiological studies are required to clarify these aspects. - Highlights: Black-Right-Pointing-Pointer Nickel released was higher than the limits imposed in EU in contact with the skin. Black-Right-Pointing-Pointer No direct relationship between the

  2. Ni–Cr based dental alloys; Ni release, corrosion and biological evaluation

    International Nuclear Information System (INIS)

    Reclaru, L.; Unger, R.E.; Kirkpatrick, C.J.; Susz, C.; Eschler, P.-Y.; Zuercher, M.-H.; Antoniac, I.; Lüthy, H.

    2012-01-01

    In the last years the dental alloy market has undergone dramatic changes for reasons of economy and biocompatibility. Nickel based alloys have become widely used substitute for the much more expensive precious metal alloys. In Europe the prevalence of nickel allergy is 10–15% for female adults and 1–3% for male adults. Despite the restrictions imposed by the EU for the protection of the general population in contact dermatitis, the use of Ni–Cr dental alloys is on the increase. Some questions have to be faced regarding the safety risk of nickel contained in dental alloys. We have collected based on many EU markets, 8 Ni–Cr dental alloys. Microstructure characterization, corrosion resistance (generalized, crevice and pitting) in saliva and the quantities of cations released in particular nickel and CrVI have been evaluated. We have applied non parametric classification tests (Kendall rank correlation) for all chemical results. Also cytotoxicity tests and an evaluation specific to TNF-alpha have been conducted. According to the obtained results, it was found that their behavior to corrosion was weak but that nickel release was high. The quantities of nickel released are higher than the limits imposed in the EU concerning contact with the skin or piercing. Surprisingly the biological tests did not show any cytotoxic effect on Hela and L929 cells or any change in TNF-alpha expression in monocytic cells. The alloys did not show any proinflammatory response in endothelial cells as demonstrated by the absence of ICAM-1 induction. We note therefore that there is really no direct relationship between the in vitro biological evaluation tests and the physico-chemical characterization of these dental alloys. Clinical and epidemiological studies are required to clarify these aspects. - Highlights: ► Nickel released was higher than the limits imposed in EU in contact with the skin. ► No direct relationship between the biological evaluation and chemical degradation.

  3. A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities.

    Science.gov (United States)

    Morris, Jonathan R; Vandermeer, John; Perfecto, Ivette

    2015-01-01

    Species' functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems.

  4. Biological effects of plant residues with constrasting chemical compositions on plant and soil under humid tropical conditions

    NARCIS (Netherlands)

    Tian, G.

    1992-01-01

    A study on plant residues with contrasting chemical compositions was conducted under laboratory, growth chamber and humid tropical field conditions to understand the function of the soil fauna in the breakdown of plant residues, the cycling of nutrients, in particular nitrogen, and the

  5. From Levy to Brownian: a computational model based on biological fluctuation.

    Directory of Open Access Journals (Sweden)

    Surya G Nurzaman

    Full Text Available BACKGROUND: Theoretical studies predict that Lévy walks maximizes the chance of encountering randomly distributed targets with a low density, but Brownian walks is favorable inside a patch of targets with high density. Recently, experimental data reports that some animals indeed show a Lévy and Brownian walk movement patterns when forage for foods in areas with low and high density. This paper presents a simple, Gaussian-noise utilizing computational model that can realize such behavior. METHODOLOGY/PRINCIPAL FINDINGS: We extend Lévy walks model of one of the simplest creature, Escherichia coli, based on biological fluctuation framework. We build a simulation of a simple, generic animal to observe whether Lévy or Brownian walks will be performed properly depends on the target density, and investigate the emergent behavior in a commonly faced patchy environment where the density alternates. CONCLUSIONS/SIGNIFICANCE: Based on the model, animal behavior of choosing Lévy or Brownian walk movement patterns based on the target density is able to be generated, without changing the essence of the stochastic property in Escherichia coli physiological mechanism as explained by related researches. The emergent behavior and its benefits in a patchy environment are also discussed. The model provides a framework for further investigation on the role of internal noise in realizing adaptive and efficient foraging behavior.

  6. A postprocessing method in the HMC framework for predicting gene function based on biological instrumental data

    Science.gov (United States)

    Feng, Shou; Fu, Ping; Zheng, Wenbin

    2018-03-01

    Predicting gene function based on biological instrumental data is a complicated and challenging hierarchical multi-label classification (HMC) problem. When using local approach methods to solve this problem, a preliminary results processing method is usually needed. This paper proposed a novel preliminary results processing method called the nodes interaction method. The nodes interaction method revises the preliminary results and guarantees that the predictions are consistent with the hierarchy constraint. This method exploits the label dependency and considers the hierarchical interaction between nodes when making decisions based on the Bayesian network in its first phase. In the second phase, this method further adjusts the results according to the hierarchy constraint. Implementing the nodes interaction method in the HMC framework also enhances the HMC performance for solving the gene function prediction problem based on the Gene Ontology (GO), the hierarchy of which is a directed acyclic graph that is more difficult to tackle. The experimental results validate the promising performance of the proposed method compared to state-of-the-art methods on eight benchmark yeast data sets annotated by the GO.

  7. Feature-based attentional tuning during biological motion detection measured with SSVEP.

    Science.gov (United States)

    Hasan, Rakibul; Srinivasan, Ramesh; Grossman, Emily D

    2017-08-01

    Performance in detection tasks can be improved by directing attention to task-relevant features. In this study, we evaluate the direction tuning of selective attention to motion features when observers detect point-light biological motion in noise. Feature-based attention strategy is assessed by capitalizing on the sensitivity of unattended steady-state visual-evoked potential (SSVEP) to the spreading of feature-based attention to unattended regions of space. Participants monitored for the presence of a point-light walker embedded in uniform dynamic noise in the center of the screen. We analyzed the phase-locked electroencephalogram response to a flickering random-dot kinematogram (RDK) in an unattended peripheral annulus for the 1 s prior to the onset of the target. We found the highest SSVEP power to originate from electrodes over posterior parietal cortex (PPC), with power modulated by the direction of motion in the unattended annulus. The SSVEP was strongest on trials in which the unattended motion was opposite the facing direction of the walker, consistent with the backstroke of the feet and with the global direction of perceived background motion from a translating walker. Coherence between electrodes over PPC and other brain regions successfully predicted individual participant's d-prime, with the highest regression coefficients at electrodes over ventrolateral prefrontal cortex (VLPFC). The findings are evidence that functional connectivity between frontal and parietal cortex promote perceptual feature-based attention, and subsequent perceptual sensitivity, when segregating point-light figures from masking surround.

  8. Spectroscopic studies and biological activity of some transition metal complexes of unusual Schiff base.

    Science.gov (United States)

    Abu Al-Nasr, Ahmad K; Ramadan, Ramadan M

    2013-03-15

    Unusual Schiff base ligand, 4-ethanimidoyl-6-[(1E)-N-(2-hydroxy-4-methylphenyl)ethanimidoyl]benzene-1,3-diol, L, was synthesized via catalytic process involving the interaction of some metal ions with a macrocyclic Schiff base (MSB). The transition metal derivatives [ML(H(2)O)(4)](NO(3))(3), M=Cr(III) and Fe(III), [NiL(H(2)O)(4)](NO(3))(2), [ML(H(2)O)(2)](NO(3))(2), M=Zn(II) and Cd(II), [Cl(2)Pd(μ-Cl)(2)PdL], [PtL(Cl)(2)] and [PtL(Cl)(4)] were also synthesized from the corresponding metal species with L. The Schiff bases and complexes were characterized by elemental analysis, mass spectrometry, IR and (1)H NMR spectroscopy. The crystal structure of L was determined by X-ray analysis. The spectroscopic studies revealed a variety of structure arrangements for the complexes. The biological activities of L and metal complexes against the Escherchia coli as Gram-negative bacteria and Staphylococcus aureus as Gram-positive bacteria, and the two fungus Aspergillus flavus and Candida albicans were screened. The cytotoxicity of [PtL(Cl)(2)] complex, a cis-platin analogous, was checked as an antitumor agent on two breast cancer cell lines (MCF7 and T47D) and human liver carcinoma cell line (HepG2). Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Spectroscopic studies and biological activity of some transition metal complexes of unusual Schiff base

    Science.gov (United States)

    Abu Al-Nasr, Ahmad K.; Ramadan, Ramadan M.

    2013-03-01

    Unusual Schiff base ligand, 4-ethanimidoyl-6-[(1E)-N-(2-hydroxy-4-methylphenyl)ethanimidoyl]benzene-1,3-diol, L, was synthesized via catalytic process involving the interaction of some metal ions with a macrocyclic Schiff base (MSB). The transition metal derivatives [ML(H2O)4](NO3)3, M = Cr(III) and Fe(III), [NiL(H2O)4](NO3)2, [ML(H2O)2](NO3)2, M = Zn(II) and Cd(II), [Cl2Pd(μ-Cl)2PdL], [PtL(Cl)2] and [PtL(Cl)4] were also synthesized from the corresponding metal species with L. The Schiff bases and complexes were characterized by elemental analysis, mass spectrometry, IR and 1H NMR spectroscopy. The crystal structure of L was determined by X-ray analysis. The spectroscopic studies revealed a variety of structure arrangements for the complexes. The biological activities of L and metal complexes against the Escherchia coli as Gram-negative bacteria and Staphylococcus aureus as Gram-positive bacteria, and the two fungus Aspergillus flavus and Candida albicans were screened. The cytotoxicity of [PtL(Cl)2] complex, a cis-platin analogous, was checked as an antitumor agent on two breast cancer cell lines (MCF7 and T47D) and human liver carcinoma cell line (HepG2).

  10. The sensitivity of new laboratory-based heterogeneous freezing schemes for dust and biological particles to time and temperature

    Science.gov (United States)

    Niedermeier, D.; Ervens, B.; Hartmann, S.; Wex, H.; Stratmann, F.

    2012-12-01

    Heterogeneous ice nucleation has been recently described by means of the Soccer ball model that takes into account multiple nucleation sites on individual particles [Niedermeier et al., 2011]. In order to study sensitivities of the implied contact angle distributions, a modified version of the Soccer ball model is implemented into a parcel model that describes in detail heterogeneous ice formation and ice /liquid water partitioning [Ervens and Feingold, 2012]. Soccer ball model parameters (number of surface sites, mean and width of the contact angle distribution) are determined from immersion freezing measurements of mineral dust particles and bacteria performed with the Leipzig Aerosol Cloud Interaction Simulator [LACIS, Hartmann et al., 2011]. While biological particles (e.g., bacteria) are much less frequent in the atmosphere, they can induce droplet freezing already at about -5°C as opposed to dust that shows efficient freezing only at lower temperatures (below -15°C). We will identify updraft regimes, temperature and IN concentration ranges where dust or biological particles, respectively, might dominate the number concentration of frozen droplets in mixed phase clouds. Additional model studies will focus on the importance of time versus temperature dependence and explore the usefulness of alternative descriptions of the freezing behavior that can be derived based on the respective laboratory studies using LACIS. These descriptions include the choice of a single contact angle as opposed to contact angle distributions or time-independent expressions. These results reveal that under selected conditions, it might be a satisfactory approximation to assume singular freezing behavior. Our sensitivity studies will help to refine time-independent freezing parameterizations using laboratory data and help bridging the current divergence between deterministic approaches [e.g., Hoose and Möhler, 2012] and physically-based approaches (classical nucleation theory) that

  11. Teaching Cell Biology to Dental Students with a Project-Based Learning Approach.

    Science.gov (United States)

    Costa-Silva, Daniela; Côrtes, Juliana A; Bachinski, Rober F; Spiegel, Carolina N; Alves, Gutemberg G

    2018-03-01

    Although the discipline of cell biology (CB) is part of the curricula of predoctoral dental schools, students often fail to recognize its practical relevance. The aim of this study was to assess the effectiveness of a practical-theoretical project-based course in closing the gaps among CB, scientific research, and dentistry for dental students. A project-based learning course was developed with nine sequential lessons to evaluate 108 undergraduate dental students enrolled in CB classes of a Brazilian school of dentistry during 2013-16. To highlight the relevance of in vitro studies in the preclinical evaluation of dental materials at the cellular level, the students were challenged to complete the process of drafting a protocol and performing a cytocompatibility assay for a bone substitute used in dentistry. Class activities included small group discussions, scientific database search and article presentations, protocol development, lab experimentation, and writing of a final scientific report. A control group of 31 students attended only one laboratory class on the same theme, and the final reports were compared between the two groups. The results showed that the project-based learning students had superior outcomes in acknowledging the relevance of in vitro methods during biocompatibility testing. Moreover, they produced scientifically sound reports with more content on methodological issues, the relationship with dentistry, and the scientific literature than the control group (p<0.05). The project-based learning students also recognized a higher relevance of scientific research and CB to dental practice. These results suggest that a project-based approach can help contextualize scientific research in dental curricula.

  12. A logic-based dynamic modeling approach to explicate the evolution of the central dogma of molecular biology.

    Directory of Open Access Journals (Sweden)

    Mohieddin Jafari

    Full Text Available It is nearly half a century past the age of the introduction of the Central Dogma (CD of molecular biology. This biological axiom has been developed and currently appears to be all the more complex. In this study, we modified CD by adding further species to the CD information flow and mathematically expressed CD within a dynamic framework by using Boolean network based on its present-day and 1965 editions. We show that the enhancement of the Dogma not only now entails a higher level of complexity, but it also shows a higher level of robustness, thus far more consistent with the nature of biological systems. Using this mathematical modeling approach, we put forward a logic-based expression of our conceptual view of molecular biology. Finally, we show that such biological concepts can be converted into dynamic mathematical models using a logic-based approach and thus may be useful as a framework for improving static conceptual models in biology.

  13. Novel approach for heterocyclization: a clean and efficient synthesis and biological evaluation of 4-oxothiazolidines under microwave technique

    International Nuclear Information System (INIS)

    Desai, Krunal G.; Desai, K.R.

    2006-01-01

    A new selective method has been developed for rapid synthesis of 2-(aryl)-3-[2-benzoimidazolythio)-acetamidyl]-4-oxothiazolidines 4a-j by the heterocyclization of 2-{(1H-benzemidazol)-ylthio}-N-benzylidene aceto hydrazide 3a-j with HSCH2COOH under microwave irradiation (MWI) is described. The reaction rate and yield is enhanced tremendously under MWI as compared to conventional methods. All the compounds have been screened for their antifungal activity against Candida albicans and Aspergillus niger, antibacterial activity against Escherchia coli and Staphylococcus aureus. In the primary screening, some of the compounds exhibited appreciable activity. The structures of the synthesized compounds 4a-j have been characterized on the basis of their elemental analysis, IR, HNMR and Mass spectral data. (author)

  14. [Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

    Science.gov (United States)

    Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

    1993-01-01

    The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

  15. Physical, Chemical, and Biological Properties of Soil under Decaying Wood in a Tropical Wet Forest in Puerto Rico

    Science.gov (United States)

    Marcela Zalamea; Grizelle Gonzalez; D. Jean Lodge

    2016-01-01

    Decaying wood is related to nutrient cycling through its role as either a sink or source of nutrients. However, at micro scales, what is the effect of decaying logs on the physical, chemical,and biotic characteristics of the soil underneath? We took samples from a 0 to 5 cm depth under and a 50 cm distance away from decaying logs (Dacryodes excelsa and Swietenia...

  16. Systems Biology

    Energy Technology Data Exchange (ETDEWEB)

    Wiley, H S.

    2006-06-01

    The biology revolution over the last 50 years has been driven by the ascendancy of molecular biology. This was enthusiastically embraced by most biologists because it took us into increasingly familiar territory. It took mysterious processes, such as the replication of genetic material and assigned them parts that could be readily understood by the human mind. When we think of ''molecular machines'' as being the underlying basis of life, we are using a paradigm derived from everyday experience. However, the price that we paid was a relentless drive towards reductionism and the attendant balkanization of biology. Now along comes ''systems biology'' that promises us a solution to the problem of ''knowing more and more about less and less''. Unlike molecular biology, systems biology appears to be taking us into unfamiliar intellectual territory, such as statistics, mathematics and computer modeling. Not surprisingly, systems biology has met with widespread skepticism and resistance. Why do we need systems biology anyway and how does this new area of research promise to change the face of biology in the next couple of decades?

  17. Homarus gammarus (Crustacea: Decapoda) larvae under an ocean acidification scenario: responses across different levels of biological organization.

    Science.gov (United States)

    Rato, Lénia D; Novais, Sara C; Lemos, Marco F L; Alves, Luís M F; Leandro, Sérgio M

    2017-12-01

    The present study evaluated the effects of exposure to different target pCO 2 levels: control (C: 370μatm, pH=8.15) and ocean acidification (OA: 710μatm, pH=7.85) on development and biochemical responses related with oxidative stress and energy metabolism during the crustacean Homarus gammarus (L.) larval development, integrating different levels of biological organization. After hatching in the laboratory, larvae from the same female brood were exposed to the described conditions from hatching until reaching Stage III (last larval stage - 11days). H. gammarus larvae demonstrated some susceptibility when addressing the predicted pCO 2 levels for 2100. Further analysis at the biochemical and physiological level highlighted the occurrence of oxidative stress in the OA scenario (Superoxide Dismutase reduction and higher DNA damage) that was followed by developmental effects, increased inter-moult period from SII to SIII and reduced growth. The extended exposure to these conditions may affect organisms' key life-cycle functions such as physiological resistance, growth, sexual maturation, or reproduction with implications in their future fitness and population dynamics. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Multi-cycle operation of enhanced biological phosphorus removal (EBPR) with different carbon sources under high temperature.

    Science.gov (United States)

    Shen, Nan; Chen, Yun; Zhou, Yan

    2017-05-01

    Many studies reported that it is challenging to apply enhanced biological phosphorus removal (EBPR) process at high temperature. Glycogen accumulating organisms (GAOs) could easily gain their dominance over poly-phosphate accumulating organisms (PAOs) when the operating temperature was in the range of 25 °C-30 °C. However, a few successful EBPR processes operated at high temperature have been reported recently. This study aimed to have an in-depth understanding on the impact of feeding strategy and carbon source types on EBPR performance in tropical climate. P-removal performance of two EBPR systems was monitored through tracking effluent quality and cyclic studies. The results confirmed that EBPR was successfully obtained and maintained at high temperature with a multi-cycle strategy. More stable performance was observed with acetate as the sole carbon source compared to propionate. Stoichiometric ratios of phosphorus and carbon transformation during both anaerobic and aerobic phases were higher at high temperature than low temperature (20±1 °C) except anaerobic PHA/C ratios within most of the sub-cycles. Furthermore, the fractions of PHA and glycogen in biomass were lower compared with one-cycle pulse feed operation. The microbial community structure was more stable in acetate-fed sequencing batch reactor (C2-SBR) than that in propionate-fed reactor (C3-SBR). Accumulibacter Clade IIC was found to be highly abundant in both reactors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Description of chemical and biological soil characteristics of two fields subjected to different agricultural management under mediterranean conditions

    Directory of Open Access Journals (Sweden)

    Salvatore M. Meli

    Full Text Available Several factors such as soil pollution and intensive agricultural management continuously damage the sustainability of agricultural production, with potentially adverse effects on soil quality. It is important to create applicable and valid soil quality indicators in order to both identify areas with potential productivity problems and monitor soil quality changes due to a range of perturbations. In this work we compared several chemical and biological variables between a Mediterranean soil characterized by intensive horticulture that has been irrigated for 20 years with moderately saline waters (IM and an adjacent soil, subjected to a sustainable agricultural production management and irrigated with plain water (SM. Soil sampling was repeated three times during a year in both sites. IM soil had lower pH, organic carbon and total nitrogen compared to SM soil at all sampling times, while its electrical conductivity was significantly higher at two sampling times only. Potentially mineralizable nitrogen pointed out significant differences only at the first sampling time, with lower levels in the SM soil. β-sitosterol, cholesterol and ergosterol varied significantly with sampling time and were influenced also by management. Statistical approach by Principal Component Analysis highlighted a contrast between two groups of soil variables: potentially mineralizable nitrogen and sterols mainly weighted on the first axis, while chemical properties, weighted on the second one. Moreover, the second axis separated the soil subjected to a sustainable agricultural production system from that subjected to intensive practice management, while the first axis separated the third sampling data from the first two.

  20. Study on toxigenic fungi in ruminant feeds under desert conditions with special references to its biological control

    Directory of Open Access Journals (Sweden)

    Shimaa M.S. Hegazy

    2015-06-01

    Full Text Available A total of 435 samples from feedstuff (130 samples of commercial ration feed storage from 1–30 days, 77 samples of commercial ration stored higher than 30 days, 57 samples from each of, derris, grind mixture, Tibn and wheat bran were collected from the feed store houses of private farms located at the desert regions of Ras Sudr at South Sinai and Elameria area at Alexandria Governorate, from December 2012 to May 2014. The collected samples were analyzed for fungal growth. The results revealed that, the main moulds observed in the ruminant feeds were Penicillium spp., Aspergillus (A flavus, Cladosporium spp., Mucor spp., Trichoderma spp., A. niger, Alternaria spp., Rhizopus spp., Fusarium spp., A. fumigates and A. terreus. In addition, the winter season was of higher incidence for moulds isolation than summer season. The most toxigenic aflatoxins secreted by Aspergillus flavus include Aflatoxin B1, Aflatoxin B2, Aflatoxin G1 and Aflatoxin G2. The results of biological treatment of Aflatoxins using Saccharomyces (S cerevisiae, showed that, the addition of Saccharomyces cerevisiae at a level of (1 × 106 cfu.ml−1 and (1 × 109 cfu.ml−1 decreased the level of concentration of aflatoxin B1, B2, G1 and G2 and the level of (1 × 109 cfu.ml−1 was more efficient in reducing aflatoxins than the lower concentration.

  1. Some biological effects of one water based ferrofluid in cucurbita pepo

    International Nuclear Information System (INIS)

    Racuciu, M.; Creanga, D.; Olteanu, Z.; Horga, E. I.

    2005-01-01

    Full text: The biological interest in the ferrofluid effect in living organisms represents an important application field, mainly for biotechnological use, since the small ferrophase size allows the penetration through the biological membranes. Experiments have been designed to reveal the influences of an aqueous ferrofluid on the assimilatory pigments, the peroxide level, nucleic acid level and on the substance accumulation. Water based ferrofluid, stabilized with citric acid was added in various concentrations (10-50-100- 150-200-250 micro L/L) (after vigorous shaking) in the culture medium of Cucurbita pepo plantlets (pumpkin). Spectrophotometric standard assay methods have been applied in order to get experimental data regarding the levels of assimilatory pigments (chlorophyll a, chlorophyll b, carotenes), nucleic acids and peroxydase like enzymes. JASCO V350 spectrophotometer provided with. The stimulatory effect of relatively high ferrofluid concentrations have been observed in the ratio chlorophyll a/b, known as a measure of photosynthesis ratio. Non-significant changes in the nucleic acid level were noticed. Inhibitory effect upon the enzyme biosynthesis was assigned to the ferrofluid addition. The statistic analysis was accomplished by considering five repetitions of every measurement in ferrofluid samples and control ones. Average values of ferrofluid samples and control ones have been compared by means of t-test. Statistic significance was revealed in comparison to the significance threshold of 0.05. (Also one figure included.) References: [1] C. Gro , K.Buescher, E. Romanus, C,A, Helm, W.Weitschies, European cells and Materials, 2002, 3(2), 163. [2] M.M.Zamfirache, G. Capraru, D. Creanga, M. Racuciu, Gh. Calugaru, Ferrofluid experiment for simulating pollution effect on plant growth, The Annals of University Galati, 2004(XXVII), Fasc.II, 37. [3] A.Goodarzi, Y.Sahoo, M.T.Swihart, P.N. Prasad, Mat.Res.Soc.Symp.Proc., 2004,Vol.789, N6.6.1

  2. A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides.

    Science.gov (United States)

    Roberts, Mark A J; August, Elias; Hamadeh, Abdullah; Maini, Philip K; McSharry, Patrick E; Armitage, Judith P; Papachristodoulou, Antonis

    2009-10-31

    Developing methods for understanding the connectivity of signalling pathways is a major challenge in biological research. For this purpose, mathematical models are routinely developed based on experimental observations, which also allow the prediction of the system behaviour under different experimental conditions. Often, however, the same experimental data can be represented by several competing network models. In this paper, we developed a novel mathematical model/experiment design cycle to help determine the probable network connectivity by iteratively invalidating models corresponding to competing signalling pathways. To do this, we systematically design experiments in silico that discriminate best between models of the competing signalling pathways. The method determines the inputs and parameter perturbations that will differentiate best between model outputs, corresponding to what can be measured/observed experimentally. We applied our method to the unknown connectivities in the chemotaxis pathway of the bacterium Rhodobacter sphaeroides. We first developed several models of R. sphaeroides chemotaxis corresponding to different signalling networks, all of which are biologically plausible. Parameters in these models were fitted so that they all represented wild type data equally well. The models were then compared to current mutant data and some were invalidated. To discriminate between the remaining models we used ideas from control systems theory to determine efficiently in silico an input profile that would result in the biggest difference in model outputs. However, when we applied this input to the models, we found it to be insufficient for discrimination in silico. Thus, to achieve better discrimination, we determined the best change in initial conditions (total protein concentrations) as well as the best change in the input profile. The designed experiments were then performed on live cells and the resulting data used to invalidate all but one of the

  3. A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. sphaeroides

    Directory of Open Access Journals (Sweden)

    Hamadeh Abdullah

    2009-10-01

    Full Text Available Abstract Background Developing methods for understanding the connectivity of signalling pathways is a major challenge in biological research. For this purpose, mathematical models are routinely developed based on experimental observations, which also allow the prediction of the system behaviour under different experimental conditions. Often, however, the same experimental data can be represented by several competing network models. Results In this paper, we developed a novel mathematical model/experiment design cycle to help determine the probable network connectivity by iteratively invalidating models corresponding to competing signalling pathways. To do this, we systematically design experiments in silico that discriminate best between models of the competing signalling pathways. The method determines the inputs and parameter perturbations that will differentiate best between model outputs, corresponding to what can be measured/observed experimentally. We applied our method to the unknown connectivities in the chemotaxis pathway of the bacterium Rhodobacter sphaeroides. We first developed several models of R. sphaeroides chemotaxis corresponding to different signalling networks, all of which are biologically plausible. Parameters in these models were fitted so that they all represented wild type data equally well. The models were then compared to current mutant data and some were invalidated. To discriminate between the remaining models we used ideas from control systems theory to determine efficiently in silico an input profile that would result in the biggest difference in model outputs. However, when we applied this input to the models, we found it to be insufficient for discrimination in silico. Thus, to achieve better discrimination, we determined the best change in initial conditions (total protein concentrations as well as the best change in the input profile. The designed experiments were then performed on live cells and the resulting

  4. Synthesis, Characterization and Biological Activities of Creatinine Amides and Creatinine Schiff Bases.

    Science.gov (United States)

    Mumtaz, Amara; Zahoor, Fareeha; Zaib, Sumera; Nawaz, Muhammad Azhar H; Saeed, Aamer; Waseem, Amir; Khan, Afsar; Hussain, Izhar; Iqbal, Jamshed

    2017-01-30

    In spite of substantial progress in scientific cognizance and medical technology, still infectious diseases are among the leading cause of morbidity and mortality. Creatinine and Schiff bases are well known for their diverse range of biological activities and thought to be emerging and useful therapeutic target for the treatment of several diseases. The present work was aimed to illustrate the influence of substitution of amides and Schiff bases on creatinine and their antimicrobial, antioxidant and anti-urease effectiveness was determined. Creatinine substituted amides (1-2) and creatinine Schiff bases (3-7) were synthesized and characterized by NMR and IR spectral data in combination with elemental analysis. All the compounds (1-7) were investigated on Jack bean urease for their urease inhibitory potential. Investigation of antimicrobial activity of the compounds was made by the agar dilution method. Moreover, 1,1-diphenyl-2- picrylhydrazyl (DPPH) method was used to determine their antioxidant potential. Molecular docking studies were also carried out to elucidate their relationship with the binding pockets of the enzyme. The compounds were found to be potent inhibitors of urease. The synthesized derivatives exhibited significant inhibition against Gram-positive and Gram-negative bacterial strains, as compared to standard, ciprofloxacin. Creatinine based derivatives exhibited potential antifungal activity when tested on infectious and pathogenic fungal strains. Similarly, most of the compounds exhibited good antioxidant activity. These derivatives may serve as a source of potential antioxidants and also help to retard microbial growth in food industry. Similarly, the studies provide a basis for further research to develop more potent urease inhibitory compounds of medicinal /agricultural interest. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  5. Novel Study Guides for Biochemistry Meaningful Learning in Biology: a Design-Based Research

    Directory of Open Access Journals (Sweden)

    Costa, C ; Galembeck, E. Costa, C ; Galembeck, E.

    2017-07-01

    Full Text Available One of the difficulties for biochemistry learning is the persistence of traditional teaching methods, based on transmission and memorization of abstract and detailed information, usually in a decontextualized way. Such scenario results in surface learning and content reproduction. In order to address these problems, three interventions in a discipline (Metabolism for Biology majors were applied, in the form of innovative teaching tools (study guides. OBJECTIVES: The main goal is to evaluate the impact of these interventions on interest, motivation, and learning of the metabolic pathways. MATERIALS AND METHODS: We describe the development, application, and evaluation of two study guides – one created from a problem used as a contextual connection for glycogen metabolism study and another embedding an integrative view based on glutamate metabolism. Both materials were guided by broad themes like evolution, metabolic adaptation, and comparative biochemistry. The development of the study guides combined submicroscopic (molecular and macroscopic (body, environment levels, aiming to motivate reading and discussion. A design-based research with cycles of application and assessment was carried out, by means of classroom observation, grade analysis in written exams, and students’ interviews. RESULTS AND DISCUSSION: In general, based on in-class student feedback to professors and to the researcher in the interviews, the study guides arouse curiosity and fostered peer discussion. Final average grades indicate a good global performance in all proposed activities. Whole data from study guides’ application in classroom evidenced their impact on interest, motivation, and learning. The strategy of developing problem or integrative situation linking molecular (micro and contextual (macro levels were helpful to foster critical thinking and to value topics of scientific literacy. CONCLUSIONS: Analysis and interpretation of the results point to benefits for

  6. Impact of organic and mineral inputs onto soil biological and metabolic activities under a long-term rice-wheat cropping system in sub-tropical Indian Inceptisols.

    Science.gov (United States)

    Basak, Nirmalendu; Datta, Ashim; Mitran, Tarik; Mandal, Biswapati; Mani, P K

    2016-01-01

    Long-term use of organic and mineral inputs has an overriding impact on soil biological and metabolic activities and crop management. Farm yard manure (FYM), paddy straw (PS) and green manure (GM, Sesbania sesban L.) were used for 24- years old rice (Oyza sativa L.) -wheat (Triticum aestivum L.) cropping system in sub-tropical India to predict whether the screened soil biological and metabolic activities are correlated with system yield. The integrated approaches viz., NPK + FYM, NPK + PS and NPK + GM significantly increased both rice and wheat yield together by 67.5, 44.4 and 55.4%, respectively over control. However, for a few exceptions both soil microbial activity and metabolic activity were remarkably enhanced under integrated treatment NPK + FYM followed by NPK + PS, and NPK + GM, respectively. Among the studied attributes fluorescein diacetate hydrolyzing, dehydrogenase, β-glucosidase activity (β-glu) and microbial biomass C (C(mic)) were screened through principal component (PCA) and discriminate analysis (DA) that explained nearly 89% of total variations of the entire data set. Among the four identified attributes, only β-glu assay value could predict system yield (R2 = 0.65). Further, estimation of β-glu activity in soil can predict other soil biological properties (R2 = 0.96).

  7. Visible light sensitized attapulgite-based lanthanide composites: microstructure, photophysical behaviour and biological application.

    Science.gov (United States)

    Xu, Jun; Sun, Zhihong; Jia, Lei; Li, Bo; Zhao, Long; Liu, Xiao; Ma, Yufei; Tian, Hao; Wang, Qin; Liu, Weisheng; Tang, Yu

    2011-12-28

    Attapulgite, an extremely stable fibrillar mineral present in nature, is a promising new carrier of luminescent lanthanide complexes for further applications. A europium complex Eu(DBM)(3)(H(2)O)(2) (HDBM = dibenzoylmethane) was covalently coupled onto modified attapulgites (or silica nanoparticles) via a ligand exchange reaction, generating attapulgite-based ternary europium complexes. The composites were characterized by CHN elemental analysis, inductively coupled plasma-atomic emission spectroscopy (ICP-AES) for Eu(3+) content, powder X-ray diffraction (XRD), thermogravimetry (TG) and UV-vis absorption spectra. The results indicate that the Eu(3+) complex was grafted covalently to the outer surfaces of attapulgites (or silica nanoparticles) and modifications by coupling agents containing different alkoxide groups (aminopropyltriethoxysilane (APTES) or aminopropylmethyldiethoxysilane (APMDES)) led to different grafting ratios. The structures of these composites were further evidenced by the determination of photophysical behaviours and coordinated water molecules of the complexes linked to matrices. Attapulgite-based lanthanide composites linked by APTES can be excited by visible light, with a wide excitation wavelength range from UV to visible light (a maximum at 398 nm), long luminescence lifetime (503 μs), high quantum yield (48%) and improved exposure durability. When incubated with HeLa cells at 37 °C, the fluorescence of matrix-APTES-cpa-Eu(DBM)(3) is observed on the cell membrane. Moreover, the low cytotoxicity of our present system results in potential applications for cell imaging in biological systems. This journal is © The Royal Society of Chemistry 2011

  8. The future of cytotoxic therapy: selective cytotoxicity based on biology is the key

    International Nuclear Information System (INIS)

    Bono, Johann S de; Tolcher, Anthony W; Rowinsky, Eric K

    2003-01-01

    Although mortality from breast cancer is decreasing, 15% or more of all patients ultimately develop incurable metastatic disease. It is hoped that new classes of target-based cytotoxic therapeutics will significantly improve the outcome for these patients. Many of these novel agents have displayed cytotoxic activity in preclinical and clinical evaluations, with little toxicity. Such preferential cytotoxicity against malignant tissues will remain tantamount to the Holy Grail in oncologic therapeutics because this portends improved patient tolerance and overall quality of life, and the capacity to deliver combination therapy. Combinations of such rationally designed target-based therapies are likely to be increasingly important in treating patients with breast carcinoma. The anticancer efficacy of these agents will, however, remain dependent on the involvement of the targets of these agents in the biology of the individual patient's disease. Results of DNA microarray analyses have raised high hopes that the analyses of RNA expression levels can successfully predict patient prognosis, and indicate that the ability to rapidly 'fingerprint' the oncogenic profile of a patient's tumor is now possible. It is hoped that these studies will support the identification of the molecules driving a tumor's growth, and the selection of the appropriate combination of targeted agents in the near future

  9. Biological Characterization of an Improved Pyrrole-Based Colchicine Site Agent Identified through Structure-Based Design.

    Science.gov (United States)

    Rohena, Cristina C; Telang, Nakul S; Da, Chenxiao; Risinger, April L; Sikorski, James A; Kellogg, Glen E; Gupton, John T; Mooberry, Susan L

    2016-02-01

    A refined model of the colchicine site on tubulin was used to design an improved analog of the pyrrole parent compound, JG-03-14. The optimized compound, NT-7-16, was evaluated in biological assays that confirm that it has potent activities as a new colchicine site microtubule depolymerizer. NT-7-16 exhibits antiproliferative and cytotoxic activities against multiple cancer cell lines, with IC(50) values of 10-16 nM, and it is able to overcome drug resistance mediated by the expression of P-glycoprotein and the βIII isotype of tubulin. NT-7-16 initiated the concentration-dependent loss of cellular microtubules and caused the formation of abnormal mitotic spindles, leading to mitotic accumulation. The direct interaction of NT-7-16 with purified tubulin was confirmed, and it was more potent than combretastatin A-4 in these assays. Binding studies verified that NT-7-16 binds to tubulin within the colchicine site. The antitumor effects of NT-7-16 were evaluated in an MDA-MB-435 xenograft model and it had excellent activity at concentrations that were not toxic. A second compound, NT-9-21, which contains dichloro moieties in place of the 3,5-dibromo substituents of NT-7-16, had a poorer fit within the colchicine site as predicted by modeling and the Hydropathic INTeractions score. Biological evaluations showed that NT-9-21 has 10-fold lower potency than NT-7-16, confirming the modeling predictions. These studies highlight the value of the refined colchicine-site model and identify a new pyrrole-based colchicine-site agent with potent in vitro activities and promising in vivo antitumor actions. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  10. Petroleum contamination impact on macrobenthic communities under the influence of an oil refinery: Integrating chemical and biological multivariate data

    Science.gov (United States)

    Venturini, Natalia; Muniz, Pablo; Bícego, Márcia C.; Martins, César C.; Tommasi, Luiz Roberto

    2008-07-01

    ratios and specific compound concentrations with biological data to improve the assessment of anthropogenic impact on marine ecosystems.

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

    Science.gov (United States)

    Toshima, Kazunobu

    2013-05-01

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

  12. SOGI-FLL Based Adaptive Filter for DSTATCOM Under Variable Supply Frequency

    Science.gov (United States)

    Puranik, Vishal; Arya, Sabha Raj

    2017-08-01

    This paper presents an adaptive filter based on second order generalized integrator-frequency locked loop (SOGI-FLL) for distribution static compensator (DSTATCOM) operating under variable supply frequency with nonlinear load. It is observed that under variable supply frequency, the FLL provides an excellent frequency tracking performance. Necessary compensation can be provided by DSTATCOM at any frequency with the help of SOGI-FLL. The MATLAB simulink model of DSTATCOM is developed with SOGI-FLL based control algorithm and rectifier based nonlinear load. This three wire system is simulated in power factor correction and zero voltage regulation mode under variable supply frequency.

  13. A systematic literature review on reviews and meta-analyses of biologically based CAM-practices for cancer patients

    DEFF Research Database (Denmark)

    Paludan-Müller, Christine; Lunde, Anita; Johannessen, Helle

    2010-01-01

    levels of evidence and were excluded from further evaluation. Among the 32 high-quality reviews the most reviewed practices were soy/plant hormones (7), Chinese herbal medicine (7), antioxidants (5) and mistletoe (4). Fifteen of the 32 reviews included data on the efficacy of biologically-based CAM......-practices against cancer, but none of the reviews concluded a positive effect on the cancer. Reviews including data on quality of life (10) and/or reduction of side effects (12) showed promising, but yet insufficient evidence for Chinese herbal medicine against pain  and side effects of chemotherapy, and mistletoe......Purpose To provide an overview and evaluate the evidence of biologically based CAM-practices for cancer patients. Methods Pubmed, Social Science Citation Index, AMED and the Cochrane library were systematically searched for reviews on effects of biologically based CAM-practices, including herbal...

  14. The development of peptide-based interfacial biomaterials for generating biological functionality on the surface of bioinert materials.

    Science.gov (United States)

    Meyers, Steven R; Khoo, Xiaojuan; Huang, Xin; Walsh, Elisabeth B; Grinstaff, Mark W; Kenan, Daniel J

    2009-01-01

    Biomaterials used in implants have traditionally been selected based on their mechanical properties, chemical stability, and biocompatibility. However, the durability and clinical efficacy of implantable biomedical devices remain limited in part due to the absence of appropriate biological interactions at the implant interface and the lack of integration into adjacent tissues. Herein, we describe a robust peptide-based coating technology capable of modifying the surface of existing biomaterials and medical devices through the non-covalent binding of modular biofunctional peptides. These peptides contain at least one material binding sequence and at least one biologically active sequence and thus are termed, "Interfacial Biomaterials" (IFBMs). IFBMs can simultaneously bind the biomaterial surface while endowing it with desired biological functionalities at the interface between the material and biological realms. We demonstrate the capabilities of model IFBMs to convert native polystyrene, a bioinert surface, into a bioactive surface that can support a range of cell activities. We further distinguish between simple cell attachment with insufficient integrin interactions, which in some cases can adversely impact downstream biology, versus biologically appropriate adhesion, cell spreading, and cell survival mediated by IFBMs. Moreover, we show that we can use the coating technology to create spatially resolved patterns of fluorophores and cells on substrates and that these patterns retain their borders in culture.

  15. The Immunogenicity of a Biological Simulant: Strategies for the Improvement of Antibody-Based Detection

    National Research Council Canada - National Science Library

    Grahame, David A; Gencic, Simonida; Bronk, Burt V

    2005-01-01

    .... The bacterium Pantoea agglomerans (formerly Erwinia herbicola, Eh) presently is used to simulate vegetative biological agents, however, anti-Eh antibodies of high affinity and specificity are needed...

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

    Science.gov (United States)

    Regier, Kimberly Fayette

    2016-01-01

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

  17. Miniaturized ionophore-based potentiometric sensors for the flow-injection determination of metformin in pharmaceutical formulations and biological fluids.

    Science.gov (United States)

    Khaled, Elmorsy; Kamel, Manal S; Hassan, Hassan N; Abd El-Alim, Sameh H; Aboul-Enein, Hassan Y

    2012-12-07

    Miniaturized potentiometric sensors based on β-cyclodextrins (β-CDs) are described for determination of metformin (Mf) in pharmaceutical preparations and biological fluids. Electrode matrix compositions are optimized on the basis of the nature and content of sensing ionophore, ionic sites and plasticizers. Coated wire electrodes (CWEs) modified with heptakis(2,3,6-tri-O-methyl)-β-CD, sodium tetrakis(4-fluorophenyl)borate (NaTFPB) and 2-fluorophenyl 2-nitrophenyl ether (f-NPE), work satisfactorily in the concentration range from 10(-6) to 10(-1) mol L(-1) with Nernstian compliance (55.7 ± 0.4 mV per decade activity) and a detection limit of 8 × 10(-7) mol L(-1). Incorporation of β-CD as a molecular recognition element improved the electrode sensitivity and selectivity due to encapsulation of Mf into the β-CD cavity (host-guest interaction). The developed electrodes have been successfully applied for the potentiometric determination of Mf under batch and flow injection analysis (FIA). FIA allows analysis of 90 samples per h offering the advantages of simplicity, accuracy and automation feasibility. The dissolution profile for metformin pharmaceutical samples (Cidophage®) was monitored using the proposed electrode in comparison with the official spectrophotometric methods. Characterization of the formed Mf-β-CD inclusion complexes is discussed in detail.

  18. Three-Dimensional Biologically Relevant Spectrum (BRS-3D: Shape Similarity Profile Based on PDB Ligands as Molecular Descriptors

    Directory of Open Access Journals (Sweden)

    Ben Hu

    2016-11-01

    Full Text Available The crystallized ligands in the Protein Data Bank (PDB can be treated as the inverse shapes of the active sites of corresponding proteins. Therefore, the shape similarity between a molecule and PDB ligands indicated the possibility of the molecule to bind with the targets. In this paper, we proposed a shape similarity profile that can be used as a molecular descriptor for ligand-based virtual screening. First, through three-dimensional (3D structural clustering, 300 diverse ligands were extracted from the druggable protein–ligand database, sc-PDB. Then, each of the molecules under scrutiny was flexibly superimposed onto the 300 ligands. Superimpositions were scored by shape overlap and property similarity, producing a 300 dimensional similarity array termed the “Three-Dimensional Biologically Relevant Spectrum (BRS-3D”. Finally, quantitative or discriminant models were developed with the 300 dimensional descriptor using machine learning methods (support vector machine. The effectiveness of this approach was evaluated using 42 benchmark data sets from the G protein-coupled receptor (GPCR ligand library and the GPCR decoy database (GLL/GDD. We compared the performance of BRS-3D with other 2D and 3D state-of-the-art molecular descriptors. The results showed that models built with BRS-3D performed best for most GLL/GDD data sets. We also applied BRS-3D in histone deacetylase 1 inhibitors screening and GPCR subtype selectivity prediction. The advantages and disadvantages of this approach are discussed.

  19. Microwave-Assisted Synthesis of Some Quinoxaline-Incorporated Schiff Bases and Their Biological Evaluation

    Directory of Open Access Journals (Sweden)

    L. Achutha

    2013-01-01

    Full Text Available Quinoxaline-incorporated Schiff bases (4a–j were synthesized by the condensation of 2-[(3-methylquinoxalin-2-yloxy]acetohydrazide (3 with indole-3-carbaldehyde, furfuraldehyde, 5-(4-nitrophenyl-2-furfuraldehyde, and substituted benzaldehydes under conventional and microwave irradiation methods. The microwave method was found to be remarkably successful with higher yields, less reaction time, and environmentally friendly compared to conventional heating method. The chemical structures of the synthesized compounds have been confirmed by analytical and spectral data. All the compounds have been evaluated for antitubercular and anti-inflammatory activities.

  20. Comparison of biological stability and metabolism of CCK2 receptor targeting peptides, a collaborative project under COST BM0607

    Energy Technology Data Exchange (ETDEWEB)

    Ocak, Meltem [Innsbruck Medical University, Clinical Department of Nuclear Medicine, Innsbruck (Austria); Istanbul University, Department of Pharmaceutical Technology, Pharmacy Faculty, Istanbul (Turkey); Helbok, Anna; Rangger, Christine; Decristoforo, Clemens [Innsbruck Medical University, Clinical Department of Nuclear Medicine, Innsbruck (Austria); Peitl, Petra Kolenc [University Medical Centre Ljubljana, Department for Nuclear Medicine, Ljubljana (Slovenia); Nock, Berthold A. [National Center for Scientific Research Demokritos, Molecular Radiopharmacy, Institute of Radioisotopes-Radiodiagnostic Products, Athens (Greece); Morelli, Giancarlo [University of Naples ' ' Federico II' ' and IBB-CN, Department of Biological Sciences, CIRPeB, Naples (Italy); Eek, Annemarie [Radboud University Nijmegen Medical Centre, Department of Nuclear Medicine, Nijmegen (Netherlands); Sosabowski, Jane K. [Institute of Cancer, Barts and the London Queen Mary' s School of Medicine and Dentistry, Centre for Molecular Oncology and Imaging, London (United Kingdom); Breeman, W.A.P. [Erasmus MC Rotterdam, Department of Nuclear Medicine, Rotterdam (Netherlands); Reubi, Jean Claude [University of Berne, Division of Cell Biology and Experimental Cancer Research Institute of Pathology, Berne (Switzerland)

    2011-08-15

    Stability of radiolabelled cholecystokinin 2 (CCK2) receptor targeting peptides has been a major limitation in the use of such radiopharmaceuticals especially for targeted radionuclide therapy applications, e.g. for treatment of medullary thyroid carcinoma (MTC). The purpose of this study was to compare the in vitro stability of a series of peptides binding to the CCK2 receptor [selected as part of the COST Action on Targeted Radionuclide Therapy (BM0607)] and to identify major cleavage sites. Twelve different 1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid (DOTA)-minigastrin/CCK conjugates were provided within an European COST Action (BM0607) by different laboratories and radiolabelled with {sup 177}Lu. Their in vitro stabilities were tested in fresh human serum. Radiochemical yields (RCY) and intact radioligands for half-life calculations were determined by radio-HPLC. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) analysis of metabolites was performed to identify cleavage products using conjugates labelled with excess stable {sup nat}Lu, incubated in serum at 37 C. Urine metabolite analysis after injection in normal mice was performed by radio-HPLC analysis. Variable stability in human serum was found for the different peptides with calculated half-lives between 4.5 {+-} 0.1 h and 198 {+-} 0.1 h (n = 2). In urine of normal mice only metabolised peptide fragments were detected even at short times after injection for all peptides. MALDI-TOF MS revealed a major cleavage site of all minigastrin derivatives between Asp and Phe-NH{sub 2} at the C-terminal end. Development of CCK2 receptor ligands especially for therapeutic purposes in patients with MTC or small cell lung cancer (SCLC) is still ongoing in different laboratories. This comparative study provided valuable insight into the importance of biological stability especially in the context of other results of this comparative

  1. Testing the effectiveness of problem-based learning with learning-disabled students in biology

    Science.gov (United States)

    Guerrera, Claudia Patrizia

    The purpose of the present study was to investigate the effects of problem-based learning (PBL) with learning-disabled (LD) students. Twenty-four students (12 dyads) classified as LD and attending a school for the learning-disabled participated in the study. Students engaged in either a computer-based environment involving BioWorld, a hospital simulation designed to teach biology students problem-solving skills, or a paper-and-pencil version based on the computer program. A hybrid model of learning was adopted whereby students were provided with direct instruction on the digestive system prior to participating in a problem-solving activity. Students worked in dyads and solved three problems involving the digestive system in either a computerized or a paper-and-pencil condition. The experimenter acted as a coach to assist students throughout the problem-solving process. A follow-up study was conducted, one month later, to measure the long-term learning gains. Quantitative and qualitative methods were used to analyze three types of data: process data, outcome data, and follow-up data. Results from the process data showed that all students engaged in effective collaboration and became more systematic in their problem solving over time. Findings from the outcome and follow-up data showed that students in both treatment conditions, made both learning and motivational gains and that these benefits were still evident one month later. Overall, results demonstrated that the computer facilitated students' problem solving and scientific reasoning skills. Some differences were noted in students' collaboration and the amount of assistance required from the coach in both conditions. Thus, PBL is an effective learning approach with LD students in science, regardless of the type of learning environment. These results have implications for teaching science to LD students, as well as for future designs of educational software for this population.

  2. Polymer-based precipitation preserves biological activities of extracellular vesicles from an endometrial cell line.

    Science.gov (United States)

    Niu, Ziru; Pang, Ronald T K; Liu, Weimin; Li, Qian; Cheng, Ranran; Yeung, William S B

    2017-01-01

    Extracellular vesicles (EVs) are membrane-bound vesicles released by cells and act as media for transfer of proteins, small RNAs and mRNAs to distant sites. They can be isolated by different methods. However, the biological activities of the purified EVs have seldom been studied. In this study, we compared the use of ultracentrifugation (UC), ultra-filtration (UF), polymer-based precipitation (PBP), and PBP with size-based purification (PBP+SP) for isolation of EVs from human endometrial cells and mouse uterine luminal fluid (ULF). Electron microscopy revealed that the diameters of the isolated EVs were similar among the tested methods. UF recovered the highest number of EVs followed by PBP, while UC and PBP+SP were significantly less efficient (P<0.05). Based on the number of EVs-to-protein ratios, PBP had the least protein contamination, significantly better than the other methods (P<0.05). All the isolated EVs expressed exosome-enriched proteins CD63, TSG101 and HSP70. Incubation of the trophoblast JEG-3 cells with an equal amount of the fluorescence-labelled EVs isolated by the studied methods showed that many of the PBP-EVs treated cells were fluorescence positive but only a few cells were labelled in the UC- and UF-EVs treated groups. Moreover, the PBP-EVs could transfer significantly more miRNA to the recipient cells than the other 3 methods (P<0.05). The PBP method could isolate EVs from mouse ULF; the diameter of the isolated EVs was 62±19 nm and expressed CD63, TSG101 and HSP70 proteins. In conclusion, PBP could best preserve the activities of the isolated EVs among the 4 methods studied and was able to isolate EVs from a small volume of sample. The simple setup and low equipment demands makes PBP the most suitable method for rapid EV assessment and isolation of EVs in clinical and basic research settings.

  3. Stability-based sorting: The forgotten process behind (not only) biological evolution.

    Science.gov (United States)

    Toman, Jan; Flegr, Jaroslav

    2017-12-21

    Natural selection is considered to be the main process that drives biological evolution. It requires selected entities to originate dependent upon one another by the means of reproduction or copying, and for the progeny to inherit the qualities of their ancestors. However, natural selection is a manifestation of a more general persistence principle, whose temporal consequences we propose to name "stability-based sorting" (SBS). Sorting based on static stability, i.e., SBS in its strict sense and usual conception, favours characters that increase the persistence of their holders and act on all material and immaterial entities. Sorted entities could originate independently from each other, are not required to propagate and need not exhibit heredity. Natural selection is a specific form of SBS-sorting based on dynamic stability. It requires some form of heredity and is based on competition for the largest difference between the speed of generating its own copies and their expiration. SBS in its strict sense and selection thus have markedly different evolutionary consequences that are stressed in this paper. In contrast to selection, which is opportunistic, SBS is able to accumulate even momentarily detrimental characters that are advantageous for the long-term persistence of sorted entities. However, it lacks the amplification effect based on the preferential propagation of holders of advantageous characters. Thus, it works slower than selection and normally is unable to create complex adaptations. From a long-term perspective, SBS is a decisive force in evolution-especially macroevolution. SBS offers a new explanation for numerous evolutionary phenomena, including broad distribution and persistence of sexuality, altruistic behaviour, horizontal gene transfer, patterns of evolutionary stasis, planetary homeostasis, increasing ecosystem resistance to disturbances, and the universal decline of disparity in the evolution of metazoan lineages. SBS acts on all levels in

  4. Influence of the blood meal source on the biology of Meccus picturatus Usinger 1939 (Hemiptera: Reduviidae: Triatominae under laboratory conditions

    Directory of Open Access Journals (Sweden)

    Martínez-Ibarra José Alejandro

    2003-01-01

    Full Text Available Aspects related to hatching, time-lapse between presenting the blood meal and beginning of feeding, feeding time, postfeed defecation delay,life time, mortality and fecundity for each stage of Meccus picturatus, life-cycle were evaluated and compared in two cohorts of M. picturatus fed on hens or rabbits. The hatching rate observed for each of the two studied groups of eggs was 78.1% (n = 2298 on the group fed on hens and 82.1% (n = 2704 on that fed on rabbits, and the average time of hatching was 20 days. Mean time-lapse for beginning feeding was under 3 min in nymphal stages and postfeed defecation delay was under 10 min in all stages, in both cohorts. Mean feeding time was significantly (P 0.05 differences were recorded among the average times from NI to adult in the cohort fed on hens (196.8 ± 15.8 days and the average time in the cohort fed on rabbits (189.5 ± 22.9. The average span in days for each stage fed on hens was not significantly different to the average span for each stage fed on rabbits. The number of blood meals at each nymphal stage varied from 1 to 6 in both cohorts. The mortality rates were higher on fifth nymphal stage, in both cohorts. No significant (P > 0.05 differences were recorded on mortality rates on most nymphal stages of both cohorts. The average number of eggs laid per female from the cohort fed on hens in a 9-month period was 791.1, whereas the average number of eggs in the cohort fed on rabbits was 928.3.

  5. Effect of sound on gap-junction-based intercellular signaling: Calcium waves under acoustic irradiation.

    Science.gov (United States)

    Deymier, P A; Swinteck, N; Runge, K; Deymier-Black, A; Hoying, J B

    2015-01-01

    We present a previously unrecognized effect of sound waves on gap-junction-based intercellular signaling such as in biological tissues composed of endothelial cells. We suggest that sound irradiation may, through temporal and spatial modulation of cell-to-cell conductance, create intercellular calcium waves with unidirectional signal propagation associated with nonconventional topologies. Nonreciprocity in calcium wave propagation induced by sound wave irradiation is demonstrated in the case of a linear and a nonlinear reaction-diffusion model. This demonstration should be applicable to other types of gap-junction-based intercellular signals, and it is thought that it should be of help in interpreting a broad range of biological phenomena associated with the beneficial therapeutic effects of sound irradiation and possibly the harmful effects of sound waves on health.

  6. Using a Module-Based Laboratory to Incorporate Inquiry into a Large Cell Biology Course

    Science.gov (United States)

    Howard, David R.; Miskowski, Jennifer A.

    2005-01-01

    Because cell biology has rapidly increased in breadth and depth, instructors are challenged not only to provide undergraduate science students with a strong, up-to-date foundation of knowledge, but also to engage them in the scientific process. To these ends, revision of the Cell Biology Lab course at the University of Wisconsin-La Crosse was…

  7. A knowledge base for teaching biology situated in the context of genetic testing

    NARCIS (Netherlands)

    van der Zande, P.A.M.; Waarlo, A.J.; Brekelmans, M.; Akkerman, S.F.; Vermunt, J. D.

    2011-01-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic

  8. A Knowledge Base for Teaching Biology Situated in the Context of Genetic Testing

    Science.gov (United States)

    van der Zande, Paul; Waarlo, Arend Jan; Brekelmans, Mieke; Akkerman, Sanne F.; Vermunt, Jan D.

    2011-01-01

    Recent developments in the field of genomics will impact the daily practice of biology teachers who teach genetics in secondary education. This study reports on the first results of a research project aimed at enhancing biology teacher knowledge for teaching genetics in the context of genetic testing. The increasing body of scientific knowledge…

  9. Students’ experienced coherence between chemistry and biology in context-based secondary science education

    NARCIS (Netherlands)

    Boer, H.J.; Prins, Gjalt; Goedhart, M.J.; Boersma, Kerst

    2014-01-01

    In current biology and chemistry secondary school practice, coherence between the subjects chemistry and biology is underexposed or even ignored. This is incongruent with the current scientific practice, in which the emphasis is shifting towards inter- and multidisciplinarity. These problems have

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

    Czech Academy of Sciences Publication Activity Database

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

    2013-01-01

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

  11. A Standards-Based Content Analysis of Selected Biological Science Websites

    Science.gov (United States)

    Stewart, Joy E.

    2010-01-01

    The purpose of this study was to analyze the biology content, instructional strategies, and assessment methods of 100 biological science websites that were appropriate for Grade 12 educational purposes. For the analysis of each website, an instrument, developed from the National Science Education Standards (NSES) for Grade 12 Life Science coupled…

  12. A Fractionated Spacecraft System Assessment Tool Based on Lifecycle Simulation Under Uncertainty

    NARCIS (Netherlands)

    Yao, W.; Chen, X.; Zhao, Y.; Van Tooren, M.J.L.

    2012-01-01

    To comprehensively assess fractionated spacecraft, an assessment tool is developed based on lifecycle simulation under uncertainty driven by modular evolutionary stochastic models. First, fractionated spacecraft nomenclature and architecture are clarified, and assessment criteria are analyzed. The

  13. Electrically Injected Polariton Lasing from a GaAs-Based Microcavity under Magnetic Field

    KAUST Repository

    Bhattacharya, Pallab

    2012-01-01

    Suppression of relaxation bottleneck and subsequent polariton lasing is observed in a GaAs-based microcavity under the application of a magnetic field. The threshold injection current density is 0.32 A/cm2 at 7 Tesla.

  14. Predicting biological parameters of estuarine benthic communities using models based on environmental data

    Directory of Open Access Journals (Sweden)

    José Souto Rosa-Filho

    2004-08-01

    Full Text Available This study aimed to predict the biological parameters (species composition, abundance, richness, diversity and evenness of benthic assemblages in southern Brazil estuaries using models based on environmental data (sediment characteristics, salinity, air and water temperature and depth. Samples were collected seasonally from five estuaries between the winter of 1996 and the summer of 1998. At each estuary, samples were taken in unpolluted areas with similar characteristics related to presence or absence of vegetation, depth and distance from the mouth. In order to obtain predictive models, two methods were used, the first one based on Multiple Discriminant Analysis (MDA, and the second based on Multiple Linear Regression (MLR. Models using MDA had better results than those based on linear regression. The best results using MLR were obtained for diversity and richness. It could be concluded that the use predictions models based on environmental data would be very useful in environmental monitoring studies in estuaries.Este trabalho objetivou predizer parâmetros da estrutura de associações macrobentônicas (composição específica, abundância, riqueza, diversidade e equitatividade em estuários do Sul do Brasil, utilizando modelos baseados em dados ambientais (características dos sedimentos, salinidade, temperaturas do ar e da água, e profundidade. As amostragens foram realizadas sazonalmente em cinco estuários entre o inverno de 1996 e o verão de 1998. Em cada estuário as amostras foram coletadas em áreas não poluídas, com características semelhantes quanto a presença ou ausência de vegetação, profundidade e distância da desenbocadura. Para a obtenção dos modelos de predição, foram utilizados dois métodos: o primeiro baseado em Análise Discriminante Múltipla (ADM e o segundo em Regressão Linear Múltipla (RLM. Os modelos baseados em ADM apresentaram resultados melhores do que os baseados em regressão linear. Os melhores

  15. Quantitative generalized ratiometric fluorescence spectroscopy for turbid media based on probe encapsulated by biologically localized embedding

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Xiu-Fang; Chen, Zeng-Ping, E-mail: zpchen2002@hotmail.com; Cui, Yin-Yin; Hu, Yuan-Liang; Yu, Ru-Qin

    2016-05-19

    PEBBLE (probe encapsulated by biologically localized embedding) nanosensor encapsulating an intensity-based fluorescence indicator and an inert reference fluorescence dye inside the pores of stable matrix can be used as a generalized wavelength-ratiometric probe. However, the lack of an efficient quantitative model render the choices of inert reference dyes and intensity-based fluorescence indicators used in PEBBLEs based generalized wavelength-ratiometric probes rather limited. In this contribution, an extended quantitative fluorescence model was derived specifically for generalized wavelength-ratiometric probes based on PEBBLE technique (QFM{sub GRP}) with a view to simplify the design of PEBBLEs and hence further extend their application potentials. The effectiveness of QFM{sub GRP} has been tested on the quantitative determination of free Ca{sup 2+} in both simulated and real turbid media using a Ca{sup 2+} sensitive PEBBLE nanosensor encapsulating Rhod-2 and eosin B inside the micropores of stable polyacrylamide matrix. Experimental results demonstrated that QFM{sub GRP} could realize precise and accurate quantification of free Ca{sup 2+} in turbid samples, even though there is serious overlapping between the fluorescence excitation peaks of eosin B and Ca{sup 2+} bound Rhod-2. The average relative predictive error value of QFM{sub GRP} for the test simulated turbid samples was 5.9%, about 2–4 times lower than the corresponding values of partial least squares calibration model and the empirical ratiometric model based on the ratio of fluorescence intensities at the excitation peaks of Ca{sup 2+} bound Rhod-2 and eosin B. The recovery rates of QFM{sub GRP} for the real and spiked turbid samples varied from 93.1% to 101%, comparable to the corresponding results of atomic absorption spectrometry. - Highlights: • An advanced model was derived for generalized wavelength-ratiometric PEBBLEs. • The model can simplify the design of generalized wavelength

  16. Correlation-Based Network Generation, Visualization, and Analysis as a Powerful Tool in Biological Studies: A Case Study in Cancer Cell Metabolism

    Directory of Open Access Journals (Sweden)

    Albert Batushansky

    2016-01-01

    Full Text Available In the last decade vast data sets are being generated in biological and medical studies. The challenge lies in their summary, complexity reduction, and interpretation. Correlation-based networks and graph-theory based properties of this type of networks can be successfully used during this process. However, the procedure has its pitfalls and requires specific knowledge that often lays beyond classical biology and includes many computational tools and software. Here we introduce one of a series of methods for correlation-based network generation and analysis using freely available software. The pipeline allows the user to control each step of the network generation and provides flexibility in selection of correlation methods and thresholds. The pipeline was implemented on published metabolomics data of a population of human breast carcinoma cell lines MDA-MB-231 under two conditions: normal and hypoxia. The analysis revealed significant differences between the metabolic networks in response to the tested conditions. The network under hypoxia had 1.7 times more significant correlations between metabolites, compared to normal conditions. Unique metabolic interactions were identified which could lead to the identification of improved markers or aid in elucidating the mechanism of regulation between distantly related metabolites induced by the cancer growth.

  17. Exploring new Probenecid-based carbonic anhydrase inhibitors: Synthesis, biological evaluation and docking studies.

    Science.gov (United States)

    Mollica, Adriano; Costante, Roberto; Akdemir, Atilla; Carradori, Simone; Stefanucci, Azzurra; Macedonio, Giorgia; Ceruso, Mariangela; Supuran, Claudiu T

    2015-09-01

    Novel Probenecid-based amide derivatives, incorporating different natural amino acids, were synthesized and assayed to test their effect on the human carbonic anhydrase (hCA, EC 4.2.1.1) transmembrane isoforms hCA IX and XII over the ubiquitous isoforms hCA I and II. Most of them presented a complete loss of hCA II inhibition (K(i)s > 10,000 nM) and strong inhibitory activity against hCA IX and XII in the nanomolar range with respect to the parent compound. A residual activity against hCA I was observed for some of them. These biological results have been explained by docking studies within the active sites of the four studied human carbonic anhydrases (with or without the zinc-bound water) and helped us to better comprehend the rationale behind the design of tertiary sulfonamide compounds as potent but atypical inhibitors of specific isoforms of human carbonic anhydrase. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Knowledge-based fuzzy system for diagnosis and control of an integrated biological wastewater treatment process.

    Science.gov (United States)

    Pires, O C; Palma, C; Costa, J C; Moita, I; Alves, M M; Ferreira, E C

    2006-01-01

    A supervisory expert system based on fuzzy logic rules was developed for diagnosis and control of a laboratory- scale plant comprising anaerobic digestion and anoxic/aerobic modules for combined high rate biological N and C removal. The design and implementation of a computational environment in LabVIEW for data acquisition, plant operation and distributed equipment control is described. A step increase in ammonia concentration from 20 to 60 mg N/L was applied during a trial period of 73 h. Recycle flow rate from the aerobic to the anoxic module and bypass flow rate from the influent directly to the anoxic reactor were the output variables of the fuzzy system. They were automatically changed (from 34 to 111 L/day and from 8 to 13 L/day, respectively), when new plant conditions were recognised by the expert system. Denitrification efficiency higher than 85% was achieved 30 h after the disturbance and 15 h after the system response at an HRT as low as 1.5 h. Nitrification efficiency gradually increased from 12 to 50% at an HRT of 3 h. The system proved to react properly in order to set adequate operating conditions that led to timely and efficient recovery of N and C removal rates.

  19. Community-based inquiry improves critical thinking in general education biology.

    Science.gov (United States)

    Quitadamo, Ian J; Faiola, Celia L; Johnson, James E; Kurtz, Martha J

    2008-01-01

    National stakeholders are becoming increasingly concerned about the inability of college graduates to think critically. Research shows that, while both faculty and students deem critical thinking essential, only a small fraction of graduates can demonstrate the thinking skills necessary for academic and professional success. Many faculty are considering nontraditional teaching methods that incorporate undergraduate research because they more closely align with the process of doing investigative science. This study compared a research-focused teaching method called community-based inquiry (CBI) with traditional lecture/laboratory in general education biology to discover which method would elicit greater gains in critical thinking. Results showed significant critical-thinking gains in the CBI group but decreases in a traditional group and a mixed CBI/traditional group. Prior critical-thinking skill, instructor, and ethnicity also significantly influenced critical-thinking gains, with nearly all ethnicities in the CBI group outperforming peers in both the mixed and traditional groups. Females, who showed decreased critical thinking in traditional courses relative to males, outperformed their male counterparts in CBI courses. Through the results of this study, it is hoped that faculty who value both research and critical thinking will consider using the CBI method.

  20. New, national bottom-up estimate for tree-based biological ...

    Science.gov (United States)

    Nitrogen is a limiting nutrient in many ecosystems, but is also a chief pollutant from human activity. Quantifying human impacts on the nitrogen cycle and investigating natural ecosystem nitrogen cycling both require an understanding of the magnitude of nitrogen inputs from biological nitrogen fixation (BNF). A bottom-up approach to estimating BNF—scaling rates up from measurements to broader scales—is attractive because it is rooted in actual BNF measurements. However, bottom-up approaches have been hindered by scaling difficulties, and a recent top-down approach suggested that the previous bottom-up estimate was much too large. Here, we used a bottom-up approach for tree-based BNF, overcoming scaling difficulties with the systematic, immense (>70,000 N-fixing trees) Forest Inventory and Analysis (FIA) database. We employed two approaches to estimate species-specific BNF rates: published ecosystem-scale rates (kg N ha-1 yr-1) and published estimates of the percent of N derived from the atmosphere (%Ndfa) combined with FIA-derived growth rates. Species-specific rates can vary for a variety of reasons, so for each approach we examined how different assumptions influenced our results. Specifically, we allowed BNF rates to vary with stand age, N-fixer density, and canopy position (since N-fixation is known to require substantial light).Our estimates from this bottom-up technique are several orders of magnitude lower than previous estimates indicating

  1. Photonic chip-based soliton frequency combs covering the biological imaging window.

    Science.gov (United States)

    Karpov, Maxim; Pfeiffer, Martin H P; Liu, Junqiu; Lukashchuk, Anton; Kippenberg, Tobias J

    2018-03-20

    Dissipative Kerr solitons (DKS) in optical microresonators provide a highly miniaturised, chip-integrated frequency comb source with unprecedentedly high repetition rates and spectral bandwidth. To date, such frequency comb sources have been successfully applied in the optical telecommunication band for dual-comb spectroscopy, coherent telecommunications, counting of optical frequencies and distance measurements. Yet, the range of applications could be significantly extended by operating in the near-infrared spectral domain, which is a prerequisite for biomedical and Raman imaging applications, and hosts commonly used optical atomic transitions. Here we show the operation of photonic-chip-based soliton Kerr combs driven with 1 micron laser light. By engineering the dispersion properties of a Si 3 N 4 microring resonator, octave-spanning soliton Kerr combs extending to 776 nm are attained, thereby covering the optical biological imaging window. Moreover, we show that soliton states can be generated in normal group-velocity dispersion regions when exploiting mode hybridisation with other mode families.

  2. Harnessing Biology to Deliver Therapeutic and Imaging Entities via Cell-Based Methods.

    Science.gov (United States)

    Joshi, Bishnu P; Hardie, Joseph; Farkas, Michelle E

    2018-03-15

    The accumulation of therapeutic and imaging agents at sites of interest is critical to their efficacy. Similarly, off-target effects (especially toxicity) are a major liability for these agents. For this reason, the use of delivery vehicles to improve the distribution characteristics of bio-active agents has become ubiquitous in the field. However, the majority of traditionally employed, cargo-bearing entities rely on passive accumulation. Even in cases where 'targeting' functionalities are used, the agents must first reach the site in order for the ligand-receptor interaction to occur. The next stage of vehicle development is the use of 'recruited' entities, which respond to biological signals produced in the tissues to be targeted, resulting in improved specificities. Recently, many advances have been made in the utilization of cells as delivery agents. They are biocompatible, exhibit excellent circulation lifetimes and tissue penetration capabilities, and respond to chemotactic signals. In this mini-review, we will explore various cell types, modifications, and applications where cell-based delivery agents are used. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. A shift in paradigm towards human biology-based systems for cholestatic-liver diseases.

    Science.gov (United States)

    Noor, Fozia

    2015-12-01

    Cholestatic-liver diseases (CLDs) arise from diverse causes ranging from genetic factors to drug-induced cholestasis. The so-called diseases of civilization (obesity, diabetes, metabolic disorders, non-alcoholic liver disease, cardiovascular diseases, etc.) are intricately implicated in liver and gall bladder diseases. Although CLDs have been extensively studied, there seem to be important gaps in the understanding of human disease. Despite the fact that many animal models exist and substantial clinical data are available, translation of this knowledge towards therapy has been disappointingly limited. Recent advances in liver cell culture such as in vivo-like 3D cultivation of human primary hepatic cells, human induced pluripotent stem cell-derived hepatocytes; and cutting-edge analytical techniques such as 'omics' technologies and high-content screenings could play a decisive role in deeper mechanistic understanding of CLDs. This Topical Review proposes a roadmap to human biology-based research using omics technologies providing quantitative information on mechanisms in an adverse outcome/disease pathway framework. With modern sensitive tools, a shift in paradigm in human disease research seems timely and even inevitable to overcome species barriers in translation. © 2015 The Authors. The Journal of Physiology © 2015 The Physiological Society.

  4. A novel cell weighing method based on the minimum immobilization pressure for biological applications

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Qili [Robotics and Mechatronics Research Laboratory, Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3800 (Australia); Institute of Robotics and Automatic Information System, Nankai University, Tianjin 300071 (China); Shirinzadeh, Bijan [Robotics and Mechatronics Research Laboratory, Department of Mechanical and Aerospace Engineering, Monash University, Clayton 3800 (Australia); Cui, Maosheng [Biotechnology Lab of Animal Reproduction, Tianjin Animal Sciences, Tianjin 300112 (China); Sun, Mingzhu; Liu, Yaowei; Zhao, Xin, E-mail: zhaoxin@nankai.edu.cn [Institute of Robotics and Automatic Information System, Nankai University, Tianjin 300071 (China)

    2015-07-28

    A novel weighing method for cells with spherical and other regular shapes is proposed in this paper. In this method, the relationship between the cell mass and the minimum aspiration pressure to immobilize the cell (referred to as minimum immobilization pressure) is derived for the first time according to static theory. Based on this relationship, a robotic cell weighing process is established using a traditional micro-injection system. Experimental results on porcine oocytes demonstrate that the proposed method is able to weigh cells at an average speed of 16.3 s/cell and with a success rate of more than 90%. The derived cell mass and density are in accordance with those reported in other published results. The experimental results also demonstrated that this method is able to detect less than 1% variation of the porcine oocyte mass quantitatively. It can be conducted by a pair of traditional micropipettes and a commercial pneumatic micro-injection system, and is expected to perform robotic operation on batch cells. At present, the minimum resolution of the proposed method for measuring the cell mass can be 1.25 × 10{sup −15 }kg. Above advantages make it very appropriate for quantifying the amount of the materials injected into or moved out of the cells in the biological applications, such as nuclear enucleations and embryo microinjections.

  5. Biologically based neural circuit modelling for the study of fear learning and extinction

    Science.gov (United States)

    Nair, Satish S.; Paré, Denis; Vicentic, Aleksandra

    2016-11-01

    The neuronal systems that promote protective defensive behaviours have been studied extensively using Pavlovian conditioning. In this paradigm, an initially neutral-conditioned stimulus is paired with an aversive unconditioned stimulus leading the subjects to display behavioural signs of fear. Decades of research into the neural bases of this simple behavioural paradigm uncovered that the amygdala, a complex structure comprised of several interconnected nuclei, is an essential part of the neural circuits required for the acquisition, consolidation and expression of fear memory. However, emerging evidence from the confluence of electrophysiological, tract tracing, imaging, molecular, optogenetic and chemogenetic methodologies, reveals that fear learning is mediated by multiple connections between several amygdala nuclei and their distributed targets, dynamical changes in plasticity in local circuit elements as well as neuromodulatory mechanisms that promote synaptic plasticity. To uncover these complex relations and analyse multi-modal data sets acquired from these studies, we argue that biologically realistic computational modelling, in conjunction with experiments, offers an opportunity to advance our understanding of the neural circuit mechanisms of fear learning and to address how their dysfunction may lead to maladaptive fear responses in mental disorders.

  6. Recent developments in solution nuclear magnetic resonance (NMR)-based molecular biology.

    Science.gov (United States)

    Ziarek, Joshua J; Baptista, Diego; Wagner, Gerhard

    2018-01-01

    Visualizing post-translational modifications, conformations, and interaction surfaces of protein structures at atomic resolution underpins the development of novel therapeutics to combat disease. As computational resources expand, in silico calculations coupled with experimentally derived structures and functional assays have led to an explosion in structure-based drug design (SBDD) with several compounds in clinical trials. It is increasingly clear that "hidden" transition-state structures along activation trajectories can be harnessed to develop novel classes of allosteric inhibitors. The goal of this mini-review is to empower the clinical researcher with a general knowledge of the strengths and weaknesses of nuclear magnetic resonance (NMR) spectroscopy in molecular medicine. Although NMR can determine protein structures at atomic resolution, its unrivaled strength lies in sensing