WorldWideScience

Sample records for biology based study

  1. 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.

  2. 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

  3. 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).

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

    Science.gov (United States)

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

    2010-10-27

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

  6. 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.

  7. 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

  8. The Effectiveness of a Case Study-Based First-Year Biology Class at a Black Women's College

    Science.gov (United States)

    Pai, Aditi; Benning, Tracy; Woods, Natasha; McGinnis, Gene; Chu, Joanne; Netherton, Josh; Bauerle, Cynthia

    2010-01-01

    The authors used a case study-based approach in the introductory biology course at Spelman College. The course taught to entering freshmen was divided into three modules--ecology, evolution, and biodiversity, each designed around a case study. They noted that (1) case study teaching was dramatically more effective than the traditional lecture…

  9. Student and Teacher Perceptions of a Mobile-Based Biology Vocabulary Study Tool for English Language Learners

    Science.gov (United States)

    Cruz, Maria B.

    English language learners studying biology face a dual challenge of mastering both content and language. Teaching ELLs how to engage in scientific discourse using appropriate language to ask, answer, explain, and make predictions about science requires a foundational knowledge of content-specific vocabulary. This study used qualitative interviews with intermediate-level ELLs at an American high school to learn how a supplemental iPod-based vocabulary review tool influenced their perceptions of learning biology vocabulary outside of classroom hours. Interviews with their biology teacher were also used to complement student testimony from the point of view of an educational professional with ELL teaching experience. Past studies in the area of mobile learning have primarily employed questionnaires to gather feedback from participants. This research study adds greater participant voice to the body of literature that encompasses mobile language learning, second language acquisition, and science education by presenting nuanced opinions from both students and teachers. This dissertation concludes with a discussion on the influence that this study could have on further research in the fields of mobile learning, academic vocabulary, and student learning behaviors.

  10. 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).

  11. 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

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

    Science.gov (United States)

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

    2013-05-01

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

  13. Tritium biological effects and perspective of the biological study

    International Nuclear Information System (INIS)

    Komatsu, Kenshi

    1998-01-01

    Since tritium is an emitter of weak β-rays (5.7keV) and is able to bind to DNA, i.e., the most important genome component, the biological effects should be expected to be more profound than that of X-rays and γ-rays. When carcinogenesis, genetical effects and the detriments for fetus and embryo were used as a biological endpoint, most of tritium RBE (relative biological effectiveness) ranged from 1 to 2. The tritium risk in man could be calculated from these RBEs and γ-ray risk for human exposure, which are obtained mainly from the data on Atomic Bomb survivors. However, the exposure modality from environmental tritium should be a chronic irradiation with ultra low dose rate or a fractionated irradiation. We must estimate the tritium effect in man based on biological experiments alone, due to lack of such epidemiological data. Low dose rate experiment should be always accompanied by the statistical problem of data, since their biological effects are fairy low, and they should involve a possible repair system, such as adaptive response (or hormesis effect) and 'Kada effect' observed in bacteria. Here we discuss future works for the tritium assessment in man, such as (1) developing a high radiation sensitive assay system with rodent hybrid cells containing a single human chromosome and also (2) study on mammal DNA repair at molecular levels using a radiosensitive hereditary disease, Nijmegen Breakage Syndrome. (author)

  14. 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.

  15. 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.

  16. Guiding Development Based Approach Practicum Vertebrates Taxonomy Scientific Study Program for Students of Biology Education

    Science.gov (United States)

    Arieska, M.; Syamsurizal, S.; Sumarmin, R.

    2018-04-01

    Students having difficulty in identifying and describing the vertebrate animals as well as less skilled in science process as practical. Increased expertise in scientific skills, one of which is through practical activities using practical guidance based on scientific approach. This study aims to produce practical guidance vertebrate taxonomy for biology education students PGRI STKIP West Sumatra valid. This study uses a model of Plomp development consisting of three phases: the initial investigation, floating or prototype stage, and the stage of assessment. Data collection instruments used in this study is a validation sheet guiding practicum. Data were analyzed descriptively based on data obtained from the field. The result of the development of practical guidance vertebrate taxonomic validity value of 3.22 is obtained with very valid category. Research and development has produced a practical guide based vertebrate taxonomic scientific approach very valid.

  17. 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.

  18. 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.

  19. Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from amoxicillin and sugars

    International Nuclear Information System (INIS)

    Naz, N.

    2009-01-01

    Fe (II), Co (II) and Ni (II) metal complexes of new Schiff bases derived from amoxicillin with sugars (D-Glucose, D-Galactose and D-Mannose) have been synthesized and characterized by elemental analysis, FTIR, electronic absorption, and atomic absorption spectroscopy, magnetic moment measurements and thermal analysis. It has been found that Schiff bases behave as bi-dentate ligands forming complexes with 1:2 (metal:ligand) stoichiometry. The complexes were neutral as confirmed by their low conductance values. The biological applications of complexes have been studied on two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and Staphylococcus aureus) microorganisms by Agar diffusion disc method. It has been found that all the complexes have higher biological activities than the pure amoxicillin. (author)

  20. Biological interactions of carbon-based nanomaterials: From coronation to degradation.

    Science.gov (United States)

    Bhattacharya, Kunal; Mukherjee, Sourav P; Gallud, Audrey; Burkert, Seth C; Bistarelli, Silvia; Bellucci, Stefano; Bottini, Massimo; Star, Alexander; Fadeel, Bengt

    2016-02-01

    Carbon-based nanomaterials including carbon nanotubes, graphene oxide, fullerenes and nanodiamonds are potential candidates for various applications in medicine such as drug delivery and imaging. However, the successful translation of nanomaterials for biomedical applications is predicated on a detailed understanding of the biological interactions of these materials. Indeed, the potential impact of the so-called bio-corona of proteins, lipids, and other biomolecules on the fate of nanomaterials in the body should not be ignored. Enzymatic degradation of carbon-based nanomaterials by immune-competent cells serves as a special case of bio-corona interactions with important implications for the medical use of such nanomaterials. In the present review, we highlight emerging biomedical applications of carbon-based nanomaterials. We also discuss recent studies on nanomaterial 'coronation' and how this impacts on biodistribution and targeting along with studies on the enzymatic degradation of carbon-based nanomaterials, and the role of surface modification of nanomaterials for these biological interactions. Advances in technology have produced many carbon-based nanomaterials. These are increasingly being investigated for the use in diagnostics and therapeutics. Nonetheless, there remains a knowledge gap in terms of the understanding of the biological interactions of these materials. In this paper, the authors provided a comprehensive review on the recent biomedical applications and the interactions of various carbon-based nanomaterials. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  1. Novel study guides for biochemistry meaningful learning in biology: a design-based research

    Directory of Open Access Journals (Sweden)

    Caetano da Costa

    2017-12-01

    Full Text Available To address the usually decontextualized transmission of information in biochemistry teaching, three interventions in a discipline (Metabolism for Biology majors were applied as innovative study guides. We describe the development, application, and evaluation of two study guides, contextualized with a real problem or an integrative view, using broad themes like evolution and metabolic adaptation. In order to evaluate the impact of both interventions on interest, motivation, and learning of the metabolic pathways, 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. Analysis and interpretation of the results point to benefits for teaching and learning, with helpful information to guide elaboration and refinement of new teaching materials and to make active learning more meaningful.

  2. Synthesis, biological evaluation and molecular docking studies of ...

    African Journals Online (AJOL)

    Synthesis, biological evaluation and molecular docking studies of Mannich bases derived from 1, 3, 4-oxadiazole- 2-thiones as potential urease inhibitors. ... Mannich bases (5-17) were subjected to in silico screening as urease inhibitors, using crystal structure of urease (Protein Data Bank ID: 5FSE) as a model enzyme.

  3. 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

  4. 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

  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. 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

  7. 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…

  8. Rethinking biology instruction: The application of DNR-based instruction to the learning and teaching of biology

    Science.gov (United States)

    Maskiewicz, April Lee

    Educational studies report that secondary and college level students have developed only limited understandings of the most basic biological processes and their interrelationships from typical classroom experiences. Furthermore, students have developed undesirable reasoning schemes and beliefs that directly affect how they make sense of and account for biological phenomena. For these reasons, there exists a need to rethink instructional practices in biology. This dissertation discusses how the principles of Harel's (1998, 2001) DNR-based instruction in mathematics could be applied to the teaching and learning of biology. DNR is an acronym for the three foundational principles of the system: Duality, Necessity, and Repeated-reasoning. This study examines the application of these three principles to ecology instruction. Through clinical and teaching interviews, I developed models of students' existing ways of understanding in ecology and inferred their ways of thinking. From these models a hypothetical learning trajectory was developed for 16 college level freshmen enrolled in a 10-week ecology teaching experiment. Through cyclical, interpretive analysis I documented and analyzed the evolution of the participants' progress. The results provide empirical evidence to support the claim that the DNR principles are applicable to ecology instruction. With respect to the Duality Principle, helping students develop specific ways of understanding led to the development of model-based reasoning---a way of thinking and the cognitive objective guiding instruction. Through carefully structured problem solving tasks, the students developed a biological understanding of the relationship between matter cycling, energy flow, and cellular processes such as photosynthesis and respiration, and used this understanding to account for observable phenomena in nature. In the case of intellectual necessity, the results illuminate how problem situations can be developed for biology learners

  9. Biological methanation of hydrogen within biogas plants: A model-based feasibility study

    International Nuclear Information System (INIS)

    Bensmann, A.; Hanke-Rauschenbach, R.; Heyer, R.; Kohrs, F.; Benndorf, D.; Reichl, U.; Sundmacher, K.

    2014-01-01

    Highlights: • Simulation study about direct methanation of hydrogen within biogas plants. • In stationary operation two limitations, namely biological and transfer limit. • Biological limit at 4m H2 3 /m CO2 3 due to stoichiometry. • Dynamic behaviour shows three qualitatively different step responses. • A simple control scheme to meet the output quality was developed. - Abstract: One option to utilize excess electric energy is its conversion to hydrogen and the subsequent methanation. An alternative to the classical chemical Sabatier process is the biological methanation (methanogenesis) within biogas plants. In conventional biogas plants methane and carbon dioxide is produced. The latter can be directly converted to methane by feeding hydrogen into the reactor, since hydrogenotrophic bacteria are present. In the present contribution, a comprehensive simulation study with respect to stationary operating conditions and disturbances is presented. It reveals two qualitative different limitations, namely a biological limit (appr. at 4m H2 3 /m CO2 3 corresponds to 4.2m H2,STP 3 /m liq 3 /d) as well as a transfer limit. A parameter region for a safe operation was defined. The temporary operation with stationary unfeasible conditions was analysed and thereby three qualitatively different disturbances can be distinguished. In one of these the operation for several days is possible. On the basis of these results, a controller was proposed and tested that meets the demands on the conversion of hydrogen and also prevents the washout of the microbial community due to hydrogen overload

  10. Undergraduate Biology Lab Courses: Comparing the Impact of Traditionally Based "Cookbook" and Authentic Research-Based Courses on Student Lab Experiences

    Science.gov (United States)

    Brownell, Sara E.; Kloser, Matthew J.; Fukami, Tadishi; Shavelson, Rich

    2012-01-01

    Over the past decade, several reports have recommended a shift in undergraduate biology laboratory courses from traditionally structured, often described as "cookbook," to authentic research-based experiences. This study compares a cookbook-type laboratory course to a research-based undergraduate biology laboratory course at a Research 1…

  11. EUD-based biological optimization for carbon ion therapy

    International Nuclear Information System (INIS)

    Brüningk, Sarah C.; Kamp, Florian; Wilkens, Jan J.

    2015-01-01

    Purpose: Treatment planning for carbon ion therapy requires an accurate modeling of the biological response of each tissue to estimate the clinical outcome of a treatment. The relative biological effectiveness (RBE) accounts for this biological response on a cellular level but does not refer to the actual impact on the organ as a whole. For photon therapy, the concept of equivalent uniform dose (EUD) represents a simple model to take the organ response into account, yet so far no formulation of EUD has been reported that is suitable to carbon ion therapy. The authors introduce the concept of an equivalent uniform effect (EUE) that is directly applicable to both ion and photon therapies and exemplarily implemented it as a basis for biological treatment plan optimization for carbon ion therapy. Methods: In addition to a classical EUD concept, which calculates a generalized mean over the RBE-weighted dose distribution, the authors propose the EUE to simplify the optimization process of carbon ion therapy plans. The EUE is defined as the biologically equivalent uniform effect that yields the same probability of injury as the inhomogeneous effect distribution in an organ. Its mathematical formulation is based on the generalized mean effect using an effect-volume parameter to account for different organ architectures and is thus independent of a reference radiation. For both EUD concepts, quadratic and logistic objective functions are implemented into a research treatment planning system. A flexible implementation allows choosing for each structure between biological effect constraints per voxel and EUD constraints per structure. Exemplary treatment plans are calculated for a head-and-neck patient for multiple combinations of objective functions and optimization parameters. Results: Treatment plans optimized using an EUE-based objective function were comparable to those optimized with an RBE-weighted EUD-based approach. In agreement with previous results from photon

  12. Agent-Based Modeling in Molecular Systems Biology.

    Science.gov (United States)

    Soheilypour, Mohammad; Mofrad, Mohammad R K

    2018-06-08

    Molecular systems orchestrating the biology of the cell typically involve a complex web of interactions among various components and span a vast range of spatial and temporal scales. Computational methods have advanced our understanding of the behavior of molecular systems by enabling us to test assumptions and hypotheses, explore the effect of different parameters on the outcome, and eventually guide experiments. While several different mathematical and computational methods are developed to study molecular systems at different spatiotemporal scales, there is still a need for methods that bridge the gap between spatially-detailed and computationally-efficient approaches. In this review, we summarize the capabilities of agent-based modeling (ABM) as an emerging molecular systems biology technique that provides researchers with a new tool in exploring the dynamics of molecular systems/pathways in health and disease. © 2018 WILEY Periodicals, Inc.

  13. A Trade Study of Two Membrane-Aerated Biological Water Processors

    Science.gov (United States)

    Allada, Ram; Lange, Kevin; Vega. Leticia; Roberts, Michael S.; Jackson, Andrew; Anderson, Molly; Pickering, Karen

    2011-01-01

    Biologically based systems are under evaluation as primary water processors for next generation life support systems due to their low power requirements and their inherent regenerative nature. This paper will summarize the results of two recent studies involving membrane aerated biological water processors and present results of a trade study comparing the two systems with regards to waste stream composition, nutrient loading and system design. Results of optimal configurations will be presented.

  14. Biologically based modelling and simulation of carcinogenesis at low doses

    International Nuclear Information System (INIS)

    Ouchi, Noriyuki B.

    2003-01-01

    The process of the carcinogenesis is studied by computer simulation. In general, we need a large number of experimental samples to detect mutations at low doses, but in practice it is difficult to get such a large number of data. To satisfy the requirements of the situation at low doses, it is good to study the process of carcinogenesis using biologically based mathematical model. We have mainly studied it by using as known as 'multi-stage model'; the model seems to get complicated, as we adopt the recent new findings of molecular biological experiments. Moreover, the basic idea of the multi-stage model is based on the epidemiologic data of log-log variation of cancer incidence with age, it seems to be difficult to compare with experimental data of irradiated cell culture system, which has been increasing in recent years. Taking above into consideration, we concluded that we had better make new model with following features: 1) a unit of the target system is a cell, 2) the new information of the molecular biology can be easily introduced, 3) having spatial coordinates for checking a colony formation or tumorigenesis. In this presentation, we will show the detail of the model and some simulation results about the carcinogenesis. (author)

  15. Biological Studies of Posttraumatic Stress Disorder

    Science.gov (United States)

    Pitman, Roger K.; Rasmusson, Ann M.; Koenen, Karestan C.; Shin, Lisa M.; Orr, Scott P.; Gilbertson, Mark W.; Milad, Mohammed R.; Liberzon, Israel

    2016-01-01

    Preface Posttraumatic stress disorder (PTSD) is the only major mental disorder for which a cause is considered to be known, viz., an event that involves threat to the physical integrity of oneself or others and induces a response of intense fear, helplessness, or horror. Although PTSD is still largely regarded as a psychological phenomenon, over the past three decades the growth of the biological PTSD literature has been explosive, and thousands of references now exist. Ultimately, the impact of an environmental event, such as a psychological trauma, must be understood at organic, cellular, and molecular levels. The present review attempts to present the current state of this understanding, based upon psychophysiological, structural and functional neuroimaging, endocrinological, genetic, and molecular biological studies in humans and in animal models. PMID:23047775

  16. The use of biologically based cancer risk models in radiation epidemiology

    International Nuclear Information System (INIS)

    Krewski, D.; Zielinski, J.M.; Hazelton, W.D.; Garner, M.J.; Moolgavkar, S.H.

    2003-01-01

    Biologically based risk projection models for radiation carcinogenesis seek to describe the fundamental biological processes involved in neoplastic transformation of somatic cells into malignant cancer cells. A validated biologically based model, whose parameters have a direct biological interpretation, can also be used to extrapolate cancer risks to different exposure conditions with some confidence. In this article, biologically based models for radiation carcinogenesis, including the two-stage clonal expansion (TSCE) model and its extensions, are reviewed. The biological and mathematical bases for such models are described, and the implications of key model parameters for cancer risk assessment examined. Specific applications of versions of the TSCE model to important epidemiologic datasets are discussed, including the Colorado uranium miners' cohort; a cohort of Chinese tin miners; the lifespan cohort of atomic bomb survivors in Hiroshima and Nagasaki; and a cohort of over 200,000 workers included in the National Dose Registry (NDR) of Canada. (author)

  17. 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

  18. 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.

  19. Biological specimens for community-based surveillance studies: Method of recruitment matters

    Directory of Open Access Journals (Sweden)

    Brenda L. Coleman

    2011-12-01

    Full Text Available Studies requiring the collection of biological specimens are often difficult to perform and costly. We compare face-to-face and telephone interviews to determine which is more effective for return of self-collected rectal swabs from subjects living in rural and semi-rural areas of Ontario, Canada. People interviewed face-to-face in 2006-2007 were asked to provide a rectal swab while the interviewer waited. Those interviewed by telephone were sent a package and asked to return the swab by mail, with one follow-up reminder call. Telephone interviewing resulted in a higher response rate for the completion of household and individual-level questionnaires. However, face-to-face interviews resulted in a significantly higher proportion of interviewees who returned swabs making the participation rate higher for this mode of contact (33.7 versus 25.0 percent. Using multivariable logistic regression, higher rates of rectal swab return were associated with face-to-face interviewing while adjusting for the impact of household size and respondent age and sex. For studies requiring the submission of intimate biological samples, face-to-face interviews can be expected to provide a higher rate of return than telephone interviews.

  20. Information fluency for undergraduate biology majors: applications of inquiry-based learning in a developmental biology course.

    Science.gov (United States)

    Gehring, Kathleen M; Eastman, Deborah A

    2008-01-01

    Many initiatives for the improvement of undergraduate science education call for inquiry-based learning that emphasizes investigative projects and reading of the primary literature. These approaches give students an understanding of science as a process and help them integrate content presented in courses. At the same time, general initiatives to promote information fluency are being promoted on many college and university campuses. Information fluency refers to discipline-specific processing of information, and it involves integration of gathered information with specific ideas to form logical conclusions. We have implemented the use of inquiry-based learning to enhance and study discipline-specific information fluency skills in an upper-level undergraduate Developmental Biology course. In this study, an information literacy tutorial and a set of linked assignments using primary literature analysis were integrated with two inquiry-based laboratory research projects. Quantitative analysis of student responses suggests that the abilities of students to identify and apply valid sources of information were enhanced. Qualitative assessment revealed a set of patterns by which students gather and apply information. Self-assessment responses indicated that students recognized the impact of the assignments on their abilities to gather and apply information and that they were more confident about these abilities for future biology courses and beyond.

  1. 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…

  2. Aquatic biology studies

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Aquatic biology studies focused on studying the hydrothermal effects of Par Pond reservoir on periphyton, plankton, zooplankton, macrophytes, human pathogens, and microbial activity; the variability between the artificial streams of the Flowing Streams Laboratory and Upper Three Runs Creek; and the bacterial production of methane in Savannah River Plant aquatic systems

  3. A CMOS active pixel sensor system for laboratory- based x-ray diffraction studies of biological tissue

    International Nuclear Information System (INIS)

    Bohndiek, Sarah E; Cook, Emily J; Arvanitis, Costas D; Olivo, Alessandro; Royle, Gary J; Clark, Andy T; Prydderch, Mark L; Turchetta, Renato; Speller, Robert D

    2008-01-01

    X-ray diffraction studies give material-specific information about biological tissue. Ideally, a large area, low noise, wide dynamic range digital x-ray detector is required for laboratory-based x-ray diffraction studies. The goal of this work is to introduce a novel imaging technology, the CMOS active pixel sensor (APS) that has the potential to fulfil all these requirements, and demonstrate its feasibility for coherent scatter imaging. A prototype CMOS APS has been included in an x-ray diffraction demonstration system. An industrial x-ray source with appropriate beam filtration is used to perform angle dispersive x-ray diffraction (ADXRD). Optimization of the experimental set-up is detailed including collimator options and detector operating parameters. Scatter signatures are measured for 11 different materials, covering three medical applications: breast cancer diagnosis, kidney stone identification and bone mineral density calculations. Scatter signatures are also recorded for three mixed samples of known composition. Results are verified using two independent models for predicting the APS scatter signature: (1) a linear systems model of the APS and (2) a linear superposition integral combining known monochromatic scatter signatures with the input polychromatic spectrum used in this case. Cross validation of experimental, modelled and literature results proves that APS are able to record biologically relevant scatter signatures. Coherent scatter signatures are sensitive to multiple materials present in a sample and provide a means to quantify composition. In the future, production of a bespoke APS imager for x-ray diffraction studies could enable simultaneous collection of the transmitted beam and scattered radiation in a laboratory-based coherent scatter system, making clinical transfer of the technique attainable

  4. Simbios: an NIH national center for physics-based simulation of biological structures.

    Science.gov (United States)

    Delp, Scott L; Ku, Joy P; Pande, Vijay S; Sherman, Michael A; Altman, Russ B

    2012-01-01

    Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations can be used by biologists to study macromolecular assemblies and by clinicians to design treatments for diseases. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. Although individual biomedical investigators make outstanding contributions to physics-based simulation, the field has been fragmented. Applications are typically limited to a single physical scale, and individual investigators usually must create their own software. These conditions created a major barrier to advancing simulation capabilities. In 2004, we established a National Center for Physics-Based Simulation of Biological Structures (Simbios) to help integrate the field and accelerate biomedical research. In 6 years, Simbios has become a vibrant national center, with collaborators in 16 states and eight countries. Simbios focuses on problems at both the molecular scale and the organismal level, with a long-term goal of uniting these in accurate multiscale simulations.

  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. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Assessment of refinery effluents and receiving waters using biologically-based effect methods

    International Nuclear Information System (INIS)

    2012-01-01

    Within the EU it is apparent that the regulatory focus on the use of biologically-based effects methods in the assessment of refinery effluents and receiving waters has increased in the past decade. This has been reflected in a recent refinery survey which revealed an increased use of such methods for assessing the quality of refinery effluents and their receiving waters. This report provides an overview of recent techniques used for this purpose. Several case studies provided by CONCAWE member companies describe the application of biological methods to effluent discharge assessment and surface water monitoring. The case studies show that when biological methods are applied to refinery effluents and receiving waters they raise different questions compared with those obtained using physical and chemical methods. Although direct measurement of the toxicity of effluent and receiving to aquatic organisms is the most cited technique, more recent efforts include tests that also address the persistence of effluent toxicity once discharged into the receiving water. Similarly, ecological monitoring of receiving waters can identify effects of effluent inputs arising from species interactions and other secondary effects that would not always be apparent from the results of biological tests conducted on single aquatic organisms. In light of recent and proposed regulatory developments the objectives of this report are therefore to: Discuss the application of biologically-based effects methods (including ecological monitoring) to refinery discharges and receiving waters; Assess the implications of such methods for future regulation of refinery discharges; and Provide guidance on good practice that can be used by refineries and the downstream oil industry to carry out and interpret data obtained using biologically-based effects methods. While the emphasis is on the toxic effects of effluents, other properties will also be covered because of their interdependency in determining

  11. Assessment of refinery effluents and receiving waters using biologically-based effect methods

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-01-15

    Within the EU it is apparent that the regulatory focus on the use of biologically-based effects methods in the assessment of refinery effluents and receiving waters has increased in the past decade. This has been reflected in a recent refinery survey which revealed an increased use of such methods for assessing the quality of refinery effluents and their receiving waters. This report provides an overview of recent techniques used for this purpose. Several case studies provided by CONCAWE member companies describe the application of biological methods to effluent discharge assessment and surface water monitoring. The case studies show that when biological methods are applied to refinery effluents and receiving waters they raise different questions compared with those obtained using physical and chemical methods. Although direct measurement of the toxicity of effluent and receiving to aquatic organisms is the most cited technique, more recent efforts include tests that also address the persistence of effluent toxicity once discharged into the receiving water. Similarly, ecological monitoring of receiving waters can identify effects of effluent inputs arising from species interactions and other secondary effects that would not always be apparent from the results of biological tests conducted on single aquatic organisms. In light of recent and proposed regulatory developments the objectives of this report are therefore to: Discuss the application of biologically-based effects methods (including ecological monitoring) to refinery discharges and receiving waters; Assess the implications of such methods for future regulation of refinery discharges; and Provide guidance on good practice that can be used by refineries and the downstream oil industry to carry out and interpret data obtained using biologically-based effects methods. While the emphasis is on the toxic effects of effluents, other properties will also be covered because of their interdependency in determining

  12. Study of β-NMR for Liquid Biological Samples

    CERN Document Server

    Beattie, Caitlin

    2017-01-01

    β-NMR is an exotic form of NMR spectroscopy that allows for the characterization of matter based on the anisotropic β-decay of radioactive probe nuclei. This has been shown to be an effective spectroscopic technique for many different compounds, but its use for liquid biological samples is relatively unexplored. The work at the VITO line of ISOLDE seeks to employ this technique to study such samples. Currently, preparations are being made for an experiment to characterize DNA G-quadruplexes and their interactions with stabilizing cations. More specifically, the work in which I engaged as a summer student focused on the experiment’s liquid handling system and the stability of the relevant biological samples under vacuum.

  13. Structural biology studies of CagA from Helicobacter pylori and histone chaperone CIA/ASF1

    International Nuclear Information System (INIS)

    Senda, Toshiya

    2015-01-01

    Crystal structures of proteins and their complexes have become critical information for molecular-based life science. Biochemical and biological analysis based on tertiary structural information is a powerful tool to unveil complex molecular processes in the cell. Here, we present two examples of the structure-based life science study, structural biology studies of CagA, an effector protein from Helicobacter pylori, and histone chaperone CIA/ASF1, which is involved in transcription initiation. (author)

  14. 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.

  15. 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 ...

  16. 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...

  17. Design of synthetic biological logic circuits based on evolutionary algorithm.

    Science.gov (United States)

    Chuang, Chia-Hua; Lin, Chun-Liang; Chang, Yen-Chang; Jennawasin, Tanagorn; Chen, Po-Kuei

    2013-08-01

    The construction of an artificial biological logic circuit using systematic strategy is recognised as one of the most important topics for the development of synthetic biology. In this study, a real-structured genetic algorithm (RSGA), which combines general advantages of the traditional real genetic algorithm with those of the structured genetic algorithm, is proposed to deal with the biological logic circuit design problem. A general model with the cis-regulatory input function and appropriate promoter activity functions is proposed to synthesise a wide variety of fundamental logic gates such as NOT, Buffer, AND, OR, NAND, NOR and XOR. The results obtained can be extended to synthesise advanced combinational and sequential logic circuits by topologically distinct connections. The resulting optimal design of these logic gates and circuits are established via the RSGA. The in silico computer-based modelling technology has been verified showing its great advantages in the purpose.

  18. Study on the radiation-induced biological responses based on the analysis of metabolites

    International Nuclear Information System (INIS)

    Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

    2013-01-01

    1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation

  19. Study on the radiation-induced biological responses based on the analysis of metabolites

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Sungkee; Jung, Uhee; Park, Haeran; Roh, Changhyun; Shin, Heejune; Ryu, Dongkyoung

    2013-01-15

    1. Objectives □ Establishment of basis of biological radiation response study by metabolite analysis 2. Project results □ Establishment of analytical basis of radiation-responsive metabolites in biological samples - Large scale collection of tissue samples from irradiated animal for radiation metabolomics research - Establishment of mass spectromety (GC MS, LC MS-MS) analysis methods of biological samples - 3 Standard Operation Protocols (SOP) for ultra high resolution mass spectrometry (FT-ICR MS, Q-TOF MS) analysis of metabolites from biological samples - Establishment of database for radiation metabolites □ Basic research on radiation-responsive metabolites and the interpretation of their functions - Validation of spermidine as a candidate biomarker of acute radiation response in mouse blood - Verification of 5 radiation-responsive steroid hormones and alteration of their metabolic enzyme activities in mouse blood - Verification of 13 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain -Verification of 10 radiation-responsive amino acids (related to oxidative stress, neurotransmission, energy metabolism) in regional mouse brain - Verification of 74 radiation-responsive metabolites in whole rat brain by ultra high resolution FT-ICR MS and Q-TOF MS analysis 3. Expected benefits and plan of application □ Establishment of research basis of radiation metabolomics in Korea □ Provision of core technology in radiation bioscience and safety field by application of radiation metabolomics results to the technology development in radiation biodosimetry, and radiation response evaluation and modulation.

  20. Updating biological bases of social behavior.

    Science.gov (United States)

    O'Connor, Thomas G

    2014-09-01

    This month's collation of papers deals with social behaviors that operationalize key constructs in fields covered by the journal, including attachment theory and parenting; emotional regulation; psychopathology of several forms; general and specific cognitive abilities. Notably, many examples are offered of how these social behaviors link with biology. That is an obvious and important direction for clinical research insofar as it helps to erase a perceptual chasm and artificial duality between 'behavior' and 'biology'. But, although it must be the case that social behavior has biological connections of one sort or other, identifying reliable connections with practical application has proved to be a non-trivial challenge. In particular, the challenge seems to be in measuring social behavior meaningfully enough that it could be expected to have a biological pulse, and in measuring biological markers systematically enough that emergent-downstream effects would surface. Associations are not especially uncommon, but it has been a frustrating task in constructing a practically broad model from a bricolage of scattered and disconnected parts and findings in the literature. Several reports in this issue offer contrasts that may help move along this line of study. © 2014 Association for Child and Adolescent Mental Health.

  1. Carbon nanostructure-based field-effect transistors for label-free chemical/biological sensors.

    Science.gov (United States)

    Hu, PingAn; Zhang, Jia; Li, Le; Wang, Zhenlong; O'Neill, William; Estrela, Pedro

    2010-01-01

    Over the past decade, electrical detection of chemical and biological species using novel nanostructure-based devices has attracted significant attention for chemical, genomics, biomedical diagnostics, and drug discovery applications. The use of nanostructured devices in chemical/biological sensors in place of conventional sensing technologies has advantages of high sensitivity, low decreased energy consumption and potentially highly miniaturized integration. Owing to their particular structure, excellent electrical properties and high chemical stability, carbon nanotube and graphene based electrical devices have been widely developed for high performance label-free chemical/biological sensors. Here, we review the latest developments of carbon nanostructure-based transistor sensors in ultrasensitive detection of chemical/biological entities, such as poisonous gases, nucleic acids, proteins and cells.

  2. Study of biological compartments

    International Nuclear Information System (INIS)

    Rocha, A.F.G. da

    1976-01-01

    The several types of biological compartments are studied such as monocompartmental system, one-compartment balanced system irreversible fluxes, two closed compartment system, three compartment systems, catenary systems and mammilary systems [pt

  3. Biological dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in hematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes cytokinetic blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree celsius has been produced. Experimental data is fitted to model Y=c+ α D+β D 2 where. Y is the number micronuclei per cell and D the dose. the curve is compared with those produced elsewhere

  4. 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.

  5. 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.

  6. Biological effective dose studies in carcinoma of uterine cervix

    International Nuclear Information System (INIS)

    Yadav, Poonam; Ramasubramanian, V.

    2008-01-01

    Cancer of cervix is the second most common cancer worldwide among women. Several treatments related protocols of radiotherapy have been followed over few decades in its treatment for evaluating the response. These physical doses varying on the basics of fractionation size, dose rate and total dose needed to be indicated as biological effective dose (BED) to rationalize these treatments. The curative potential of radiation therapy in the management of carcinoma of the cervix is greatly enhanced by the use of intracavitary brachytherapy. Successful brachytherapy requires the high radiation dose to be delivered to the tumor where as minimum radiation dose reach to surrounding normal tissue. Present study is aimed to evaluate biologically effective dose in patients receiving high dose-rate brachytherapy plus external beam radiotherapy based on tumor cell proliferation values in cancer of the cervix patients. The study includes 30 patients' data as a retrospective analysis. In addition determine extent of a dose-response relationship existing between the biological effective dose at Point A and the bladder and rectum and the clinical outcomes

  7. 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.

  8. A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

    Science.gov (United States)

    Mungall, Christopher J; Emmert, David B

    2007-07-01

    A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http

  9. Mobile-based biology edutainment application for secondary schools

    Science.gov (United States)

    AL-Modwahi, Ashraf Abbas M.; Kaisara, Onalenna; Parkizkar, Behrang; Habibi Lashkari, Arash

    2013-03-01

    The high increase of mobile technology is leading to mobilized learning environment, thus making traditional learning to diminish slowly and become inactive and unproductive. Learners worldwide are being attracted to mobile environment more so that it promotes anytime, anywhere learning. Biology as a secondary school subject will be applicable for mobile learning for such a time and generation as this. This paper is therefore an attempt to mobile based biology edutainment system for the students who normally range from the ages of thirteen to sixteen.

  10. Gene expression-based biological test for major depressive disorder: an advanced study

    Directory of Open Access Journals (Sweden)

    Watanabe S

    2017-02-01

    Full Text Available Shin-ya Watanabe,1 Shusuke Numata,1 Jun-ichi Iga,2 Makoto Kinoshita,1 Hidehiro Umehara,1 Kazuo Ishii,3 Tetsuro Ohmori1 1Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, 2Department of Neuropsychiatry, Molecules and Function, Ehime University Graduate School of Medicine, Ehime, 3Department of Applied Biological Science, Faculty of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan Purpose: Recently, we could distinguished patients with major depressive disorder (MDD from nonpsychiatric controls with high accuracy using a panel of five gene expression markers (ARHGAP24, HDAC5, PDGFC, PRNP, and SLC6A4 in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder.Patients and methods: We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR, and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD.Results: This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively.Conclusion: Further research to identify MDD-specific markers is needed to improve the performance of this biological test. Keywords: depressive disorder, biomarker, gene expression, schizophrenia, bipolar disorder

  11. PENGEMBANGAN PENUNTUN PRAKTIKUM BIOLOGI UMUM BERBASIS INKUIRI TERBIMBING MAHASISWA BIOLOGI STKIP PAYAKUMBUH

    Directory of Open Access Journals (Sweden)

    Sri Nengsi

    2016-05-01

    Full Text Available One of supporting the implementation of the practicum is the practical guidence. To increase motivation, activities, and learning outcomes it is used inquiry based practical guide for students are invited to experiment with doing practical activities with scientific. The purpose of this study was to reveal the validity, practicalities, and guiding the resulting effectiveness of guidence inquiry based on the general biology lesson for students of biology education STKIP Payakumbuh. This research is the development of Plomp development model which consists of three phases: problem identification and needs analysis, design development and implementation, evaluation. The results of this study indicate that the development of practical guidance guided inquiry based general biology for students of biology education STKIP Payakumbuh valid, practically and effectively.

  12. Studying cell biology in the skin.

    Science.gov (United States)

    Morrow, Angel; Lechler, Terry

    2015-11-15

    Advances in cell biology have often been driven by studies in diverse organisms and cell types. Although there are technical reasons for why different cell types are used, there are also important physiological reasons. For example, ultrastructural studies of vesicle transport were aided by the use of professional secretory cell types. The use of tissues/primary cells has the advantage not only of using cells that are adapted to the use of certain cell biological machinery, but also of highlighting the physiological roles of this machinery. Here we discuss advantages of the skin as a model system. We discuss both advances in cell biology that used the skin as a driving force and future prospects for use of the skin to understand basic cell biology. A unique combination of characteristics and tools makes the skin a useful in vivo model system for many cell biologists. © 2015 Morrow and Lechler. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  13. Biological Dosimetry of X-rays by micronuclei study

    International Nuclear Information System (INIS)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-01-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ αD+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs

  14. The emerging molecular biology toolbox for the study of long noncoding RNA biology.

    Science.gov (United States)

    Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

    2017-10-01

    Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

  15. 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…

  16. 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

  17. Mammalian synthetic biology for studying the cell.

    Science.gov (United States)

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

    2017-01-02

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

  18. 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

  19. 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

  20. BicPAMS: software for biological data analysis with pattern-based biclustering.

    Science.gov (United States)

    Henriques, Rui; Ferreira, Francisco L; Madeira, Sara C

    2017-02-02

    Biclustering has been largely applied for the unsupervised analysis of biological data, being recognised today as a key technique to discover putative modules in both expression data (subsets of genes correlated in subsets of conditions) and network data (groups of coherently interconnected biological entities). However, given its computational complexity, only recent breakthroughs on pattern-based biclustering enabled efficient searches without the restrictions that state-of-the-art biclustering algorithms place on the structure and homogeneity of biclusters. As a result, pattern-based biclustering provides the unprecedented opportunity to discover non-trivial yet meaningful biological modules with putative functions, whose coherency and tolerance to noise can be tuned and made problem-specific. To enable the effective use of pattern-based biclustering by the scientific community, we developed BicPAMS (Biclustering based on PAttern Mining Software), a software that: 1) makes available state-of-the-art pattern-based biclustering algorithms (BicPAM (Henriques and Madeira, Alg Mol Biol 9:27, 2014), BicNET (Henriques and Madeira, Alg Mol Biol 11:23, 2016), BicSPAM (Henriques and Madeira, BMC Bioinforma 15:130, 2014), BiC2PAM (Henriques and Madeira, Alg Mol Biol 11:1-30, 2016), BiP (Henriques and Madeira, IEEE/ACM Trans Comput Biol Bioinforma, 2015), DeBi (Serin and Vingron, AMB 6:1-12, 2011) and BiModule (Okada et al., IPSJ Trans Bioinf 48(SIG5):39-48, 2007)); 2) consistently integrates their dispersed contributions; 3) further explores additional accuracy and efficiency gains; and 4) makes available graphical and application programming interfaces. Results on both synthetic and real data confirm the relevance of BicPAMS for biological data analysis, highlighting its essential role for the discovery of putative modules with non-trivial yet biologically significant functions from expression and network data. BicPAMS is the first biclustering tool offering the

  1. 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.

  2. Design and validation of general biology learning program based on scientific inquiry skills

    Science.gov (United States)

    Cahyani, R.; Mardiana, D.; Noviantoro, N.

    2018-03-01

    Scientific inquiry is highly recommended to teach science. The reality in the schools and colleges is that many educators still have not implemented inquiry learning because of their lack of understanding. The study aims to1) analyze students’ difficulties in learning General Biology, 2) design General Biology learning program based on multimedia-assisted scientific inquiry learning, and 3) validate the proposed design. The method used was Research and Development. The subjects of the study were 27 pre-service students of general elementary school/Islamic elementary schools. The workflow of program design includes identifying learning difficulties of General Biology, designing course programs, and designing instruments and assessment rubrics. The program design is made for four lecture sessions. Validation of all learning tools were performed by expert judge. The results showed that: 1) there are some problems identified in General Biology lectures; 2) the designed products include learning programs, multimedia characteristics, worksheet characteristics, and, scientific attitudes; and 3) expert validation shows that all program designs are valid and can be used with minor revisions. The first section in your paper.

  3. Synthesis, spectroscopic and biological studies of transition metal complexes of novel schiff bases derived from cephradine and sugars

    International Nuclear Information System (INIS)

    Naz, N.; Iqbal, M.Z.

    2011-01-01

    Fe(II), Co(II) and Ni(II) metal complexes of novel schiff bases derived from Cephradine and sugars (D-Glucose, L. Arabinose and D-Galactose) were synthesized and characterized by elemental analysis, magnetic susceptibility, thermal analysis, electronic absorption and FT-IR spectral studies. It has been found that schiff bases behave as bi-dentate-ligands forming complexes with 1:2 (metal:ligand) stoichiometry. the neutral nature of the complexes was confirmed by their low conductance values. The biological activities of complexes have been evaluated against two gram negative (Escherichia coli and Pseudomonas aeruginosa) and two gram positive (Bacillus subtilis and staphylococcus aureus) bacteria by Agar diffusion disc method. It has been found that the complexes have higher activity as compared to the pure Cephradine against the same bacteria. (author)

  4. 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

  5. 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.

  6. Using Zebrafish to Implement a Course-Based Undergraduate Research Experience to Study Teratogenesis in Two Biology Laboratory Courses

    Science.gov (United States)

    Chism, Grady W.; Vaughan, Martin A.; Muralidharan, Pooja; Marrs, Jim A.

    2016-01-01

    Abstract A course-based undergraduate research experience (CURE) spanning three semesters was introduced into freshman and sophomore biology classes, with the hypothesis that participation in a CURE affects skills in research, communication, and collaboration, which may help students persist in science. Student research projects were centered on the hypothesis that nicotine and caffeine exposure during early development affects gastrulation and heart development in zebrafish. First, freshmen generated original data showing distinct effects of embryonic nicotine and caffeine exposure on zebrafish heart development and function. Next, Cell Biology laboratory students continued the CURE studies and identified novel teratogenic effects of nicotine and caffeine during gastrulation. Finally, new freshmen continued the CURE research, examining additional toxicant effects on development. Students designed new protocols, made measurements, presented results, and generated high-quality preliminary data that were studied in successive semesters. By implementing this project, the CURE extended faculty research and provided a scalable model to address national goals to involve more undergraduates in authentic scientific research. In addition, student survey results support the hypothesis that CUREs provide significant gains in student ability to (1) design experiments, (2) analyze data, and (3) make scientific presentations, translating into high student satisfaction and enhanced learning. PMID:26829498

  7. Giant Ants and Walking Plants: Using Science Fiction to Teach a Writing-Intensive, Lab-Based Biology Class for Nonmajors

    Science.gov (United States)

    Firooznia, Fardad

    2006-01-01

    This writing-intensive, lab-based, nonmajor biology course explores scientific inquiry and biological concepts through specific topics illustrated or inaccurately depicted in works of science fiction. The laboratory emphasizes the scientific method and introduces several techniques used in biological research related to the works we study.…

  8. A mathematical framework for agent based models of complex biological networks.

    Science.gov (United States)

    Hinkelmann, Franziska; Murrugarra, David; Jarrah, Abdul Salam; Laubenbacher, Reinhard

    2011-07-01

    Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models, it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis. This mathematical framework can also accommodate other model types such as Boolean networks and the more general logical models, as well as Petri nets.

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

    Science.gov (United States)

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

    2013-01-01

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

  10. 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.

  11. [Application of network biology on study of traditional Chinese medicine].

    Science.gov (United States)

    Tian, Sai-Sai; Yang, Jian; Zhao, Jing; Zhang, Wei-Dong

    2018-01-01

    With the completion of the human genome project, people have gradually recognized that the functions of the biological system are fulfilled through network-type interaction between genes, proteins and small molecules, while complex diseases are caused by the imbalance of biological processes due to a number of gene expression disorders. These have contributed to the rise of the concept of the "multi-target" drug discovery. Treatment and diagnosis of traditional Chinese medicine are based on holism and syndrome differentiation. At the molecular level, traditional Chinese medicine is characterized by multi-component and multi-target prescriptions, which is expected to provide a reference for the development of multi-target drugs. This paper reviews the application of network biology in traditional Chinese medicine in six aspects, in expectation to provide a reference to the modernized study of traditional Chinese medicine. Copyright© by the Chinese Pharmaceutical Association.

  12. 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.)

  13. Designing and evaluating a context-based lesson sequence promoting conceptual coherence in biology

    NARCIS (Netherlands)

    Ummels, M. H J; Kamp, M. J A; De Kroon, H.; Boersma, K. Th|info:eu-repo/dai/nl/073043141

    2015-01-01

    Context-based education, in which students deal with biological concepts in a meaningful way, is showing promise in promoting the development of students conceptual coherence. However, literature gives little guidance about how this kind of education should be designed. Therefore, our study aims at

  14. WORKSHOP ON APPLICATION OF STATISTICAL METHODS TO BIOLOGICALLY-BASED PHARMACOKINETIC MODELING FOR RISK ASSESSMENT

    Science.gov (United States)

    Biologically-based pharmacokinetic models are being increasingly used in the risk assessment of environmental chemicals. These models are based on biological, mathematical, statistical and engineering principles. Their potential uses in risk assessment include extrapolation betwe...

  15. Interaction of Herbal Compounds with Biological Targets: A Case Study with Berberine

    Directory of Open Access Journals (Sweden)

    Xiao-Wu Chen

    2012-01-01

    Full Text Available Berberine is one of the main alkaloids found in the Chinese herb Huang lian (Rhizoma Coptidis, which has been reported to have multiple pharmacological activities. This study aimed to analyze the molecular targets of berberine based on literature data followed by a pathway analysis using the PANTHER program. PANTHER analysis of berberine targets showed that the most classes of molecular functions include receptor binding, kinase activity, protein binding, transcription activity, DNA binding, and kinase regulator activity. Based on the biological process classification of in vitro berberine targets, those targets related to signal transduction, intracellular signalling cascade, cell surface receptor-linked signal transduction, cell motion, cell cycle control, immunity system process, and protein metabolic process are most frequently involved. In addition, berberine was found to interact with a mixture of biological pathways, such as Alzheimer’s disease-presenilin and -secretase pathways, angiogenesis, apoptosis signalling pathway, FAS signalling pathway, Hungtington disease, inflammation mediated by chemokine and cytokine signalling pathways, interleukin signalling pathway, and p53 pathways. We also explored the possible mechanism of action for the anti-diabetic effect of berberine. Further studies are warranted to elucidate the mechanisms of action of berberine using systems biology approach.

  16. 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.

  17. 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

  18. 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.

  19. Review of Biological Network Data and Its Applications

    Directory of Open Access Journals (Sweden)

    Donghyeon Yu

    2013-12-01

    Full Text Available Studying biological networks, such as protein-protein interactions, is key to understanding complex biological activities. Various types of large-scale biological datasets have been collected and analyzed with high-throughput technologies, including DNA microarray, next-generation sequencing, and the two-hybrid screening system, for this purpose. In this review, we focus on network-based approaches that help in understanding biological systems and identifying biological functions. Accordingly, this paper covers two major topics in network biology: reconstruction of gene regulatory networks and network-based applications, including protein function prediction, disease gene prioritization, and network-based genome-wide association study.

  20. Synthesis, biological evaluation and structure-activity correlation study of a series of imidazol-based compounds as Candida albicans inhibitors.

    Science.gov (United States)

    Moraca, Francesca; De Vita, Daniela; Pandolfi, Fabiana; Di Santo, Roberto; Costi, Roberta; Cirilli, Roberto; D'Auria, Felicia Diodata; Panella, Simona; Palamara, Anna Teresa; Simonetti, Giovanna; Botta, Maurizio; Scipione, Luigi

    2014-08-18

    A new series of 2-(1H-imidazol-1-yl)-1-phenylethanol derivatives was synthesized. The antifungal activity was evaluated in vitro against different fungal species. The biological results show that the most active compounds possess an antifungal activity comparable or higher than Fluconazole against Candida albicans, non-albicans Candida species, Cryptococcus neoformans and dermathophytes. Because of their racemic nature, the most active compounds 5f and 6c were tested as pure enantiomers. For 6c the (R)-enantiomer resulted more active than the (S)-one, otherwise for 5f the (S)-enantiomer resulted the most active. To rationalize the experimental data, a ligand-based computational study was carried out; the results of the modelling study show that (S)-5f and (R)-6c perfectly align to the ligand-based model, showing the same relative configuration. Preliminary studies on the human lung adenocarcinoma epithelial cells (A549) have shown that 6c, 5e and 5f possess a low cytotoxicity. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  1. Biological interaction of living cells with COSAN-based synthetic vesicles.

    Science.gov (United States)

    Tarrés, Màrius; Canetta, Elisabetta; Paul, Eleanor; Forbes, Jordan; Azzouni, Karima; Viñas, Clara; Teixidor, Francesc; Harwood, Adrian J

    2015-01-15

    Cobaltabisdicarbollide (COSAN) [3,3'-Co(1,2-C2B9H11)2](-), is a complex boron-based anion that has the unusual property of self-assembly into membranes and vesicles. These membranes have similar dimensions to biological membranes found in cells, and previously COSAN has been shown to pass through synthetic lipid membranes and those of living cells without causing breakdown of membrane barrier properties. Here, we investigate the interaction of this inorganic membrane system with living cells. We show that COSAN has no immediate effect on cell viability, and cells fully recover when COSAN is removed following exposure for hours to days. COSAN elicits a range of cell biological effects, including altered cell morphology, inhibition of cell growth and, in some cases, apoptosis. These observations reveal a new biology at the interface between inorganic, synthetic COSAN membranes and naturally occurring biological membranes.

  2. 1H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    International Nuclear Information System (INIS)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D.

    2011-01-01

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in 1 H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

  3. Effects of socioscientific issues-based instruction on argumentation ability and biology concepts of upper secondary school students

    Science.gov (United States)

    Faelt, Surasak; Samiphak, Sara; Pattaradilokrat, Sittiporn

    2018-01-01

    Argumentation skill is an essential skill needed in students, and one of the competencies in scientific literacy. Through arguing on socioscientific issues, students may gain deeper conceptual understanding. The purpose of this research is to examine the efficacy of a socioscientific issues-based instruction compared with an inquirybased instruction. This is to determine which one is better in promoting 10th grade students' argumentation ability and biology concepts of digestive system and cellular respiration. The forty 10th grade students included in this study were from two mathematics-science program classes in a medium-sized secondary school located in a suburb of Buriram province, Thailand. The research utilizes a quasi-experimental design; pre-test post-test control group design. We developed and implemented 4 lesson plans for both socioscientific issues-based instruction and inquiry-based instruction. Ten weeks were used to collect the data. A paper-based questionnaire and informal interviews were designed to test students' argumentation ability, and the two-tier multiple-choice test was designed to test their biology concepts. This research explore qualitatively and quantitatively students' argumentation abilities and biology concepts, using arithmetic mean, mean of percentage, standard deviation and t-test. Results show that there is no significant difference between the two group regarding mean scores of the argumentation ability. However, there is significant difference between the two groups regarding mean scores of the biology concepts. This suggests that socioscientific issues-based instruction could be used to improve students' biology concepts.

  4. Revisit of Machine Learning Supported Biological and Biomedical Studies.

    Science.gov (United States)

    Yu, Xiang-Tian; Wang, Lu; Zeng, Tao

    2018-01-01

    Generally, machine learning includes many in silico methods to transform the principles underlying natural phenomenon to human understanding information, which aim to save human labor, to assist human judge, and to create human knowledge. It should have wide application potential in biological and biomedical studies, especially in the era of big biological data. To look through the application of machine learning along with biological development, this review provides wide cases to introduce the selection of machine learning methods in different practice scenarios involved in the whole biological and biomedical study cycle and further discusses the machine learning strategies for analyzing omics data in some cutting-edge biological studies. Finally, the notes on new challenges for machine learning due to small-sample high-dimension are summarized from the key points of sample unbalance, white box, and causality.

  5. 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…

  6. A Systems’ Biology Approach to Study MicroRNA-Mediated Gene Regulatory Networks

    Directory of Open Access Journals (Sweden)

    Xin Lai

    2013-01-01

    Full Text Available MicroRNAs (miRNAs are potent effectors in gene regulatory networks where aberrant miRNA expression can contribute to human diseases such as cancer. For a better understanding of the regulatory role of miRNAs in coordinating gene expression, we here present a systems biology approach combining data-driven modeling and model-driven experiments. Such an approach is characterized by an iterative process, including biological data acquisition and integration, network construction, mathematical modeling and experimental validation. To demonstrate the application of this approach, we adopt it to investigate mechanisms of collective repression on p21 by multiple miRNAs. We first construct a p21 regulatory network based on data from the literature and further expand it using algorithms that predict molecular interactions. Based on the network structure, a detailed mechanistic model is established and its parameter values are determined using data. Finally, the calibrated model is used to study the effect of different miRNA expression profiles and cooperative target regulation on p21 expression levels in different biological contexts.

  7. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology

    Directory of Open Access Journals (Sweden)

    Ina Aretz

    2016-04-01

    Full Text Available Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  8. Advantages and Pitfalls of Mass Spectrometry Based Metabolome Profiling in Systems Biology.

    Science.gov (United States)

    Aretz, Ina; Meierhofer, David

    2016-04-27

    Mass spectrometry-based metabolome profiling became the method of choice in systems biology approaches and aims to enhance biological understanding of complex biological systems. Genomics, transcriptomics, and proteomics are well established technologies and are commonly used by many scientists. In comparison, metabolomics is an emerging field and has not reached such high-throughput, routine and coverage than other omics technologies. Nevertheless, substantial improvements were achieved during the last years. Integrated data derived from multi-omics approaches will provide a deeper understanding of entire biological systems. Metabolome profiling is mainly hampered by its diversity, variation of metabolite concentration by several orders of magnitude and biological data interpretation. Thus, multiple approaches are required to cover most of the metabolites. No software tool is capable of comprehensively translating all the data into a biologically meaningful context yet. In this review, we discuss the advantages of metabolome profiling and main obstacles limiting progress in systems biology.

  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. 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

  11. Modeling of various contact theories for the manipulation of different biological micro/nanoparticles based on AFM

    Science.gov (United States)

    Korayem, M. H.; Taheri, M.

    2014-01-01

    In this article, the modeling of various contact theories to be applied in the biomanipulation of different micro/nanoparticles based on the atomic force microscope has been studied, and the effect of adhesion force in different contact models on indentation depth and contact angle between tip and substrate has been explored for the target biological micro/nanoparticle. The contact models used in this research include the Hertz, JKR, DMT, BCP, COS, PT, and the SUN models. Also, the target particles comprise the biological micro/nanoparticles of DNA, yeast, platelet, and nanobacterium. Previous research works have investigated the contact models for the manipulation of non-biological gold micro/nanoparticles in the air environment. Since in a real biomanipulation situation, the biological micro/nanoparticles are displaced in biological environments; in this article, various contact theories for the biomanipulation of biological micro/nanoparticles in different biological environments have been modeled and compared for the first time. The results of modeling indicate that the use of Hertz contact model in analyzing the biomanipulation of biological nanoparticles is not appropriate, because it does not take the adhesion force into consideration and thus produces a significant error. Also, all the six contact models developed in this article show larger deformations for studied bionanoparticles in comparison to the gold nanoparticles, which can be justified with regards to the mechanical properties of gold.

  12. Evaluation of the published biological bases for regulations concerning non-coherent light

    International Nuclear Information System (INIS)

    Sykes, S.M.; Bockstahler, L.; Felten, R.; Hellman, K.; Jacobson, E.; Krell, K.; Lytle, C.D.; Waxler, M.; Withrow, T.; Zaremba, T.

    1981-01-01

    The development of an information base of light-induced bioeffects data to support regulatory activities is a continuing process. Though standards covering the three spectral regions of light, ultraviolet (UV), visible, and infrared (IR), currently exist, attempts must regularly be made to assess the adequacy of these standards with respect to currently available biological information. In order to establish a starting point for these reassessments, the biological effects of light considered in establishing the standards must first be determined. Using this information, the strengths and weaknesses of each standard can be evaluated, and particularly important areas of future research can be determined. This document analyzes current standards covering non-coherent light with respect to the biological effects considered in their adoption. The current standards covering non-coherent light are based on few biological endpoints. The ACGIH standard for ultraviolet considers only skin erythema and eye keratitis; the visible light standard considers only retinal damage; and the infrared standard considers only lens cataracts. Clearly, other biological effects need to be considered. But any standard represents a state-of-the-art estimate of maximum allowable exposure levels, and while there is considerable qualitative information on many additional biological effects of light, there is little quantitative information. Without this information it is difficult either to incorporate these effects into the regulatory process or to determine if the current standards are adequate to cover them

  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. PMID:24147138

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

    OpenAIRE

    Beach, Dale L.; Alvarez, Consuelo J.

    2015-01-01

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

  15. 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.

  16. 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.

  17. 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.

  18. Biologically based neural network for mobile robot navigation

    Science.gov (United States)

    Torres Muniz, Raul E.

    1999-01-01

    The new tendency in mobile robots is to crete non-Cartesian system based on reactions to their environment. This emerging technology is known as Evolutionary Robotics, which is combined with the Biorobotic field. This new approach brings cost-effective solutions, flexibility, robustness, and dynamism into the design of mobile robots. It also provides fast reactions to the sensory inputs, and new interpretation of the environment or surroundings of the mobile robot. The Subsumption Architecture (SA) and the action selection dynamics developed by Brooks and Maes, respectively, have successfully obtained autonomous mobile robots initiating this new trend of the Evolutionary Robotics. Their design keeps the mobile robot control simple. This work present a biologically inspired modification of these schemes. The hippocampal-CA3-based neural network developed by Williams Levy is used to implement the SA, while the action selection dynamics emerge from iterations of the levels of competence implemented with the HCA3. This replacement by the HCA3 results in a closer biological model than the SA, combining the Behavior-based intelligence theory with neuroscience. The design is kept simple, and it is implemented in the Khepera Miniature Mobile Robot. The used control scheme obtains an autonomous mobile robot that can be used to execute a mail delivery system and surveillance task inside a building floor.

  19. Molecular biology in studies of oceanic primary production

    International Nuclear Information System (INIS)

    LaRoche, J.; Falkowski, P.G.; Geider, R.

    1992-01-01

    Remote sensing and the use of moored in situ instrumentation has greatly improved our ability to measure phytoplankton chlorophyll and photosynthesis on global scales with high temporal resolution. However, the interpretation of these measurements and their significance with respect to the biogeochemical cycling of carbon relies on their relationship with physiological and biochemical processes in phytoplankton. For example, the use of satellite images of surface chlorophyll to estimate primary production is often based on the functional relationship between photosynthesis and irradiance. A variety of environmental factors such as light, temperature, nutrient availability affect the photosynthesis/irradiance (P vs I) relationship in phytoplankton. We present three examples showing how molecular biology can be used to provide basic insight into the factors controlling primary productivity at three different levels of complexity: 1. Studies of light intensity regulation in unicellular alga show how molecular biology can help understand the processing of environmental cues leading to the regulation of photosynthetic gene expression. 2. Probing of the photosynthetic apparatus using molecular techniques can be used to test existing mechanistic models derived from the interpretation of physiological and biophysical measurements. 3. Exploratory work on the expression of specific proteins during nutrient-limited growth of phytoplankton may lead to the identification and production of molecular probes for field studies

  20. Implementation of biological tissue Mueller matrix for polarization-sensitive optical coherence tomography based on LabVIEW

    Science.gov (United States)

    Lin, Yongping; Zhang, Xiyang; He, Youwu; Cai, Jianyong; Li, Hui

    2018-02-01

    The Jones matrix and the Mueller matrix are main tools to study polarization devices. The Mueller matrix can also be used for biological tissue research to get complete tissue properties, while the commercial optical coherence tomography system does not give relevant analysis function. Based on the LabVIEW, a near real time display method of Mueller matrix image of biological tissue is developed and it gives the corresponding phase retardant image simultaneously. A quarter-wave plate was placed at 45 in the sample arm. Experimental results of the two orthogonal channels show that the phase retardance based on incident light vector fixed mode and the Mueller matrix based on incident light vector dynamic mode can provide an effective analysis method of the existing system.

  1. BETAview: a digital {beta}-imaging system for dynamic studies of biological phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C. E-mail: montesi@na.infn.it; Russo, P

    2002-02-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of {beta}-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 {mu}m thick, segmented into 64x64 170 {mu}m size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm{sup 2}. Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [{sup 14}C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 {mu}m pixel size) is soon to come.

  2. BETAview: a digital β-imaging system for dynamic studies of biological phenomena

    International Nuclear Information System (INIS)

    Bertolucci, E.; Conti, M.; Mettivier, G.; Montesi, M.C.; Russo, P.

    2002-01-01

    We present a digital autoradiography (DAR) system, named BETAview, based on semiconductor pixel detectors and a single particle counting chip, for quantitative analysis of β-emitting radioactive tracers in biological samples. The system is able to perform a real time monitoring of time-dependent biological phenomena. BETAview could be equipped either with GaAs or with Si semiconductor pixellated detectors. In this paper, we describe the results obtained with an assembly based on a Si detector, 300 μm thick, segmented into 64x64 170 μm size square pixels. The detector is bump-bonded to the low threshold, single particle counting chip named Medipix1, developed by a CERN-based European collaboration. The sensitive area is about 1 cm 2 . Studies of background noise and detection efficiency have been performed. Moreover, time-resolved cellular uptake studies with radiolabelled molecules have been monitored. Specifically, we have followed in vivo and in real time, the [ 14 C]L-leucine amino acid uptake by eggs of Octopus vulgaris confirming the preliminary results of a previous paper. This opens the field of biomolecular kynetic studies with this new class of semiconductor DAR systems, whose evolution (using the Medipix2 chip, 256x256 pixels, 55 μm pixel size) is soon to come

  3. 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…

  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. Receptor studies in biological psychiatry

    International Nuclear Information System (INIS)

    Fujiwara, Yutaka

    1992-01-01

    Recent advances in the pharmacological treatment of endogenous psychosis have led to the development of biological studies in psychiatry. Studies on neurotransmitter receptors were reviewed in order to apply positron-emission tomograph (PET) for biological psychiatry. The dopamine (DA) hypothesis for schizophrenia was advanced on the basis of the observed effects of neuroleptics and methamphetamine, and DA(D 2 ) receptor supersensitivity measured by PET and receptor binding in the schizophrenic brain. The clinical potencies of neuroleptics for schizophrenia were correlated with their abilities to inhibit the D 2 receptor, and not other receptors. The σ receptor was expected to be a site of antipsychotic action. However, the potency of drugs action on it was not correlated with clinical efficacy. Haloperidol binds with high affinity to the σ receptor, which may mediate acute dystonia, an extrapyramidal side effect of neuroleptics. Behavioral and neurochemical changes induced by methamphetamine treatment were studied as an animal model of schizophrenia, and both a decrease of D 2 receptor density and an increase of DA release were detected. The monoamine hypothesis for manic-depressive psychosis was advanced on the basis of the effect of reserpine, monoamine oxidase inhibitor and antidepressants. 3 H-clonidine binding sites were increased in platelet membranes of depressive patients, 3 H-imipramine binding sites were decreased. The GABA A receptor is the target site for the action of anxiolytics and antiepileptics such as benzodiazepines and barbiturates. Recent developments in molecular biology techniques have revealed the structure of receptor proteins, which are classified into two receptor families, the G-protein coupled type (D 2 ) and the ion-channel type (GABA A ). (J.P.N.)

  6. 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.

  7. Relations between Intuitive Biological Thinking and Biological Misconceptions in Biology Majors and Nonmajors

    Science.gov (United States)

    Coley, John D.; Tanner, Kimberly

    2015-01-01

    Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems—teleological, essentialist, and anthropocentric thinking—that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. PMID:25713093

  8. 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

  9. 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

  10. A systems biology-based classifier for hepatocellular carcinoma diagnosis.

    Directory of Open Access Journals (Sweden)

    Yanqiong Zhang

    Full Text Available AIM: The diagnosis of hepatocellular carcinoma (HCC in the early stage is crucial to the application of curative treatments which are the only hope for increasing the life expectancy of patients. Recently, several large-scale studies have shed light on this problem through analysis of gene expression profiles to identify markers correlated with HCC progression. However, those marker sets shared few genes in common and were poorly validated using independent data. Therefore, we developed a systems biology based classifier by combining the differential gene expression with topological features of human protein interaction networks to enhance the ability of HCC diagnosis. METHODS AND RESULTS: In the Oncomine platform, genes differentially expressed in HCC tissues relative to their corresponding normal tissues were filtered by a corrected Q value cut-off and Concept filters. The identified genes that are common to different microarray datasets were chosen as the candidate markers. Then, their networks were analyzed by GeneGO Meta-Core software and the hub genes were chosen. After that, an HCC diagnostic classifier was constructed by Partial Least Squares modeling based on the microarray gene expression data of the hub genes. Validations of diagnostic performance showed that this classifier had high predictive accuracy (85.88∼92.71% and area under ROC curve (approximating 1.0, and that the network topological features integrated into this classifier contribute greatly to improving the predictive performance. Furthermore, it has been demonstrated that this modeling strategy is not only applicable to HCC, but also to other cancers. CONCLUSION: Our analysis suggests that the systems biology-based classifier that combines the differential gene expression and topological features of human protein interaction network may enhance the diagnostic performance of HCC classifier.

  11. Nuclear biological studies in France

    International Nuclear Information System (INIS)

    Coursaget, J.

    1961-01-01

    On the occasion of a colloquium on radiobiological research programmes, a number of documents dealing with French accomplishments and projects in this field were collected together. We felt that it would be useful to assemble these papers in one report; although they are brief and leave gaps to be filled in, they provide certain data, give an overall view of the situation, and can also suggest a rough plan for the general policy to adopt in the field of 'nuclear' biological research; i.e. research based on the nuclear tracer method or devoted to the action of ionising radiations. (author) [fr

  12. 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.

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

    KAUST Repository

    Smaili, Fatima Z.; Gao, Xin; Hoehndorf, Robert

    2018-01-01

    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.

  14. 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.

  15. [Biologic therapy in idiopathic inflammatory myopathy].

    Science.gov (United States)

    Selva-O'Callaghan, Albert; Ramos Casals, Manel; Grau Junyent, Josep M

    2014-09-15

    The aim of this article is to study the evidence-based knowledge related to the use of biological therapies in patients diagnosed with idiopathic inflammatory myopathy (dermatomyositis, polymyositis and inclusion body myositis). In this review the leading published studies related to the use of biological therapy in patients with myositis are analysed; mainly those with high methodological standards, that means randomized and controlled studies. Methodological drawbacks due to the rarity and heterogeneity of these complex diseases are also addressed. Up to now is not possible to ascertain the biologics as a recommended therapy in patients with myositis, at least based in the current evidence-based knowledge, although it can not be neglected as a therapeutic option in some clinical situations, taking into account the scarce of effective treatments in those patients, especially in refractory myositis. Future studies probably will help to better define the role of biological therapies in patients with idiopathic inflammatory myopathy. Copyright © 2013 Elsevier España, S.L.U. All rights reserved.

  16. 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

  17. 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

  18. 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.

  19. Recommendations for designing and conducting veterinary clinical pathology biologic variation studies

    DEFF Research Database (Denmark)

    Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K

    2017-01-01

    The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review......). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing....

  20. The Relationships Between Epistemic Beliefs in Biology and Approaches to Learning Biology Among Biology-Major University Students in Taiwan

    Science.gov (United States)

    Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung

    2012-12-01

    The aim of this study was to investigate the relationships between students' epistemic beliefs in biology and their approaches to learning biology. To this end, two instruments, the epistemic beliefs in biology and the approaches to learning biology surveys, were developed and administered to 520 university biology students, respectively. By and large, it was found that the students reflected "mixed" motives in biology learning, while those who had more sophisticated epistemic beliefs tended to employ deep strategies. In addition, the results of paired t tests revealed that the female students were more likely to possess beliefs about biological knowledge residing in external authorities, to believe in a right answer, and to utilize rote learning as a learning strategy. Moreover, compared to juniors and seniors, freshmen and sophomores tended to hold less mature views on all factors of epistemic beliefs regarding biology. Another comparison indicated that theoretical biology students (e.g. students majoring in the Department of Biology) tended to have more mature beliefs in learning biology and more advanced strategies for biology learning than those students studying applied biology (e.g. in the Department of Biotechnology). Stepwise regression analysis, in general, indicated that students who valued the role of experiments and justify epistemic assumptions and knowledge claims based on evidence were more oriented towards having mixed motives and utilizing deep strategies to learn biology. In contrast, students who believed in the certainty of biological knowledge were more likely to adopt rote learning strategies and to aim to qualify in biology.

  1. 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

  2. Effects of Conceptual Change Text Based Instruction on Ecology, Attitudes toward Biology and Environment

    Science.gov (United States)

    Çetin, Gülcan; Ertepinar, Hamide; Geban, Ömer

    2015-01-01

    The purpose of this study is to investigate the effects of the conceptual change text based instruction on ninth grade students' understanding of ecological concepts, and attitudes toward biology and environment. Participants were 82 ninth grade students in a public high school in the Northwestern Turkey. A treatment was employed over a five-week…

  3. {sup 1}H NMR-based metabolic profiling reveals inherent biological variation in yeast and nematode model systems

    Energy Technology Data Exchange (ETDEWEB)

    Szeto, Samuel S. W.; Reinke, Stacey N.; Lemire, Bernard D., E-mail: bernard.lemire@ualberta.ca [University of Alberta, Department of Biochemistry, School of Molecular and Systems Medicine (Canada)

    2011-04-15

    The application of metabolomics to human and animal model systems is poised to provide great insight into our understanding of disease etiology and the metabolic changes that are associated with these conditions. However, metabolomic studies have also revealed that there is significant, inherent biological variation in human samples and even in samples from animal model systems where the animals are housed under carefully controlled conditions. This inherent biological variability is an important consideration for all metabolomics analyses. In this study, we examined the biological variation in {sup 1}H NMR-based metabolic profiling of two model systems, the yeast Saccharomyces cerevisiae and the nematode Caenorhabditis elegans. Using relative standard deviations (RSD) as a measure of variability, our results reveal that both model systems have significant amounts of biological variation. The C. elegans metabolome possesses greater metabolic variance with average RSD values of 29 and 39%, depending on the food source that was used. The S. cerevisiae exometabolome RSD values ranged from 8% to 12% for the four strains examined. We also determined whether biological variation occurs between pairs of phenotypically identical yeast strains. Multivariate statistical analysis allowed us to discriminate between pair members based on their metabolic phenotypes. Our results highlight the variability of the metabolome that exists even for less complex model systems cultured under defined conditions. We also highlight the efficacy of metabolic profiling for defining these subtle metabolic alterations.

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

    LENUS (Irish Health Repository)

    Anney, Richard J L

    2012-02-01

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

  5. 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.

  6. Capturing microscopic features of bone remodeling into a macroscopic model based on biological rationales of bone adaptation.

    Science.gov (United States)

    Kim, Young Kwan; Kameo, Yoshitaka; Tanaka, Sakae; Adachi, Taiji

    2017-10-01

    To understand Wolff's law, bone adaptation by remodeling at the cellular and tissue levels has been discussed extensively through experimental and simulation studies. For the clinical application of a bone remodeling simulation, it is significant to establish a macroscopic model that incorporates clarified microscopic mechanisms. In this study, we proposed novel macroscopic models based on the microscopic mechanism of osteocytic mechanosensing, in which the flow of fluid in the lacuno-canalicular porosity generated by fluid pressure gradients plays an important role, and theoretically evaluated the proposed models, taking biological rationales of bone adaptation into account. The proposed models were categorized into two groups according to whether the remodeling equilibrium state was defined globally or locally, i.e., the global or local uniformity models. Each remodeling stimulus in the proposed models was quantitatively evaluated through image-based finite element analyses of a swine cancellous bone, according to two introduced criteria associated with the trabecular volume and orientation at remodeling equilibrium based on biological rationales. The evaluation suggested that nonuniformity of the mean stress gradient in the local uniformity model, one of the proposed stimuli, has high validity. Furthermore, the adaptive potential of each stimulus was discussed based on spatial distribution of a remodeling stimulus on the trabecular surface. The theoretical consideration of a remodeling stimulus based on biological rationales of bone adaptation would contribute to the establishment of a clinically applicable and reliable simulation model of bone remodeling.

  7. 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

  8. Recommendations for designing and conducting veterinary clinical pathology biologic variation studies.

    Science.gov (United States)

    Freeman, Kathleen P; Baral, Randolph M; Dhand, Navneet K; Nielsen, Søren Saxmose; Jensen, Asger L

    2017-06-01

    The recent creation of a veterinary clinical pathology biologic variation website has highlighted the need to provide recommendations for future studies of biologic variation in animals in order to help standardize and improve the quality of published information and to facilitate review and selection of publications as standard references. The following recommendations are provided in the format and order commonly found in veterinary publications. A checklist is provided to aid in planning, implementing, and evaluating veterinary studies on biologic variation (Appendix S1). These recommendations provide a valuable resource for clinicians, laboratorians, and researchers interested in conducting studies of biologic variation and in determining the quality of studies of biologic variation in veterinary laboratory testing. © 2017 American Society for Veterinary Clinical Pathology.

  9. Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

    Directory of Open Access Journals (Sweden)

    Bryan E. Dutton

    2002-12-01

    Full Text Available We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

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

    Science.gov (United States)

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

    2016-08-20

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

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. Application of X-ray fluorescence analytical techniques in phytoremediation and plant biology studies

    International Nuclear Information System (INIS)

    Necemer, Marijan; Kump, Peter; Scancar, Janez; Jacimovic, Radojko; Simcic, Jurij; Pelicon, Primoz; Budnar, Milos; Jeran, Zvonka; Pongrac, Paula; Regvar, Marjana; Vogel-Mikus, Katarina

    2008-01-01

    Phytoremediation is an emerging technology that employs the use of higher plants for the clean-up of contaminated environments. Progress in the field is however handicapped by limited knowledge of the biological processes involved in plant metal uptake, translocation, tolerance and plant-microbe-soil interactions; therefore a better understanding of the basic biological mechanisms involved in plant/microbe/soil/contaminant interactions would allow further optimization of phytoremediation technologies. In view of the needs of global environmental protection, it is important that in phytoremediation and plant biology studies the analytical procedures for elemental determination in plant tissues and soil should be fast and cheap, with simple sample preparation, and of adequate accuracy and reproducibility. The aim of this study was therefore to present the main characteristics, sample preparation protocols and applications of X-ray fluorescence-based analytical techniques (energy dispersive X-ray fluorescence spectrometry-EDXRF, total reflection X-ray fluorescence spectrometry-TXRF and micro-proton induced X-ray emission-micro-PIXE). Element concentrations in plant leaves from metal polluted and non-polluted sites, as well as standard reference materials, were analyzed by the mentioned techniques, and additionally by instrumental neutron activation analysis (INAA) and atomic absorption spectrometry (AAS). The results were compared and critically evaluated in order to assess the performance and capability of X-ray fluorescence-based techniques in phytoremediation and plant biology studies. It is the EDXRF, which is recommended as suitable to be used in the analyses of a large number of samples, because it is multi-elemental, requires only simple preparation of sample material, and it is analytically comparable to the most frequently used instrumental chemical techniques. The TXRF is compatible to FAAS in sample preparation, but relative to AAS it is fast, sensitive and

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

    Science.gov (United States)

    Lents, Nathan H.; Cifuentes, Oscar E.

    2009-01-01

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

  17. Relations between intuitive biological thinking and biological misconceptions in biology majors and nonmajors.

    Science.gov (United States)

    Coley, John D; Tanner, Kimberly

    2015-03-02

    Research and theory development in cognitive psychology and science education research remain largely isolated. Biology education researchers have documented persistent scientifically inaccurate ideas, often termed misconceptions, among biology students across biological domains. In parallel, cognitive and developmental psychologists have described intuitive conceptual systems--teleological, essentialist, and anthropocentric thinking--that humans use to reason about biology. We hypothesize that seemingly unrelated biological misconceptions may have common origins in these intuitive ways of knowing, termed cognitive construals. We presented 137 undergraduate biology majors and nonmajors with six biological misconceptions. They indicated their agreement with each statement, and explained their rationale for their response. Results indicate frequent agreement with misconceptions, and frequent use of construal-based reasoning among both biology majors and nonmajors in their written explanations. Moreover, results also show associations between specific construals and the misconceptions hypothesized to arise from those construals. Strikingly, such associations were stronger among biology majors than nonmajors. These results demonstrate important linkages between intuitive ways of thinking and misconceptions in discipline-based reasoning, and raise questions about the origins, persistence, and generality of relations between intuitive reasoning and biological misconceptions. © 2015 J. D. Coley and K. Tanner. 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).

  18. Generation of structurally novel short carotenoids and study of their biological activity.

    Science.gov (United States)

    Kim, Se H; Kim, Moon S; Lee, Bun Y; Lee, Pyung C

    2016-02-23

    Recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. In spite of systematic studies, the possibility of using C30 carotenoids as biologically functional compounds has not been explored thus far. Here, we generated 13 novel structures of C30 carotenoids and one C35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthesis, in Escherichia coli. Measurement of radical scavenging activity of various C30 carotenoid structures revealed that acyclic C30 carotenoids showed higher radical scavenging activity than did DL-α-tocopherol. We could assume high potential biological activity of the novel structures of C30 carotenoids as well, based on the neuronal differentiation activity observed for the monocyclic C30 carotenoid 4,4'-diapotorulene on rat bone marrow mesenchymal stem cells. Our results demonstrate that a series of structurally novel carotenoids possessing biologically beneficial properties can be synthesized in E. coli.

  19. ChemProt: a disease chemical biology database

    DEFF Research Database (Denmark)

    Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine Marie Laure

    2011-01-01

    Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network...... biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated protein-protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30...... evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram...

  20. Biological dosimetry study in differentiated thyroid carcinoma patients treated with 131Iodine

    International Nuclear Information System (INIS)

    Vallerga, Maria Belen

    2008-11-01

    Biological Dosimetry allows individual dose assessments based on the effect produced by ionizing radiation on a given biological parameter. The current biological endpoint being scored is chromosomal aberrations, relying on a lymphocytes culture from the patient's blood. The measured yield of chromosome aberrations is referred to a calibration curve obtaining the whole body dose. Different scenarios of overexposure can be taken into account by modifying the calculations leading to the dose estimate. Differentiated Thyroid Carcinoma patients undergo thyroidectomy followed by internal radiotherapy with 131 I. The treatment's success entails the delivery of a lethal dose to the tumour within the maximum tolerable dose to a critical organ (blood doses over 2 Gy could lead to bone marrow depression). Currently, there is no established agreement for the selection of radioiodine dosage. Historically, the empiric approach, based on clinical and biochemical data, has been recommended. Nevertheless, this method may not be associated with optimal outcomes. On the other hand, the dosimetric approach attempts to determine the maximum allowable activity to be administered, establishing its biokinetics by a diagnostic 131 I study. The methodology may be modified to further individualized treatment, however it requires validation. Biological dosimetry provides an independent measure of radiotherapy effect, as such it might aid in the validation process. Nonetheless, biological dosimetry has traditionally been applied in cases of external and accidental overexposure to ionizing radiation. Accordingly, it is mandatory to assess its value in medical internal incorporations (main objective of the present study). The applied treatment strategy comprises whole body dose assessment by biological and internal dosimetry in order to administer a personalized therapeutic activity. Overall, 20 patients with differentiated thyroid carcinoma were included in the study. For biological dosimetry

  1. 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

  2. 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.

  3. US Subseabed Disposal Program radioecological data base: summaries of available radionuclide concentration factors and biological half-lives

    International Nuclear Information System (INIS)

    Gomez, L.S.; Marietta, M.G.; Jackson, D.W.

    1984-01-01

    The US Subseabed Disposal Program has compiled an extensive objective concentration factor and biological half-life data base from the international marine radioecological literature. A microcomputer-based data management system has been implemented to provide statistical and graphical summaries of these data. The data base is constructed in a manner which allows subsets to be sorted using a number of inter-study variables such as organism category, tissue/organ category, geographic location (for in situ studies), and several laboratory-related conditions (e.g., exposure time and exposure concentration). We discuss concentration factor data summaries for many elements. We also discuss summary material for biological half-life data. We discuss the results of our review with the estimates of mean concentration factors provided by the IAEA. It is proposed that this presentation scheme will enable those concerned with predictive assessment of radiation dose in the marine environment to make a more judicious selection of data for a given application. 7 references

  4. Soil and terrestrial biology studies

    International Nuclear Information System (INIS)

    Anon.

    1976-01-01

    Soil and terrestrial biology studies focused on developing an understanding of the uptake of gaseous substances from the atmosphere by plants, biodegradation of oil, and the movement of Pu in the terrestrial ecosystems of the southeastern United States. Mathematical models were developed for SO 2 and tritium uptake from the atmosphere by plants; the uptake of tritium by soil microorganisms was measured; and the relationships among the Pu content of soil, plants, and animals of the Savannah River Plant area were studied. Preliminary results are reported for studies on the biodegradation of waste oil on soil surfaces

  5. 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.

  6. 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.

  7. 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

  8. Computerised modelling for developmental biology : an exploration with case studies

    NARCIS (Netherlands)

    Bertens, Laura M.F.

    2012-01-01

    Many studies in developmental biology rely on the construction and analysis of models. This research presents a broad view of modelling approaches for developmental biology, with a focus on computational methods. An overview of modelling techniques is given, followed by several case studies. Using

  9. Correlation studies between the results of workplace monitoring and biological parameters

    International Nuclear Information System (INIS)

    Khan, A.H.

    1987-10-01

    Some nuclear-based and non-nuclear analytical techniques have been used to look for correlations between the results of workplace monitoring and biological parameters of exposed workers in various workplace environments. The analytical competence of the external beam thick and thin target particle-induced X-ray emission (PIXE) analysis has been established for elemental analysis of air particulates and biological materials. The capability of low-energy photon spectrometry (LEPS) has also been demonstrated. Using the methods of PIXE and flame AAS, some studies have been performed on the elemental composition of air particulates, human head hair, nail and urine collected in different workplace environments in Dhaka. This report contains a brief account of this research along with an outline of future research projects to be carried out in this and other related areas. 13 refs, 5 figs, 7 tabs

  10. 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.

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

    Science.gov (United States)

    Marbach-Ad, Gili; Hunt Rietschel, Carly

    2016-01-01

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

  12. Development trend of radiation biology research-systems radiation biology

    International Nuclear Information System (INIS)

    Min Rui

    2010-01-01

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

  13. Emerging systems biology approaches in nanotoxicology: Towards a mechanism-based understanding of nanomaterial hazard and risk

    Energy Technology Data Exchange (ETDEWEB)

    Costa, Pedro M.; Fadeel, Bengt, E-mail: Bengt.Fadeel@ki.se

    2016-05-15

    Engineered nanomaterials are being developed for a variety of technological applications. However, the increasing use of nanomaterials in society has led to concerns about their potential adverse effects on human health and the environment. During the first decade of nanotoxicological research, the realization has emerged that effective risk assessment of the multitudes of new nanomaterials would benefit from a comprehensive understanding of their toxicological mechanisms, which is difficult to achieve with traditional, low-throughput, single end-point oriented approaches. Therefore, systems biology approaches are being progressively applied within the nano(eco)toxicological sciences. This novel paradigm implies that the study of biological systems should be integrative resulting in quantitative and predictive models of nanomaterial behaviour in a biological system. To this end, global ‘omics’ approaches with which to assess changes in genes, proteins, metabolites, etc. are deployed allowing for computational modelling of the biological effects of nanomaterials. Here, we highlight omics and systems biology studies in nanotoxicology, aiming towards the implementation of a systems nanotoxicology and mechanism-based risk assessment of nanomaterials. - Highlights: • Systems nanotoxicology is a multi-disciplinary approach to quantitative modelling. • Transcriptomics, proteomics and metabolomics remain the most common methods. • Global “omics” techniques should be coupled to computational modelling approaches. • The discovery of nano-specific toxicity pathways and biomarkers is a prioritized goal. • Overall, experimental nanosafety research must endeavour reproducibility and relevance.

  14. Emerging systems biology approaches in nanotoxicology: Towards a mechanism-based understanding of nanomaterial hazard and risk

    International Nuclear Information System (INIS)

    Costa, Pedro M.; Fadeel, Bengt

    2016-01-01

    Engineered nanomaterials are being developed for a variety of technological applications. However, the increasing use of nanomaterials in society has led to concerns about their potential adverse effects on human health and the environment. During the first decade of nanotoxicological research, the realization has emerged that effective risk assessment of the multitudes of new nanomaterials would benefit from a comprehensive understanding of their toxicological mechanisms, which is difficult to achieve with traditional, low-throughput, single end-point oriented approaches. Therefore, systems biology approaches are being progressively applied within the nano(eco)toxicological sciences. This novel paradigm implies that the study of biological systems should be integrative resulting in quantitative and predictive models of nanomaterial behaviour in a biological system. To this end, global ‘omics’ approaches with which to assess changes in genes, proteins, metabolites, etc. are deployed allowing for computational modelling of the biological effects of nanomaterials. Here, we highlight omics and systems biology studies in nanotoxicology, aiming towards the implementation of a systems nanotoxicology and mechanism-based risk assessment of nanomaterials. - Highlights: • Systems nanotoxicology is a multi-disciplinary approach to quantitative modelling. • Transcriptomics, proteomics and metabolomics remain the most common methods. • Global “omics” techniques should be coupled to computational modelling approaches. • The discovery of nano-specific toxicity pathways and biomarkers is a prioritized goal. • Overall, experimental nanosafety research must endeavour reproducibility and relevance.

  15. Vitamin D and depression: a systematic review and meta-analysis comparing studies with and without biological flaws.

    Science.gov (United States)

    Spedding, Simon

    2014-04-11

    Efficacy of Vitamin D supplements in depression is controversial, awaiting further literature analysis. Biological flaws in primary studies is a possible reason meta-analyses of Vitamin D have failed to demonstrate efficacy. This systematic review and meta-analysis of Vitamin D and depression compared studies with and without biological flaws. The systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The literature search was undertaken through four databases for randomized controlled trials (RCTs). Studies were critically appraised for methodological quality and biological flaws, in relation to the hypothesis and study design. Meta-analyses were performed for studies according to the presence of biological flaws. The 15 RCTs identified provide a more comprehensive evidence-base than previous systematic reviews; methodological quality of studies was generally good and methodology was diverse. A meta-analysis of all studies without flaws demonstrated a statistically significant improvement in depression with Vitamin D supplements (+0.78 CI +0.24, +1.27). Studies with biological flaws were mainly inconclusive, with the meta-analysis demonstrating a statistically significant worsening in depression by taking Vitamin D supplements (-1.1 CI -0.7, -1.5). Vitamin D supplementation (≥800 I.U. daily) was somewhat favorable in the management of depression in studies that demonstrate a change in vitamin levels, and the effect size was comparable to that of anti-depressant medication.

  16. Biologically Based Restorative Management of Tooth Wear

    Directory of Open Access Journals (Sweden)

    Martin G. D. Kelleher

    2012-01-01

    Full Text Available The prevalence and severity of tooth wear is increasing in industrialised nations. Yet, there is no high-level evidence to support or refute any therapeutic intervention. In the absence of such evidence, many currently prevailing management strategies for tooth wear may be failing in their duty of care to first and foremost improve the oral health of patients with this disease. This paper promotes biologically sound approaches to the management of tooth wear on the basis of current best evidence of the aetiology and clinical features of this disease. The relative risks and benefits of the varying approaches to managing tooth wear are discussed with reference to long-term follow-up studies. Using reference to ethical standards such as “The Daughter Test”, this paper presents case reports of patients with moderate-to-severe levels of tooth wear managed in line with these biologically sound principles.

  17. CASPIAN BIOLOGICAL RESOURCES

    Directory of Open Access Journals (Sweden)

    M. K. Guseynov

    2015-01-01

    Full Text Available Aim. We present the data on the biological resources of the Caspian Sea, based on the analysis of numerous scientific sources published between years of 1965 and 2011. Due to changes in various biotic and abiotic factors we find it important to discuss the state of the major groups of aquatic biocenosis including algae, crayfish, shrimp, pontogammarus, fish and Caspian seal. Methods. Long-term data has been analyzed on the biology and ecology of the main commercial fish stocks and their projected catches for qualitative and quantitative composition, abundance and biomass of aquatic organisms that make up the food base for fish. Results and discussion. It has been found that the widespread commercial invertebrates in the Caspian Sea are still poorly studied; their stocks are not identified and not used commercially. There is a great concern about the current state of the main commercial fish stocks of the Caspian Sea. A critical challenge is to preserve the pool of biological resources and the restoration of commercial stocks of Caspian fish. For more information about the state of the marine ecosystem in modern conditions, expedition on Caspian Sea should be carried out to study the hydrochemical regime and fish stocks, assessment of sturgeon stocks, as well as the need to conduct sonar survey for sprat stocks. Conclusions. The main condition for preserving the ecosystem of the Caspian Sea and its unique biological resources is to develop and apply environmentally-friendly methods of oil, issuing concerted common fisheries rules in various regions of theCaspian Sea, strengthening of control for sturgeon by all Caspian littoral states. The basic principle of the protection of biological resources is their rational use, based on the preservation of optimal conditions of their natural or artificial reproduction. 

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

    Science.gov (United States)

    Marbach-Ad, Gili; Hunt Rietschel, Carly

    2016-01-01

    In this study, we used a case study approach to obtain an in-depth understanding of the change process of two university instructors who were involved with redesigning a biology course. Given the hesitancy of many biology instructors to adopt evidence-based, learner-centered teaching methods, there is a critical need to understand how biology instructors transition from teacher-centered (i.e., lecture-based) instruction to teaching that focuses on the students. Using the innovation-decision model for change, we explored the motivation, decision-making, and reflective processes of the two instructors through two consecutive, large-enrollment biology course offerings. Our data reveal that the change process is somewhat unpredictable, requiring patience and persistence during inevitable challenges that arise for instructors and students. For example, the change process requires instructors to adopt a teacher-facilitator role as opposed to an expert role, to cover fewer course topics in greater depth, and to give students a degree of control over their own learning. Students must adjust to taking responsibility for their own learning, working collaboratively, and relinquishing the anonymity afforded by lecture-based teaching. We suggest implications for instructors wishing to change their teaching and administrators wishing to encourage adoption of learner-centered teaching at their institutions. © 2016 G. Marbach-Ad and C. H. Rietschel. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  19. The Dominance Behavioral System and Psychopathology: Evidence from Self-Report, Observational, and Biological Studies

    Science.gov (United States)

    Johnson, Sheri L.; Leedom, Liane J.; Muhtadie, Luma

    2012-01-01

    The dominance behavioral system (DBS) can be conceptualized as a biologically-based system which guides dominance motivation, dominant and subordinate behavior, and responsivity to perceptions of power and subordination. A growing body of research suggests that problems with the DBS are evident across a broad range of psychopathologies. We begin by describing psychological, social, and biological correlates of the dominance behavioral system (DBS). Extensive research suggests that externalizing disorders, mania-proneness, and narcissistic traits are related to heightened dominance motivation and behaviors. Mania and narcissistic traits also appear related to inflated self-perceptions of power. Anxiety and depression are related to subordination and submissiveness, as well as a desire to avoid subordination. Models of the DBS have received support from research with humans and animals; from self-report, observational, and biological methods; and using naturalistic and experimental paradigms. Limitations of available research include the relative lack of longitudinal studies using multiple measures of the DBS and the absence of relevant studies using diagnosed samples to study narcissistic personality disorder and bipolar disorder. We provide suggestions for future research on the DBS and psychopathology, including investigations of whether the DBS can be used to differentiate specific disorder outcomes; the need for more sophisticated biological research; and the value of longitudinal dynamical research. Implications of using the DBS as a tool in clinical assessment and treatment are discussed. PMID:22506751

  20. Supporting read-across using biological data.

    Science.gov (United States)

    Zhu, Hao; Bouhifd, Mounir; Donley, Elizabeth; Egnash, Laura; Kleinstreuer, Nicole; Kroese, E Dinant; Liu, Zhichao; Luechtefeld, Thomas; Palmer, Jessica; Pamies, David; Shen, Jie; Strauss, Volker; Wu, Shengde; Hartung, Thomas

    2016-01-01

    Read-across, i.e. filling toxicological data gaps by relating to similar chemicals, for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, however, biological similarity based on biological data adds extra strength to this process. In the context of developing Good Read-Across Practice guidance, a number of case studies were evaluated to demonstrate the use of biological data to enrich read-across. In the simplest case, chemically similar substances also show similar test results in relevant in vitro assays. This is a well-established method for the read-across of e.g. genotoxicity assays. Larger datasets of biological and toxicological properties of hundreds and thousands of substances become increasingly available enabling big data approaches in read-across studies. Several case studies using various big data sources are described in this paper. An example is given for the US EPA's ToxCast dataset allowing read-across for high quality uterotrophic assays for estrogenic endocrine disruption. Similarly, an example for REACH registration data enhancing read-across for acute toxicity studies is given. A different approach is taken using omics data to establish biological similarity: Examples are given for stem cell models in vitro and short-term repeated dose studies in rats in vivo to support read-across and category formation. These preliminary biological data-driven read-across studies highlight the road to the new generation of read-across approaches that can be applied in chemical safety assessment.

  1. Generation of structurally novel short carotenoids and study of their biological activity

    DEFF Research Database (Denmark)

    Kim, Se Hyeuk; Kim, Moon S.; Lee, Bun Y.

    2016-01-01

    Recent research interest in phytochemicals has consistently driven the efforts in the metabolic engineering field toward microbial production of various carotenoids. In spite of systematic studies, the possibility of using C30 carotenoids as biologically functional compounds has not been explored...... thus far. Here, we generated 13 novel structures of C30 carotenoids and one C35 carotenoid, including acyclic, monocyclic, and bicyclic structures, through directed evolution and combinatorial biosynthesis, in Escherichia coli. Measurement of radical scavenging activity of various C30 carotenoid...... structures revealed that acyclic C30 carotenoids showed higher radical scavenging activity than did DL-atocopherol. We could assume high potential biological activity of the novel structures of C30 carotenoids as well, based on the neuronal differentiation activity observed for the monocyclic C30 carotenoid...

  2. 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.

  3. 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.

  4. NMR spectroscopy, Hammett correlations and biological activity of some Schiff bases derived from piperonal

    International Nuclear Information System (INIS)

    Echevarria, Aurea; Giesbrecht, Astrea

    1999-01-01

    A series of eleven Schiff Bases have been synthesized. They were obtained by condensation of piperonal (3,4-methylenedioxybenzaldehyde) with the corresponding aromatic primary amines. Their 1 H and 13 C-NMR spectra have been obtained and the Hammett correlations including chemical shifts and the substituent constants (σ p , σR e σI) were studied. Linear and bilinear significant correlations were observed for iminic carbon (C-α) and C-1 ' , showing a more significant resonance effect on chemical shifts. The chemical shifts for C-4 ' were highly affected by substituent effects, especially for halogens in the expected direction. Their biological activity against microorganisms has also been measured and significant activity was showed against Epidermophyton floccosum. The biological activity did not give a reasonable relationship with electronic effects. (author)

  5. Compartmental study of biological systems

    International Nuclear Information System (INIS)

    Moretti, J.L.

    1975-01-01

    The compartmental analysis of biological system is dealt with on several chapters devoted successively to: terminology; a mathematical and symbolic account of a system at equilibrium; different compartment systems; analysis of the experimental results. For this it is pointed out that the application of compartmental systems to biological phenomena is not always without danger. Sometimes the compartmental system established in a reference subject fails to conform in the patient. The compartments can divide into two or join together, completely changing the aspect of the system so that parameters calculated with the old model become entirely false. The conclusion is that the setting up of a compartmental system to represent a biological phenomenon is a tricky undertaking and the results must be constantly criticized and questioned [fr

  6. 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.

  7. Comparison of Learner Involvement in Biology Laboratory ...

    African Journals Online (AJOL)

    Performance in the biology practical paper has been poor at Kenya national examinations in the past five years (1998-2002). This may imply a lack of emphasis on the teaching of biology through the process-based approach. This study investigated the level of learner involvement in biology practical investigations in ...

  8. 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.

  9. Vitamin D and Depression: A Systematic Review and Meta-Analysis Comparing Studies with and without Biological Flaws

    Directory of Open Access Journals (Sweden)

    Simon Spedding

    2014-04-01

    Full Text Available Efficacy of Vitamin D supplements in depression is controversial, awaiting further literature analysis. Biological flaws in primary studies is a possible reason meta-analyses of Vitamin D have failed to demonstrate efficacy. This systematic review and meta-analysis of Vitamin D and depression compared studies with and without biological flaws. The systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA guidelines. The literature search was undertaken through four databases for randomized controlled trials (RCTs. Studies were critically appraised for methodological quality and biological flaws, in relation to the hypothesis and study design. Meta-analyses were performed for studies according to the presence of biological flaws. The 15 RCTs identified provide a more comprehensive evidence-base than previous systematic reviews; methodological quality of studies was generally good and methodology was diverse. A meta-analysis of all studies without flaws demonstrated a statistically significant improvement in depression with Vitamin D supplements (+0.78 CI +0.24, +1.27. Studies with biological flaws were mainly inconclusive, with the meta-analysis demonstrating a statistically significant worsening in depression by taking Vitamin D supplements (−1.1 CI −0.7, −1.5. Vitamin D supplementation (≥800 I.U. daily was somewhat favorable in the management of depression in studies that demonstrate a change in vitamin levels, and the effect size was comparable to that of anti-depressant medication.

  10. Development of a web-based register for the Dutch national study on biologicals in JIA : www.ABC-register.nl

    NARCIS (Netherlands)

    Prince, F H M; Ferket, I S; Kamphuis, S.; Armbrust, W; Ten Cate, R; Hoppenreijs, E P A H; Koopman-Keemink, Y; van Rossum, M A J; van Santen-Hoeufft, M; Twilt, M; van Suijlekom-Smit, L W A

    OBJECTIVES: Most clinical studies use paper case record forms (CRFs) to collect data. In the Dutch multi-centre observational study on biologicals we encountered several disadvantages of using the paper CRFs. These are delay in data collection, lack of overview in collected data and difficulties in

  11. 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.

  12. Systems-based biological concordance and predictive reproducibility of gene set discovery methods in cardiovascular disease.

    Science.gov (United States)

    Azuaje, Francisco; Zheng, Huiru; Camargo, Anyela; Wang, Haiying

    2011-08-01

    The discovery of novel disease biomarkers is a crucial challenge for translational bioinformatics. Demonstration of both their classification power and reproducibility across independent datasets are essential requirements to assess their potential clinical relevance. Small datasets and multiplicity of putative biomarker sets may explain lack of predictive reproducibility. Studies based on pathway-driven discovery approaches have suggested that, despite such discrepancies, the resulting putative biomarkers tend to be implicated in common biological processes. Investigations of this problem have been mainly focused on datasets derived from cancer research. We investigated the predictive and functional concordance of five methods for discovering putative biomarkers in four independently-generated datasets from the cardiovascular disease domain. A diversity of biosignatures was identified by the different methods. However, we found strong biological process concordance between them, especially in the case of methods based on gene set analysis. With a few exceptions, we observed lack of classification reproducibility using independent datasets. Partial overlaps between our putative sets of biomarkers and the primary studies exist. Despite the observed limitations, pathway-driven or gene set analysis can predict potentially novel biomarkers and can jointly point to biomedically-relevant underlying molecular mechanisms. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. 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

  14. The effects of problem-based learning on the self-efficacy and attitudes of beginning biology majors

    Science.gov (United States)

    Rajab, Adel Mohammad

    The problem of low persistence of science majors has resulted in calls for changes in undergraduate instruction toward environments that foster positive self-efficacy among beginning science majors. Low science self-efficacy and poor attitudes toward science may contribute to high attrition rates of science majors. Classroom environments that foster positive self-efficacy development include pedagogies that promote authentic learning contexts and involve collaborative learning teams. Problem-based learning (PBL) is an instructional model that attempts to create both conditions and may provide every source of information needed for the development of self-efficacy (i.e., mastery experiences, vicarious experiences, verbal persuasion, and physiological states) as postulated by Albert Bandura. The degree to which these sources of self-efficacy are delivered to individuals within a PBL group may depend on how the group members interact and how students perceive the PBL process itself. This study examined the development of biology self-efficacy and attitudes among biology majors in a PBL setting and in a traditional lecture-based setting. Specifically, this project investigated changes in students' biology self-efficacy beliefs, mediating aspects of PBL in self-efficacy development, the relationship between PBL processes and group collective efficacy, the predictive nature of entering self-efficacy levels on attitudes toward PBL and mid-term grades, and changes in student attitudes toward biology. The study design was quasi-experimental and included quantitative pre- and post-surveys, qualitative interviews, and classroom observations. Findings revealed that students enrolled in a PBL class exhibited greater gains in biology self-efficacy and were likely to report more favorable attitudes toward biology compared to students enrolled in a traditional class. The aspects of PBL that most accounted for these findings were students' ownership of the learning process, their

  15. Study of biological effect of radiation

    International Nuclear Information System (INIS)

    Li Guisheng

    1992-01-01

    The some progress on the study of biological effect for protract exposure to low dose rate radiation is reported, and it is indicated that the potential risk of this exposure for the human health and the importance of the routine monitoring of radiation dose for various nuclear installations. The potential exposure to the low dose rate radiation would attract people's extra attention

  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. Comparison Between Water Quality Index (WQI) and Biological Water Quality Index (BWQI) for Water Quality Assessment: Case Study of Melana River, Johor

    International Nuclear Information System (INIS)

    Nor Zaiha Arman; Mohd Ismid Mohd Said; Shamila Azman; Muhammad Hazim Mat Hussin

    2013-01-01

    A study of water quality in Melana River, Johor was carried out in three consecutive months (March - May 2012). This study aims to determine the comparative results through biological monitoring as well as conventional method (physical and chemical analysis). Assessment is carried out through collection and identification of the biological indicator which comprises of macro benthos based on Biological Water Quality Index (BWQI). Comparison was done based on two methods namely invertebrate analysis and also laboratory analysis. For invertebrate analysis, Melana River consist of three types of Family groups namely Nymphs, Larvae and Molluscs. The result for Water Quality Index (WQI) and also Biological Water Quality Index (BWQI) analysis showed that the level of Melana River is polluted and classified in Class III. This study shows that even though different methods were used, the similar results were obtained for both rivers and can be applied to any river to identify their level of cleanliness. (author)

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

    International Nuclear Information System (INIS)

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

    1995-01-01

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

  19. Students’ learning activities while studying biological process diagrams

    NARCIS (Netherlands)

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

    2015-01-01

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

  20. Improvement of the titanium implant biological properties by coating with poly (ε-caprolactone)-based hybrid nanocomposites synthesized via sol-gel

    Energy Technology Data Exchange (ETDEWEB)

    Catauro, Michelina; Bollino, Flavia; Papale, Ferdinando [Department of Industrial and Information Engineering, Second University of Naples, Via Roma 21, 81031 Aversa (Italy)

    2016-05-18

    When bioactive coatings are applied to medical implants by means of sol-gel dip coating technique, the biological proprieties of the implant surface can be modified to match the properties of the surrounding tissues. In this study organo-inorganic nanocomposites materials were synthesized via sol-gel. They consisted of an inorganic zirconium-based and silica-based matrix, in which a biodegradable polymer (the poly-ε-caprolactone, PCL) was incorporated in different weight percentages. The synthesized materials, in sol phase, were used to dip-coat a substrate of commercially pure titanium grade 4 (CP Ti gr. 4) in order to improve its biological properties. A microstructural analysis of the obtained films was carried out by scanning electron microscopy (SEM) and attenuated total reflectance (ATR) Fourier transform infrared spectroscopy (FT-IR). Biological proprieties of the coated substrates were investigated by means of in vitro tests.

  1. Value-Based Medicine and Integration of Tumor Biology.

    Science.gov (United States)

    Brooks, Gabriel A; Bosserman, Linda D; Mambetsariev, Isa; Salgia, Ravi

    2017-01-01

    Clinical oncology is in the midst of a genomic revolution, as molecular insights redefine our understanding of cancer biology. Greater awareness of the distinct aberrations that drive carcinogenesis is also contributing to a growing armamentarium of genomically targeted therapies. Although much work remains to better understand how to combine and sequence these therapies, improved outcomes for patients are becoming manifest. As we welcome this genomic revolution in cancer care, oncologists also must grapple with a number of practical problems. Costs of cancer care continue to grow, with targeted therapies responsible for an increasing proportion of spending. Rising costs are bringing the concept of value into sharper focus and challenging the oncology community with implementation of value-based cancer care. This article explores the ways that the genomic revolution is transforming cancer care, describes various frameworks for considering the value of genomically targeted therapies, and outlines key challenges for delivering on the promise of personalized cancer care. It highlights practical solutions for the implementation of value-based care, including investment in biomarker development and clinical trials to improve the efficacy of targeted therapy, the use of evidence-based clinical pathways, team-based care, computerized clinical decision support, and value-based payment approaches.

  2. Synchrotron-based X-ray microscopic studies for bioeffects of nanomaterials.

    Science.gov (United States)

    Zhu, Ying; Cai, Xiaoqing; Li, Jiang; Zhong, Zengtao; Huang, Qing; Fan, Chunhai

    2014-04-01

    There have been increasing interests in studying biological effects of nanomaterials, which are nevertheless faced up with many challenges due to the nanoscale dimensions and unique chemical properties of nanomaterials. Synchrotron-based X-ray microscopy, an advanced imaging technology with high spatial resolution and excellent elemental specificity, provides a new platform for studying interactions between nanomaterials and living systems. In this article, we review the recent progress of X-ray microscopic studies on bioeffects of nanomaterials in several living systems including cells, model organisms, animals and plants. We aim to provide an overview of the state of the art, and the advantages of using synchrotron-based X-ray microscopy for characterizing in vitro and in vivo behaviors and biodistribution of nanomaterials. We also expect that the use of a combination of new synchrotron techniques should offer unprecedented opportunities for better understanding complex interactions at the nano-biological interface and accounting for unique bioeffects of nanomaterials. Synchrotron-based X-ray microscopy is a non-destructive imaging technique that enables high resolution spatial mapping of metals with elemental level detection methods. This review summarizes the current use and perspectives of this novel technique in studying the biology and tissue interactions of nanomaterials. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Spectroscopic, thermal and biological studies of coordination

    Indian Academy of Sciences (India)

    Spectroscopic, thermal and biological studies of coordination compounds of sulfasalazine drug: Mn(II), Hg(II), Cr(III), ZrO(II), VO(II) and Y(III) transition metal ... The thermal decomposition of the complexes as well as thermodynamic parameters ( *}, *, * and *) were estimated using Coats–Redfern and ...

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

    Science.gov (United States)

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

    2012-07-01

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

  5. Ethnographic Observational Study of the Biologic Initiation Conversation Between Rheumatologists and Biologic-Naive Rheumatoid Arthritis Patients.

    Science.gov (United States)

    Kottak, Nicholas; Tesser, John; Leibowitz, Evan; Rosenberg, Melissa; Parenti, Dennis; DeHoratius, Raphael

    2018-01-30

    This ethnographic market research study investigated the biologic initiation conversation between rheumatologists and biologic-naive patients with rheumatoid arthritis to assess how therapy options, particularly mode of administration, were discussed. Consenting rheumatologists (n = 16) and patients (n = 48) were videotaped during medical visits and interviewed by a trained ethnographer. The content, structure, and timing of conversations regarding biologic initiation were analyzed. The mean duration of physician-patient visits was approximately 15 minutes; biologic therapies were discussed for a mean of 5.6 minutes. Subcutaneous (SC) and intravenous (IV) therapy options were mentioned in 45 and 35 visits, respectively, out of a total of 48 visits. All patients had some familiarity with SC administration, but nearly half of patients (22 of 48) were unfamiliar with IV therapy going into the visit. IV administration was not defined or described by rheumatologists in 77% of visits (27 of 35) mentioning IV therapy. Thus, 19 of 22 patients who were initially unfamiliar with IV therapy remained unfamiliar after the visit. Disparities in physician-patient perceptions were revealed, as all rheumatologists (16 of 16) believed IV therapy would be less convenient than SC therapy for patients, while 46% of patients (22 of 48) felt this way. In post-visit interviews, some patients seemed confused and overwhelmed, particularly when presented with many treatment choices in a visit. Some patients stated they would benefit from visual aids or summary sheets of key points. This study revealed significant educational opportunities to improve the biologic initiation conversation and indicated a disparity between patients' and rheumatologists' perception of IV therapy. © 2018 The Authors. Arthritis Care & Research published by Wiley Periodicals, Inc. on behalf of American College of Rheumatology.

  6. Biological and chemical sensors based on graphene materials.

    Science.gov (United States)

    Liu, Yuxin; Dong, Xiaochen; Chen, Peng

    2012-03-21

    Owing to their extraordinary electrical, chemical, optical, mechanical and structural properties, graphene and its derivatives have stimulated exploding interests in their sensor applications ever since the first isolation of free-standing graphene sheets in year 2004. This article critically and comprehensively reviews the emerging graphene-based electrochemical sensors, electronic sensors, optical sensors, and nanopore sensors for biological or chemical detection. We emphasize on the underlying detection (or signal transduction) mechanisms, the unique roles and advantages of the used graphene materials. Properties and preparations of different graphene materials, their functionalizations are also comparatively discussed in view of sensor development. Finally, the perspective and current challenges of graphene sensors are outlined (312 references).

  7. SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases.

    Science.gov (United States)

    Schweiger, Dominik; Trajanoski, Zlatko; Pabinger, Stephan

    2014-08-15

    Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely available at http://sparqlgraph.i-med.ac.at.

  8. 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

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

    KAUST Repository

    Bera, Tushar Kanti; Jampana, Nagaraju; Lubineau, Gilles

    2016-01-01

    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

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

    Science.gov (United States)

    Beach, Dale L; Alvarez, Consuelo J

    2015-12-01

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

  11. 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).

  12. Study Finds Association between Biological Marker and Susceptibility to the Common Cold

    Science.gov (United States)

    ... W X Y Z Study Finds Association Between Biological Marker and Susceptibility to the Common Cold Share: © ... a cold caused by a particular rhinovirus. The biological marker identified in the study was the length ...

  13. Deep learning: Using machine learning to study biological vision

    OpenAIRE

    Majaj, Najib; Pelli, Denis

    2017-01-01

    Today most vision-science presentations mention machine learning. Many neuroscientists use machine learning to decode neural responses. Many perception scientists try to understand recognition by living organisms. To them, machine learning offers a reference of attainable performance based on learned stimuli. This brief overview of the use of machine learning in biological vision touches on its strengths, weaknesses, milestones, controversies, and current directions.

  14. Identifying Ant-Mirid Spatial Interactions to Improve Biological Control in Cacao-Based Agroforestry System.

    Science.gov (United States)

    Bagny Beilhe, Leïla; Piou, Cyril; Tadu, Zéphirin; Babin, Régis

    2018-06-06

    The use of ants for biological control of insect pests was the first reported case of conservation biological control. Direct and indirect community interactions between ants and pests lead to differential spatial pattern. We investigated spatial interactions between mirids, the major cocoa pest in West Africa and numerically dominant ant species, using bivariate point pattern analysis to identify potential biological control agents. We assume that potential biological control agents should display negative spatial interactions with mirids considering their niche overlap. The mirid/ant data were collected in complex cacao-based agroforestry systems sampled in three agroecological areas over a forest-savannah gradient in Cameroon. Three species, Crematogaster striatula Emery (Hymenoptera: Formicidae), Crematogaster clariventris Mayr (Hymenoptera: Formicidae), and Oecophylla longinoda Latreille (Hymenoptera: Formicidae) with high predator and aggressive behaviors were identified as dominant and showed negative spatial relationships with mirids. The weaver ant, O. longinoda was identified as the only potential biological control agent, considering its ubiquity in the plots, the similarity in niche requirements, and the spatial segregation with mirids resulting probably from exclusion mechanisms. Combining bivariate point pattern analysis to good knowledge of insect ecology was an effective method to identify a potentially good biological control agent.

  15. Development of the Biology Card Sorting Task to Measure Conceptual Expertise in Biology

    Science.gov (United States)

    Smith, Julia I.; Combs, Elijah D.; Nagami, Paul H.; Alto, Valerie M.; Goh, Henry G.; Gourdet, Muryam A. A.; Hough, Christina M.; Nickell, Ashley E.; Peer, Adrian G.; Coley, John D.; Tanner, Kimberly D.

    2013-01-01

    There are widespread aspirations to focus undergraduate biology education on teaching students to think conceptually like biologists; however, there is a dearth of assessment tools designed to measure progress from novice to expert biological conceptual thinking. We present the development of a novel assessment tool, the Biology Card Sorting Task, designed to probe how individuals organize their conceptual knowledge of biology. While modeled on tasks from cognitive psychology, this task is unique in its design to test two hypothesized conceptual frameworks for the organization of biological knowledge: 1) a surface feature organization focused on organism type and 2) a deep feature organization focused on fundamental biological concepts. In this initial investigation of the Biology Card Sorting Task, each of six analytical measures showed statistically significant differences when used to compare the card sorting results of putative biological experts (biology faculty) and novices (non–biology major undergraduates). Consistently, biology faculty appeared to sort based on hypothesized deep features, while non–biology majors appeared to sort based on either surface features or nonhypothesized organizational frameworks. Results suggest that this novel task is robust in distinguishing populations of biology experts and biology novices and may be an adaptable tool for tracking emerging biology conceptual expertise. PMID:24297290

  16. Quantum mechanical simulation methods for studying biological systems

    International Nuclear Information System (INIS)

    Bicout, D.; Field, M.

    1996-01-01

    Most known biological mechanisms can be explained using fundamental laws of physics and chemistry and a full understanding of biological processes requires a multidisciplinary approach in which all the tools of biology, chemistry and physics are employed. An area of research becoming increasingly important is the theoretical study of biological macromolecules where numerical experimentation plays a double role of establishing a link between theoretical models and predictions and allowing a quantitative comparison between experiments and models. This workshop brought researchers working on different aspects of the development and application of quantum mechanical simulation together, assessed the state-of-the-art in the field and highlighted directions for future research. Fourteen lectures (theoretical courses and specialized seminars) deal with following themes: 1) quantum mechanical calculations of large systems, 2) ab initio molecular dynamics where the calculation of the wavefunction and hence the energy and forces on the atoms for a system at a single nuclear configuration are combined with classical molecular dynamics algorithms in order to perform simulations which use a quantum mechanical potential energy surface, 3) quantum dynamical simulations, electron and proton transfer processes in proteins and in solutions and finally, 4) free seminars that helped to enlarge the scope of the workshop. (N.T.)

  17. Statistical approach for selection of biologically informative genes.

    Science.gov (United States)

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

    2018-05-20

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

  18. A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

    Science.gov (United States)

    Kang, Tianyu; Ding, Wei; Zhang, Luoyan; Ziemek, Daniel; Zarringhalam, Kourosh

    2017-12-19

    Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers. In this paper, we develop a biological network-based regularized artificial neural network model for prediction of phenotype from transcriptomic measurements in clinical trials. To improve model sparsity and the overall reproducibility of the model, we incorporate regularization for simultaneous shrinkage of gene sets based on active upstream regulatory mechanisms into the model. We benchmark our method against various regression, support vector machines and artificial neural network models and demonstrate the ability of our method in predicting the clinical outcomes using clinical trial data on acute rejection in kidney transplantation and response to Infliximab in ulcerative colitis. We show that integration of prior biological knowledge into the classification as developed in this paper, significantly improves the robustness and generalizability of predictions to independent datasets. We provide a Java code of our algorithm along with a parsed version of the STRING DB database. In summary, we present a method for prediction of clinical phenotypes using baseline genome-wide expression data that makes use of prior biological knowledge on gene-regulatory interactions in order to increase robustness and reproducibility of omic-scale markers. The integrated group-wise regularization methods increases the interpretability of biological signatures and gives stable performance estimates across independent test sets.

  19. Generation and characterization of biological aerosols for laser measurements

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Yung-Sung; Barr, E.B.

    1995-12-01

    Concerns for proliferation of biological weapons including bacteria, fungi, and viruses have prompted research and development on methods for the rapid detection of biological aerosols in the field. Real-time instruments that can distinguish biological aerosols from background dust would be especially useful. Sandia National Laboratories (SNL) is developing a laser-based, real-time instrument for rapid detection of biological aerosols, and ITRI is working with SNL scientists and engineers to evaluate this technology for a wide range of biological aerosols. This paper describes methods being used to generate the characterize the biological aerosols for these tests. In summary, a biosafe system has been developed for generating and characterizing biological aerosols and using those aerosols to test the SNL laser-based real-time instrument. Such tests are essential in studying methods for rapid detection of airborne biological materials.

  20. Graphics processing units in bioinformatics, computational biology and systems biology.

    Science.gov (United States)

    Nobile, Marco S; Cazzaniga, Paolo; Tangherloni, Andrea; Besozzi, Daniela

    2017-09-01

    Several studies in Bioinformatics, Computational Biology and Systems Biology rely on the definition of physico-chemical or mathematical models of biological systems at different scales and levels of complexity, ranging from the interaction of atoms in single molecules up to genome-wide interaction networks. Traditional computational methods and software tools developed in these research fields share a common trait: they can be computationally demanding on Central Processing Units (CPUs), therefore limiting their applicability in many circumstances. To overcome this issue, general-purpose Graphics Processing Units (GPUs) are gaining an increasing attention by the scientific community, as they can considerably reduce the running time required by standard CPU-based software, and allow more intensive investigations of biological systems. In this review, we present a collection of GPU tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. The complete list of GPU-powered tools here reviewed is available at http://bit.ly/gputools. © The Author 2016. Published by Oxford University Press.

  1. External irradiation facilities open for biological studies - progress in july 2005

    International Nuclear Information System (INIS)

    Gaillard-Lecanu, E.; Authier, N.; Verrey, B.; Bailly, I.; Bordy, J.M.; Coffigny, H.; Cortela, L.; Duval, D.; Leplat, J.J.; Poncy, J.L.; Testard, I.; Thuret, J.Y.

    2005-01-01

    The Life Science Division of the Atomic Energy Commission is making an inventory of the various radiation sources accessible for investigation on the biological effects of ionizing radiation. In this field, a wide range of studies is being carried out at the Life Science Division, attempting to characterize the kind of lesions with their early biological consequences (on the various cell compartments) and their late biological consequences (deterministic or stochastic effects), in relation to the radiation type and dose, especially at low doses. Several experimental models are available: plants, bacteria, eukaryotic cells from yeast up to mammalian cells and in vivo studies, mostly on rodents, in order to characterize the somatic late effects and the hereditary effects. Due to the significant cost of these facilities, also to their specific properties (nature of the radiation, dose and dose rate, possible accuracy of the irradiation at the molecular level), the closeness is no longer the only criteria for biologists to make a choice. The current evolution is to set up irradiation infrastructures combining ionizing radiation sources themselves and specific tools dedicated to biological studies: cell or molecular biology laboratories, animal facilities. The purpose, in this new frame, is to provide biologists with the most suitable facilities, and, if possible, to change these facilities according to requirements in radiobiology. In this report, the basics of interactions of ionizing radiation with biological tissues are briefly introduced, followed by a presentation of some of the facilities available for radiobiological studies especially at CEA. This panorama is not a comprehensive one, new data will be included as they advance, whether reporting existing facilities or if a new one is developed. (authors)

  2. 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.

  3. Biological Studies with Laser-Polarized ^129Xe

    Science.gov (United States)

    Tseng, C. H.; Oteiza, E. R.; Wong, G. A.; Walsworth, R. L.; Albert, M. S.; Nascimben, L.; Peled, S.; Sakai, K.; Jolesz, F. A.

    1996-05-01

    We have studied several biological systems using laser-polarized ^129Xe. In certain tissues magnetic resonance imaging (MRI) using inhaled laser-polarized noble gases may provide images superior to those from conventional proton MRI. High resolution laser-polarized ^3He images of air spaces in the human lung were recently obtained by the Princeton/Duke group. However, ^3He is not very soluble in tissue. Therefore, we are using laser polarized ^129Xe (tissue-soluble), with the long term goal of biomedical functional imaging. We have investigated multi-echo and multi-excitation magnetic resonance detection schemes to exploit the highly non-thermal ^129Xe magnetization produced by the laser polarization technique. We have inhalated live rats with laser-polarized ^129Xe gas and measured three distinct ^129Xe tissue resonances that last 20 to 40 sec. As a demonstration, we obtained a laser polarized ^129Xe image of the human oral cavity. Currently we are measuring the polarization lifetime of ^129Xe dissolved in human blood, the biological transporting medium. These studies and other recent developments will be reported.

  4. Two Project-Based Strategies in an Interdisciplinary Mathematical Modeling in Biology Course

    Science.gov (United States)

    Ludwig, Patrice; Tongen, Anthony; Walton, Brian

    2018-01-01

    James Madison University faculty team-teach an interdisciplinary mathematical modeling course for mathematics and biology students. We have used two different project-based approaches to emphasize the mathematical concepts taught in class, while also exposing students to new areas of mathematics not formally covered in class. The first method…

  5. Mathematical biology

    CERN Document Server

    Murray, James D

    1993-01-01

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

  6. Ways of incorporating photographic images in learning and assessing high school biology: A study of visual perception and visual cognition

    Science.gov (United States)

    Nixon, Brenda Chaumont

    This study evaluated the cognitive benefits and costs of incorporating biology-textbook and student-generated photographic images into the learning and assessment processes within a 10th grade biology classroom. The study implemented Wandersee's (2000) 20-Q Model of Image-Based Biology Test-Item Design (20-Q Model) to explore the use of photographic images to assess students' understanding of complex biological processes. A thorough review of the students' textbook using ScaleMaster R with PC Interface was also conducted. The photographs, diagrams, and other representations found in the textbook were measured to determine the percentage of each graphic depicted in the book and comparisons were made to the text. The theoretical framework that guided the research included Human Constructivist tenets espoused by Mintzes, Wandersee and Novak (2000). Physiological and cognitive factors of images and image-based learning as described by Robin (1992), Solso (1997) and Wandersee (2000) were examined. Qualitative case study design presented by Yin (1994), Denzin and Lincoln (1994) was applied and data were collected through interviews, observations, student activities, student and school artifacts and Scale Master IIRTM measurements. The results of the study indicate that although 24% of the high school biology textbook is devoted to photographic images which contribute significantly to textbook cost, the teacher and students paid little attention to photographic images other than as aesthetic elements for creating biological ambiance, wasting valuable opportunities for learning. The analysis of the photographs corroborated findings published by the Association American Association for the Advancement of Science that indicated "While most of the books are lavishly illustrated, these representations are rarely helpful, because they are too abstract, needlessly complicated, or inadequately explained" (Roseman, 2000, p. 2). The findings also indicate that applying the 20-Q

  7. 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...

  8. Capacity for DNA-barcode based taxonomy in support of Great Lakes biological monitoring

    Science.gov (United States)

    Enumerating organisms collected via nets and sediment grabs is a mainstay of aquatic ecology. Since morphological taxonomy can require considerable resources and expertise, DNA barcode-based identification of mixed-organism samples offers a valuable tool in support of biological...

  9. The Effect of Using Evolution Textbook Based on ICT and Metacognitive on Cognitive Competence of Biology Students at State University of Padang

    Science.gov (United States)

    Helendra, H.; Fadilah, M.; Arsih, F.

    2018-04-01

    Implementation of evolution lectures at Biology Department Faculty of Mathematics and Natural Sciences State University of Padang has been considered not optimal. The reasons are the limited availability of textbooks and students' learning attitudes. Because currently the students are very familiar with the internet and even has become a necessity, it has developed textbooks of evolution based on ICT and metacognitive. Selection of ICT based is in order to optimize the utilization of multimedia, and this is very compatible with the development of learning technology. While metacognitive based is in order to train students' learning attitudes to be able to think analysis, creative and evaluative. The aim of this study is to determine the effect of the use of evolution textbooks based on ICT and metacognitive to the cognitive competence of students of Biology Department State University of Padang. The data of this research is students' cognitive competence obtained from the implementation of effectiveness test of evolution textbook in the form of student learning outcomes. The research instrument is a learning result test designed to determine students’ cognitive competence. The subject of the study is a group of students in evolution course consisting of 33 students. Lectures are conducted through face-to-face and online lectures on Edmodo’s platform. The result of data analysis shows that there is an increase of cognitive competence of biology students after learning using ICT and metacognitive based evolution textbook, where average achievement is 77.72 with Percentage of achievement of criteria mastery is 81.25%. Therefore, it can be concluded that the evolution textbook based on ICT and metacognitive is effective in improving cognitive competence of students of Biology Department, Universitas Negeri Padang.

  10. 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

  11. Inquiry-based Investigation in Biology Laboratories: Does Neem Provide Bioprotection against Bean Beetles?

    Science.gov (United States)

    Pearce, Amy R.; Sale, Amanda Lovelace; Srivatsan, Malathi; Beck, Christopher W.; Blumer, Lawrence S.; Grippo, Anne A.

    2013-01-01

    We developed an inquiry-based biology laboratory exercise in which undergraduate students designed experiments addressing whether material from the neem tree ("Azadirachta indica") altered bean beetle ("Callosobruchus maculatus") movements and oviposition. Students were introduced to the bean beetle life cycle, experimental…

  12. [Side effects of biologic therapies in psoriasis].

    Science.gov (United States)

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

    2018-04-01

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

  13. 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..

  14. Machine learning based methods for the study of metabolism and its effect on the behavior of biological systems

    OpenAIRE

    Higuera Cabañes, Clara

    2015-01-01

    Las disciplinas de bioinformática y biología computacional, que se sirven de técnicas informáticas para dar solución a problemas en biología, se han posicionado como piezas clave en la investigación en biología molecular. Tanto por la gran cantidad de información compleja generada en los laboratorios como por la necesidad de simular in silico determinados procesos biológicos para su estudio, actualmente es esencial el desarrollo de nuevos métodos computacionales que asistan en la investigació...

  15. 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.

  16. Drawing-to-Learn: A Framework for Using Drawings to Promote Model-Based Reasoning in Biology

    Science.gov (United States)

    Quillin, Kim; Thomas, Stephen

    2015-01-01

    The drawing of visual representations is important for learners and scientists alike, such as the drawing of models to enable visual model-based reasoning. Yet few biology instructors recognize drawing as a teachable science process skill, as reflected by its absence in the Vision and Change report’s Modeling and Simulation core competency. Further, the diffuse research on drawing can be difficult to access, synthesize, and apply to classroom practice. We have created a framework of drawing-to-learn that defines drawing, categorizes the reasons for using drawing in the biology classroom, and outlines a number of interventions that can help instructors create an environment conducive to student drawing in general and visual model-based reasoning in particular. The suggested interventions are organized to address elements of affect, visual literacy, and visual model-based reasoning, with specific examples cited for each. Further, a Blooming tool for drawing exercises is provided, as are suggestions to help instructors address possible barriers to implementing and assessing drawing-to-learn in the classroom. Overall, the goal of the framework is to increase the visibility of drawing as a skill in biology and to promote the research and implementation of best practices. PMID:25713094

  17. Autonomy and Fear of Synthetic Biology: How Can Patients' Autonomy Be Enhanced in the Field of Synthetic Biology? A Qualitative Study with Stable Patients.

    Science.gov (United States)

    Rakic, Milenko; Wienand, Isabelle; Shaw, David; Nast, Rebecca; Elger, Bernice S

    2017-04-01

    We analyzed stable patients' views regarding synthetic biology in general, the medical application of synthetic biology, and their potential participation in trials of synthetic biology in particular. The aim of the study was to find out whether patients' views and preferences change after receiving more detailed information about synthetic biology and its clinical applications. The qualitative study was carried out with a purposive sample of 36 stable patients, who suffered from diabetes or gout. Interviews were transcribed verbatim, translated and fully anonymized. Thematic analysis was applied in order to examine stable patients' attitudes towards synthetic biology, its medical application, and their participation in trials. When patients were asked about synthetic biology in general, most of them were anxious that something uncontrollable could be created. After a concrete example of possible future treatment options, patients started to see synthetic biology in a more positive way. Our study constitutes an important first empirical insight into stable patients' views on synthetic biology and into the kind of fears triggered by the term "synthetic biology." Our results show that clear and concrete information can change patients' initial negative feelings towards synthetic biology. Information should thus be transmitted with great accuracy and transparency in order to reduce irrational fears of patients and to minimize the risk that researchers present facts too positively for the purposes of persuading patients to participate in clinical trials. Potential participants need to be adequately informed in order to be able to autonomously decide whether to participate in human subject research involving synthetic biology.

  18. Operational and biological effects zones from base stations of cellular telephony

    Energy Technology Data Exchange (ETDEWEB)

    Geronikolou, St. A., E-mail: sgeronik@bioacademy.gr [Biomedical Research Foundation Academy of Athens, Athens (Greece); Zimeras, S., E-mail: zimste@aegean.gr [University of the Aegean, Karlovassi, Samos (Greece); Tsitomeneas, S. Th., E-mail: stsit@teipir.gr [Piraeus University of Applied Sciences, Aigaleo (Greece)

    2016-03-25

    The possible environmental impacts of cellular base stations are operational and biological. The operational effects comprise Εlectro-Μagnetic Interference (EMI), lightning alterations and aesthetic degradation. Both thermal and non-thermal biological effects depend on the absorption of UHF radiofrequencies used. We measured, calculated and estimated the impact zones. The results are: (a) The lightning lethal zone equal to the antenna height, (b) the EMI impact in a zone up to 40m and (c) the ICNIRP’s limits exceed to a zone of 8∼20m into the antenna’s radiation pattern (for 2G GSM and 3G UMTS station). Finally we conclude the adverse effects must not expected in a zone of more than 150m from the radiated antenna, whereas, there is possibility of stochastic effects in intermediate distances (20/40-150m).

  19. Study of energetic-particle-irradiation induced biological effect on Rhizopus oryzae through synchrotron-FTIR micro-spectroscopy

    Science.gov (United States)

    Liu, Jinghua; Qi, Zeming; Huang, Qing; Wei, Xiaoli; Ke, Zhigang; Fang, Yusheng; Tian, Yangchao; Yu, Zengliang

    2013-01-01

    Energetic particles exist ubiquitously and cause varied biological effects such as DNA strand breaks, lipid peroxidation, protein modification, cell apoptosis or death. An emerging biotechnology based on ion-beam technique has been developed to serve as an effective tool for mutation breeding of crops and microbes. In order to improve the effectiveness of ion-beam biotechnology for mutation breeding, it is indispensible to gain a better understanding of the mechanism of the interactions between the energetic ions and biological systems which is still elusive. A new trend is to conduct more comprehensive research which is based on micro-scaled observation of the changes of the cellular structures and compositions under the interactions. For this purpose, advanced synchrotron FTIR (s-FTIR) microscopy was employed to monitor the cellular changes of single fungal hyphae under irradiation of α-particles from 241Am. Intracellular contents of ROS, MDA, GSSG/GSH and activities of CAT and SOD were measured via biochemical assay. Ion-irradiation on Rhizopus oryzae causes localized vacuolation, autolysis of cell wall and membrane, lipid peroxidation, DNA damage and conformational changes of proteins, which have been clearly revealed by the s-FTIR microspectroscopy. The different changes of cell viability, SOD and CAT activities can be explained by the ROS-involved chemical reactions. Evidently, the elevated level of ROS in hyphal cells upon irradiation plays the key role in the caused biological effect. This study demonstrates that s-FTIR microspectroscopy is an effective tool to study the damage of fungal hyphae caused by ionizing radiation and it facilitates the exploit of the mechanism for the interactions between the energetic ions and biological systems.

  20. Researchers study decontamination of chemical, biological warfare agents

    OpenAIRE

    Trulove, Susan

    2007-01-01

    The U.S. Army Research Office has awarded Virginia Tech a $680,000 grant over two years to build an instrument that can be used to study the chemistry of gases that will decompose both chemical and biological warfare agents on surfaces.

  1. Systems biology in critical-care nursing.

    Science.gov (United States)

    Schallom, Lynn; Thimmesch, Amanda R; Pierce, Janet D

    2011-01-01

    Systems biology applies advances in technology and new fields of study including genomics, transcriptomics, proteomics, and metabolomics to the development of new treatments and approaches of care for the critically ill and injured patient. An understanding of systems biology enhances a nurse's ability to implement evidence-based practice and to educate patients and families on novel testing and therapies. Systems biology is an integrated and holistic view of humans in relationship with the environment. Biomarkers are used to measure the presence and severity of disease and are rapidly expanding in systems biology endeavors. A systems biology approach using predictive, preventive, and participatory involvement is being utilized in a plethora of conditions of critical illness and injury including sepsis, cancer, pulmonary disease, and traumatic injuries.

  2. 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...

  3. 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

  4. 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

  5. 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

  6. Electrical impedance spectroscopy (EIS)-based evaluation of biological tissue phantoms to study multifrequency electrical impedance tomography (Mf-EIT) systems

    KAUST Repository

    Bera, Tushar Kanti

    2016-03-18

    Abstract: Electrical impedance tomography (EIT) phantoms are essential for the calibration, comparison and evaluation of the EIT systems. In EIT, the practical phantoms are typically developed based on inhomogeneities surrounded by a homogeneous background to simulate a suitable conductivity contrast. In multifrequency EIT (Mf-EIT) evaluation, the phantoms must be developed with the materials which have recognizable or distinguishable impedance variations over a wide range of frequencies. In this direction the impedance responses of the saline solution (background) and a number vegetable and fruit tissues (inhomogeneities) are studied with electrical impedance spectroscopy (EIS) and the frequency responses of bioelectrical impedance and conductivity are analyzed. A number of practical phantoms with different tissue inhomogeneities and different inhomogeneity configurations are developed and the multifrequency impedance imaging is studied with the Mf-EIT system to evaluate the phantoms. The conductivity of the vegetable inhomogeneities reconstructed from the EIT imaging is compared with the conductivity values obtained from the EIS studies. Experimental results obtained from multifrequency EIT reconstruction demonstrate that the electrical impedance of all the biological tissues inhomogenity decreases with frequency. The potato tissue phantom produces better impedance image in high frequency ranges compared to the cucumber phantom, because the cucumber impedance at high frequency becomes lesser than that of the potato at the same frequency range. Graphical Abstract: [Figure not available: see fulltext.] © 2016 The Visualization Society of Japan

  7. 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.

  8. Large Scale Proteomic Data and Network-Based Systems Biology Approaches to Explore the Plant World.

    Science.gov (United States)

    Di Silvestre, Dario; Bergamaschi, Andrea; Bellini, Edoardo; Mauri, PierLuigi

    2018-06-03

    The investigation of plant organisms by means of data-derived systems biology approaches based on network modeling is mainly characterized by genomic data, while the potential of proteomics is largely unexplored. This delay is mainly caused by the paucity of plant genomic/proteomic sequences and annotations which are fundamental to perform mass-spectrometry (MS) data interpretation. However, Next Generation Sequencing (NGS) techniques are contributing to filling this gap and an increasing number of studies are focusing on plant proteome profiling and protein-protein interactions (PPIs) identification. Interesting results were obtained by evaluating the topology of PPI networks in the context of organ-associated biological processes as well as plant-pathogen relationships. These examples foreshadow well the benefits that these approaches may provide to plant research. Thus, in addition to providing an overview of the main-omic technologies recently used on plant organisms, we will focus on studies that rely on concepts of module, hub and shortest path, and how they can contribute to the plant discovery processes. In this scenario, we will also consider gene co-expression networks, and some examples of integration with metabolomic data and genome-wide association studies (GWAS) to select candidate genes will be mentioned.

  9. 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.

  10. The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) Based Typing: Employment of Bioinformatics in a Multicenter Study.

    Science.gov (United States)

    Oberle, Michael; Wohlwend, Nadia; Jonas, Daniel; Maurer, Florian P; Jost, Geraldine; Tschudin-Sutter, Sarah; Vranckx, Katleen; Egli, Adrian

    2016-01-01

    The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS) typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains. Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP) including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany). Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium). Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster. Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.

  11. The Technical and Biological Reproducibility of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS Based Typing: Employment of Bioinformatics in a Multicenter Study.

    Directory of Open Access Journals (Sweden)

    Michael Oberle

    Full Text Available The technical, biological, and inter-center reproducibility of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI TOF MS typing data has not yet been explored. The aim of this study is to compare typing data from multiple centers employing bioinformatics using bacterial strains from two past outbreaks and non-related strains.Participants received twelve extended spectrum betalactamase-producing E. coli isolates and followed the same standard operating procedure (SOP including a full-protein extraction protocol. All laboratories provided visually read spectra via flexAnalysis (Bruker, Germany. Raw data from each laboratory allowed calculating the technical and biological reproducibility between centers using BioNumerics (Applied Maths NV, Belgium.Technical and biological reproducibility ranged between 96.8-99.4% and 47.6-94.4%, respectively. The inter-center reproducibility showed a comparable clustering among identical isolates. Principal component analysis indicated a higher tendency to cluster within the same center. Therefore, we used a discriminant analysis, which completely separated the clusters. Next, we defined a reference center and performed a statistical analysis to identify specific peaks to identify the outbreak clusters. Finally, we used a classifier algorithm and a linear support vector machine on the determined peaks as classifier. A validation showed that within the set of the reference center, the identification of the cluster was 100% correct with a large contrast between the score with the correct cluster and the next best scoring cluster.Based on the sufficient technical and biological reproducibility of MALDI-TOF MS based spectra, detection of specific clusters is possible from spectra obtained from different centers. However, we believe that a shared SOP and a bioinformatics approach are required to make the analysis robust and reliable.

  12. CyBy(2): a structure-based data management tool for chemical and biological data.

    Science.gov (United States)

    Höck, Stefan; Riedl, Rainer

    2012-01-01

    We report the development of a powerful data management tool for chemical and biological data: CyBy(2). CyBy(2) is a structure-based information management tool used to store and visualize structural data alongside additional information such as project assignment, physical information, spectroscopic data, biological activity, functional data and synthetic procedures. The application consists of a database, an application server, used to query and update the database, and a client application with a rich graphical user interface (GUI) used to interact with the server.

  13. Radiochemistry - Applications in the study of radical mechanisms of biological interest

    International Nuclear Information System (INIS)

    Foos, Jacques

    1982-01-01

    In biology, oxygen reducing processes give rise to the formation of intermediate radicals. One of the major breakthroughs of radiation chemistry of aqueous solutions is the identification of these compounds. The author describes the techniques used to study the reaction of these radicals (of radiolytic origin) with biological molecules [fr

  14. The Effects of Case-Based Instruction on Undergraduate Biology Students' Understanding of the Nature of Science

    Science.gov (United States)

    Burniston, Amy Lucinda

    Undergraduate science education is currently seeing a dramatic pedagogical push towards teaching the philosophies underpinning science as well as an increase in strategies that employ active learning. Many active learning strategies stem from constructivist ideals and have been shown to affect a student's understanding of how science operates and its impact on society- commonly referred to as the nature of science (NOS). One particular constructivist teaching strategy, case-based instruction (CBI), has been recommended by researchers and science education reformists as an effective instructional strategy for teaching NOS. Furthermore, when coupled with explicit-reflective instruction, CBI has been found to significantly increasing understanding of NOS in elementary and secondary students. However, few studies aimed their research on CBI and NOS towards higher education. Thus, this study uses a quasi-experimental, nonequivalent group design to study the effects of CBI on undergraduate science students understandings of NOS. Undergraduate biology student's understanding of NOS were assessed using the Views of Science Education (VOSE) instrument pre and post CBI intervention in Cellular and Molecular Biology and Human Anatomy and Physiology II. Data analysis indicated statistically significant differences between students NOS scores in experimental versus control sections for both courses, with experimental groups obtaining higher posttest scores. The results of this study indicate that undergraduate male and female students have similarly poor understandings of NOS and the use of historical case based instruction can be used as a means to increase undergraduate understanding of NOS.

  15. Radiolabelled substrates for studying biological effects of trace contaminants

    International Nuclear Information System (INIS)

    1975-01-01

    A programme of coordinated isotopic tracer-aided investigations of the biological side-effects of foreign chemical residues in food and agriculture, initiated in 1973, was reviewed. The current status of representative investigations from the point of view of techniques and priorities was assessed. Such investigations involved radioactive substrates for studying DNA injury and its repair; 14 C-labelled acetylcholine as substrate for measuring enzyme inhibition due to the presence of, or exposure to, anticholinesteratic contaminants; radioactive substrates as indication of side-effects in non-target organisms and of their comparative susceptibilities; radioactive substrates as indicators of persistence or biodegradability of trace contaminants of soil or water; and labelled pools for studying the biological side-effects of trace contaminants. Priorities were identified

  16. Logic-based models in systems biology: a predictive and parameter-free network analysis method.

    Science.gov (United States)

    Wynn, Michelle L; Consul, Nikita; Merajver, Sofia D; Schnell, Santiago

    2012-11-01

    Highly complex molecular networks, which play fundamental roles in almost all cellular processes, are known to be dysregulated in a number of diseases, most notably in cancer. As a consequence, there is a critical need to develop practical methodologies for constructing and analysing molecular networks at a systems level. Mathematical models built with continuous differential equations are an ideal methodology because they can provide a detailed picture of a network's dynamics. To be predictive, however, differential equation models require that numerous parameters be known a priori and this information is almost never available. An alternative dynamical approach is the use of discrete logic-based models that can provide a good approximation of the qualitative behaviour of a biochemical system without the burden of a large parameter space. Despite their advantages, there remains significant resistance to the use of logic-based models in biology. Here, we address some common concerns and provide a brief tutorial on the use of logic-based models, which we motivate with biological examples.

  17. Computational Systems Chemical Biology

    OpenAIRE

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

    2011-01-01

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

  18. The Biological Responses to Magnesium-Based Biodegradable Medical Devices

    Directory of Open Access Journals (Sweden)

    Lumei Liu

    2017-11-01

    Full Text Available The biocompatibility of Magnesium-based materials (MBMs is critical to the safety of biodegradable medical devices. As a promising metallic biomaterial for medical devices, the issue of greatest concern is devices’ safety as degrading products are possibly interacting with local tissue during complete degradation. The aim of this review is to summarize the biological responses to MBMs at the cellular/molecular level, including cell adhesion, transportation signaling, immune response, and tissue growth during the complex degradation process. We review the influence of MBMs on gene/protein biosynthesis and expression at the site of implantation, as well as throughout the body. This paper provides a systematic review of the cellular/molecular behavior of local tissue on the response to Mg degradation, which may facilitate a better prediction of long-term degradation and the safe use of magnesium-based implants through metal innovation.

  19. 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.

  20. 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.

  1. 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.

  2. 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 .

  3. Synthetic biology devices and circuits for RNA-based 'smart vaccines': a propositional review.

    Science.gov (United States)

    Andries, Oliwia; Kitada, Tasuku; Bodner, Katie; Sanders, Niek N; Weiss, Ron

    2015-02-01

    Nucleic acid vaccines have been gaining attention as an alternative to the standard attenuated pathogen or protein based vaccine. However, an unrealized advantage of using such DNA or RNA based vaccination modalities is the ability to program within these nucleic acids regulatory devices that would provide an immunologist with the power to control the production of antigens and adjuvants in a desirable manner by administering small molecule drugs as chemical triggers. Advances in synthetic biology have resulted in the creation of highly predictable and modular genetic parts and devices that can be composed into synthetic gene circuits with complex behaviors. With the recent advent of modified RNA gene delivery methods and developments in the RNA replicon platform, we foresee a future in which mammalian synthetic biologists will create genetic circuits encoded exclusively on RNA. Here, we review the current repertoire of devices used in RNA synthetic biology and propose how programmable 'smart vaccines' will revolutionize the field of RNA vaccination.

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

    Science.gov (United States)

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

    2014-12-01

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

  5. In silico model-based inference: a contemporary approach for hypothesis testing in network biology.

    Science.gov (United States)

    Klinke, David J

    2014-01-01

    Inductive inference plays a central role in the study of biological systems where one aims to increase their understanding of the system by reasoning backwards from uncertain observations to identify causal relationships among components of the system. These causal relationships are postulated from prior knowledge as a hypothesis or simply a model. Experiments are designed to test the model. Inferential statistics are used to establish a level of confidence in how well our postulated model explains the acquired data. This iterative process, commonly referred to as the scientific method, either improves our confidence in a model or suggests that we revisit our prior knowledge to develop a new model. Advances in technology impact how we use prior knowledge and data to formulate models of biological networks and how we observe cellular behavior. However, the approach for model-based inference has remained largely unchanged since Fisher, Neyman and Pearson developed the ideas in the early 1900s that gave rise to what is now known as classical statistical hypothesis (model) testing. Here, I will summarize conventional methods for model-based inference and suggest a contemporary approach to aid in our quest to discover how cells dynamically interpret and transmit information for therapeutic aims that integrates ideas drawn from high performance computing, Bayesian statistics, and chemical kinetics. © 2014 American Institute of Chemical Engineers.

  6. 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.

  7. Comparative study of biological activity of glutathione, sodium ...

    African Journals Online (AJOL)

    Glutathione (GSH) and sodium tungstate (Na2WO4) are important pharmacological agents. They provide protection to cells against cytotoxic agents and thus reduce their cytotoxicity. It was of interest to study the biological activity of these two pharmacological active agents. Different strains of bacteria were used and the ...

  8. Emergence of communication in socio-biological networks

    CERN Document Server

    Berea, Anamaria

    2018-01-01

    This book integrates current advances in biology, economics of information and linguistics research through applications using agent-based modeling and social network analysis to develop scenarios of communication and language emergence in the social aspects of biological communications. The book presents a model of communication emergence that can be applied both to human and non-human living organism networks. The model is based on economic concepts and individual behavior fundamental for the study of trust and reputation networks in social science, particularly in economics; it is also based on the theory of the emergence of norms and historical path dependence that has been influential in institutional economics. Also included are mathematical models and code for agent-based models to explore various scenarios of language evolution, as well as a computer application that explores language and communication in biological versus social organisms, and the emergence of various meanings and grammars in human ...

  9. A Collective Case Study of Secondary Students' Model-Based Inquiry on Natural Selection through Programming in an Agent-Based Modeling Environment

    Science.gov (United States)

    Xiang, Lin

    2011-01-01

    This is a collective case study seeking to develop detailed descriptions of how programming an agent-based simulation influences a group of 8th grade students' model-based inquiry (MBI) by examining students' agent-based programmable modeling (ABPM) processes and the learning outcomes. The context of the present study was a biology unit on…

  10. Context matters: volunteer bias, small sample size, and the value of comparison groups in the assessment of research-based undergraduate introductory biology lab courses.

    Science.gov (United States)

    Brownell, Sara E; Kloser, Matthew J; Fukami, Tadashi; Shavelson, Richard J

    2013-01-01

    The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.

  11. Study of the effects of radon in three biological systems

    International Nuclear Information System (INIS)

    Tavera, L.; Balcazar, M.; Lopez, A.; Brena, M.; Rosa, M.E. De la; Villalobos P, R.

    2002-01-01

    The radon and its decay products are responsible of the 3/4 parts of the exposure of the persons to the environmental radiation. The discovery at the end of XIX Century of the illnesses, mainly of cancer, which appeared in the presence of radon, lead to an accelerated growing of the radon studies: monitoring, dosimetry, effects on the persons, etc. Several epidemiological studies of radon in miners and population in general have been realized; advancing in the knowledge about the concentration-lung cancer risk relationship, but with discrepancies in the results depending on the concentration levels. Therefor, studies which consuming time, efforts and money go on doing. The research of the radon effects in biological systems different to human, allows to realize studies in less time, in controlled conditions and generally at lower cost, generating information about the alpha radiation effects in the cellular field. Therefor it was decided to study the response of three biological systems exposed to radon: an unicellular bacteria Escherichia Coli which was exposed directly to alpha particles from an electrodeposited source for determining the sensitivity limit of the chose technique. A plant, Tradescantia, for studying the cytogenetic effect of the system exposed to controlled concentrations of radon. An insect, Drosophila Melanogaster, for studying the genetic effects and the accumulated effects in several generations exposed to radon. In this work the experimental settlements are presented for the expositions of the systems and the biological results commenting the importance of these. (Author)

  12. Synthesis of C-di-saccharidic compounds by radical cyclisation. Study of biological, structural and dynamic properties

    International Nuclear Information System (INIS)

    Rubinstenn, Gilles

    1996-01-01

    The synthesis of carbohydrate mimics and particularly of C-disaccharides, molecules in which the inter-glycosidic oxygen atom has been replaced by a methylene group, has become, this past two decades, an important challenge in organic chemistry. In the first chapter we present the synthesis of C-disaccharides from the neutral series by a silaketal tethering. The key step of this C-glycosylation is a radical macro-cyclisation. This strategy is applied to the synthesis of two analogues of natural, biologically active, products, the lactose and the Lewis x tri-saccharide. The biological activity of this mimetics is then evaluated. A new tethering strategy, based on the use of phosphorus III compounds, is applied, in the second chapter, to the building of C-disaccharides of the 2'-amino 2'- deoxy series. The third chapter deals with the structural and dynamics study of the C-glycosides prepared in chapter 1 by Nuclear Magnetic Resonance. A new methodology, studying the dipolar relaxation along an effective field, generated through an off-resonance RF field, allowed the precise measurement of longitudinal and transverse cross-relaxation rates. Structural and dynamics parameter thus derived are used as restraints for molecular modeling. The results of this study are then compared to those of the biological tests. (author) [fr

  13. Evaluation of the Redesign of an Undergraduate Cell Biology Course

    Science.gov (United States)

    McEwen, Laura April; Harris, dik; Schmid, Richard F.; Vogel, Jackie; Western, Tamara; Harrison, Paul

    2009-01-01

    This article offers a case study of the evaluation of a redesigned and redeveloped laboratory-based cell biology course. The course was a compulsory element of the biology program, but the laboratory had become outdated and was inadequately equipped. With the support of a faculty-based teaching improvement project, the teaching team redesigned the…

  14. Column adsorption of perchlorate by amine-crosslinked biopolymer based resin and its biological, chemical regeneration properties.

    Science.gov (United States)

    Song, Wen; Xu, Xing; Tan, Xin; Wang, Yan; Ling, Jianya; Gao, Baoyu; Yue, Qinyan

    2015-01-22

    Column adsorption of perchlorate by amine-crosslinked biopolymer based resin was investigated by considering the bed depth, stream flow rate and influent pH. The empty bed contact time (EBCT) increased with the growth of bed depths, meanwhile rising flow rate at constant bed depth (3.4 cm) decreased the breakthrough time. It was observed that perchlorate adsorption capacity was optimum at neutral condition (pH: 6.0, 170.4 mg/g), and decreased at acidic (pH: 3.0, 96.4 mg/g) or alkalic (pH: 12.0, 72.8 mg/g) influents. The predominant strains of the acclimated sludge for resin biological regeneration were the β-subclass of Proteobacteria. Biological regeneration of the saturated amine-crosslinked biopolymer based resin with mixed bacteria have shown its merit with regeneration and biological perchlorate destruction simultaneously, although its regeneration efficiency was only 61.2-84.1% by contrast to chemical regeneration with efficiency more than 95%. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. 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.

  16. Non-nitric oxide based metallovasodilators: synthesis, reactivity and biological studies.

    Science.gov (United States)

    Sá, Denise S; Fernandes, André F; Silva, Carlos D S; Costa, Paula P C; Fonteles, Manassés C; Nascimento, Nilberto R F; Lopes, Luiz G F; Sousa, Eduardo H S

    2015-08-14

    There is an increasing number of compounds developed to target one or more pathways involved in vasodilation. Some studies conducted with azaindole and indazole derivatives showed cardiovascular activity associated with these compounds. Fast and easy structural modification of these organic molecules can be achieved using metal complexes promoting a much larger spatial change than organic strategies, potentially leading to novel drugs. Here, we have prepared a series of complexes with a formula cis-[RuCl(L)(bpy)(2)]PF(6), where L = 7-azaindole (ain), 5-azaindole (5-ain), 4-azaindole (4-ain), indazole (indz), benzimidazole (bzim) or quinoline (qui), which were characterized by spectroscopic and electrochemical techniques (CV, DPV). These compounds showed reasonable stability exhibiting photoreactivity only at low wavelength along with superoxide scavenger activity. Cytotoxicity assays indicated their low activity preliminarily supporting in vivo application. Interestingly, vasodilation assays conducted in rat aorta exhibited great activity that largely improved compared to free ligands and even better than the well-studied organic compound (BAY 41-42272), with IC(50) reaching 55 nM. These results have validated this strategy opening new opportunities to further develop cardiovascular agents based on metallo-bicyclic rings.

  17. Strategi Pembelajaran Biologi Berbasis Kompetensi dan Konservasi

    Directory of Open Access Journals (Sweden)

    Saiful Ridlo

    2013-09-01

    Full Text Available AbstrakPembelajaran melibatkan interaksi dosen, mahasiswa, dan sumber belajar. Interaksi antara ketiganya membutuhkan strategi pembelajaran. Penelitian ini bertujuan menghasilkan strategi pembelajaran biologi di Jurusan Biologi Unnes yang telah berkomitmen mengaplikasikan kurikulum berbasis kompetensi dan konservasi dengan ciri pendekatan jelajah alam sekitar (JAS. Metodologi penelitian menggunakan pendekatan kualitatif. Informannya dosen dan mahasiswa yang mengajar dan belajar biologi umum, mikrobiologi, dan taksonomi hewan. Data yang diperoleh berupa deskripsi kegiatan belajar mengajar dan lesson study.  Data-data dianalisis kemudian dinarasikan. Hasil penelitian menunjukkan pembelajaran biologi dengan pendekatan berpusat pada siswa yang dikhususkan pada kegiatan penjelajahan alam sekitar dapat dilakukan menggunakan strategi yang berbasis pada cara belajar siswa aktif dan kooperatif. Strategi-strategi tersebut adalah pembelajaran kontekstual, pembelajaran partisipatif, dan pembelajaran inkuiri. AbstractLearning involves the interaction of lecturer, students, and learning resources. The interaction between them requires a learning strategy. This research aims to generate learning strategies of biology in the Department of Biology Unnes which has committed to apply the competence- and conservation-based curriculum of features the environmental exploration (JAS approach. The research methodology uses a qualitative approach. The informants are the faculty members and the students who, respectively, teach and learn biology, microbiology, and animal taxonomy subjects. The data obtained were in the form of description of learning activities and lesson studies. The data were then analyzed narratively. The results showed that the student-centered learning of environmental exploration may be conducted using active- and cooperative-based strategies. Examples of these strategies are contextual learning, participatory learning, and inquiry learning.

  18. 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.

  19. 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.

  20. [The safety of biologics : a risk-benefit assessment of treating rheumatoid arthritis with biologics based on registry data on mortality].

    Science.gov (United States)

    Sander, O

    2010-11-01

    The aim of this study is a risk-benefit assessment of treating rheumatoid arthritis with biologics based on registry data on mortality.UK, Sweden and Spain have published evaluable data on mortality. A parallel control group was conducted in the UK. Sweden and Spain used an historical cohort for comparison.Central registries supported British and Swedish research by sending details on all deaths. The variety of possible confounders prevents direct comparisons of the registers and safe predictions for individual patients.The death rate in TNF-inhibitor-treated patients is higher than in the general population but lower than in the control groups with RA. Thus comorbidities are not balanced, the weighted mortality rate scaled down the difference between exposed patients and controls. When TNF-inhibitors are given for the usual indication, mortality is reduced compared to conventional therapy.

  1. Improving Satellite Compatible Microdevices to Study Biology in Space

    Science.gov (United States)

    Kalkus, Trevor; Snyder, Jessica; Paulino-Lima, Ivan; Rothschild, Lynn

    2017-01-01

    sense for biochemicals. (3) Developing a modular, semi-autonomous microfluidic device that can be easily adapted for a variety of common biological experiments. This versatility will allow for quicker and cheaper experimentation. These improvements to satellite experiment platforms have the potential to radically increase the return from NASA's biological and field studies with reduced development time, mass, and cost with increased robustness data and interpretation.

  2. COMPUTATIONAL MODELING AND SIMULATION IN BIOLOGY TEACHING: A MINIMALLY EXPLORED FIELD OF STUDY WITH A LOT OF POTENTIAL

    Directory of Open Access Journals (Sweden)

    Sonia López

    2016-09-01

    Full Text Available This study is part of a research project that aims to characterize the epistemological, psychological and didactic presuppositions of science teachers (Biology, Physics, Chemistry that implement Computational Modeling and Simulation (CMS activities as a part of their teaching practice. We present here a synthesis of a literature review on the subject, evidencing how in the last two decades this form of computer usage for science teaching has boomed in disciplines such as Physics and Chemistry, but in a lesser degree in Biology. Additionally, in the works that dwell on the use of CMS in Biology, we identified a lack of theoretical bases that support their epistemological, psychological and/or didactic postures. Accordingly, this generates significant considerations for the fields of research and teacher instruction in Science Education.

  3. 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...

  4. Occupational cosmic radiation exposure in Portuguese airline pilots: study of a possible correlation with oxidative biological markers.

    Science.gov (United States)

    Silva, Rodrigo; Folgosa, Filipe; Soares, Paulo; Pereira, Alice S; Garcia, Raquel; Gestal-Otero, Juan Jesus; Tavares, Pedro; Gomes da Silva, Marco D R

    2013-05-01

    Several studies have sought to understand the health effects of occupational exposure to cosmic radiation. However, only few biologic markers or associations with disease outcomes have so far been identified. In the present study, 22 long- and 26 medium-haul male Portuguese airline pilots and 36 factory workers who did not fly regularly were investigated. The two groups were comparable in age and diet, were non-smokers, never treated with ionizing radiation and other factors. Cosmic radiation exposure in pilots was quantified based on direct monitoring of 51 flights within Europe, and from Europe to North and South America, and to Africa. Indirect dose estimates in pilots were performed based on the SIEVERT (Système informatisé d'évaluation par vol de l'exposition au rayonnement cosmique dans les transports aériens) software for 6,039 medium- and 1,366 long-haul flights. Medium-haul pilots had a higher cosmic radiation dose rate than long-haul pilots, that is, 3.3 ± 0.2 μSv/h and 2.7 ± 0.3 μSv/h, respectively. Biological tests for oxidative stress on blood and urine, as appropriate, at two time periods separated by 1 year, included measurements of antioxidant capacity, total protein, ferritin, hemoglobin, creatinine and 8-hydroxy-2-deoxyguanosine (8OHdG). Principal components analysis was used to discriminate between the exposed and unexposed groups based on all the biological tests. According to this analysis, creatinine and 8OHdG levels were different for the pilots and the unexposed group, but no distinctions could be made among the medium- and the long-haul pilots. While hemoglobin levels seem to be comparable between the studied groups, they were directly correlated with ferritin values, which were lower for the airline pilots.

  5. Segmentation and classification of biological objects

    DEFF Research Database (Denmark)

    Schultz, Nette

    1995-01-01

    The present thesis is on segmentation and classification of biological objects using statistical methods. It is based on case studies dealing with different kinds of pork meat images, and we introduce appropriate statistical methods to solve the tasks in the case studies. The case studies concern...

  6. Unified Deep Learning Architecture for Modeling Biology Sequence.

    Science.gov (United States)

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

    2017-10-09

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

  7. Effect of a care plan based on Roy adaptation model biological dimension on stroke patients' physiologic adaptation level.

    Science.gov (United States)

    Alimohammadi, Nasrollah; Maleki, Bibi; Shahriari, Mohsen; Chitsaz, Ahmad

    2015-01-01

    Stroke is a stressful event with several functional, physical, psychological, social, and economic problems that affect individuals' different living balances. With coping strategies, patients try to control these problems and return to their natural life. The aim of this study is to investigate the effect of a care plan based on Roy adaptation model biological dimension on stroke patients' physiologic adaptation level. This study is a clinical trial in which 50 patients, affected by brain stroke and being admitted in the neurology ward of Kashani and Alzahra hospitals, were randomly assigned to control and study groups in Isfahan in 2013. Roy adaptation model care plan was administered in biological dimension in the form of four sessions and phone call follow-ups for 1 month. The forms related to Roy adaptation model were completed before and after intervention in the two groups. Chi-square test and t-test were used to analyze the data through SPSS 18. There was a significant difference in mean score of adaptation in physiological dimension in the study group after intervention (P adaptation in the patients affected by brain stroke in the study and control groups showed a significant increase in physiological dimension in the study group by 47.30 after intervention (P adaptation model biological dimension care plan can result in an increase in adaptation in patients with stroke in physiological dimension. Nurses can use this model for increasing patients' adaptation.

  8. Academic Preparation in Biology and Advocacy for Teaching Evolution: Biology versus Non-Biology Teachers

    Science.gov (United States)

    Nehm, Ross H.; Kim, Sun Young; Sheppard, Keith

    2009-01-01

    Despite considerable focus on evolution knowledge-belief relationships, little research has targeted populations with strong content backgrounds, such as undergraduate degrees in biology. This study (1) measured precertified biology and non-biology teachers' (n = 167) knowledge of evolution and the nature of science; (2) quantified teacher…

  9. Logic-based models in systems biology: a predictive and parameter-free network analysis method†

    Science.gov (United States)

    Wynn, Michelle L.; Consul, Nikita; Merajver, Sofia D.

    2012-01-01

    Highly complex molecular networks, which play fundamental roles in almost all cellular processes, are known to be dysregulated in a number of diseases, most notably in cancer. As a consequence, there is a critical need to develop practical methodologies for constructing and analysing molecular networks at a systems level. Mathematical models built with continuous differential equations are an ideal methodology because they can provide a detailed picture of a network’s dynamics. To be predictive, however, differential equation models require that numerous parameters be known a priori and this information is almost never available. An alternative dynamical approach is the use of discrete logic-based models that can provide a good approximation of the qualitative behaviour of a biochemical system without the burden of a large parameter space. Despite their advantages, there remains significant resistance to the use of logic-based models in biology. Here, we address some common concerns and provide a brief tutorial on the use of logic-based models, which we motivate with biological examples. PMID:23072820

  10. 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.

  11. Using Case Studies in Calculus-based Physics

    Science.gov (United States)

    Katz, Debora M.

    2006-12-01

    Do your students believe that the physics only works in your classroom or laboratory? Or do they see that physics underlies their everyday experience? Case studies in physics help students connect physics principles to their everyday experience. For decades, case studies have been used to teach law, medicine and biology, but they are rarely used in physics. I am working on a calculus-based physics textbook for scientists and engineers. Case studies are woven into each chapter. Stop by and get a case study to test out in your classroom. I would love to get your feedback.

  12. Biological performance of titania containing phosphate-based glasses for bone tissue engineering applications

    International Nuclear Information System (INIS)

    Abou Neel, Ensanya Ali; Chrzanowski, Wojciech; Knowles, Jonathan Campbell

    2014-01-01

    The interplay between glass chemistry, structure, degradation kinetics, and biological activity provides flexibility for the development of scaffolds with highly specific cellular response. The aim of this study was therefore to investigate the role of titania inclusion into the phosphate-based glass on its ability to stimulate osteoblast-like human osteosarcoma (HOS) cells to adhere, proliferate and differentiate. In depth morphological and biochemical characterisation was performed on HOS cells cultured on the surface of glass discs. Cell proliferation was also studied in the presence of the glass extract. Cell differentiation, through osteoblast phenotype genes, alkaline phosphatase (ALP) activity and osteocalcin production, was carried out using normal or osteogenic media. Both Thermanox® and titania free glass were used as controls. The data demonstrated that titania inclusion provides desired cytocompatible surface that supported initial cell attachment, sustained viability, and increased cell proliferation similar or significantly higher than Thermanox®. The modified glasses regulated osteoblastic cell differentiation as detected by osteoblast phenotype gene transcription and upregulated ALP and osteocalcin expression. Using osteogenic media had no significant effect on ALP activity and osteocalcin expression. Therefore, titania modified phosphate glasses may have future use as bone tissue engineering scaffolds. - Highlights: • This study investigated the role of titania on the biological response of phosphate glasses. • Incorporation of titania improved HOS cell attachment, viability and proliferation. • Titania modified glasses regulated osteoblastic cell differentiation. • Using osteogenic media had no significant effect on cell differentiation. • Titania modified glasses may have future use as bone tissue engineering scaffolds

  13. Moessbauer spectroscopic studies of magnetically ordered biological materials

    International Nuclear Information System (INIS)

    Dickson, D.P.E.

    1987-01-01

    This paper discusses recent work showing the application of Moessbauer spectroscopy to the study of the properties of the magnetically ordered materials which occur in a variety of biological systems. These materials display a diversity of behaviour which provides good examples of the various possibilities which can arise with iron-containing particles of different compositions and sizes. (orig.)

  14. Biologically inspired technologies in NASA's morphing project

    Science.gov (United States)

    McGowan, Anna-Maria R.; Cox, David E.; Lazos, Barry S.; Waszak, Martin R.; Raney, David L.; Siochi, Emilie J.; Pao, S. Paul

    2003-07-01

    For centuries, biology has provided fertile ground for hypothesis, discovery, and inspiration. Time-tested methods used in nature are being used as a basis for several research studies conducted at the NASA Langley Research Center as a part of Morphing Project, which develops and assesses breakthrough vehicle technologies. These studies range from low drag airfoil design guided by marine and avian morphologies to soaring techniques inspired by birds and the study of small flexible wing vehicles. Biology often suggests unconventional yet effective approaches such as non-planar wings, dynamic soaring, exploiting aeroelastic effects, collaborative control, flapping, and fibrous active materials. These approaches and other novel technologies for future flight vehicles are being studied in NASA's Morphing Project. This paper will discuss recent findings in the aeronautics-based, biologically-inspired research in the project.

  15. Optimization of labeling conditions of n-isopropyl-p-iodoamphetamine chloridate (IMP) with radioiodine. Biological distribution studies

    International Nuclear Information System (INIS)

    Colturato, Maria Tereza

    2000-01-01

    The development of this work was based on a great interest from the medical community in the utilization of N-isopropyl-p-iodoamphetamine chloridate (IMP) labeled with 123 l, for brain perfusion evaluation. The IMP was initially characterized by: Melting Point (MP), Infrared Spectrophotometry (IR), Nuclear Magnetic Resonance Spectrometry (NMR), Elemental Analysis and High Performance Liquid Chromatography (HPLC). After having chosen the ideal method (nucleophilic substitution) to label IMP with that used Cu(I) as reducing agent and ascorbic acid as catalyzing of Cu(II), studies were performed to optimize the labeling parameters of 123 l-IMP: temperature reaction, time reaction, ascorbic acid mass, pH and molar ratio, and stability of the final product. The quality control method (ascending paper chromatographic) used to determine the radiochemistry purity showed to be efficient, fast and of easily handling for routine production. Biological distribution studies were performed with laboratory animals (mice) to determine the percent administered dose in the blood, different organs and whole body after intravenous administration of the radiopharmaceutical. Toxicological evaluation and in vitro study to determine the plasmatic protein binding were also done. The data of the biological distribution in mice have shown that the product crossed the intact blood brain barrier, for a enough time to obtain brain scintigraphic image, thus, allowing a follow up of further studies after the intravenous administration of the radiopharmaceutical. The 123 l-IMP showed a blood clearance and then the principal elimination route was the urinary. The kinetic study of 123 l-IMP, submitting blood samples data to BIEXP.BAS program, showed a biexponential pattern which allowed demonstrating that the compound presents a first phase of quick distribution and a second one slower corresponding to the equilibrium and elimination. Based on the results from radiochemical purity, stability and

  16. 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

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

    Science.gov (United States)

    2003-06-01

    parenthesis in figure 1.8 is a bi-stable toggle switch. Introduction: Molecular assembly lines O=P-O- O O HOH H0P-0- O -O- 4 Polymerase HO H--- O HHO ...sample. Therefore, the samples are self-consistent. From here on, the calculated temperature based on FAM emission MNSowmm" RF Biology: Results and...irradiation for one hour. Figure 2.11 shows the fluorescence spectra of FAM emission (4 scans averaged over 200 seconds) in a 300MHz field. The increased

  18. Artificial cell mimics as simplified models for the study of cell biology.

    Science.gov (United States)

    Salehi-Reyhani, Ali; Ces, Oscar; Elani, Yuval

    2017-07-01

    Living cells are hugely complex chemical systems composed of a milieu of distinct chemical species (including DNA, proteins, lipids, and metabolites) interconnected with one another through a vast web of interactions: this complexity renders the study of cell biology in a quantitative and systematic manner a difficult task. There has been an increasing drive towards the utilization of artificial cells as cell mimics to alleviate this, a development that has been aided by recent advances in artificial cell construction. Cell mimics are simplified cell-like structures, composed from the bottom-up with precisely defined and tunable compositions. They allow specific facets of cell biology to be studied in isolation, in a simplified environment where control of variables can be achieved without interference from a living and responsive cell. This mini-review outlines the core principles of this approach and surveys recent key investigations that use cell mimics to address a wide range of biological questions. It will also place the field in the context of emerging trends, discuss the associated limitations, and outline future directions of the field. Impact statement Recent years have seen an increasing drive to construct cell mimics and use them as simplified experimental models to replicate and understand biological phenomena in a well-defined and controlled system. By summarizing the advances in this burgeoning field, and using case studies as a basis for discussion on the limitations and future directions of this approach, it is hoped that this minireview will spur others in the experimental biology community to use artificial cells as simplified models with which to probe biological systems.

  19. 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.

  20. Context Matters: Volunteer Bias, Small Sample Size, and the Value of Comparison Groups in the Assessment of Research-Based Undergraduate Introductory Biology Lab Courses

    Directory of Open Access Journals (Sweden)

    Sara E. Brownell

    2013-08-01

    Full Text Available The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.

  1. Cell attachment properties of Portland cement-based endodontic materials: biological and methodological considerations.

    Science.gov (United States)

    Ahmed, Hany Mohamed Aly; Luddin, Norhayati; Kannan, Thirumulu Ponnuraj; Mokhtar, Khairani Idah; Ahmad, Azlina

    2014-10-01

    The attachment and spreading of mammalian cells on endodontic biomaterials are an area of active research. The purpose of this review is to discuss the cell attachment properties of Portland cement (PC)-based materials by using scanning electron microscope (SEM). In addition, methodological aspects and technical challenges are discussed. A PubMed electronic search was conducted by using appropriate key words to identify the available investigations on the cell attachment properties of PC-based endodontic materials. After retrieving the full text of related articles, the cross citations were also identified. A total of 23 articles published between January 1993 and October 2013 were identified. This review summarizes the cell attachment properties of commercial and experimental PC-based materials on different cell cultures by using SEM. Methodological procedures, technical challenges, and relevance of SEM in determining the biological profile of PC-based materials are discussed. SEM observations demonstrate that commercial MTA formulations show favorable cell attachment properties, which is consistent with their successful clinical outcomes. The favorable cell attachment properties of PC and its modified formulations support its potential use as a substitute for mineral trioxide aggregate. However, researchers should carefully select cell types for their SEM investigations that would be in contact with the proposed PC-based combinations in the clinical situation. Despite being a technical challenge, SEM provides useful information on the cell attachment properties of PC-based materials; however, other assays for cell proliferation and viability are essential to come up with an accurate in vitro biological profile of any given PC-based formulation. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  2. 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.

  3. Biological studies of the U.S. subseabed disposal program

    International Nuclear Information System (INIS)

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

    1980-01-01

    The Subseabed Disposal Program (SDP) of the U.S. is assessing the feasibility of emplacing high level radioactive wastes (HLW) within deep-sea sediments and is developing the means for assessing the feasibility of the disposal practices of other nations. This paper discusses the role and status of biological research in the SDP. Studies of the disposal methods and of the conceived barriers (canister, waste form and sediment) suggest that biological knowledge will be principally needed to address the impact of accidental releases of radionuclides. Current experimental work is focusing on the deep-sea ecosystem to determine: (1) the structure of benthic communities, including their microbial component; (2) the faunal composition of deep midwater nekton; (3) the biology of deep-sea amphipods; (4) benthic community metabolism; (5) the rates of bacterial processes; (6) the metabolism of deep-sea animals, and (7) the radiation sensitivity of deep-sea organisms. A multi-compartment model is being developed to assess quantitatively, the impact (on the environment and on man) of releases of radionuclides into the sea

  4. Visual Literacy in Preservice Teachers: a Case Study in Biology

    Science.gov (United States)

    Ruiz-Gallardo, José Reyes; García Fernández, Beatriz; Mateos Jiménez, Antonio

    2017-07-01

    In this study, we explore the competence of preservice teachers (n = 161) in labelling and creating new cross-sectional human diagrams, based on anatomy knowledge depicted in longitudinal sections. Using educational standards to assess visual literacy and ad hoc open questions, results indicate limited skills for both tasks. However, their competence is particularly poor creating diagrams, where shortcomings were observed not only in visual literacy but in content knowledge. We discuss the misconceptions detected during these assessments. Visual literacy training should be strengthened for these students, as it is a skill that is especially important for future teachers to use in learning, assessing, and reflecting on content in science education. This is particularly important in preservice teachers since they should be fluent in the use of visual teaching tools in teaching anatomy and other content in the biology curriculum.

  5. [A novel biologic electricity signal measurement based on neuron chip].

    Science.gov (United States)

    Lei, Yinsheng; Wang, Mingshi; Sun, Tongjing; Zhu, Qiang; Qin, Ran

    2006-06-01

    Neuron chip is a multiprocessor with three pipeline CPU; its communication protocol and control processor are integrated in effect to carry out the function of communication, control, attemper, I/O, etc. A novel biologic electronic signal measurement network system is composed of intelligent measurement nodes with neuron chip at the core. In this study, the electronic signals such as ECG, EEG, EMG and BOS can be synthetically measured by those intelligent nodes, and some valuable diagnostic messages are found. Wavelet transform is employed in this system to analyze various biologic electronic signals due to its strong time-frequency ability of decomposing signal local character. Better effect is gained. This paper introduces the hardware structure of network and intelligent measurement node, the measurement theory and the signal figure of data acquisition and processing.

  6. Thinking about Digestive System in Early Childhood: A Comparative Study about Biological Knowledge

    Science.gov (United States)

    AHI, Berat

    2017-01-01

    The current study aims to explore how children explain the concepts of biology and how biological knowledge develops across ages by focusing on the structure and functions of the digestive system. The study was conducted with 60 children. The data were collected through the interviews conducted within a think-aloud protocol. The interview data…

  7. Novel nuclear magnetic resonance techniques for studying biological molecules

    International Nuclear Information System (INIS)

    Laws, David D.

    2000-01-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (φ/ψ) dihedral angles by comparing experimentally determined 13 C a , chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.

  8. [Biology and culture: a dimension of collaboration between anthropology and epidemiology].

    Science.gov (United States)

    Song, Leiming; Wang, Ning

    2016-01-01

    Biology is the important basis of epidemiological study. Based on biology, psychology, social and cultural factors can influence human's health and disease incidence. The medical mode has changed from "biomedical mode" to "bio-psycho-social medical model" , but culture factor was neglected somewhat during this process, so paying attention to culture factor in anthropologic study and using it as biologic basis in epidemiologic study might be a dimension of collaboration between of anthropology and epidemiology.

  9. IMRT optimization with pseudo-biologic objective function

    International Nuclear Information System (INIS)

    Yi, B. Y.; Ahn, S. D.; Kim, J. H.; Lee, S. W.; Choi, E. K.

    2002-01-01

    The pseudo-biologic objective function has been proposed for the IMRT optimization. It is similar to the biological objective function in mathematical shape, but uses physical parameters. The pseudo-biologic objective function concept is consisted of the target coverage index (TCI) and the organ score index (OSI), was introduced. The TCI was expressed as the sum of all of the weighted bins of target dose volume histogram (DVH). The weights were given as the normal distribution of which the average is 100 % and the standard deviation is ±. The OSI was expressed as similar way. The average of the normal distribution was 0% of the dose and that of standard deviation was selected as a function of limiting dose and its importance. The objective function could be calculated as the product of the TCI and OSI's. The RTP Tool Box (RTB) was used for this study. The constraints applied in the optimization was intuitively clinical experience based numbers, while the physical objective function asks just numbers which are not necessarily based on the clinic, and the parameters for the biologic objective functions are uncertain. The OSI's from the pseudo-biological function showed better results than from the physical functions, while TCI's showed similar tendency. We could show that the pseudo-biologic function can be used for an IMRT objective function on behalf of the biological objective function

  10. WE-B-304-03: Biological Treatment Planning

    International Nuclear Information System (INIS)

    Orton, C.

    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

  11. Graphene and graphene-like two-denominational materials based fluorescence resonance energy transfer (FRET) assays for biological applications.

    Science.gov (United States)

    Tian, Feng; Lyu, Jing; Shi, Jingyu; Yang, Mo

    2017-03-15

    In the past decades, Förster resonance energy transfer (FRET) has been applied in many biological applications to reveal the biological information at the nanoscale. Recently, graphene and graphene-like two-dimensional (2D) nanomaterials started to be used in FRET assays as donors or acceptors including graphene oxide (GO), graphene quantum dot (GQD), graphitic-carbon nitride nanosheets (g-C 3 N 4 ) and transition metal dichalcogenides (e.g. MoS 2 , MnO 2, and WS 2 ). Due to the remarkable properties such as large surface to volume ratio, tunable energy band, photoluminescence and excellent biocompatibility, these 2D nanomaterials based FRET assays have shown great potential in various biological applications. This review summarizes the recent development of graphene and graphene-like 2D nanomaterials based FRET assays in applications of biosensing, bioimaging, and drug delivery monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Healthy Foundations Study: a randomised controlled trial to evaluate biological embedding of early-life experiences.

    Science.gov (United States)

    Gonzalez, Andrea; Catherine, Nicole; Boyle, Michael; Jack, Susan M; Atkinson, Leslie; Kobor, Michael; Sheehan, Debbie; Tonmyr, Lil; Waddell, Charlotte; MacMillan, Harriet L

    2018-01-26

    Adverse early experiences are associated with long-lasting disruptions in physiology, development and health. These experiences may be 'biologically embedded' into molecular and genomic systems that determine later expressions of vulnerability. Most studies to date have not examined whether preventive interventions can potentially reverse biological embedding. The Nurse-Family Partnership (NFP) is an evidence-based intervention with demonstrated efficacy in improving prenatal health, parenting and child functioning. The Healthy Foundations Study is an innovative birth cohort which will evaluate the impact of the NFP on biological outcomes of mothers and their infants. Starting in 2013, up to 400 pregnant mothers and their newborns were recruited from the British Columbia Healthy Connections Project-a randomised controlled trial of the NFP, and will be followed to child aged 2 years. Women were recruited prior to 28 weeks' gestation and then individually randomised to receive existing services (comparison group) or NFP plus existing services (intervention group). Hair samples are collected from mothers at baseline and 2 months post partum to measure physiological stress. Saliva samples are collected from infants during all visits for analyses of stress and immune function. Buccal swabs are collected from infants at 2 and 24 months to assess DNA methylation. Biological samples will be related to child outcome measures at age 2 years. The study received ethical approval from seven research ethics boards. Findings from this study will be shared broadly with the research community through peer-reviewed publications, and conference presentations, as well as seminars with our policy partners and relevant healthcare providers. The outcomes of this study will provide all stakeholders with important information regarding how early adversity may lead to health and behavioural disparities and how these may be altered through early interventions. NCT01672060; Pre-results.

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

    DEFF Research Database (Denmark)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas

    2015-01-01

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

  14. Evaluation rate of aging person based on determination of biological age

    Directory of Open Access Journals (Sweden)

    V. Fil

    2015-01-01

    2Kazimierz Wielki University, Bydgoszcz, Poland   Abstract The article considers the value of biological and passport age of student youth. In experiment participated 140 students aged 17-19 years. Calculated their biological age. Reviewed pace of aging of the body of students. Detected indexes that have the strongest relationship with indicators of biological age. The results compared with researchers of other regions of Ukraine.   Keywords: chronological (passport age, biological age, appropriate biological age, pulse blood pressure, rate of aging, static balancing, self-reported level of health.

  15. A concept for biological valuation in the marine environment

    Directory of Open Access Journals (Sweden)

    Eric Willem Maria Stienen

    2007-03-01

    Full Text Available In order to develop management strategies for sustainable useand conservation in the marine environment, reliable and meaningful,but integrated ecological information is needed. Biological valuationmaps that compile and summarize all available biological andecological information for a study area, and that allocate anoverall biological value to subzones, can be used as baselinemaps for future spatial planning at sea. This paper providesa concept for marine biological valuation which is based on aliterature review of existing valuation criteria and the consensusreached by a discussion group of experts.

  16. Biological and Chemical Information Technologies

    DEFF Research Database (Denmark)

    Amos, Martyn; Dittrich, Peter; McCaskill, John

    2011-01-01

    Biological and chemical information technologies (bio/chem IT) have the potential to reshape the scientific and technological landscape. In this paper we briefly review the main challenges and opportunities in the field, before presenting several case studies based on ongoing FP7 research projects....

  17. From Lévy to Brownian: a computational model based on biological fluctuation.

    Science.gov (United States)

    Nurzaman, Surya G; Matsumoto, Yoshio; Nakamura, Yutaka; Shirai, Kazumichi; Koizumi, Satoshi; Ishiguro, Hiroshi

    2011-02-03

    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. 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. 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.

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

    Science.gov (United States)

    Ferragina, Paolo; Giancarlo, Raffaele; Greco, Valentina; Manzini, Giovanni; Valiente, Gabriel

    2007-07-13

    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. 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 (Receiver Operating Curve) analysis, aims at

  19. 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

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

    International Nuclear Information System (INIS)

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

    1991-01-01

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

  1. 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.

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

    Science.gov (United States)

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

    2015-07-01

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

  3. Effectiveness of a Low-Cost, Graduate Student-Led Intervention on Study Habits and Performance in Introductory Biology.

    Science.gov (United States)

    Hoskins, Tyler D; Gantz, J D; Chaffee, Blake R; Arlinghaus, Kel; Wiebler, James; Hughes, Michael; Fernandes, Joyce J

    2017-01-01

    Institutions have developed diverse approaches that vary in effectiveness and cost to improve student performance in introductory science, technology, engineering, and mathematics courses. We developed a low-cost, graduate student-led, metacognition-based study skills course taught in conjunction with the introductory biology series at Miami University. Our approach aimed to improve performance for underachieving students by combining an existing framework for the process of learning (the study cycle) with concrete tools (outlines and concept maps) that have been shown to encourage deep understanding. To assess the effectiveness of our efforts, we asked 1) how effective our voluntary recruitment model was at enrolling the target cohort, 2) how the course impacted performance on lecture exams, 3) how the course impacted study habits and techniques, and 4) whether there are particular study habits or techniques that are associated with large improvements on exam scores. Voluntary recruitment attracted only 11-17% of our target cohort. While focal students improved on lecture exams relative to their peers who did not enroll, gains were relatively modest, and not all students improved. Further, although students across both semesters of our study reported improved study habits (based on pre and post surveys) and on outlines and concept maps (based on retrospectively scored assignments), gains were more dramatic in the Fall semester. Multivariate models revealed that, while changes in study habits and in the quality of outlines and concept maps were weakly associated with change in performance on lecture exams, relationships were only significant in the Fall semester and were sometimes counterintuitive. Although benefits of the course were offset somewhat by the inefficiency of voluntary recruitment, we demonstrate the effectiveness our course, which is inexpensive to implement and has advantage of providing pedagogical experience to future educators. © 2017 T. D

  4. 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.

  5. 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.

  6. VISUALIZATION OF BIOLOGICAL TISSUE IMPEDANCE PARAMETERS

    Directory of Open Access Journals (Sweden)

    V. I. Bankov

    2016-01-01

    Full Text Available Objective. Investigation the opportunity for measurement of biological tissue impedance to visualize its parameters.Materials and methods. Studies were undertook on the experimental facility, consists of registrating measuring cell, constructed from flat inductors system, formed in oscillatory circuit, herewith investigated biological tissue is the part of this oscillatory circuit. An excitation of oscillatory circuit fulfilled by means of exciter inductor which forms impulse complex modulated electromagnetic field (ICM EMF. The measurement process and visualizations provided by set of certificated instruments: a digital oscillograph AKTAKOM ADS-2221MV, a digital generator АКТАКОМ AWG-4150 (both with software and a gauge RLC E7-22. Comparative dynamic studies of fixed volume and weight pig’s blood, adipose tissue, muscular tissue impedance were conducted by contact versus contactless methods. Contactless method in contrast to contact method gives opportunity to obtain the real morphological visualization of biological tissue irrespective of their nature.Results. Comparison of contact and contactless methods of impedance measurement shows that the inductance to capacitance ratio X(L / X(C was equal: 17 – for muscular tissue, 4 – for blood, 1 – for adipose tissue. It demonstrates the technical correspondence of both impedance registration methods. If propose the base relevance of X (L and X (C parameters for biological tissue impedance so contactless measurement method for sure shows insulating properties of adipose tissue and high conductivity for blood and muscular tissue in fixed volume-weight parameters. Registration of biological tissue impedance complex parameters by contactless method with the help of induced ICM EMF in fixed volume of biological tissue uncovers the most important informative volumes to characterize morphofunctional condition of biological tissue namely X (L / X (C.Conclusion. Contactless method of biological

  7. 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.

  8. Patterns of Care for Biologic-Dosing Outliers and Nonoutliers in Biologic-Naive Patients with Rheumatoid Arthritis.

    Science.gov (United States)

    Delate, Thomas; Meyer, Roxanne; Jenkins, Daniel

    2017-08-01

    Although most biologic medications for patients with rheumatoid arthritis (RA) have recommended fixed dosing, actual biologic dosing may vary among real-world patients, since some patients can receive higher (high-dose outliers) or lower (low-dose outliers) doses than what is recommended in medication package inserts. To describe the patterns of care for biologic-dosing outliers and nonoutliers in biologic-naive patients with RA. This was a retrospective, longitudinal cohort study of patients with RA who were not pregnant and were aged ≥ 18 and 110% of the approved dose in the package insert at any time during the study period. Baseline patient profiles, treatment exposures, and outcomes were collected during the 180 days before and up to 2 years after biologic initiation and compared across index biologic outlier groups. Patients were followed for at least 1 year, with a subanalysis of those patients who remained as members for 2 years. This study included 434 RA patients with 1 year of follow-up and 372 RA patients with 2 years of follow-up. Overall, the vast majority of patients were female (≈75%) and had similar baseline characteristics. Approximately 10% of patients were outliers in both follow-up cohorts. ETN patients were least likely to become outliers, and ADA patients were most likely to become outliers. Of all outliers during the 1-year follow-up, patients were more likely to be a high-dose outlier (55%) than a low-dose outlier (45%). Median 1- and 2-year adjusted total biologic costs (based on wholesale acquisition costs) were higher for ADA and ETA nonoutliers than for IFX nonoutliers. Biologic persistence was highest for IFX patients. Charlson Comorbidity Index score, ETN and IFX index biologic, and treatment with a nonbiologic disease-modifying antirheumatic drug (DMARD) before biologic initiation were associated with becoming high- or low-dose outliers (c-statistic = 0.79). Approximately 1 in 10 study patients with RA was identified as a

  9. Manufacturing economics of plant-made biologics: case studies in therapeutic and industrial enzymes.

    Science.gov (United States)

    Tusé, Daniel; Tu, Tiffany; McDonald, Karen A

    2014-01-01

    Production of recombinant biologics in plants has received considerable attention as an alternative platform to traditional microbial and animal cell culture. Industrially relevant features of plant systems include proper eukaryotic protein processing, inherent safety due to lack of adventitious agents, more facile scalability, faster production (transient systems), and potentially lower costs. Lower manufacturing cost has been widely claimed as an intuitive feature of the platform by the plant-made biologics community, even though cost information resides within a few private companies and studies accurately documenting such an advantage have been lacking. We present two technoeconomic case studies representing plant-made enzymes for diverse applications: human butyrylcholinesterase produced indoors for use as a medical countermeasure and cellulases produced in the field for the conversion of cellulosic biomass into ethanol as a fuel extender. Production economics were modeled based on results reported with the latest-generation expression technologies on Nicotiana host plants. We evaluated process unit operations and calculated bulk active and per-dose or per-unit costs using SuperPro Designer modeling software. Our analyses indicate that substantial cost advantages over alternative platforms can be achieved with plant systems, but these advantages are molecule/product-specific and depend on the relative cost-efficiencies of alternative sources of the same product.

  10. Manufacturing Economics of Plant-Made Biologics: Case Studies in Therapeutic and Industrial Enzymes

    Directory of Open Access Journals (Sweden)

    Daniel Tusé

    2014-01-01

    Full Text Available Production of recombinant biologics in plants has received considerable attention as an alternative platform to traditional microbial and animal cell culture. Industrially relevant features of plant systems include proper eukaryotic protein processing, inherent safety due to lack of adventitious agents, more facile scalability, faster production (transient systems, and potentially lower costs. Lower manufacturing cost has been widely claimed as an intuitive feature of the platform by the plant-made biologics community, even though cost information resides within a few private companies and studies accurately documenting such an advantage have been lacking. We present two technoeconomic case studies representing plant-made enzymes for diverse applications: human butyrylcholinesterase produced indoors for use as a medical countermeasure and cellulases produced in the field for the conversion of cellulosic biomass into ethanol as a fuel extender. Production economics were modeled based on results reported with the latest-generation expression technologies on Nicotiana host plants. We evaluated process unit operations and calculated bulk active and per-dose or per-unit costs using SuperPro Designer modeling software. Our analyses indicate that substantial cost advantages over alternative platforms can be achieved with plant systems, but these advantages are molecule/product-specific and depend on the relative cost-efficiencies of alternative sources of the same product.

  11. 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…

  12. Biological life support systems for a Mars mission planetary base: Problems and prospects

    Science.gov (United States)

    Tikhomirov, A. A.; Ushakova, S. A.; Kovaleva, N. P.; Lamaze, B.; Lobo, M.; Lasseur, Ch.

    The study develops approaches to designing biological life support systems for the Mars mission - for the flight conditions and for a planetary base - using experience of the Institute of Biophysics of the Siberian Branch of the Russian Academy of Sciences (IBP SB RAS) with the Bios-3 system and ESA's experience with the MELISSA program. Variants of a BLSS based on using Chlorella and/or Spirulina and higher plants for the flight period of the Mars mission are analyzed. It is proposed constructing a BLSS with a closed-loop material cycle for gas and water and for part of human waste. A higher-plant-based BLSS with the mass exchange loop closed to various degrees is proposed for a Mars planetary base. Various versions of BLSS configuration and degree of closure of mass exchange are considered, depending on the duration of the Mars mission, the diet of the crew, and some other conditions. Special consideration is given to problems of reliability and sustainability of material cycling in BLSS, which are related to production of additional oxygen inside the system. Technologies of constructing BLSS of various configurations are proposed and substantiated. Reasons are given for using physicochemical methods in BLSS as secondary tools both during the flight and the stay on Mars.

  13. Fibrin Gels Exhibit Improved Biological, Structural, and Mechanical Properties Compared with Collagen Gels in Cell-Based Tendon Tissue-Engineered Constructs

    Science.gov (United States)

    Dyment, Nathaniel A.; Lu, Yinhui; Rao, Marepalli; Shearn, Jason T.; Rowe, David W.; Kadler, Karl E.; Butler, David L.

    2015-01-01

    The prevalence of tendon and ligament injuries and inadequacies of current treatments is driving the need for alternative strategies such as tissue engineering. Fibrin and collagen biopolymers have been popular materials for creating tissue-engineered constructs (TECs), as they exhibit advantages of biocompatibility and flexibility in construct design. Unfortunately, a few studies have directly compared these materials for tendon and ligament applications. Therefore, this study aims at determining how collagen versus fibrin hydrogels affect the biological, structural, and mechanical properties of TECs during formation in vitro. Our findings show that tendon and ligament progenitor cells seeded in fibrin constructs exhibit improved tenogenic gene expression patterns compared with their collagen-based counterparts for approximately 14 days in culture. Fibrin-based constructs also exhibit improved cell-derived collagen alignment, increased linear modulus (2.2-fold greater) compared with collagen-based constructs. Cyclic tensile loading, which promotes the maturation of tendon constructs in a previous work, exhibits a material-dependent effect in this study. Fibrin constructs show trending reductions in mechanical, biological, and structural properties, whereas collagen constructs only show improved tenogenic expression in the presence of mechanical stimulation. These findings highlight that components of the mechanical stimulus (e.g., strain amplitude or time of initiation) need to be tailored to the material and cell type. Given the improvements in tenogenic expression, extracellular matrix organization, and material properties during static culture, in vitro findings presented here suggest that fibrin-based constructs may be a more suitable alternative to collagen-based constructs for tissue-engineered tendon/ligament repair. PMID:25266738

  14. Studies of the electronic structure and biological activity of chosen 1,4-benzodiazepines by {sup 35}Cl NQR spectroscopy and DFT calculations

    Energy Technology Data Exchange (ETDEWEB)

    Bronisz, K. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland); Ostafin, M. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland)], E-mail: ostifnqr@amu.edu.pl; Poleshchuk, O. Kh. [Department of Chemistry, Tomsk Pedagogical University, Komsomolskii 75, 634041 Tomsk (Russian Federation); Mielcarek, J. [Faculty of Pharmacy, University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan (Poland); Nogaj, B. [Department of Physics, Adam Mickiewicz University, Umultowska 85, 61-614 Poznan (Poland)

    2006-11-08

    Selected derivatives of 1,4-benzodiazepine: lorazepam, lormetazepam, oxazepam and temazepam, used as active substances in anxiolytic drugs, have been studied by {sup 35}Cl NQR method in order to find the correlation between electronic structure and biological activity. The {sup 35}Cl NQR resonance frequencies ({nu} {sub Q}) measured at 77 K have been correlated with the following parameters characterising their biological activity: biological half-life period (t {sub 0.5}), affinity to benzodiazepine receptor (IC{sub 50}) and mean dose equivalent. The results of experimental study of some benzodiazepine derivatives by nuclear quadrupole resonance of {sup 35}Cl nuclei are compared with theoretical results based on DFT calculations which were carried out by means of Gaussian'98 W software.

  15. Models for synthetic biology.

    Science.gov (United States)

    Kaznessis, Yiannis N

    2007-11-06

    Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

  16. Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Papini, Marta; Nookaew, Intawat; Uhlén, Mathias

    2012-01-01

    , but is regulated by a decrease in oxygen levels. Even though S. stipitis has been extensively studied due to its potential application in pentoses fermentation, a limited amount of information is available about its metabolism during aerobic growth on glucose. Here, we provide a systems biology based comparison....... To describe gene expression levels under the two conditions, we performed RNA sequencing and the results were used to quantify transcript abundances of genes from the central carbon metabolism and compared with those obtained with S. cerevisiae. Interestingly, genes involved in central pathways showed...

  17. 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.

  18. Prior knowledge-based approach for associating contaminants with biological effects: A case study in the St. Croix River basin, MN, WI, USA

    Science.gov (United States)

    Schroeder, Anthony L.; Martinovic-Weigelt, Dalma; Ankley, Gerald T.; Lee, Kathy E.; Garcia-Reyero, Natalia; Perkins, Edward J.; Schoenfuss, Heiko L.; Villeneuve, Daniel L.

    2017-01-01

    Evaluating potential adverse effects of complex chemical mixtures in the environment is challenging. One way to address that challenge is through more integrated analysis of chemical monitoring and biological effects data. In the present study, water samples from five locations near two municipal wastewater treatment plants in the St. Croix River basin, on the border of MN and WI, USA, were analyzed for 127 organic contaminants. Known chemical-gene interactions were used to develop site-specific knowledge assembly models (KAMs) and formulate hypotheses concerning possible biological effects associated with chemicals detected in water samples from each location. Additionally, hepatic gene expression data were collected for fathead minnows (Pimephales promelas) exposed in situ, for 12 d, at each location. Expression data from oligonucleotide microarrays were analyzed to identify functional annotation terms enriched among the differentially-expressed probes. The general nature of many of the terms made hypothesis formulation on the basis of the transcriptome-level response alone difficult. However, integrated analysis of the transcriptome data in the context of the site-specific KAMs allowed for evaluation of the likelihood of specific chemicals contributing to observed biological responses. Thirteen chemicals (atrazine, carbamazepine, metformin, thiabendazole, diazepam, cholesterol, p-cresol, phenytoin, omeprazole, ethyromycin, 17β-estradiol, cimetidine, and estrone), for which there was statistically significant concordance between occurrence at a site and expected biological response as represented in the KAM, were identified. While not definitive, the approach provides a line of evidence for evaluating potential cause-effect relationships between components of a complex mixture of contaminants and biological effects data, which can inform subsequent monitoring and investigation.

  19. The Relationships between Epistemic Beliefs in Biology and Approaches to Learning Biology among Biology-Major University Students in Taiwan

    Science.gov (United States)

    Lin, Yi-Chun; Liang, Jyh-Chong; Tsai, Chin-Chung

    2012-01-01

    The aim of this study was to investigate the relationships between students' epistemic beliefs in biology and their approaches to learning biology. To this end, two instruments, the epistemic beliefs in biology and the approaches to learning biology surveys, were developed and administered to 520 university biology students, respectively. By and…

  20. Approaches to chemical synthetic biology.

    Science.gov (United States)

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

    2012-07-16

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

  1. WebBio, a web-based management and analysis system for patient data of biological products in hospital.

    Science.gov (United States)

    Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

    2011-08-01

    We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

  2. Systems biology of bacterial nitrogen fixation: High-throughput technology and its integrative description with constraint-based modeling

    Directory of Open Access Journals (Sweden)

    Resendis-Antonio Osbaldo

    2011-07-01

    Full Text Available Abstract Background Bacterial nitrogen fixation is the biological process by which atmospheric nitrogen is uptaken by bacteroids located in plant root nodules and converted into ammonium through the enzymatic activity of nitrogenase. In practice, this biological process serves as a natural form of fertilization and its optimization has significant implications in sustainable agricultural programs. Currently, the advent of high-throughput technology supplies with valuable data that contribute to understanding the metabolic activity during bacterial nitrogen fixation. This undertaking is not trivial, and the development of computational methods useful in accomplishing an integrative, descriptive and predictive framework is a crucial issue to decoding the principles that regulated the metabolic activity of this biological process. Results In this work we present a systems biology description of the metabolic activity in bacterial nitrogen fixation. This was accomplished by an integrative analysis involving high-throughput data and constraint-based modeling to characterize the metabolic activity in Rhizobium etli bacteroids located at the root nodules of Phaseolus vulgaris (bean plant. Proteome and transcriptome technologies led us to identify 415 proteins and 689 up-regulated genes that orchestrate this biological process. Taking into account these data, we: 1 extended the metabolic reconstruction reported for R. etli; 2 simulated the metabolic activity during symbiotic nitrogen fixation; and 3 evaluated the in silico results in terms of bacteria phenotype. Notably, constraint-based modeling simulated nitrogen fixation activity in such a way that 76.83% of the enzymes and 69.48% of the genes were experimentally justified. Finally, to further assess the predictive scope of the computational model, gene deletion analysis was carried out on nine metabolic enzymes. Our model concluded that an altered metabolic activity on these enzymes induced

  3. OWL Reasoning Framework over Big Biological Knowledge Network

    Science.gov (United States)

    Chen, Huajun; Chen, Xi; Gu, Peiqin; Wu, Zhaohui; Yu, Tong

    2014-01-01

    Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity. PMID:24877076

  4. Spectroscopic study of biologically active glasses

    Science.gov (United States)

    Szumera, M.; Wacławska, I.; Mozgawa, W.; Sitarz, M.

    2005-06-01

    It is known that the chemical activity phenomenon is characteristic for some inorganic glasses and they are able to participate in biological processes of living organisms (plants, animals and human bodies). An example here is the selective removal of silicate-phosphate glass components under the influence of biological solutions, which has been applied in designing glasses acting as ecological fertilizers of controlled release rate of the nutrients for plants. The structure of model silicate-phosphate glasses containing the different amounts of the glass network formers, i.e. Ca 2+ and Mg 2+, as a binding components were studied. These elements besides other are indispensable of the normal growth of plants. In order to establish the function and position occupied by the particular components in the glass structure, the glasses were examined by FTIR spectroscopy (with spectra decomposition) and XRD methods. It has been found that the increasing amount of MgO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes systematically from a structure of the cristobalite type to a structure corresponding to forsterite type. Whilst the increasing content of CaO in the structure of silicate-phosphate glasses causes the formation of domains the structure of which changes from a structure typical for cristobalite through one similar to the structure of calcium orthophosphate, to a structure corresponding to calcium silicates. The changing character of domains structure is the reason of different chemical activity of glasses.

  5. 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.

  6. Quantum biological information theory

    CERN Document Server

    Djordjevic, Ivan B

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Nora A. Gutierrez Najera

    2017-05-01

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

  8. Analisis Aplikasi Konsep Gaya dalam Fisika yang Berkaitan dengan Bidang Biologi

    Directory of Open Access Journals (Sweden)

    Toto Toto

    2017-06-01

    Full Text Available Abstract In general, students of Biology faculty study program of Universitas Galuh Ciamis viewed physics as a difficult subject (based on interview result of writer with some students. This statement is reinforced by the acquisition of less satisfactory physics courses. They are less interested in the subject of physics with a variety of reasons including counting material that requires them to memorize many formulas and theories. In the course of physics in the biology program should be equipped application of concepts and principles of physics in the field of biology. It is very important to facilitate students in mastering and enjoying physics courses. In this study, documentation study of biology books in the subjects of General Biology in 1st semester. Based on the analysis there are application of the concept of style in the subject material of General Biology namely: capillarity style on xylem and phloem; Force on muscle tissue; And food peristaltic style. The results of this study are useful as a basis for the preparation of physics-oriented teaching materials of biological science, so that biology students are expected to be interested in physics. As a recommendation that analysis of the application of concepts and principles of physics in biology must be done in a continuous manner. Keywords: Style concept application. Abstrak Pada umumnya  mahasiswa prodi pendidikan biologi FKIP Universitas Galuh Ciamis  memandang fisika sebagai mata kuliah yang sulit (berdasarkan hasil wawancara penulis dengan beberapa mahasiswa. Pernyataan ini diperkuat  dengan perolehan nilai mata kuliah fisika yang kurang memuaskan. Mereka kurang tertarik pada mata kuliah fisika dengan berbagai alasan diantaranya banyak materi hitungan yang mengharuskan mereka menghapal banyak rumus dan teori. Dalam perkuliahan fisika pada prodi biologi seharusnya dilengkapi aplikasi konsep dan prinsip-prinsip fisika dalam bidang biologi. Hal tersebut sangat penting untuk

  9. Proteomics in studying cancer stem cell biology.

    Science.gov (United States)

    Kranenburg, Onno; Emmink, Benjamin L; Knol, Jaco; van Houdt, Winan J; Rinkes, Inne H M Borel; Jimenez, Connie R

    2012-06-01

    Normal multipotent tissue stem cells (SCs) are the driving force behind tissue turnover and repair. The cancer stem cell theory holds that tumors also contain stem-like cells that drive tumor growth and metastasis formation. However, very little is known about the regulation of SC maintenance pathways in cancer and how these are affected by cancer-specific genetic alterations and by treatment. Proteomics is emerging as a powerful tool to identify the signaling complexes and pathways that control multi- and pluri-potency and SC differentiation. Here, the authors review the novel insights that these studies have provided and present a comprehensive strategy for the use of proteomics in studying cancer SC biology.

  10. Treating moderate to severe psoriasis - best use of biologics.

    LENUS (Irish Health Repository)

    Lynch, Maeve

    2014-02-01

    This review focuses on the efficacy, safety and best use of biologic agents in moderate-to-severe psoriasis. Recommendations from two recent guidelines are summarised. The NICE Guidelines 2012 provide recommendations on best practice for prescribing biologics. The German S3 Guidelines are based on a systematic review of published studies and report the efficacy of biologics and guidelines for treatment. Data on the safety of biologics are available for up to 5 years in psoriasis and are on the whole reassuring. Registry data is evolving and will provide data on safety to help inform long-term monitoring of patients with psoriasis on biologics agents. New anti-interleukin-17 (IL17) and anti-IL17RA biologics are in Phase 3 clinical trials and may prove to be more effective than existing biologics.

  11. A case study of technology-enhanced active learning in introductory cellular biology

    Science.gov (United States)

    Chacon Diaz, Lucia Bernardette

    Science teaching and learning in higher education has been evolving over the years to encourage student retention in STEM fields and reduce student attrition. As novel pedagogical practices emerge in the college science classroom, research on the effectiveness of such approaches must be undertaken. The following research applied a case study research design in order to evaluate the experiences of college students in a TEAL classroom. This case study was conducted during the 2017 Summer Cellular and Organismal Biology course at a four-year Hispanic Serving Institution located in the Southwest region of the United States. The main components evaluated were students' exam performance, self-efficacy beliefs, and behaviors and interactions in the Technology-Enhanced Active Learning (TEAL) classroom. The findings suggest that students enrolled in a TEAL classroom are equally capable of answering high and low order thinking questions. Additionally, students are equally confident in answering high and low order thinking items related to cellular biology. In the TEAL classroom, student-student interactions are encouraged and collaborative behaviors are exhibited. Gender and ethnicity do not influence self-efficacy beliefs in students in the TEAL room, and the overall class average of self-efficacy beliefs tended to be higher compared to exam performance. Based on the findings of this case study, TEAL classrooms are greatly encouraged in science higher education in order to facilitate learning and class engagement for all students. Providing students with the opportunity to expand their academic talents in the science classroom accomplishes a crucial goal in STEM higher education.

  12. 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.

  13. Studies of the reproductive biology of deep-sea megabenthos IV. The echinoderm species Peniagone azorica and P. diaphana (elasipodida: holothuroidea)

    International Nuclear Information System (INIS)

    Tyler, P.A.; Muirhead, A.

    1984-01-01

    This report is the fourth in a series from a study of the reproductive processes in deep-sea benthic megainvertebrates. The concept of this study is based on the premise that reproduction is the most sensitive physiological process of marine invertebrates and will therefore be the first to be affected by any undue stress. Benthic megainvertebrates were selected as these are readily visible in both deep-sea photographs and television. However studies of sublethal levels of contaminants in shallow water marine invertebrates have shown that when these organisms are exposed to stress, their general biology, e.g., respiration, growth, etc. may not be affected, whilst the gametogenic biology may be totally disrupted. Thus the present study of the gametogenic biology of deep-sea megainvertebrates provides a benchmark study against which 'post-disposal' specimens could be compared. This would provide a sensitive indicator of radioactive release that may not be determined from other studies of adult ecology. If the gametogenic process is not affected by the uptake of radionuclides it is possible that any dispersal of spawned eggs or larvae may transfer these radionuclides into another part of the deep-sea food chain or deep-sea environment. (author)

  14. Proteomics Improves the New Understanding of Honeybee Biology.

    Science.gov (United States)

    Hora, Zewdu Ararso; Altaye, Solomon Zewdu; Wubie, Abebe Jemberie; Li, Jianke

    2018-04-11

    The honeybee is one of the most valuable insect pollinators, playing a key role in pollinating wild vegetation and agricultural crops, with significant contribution to the world's food production. Although honeybees have long been studied as model for social evolution, honeybee biology at the molecular level remained poorly understood until the year 2006. With the availability of the honeybee genome sequence and technological advancements in protein separation, mass spectrometry, and bioinformatics, aspects of honeybee biology such as developmental biology, physiology, behavior, neurobiology, and immunology have been explored to new depths at molecular and biochemical levels. This Review comprehensively summarizes the recent progress in honeybee biology using proteomics to study developmental physiology, task transition, and physiological changes in some of the organs, tissues, and cells based on achievements from the authors' laboratory in this field. The research advances of honeybee proteomics provide new insights for understanding of honeybee biology and future research directions.

  15. An overview of surface radiance and biology studies in FIFE

    Science.gov (United States)

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

    1992-01-01

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

  16. An overview of surface radiance and biology studies in FIFE

    Science.gov (United States)

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

    1992-11-01

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

  17. Biological mineralization of iron: Studies using Moesbauer spectroscopy and complementary techniques

    International Nuclear Information System (INIS)

    Webb, J.; Kim, K.S.; Tran, K.C.; Pierre, T.G.S.

    1988-01-01

    Biological deposition of solid Fe-containing phases can be studied using 57 Fe Moessbauer spectroscopy. Other techniques are needed in order to understand this complex process. These include proton-induced X-ray and γ-ray emission (PIXE/PIGME), electron microscopy, electron and X-ray diffraction, infrared spectroscopy and chemical characterization of organic components. This paper reviews and evaluates the application of these techniques to biological mineralization of Fe, particularly that occurring in the radula teeth of the marine molluscs, chitons and limpets. (orig.)

  18. Biological Control of Bacterial Wilt in South East Asia

    OpenAIRE

    Arwiyanto, Triwidodo

    2014-01-01

    Bacterial wilt disease caused by Ralstonia solanacearum destroys many crops of different plant families in South East Asia despite many researches about the disease, and the availability of developed control method in other parts of the world. There is no chemical available for the bacterial wilt pathogen and biological control is then chosen as an alternative to save the crops. Most of the biological control studies were based on antagonism between biological control agent and the pathogen. ...

  19. Applications of Microfluidics in Quantitative Biology.

    Science.gov (United States)

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

    2018-05-01

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

  20. 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.

  1. e-Biologics: Fabrication of Sustainable Electronics with "Green" Biological Materials.

    Science.gov (United States)

    Lovley, Derek R

    2017-06-27

    The growing ubiquity of electronic devices is increasingly consuming substantial energy and rare resources for materials fabrication, as well as creating expansive volumes of toxic waste. This is not sustainable. Electronic biological materials (e-biologics) that are produced with microbes, or designed with microbial components as the guide for synthesis, are a potential green solution. Some e-biologics can be fabricated from renewable feedstocks with relatively low energy inputs, often while avoiding the harsh chemicals used for synthesizing more traditional electronic materials. Several are completely free of toxic components, can be readily recycled, and offer unique features not found in traditional electronic materials in terms of size, performance, and opportunities for diverse functionalization. An appropriate investment in the concerted multidisciplinary collaborative research required to identify and characterize e-biologics and to engineer materials and devices based on e-biologics could be rewarded with a new "green age" of sustainable electronic materials and devices. Copyright © 2017 Lovley.

  2. Investigating Lebanese Grade Seven Biology Teachers Mathematical Knowledge and Skills: A Case Study

    Science.gov (United States)

    Raad, Nawal Abou; Chatila, Hanadi

    2016-01-01

    This paper investigates Lebanese grade 7 biology teachers' mathematical knowledge and skills, by exploring how they explain a visual representation in an activity depending on the mathematical concept "Function". Twenty Lebanese in-service biology teachers participated in the study, and were interviewed about their explanation for the…

  3. World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia, Part 2

    DEFF Research Database (Denmark)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas

    2013-01-01

    These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry (WFSBP) guidelines for biological treatment of schizophrenia published in 2006. For this 2012 revision, all available publications pertaining to the biological treatment of schizoph...

  4. World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia, part 1

    DEFF Research Database (Denmark)

    Hasan, Alkomiet; Falkai, Peter; Wobrock, Thomas

    2012-01-01

    These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry Guidelines for Biological Treatment of Schizophrenia published in 2005. For this 2012 revision, all available publications pertaining to the biological treatment of schizophrenia we...

  5. [Undergraduate and postgraduate studies in the biological sciences in Chile (1985)].

    Science.gov (United States)

    Niemeyer, H

    1986-01-01

    A study group of scientists was convened by the Sociedad de Biología de Chile (Biological Society of Chile) and the Regional Program for Graduate Training in Biological Sciences, PNUD-Unesco, RLA 78/024, to assess undergraduate and graduate studies in life sciences in Chile. The group presented this report at the 28th Annual Meeting of the Society. Discussion centered on the features that should characterize the studies leading to the academic degrees of Licenciado (Licenciate), Magíster (Master) and Doctor (Ph. D) in Sciences, and also on the qualifications that the universities should satisfy in order to grant them. After analyzing the present situation of undergraduate and graduate studies in Biological Sciences in Chilean universities, the group made the following main suggestions: 1. It is recommended that Chilean universities agree on a 4-year plan for the Licenciado degree, without the requirement of a thesis. The importance of providing the students with good laboratory exercises and field experience and with the opportunity to perform short research projects is stressed. In addition, a sound theoretical training on mathematics, physics and chemistry in the education of a modern Biologist is important. Licenciate studies ought to be the basis for professional careers and the universities should offer to the Licenciados free access to their professional schools. 2. It is considered appropriate for Chile and its universities to develop graduate programs in those disciplines that have reached a level of excellence. To accomplish this aim, adequate finance of the universities is necessary to permit them to provide the essential facilities for doing research, and to create a wide system of fellowships for graduate students. Direct government support for research and graduate student fellowships is requested. 3. Research experience of the kind needed for the preparation of a doctoral thesis is recommended as the academic level appropriate for those engaged in

  6. Novel nuclear magnetic resonance techniques for studying biological molecules

    Energy Technology Data Exchange (ETDEWEB)

    Laws, David Douglas [Univ. of California, Berkeley, CA (United States)

    2000-06-01

    Over the fifty-five year history of Nuclear Magnetic Resonance (NMR), considerable progress has been made in the development of techniques for studying the structure, function, and dynamics of biological molecules. The majority of this research has involved the development of multi-dimensional NMR experiments for studying molecules in solution, although in recent years a number of groups have begun to explore NMR methods for studying biological systems in the solid-state. Despite this new effort, a need still exists for the development of techniques that improve sensitivity, maximize information, and take advantage of all the NMR interactions available in biological molecules. In this dissertation, a variety of novel NMR techniques for studying biomolecules are discussed. A method for determining backbone (Φ/Ψ) dihedral angles by comparing experimentally determined 13Ca, chemical-shift anisotropies with theoretical calculations is presented, along with a brief description of the theory behind chemical-shift computation in proteins and peptides. The utility of the Spin-Polarization Induced Nuclear Overhauser Effect (SPINOE) to selectively enhance NMR signals in solution is examined in a variety of systems, as are methods for extracting structural information from cross-relaxation rates that can be measured in SPINOE experiments. Techniques for the production of supercritical and liquid laser-polarized xenon are discussed, as well as the prospects for using optically pumped xenon as a polarizing solvent. In addition, a detailed study of the structure of PrP 89-143 is presented. PrP 89-143 is a 54 residue fragment of the prion proteins which, upon mutation and aggregation, can induce prion diseases in transgenic mice. Whereas the structure of the wild-type PrP 89-143 is a generally unstructured mixture of α-helical and β-sheet conformers in the solid state, the aggregates formed from the PrP 89-143 mutants appear to be mostly β-sheet.

  7. Subject and authorship of records related to the Organization for Tropical Studies (OTS in BINABITROP, a comprehensive database about Costa Rican biology

    Directory of Open Access Journals (Sweden)

    Julián Monge-Nájera

    2013-06-01

    Full Text Available BINABITROP is a bibliographical database of more than 38 000 records about the ecosystems and organisms of Costa Rica. In contrast with commercial databases, such as Web of Knowledge and Scopus, which exclude most of the scientific journals published in tropical countries, BINABITROP is a comprehensive record of knowledge on the tropical ecosystems and organisms of Costa Rica. We analyzed its contents in three sites (La Selva, Palo Verde and Las Cruces and recorded scientific field, taxonomic group and authorship. We found that most records dealt with ecology and systematics, and that most authors published only one article in the study period (1963-2011. Most research was published in four journals: Biotropica, Revista de Biología Tropical/ International Journal of Tropical Biology and Conservation, Zootaxa and Brenesia. This may be the first study of a such a comprehensive database for any case of tropical biology literature.BINABITROP es una base de datos bibliográfica con más de 38 000 registros sobre los ecosistemas y organismos de Costa Rica. En contraste con bases de datos comerciales como Web of Knowledge y Scopus, que excluyen a la mayoría de las revistas científicas publicadas en los países tropicales, BINABITROP registra casi por completo la literatura biológica sobre Costa Rica. Analizamos los registros de La Selva, Palo Verde y Las Cruces. Hallamos que la mayoría de los registros corresponden a estudios sobre ecología y sistemática; que la mayoría de los autores sólo registraron un artículo en el período de estudio (1963-2011 y que la mayoría de la investigación formalmente publicada apareció en cuatro revistas: Biotropica, Revista de Biología Tropical/International Journal of Tropical Biology, Zootaxa y Brenesia. Este parece ser el primer estudio de una base de datos integral sobre literatura de biología tropical.

  8. Structural Biology Fact Sheet

    Science.gov (United States)

    ... NIGMS NIGMS Home > Science Education > Structural Biology Structural Biology Tagline (Optional) Middle/Main Content Area PDF Version (688 KB) Other Fact Sheets What is structural biology? Structural biology is the study of how biological ...

  9. Biological trade and markets.

    Science.gov (United States)

    Hammerstein, Peter; Noë, Ronald

    2016-02-05

    Cooperation between organisms can often be understood, like trade between merchants, as a mutually beneficial exchange of services, resources or other 'commodities'. Mutual benefits alone, however, are not sufficient to explain the evolution of trade-based cooperation. First, organisms may reject a particular trade if another partner offers a better deal. Second, while human trade often entails binding contracts, non-human trade requires unwritten 'terms of contract' that 'self-stabilize' trade and prevent cheating even if all traders strive to maximize fitness. Whenever trading partners can be chosen, market-like situations arise in nature that biologists studying cooperation need to account for. The mere possibility of exerting partner choice stabilizes many forms of otherwise cheatable trade, induces competition, facilitates the evolution of specialization and often leads to intricate forms of cooperation. We discuss selected examples to illustrate these general points and review basic conceptual approaches that are important in the theory of biological trade and markets. Comparing these approaches with theory in economics, it turns out that conventional models-often called 'Walrasian' markets-are of limited relevance to biology. In contrast, early approaches to trade and markets, as found in the works of Ricardo and Cournot, contain elements of thought that have inspired useful models in biology. For example, the concept of comparative advantage has biological applications in trade, signalling and ecological competition. We also see convergence between post-Walrasian economics and biological markets. For example, both economists and biologists are studying 'principal-agent' problems with principals offering jobs to agents without being sure that the agents will do a proper job. Finally, we show that mating markets have many peculiarities not shared with conventional economic markets. Ideas from economics are useful for biologists studying cooperation but need

  10. Epistemological Syncretism in a Biology Classroom: A Case Study

    Science.gov (United States)

    Bennett, William D.; Park, Soonhye

    2011-01-01

    In teaching science, the beliefs of teachers may come into conflict and inhibit the implementation of reformed teaching practice. An experienced biology teacher, Mr. Hobbs, was found to have two different sets of epistemological beliefs while his classroom practice was predominantly teacher-centered. A case study was then performed in order to…

  11. The effect of abstract versus concrete framing on judgments of biological and psychological bases of behavior.

    Science.gov (United States)

    Kim, Nancy S; Johnson, Samuel G B; Ahn, Woo-Kyoung; Knobe, Joshua

    2017-01-01

    Human behavior is frequently described both in abstract, general terms and in concrete, specific terms. We asked whether these two ways of framing equivalent behaviors shift the inferences people make about the biological and psychological bases of those behaviors. In five experiments, we manipulated whether behaviors are presented concretely (i.e. with reference to a specific person, instantiated in the particular context of that person's life) or abstractly (i.e. with reference to a category of people or behaviors across generalized contexts). People judged concretely framed behaviors to be less biologically based and, on some dimensions, more psychologically based than the same behaviors framed in the abstract. These findings held true for both mental disorders (Experiments 1 and 2) and everyday behaviors (Experiments 4 and 5), and yielded downstream consequences for the perceived efficacy of disorder treatments (Experiment 3). Implications for science educators, students of science, and members of the lay public are discussed.

  12. Treatability study of pesticide-based industrial wastewater.

    Science.gov (United States)

    Shah, Kinnari; Chauhan, L I; Galgale, A D

    2012-10-01

    This paper finds out appropriate treatment methods for wastewater of an Organophosphorus viz, chloropyrifos pesticide manufacturing industry. The characterization of wastewater generated during trial production of chloropyrifos was carried out. Based on the characterization of wastewater, various treatability studies were conducted. The most desirable results were obtained with treatment scheme employing acidification, chlorination with NaOCl, suspended growth biological treatment, chemical precipitation for phosphorous removal and activated carbon treatment. Acidification of wastewater helps in by-product recovery as well as reduction in COD upto 36.26%. Chlorination followed by biological treatment was found to be effective to reduce the COD level by 62.06%. To comply with permissible limits prescribed by Effluent Channel Project Ltd.(ECPL)* and Gujarat Pollution Control Board (GPCB) for discharge of industrial effluent into channel, further treatment in the form of chemical precipitation (for phosphorous removal) and granular activated carbon is suggested.

  13. Biological and ecological responses to carbon-based nanomaterials

    Science.gov (United States)

    Ratnikova, Tatsiana A.

    This dissertation examines the biological and ecological responses to carbon nanoparticles, a major class of nanomaterials which have been mass produced and extensively studied for their rich physical properties and commercial values. Chapter I of this dissertation offers a comprehensive review on the structures, properties, applications, and implications of carbon nanomaterials, especially related to the perspectives of biological and ecosystems. Given that there are many types of carbon nanomaterials available, this chapter is focused on three major types of carbon-based nanomaterials only, namely, fullerenes, single walled and multi-walled carbon nanotubes. On the whole organism level, specifically, Chapter II presents a first study on the fate of fullerenes and multiwalled carbon nanotubes in rice plants, which was facilitated by the self assembly of these nanomaterials with NOM. The aspects of fullerene uptake, translocation, biodistribution, and generational transfer in the plants were examined and quantified using bright field and electron microscopy, FT-Raman, and FTIR spectroscopy. The uptake and transport of fullerene in the plant vascular system were attributed to water transpiration, convection, capillary force, and the fullerene concentration gradient from the roots to the leaves of the plants. On the cellular level, Chapter III documents the differential uptake of hydrophilic C60(OH)20 vs. amphiphilic C70-NOM complex in Allium cepa plant cells and HT-29 colon carcinoma cells. This study was conducted using a plant cell viability assay, and complemented by bright field, fluorescence and electron microscopy imaging. In particular, C60(OH)20 and C70-NOM showed contrasting uptake in both the plant and mammalian cells, due to their significant differences in physicochemistry and the presence of an extra hydrophobic plant cell wall in the plant cells. Consequently, C60(OH)20 was found to induce toxicity in Allium cepa cells but not in HT-29 cells, while C70

  14. Physical and biological predictors of radiation-induced whole lung injury: early results of a prospective study

    International Nuclear Information System (INIS)

    Marks, L.B.; Munley, M.; Bentel, G.; Hollis, D.; Zhou, S.; Jirtle, R.; Kong, F.M.; Scarfone, C.; Antoine, P.; Chew, M.; Tapson, V.; Spencer, D.; Jaszczak, R.; Coleman, E.; Anscher, M.

    1996-01-01

    Purpose: To develop methods of predicting the pulmonary consequences of thoracic irradiation (RT) by prospectively studying changes in pulmonary function following RT. Methods: 105 patients receiving incidental partial lung irradiation during treatment of tumors in/around the thorax (lung-70, breast-18, lymphoma-4, misc-3) had whole lung function assessed (symptoms and pulmonary function tests [PFTs: FEV1-forced expiratory volume 1 sec; DLCO-diffusion capacity]) before and repeatedly 6-48 months following RT. All had computed tomography-based 3-dimensional (3D) dose calculations with lung density heterogeneity corrections for dose-volume histogram (DVH) and NTCP (normal tissue complication probability) calculations. Functional DVHs (DVfH) based on SPECT (single photon emission computed tomography) lung perfusion scans, and serial transforming growth factor-beta (TGF-β) levels were available in 50 and 30 patients, respectively. The incidence and severity of changes in whole lung function were correlated with clinical, physical and biological factors outlined in the results. Exploratory statistical analyses were preformed using chi-square, logistic regression, and multiple linear regression. Mean pt age=57, range 21-87; sex: 63 F, 42 M; 29 had chemotherapy (CT) before/with RT; Follow-up 6-48 months (mean 15, median 12). Results RT-induced symptoms developed in 26 patients (7-grade I-no intervention; 16 grade II-steroids; 3 grade III-oxygen and steroids). A mixed model based on pre-RT DLCO and CT-based NTCP was strongly predictive for the development of symptoms (p 30 Gy. In patients with 'good' pre-RT PFTs, there may be a relationship between the % reduction in PFT and % lung volume receiving >30 Gy (figure). Conclusion: Whole lung injury (symptoms or PFT changes) appears to be related to a variety of physical, biological and clinical factors. The data suggest that no one variable is likely to be an adequate predictor and that multi-faceted predictive models will be

  15. 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.

  16. Validation and selection of ODE based systems biology models: how to arrive at more reliable decisions.

    Science.gov (United States)

    Hasdemir, Dicle; Hoefsloot, Huub C J; Smilde, Age K

    2015-07-08

    Most ordinary differential equation (ODE) based modeling studies in systems biology involve a hold-out validation step for model validation. In this framework a pre-determined part of the data is used as validation data and, therefore it is not used for estimating the parameters of the model. The model is assumed to be validated if the model predictions on the validation dataset show good agreement with the data. Model selection between alternative model structures can also be performed in the same setting, based on the predictive power of the model structures on the validation dataset. However, drawbacks associated with this approach are usually under-estimated. We have carried out simulations by using a recently published High Osmolarity Glycerol (HOG) pathway from S.cerevisiae to demonstrate these drawbacks. We have shown that it is very important how the data is partitioned and which part of the data is used for validation purposes. The hold-out validation strategy leads to biased conclusions, since it can lead to different validation and selection decisions when different partitioning schemes are used. Furthermore, finding sensible partitioning schemes that would lead to reliable decisions are heavily dependent on the biology and unknown model parameters which turns the problem into a paradox. This brings the need for alternative validation approaches that offer flexible partitioning of the data. For this purpose, we have introduced a stratified random cross-validation (SRCV) approach that successfully overcomes these limitations. SRCV leads to more stable decisions for both validation and selection which are not biased by underlying biological phenomena. Furthermore, it is less dependent on the specific noise realization in the data. Therefore, it proves to be a promising alternative to the standard hold-out validation strategy.

  17. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  18. Exploring Pedagogical Content Knowledge of Biology Graduate Teaching Assistants through Their Participation in Lesson Study

    Science.gov (United States)

    Lampley, Sandra A.; Gardner, Grant E.; Barlow, Angela T.

    2018-01-01

    Graduate teaching assistants (GTAs) are responsible for teaching the majority of biology undergraduate laboratory sections, although many feel underprepared to do so. This study explored the impact of biology GTA participation in a professional development model known as lesson study. Using a case study methodology with multiple qualitative data…

  19. Remote Sensing Dynamic Monitoring of Biological Invasive Species Based on Adaptive PCNN and Improved C-V Model

    Directory of Open Access Journals (Sweden)

    PENG Gang

    2014-12-01

    Full Text Available Biological species invasion problem bring serious damage to the ecosystem, and have become one of the six major enviromental problems that affect the future economic development, also have become one of the hot topic in domestic and foreign scholars. Remote sensing technology has been successfully used in the investigation of coastal zone resources, dynamic monitoring of the resources and environment, and other fields. It will cite a new remote sensing image change detection algorithm based on adaptive pulse coupled neural network (PCNN and improved C-V model, for remote sensing dynamic monitoring of biological species invasion. The experimental results show that the algorithm is effective in the test results of biological species invasions.

  20. Membrane materials for storing biological samples intended for comparative nanotoxicological testing

    Science.gov (United States)

    Metelkin, A.; Kuznetsov, D.; Kolesnikov, E.; Chuprunov, K.; Kondakov, S.; Osipov, A.; Samsonova, J.

    2015-11-01

    The study is aimed at identifying the samples of most promising membrane materials for storing dry specimens of biological fluids (Dried Blood Spots, DBS technology). Existing sampling systems using cellulose fiber filter paper have a number of drawbacks such as uneven distribution of the sample spot, dependence of the spot spreading area on the individual biosample properties, incomplete washing-off of the sample due to partially inconvertible sorption of blood components on cellulose fibers, etc. Samples of membrane materials based on cellulose, polymers and glass fiber with applied biosamples were studied using methods of scanning electron microscopy, FT-IR spectroscopy and surface-wetting measurement. It was discovered that cellulose-based membrane materials sorb components of biological fluids inside their structure, while membranes based on glass fiber display almost no interaction with the samples and biological fluid components dry to films in the membrane pores between the structural fibers. This characteristic, together with the fact that membrane materials based on glass fiber possess sufficient strength, high wetting properties and good storage capacity, attests them as promising material for dry samples of biological fluids storage systems.

  1. Membrane materials for storing biological samples intended for comparative nanotoxicological testing

    International Nuclear Information System (INIS)

    Metelkin, A; Kuznetsov, D; Kolesnikov, E; Chuprunov, K; Kondakov, S; Osipov, A; Samsonova, J

    2015-01-01

    The study is aimed at identifying the samples of most promising membrane materials for storing dry specimens of biological fluids (Dried Blood Spots, DBS technology). Existing sampling systems using cellulose fiber filter paper have a number of drawbacks such as uneven distribution of the sample spot, dependence of the spot spreading area on the individual biosample properties, incomplete washing-off of the sample due to partially inconvertible sorption of blood components on cellulose fibers, etc. Samples of membrane materials based on cellulose, polymers and glass fiber with applied biosamples were studied using methods of scanning electron microscopy, FT-IR spectroscopy and surface-wetting measurement. It was discovered that cellulose-based membrane materials sorb components of biological fluids inside their structure, while membranes based on glass fiber display almost no interaction with the samples and biological fluid components dry to films in the membrane pores between the structural fibers. This characteristic, together with the fact that membrane materials based on glass fiber possess sufficient strength, high wetting properties and good storage capacity, attests them as promising material for dry samples of biological fluids storage systems. (paper)

  2. Standard biological parts knowledgebase.

    Directory of Open Access Journals (Sweden)

    Michal Galdzicki

    2011-02-01

    Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org. The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org. SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL, a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  3. Standard Biological Parts Knowledgebase

    Science.gov (United States)

    Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

    2011-01-01

    We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

  4. Standard biological parts knowledgebase.

    Science.gov (United States)

    Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

    2011-02-24

    We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

  5. Patient Adherence to Biologic Agents in Psoriasis

    DEFF Research Database (Denmark)

    Hsu, Der Yi; Gniadecki, Robert

    2016-01-01

    BACKGROUND: Low adherence to therapies in psoriasis decreases treatment outcomes and increases the total health care costs. In spite of the wide use of biologic agents, patients' adherence to these drugs has not been extensively investigated. OBJECTIVE: The aim of this study is to measure adherence...... to the biologic drugs in a population of patients treated for psoriasis vulgaris using the medication possession ratio (MPR) index and to survey patients' attitudes to the treatment. METHODS: This is a single-center study on 247 patients with psoriasis vulgaris treated with adalimumab (n = 113), etanercept (n...... = 39), and ustekinumab (n = 95). MPR calculation was calculated monthly based on the hospital records documenting the dispensing of biologics to the patients. Clinical data [Psoriasis Area and Severity Index (PASI), Dermatology Life Quality Index (DLQI), presence of psoriatic arthritis, concomitant...

  6. Supporting read-across using biological data

    NARCIS (Netherlands)

    Zhu, H.; Bouhifd, M.; Donley, E.; Egnash, L.; Kleinstreuer, N.; Kroese, E.D.; Liu, Z.; Luechtefeld, T.; Palmer, J.; Pamies, D.; Shen, J.; Strauss, V.; Wu, S.; Hartung, T.

    2016-01-01

    Read-across, i.e., filling toxicological data gaps by relating to similar chemicals for which test data are available, is usually done based on chemical similarity. Besides structure and physico-chemical properties, biological similarity based on biological data adds extra strength to this process.

  7. Biological and Clinical Aspects of an Olive Oil-Based Lipid Emulsion—A Review

    Directory of Open Access Journals (Sweden)

    Wei Cai

    2018-06-01

    Full Text Available Intravenous lipid emulsions (ILEs have been an integral component of parenteral nutrition for more than 50 years. Numerous formulations are available and are based on vegetable (soybean, olive, coconut and animal (fish oils. Therefore, each of these formulations has a unique fatty acid composition that offers both benefits and limitations. As clinical experience and our understanding of the effects of fatty acids on various physiological processes has grown, there is evidence to suggest that some ILEs may have benefits compared with others. Current evidence suggests that olive oil-based ILE may preserve immune, hepatobiliary, and endothelial cell function, and may reduce lipid peroxidation and plasma lipid levels. There is good evidence from a large randomized controlled study to support a benefit of olive oil-based ILE over soybean oil-based ILE on reducing infections in critically ill patients. At present there is limited evidence to demonstrate a benefit of olive oil-based ILE over other ILEs on glucose metabolism, and few data exist to demonstrate a benefit on clinical outcomes such as hospital or intensive care unit stay, duration of mechanical ventilation, or mortality. We review the current research and clinical evidence supporting the potential positive biological and clinical aspects of olive oil-based ILE and conclude that olive oil-based ILE is well tolerated and provides effective nutritional support to various PN-requiring patient populations. Olive oil-based ILE appears to support the innate immune system, is associated with fewer infections, induces less lipid peroxidation, and is not associated with increased hepatobiliary or lipid disturbances. These data would suggest that olive oil-based ILE is a valuable option in various PN-requiring patient populations.

  8. Can a Multimedia Tool Help Students' Learning Performance in Complex Biology Subjects?

    Science.gov (United States)

    Koseoglu, Pinar; Efendioglu, Akin

    2015-01-01

    The aim of the present study was to determine the effects of multimedia-based biology teaching (Mbio) and teacher-centered biology (TCbio) instruction approaches on learners' biology achievements, as well as their views towards learning approaches. During the research process, an experimental design with two groups, TCbio (n = 22) and Mbio (n =…

  9. 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

  10. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Directory of Open Access Journals (Sweden)

    Kuan Peng

    2010-01-01

    Full Text Available As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SPn, and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  11. Study on photon transport problem based on the platform of molecular optical simulation environment.

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  12. Appendix U: benthic biological studies

    International Nuclear Information System (INIS)

    Hessler, R.R.

    1981-01-01

    Characterization of the biology and standing crop of the benthic organisms is divided into two major categories: (1) those organisms (sessile or with limited mobility) that live on or within the sediment (infauna); and (2) highly mobile organisms that have contact (if only occasionally) with the sediment (benthopelagic organisms). At this time our studies of benthopelagic organisms are restricted to amphipods. The amphipods trapped at MPG-I (30 to 31 0 N, 159 0 W) in 1978 have been sorted to species and compared with those trapped at Climax II (28 0 N, 155 to 156 0 W) in 1977. The species composition is the same at both stations and the numerical representation of the various species appears to be equivalent. Instar categories based on morphological and size criteria have been determined for Eurythenes gryllus. Comparison of the size range of the instar categories, morphological characters and female to male ratio show no detectable differences in E. gryllus from the two areas. Individuals of one of the smaller species of amphipods (Paralicella caperesca) were trapped at 710 m above the sediment, demonstrating that although the primary range of this species is 0-1 m off the bottom, it is capable of wide bathymetric movements. Males mature at a much smaller size (7 cm vs 11.5 cm) than females. Females appear to breed only once while males seem to be reproductively mature for several instars. After attaining maturity, male growth decreases to almost half the previous rate, and the time interval between molts appears to increase substantially. Females approximate a linear growth rate throughout their instar stages. The data are insufficient to determine if a decrease in growth rate occurs at the molt to maturity (female 14). The apparent difference in the time to maturity for males and females results in a high number of mature males present in the population to fertilize relatively few females

  13. Biological, Histological and Ultra-Structural Studies of Female Mullet ...

    African Journals Online (AJOL)

    Biological, Histological and Ultra-Structural Studies of Female Mullet, Mugil cephalus , Ovaries Collected from Different Habitats during Annual Reproductive Cycle. ... 35 and 52 cm, respectively; whereas, the total number of ripe ova in brackish water fish ranged from 0.57±0.14 to 3.81±0.59 x106 for the same length groups.

  14. Synthesis and study of biological behavior of radiopharmaceutical preparations on the base of specific to receptors compounds

    International Nuclear Information System (INIS)

    Bruskin, A.B.; Klement'eva, O.E.; Kodina, G.E.; Korsunskij, V.N.; Korshunov, V.B.; Slobodnyak, I.I.

    2005-01-01

    Aim of the present work is study of conditions radionuclide administration in modified biomolecules and study of its conjugation with tumor cells in vivo and in vitro. Octreotide labelling by the 111 In reactions in different buffer systems with yield ≥95 % were carried out. Demands making to quality of initial solution 111 In chloride for providing of radiochemical purity of the labelled compound were determined. Time of maximal accumulation of peptide by tumor cells has been defined. It is shown, that accumulation of control preparation 111 In-DTPA - in dependence on selected cell culture and experiment conditions - in 5-10 time lower, than accumulation of labeled peptide. Lyophilized forms of reagents providing one-stage opportunity of the preparation production at clinic conditions were obtained. The product is stable in laboratory animals blood serum. By the data of biological distribution the differential accumulation coefficients making up: tumor/blood -5-30; tumor-muscle - 2-10. The scintigraphic image of mouse malice's tumor was get

  15. A systems biology approach to study systemic inflammation.

    Science.gov (United States)

    Chen, Bor-Sen; Wu, Chia-Chou

    2014-01-01

    Systemic inflammation needs a precise control on the sequence and magnitude of occurring events. The high throughput data on the host-pathogen interactions gives us an opportunity to have a glimpse on the systemic inflammation. In this article, a dynamic Candida albicans-zebrafish interactive infectious network is built as an example to demonstrate how systems biology approach can be used to study systematic inflammation. In particular, based on microarray data of C. albicans and zebrafish during infection, the hyphal growth, zebrafish, and host-pathogen intercellular PPI networks were combined to form an integrated infectious PPI network that helps us understand the systematic mechanisms underlying the pathogenicity of C. albicans and the immune response of the host. The signaling pathways for morphogenesis and hyphal growth of C. albicans were 2 significant interactions found in the intercellular PPI network. Two cellular networks were also developed corresponding to the different infection stages (adhesion and invasion), and then compared with each other to identify proteins to gain more insight into the pathogenic role of hyphal development in the C. albicans infection process. Important defense-related proteins in zebrafish were predicted using the same approach. This integrated network consisting of intercellular invasion and cellular defense processes during infection can improve medical therapies and facilitate development of new antifungal drugs.

  16. Biological Dialogues: How to Teach Your Students to Learn Fluency in Biology

    Science.gov (United States)

    May, S. Randolph; Cook, David L.; May, Marilyn K.

    2013-01-01

    Biology courses have thousands of words to learn in order to intelligently discuss the subject and take tests over the material. Biological fluency is an important goal for students, and practical methods based on constructivist pedagogies can be employed to promote it. We present a method in which pairs of students write dialogues from…

  17. A Friendly-Biological Reactor SIMulator (BioReSIM for studying biological processes in wastewater treatment processes

    Directory of Open Access Journals (Sweden)

    Raul Molina

    2014-12-01

    Full Text Available Biological processes for wastewater treatments are inherently dynamic systems because of the large variations in the influent wastewater flow rate, concentration composition and the adaptive behavior of the involved microorganisms. Moreover, the sludge retention time (SRT is a critical factor to understand the bioreactor performances when changes in the influent or in the operation conditions take place. Since SRT are usually in the range of 10-30 days, the performance of biological reactors needs a long time to be monitored in a regular laboratory demonstration, limiting the knowledge that can be obtained in the experimental lab practice. In order to overcome this lack, mathematical models and computer simulations are useful tools to describe biochemical processes and predict the overall performance of bioreactors under different working operation conditions and variations of the inlet wastewater composition. The mathematical solution of the model could be difficult as numerous biochemical processes can be considered. Additionally, biological reactors description (mass balance, etc. needs models represented by partial or/and ordinary differential equations associated to algebraic expressions, that require complex computational codes to obtain the numerical solutions. Different kind of software for mathematical modeling can be used, from large degree of freedom simulators capable of free models definition (as AQUASIM, to closed predefined model structure programs (as BIOWIN. The first ones usually require long learning curves, whereas the second ones could be excessively rigid for specific wastewater treatment systems. As alternative, we present Biological Reactor SIMulator (BioReSIM, a MATLAB code for the simulation of sequencing batch reactors (SBR and rotating biological contactors (RBC as biological systems of suspended and attached biomass for wastewater treatment, respectively. This BioReSIM allows the evaluation of simple and complex

  18. Integrating biological indicators in a Soil Monitoring Network (SMN to improve soil quality diagnosis - a case study in Southern Belgium (Wallonia

    Directory of Open Access Journals (Sweden)

    Krüger, I.

    2017-01-01

    Full Text Available Description of the subject. Soil organisms and their activities are essential for soil ecosystem functioning and they can thus be used as pertinent indicators of soil quality. Recent efforts have been undertaken to include biological indicators of soil quality into regional/national monitoring networks. Objectives. The aim of this study was to provide a first dataset of six biological indicators and two eco-physiological quotients for two landscape units in Wallonia. These spatial units are characterized by homogeneous climate conditions, soil type, land-use and management (here, grasslands in the Ardennes, and croplands in the Loam Region. Method. Respiration potential, microbial biomass carbon and nitrogen, net nitrogen mineralization, metabolic potential of soil bacteria and earthworm abundance were measured at a total of 60 sites in two different landscape units (LSU. Variability within each LSU was studied. Data was synthesized through calculation of a comprehensive score and presentation as radar plots. Results. All selected biological indicators were significantly higher under grassland than under cropland soils, highlighting the biological indicators' power of discrimination between main land use types. Variability within LSU depended on the biological indicator and was generally higher in grassland than in cropland soils. Each site could unambiguously be assigned to its landscape unit based on its calculated comprehensive score. Radar plots allowed an assessment of the distribution of values within a landscape unit at a glance. Conclusions. The pilot-study defined the first baseline values for agricultural soils in Wallonia and laid the foundation for a monitoring network of biological soil quality.

  19. Background study of absorbed dose in biological experiments at the Modane Underground Laboratory

    Directory of Open Access Journals (Sweden)

    Lampe Nathanael

    2016-01-01

    Full Text Available Aiming to explore how biological systems respond to ultra-low background environ-ments, we report here our background studies for biological experiments in the Modane Under-ground Laboratory. We find that the minimum radioactive background for biology experiments is limited by the potassium content of the biological sample itself, coming from its nutritive me-dium, which we find in our experimental set-up to be 26 nGy hr-1. Compared to our reference radiation environment in Clermont-Ferrand, biological experiments can be conducted in the Modane laboratory with a radiation background 8.2 times lower than the reference above-ground level. As the radiation background may be further reduced by using different nutritive media, we also provide measurements of the potassium concentration by gamma spectroscopy of yeast extract (63.3±1.2 mg g-1 and tryptone (2.5±0.2 mg g-1 in order to guide media selection in future experiments.

  20. Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Teacher's Guide.

    Science.gov (United States)

    Alberta Environment, Edmonton. Environmental Education Resources Branch.

    The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

  1. Water Quality Monitoring: An Environmental Studies Unit for Biology 20/30. Student Manual.

    Science.gov (United States)

    Alberta Environment, Edmonton. Environmental Education Resources Branch.

    The objective of this environmental studies unit is to establish a water quality monitoring project for high school students in Alberta while simultaneously providing a unit which meets the objectives of the Biology 20 program (and which may also be used in Biology 10 and 30). Through this project, students assist in the collection,…

  2. Review of low dose-rate epidemiological studies and biological mechanisms of dose-rate effects on radiation induced carcinogenesis

    International Nuclear Information System (INIS)

    Iwasaki, Toshiyasu; Otsuka, Kensuke; Yoshida, Kazuo

    2015-01-01

    Radiation protection system adopts the linear non-threshold model with using dose and dose-rate effectiveness factor (DDREF). The dose-rate range where DDREF is applied is below 100 mGy per hour, and it is regarded that there are no dose-rate effects at very low dose rate, less than of the order of 10 mGy per year, even from the biological risk evaluation model based on cellular and molecular level mechanisms for maintenance of genetic integrity. Among low dose-rate epidemiological studies, studies of residents in high natural background areas showed no increase of cancer risks at less than about 10 mGy per year. On the other hand, some studies include a study of the Techa River cohort suggested the increase of cancer risks to the similar degree of Atomic bomb survivor data. The difference of those results was supposed due to the difference of dose rate. In 2014, International Commission on Radiological Protection opened a draft report on stem cell biology for public consultations. The report proposed a hypothesis based on the new idea of stem cell competition as a tissue level quality control mechanism, and suggested that it could explain the dose-rate effects around a few milligray per year. To verify this hypothesis, it would be needed to clarify the existence and the lowest dose of radiation-induced stem cell competition, and to elucidate the rate of stem cell turnover and radiation effects on it. As for the turnover, replenishment of damaged stem cells would be the important biological process. It would be meaningful to collect the information to show the difference of dose rates where the competition and the replenishment would be the predominant processes. (author)

  3. Biomaterials-based electronics: polymers and interfaces for biology and medicine.

    Science.gov (United States)

    Muskovich, Meredith; Bettinger, Christopher J

    2012-05-01

    Advanced polymeric biomaterials continue to serve as a cornerstone for new medical technologies and therapies. The vast majority of these materials, both natural and synthetic, interact with biological matter in the absence of direct electronic communication. However, biological systems have evolved to synthesize and utilize naturally-derived materials for the generation and modulation of electrical potentials, voltage gradients, and ion flows. Bioelectric phenomena can be translated into potent signaling cues for intra- and inter-cellular communication. These cues can serve as a gateway to link synthetic devices with biological systems. This progress report will provide an update on advances in the application of electronically active biomaterials for use in organic electronics and bio-interfaces. Specific focus will be granted to covering technologies where natural and synthetic biological materials serve as integral components such as thin film electronics, in vitro cell culture models, and implantable medical devices. Future perspectives and emerging challenges will also be highlighted. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Numerical study of water diffusion in biological tissues using an improved finite difference method

    International Nuclear Information System (INIS)

    Xu Junzhong; Does, Mark D; Gore, John C

    2007-01-01

    An improved finite difference (FD) method has been developed in order to calculate the behaviour of the nuclear magnetic resonance signal variations caused by water diffusion in biological tissues more accurately and efficiently. The algorithm converts the conventional image-based finite difference method into a convenient matrix-based approach and includes a revised periodic boundary condition which eliminates the edge effects caused by artificial boundaries in conventional FD methods. Simulated results for some modelled tissues are consistent with analytical solutions for commonly used diffusion-weighted pulse sequences, whereas the improved FD method shows improved efficiency and accuracy. A tightly coupled parallel computing approach was also developed to implement the FD methods to enable large-scale simulations of realistic biological tissues. The potential applications of the improved FD method for understanding diffusion in tissues are also discussed. (note)

  5. Modelling and Simulating Complex Systems in Biology: introducing NetBioDyn : A Pedagogical and Intuitive Agent-Based Software

    OpenAIRE

    Ballet, Pascal; Rivière, Jérémy; Pothet, Alain; Théron, Michaël; Pichavant, Karine; Abautret, Frank; Fronville, Alexandra; Rodin, Vincent

    2017-01-01

    International audience; Modelling and teaching complex biological systems is a difficult process. Multi-Agent Based Simulations (MABS) have proved to be an appropriate approach both in research and education when dealing with such systems including emergent, self-organizing phenomena. This chapter presents NetBioDyn, an original software aimed at biologists (students, teachers, researchers) to easily build and simulate complex biological mechanisms observed in multicellular and molecular syst...

  6. Automated radiofrequency-based US measurement of common carotid intima-media thickness in RA patients treated with synthetic vs synthetic and biologic DMARDs.

    Science.gov (United States)

    Naredo, Esperanza; Möller, Ingrid; Corrales, Alfonso; Bong, David A; Cobo-Ibáñez, Tatiana; Corominas, Hector; Garcia-Vivar, Ma Luz; Macarrón, Pilar; Navio, Teresa; Richi, Patricia; Iagnocco, Annamaria; Garrido, Jesús; Martínez-Hernández, David

    2013-02-01

    To compare the carotid intima-media thickness (IMT) assessed with automated radiofrequency-based US in RA patients treated with synthetic vs synthetic and biologic DMARDs and controls. Ninety-four RA patients and 94 sex- and age-matched controls were prospectively recruited at seven centres. Cardiovascular (CV) risk factors and co-morbidities, RA characteristics and therapy were recorded. Common carotid artery (CCA)-IMT was assessed in RA patients and controls with automated radiofrequency-based US by the same investigator at each centre. Forty-five (47.9%) RA patients had been treated with synthetic DMARDs and 49 (52.1%) with synthetic and biologic DMARDs. There were no significant differences between the RA patients and controls in demographics, CV co-morbidities and CV disease. There were significantly more smokers among RA patients treated with synthetic and biologic DMARDs (P = 0.036). Disease duration and duration of CS and synthetic DMARD therapy was significantly longer in RA patients treated with synthetic and biologic DMARDs (P radiofrequency-based measurement of CCA-IMT can discriminate between RA patients treated with synthetic DMARDs vs RA patients treated with synthetic and biologic DMARDs.

  7. 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.

  8. 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.

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

    Science.gov (United States)

    Malacinski, George M

    2003-01-01

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

  10. A Study Assessing the Potential of Negative Effects in Interdisciplinary Math–Biology Instruction

    Science.gov (United States)

    Madlung, Andreas; Bremer, Martina; Himelblau, Edward; Tullis, Alexa

    2011-01-01

    There is increasing enthusiasm for teaching approaches that combine mathematics and biology. The call for integrating more quantitative work in biology education has led to new teaching tools that improve quantitative skills. Little is known, however, about whether increasing interdisciplinary work can lead to adverse effects, such as the development of broader but shallower skills or the possibility that math anxiety causes some students to disengage in the classroom, or, paradoxically, to focus so much on the mathematics that they lose sight of its application for the biological concepts in the center of the unit at hand. We have developed and assessed an integrative learning module and found disciplinary learning gains to be equally strong in first-year students who actively engaged in embedded quantitative calculations as in those students who were merely presented with quantitative data in the context of interpreting biological and biostatistical results. When presented to advanced biology students, our quantitative learning tool increased test performance significantly. We conclude from our study that the addition of mathematical calculations to the first year and advanced biology curricula did not hinder overall student learning, and may increase disciplinary learning and data interpretation skills in advanced students. PMID:21364099

  11. New Approaches in Cancer Biology Can Inform the Biology Curriculum.

    Science.gov (United States)

    Jones, Lynda; Gordon, Diana; Zelinski, Mary

    2018-03-01

    Students tend to be very interested in medical issues that affect them and their friends and family. Using cancer as a hook, the ART of Reproductive Medicine: Oncofertility curriculum (free, online, and NIH sponsored) has been developed to supplement the teaching of basic biological concepts and to connect biology and biomedical research. This approach allows integration of up-to-date information on cancer and cancer treatment, cell division, male and female reproductive anatomy and physiology, cryopreservation, fertility preservation, stem cells, ethics, and epigenetics into an existing biology curriculum. Many of the topics covered in the curriculum relate to other scientific disciplines, such as the latest developments in stem cell research including tissue bioengineering and gene therapy for inherited mitochondrial disease, how epigenetics occurs chemically to affect gene expression or suppression and how it can be passed down through the generations, and the variety of biomedical careers students could pursue. The labs are designed to be open-ended and inquiry-based, and extensions to the experiments are provided so that students can explore questions further. Case studies and ethical dilemmas are provided to encourage thoughtful discussion. In addition, each chapter of the curriculum includes links to scientific papers, additional resources on each topic, and NGSS alignment.

  12. Review of Russian language studies on radionuclide behaviour in agricultural animals: biological half-lives.

    Science.gov (United States)

    Fesenko, S; Isamov, N; Barnett, C L; Beresford, N A; Howard, B J; Sanzharova, N; Fesenko, E

    2015-04-01

    Extensive studies on transfer of radionuclides to animals were carried out in the USSR from the 1950s. Few of these studies were published in the international refereed literature or taken into account in international reviews. This paper continues a series of reviews of Russian language literature on radionuclide transfer to animals, providing information on biological half-lives of radionuclides in various animal tissues. The data are compared, where possible, with those reported in other countries. The data are normally quantified using a single or double exponential accounting for different proportions of the loss. For some products, such as milk, biological half-lives tend to be rapid at 1-3 d for most radionuclides and largely described by a single exponential. However, for other animal products biological half-lives can vary widely as they are influenced by many factors such as the age and size of the animal. Experimental protocols, such as the duration of the study, radionuclide administration and/or sample collection protocol also influence the value of biological half-lives estimated. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Study on the uptake and distribution of gadolinium based contrast agents in biological samples using laser ablation with inductively coupled plasma mass spectroscopy

    International Nuclear Information System (INIS)

    Lingott, Jana

    2016-01-01

    Gadolinium based contrast agents are used for magnetic resonance imaging. After their excretion by medicated patients they reach surface water passing waste water treatment plants where they are not removed sufficiently. The behavior of the contrast agents in the environment and the interaction with organisms was investigated in this work due to the toxicity of the free Gd 3+ ion and the associated risks, such as accumulation in the human food chain. In this work, the two elemental analytical imaging methods laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) and synchrotron radiation X-ray fluorescence analysis (SRXRF) have been used to investigate the uptake, distribution, and excretion of Gd-based contrast agents by various biological systems. Both methods were analytically characterized and compared for this application. The detection limits of gadolinium were determined under optimized conditions by LA-ICP-MS and SRXRF. With calibration by remains of dried elemental standard droplets detection limits of 0.78 pg absolute amount of gadolinium (LA-ICP-MS), respectively 89 pg (SRXRF) were reached. Based on filamentous algae as water plants the uptake and the excretion of Gd-based contrast agents were revealed. The dependence on concentration of the contrast agent in the exposition solution and the independence of temporal uptake within one to seven days were studied for duckweed. By LA-ICP-MS gadolinium was quantified in a leaf of cress plant. The verification of the results was performed by SRXRF and ICP-MS after digestion. Furthermore, the uptake and distribution of Gd-based contrast agents in higher organisms (water flea) were observed. The exact location of gadolinium was resolved by three-dimensional μ-computed tomography by the comparison of an exposed with a Gd-free water flea. In all studies, gadolinium was detected in the investigated exposed model organisms. It can be concluded that the contrast agents were taken from the environment.

  14. 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

    analysis (GSEA to evaluate the clustering results; (2 Leave-one-out cross-validation (LOOCV to ensure that the SVM classifiers assign TFs to NM categories with high confidence; (3 Binding site enrichment analysis (BSEA to determine enrichment of the gene clusters for the cognate binding sites of their predicted TFs; (4 Comparison with previously reported results in the literatures to confirm the inferred regulations. Conclusion The major contribution of this study is the development of a computational framework to assist the inference of TRN by integrating heterogeneous data from multiple sources and by decomposing a TRN into NM-based modules. The inference capability of the proposed framework is verified statistically (e.g., LOOCV and biologically (e.g., GSEA, BSEA, and literature validation. The proposed framework is useful for inferring small NM-based modules of TF-target gene relationships that can serve as a basis for generating new testable hypotheses.

  15. Postgraduate studies in radiation biology in Europe

    International Nuclear Information System (INIS)

    Trott, K.R.; Lohmann, P.H.M.; Zeeland, A.A. van; Natarajan, A.T.; Schibilla, H.; Chadwick, K.; Kellerer, A.M.; Steinhaeusler, F.

    1998-01-01

    The present system of radiobiological research in universities and research centres is no longer able to train radiobiologists who have a comprehensive understanding of the entire field of radiation biology including both 'classical' and molecular radiation biology. However, such experts are needed in view of the role radiation protection plays in our societies. No single institution in Europe could now run a 1-year, full-time course which covers all aspects of the radiobiological basis of radiation protection. Therefore, a cooperative action of several universities from different EU member states has been developed and is described herein. (orig.)

  16. Biological and medical sensor technologies

    CERN Document Server

    Iniewski, Krzysztof

    2012-01-01

    Biological and Medical Sensor Technologies presents contributions from top experts who explore the development and implementation of sensors for various applications used in medicine and biology. Edited by a pioneer in the area of advanced semiconductor materials, the book is divided into two sections. The first part covers sensors for biological applications. Topics include: Advanced sensing and communication in the biological world DNA-derivative architectures for long-wavelength bio-sensing Label-free silicon photonics Quartz crystal microbalance-based biosensors Lab-on-chip technologies fo

  17. Biology task group

    International Nuclear Information System (INIS)

    Anon.

    1981-01-01

    The accomplishments of the task group studies over the past year are reviewed. The purposes of biological investigations, in the context of subseabed disposal, are: an evaluation of the dose to man; an estimation of effects on the ecosystem; and an estimation of the influence of organisms on and as barriers to radionuclide migration. To accomplish these ends, the task group adopted the following research goals: (1) acquire more data on biological accumulation of specific radionuclides, such as those of Tc, Np, Ra, and Sr; (2) acquire more data on transfer coefficients from sediment to organism; (3) Calculate mass transfer rates, construct simple models using them, and estimate collective dose commitment; (4) Identify specific pathways or transfer routes, determine the rates of transfer, and make dose limit calculations with simple models; (5) Calculate dose rates to and estimate irradiation effects on the biota as a result of waste emplacement, by reference to background irradiation calculations. (6) Examine the effect of the biota on altering sediment/water radionuclide exchange; (7) Consider the biological data required to address different accident scenarios; (8) Continue to provide the basic biological information for all of the above, and ensure that the system analysis model is based on the most realistic and up-to-date concepts of marine biologists; and (9) Ensure by way of free exchange of information that the data used in any model are the best currently available

  18. SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

    Science.gov (United States)

    Zi, Zhike

    2011-04-01

    Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors. SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

  19. Biological methods used to assess surface water quality

    Directory of Open Access Journals (Sweden)

    Szczerbiñska Natalia

    2015-12-01

    Full Text Available In accordance with the guidelines of the Water Framework Directive 2000/60 (WFD, both ecological and chemical statuses determine the assessment of surface waters. The profile of ecological status is based on the analysis of various biological components, and physicochemical and hydromorphological indicators complement this assessment. The aim of this article is to present the biological methods used in the assessment of water status with a special focus on bioassay, as well as to provide a review of methods of monitoring water status. Biological test methods include both biomonitoring and bioanalytics. Water biomonitoring is used to assess and forecast the status of water. These studies aim to collect data on water pollution and forecast its impact. Biomonitoring uses organisms which are characterized by particular vulnerability to contaminants. Bioindicator organisms are algae, fungi, bacteria, larval invertebrates, cyanobacteria, macroinvertebrates, and fish. Bioanalytics is based on the receptors of contaminants that can be biologically active substances. In bioanalytics, biosensors such as viruses, bacteria, antibodies, enzymes, and biotests are used to assess degrees of pollution.

  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. Synthetic Biology: Mapping the Scientific Landscape

    Science.gov (United States)

    Oldham, Paul; Hall, Stephen; Burton, Geoff

    2012-01-01

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

  2. Nutritional Systems Biology

    DEFF Research Database (Denmark)

    Jensen, Kasper

    and network biology has the potential to increase our understanding of how small molecules affect metabolic pathways and homeostasis, how this perturbation changes at the disease state, and to what extent individual genotypes contribute to this. A fruitful strategy in approaching and exploring the field...... biology research. The paper also shows as a proof-of-concept that a systems biology approach to diet is meaningful and demonstrates some basic principles on how to work with diet systematic. The second chapter of this thesis we developed the resource NutriChem v1.0. A foodchemical database linking...... sites of diet on the disease pathway. We propose a framework for interrogating the critical targets in colon cancer process and identifying plant-based dietary interventions as important modifiers using a systems chemical biology approach. The fifth chapter of the thesis is on discovering of novel anti...

  3. An Error Analysis of Structured Light Scanning of Biological Tissue

    DEFF Research Database (Denmark)

    Jensen, Sebastian Hoppe Nesgaard; Wilm, Jakob; Aanæs, Henrik

    2017-01-01

    This paper presents an error analysis and correction model for four structured light methods applied to three common types of biological tissue; skin, fat and muscle. Despite its many advantages, structured light is based on the assumption of direct reflection at the object surface only......, statistical linear model based on the scan geometry. As such, scans can be corrected without introducing any specially designed pattern strategy or hardware. We can effectively reduce the error in a structured light scanner applied to biological tissue by as much as factor of two or three........ This assumption is violated by most biological material e.g. human skin, which exhibits subsurface scattering. In this study, we find that in general, structured light scans of biological tissue deviate significantly from the ground truth. We show that a large portion of this error can be predicted with a simple...

  4. Biology Factual Knowledge at Eleventh Grade of Senior High School Students in Pacitan based on Favorite Schools

    Science.gov (United States)

    Yustiana, I. A.; Paidi; Mercuriani, I. S.

    2018-03-01

    This study aimed to determine the Biology factual knowledge at eleventh grade of senior high school students in Pacitan based on favorite schools. This research was a descriptive research by using survey method. The population in this study was all of senior high school students in Pacitan. The sampling technique used purposive sampling technique and obtained 3 favorite schools and 3 non-favorite schools. The technique of collecting data used test form which was as the instrument of the research. Data analysis technique used Mann-Whitney U test. Based on the test, it was obtained p = 0,000 (p <0,05) so there was a significant difference between the factual knowledge of the students in the favorite schools and non-favorite schools in Pacitan. The factual knowledge of students in favorite schools was higher with an average of 5.32 while non-favorite schools were obtained an average of 4.36.

  5. Biologics in pediatric psoriasis - efficacy and safety.

    Science.gov (United States)

    Dogra, Sunil; Mahajan, Rahul

    2018-01-01

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

  6. A prospective observational study of pigmented naevi changes in psoriasis patients on biologic therapy.

    Science.gov (United States)

    Choi, Seohee Deanne; D'Souza, Mario I; Menzies, Scott W; Weninger, Wolfgang

    2018-05-23

    Patients on biologic therapy are thought to be at increased risk of developing non-melanoma skin cancers and melanomas. It is unknown whether biologic therapy alters the natural history of melanocytic naevi. Therefore, a prospective observational study was conducted to determine whether psoriasis patients on biologic therapy develop changes in naevi. Clinical and dermoscopic assessment of all melanocytic naevi was performed in 45 psoriasis patients on biologic therapy versus a control cohort of 43 subjects, using sequential digital dermoscopic imaging and total body photography. The mean follow-up period was 1.5 years. The study and control patients had comparable age, gender, previous and family history of non-melanoma skin cancers and melanomas, as well as previous sun exposure and total number of naevi. The number of naevi with major dermoscopic changes was 3% in the study and 1.9% in the control group, with an adjusted incidence rate ratio of 1.45 (95% confidence interval 0.90-2.33; P = 0.125). The rate of minor changes was 15.9% in the study group versus 19.4% in the control (adjusted incidence rate ratio 0.77, 95% confidence interval 0.57-1.08; P = 0.14). There were six new dysplastic naevi in 4/45 biologic patients and four in 4/43 controls; however, the difference was not significant (relative risk 0.96, 95% confidence interval -0.12 to 0.12; P = 0.95). There were no melanomas in either group. Over a mean follow-up period of 1.5 years there was no evidence of significantly different changes in naevi or development of new dysplastic naevi in psoriasis patients on biologic treatment compared to controls. © 2018 The Australasian College of Dermatologists.

  7. Using Femtosecond Laser Subcellular Surgery as a Tool to Study Cell Biology

    Energy Technology Data Exchange (ETDEWEB)

    Shen, N; Colvin, M E; Huser, T

    2007-02-27

    Research on cellular function and regulation would be greatly advanced by new instrumentation using methods to alter cellular processes with spatial discrimination on the nanometer-scale. We present a novel technique for targeting submicrometer sized organelles or other biologically important regions in living cells using femtosecond laser pulses. By tightly focusing these pulses beneath the cell membrane, we can vaporize cellular material inside the cell through nonlinear optical processes. This technique enables non-invasive manipulation of the physical structure of a cell with sub-micrometer resolution. We propose to study the role mitochondria play in cell proliferation and apoptosis. Our technique provides a unique tool for the study of cell biology.

  8. A resource about fungi for intercultural dialogue in biology teaching

    Directory of Open Access Journals (Sweden)

    Edilaine Almeida Oliveira Silva

    2017-07-01

    Full Text Available We are presenting results of a collaborative study with a teacher from a public school in the Bahia State (northeastern Brazil. The main objective was to develop a didactic resource that could be applied in biology teaching based on intercultural dialogue, between students’ cultural knowledge and the school’s biological knowledge about mushrooms. In other words, this didactics of biology links the knowledge inherited culturally. It was applied a questionnaire with students of this school, and from the answers it was prepared Comparative Cognition tables. Relations of similarity and differences between prior knowledge of students and school biological knowledge were scored in these tables. The results revealed relationships between these two forms of knowledge, being mandatory similarity relations. These revelations were important for planning and construction of an educational game based on intercultural dialogue. The present study aims to continue with the application of this teaching resource in the classrooms of the participating teacher, looking for its viability in educational interventions in relation to the intercultural dialogue between students’ preconceptions and school science knowledge about fungi.

  9. MEMS-Based Microanalytical System for Dielectrophoresis Studies of Biological Macromolecules

    National Research Council Canada - National Science Library

    Crippen, Shane

    2000-01-01

    ...s such as DNA and bovine serum albumin (BSA). Through a process of discovery that involved extensive theoretical and literature based analysis coupled with laboratory validation and extension of current dielectrophoresis knowledge...

  10. A comparison of biological and cultural evolution

    Indian Academy of Sciences (India)

    the intellectual and moral characters of man have emerged as results of biological ..... tural selection is at least partly based on conscious action. In cultural evolution .... Transfer of information in biological and cultural evolution. In biological.

  11. Integrating biological redesign: where synthetic biology came from and where it needs to go.

    Science.gov (United States)

    Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

    2014-03-27

    Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. The role of bacillus-based biological control agents in integrated pest management systems: plant diseases.

    Science.gov (United States)

    Jacobsen, B J; Zidack, N K; Larson, B J

    2004-11-01

    ABSTRACT Bacillus-based biological control agents (BCAs) have great potential in integrated pest management (IPM) systems; however, relatively little work has been published on integration with other IPM management tools. Unfortunately, most research has focused on BCAs as alternatives to synthetic chemical fungicides or bactericides and not as part of an integrated management system. IPM has had many definitions and this review will use the national coalition for IPM definition: "A sustainable approach to managing pests by combining biological, cultural, physical and chemical tools in a way that minimizes economic, health and environmental risks." This review will examine the integrated use of Bacillus-based BCAs with disease management tools, including resistant cultivars, fungicides or bactericides, or other BCAs. This integration is important because the consistency and degree of disease control by Bacillus-based BCAs is rarely equal to the control afforded by the best fungicides or bactericides. In theory, integration of several tools brings stability to disease management programs. Integration of BCAs with other disease management tools often provides broader crop adaptation and both more efficacious and consistent levels of disease control. This review will also discuss the use of Bacillus-based BCAs in fungicide resistance management. Work with Bacillus thuringiensis and insect pest management is the exception to the relative paucity of reports but will not be the focus of this review.

  13. View of environmental radiation effects from the study of radiation biology in C. elegans

    International Nuclear Information System (INIS)

    Sakashita, Tetsuya

    2011-01-01

    Caenorhabditis (C.) elegans is a non-parasitic soil nematode and is well-known as a unique model organism, because of its complete cell-lineage, nervous network and genome sequences. Also, C. elegans can be easily manipulated in the laboratory. These advantages make C. elegans as a good in vivo model system in the field of radiation biology. Radiation effects in C. elegans have been studied for three decades. Here, I briefly review the current knowledge of the biological effects of ionizing irradiation in C. elegans with a scope of environmental radiation effects. Firstly, basic information of C. elegans as a model organism is described. Secondly, historical view is reported on the study of radiation biology in C. elegans. Thirdly, our research on learning behavior is presented. Finally, an opinion of the use of C. elegans for environmental radiation protection is referred. I believe that C. elegans may be a good promising in vivo model system in the field of environmental radiation biology. (author)

  14. Polyvinylpyrrolidone and arsenic-induced changes in biological responses of model aquatic organisms exposed to iron-based nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Llaneza, Verónica [University of Florida, Engineering School of Sustainable Infrastructure and Environment, Department of Environmental Engineering Sciences (United States); Rodea-Palomares, Ismael [Univ. Autonoma de Madrid, Dept. de Biologia, Facultad de Ciencias (Spain); Zhou, Zuo [University of Florida, Engineering School of Sustainable Infrastructure and Environment, Department of Environmental Engineering Sciences (United States); Rosal, Roberto [Univ. de Alcalá, Dept. de Ingeniería Química (Spain); Fernández-Pina, Francisca [Univ. Autonoma de Madrid, Dept. de Biologia, Facultad de Ciencias (Spain); Bonzongo, Jean-Claude J., E-mail: bonzongo@ufl.edu [University of Florida, Engineering School of Sustainable Infrastructure and Environment, Department of Environmental Engineering Sciences (United States)

    2016-08-15

    The efficiency of zero-valent iron particles used in the remediation of contaminated groundwater has, with the emergence of nanotechnology, stimulated interest on the use of nano-size particles to take advantage of high-specific surface area and reactivity characteristics of nanoparticles (NPs). Accordingly, engineered iron-NPs are among the most widely used nanomaterials for in situ remediation. However, while several ecotoxicity studies have been conducted to investigate the adverse impacts of these NPs on aquatic organisms, research on the implications of spent iron-based NPs is lacking. In this study, a comparative approach is used, in which the biological effects of three iron-based NPs (Fe{sub 3}O{sub 4} and γ-Fe{sub 2}O{sub 3} NPs with particle sizes ranging from 20 to 50 nm, and Fe{sup 0}-NPs with an average particle size of 40 nm) on Raphidocelis subcapitata (formely known as Pseudokirchneriella subcapitata) and Daphnia magna were investigated using both as-prepared and pollutant-doped Fe-based NPs. For the latter, arsenic (As) was used as example sorbed pollutant. The results show that improved degree of NP dispersion by use of polyvinylpyrrolidone overlapped with both increased arsenic adsorption capacity and toxicity to the tested organisms. For R. subcapitata, Fe-oxide NPs were more toxic than Fe{sup 0}-NPs, due primarily to differences in the degree of NPs aggregation and ability to produce reactive oxygen species. For the invertebrate D. magna, a similar trend of biological responses was observed, except that sorption of As to Fe{sup 0}-NPs significantly increased the toxic response when compared to R. subcapitata. Overall, these findings point to the need for research on downstream implications of NP-pollutant complexes generated during water treatment by injection of NPs into aquatic systems.

  15. Polyvinylpyrrolidone and arsenic-induced changes in biological responses of model aquatic organisms exposed to iron-based nanoparticles

    International Nuclear Information System (INIS)

    Llaneza, Verónica; Rodea-Palomares, Ismael; Zhou, Zuo; Rosal, Roberto; Fernández-Pina, Francisca; Bonzongo, Jean-Claude J.

    2016-01-01

    The efficiency of zero-valent iron particles used in the remediation of contaminated groundwater has, with the emergence of nanotechnology, stimulated interest on the use of nano-size particles to take advantage of high-specific surface area and reactivity characteristics of nanoparticles (NPs). Accordingly, engineered iron-NPs are among the most widely used nanomaterials for in situ remediation. However, while several ecotoxicity studies have been conducted to investigate the adverse impacts of these NPs on aquatic organisms, research on the implications of spent iron-based NPs is lacking. In this study, a comparative approach is used, in which the biological effects of three iron-based NPs (Fe_3O_4 and γ-Fe_2O_3 NPs with particle sizes ranging from 20 to 50 nm, and Fe"0-NPs with an average particle size of 40 nm) on Raphidocelis subcapitata (formely known as Pseudokirchneriella subcapitata) and Daphnia magna were investigated using both as-prepared and pollutant-doped Fe-based NPs. For the latter, arsenic (As) was used as example sorbed pollutant. The results show that improved degree of NP dispersion by use of polyvinylpyrrolidone overlapped with both increased arsenic adsorption capacity and toxicity to the tested organisms. For R. subcapitata, Fe-oxide NPs were more toxic than Fe"0-NPs, due primarily to differences in the degree of NPs aggregation and ability to produce reactive oxygen species. For the invertebrate D. magna, a similar trend of biological responses was observed, except that sorption of As to Fe"0-NPs significantly increased the toxic response when compared to R. subcapitata. Overall, these findings point to the need for research on downstream implications of NP-pollutant complexes generated during water treatment by injection of NPs into aquatic systems.

  16. Polyvinylpyrrolidone and arsenic-induced changes in biological responses of model aquatic organisms exposed to iron-based nanoparticles

    Science.gov (United States)

    Llaneza, Verónica; Rodea-Palomares, Ismael; Zhou, Zuo; Rosal, Roberto; Fernández-Pina, Francisca; Bonzongo, Jean-Claude J.

    2016-08-01

    The efficiency of zero-valent iron particles used in the remediation of contaminated groundwater has, with the emergence of nanotechnology, stimulated interest on the use of nano-size particles to take advantage of high-specific surface area and reactivity characteristics of nanoparticles (NPs). Accordingly, engineered iron-NPs are among the most widely used nanomaterials for in situ remediation. However, while several ecotoxicity studies have been conducted to investigate the adverse impacts of these NPs on aquatic organisms, research on the implications of spent iron-based NPs is lacking. In this study, a comparative approach is used, in which the biological effects of three iron-based NPs (Fe3O4 and γ-Fe2O3 NPs with particle sizes ranging from 20 to 50 nm, and Fe0-NPs with an average particle size of 40 nm) on Raphidocelis subcapitata (formely known as Pseudokirchneriella subcapitata) and Daphnia magna were investigated using both as-prepared and pollutant-doped Fe-based NPs. For the latter, arsenic (As) was used as example sorbed pollutant. The results show that improved degree of NP dispersion by use of polyvinylpyrrolidone overlapped with both increased arsenic adsorption capacity and toxicity to the tested organisms. For R. subcapitata, Fe-oxide NPs were more toxic than Fe0-NPs, due primarily to differences in the degree of NPs aggregation and ability to produce reactive oxygen species. For the invertebrate D. magna, a similar trend of biological responses was observed, except that sorption of As to Fe0-NPs significantly increased the toxic response when compared to R. subcapitata. Overall, these findings point to the need for research on downstream implications of NP-pollutant complexes generated during water treatment by injection of NPs into aquatic systems.

  17. Fast Biological Modeling for Voxel-based Heavy Ion Treatment Planning Using the Mechanistic Repair-Misrepair-Fixation Model and Nuclear Fragment Spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kamp, Florian [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States); Department of Radiation Oncology, Technische Universität München, Klinikum Rechts der Isar, München (Germany); Physik-Department, Technische Universität München, Garching (Germany); Cabal, Gonzalo [Experimental Physics–Medical Physics, Ludwig Maximilians University Munich, Garching (Germany); Mairani, Andrea [Medical Physics Unit, Centro Nazionale Adroterapia Oncologica (CNAO), Pavia (Italy); Heidelberg Ion-Beam Therapy Center, Heidelberg (Germany); Parodi, Katia [Experimental Physics–Medical Physics, Ludwig Maximilians University Munich, Garching (Germany); Wilkens, Jan J. [Department of Radiation Oncology, Technische Universität München, Klinikum Rechts der Isar, München (Germany); Physik-Department, Technische Universität München, Garching (Germany); Carlson, David J., E-mail: david.j.carlson@yale.edu [Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut (United States)

    2015-11-01

    Purpose: The physical and biological differences between heavy ions and photons have not been fully exploited and could improve treatment outcomes. In carbon ion therapy, treatment planning must account for physical properties, such as the absorbed dose and nuclear fragmentation, and for differences in the relative biological effectiveness (RBE) of ions compared with photons. We combined the mechanistic repair-misrepair-fixation (RMF) model with Monte Carlo-generated fragmentation spectra for biological optimization of carbon ion treatment plans. Methods and Materials: Relative changes in double-strand break yields and radiosensitivity parameters with particle type and energy were determined using the independently benchmarked Monte Carlo damage simulation and the RMF model to estimate the RBE values for primary carbon ions and secondary fragments. Depth-dependent energy spectra were generated with the Monte Carlo code FLUKA for clinically relevant initial carbon ion energies. The predicted trends in RBE were compared with the published experimental data. Biological optimization for carbon ions was implemented in a 3-dimensional research treatment planning tool. Results: We compared the RBE and RBE-weighted dose (RWD) distributions of different carbon ion treatment scenarios with and without nuclear fragments. The inclusion of fragments in the simulations led to smaller RBE predictions. A validation of RMF against measured cell survival data reported in published studies showed reasonable agreement. We calculated and optimized the RWD distributions on patient data and compared the RMF predictions with those from other biological models. The RBE values in an astrocytoma tumor ranged from 2.2 to 4.9 (mean 2.8) for a RWD of 3 Gy(RBE) assuming (α/β){sub X} = 2 Gy. Conclusions: These studies provide new information to quantify and assess uncertainties in the clinically relevant RBE values for carbon ion therapy based on biophysical mechanisms. We present results from

  18. 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…

  19. KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems.

    Science.gov (United States)

    Costa, Rafael S; Veríssimo, André; Vinga, Susana

    2014-08-13

    The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis. In the first step, it is usually required to set initial metabolite concentrations, and to assign kinetic rate laws, along with estimating parameter values using kinetic data through optimization when these are not known. Although the rapid development of high-throughput methods has generated much omics data, experimentalists present only a summary of obtained results for publication, the experimental data files are not usually submitted to any public repository, or simply not available at all. In order to automatize as much as possible the steps of building kinetic models, there is a growing requirement in the systems biology community for easily exchanging data in combination with models, which represents the main motivation of KiMoSys development. KiMoSys is a user-friendly platform that includes a public data repository of published experimental data, containing concentration data of metabolites and enzymes and flux data. It was designed to ensure data management, storage and sharing for a wider systems biology community. This community repository offers a web-based interface and upload facility to turn available data into publicly accessible, centralized and structured-format data files. Moreover, it compiles and integrates available kinetic models associated with the data.KiMoSys also integrates some tools to facilitate the kinetic model construction process of large-scale metabolic networks, especially when the systems biologists perform computational research. KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating data storage and sharing, thus supporting construction of ODE-based kinetic models and collaborative research projects.The web application implemented using Ruby

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

    Science.gov (United States)

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

    2010-01-01

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

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

    Science.gov (United States)

    McManus, Jeffrey M.; Shaw, Kendrick M.

    2010-01-01

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

  2. Multiple Realizability and Biological Laws

    NARCIS (Netherlands)

    Raerinne, Jani P.; Eronen, Markus I.

    2012-01-01

    We critically analyze Alexander Rosenberg's argument based on the multiple realizability of biological properties that there are no biological laws. The argument is intuitive and suggestive. Nevertheless, a closer analysis reveals that the argument rests on dubious assumptions about the nature of

  3. WE-B-304-00: Point/Counterpoint: Biological Dose Optimization

    International Nuclear Information System (INIS)

    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

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

    Science.gov (United States)

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

    2015-08-21

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

  5. Synthetic biology, inspired by synthetic chemistry.

    Science.gov (United States)

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

    2012-07-16

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

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

    Directory of Open Access Journals (Sweden)

    Clemens D Cohen

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

  7. Quantification of biologically effective environmental UV irradiance

    Science.gov (United States)

    Horneck, G.

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

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

    Science.gov (United States)

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

    2017-04-01

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

  9. G‐LoSA: An efficient computational tool for local structure‐centric biological studies and drug design

    Science.gov (United States)

    2016-01-01

    Abstract Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G‐LoSA. G‐LoSA aligns protein local structures in a sequence order independent way and provides a GA‐score, a chemical feature‐based and size‐independent structure similarity score. Our benchmark validation shows the robust performance of G‐LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure‐centric comparative biology studies. In particular, G‐LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G‐LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer‐aided drug design. We hope that G‐LoSA can be a useful computational method for exploring interesting biological problems through large‐scale comparison of protein local structures and facilitating drug discovery research and development. G‐LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. PMID:26813336

  10. G-LoSA: An efficient computational tool for local structure-centric biological studies and drug design.

    Science.gov (United States)

    Lee, Hui Sun; Im, Wonpil

    2016-04-01

    Molecular recognition by protein mostly occurs in a local region on the protein surface. Thus, an efficient computational method for accurate characterization of protein local structural conservation is necessary to better understand biology and drug design. We present a novel local structure alignment tool, G-LoSA. G-LoSA aligns protein local structures in a sequence order independent way and provides a GA-score, a chemical feature-based and size-independent structure similarity score. Our benchmark validation shows the robust performance of G-LoSA to the local structures of diverse sizes and characteristics, demonstrating its universal applicability to local structure-centric comparative biology studies. In particular, G-LoSA is highly effective in detecting conserved local regions on the entire surface of a given protein. In addition, the applications of G-LoSA to identifying template ligands and predicting ligand and protein binding sites illustrate its strong potential for computer-aided drug design. We hope that G-LoSA can be a useful computational method for exploring interesting biological problems through large-scale comparison of protein local structures and facilitating drug discovery research and development. G-LoSA is freely available to academic users at http://im.compbio.ku.edu/GLoSA/. © 2016 The Protein Society.

  11. 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

  12. Studies on bacterial flora and biological control agent of Cydia ...

    African Journals Online (AJOL)

    In the present study, in order to find a more effective and safe biological control agent against Cydia pomonella, we investigated the bacterial flora and tested them for insecticidal effects on this insect. According to morphological, physiological and biochemical tests, bacterial flora were identified as Proteus rettgeri (Cp1), ...

  13. Vitamin D biology and heart failure : Clinical and experimental studies

    NARCIS (Netherlands)

    Meems, Laura

    2015-01-01

    In the last decade, vitamin D biology has been studied more extensively than ever before.. The use of vitamin D supplements is common, and so is determination of plasma vitamin D status. Besides its role in bone homeostasis, vitamin D is thought to be an important player in the development and

  14. Innovations in Undergraduate Chemical Biology Education.

    Science.gov (United States)

    Van Dyke, Aaron R; Gatazka, Daniel H; Hanania, Mariah M

    2018-01-19

    Chemical biology derives intellectual vitality from its scientific interface: applying chemical strategies and perspectives to biological questions. There is a growing need for chemical biologists to synergistically integrate their research programs with their educational activities to become holistic teacher-scholars. This review examines how course-based undergraduate research experiences (CUREs) are an innovative method to achieve this integration. Because CUREs are course-based, the review first offers strategies for creating a student-centered learning environment, which can improve students' outcomes. Exemplars of CUREs in chemical biology are then presented and organized to illustrate the five defining characteristics of CUREs: significance, scientific practices, discovery, collaboration, and iteration. Finally, strategies to overcome common barriers in CUREs are considered as well as future innovations in chemical biology education.

  15. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

  16. Creating biological nanomaterials using synthetic biology

    International Nuclear Information System (INIS)

    Rice, MaryJoe K; Ruder, Warren C

    2014-01-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems. (review)

  17. Creating biological nanomaterials using synthetic biology.

    Science.gov (United States)

    Rice, MaryJoe K; Ruder, Warren C

    2014-02-01

    Synthetic biology is a new discipline that combines science and engineering approaches to precisely control biological networks. These signaling networks are especially important in fields such as biomedicine and biochemical engineering. Additionally, biological networks can also be critical to the production of naturally occurring biological nanomaterials, and as a result, synthetic biology holds tremendous potential in creating new materials. This review introduces the field of synthetic biology, discusses how biological systems naturally produce materials, and then presents examples and strategies for incorporating synthetic biology approaches in the development of new materials. In particular, strategies for using synthetic biology to produce both organic and inorganic nanomaterials are discussed. Ultimately, synthetic biology holds the potential to dramatically impact biological materials science with significant potential applications in medical systems.

  18. The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right.

    Science.gov (United States)

    Audie, J; Boyd, C

    2010-01-01

    The case for peptide-based drugs is compelling. Due to their chemical, physical and conformational diversity, and relatively unproblematic toxicity and immunogenicity, peptides represent excellent starting material for drug discovery. Nature has solved many physiological and pharmacological problems through the use of peptides, polypeptides and proteins. If nature could solve such a diversity of challenging biological problems through the use of peptides, it seems reasonable to infer that human ingenuity will prove even more successful. And this, indeed, appears to be the case, as a number of scientific and methodological advances are making peptides and peptide-based compounds ever more promising pharmacological agents. Chief among these advances are powerful chemical and biological screening technologies for lead identification and optimization, methods for enhancing peptide in vivo stability, bioavailability and cell-permeability, and new delivery technologies. Other advances include the development and experimental validation of robust computational methods for peptide lead identification and optimization. Finally, scientific analysis, biology and chemistry indicate the prospect of designing relatively small peptides to therapeutically modulate so-called 'undruggable' protein-protein interactions. Taken together a clear picture is emerging: through the synergistic use of the scientific imagination and the computational, chemical and biological methods that are currently available, effective peptide therapeutics for novel targets can be designed that surpass even the proven peptidic designs of nature.

  19. Microbiome studies in the biological control of plant pathogens

    Science.gov (United States)

    Biological control of plant pathogens, although it has been a successful alternative that has allowed to select microorganisms for the generation of bioproducts and to understand multiple biological mechanisms, cannot be considered as a strategy defined only from the selection of a range of cultiva...

  20. INNOVATION IN ACCOUNTING BIOLOGIC ASSETS

    OpenAIRE

    Stolуarova M. A.; Shcherbina I. D.

    2016-01-01

    The article describes the innovations in the classification and measurement of biological assets according to IFRS (IAS) 41 "Agriculture". The difficulties faced by agricultural producers using standard, set out in article. The classification based on the adopted amendments, according to which the fruit-bearing plants, previously accounted for as biological assets are measured at fair value are included in the category of fixed assets. The structure of biological assets and main means has bee...

  1. 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.

  2. Radical production in biological systems

    International Nuclear Information System (INIS)

    Johnson, J.R.; Akabani, G.

    1994-10-01

    This paper describes our effort to develop a metric for radiation exposure that is more fundamental than adsorbed dose and upon which a metric for exposure to chemicals could be based. This metric is based on the production of radicals by the two agents. Radicals produced by radiation in biological systems commonly assumed to be the same as those produced in water despite the presence of a variety of complex molecules. This may explain why the extensive efforts to describe the relationship between energy deposition (track structure) and molecular damage to DNA, based on the spectrum of radicals produced, have not been successful in explaining simple biological effects such as cell killing. Current models assume that DNA and its basic elements are immersed in water-like media and only model the production and diffusion of water-based radicals and their interaction with DNA structures; these models lack the cross sections associated with each macro-component of DNA and only treat water-based radicals. It has been found that such models are not realistic because DNA is not immersed in pure water. A computer code capable of simulating electron tracks, low-energy electrons, energy deposition in small molecules, and radical production and diffusion in water like media has been developed. This code is still in at a primitive stage and development is continuing. It is being used to study radical production by radiation, and radical diffusion and interactions in simple molecular systems following their production. We are extending the code to radical production by chemicals to complement our PBPK modeling efforts. It therefore has been developed primarily for use with radionuclides that are in biological materials, and not for radiation fields

  3. Biological Dosimetry of X-rays by micronuclei study; Dosimetria Biologica de rayos-X mediante el estudio de micronucleos

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, E; Silva, A; Navlet, J

    1991-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ {alpha}D+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs.

  4. Biological Dosimetry of X-rays by micronuclei study; Dosimetria Biologica de rayos-X mediante el estudio de micronucleos

    Energy Technology Data Exchange (ETDEWEB)

    Gomez, E.; Silva, A.; Navlet, J.

    1991-07-01

    Biological dosimetry consists of estimating absorbed doses for people exposed to radiation by mean biological methods. Several indicators used are based in haematological, biochemical an cytogenetics data, although nowadays without doubt, the cytogenetic method is considered to be the most reliable, in this case, the study of micronuclei in peripheral blood lymphocytes citokinetics blocked can be related to absorbed dose through an experimental calibration curve. An experimental dose-response curve, using micronuclei assay for X-rays at 250 kVp, 43,79 rads/min and temperature 37 degree centigree has been produced. Experimental data is fitted to model Y=C+ {alpha}D+BD''2 where Y is the number of micronuclei per cell and D the dose. The curve is compared with those produced elsewhere. (Author) 24 refs.

  5. Review of Russian language studies on radionuclide behaviour in agricultural animals: biological half-lives

    International Nuclear Information System (INIS)

    Fesenko, S.; Isamov, N.; Barnett, C.L.; Beresford, N.A.; Howard, B.J.; Sanzharova, N.; Fesenko, E.

    2015-01-01

    Extensive studies on transfer of radionuclides to animals were carried out in the USSR from the 1950s. Few of these studies were published in the international refereed literature or taken into account in international reviews. This paper continues a series of reviews of Russian language literature on radionuclide transfer to animals, providing information on biological half-lives of radionuclides in various animal tissues. The data are compared, where possible, with those reported in other countries. The data are normally quantified using a single or double exponential accounting for different proportions of the loss. For some products, such as milk, biological half-lives tend to be rapid at 1–3 d for most radionuclides and largely described by a single exponential. However, for other animal products biological half-lives can vary widely as they are influenced by many factors such as the age and size of the animal. Experimental protocols, such as the duration of the study, radionuclide administration and/or sample collection protocol also influence the value of biological half-lives estimated. - Highlights: • The data on biological half-lives from Russian language literature were reviewed. • Radionuclides with the shortest half-lives in animals are those which accumulate in soft tissues. • Short term behaviour is affected by the form in which radionuclides are administered. • There is a tendency for more rapid radionuclide turnover in younger animals

  6. Biosocial Conservation: Integrating Biological and Ethnographic Methods to Study Human-Primate Interactions.

    Science.gov (United States)

    Setchell, Joanna M; Fairet, Emilie; Shutt, Kathryn; Waters, Siân; Bell, Sandra

    2017-01-01

    Biodiversity conservation is one of the grand challenges facing society. Many people interested in biodiversity conservation have a background in wildlife biology. However, the diverse social, cultural, political, and historical factors that influence the lives of people and wildlife can be investigated fully only by incorporating social science methods, ideally within an interdisciplinary framework. Cultural hierarchies of knowledge and the hegemony of the natural sciences create a barrier to interdisciplinary understandings. Here, we review three different projects that confront this difficulty, integrating biological and ethnographic methods to study conservation problems. The first project involved wildlife foraging on crops around a newly established national park in Gabon. Biological methods revealed the extent of crop loss, the species responsible, and an effect of field isolation, while ethnography revealed institutional and social vulnerability to foraging wildlife. The second project concerned great ape tourism in the Central African Republic. Biological methods revealed that gorilla tourism poses risks to gorillas, while ethnography revealed why people seek close proximity to gorillas. The third project focused on humans and other primates living alongside one another in Morocco. Incorporating shepherds in the coproduction of ecological knowledge about primates built trust and altered attitudes to the primates. These three case studies demonstrate how the integration of biological and social methods can help us to understand the sustainability of human-wildlife interactions, and thus promote coexistence. In each case, an integrated biosocial approach incorporating ethnographic data produced results that would not otherwise have come to light. Research that transcends conventional academic boundaries requires the openness and flexibility to move beyond one's comfort zone to understand and acknowledge the legitimacy of "other" kinds of knowledge. It is

  7. Modular analysis of biological networks.

    Science.gov (United States)

    Kaltenbach, Hans-Michael; Stelling, Jörg

    2012-01-01

    The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

  8. Animal protein production modules in biological life support systems: Novel combined aquaculture techniques based on the closed equilibrated biological aquatic system (C.E.B.A.S.)

    Science.gov (United States)

    Blüm, V.; Andriske, M.; Kreuzberg, K.; Schreibman, M. P.

    Based on the experiences made with the Closed Equilibrated Biological Aquatic System (C.E.B.A.S.) which was primarily deveoloped for long-term and multi-generation experiments with aquatic animals and plants in a space station highly effective fresh water recycling modules were elaborated utilizing a combination of ammonia oxidizing bacteria filters and higher plants. These exhibit a high effectivity to eliminate phosphate and anorganic nitrogen compounds and arc. in addidition. able to contribute to the oxygen supply of the aquatic animals. The C.E.B.A.S. filter system is able to keep a closed artificial aquatic ecosystem containing teleost fishes and water snails biologically stable for several month and to eliminate waste products deriving from degraded dead fishes without a decrease of the oxygen concentration down to less than 3.5 mg/l at 25 °C. More advanced C.E.B.A.S. filter systems, the BIOCURE filters, were also developed for utilization in semiintensive and intensive aquaculture systems for fishes. In fact such combined animal-plant aquaculture systems represent highly effective productions sites for human food if proper plant and fish species are selected The present papers elucidates ways to novel aquaculture systems in which herbivorous fishes are raised by feeding them with plant biomass produced in the BIOCURE filters and presents the scheme of a modification which utilizes a plant species suitable also for human nutrition. Special attention is paid to the benefits of closed aquaculture system modules which may be integrated into bioregenerative life support systems of a higher complexity for, e. g.. lunar or planetary bases including some psychologiccal aspects of the introduction of animal protein production into plant-based life support systems. Moreover, the basic reproductive biological problems of aquatic animal breeding under reduced gravity are explained leading to a disposition of essential research programs in this context.

  9. Genome-wide association study and biological pathway analysis of the Eimeria maxima response in broilers.

    Science.gov (United States)

    Hamzić, Edin; Buitenhuis, Bart; Hérault, Frédéric; Hawken, Rachel; Abrahamsen, Mitchel S; Servin, Bertrand; Elsen, Jean-Michel; Pinard-van der Laan, Marie-Hélène; Bed'Hom, Bertrand

    2015-11-25

    Coccidiosis is the most common and costly disease in the poultry industry and is caused by protozoans of the Eimeria genus. The current control of coccidiosis, based on the use of anticoccidial drugs and vaccination, faces serious obstacles such as drug resistance and the high costs for the development of efficient vaccines, respectively. Therefore, the current control programs must be expanded with complementary approaches such as the use of genetics to improve the host response to Eimeria infections. Recently, we have performed a large-scale challenge study on Cobb500 broilers using E. maxima for which we investigated variability among animals in response to the challenge. As a follow-up to this challenge study, we performed a genome-wide association study (GWAS) to identify genomic regions underlying variability of the measured traits in the response to Eimeria maxima in broilers. Furthermore, we conducted a post-GWAS functional analysis to increase our biological understanding of the underlying response to Eimeria maxima challenge. In total, we identified 22 single nucleotide polymorphisms (SNPs) with q value Eimeria maxima in broilers. Furthermore, the post-GWAS functional analysis indicates that biological pathways and networks involved in tissue proliferation and repair along with the primary innate immune response may play the most important role during the early stage of Eimeria maxima infection in broilers.

  10. Influence of Ferrocene and Transition Metals on the Biological Activities of Schiff Bases

    International Nuclear Information System (INIS)

    Sadeq, A.; Fatesh, S.A.; Ibrahim, A.A.

    2016-01-01

    A series of organic and organometallic Schiff bases bearing phenylferrocene and their six transition metal complexes have been prepared and tested for their potential biological applications by using antifungal, antibacterial, antitumor activities, toxicity testing against the brine shrimp and DNA damage analysis. The copper and cobalt complexes of organic Schiff base showed significant antibacterial activity. The antifungal activities tested against six fungal strains revealed that N-(4-hydroxybenzylidene) aniline (A5) had the highest antifungal activity. Most of these compounds showed cytotoxic activity against the brine shrimp. The results of showed that these compounds had significant antitumor activity, up to 97% in the case of N-(4-chlorobenzylidene) aniline (A3). Only two compounds N-(2-hydroxy benzylidene) 4-ferrocenylaniline (F2) and Nickel (II) complex of organic Schiff base (CO/sub 2/) had DNA damaging activity at 20mg/ml concentration. (author)

  11. Improved normal tissue sparing in head and neck radiotherapy using biological cost function based-IMRT.

    Science.gov (United States)

    Anderson, N; Lawford, C; Khoo, V; Rolfo, M; Joon, D L; Wada, M

    2011-12-01

    Intensity-modulated radiotherapy (IMRT) has reduced the impact of acute and late toxicities associated with head and neck radiotherapy. Treatment planning system (TPS) advances in biological cost function based optimization (BBO) and improved segmentation techniques have increased organ at risk (OAR) sparing compared to conventional dose-based optimization (DBO). A planning study was undertaken to compare OAR avoidance in DBO and BBO treatment planning. Simultaneous integrated boost treatment plans were produced for 10 head and neck patients using both planning systems. Plans were compared for tar get coverage and OAR avoidance. Comparisons were made using the BBO TPS Monte Carlo dose engine to eliminate differences due to inherent algorithms. Target coverage (V95%) was maintained for both solutions. BBO produced lower OAR doses, with statistically significant improvement to left (12.3%, p = 0.005) and right parotid mean dose (16.9%, p = 0.004), larynx V50_Gy (71.0%, p = 0.005), spinal cord (21.9%, p < 0.001) and brain stem dose maximums (31.5%, p = 0.002). This study observed improved OAR avoidance with BBO planning. Further investigations will be undertaken to review any clinical benefit of this improved planned dosimetry.

  12. Using Cluster Analysis to Compartmentalize a Large Managed Wetland Based on Physical, Biological, and Climatic Geospatial Attributes.

    Science.gov (United States)

    Hahus, Ian; Migliaccio, Kati; Douglas-Mankin, Kyle; Klarenberg, Geraldine; Muñoz-Carpena, Rafael

    2018-04-27

    Hierarchical and partitional cluster analyses were used to compartmentalize Water Conservation Area 1, a managed wetland within the Arthur R. Marshall Loxahatchee National Wildlife Refuge in southeast Florida, USA, based on physical, biological, and climatic geospatial attributes. Single, complete, average, and Ward's linkages were tested during the hierarchical cluster analyses, with average linkage providing the best results. In general, the partitional method, partitioning around medoids, found clusters that were more evenly sized and more spatially aggregated than those resulting from the hierarchical analyses. However, hierarchical analysis appeared to be better suited to identify outlier regions that were significantly different from other areas. The clusters identified by geospatial attributes were similar to clusters developed for the interior marsh in a separate study using water quality attributes, suggesting that similar factors have influenced variations in both the set of physical, biological, and climatic attributes selected in this study and water quality parameters. However, geospatial data allowed further subdivision of several interior marsh clusters identified from the water quality data, potentially indicating zones with important differences in function. Identification of these zones can be useful to managers and modelers by informing the distribution of monitoring equipment and personnel as well as delineating regions that may respond similarly to future changes in management or climate.

  13. Nano- and micro-fabrication for single-molecule biological studies

    NARCIS (Netherlands)

    Huang, Z.

    2012-01-01

    Heterogeneity is a general feature in biological system. In order to avoid possible misleading effects of ensemble averaging, and to ensure a correct understanding of the biological system, it is very important to look into individuals, such as a single bio-molecule or a single cell, for details.

  14. Metabolism of labeled parathyroid hormone. V. Collected biological studies

    Energy Technology Data Exchange (ETDEWEB)

    Neuman, W F; Neuman, M W; Lane, K; Miller, L; Sammon, P J

    1975-01-01

    Biologically active /sup 125/I-labeled parathyroid hormone (/sup 125/I-PTH) was used in a series of studies in dogs and chickens designed to confirm and augment earlier studies in rats. As in rats, a three exponential equation was required to describe disappearance of /sup 125/I-PTH from the blood in the dog. The first two ''half-lives'' (1.8 and 7 min) accounted for the bulk of the dose. Also as in rats, deposition of apparently intact hormone took place rapidly in kidney, liver and bone in both the dog and the chicken. Degradation occurred very rapidly in all three target organs. Three labeled hormones of different biological activities were compared in the rat. Inactive, oxidized hormone was rejected by the liver but showed markedly increased deposition in kidney and the higher the purity of the hormone the higher was its uptake by liver. Exploration of a wide range of dosages revealed few effects on distribution (smaller depositon in liver and kidney at highest dosages, 65 ..mu..g/rat). Fresh sera did not degrade hormone rapidly or extensively. There was no deposition of hormone in intestinal mucosa, marrow, and red cells. Nephrectomy increased deposition in liver and bone. Finally, the perfused liver was capable of extensive degradation of the hormone.

  15. Biological variability dominates and influences analytical variance in HPLC-ECD studies of the human plasma metabolome

    Directory of Open Access Journals (Sweden)

    Willett Walter C

    2007-11-01

    Full Text Available Abstract Background Biomarker-based assessments of biological samples are widespread in clinical, pre-clinical, and epidemiological investigations. We previously developed serum metabolomic profiles assessed by HPLC-separations coupled with coulometric array detection that can accurately identify ad libitum fed and caloric-restricted rats. These profiles are being adapted for human epidemiology studies, given the importance of energy balance in human disease. Methods Human plasma samples were biochemically analyzed using HPLC separations coupled with coulometric electrode array detection. Results We identified these markers/metabolites in human plasma, and then used them to determine which human samples represent blinded duplicates with 100% accuracy (N = 30 of 30. At least 47 of 61 metabolites tested were sufficiently stable for use even after 48 hours of exposure to shipping conditions. Stability of some metabolites differed between individuals (N = 10 at 0, 24, and 48 hours, suggesting the influence of some biological factors on parameters normally considered as analytical. Conclusion Overall analytical precision (mean median CV, ~9% and total between-person variation (median CV, ~50–70% appear well suited to enable use of metabolomics markers in human clinical trials and epidemiological studies, including studies of the effect of caloric intake and balance on long-term cancer risk.

  16. Two Dogmas of Biology

    Directory of Open Access Journals (Sweden)

    Leonore Fleming

    2017-01-01

    Full Text Available The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology.

  17. Static Analysis for Systems Biology

    DEFF Research Database (Denmark)

    Nielson, Flemming; Nielson, Hanne Riis; Rosa, D. Schuch da

    2004-01-01

    This paper shows how static analysis techniques can help understanding biological systems. Based on a simple example we illustrate the outcome of performing three different analyses extracting information of increasing precision. We conclude by reporting on the potential impact and exploitation o...... of these techniques in systems biology....

  18. Neutron scattering and diffraction instrument for structural study on biology in Japan

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Ibaraki-ken (Japan)

    1994-12-31

    Neutron scattering and diffraction instruments in Japan which can be used for structural studies in biology are briefly introduced. Main specifications and general layouts of the instruments are shown.

  19. Integrating systems biology models and biomedical ontologies.

    Science.gov (United States)

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

    2011-08-11

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

  20. The Importance of Biological Databases in Biological Discovery.

    Science.gov (United States)

    Baxevanis, Andreas D; Bateman, Alex

    2015-06-19

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

  1. Controllability and observability of Boolean networks arising from biology

    Science.gov (United States)

    Li, Rui; Yang, Meng; Chu, Tianguang

    2015-02-01

    Boolean networks are currently receiving considerable attention as a computational scheme for system level analysis and modeling of biological systems. Studying control-related problems in Boolean networks may reveal new insights into the intrinsic control in complex biological systems and enable us to develop strategies for manipulating biological systems using exogenous inputs. This paper considers controllability and observability of Boolean biological networks. We propose a new approach, which draws from the rich theory of symbolic computation, to solve the problems. Consequently, simple necessary and sufficient conditions for reachability, controllability, and observability are obtained, and algorithmic tests for controllability and observability which are based on the Gröbner basis method are presented. As practical applications, we apply the proposed approach to several different biological systems, namely, the mammalian cell-cycle network, the T-cell activation network, the large granular lymphocyte survival signaling network, and the Drosophila segment polarity network, gaining novel insights into the control and/or monitoring of the specific biological systems.

  2. Biological AMS at Uppsala University: Status report

    International Nuclear Information System (INIS)

    Salehpour, Mehran; Forsgard, Niklas; Possnert, Goeran

    2010-01-01

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

  3. 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.

  4. Biological performance of Liquidambar orientalis Mill. heartwood

    Science.gov (United States)

    Evren Terzi; S. Nami Kartal; Claudia Marcela Ibáñez; Coþkun Köse; Rachel Arango; Carol A. Clausen; Frederick. Green III

    2012-01-01

    New approaches for wood protection based on green technologies have increased interest in using heartwood portions of certain wood species for the effects (toxic and antioxidant properties, chelate formation, hydrophobicity) of extractives located in heartwood. This study evaluated the biological performance of heartwood of Liquidambar orientalis...

  5. 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

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-10-01

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

  8. Studies on digoxin derivatives in different biological media by radioimmunoassay

    International Nuclear Information System (INIS)

    Barmasch, Martha; Perez, L.N.; Altschuler, Noe.

    1978-05-01

    The fundamental aim of this study was to develop a methodology to be applied to pharmacological studies, directed to demonstrate the passage of digitalic compounds through the blood-brain barrier. This study was a comparative one between β methyl digoxin (βMD) and digitoxin (Dt). A methodology of radioimmunoassay was developed for different biological media: serum (S), plasma (P) and cerebro spinal fluid (CSF). In addition, the immunochemical behaviour (affinity, displacement, etc.) of βMD was studied when reacted with digoxin (D) and digoxin-antisera, supplied by the commercial kits utilized in these studies. (author) [es

  9. Biological validation of physical coastal waters classification along the NE Atlantic region based on rocky macroalgae distribution

    Science.gov (United States)

    Ramos, Elvira; Puente, Araceli; Juanes, José Antonio; Neto, João M.; Pedersen, Are; Bartsch, Inka; Scanlan, Clare; Wilkes, Robert; Van den Bergh, Erika; Ar Gall, Erwan; Melo, Ricardo

    2014-06-01

    A methodology to classify rocky shores along the North East Atlantic (NEA) region was developed. Previously, biotypes and the variability of environmental conditions within these were recognized based on abiotic data. A biological validation was required in order to support the ecological meaning of the physical typologies obtained. A database of intertidal macroalgae species occurring in the coastal area between Norway and the South Iberian Peninsula was generated. Semi-quantitative abundance data of the most representative macroalgal taxa were collected in three levels: common, rare or absent. Ordination and classification multivariate analyses revealed a clear latitudinal gradient in the distribution of macroalgae species resulting in two distinct groups: one northern and one southern group, separated at the coast of Brittany (France). In general, the results based on biological data coincided with the results based on physical characteristics. The ecological meaning of the coastal waters classification at a broad scale shown in this work demonstrates that it can be valuable as a practical tool for conservation and management purposes.

  10. Application of Raman Microspectroscopic and Raman imaging techniques for cell biological studies

    NARCIS (Netherlands)

    Puppels, G.J.; Puppels, G.J.; Bakker schut, T.C.; Bakker Schut, T.C.; Sijtsema, N.M.; Grond, M.; Grond, M.; Maraboeuf, F.; de Grauw, C.J.; de Grauw, C.J.; Figdor, Carl; Greve, Jan

    1995-01-01

    Raman spectroscopy is being used to study biological molecules for some three decades now. Thanks to continuing advances in instrumentation more and more applications have become feasible in which molecules are studied in situ, and this has enabled Raman spectroscopy to enter the realms of

  11. The Dominance Behavioral System and Psychopathology: Evidence from Self-Report, Observational, and Biological Studies

    Science.gov (United States)

    Johnson, Sheri L.; Leedom, Liane J.; Muhtadie, Luma

    2012-01-01

    The dominance behavioral system (DBS) can be conceptualized as a biologically based system that guides dominance motivation, dominant and subordinate behavior, and responsivity to perceptions of power and subordination. A growing body of research suggests that problems with the DBS are evident across a broad range of psychopathologies. We begin by…

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

    Science.gov (United States)

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

    2016-06-16

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

  13. Clinically Applicable Monte Carlo–based Biological Dose Optimization for the Treatment of Head and Neck Cancers With Spot-Scanning Proton Therapy

    Energy Technology Data Exchange (ETDEWEB)

    Wan Chan Tseung, Hok Seum, E-mail: wanchantseung.hok@mayo.edu; Ma, Jiasen; Kreofsky, Cole R.; Ma, Daniel J.; Beltran, Chris

    2016-08-01

    Purpose: Our aim is to demonstrate the feasibility of fast Monte Carlo (MC)–based inverse biological planning for the treatment of head and neck tumors in spot-scanning proton therapy. Methods and Materials: Recently, a fast and accurate graphics processor unit (GPU)–based MC simulation of proton transport was developed and used as the dose-calculation engine in a GPU-accelerated intensity modulated proton therapy (IMPT) optimizer. Besides dose, the MC can simultaneously score the dose-averaged linear energy transfer (LET{sub d}), which makes biological dose (BD) optimization possible. To convert from LET{sub d} to BD, a simple linear relation was assumed. By use of this novel optimizer, inverse biological planning was applied to 4 patients, including 2 small and 1 large thyroid tumor targets, as well as 1 glioma case. To create these plans, constraints were placed to maintain the physical dose (PD) within 1.25 times the prescription while maximizing target BD. For comparison, conventional intensity modulated radiation therapy (IMRT) and IMPT plans were also created using Eclipse (Varian Medical Systems) in each case. The same critical-structure PD constraints were used for the IMRT, IMPT, and biologically optimized plans. The BD distributions for the IMPT plans were obtained through MC recalculations. Results: Compared with standard IMPT, the biologically optimal plans for patients with small tumor targets displayed a BD escalation that was around twice the PD increase. Dose sparing to critical structures was improved compared with both IMRT and IMPT. No significant BD increase could be achieved for the large thyroid tumor case and when the presence of critical structures mitigated the contribution of additional fields. The calculation of the biologically optimized plans can be completed in a clinically viable time (<30 minutes) on a small 24-GPU system. Conclusions: By exploiting GPU acceleration, MC-based, biologically optimized plans were created for

  14. 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.

  15. Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

    Directory of Open Access Journals (Sweden)

    Ivan B. Djordjevic

    2015-08-01

    Full Text Available Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i Markovian classical model, (ii Markovian-like quantum model, and (iii hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage Markov chain-like models of aging, which

  16. A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

    Directory of Open Access Journals (Sweden)

    Rosalind A. Le Feuvre

    2018-06-01

    Full Text Available Society is on the cusp of harnessing recent advances in synthetic biology to discover new bio-based products and routes to their affordable and sustainable manufacture. This is no more evident than in the discovery and manufacture of Synthetic Biological Materials, where synthetic biology has the capacity to usher in a new Materials from Biology era that will revolutionise the discovery and manufacture of innovative synthetic biological materials. These will encompass novel, smart, functionalised and hybrid materials for diverse applications whose discovery and routes to bio-production will be stimulated by the fusion of new technologies positioned across physical, digital and biological spheres. This article, which developed from an international workshop held in Manchester, United Kingdom, in 2017 [1], sets out to identify opportunities in the new materials from biology era. It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches. This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products to market. Pathway opportunities are identified that will help foster expertise sharing and infrastructure development to accelerate the delivery of a new generation of synthetic biological materials and the leveraging of existing investments in synthetic biology and advanced materials research to achieve this goal. Keywords: Synthetic biology, Materials, Biological materials, Biomaterials, Advanced materials

  17. An ESR study on biological dosimeters: Human hair

    International Nuclear Information System (INIS)

    Colak, Seyda; Ozbey, Turan

    2011-01-01

    In the present work, characteristic features of the radicals found in untreated, gamma and UV-irradiated and mechanical damaged human hair samples were investigated by ESR spectroscopy. Heights of the resonance peaks measured with respect to the spectrum base line were used to monitor microwave power, dose-response, storage time and temperature dependent kinetic features of the radical species contributing to the formation of recorded experimental ESR spectra. Peak heights and g-values (2.0037-2.0052) determined from recorded spectra of hair were color dependent with ΔHpp-0.47 mT. The act of cutting hair samples gene rates sulfur centered radicals which are found in the a-keratin structure of hair. The variations of the peak heights with temperature were related with the water content found in the hair samples. In the 6-1100 Gy dose range, a linear + quadratic dose-response curve was recorded for hair and the mean radiation yield (G mean ) was calculated to be 0.4. The gamma radiation induced radicals were stable for a several hours at room temperature storage conditions. Based on these findings it was concluded that human hair samples could be used as biological/personnel dosimeters and that ESR spectroscopy could be successfully used as a potential technique for monitoring its dosimetric behaviours.

  18. Biological isotopy. Introduction to the isotopic effects and to their applications in biology

    International Nuclear Information System (INIS)

    Tcherkez, G.

    2010-01-01

    Since their discovery in the beginning of the 20. century, the study of stable isotopes has considerably developed. This domain, which remained limited in its applications until the 1990's, has become particularly important thereafter thanks to its practical applications and in particular to its economical impacts. Many techniques used in fraud control, in drugs use control, in selection of high-yield plants etc are based on isotopic abundance measurements. This reference book gives a synthesis of our actual knowledge on the use of stable isotopes and of isotope fractionation in biology. It presents the basic notions of isotopic biochemistry and explains the origin of the isotopic effects. The application principles of these effects to metabolism, to organisms physiology, to environmental biology etc are explained and detailed using examples and exercises. The first chapters present the basic knowledge which defines, from a mathematical point-of-view, the isotopic effects of chemical reactions or of physical processes taking place in biology. The measurements principle of natural isotopes abundance is then synthesised. Finally, all these notions are applied at different scales: enzymes, physiology, metabolism, environment, ecosystems and fraud crackdown. (J.S.)

  19. Materiomics: biological protein materials, from nano to macro

    Science.gov (United States)

    Cranford, Steven; Buehler, Markus J

    2010-01-01

    Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics – discovering Nature’s complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature’s materials have been hindered by our lack of fundamental understanding of these materials’ intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties

  20. Hemodynamic Evaluation of a Biological and Mechanical Aortic Valve Prosthesis Using Patient-Specific MRI-Based CFD.

    Science.gov (United States)

    Hellmeier, Florian; Nordmeyer, Sarah; Yevtushenko, Pavlo; Bruening, Jan; Berger, Felix; Kuehne, Titus; Goubergrits, Leonid; Kelm, Marcus

    2018-01-01

    Modeling different treatment options before a procedure is performed is a promising approach for surgical decision making and patient care in heart valve disease. This study investigated the hemodynamic impact of different prostheses through patient-specific MRI-based CFD simulations. Ten time-resolved MRI data sets with and without velocity encoding were obtained to reconstruct the aorta and set hemodynamic boundary conditions for simulations. Aortic hemodynamics after virtual valve replacement with a biological and mechanical valve prosthesis were investigated. Wall shear stress (WSS), secondary flow degree (SFD), transvalvular pressure drop (TPD), turbulent kinetic energy (TKE), and normalized flow displacement (NFD) were evaluated to characterize valve-induced hemodynamics. The biological prostheses induced significantly higher WSS (medians: 9.3 vs. 8.6 Pa, P = 0.027) and SFD (means: 0.78 vs. 0.49, P = 0.002) in the ascending aorta, TPD (medians: 11.4 vs. 2.7 mm Hg, P = 0.002), TKE (means: 400 vs. 283 cm 2 /s 2 , P = 0.037), and NFD (means: 0.0994 vs. 0.0607, P = 0.020) than the mechanical prostheses. The differences between the prosthesis types showed great inter-patient variability, however. Given this variability, a patient-specific evaluation is warranted. In conclusion, MRI-based CFD offers an opportunity to assess the interactions between prosthesis and patient-specific boundary conditions, which may help in optimizing surgical decision making and providing additional guidance to clinicians. © 2017 International Center for Artificial Organs and Transplantation and Wiley Periodicals, Inc.