[Advance in molecular biology of Dendrobium (Orchidaceae)].

Science.gov (United States)

Li, Qing; Li, Biao; Guo, Shun-Xing

2016-08-01

With the development of molecular biology, the process in molecular biology research of Dendrobium is going fast. Not only did it provide new ways to identify Dendrobium quickly, reveal the genetic diversity and relationship of Dendrobium, but also lay the vital foundation for explaining the mechanism of Dendrobium growth and metabolism. The present paper reviews the recent process in molecular biology research of Dendrobium from three aspects, including molecular identification, genetic diversity and functional genes. And this review will facilitate the development of this research area and Dendrobium. Copyright© by the Chinese Pharmaceutical Association.

History of the molecular biology of cytomegaloviruses.

Science.gov (United States)

Stinski, Mark F

2014-01-01

The history of the molecular biology of cytomegaloviruses from the purification of the virus and the viral DNA to the cloning and expression of the viral genes is reviewed. A key genetic element of cytomegalovirus (the CMV promoter) contributed to our understanding of eukaryotic cell molecular biology and to the development of lifesaving therapeutic proteins. The study of the molecular biology of cytomegaloviruses also contributed to the development of antivirals to control the viral infection.

Molecular biology of the cell

CERN Document Server

Alberts, Bruce; Lewis, Julian

2000-01-01

Molecular Biology of the Cell is the classic in-dept text reference in cell biology. By extracting the fundamental concepts from this enormous and ever-growing field, the authors tell the story of cell biology, and create a coherent framework through which non-expert readers may approach the subject. Written in clear and concise language, and beautifully illustrated, the book is enjoyable to read, and it provides a clear sense of the excitement of modern biology. Molecular Biology of the Cell sets forth the current understanding of cell biology (completely updated as of Autumn 2001), and it explores the intriguing implications and possibilities of the great deal that remains unknown. The hallmark features of previous editions continue in the Fourth Edition. The book is designed with a clean and open, single-column layout. The art program maintains a completely consistent format and style, and includes over 1,600 photographs, electron micrographs, and original drawings by the authors. Clear and concise concept...

Monod and the spirit of molecular biology.

Science.gov (United States)

Morange, Michel

2015-06-01

The founders of molecular biology shared views on the place of biology within science, as well as on the relations of molecular biology to Darwinism. Jacques Monod was no exception, but the study of his writings is particularly interesting because he expressed his point of view very clearly and pushed the implications of some of his choices further than most of his contemporaries. The spirit of molecular biology is no longer the same as in the 1960s but, interestingly, Monod anticipated some recent evolutions of this discipline. Copyright © 2015 Académie des sciences. Published by Elsevier SAS. All rights reserved.

The molecular biology capstone assessment: a concept assessment for upper-division molecular biology students.

Science.gov (United States)

Couch, Brian A; Wood, William B; Knight, Jennifer K

2015-03-02

Measuring students' conceptual understandings has become increasingly important to biology faculty members involved in evaluating and improving departmental programs. We developed the Molecular Biology Capstone Assessment (MBCA) to gauge comprehension of fundamental concepts in molecular and cell biology and the ability to apply these concepts in novel scenarios. Targeted at graduating students, the MBCA consists of 18 multiple-true/false (T/F) questions. Each question consists of a narrative stem followed by four T/F statements, which allows a more detailed assessment of student understanding than the traditional multiple-choice format. Questions were iteratively developed with extensive faculty and student feedback, including validation through faculty reviews and response validation through student interviews. The final assessment was taken online by 504 students in upper-division courses at seven institutions. Data from this administration indicate that the MBCA has acceptable levels of internal reliability (α=0.80) and test-retest stability (r=0.93). Students achieved a wide range of scores with a 67% overall average. Performance results suggest that students have an incomplete understanding of many molecular biology concepts and continue to hold incorrect conceptions previously documented among introductory-level students. By pinpointing areas of conceptual difficulty, the MBCA can provide faculty members with guidance for improving undergraduate biology programs. © 2015 B. A. Couch et al. 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).

The Molecular Biology of Pestiviruses.

Science.gov (United States)

Tautz, Norbert; Tews, Birke Andrea; Meyers, Gregor

2015-01-01

Pestiviruses are among the economically most important pathogens of livestock. The biology of these viruses is characterized by unique and interesting features that are both crucial for their success as pathogens and challenging from a scientific point of view. Elucidation of these features at the molecular level has made striking progress during recent years. The analyses revealed that major aspects of pestivirus biology show significant similarity to the biology of human hepatitis C virus (HCV). The detailed molecular analyses conducted for pestiviruses and HCV supported and complemented each other during the last three decades resulting in elucidation of the functions of viral proteins and RNA elements in replication and virus-host interaction. For pestiviruses, the analyses also helped to shed light on the molecular basis of persistent infection, a special strategy these viruses have evolved to be maintained within their host population. The results of these investigations are summarized in this chapter. © 2015 Elsevier Inc. All rights reserved.

Topology in Molecular Biology

CERN Document Server

Monastyrsky, Michail Ilych

2007-01-01

The book presents a class of new results in molecular biology for which topological methods and ideas are important. These include: the large-scale conformation properties of DNA; computational methods (Monte Carlo) allowing the simulation of large-scale properties of DNA; the tangle model of DNA recombination and other applications of Knot theory; dynamics of supercoiled DNA and biocatalitic properties of DNA; the structure of proteins; and other very recent problems in molecular biology. The text also provides a short course of modern topology intended for the broad audience of biologists and physicists. The authors are renowned specialists in their fields and some of the new results presented here are documented for the first time in monographic form.

Biology relevant to space radiation

International Nuclear Information System (INIS)

Fry, R.J.M.

1996-01-01

The biological effects of the radiations to which mankind on earth are exposed are becoming known with an increasing degree of detail. This knowledge is the basis of the estimates of risk that, in turn, fosters a comprehensive and evolving radiation protection system. The substantial body of information has been, and is being, applied to questions about the biological effects of radiation is space and the associated risk estimates. The purpose of this paper is not to recount all the biological effect of radiation but to concentrate on those that may occur as a result from exposure to the radiations encountered in space. In general, the biological effects of radiation in space are the same as those on earth. However, the evidence that the effects on certain tissues by the heaviest-charged particles can be interpreted on the basis of our knowledge about other high-LET radiation is equivocal. This specific question will be discussed in greater detail later. It is important to point out the that there are only limited data about the effects on humans of two components of the radiations in space, namely protons and heavy ions. Thus predictions of effects on space crews are based on experimental systems exposed on earth at rates and fluences that are higher than those in space and one the effects of gamma or x rays with estimates of the equivalent doses using quality factors

Space Biology in the 21st century

Science.gov (United States)

Halstead, Thora W.; Krauss, Robert W.

1990-01-01

Space Biology is poised to make significant contributions to science in the next century. A carefully crafted, but largely ground-based, program in the United States has evolved major questions that require answers through experiments in space. Science, scientists, and the new long-term spacecrafts designed by NASA will be available for the first time to mount a serious Space Biology effort. The scientific challenge is of such importance that success will provide countless benefits to biologically dependent areas such as medicine, food, and commerce in the decades ahead. The international community is rapidly expanding its role in this field. The United States should generate the resources that will allow progress in Space Biology to match the recognized progress made in aeronautics and the other space sciences.

Aging in a Relativistic Biological Space-Time

Directory of Open Access Journals (Sweden)

Davide Maestrini

2018-05-01

Full Text Available Here we present a theoretical and mathematical perspective on the process of aging. We extend the concepts of physical space and time to an abstract, mathematically-defined space, which we associate with a concept of “biological space-time” in which biological dynamics may be represented. We hypothesize that biological dynamics, represented as trajectories in biological space-time, may be used to model and study different rates of biological aging. As a consequence of this hypothesis, we show how dilation or contraction of time analogous to relativistic corrections of physical time resulting from accelerated or decelerated biological dynamics may be used to study precipitous or protracted aging. We show specific examples of how these principles may be used to model different rates of aging, with an emphasis on cancer in aging. We discuss how this theory may be tested or falsified, as well as novel concepts and implications of this theory that may improve our interpretation of biological aging.

Fundamental plant biology enabled by the space shuttle.

Science.gov (United States)

Paul, Anna-Lisa; Wheeler, Ray M; Levine, Howard G; Ferl, Robert J

2013-01-01

The relationship between fundamental plant biology and space biology was especially synergistic in the era of the Space Shuttle. While all terrestrial organisms are influenced by gravity, the impact of gravity as a tropic stimulus in plants has been a topic of formal study for more than a century. And while plants were parts of early space biology payloads, it was not until the advent of the Space Shuttle that the science of plant space biology enjoyed expansion that truly enabled controlled, fundamental experiments that removed gravity from the equation. The Space Shuttle presented a science platform that provided regular science flights with dedicated plant growth hardware and crew trained in inflight plant manipulations. Part of the impetus for plant biology experiments in space was the realization that plants could be important parts of bioregenerative life support on long missions, recycling water, air, and nutrients for the human crew. However, a large part of the impetus was that the Space Shuttle enabled fundamental plant science essentially in a microgravity environment. Experiments during the Space Shuttle era produced key science insights on biological adaptation to spaceflight and especially plant growth and tropisms. In this review, we present an overview of plant science in the Space Shuttle era with an emphasis on experiments dealing with fundamental plant growth in microgravity. This review discusses general conclusions from the study of plant spaceflight biology enabled by the Space Shuttle by providing historical context and reviews of select experiments that exemplify plant space biology science.

Microgravity research in plant biological systems: Realizing the potential of molecular biology

Science.gov (United States)

Lewis, Norman G.; Ryan, Clarence A.

1993-01-01

The sole all-pervasive feature of the environment that has helped shape, through evolution, all life on Earth is gravity. The near weightlessness of the Space Station Freedom space environment allows gravitational effects to be essentially uncoupled, thus providing an unprecedented opportunity to manipulate, systematically dissect, study, and exploit the role of gravity in the growth and development of all life forms. New and exciting opportunities are now available to utilize molecular biological and biochemical approaches to study the effects of microgravity on living organisms. By careful experimentation, we can determine how gravity perception occurs, how the resulting signals are produced and transduced, and how or if tissue-specific differences in gene expression occur. Microgravity research can provide unique new approaches to further our basic understanding of development and metabolic processes of cells and organisms, and to further the application of this new knowledge for the betterment of humankind.

Ins and outs of systems biology vis-à-vis molecular biology: continuation or clear cut?

Science.gov (United States)

De Backer, Philippe; De Waele, Danny; Van Speybroeck, Linda

2010-03-01

The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology 'revolutionizes' molecular biology and 'transcends' its assumed reductionism. The strength of this claim appears to depend on how molecular and systems biology are characterised and on how reductionism is interpreted. Doing credit to molecular biology and to methodological reductionism, it is argued that the distinction between molecular and systems biology is gradual rather than sharp. As such, the classical challenge in biology to manage, interpret and integrate biological data into functional wholes is further intensified by systems biology's use of modelling and bioinformatics, and by its scale enlargement.

Measurement Frontiers in Molecular Biology

Science.gov (United States)

Laderman, Stephen

2009-03-01

Developments of molecular measurements and manipulations have long enabled forefront research in evolution, genetics, biological development and its dysfunction, and the impact of external factors on the behavior of cells. Measurement remains at the heart of exciting and challenging basic and applied problems in molecular and cell biology. Methods to precisely determine the identity and abundance of particular molecules amongst a complex mixture of similar and dissimilar types require the successful design and integration of multiple steps involving biochemical manipulations, separations, physical probing, and data processing. Accordingly, today's most powerful methods for characterizing life at the molecular level depend on coordinated advances in applied physics, biochemistry, chemistry, computer science, and engineering. This is well illustrated by recent approaches to the measurement of DNA, RNA, proteins, and intact cells. Such successes underlie well founded visions of how molecular biology can further assist in answering compelling scientific questions and in enabling the development of remarkable advances in human health. These visions, in turn, are motivating the interdisciplinary creation of even more comprehensive measurements. As a further and closely related consequence, they are motivating innovations in the conceptual and practical approaches to organizing and visualizing large, complex sets of interrelated experimental results and distilling from those data compelling, informative conclusions.

The Molecular Era of Surfactant Biology

OpenAIRE

Whitsett, Jeffrey A.

2014-01-01

Advances in the physiology, biochemistry, molecular and cell biology of the pulmonary surfactant system transformed the clinical care and outcome of preterm infants with respiratory distress syndrome. The molecular era of surfactant biology provided genetic insights into the pathogenesis of pulmonary disorders, previously termed “idiopathic” that affect newborn infants, children and adults. Knowledge related to the structure and function of the surfactant proteins and their roles in alveolar ...

Characterization of Outer Space Radiation Induced Changes in Extremophiles Utilizing Deep Space Gateway Opportunities

Science.gov (United States)

Venkateswaran, K.; Wang, C.; Smith, D.; Mason, C.; Landry, K.; Rettberg, P.

2018-02-01

Extremophilic microbial survival, adaptation, biological functions, and molecular mechanisms associated with outer space radiation can be tested by exposing them onto Deep Space Gateway hardware (inside/outside) using microbiology and molecular biology techniques.

Gravitational biology on the space station

Science.gov (United States)

Keefe, J. R.; Krikorian, A. D.

1983-01-01

The current status of gravitational biology is summarized, future areas of required basic research in earth-based and spaceflight projects are presented, and potential applications of gravitational biology on a space station are demonstrated. Topics covered include vertebrate reproduction, prenatal/postnatal development, a review of plant space experiments, the facilities needed for growing plants, gravimorphogenesis, thigmomorphogenesis, centrifuges, maintaining a vivarium, tissue culture, and artificial human organ generation. It is proposed that space stations carrying out these types of long-term research be called the National Space Research Facility.

Teaching Molecular Biology with Microcomputers.

Science.gov (United States)

Reiss, Rebecca; Jameson, David

1984-01-01

Describes a series of computer programs that use simulation and gaming techniques to present the basic principles of the central dogma of molecular genetics, mutation, and the genetic code. A history of discoveries in molecular biology is presented and the evolution of these computer assisted instructional programs is described. (MBR)

Space Biology in Russia Today

Science.gov (United States)

Grigoriev, Anatoly; Sychev, Vladimir; Ilyin, Eugene

At present space biology research in Russia is making significant progress in several areas of high priority. Gravitational biology. In April-May 2013, a successful 30-day flight of the biological satellite (biosatellite) Bion-M1 was conducted, which carried rodents (mice and gerbils), geckos, fish, mollusks, crustaceans, microorganisms, insects, lower and higher plants, seeds, etc. The investigations were performed by Russian scientists as well as by researchers from NASA, CNES, DLR and South Korea. Foton-M4 carrying various biological specimens is scheduled to launch in 2014. Work has begun to develop science research programs to be implemented onboard Bion-M2 and Bion-M3 as well as on high apogee recoverable spacecraft. Study of the effects of microgravity on the growth and development of higher plants cultivated over several generations on the International Space Station (ISS) has been recently completed. Space radiobiology. Regular experiments aimed at investigating the effects of high-energy galactic cosmic rays on the animal central nervous system and behavior are being carried out using the Particle Accelerator in the town of Dubna. Biological (environmental) life support systems. In recent years, experiments have been performed on the ISS to upgrade technologies of plant cultivation in microgravity. Advanced greenhouse mockups have been built and are currentlyundergoing bioengineering tests. Technologies of waste utilization in space are being developed. Astrobiology experiments in orbital missions. In 2010, the Biorisk experiment on bacterial and fungal spores, seeds and dormant forms of organisms was completed. The payload containing the specimens was installed on the exterior wall of the ISS and was exposed to outer space for 31 months. In addition, Bion-M1 also carried seeds, bacterial spores and microbes that were exposed to outer space effects. The survival rate of bacterial spores incorporated into man-made meteorites, that were attached to the

The progress of molecular biology in radiation research

International Nuclear Information System (INIS)

Wei Kang

1989-01-01

The recent progress in application of molecular biology techniques in the study of radiation biology is reviewed. The three sections are as follows: (1) the study of DNA damage on molecular level, (2) the molecular mechanism of radiation cell genetics, including chromosome abberation and cell mutation, (3) the study on DNA repair gene with DNA mediated gene transfer techniques

Cell biology experiments conducted in space

Science.gov (United States)

Taylor, G. R.

1977-01-01

A review of cell biology experiments conducted during the first two decades of space flight is provided. References are tabulated for work done with six types of living test system: isolated viruses, bacteriophage-host, bacteria, yeasts and filamentous fungi, protozoans, and small groups of cells (such as hamster cell tissue and fertilized frog eggs). The general results of studies involving the survival of cells in space, the effect of space flight on growing cultures, the biological effects of multicharged high-energy particles, and the effects of space flight on the genetic apparatus of microorganisms are summarized. It is concluded that cell systems remain sufficiently stable during space flight to permit experimentation with models requiring a fixed cell line during the space shuttle era.

Biological challenges of true space settlement

Science.gov (United States)

Mankins, John C.; Mankins, Willa M.; Walter, Helen

2018-05-01

"Space Settlements" - i.e., permanent human communities beyond Earth's biosphere - have been discussed within the space advocacy community since the 1970s. Now, with the end of the International Space Station (ISS) program fast approaching (planned for 2024-2025) and the advent of low cost Earth-to-orbit (ETO) transportation in the near future, the concept is coming once more into mainstream. Considerable attention has been focused on various issues associated with the engineering and human health considerations of space settlement such as artificial gravity and radiation shielding. However, relatively little attention has been given to the biological implications of a self-sufficient space settlement. Three fundamental questions are explored in this paper: (1) what are the biological "foundations" of truly self-sufficient space settlements in the foreseeable future, (2) what is the minimum scale for such self-sustaining human settlements, and (3) what are the integrated biologically-driven system requirements for such settlements? The paper examines briefly the implications of the answers to these questions in relevant potential settings (including free space, the Moon and Mars). Finally, this paper suggests relevant directions for future research and development in order for such space settlements to become viable in the future.

The molecular biology in wound healing & non-healing wound.

Science.gov (United States)

Qing, Chun

2017-08-01

The development of molecular biology and other new biotechnologies helps us to recognize the wound healing and non-healing wound of skin in the past 30 years. This review mainly focuses on the molecular biology of many cytokines (including growth factors) and other molecular factors such as extracellular matrix (ECM) on wound healing. The molecular biology in cell movement such as epidermal cells in wound healing was also discussed. Moreover many common chronic wounds such as pressure ulcers, leg ulcers, diabetic foot wounds, venous stasis ulcers, etc. usually deteriorate into non-healing wounds. Therefore the molecular biology such as advanced glycation end products (AGEs) and other molecular factors in diabetes non-healing wounds were also reviewed. Copyright © 2017 Daping Hospital and the Research Institute of Surgery of the Third Military Medical University. Production and hosting by Elsevier B.V. All rights reserved.

The molecular biology of WHO grade I astrocytomas.

Science.gov (United States)

Marko, Nicholas F; Weil, Robert J

2012-12-01

World Health Organization (WHO) grade I astrocytomas include pilocytic astrocytoma (PA) and subependymal giant cell astrocytoma (SEGA). As technologies in pharmacologic neo-adjuvant therapy continue to progress and as molecular characteristics are progressively recognized as potential markers of both clinically significant tumor subtypes and response to therapy, interest in the biology of these tumors has surged. An updated review of the current knowledge of the molecular biology of these tumors is needed. We conducted a Medline search to identify published literature discussing the molecular biology of grade I astrocytomas. We then summarized this literature and discuss it in a logical framework through which the complex biology of these tumors can be clearly understood. A comprehensive review of the molecular biology of WHO grade I astrocytomas is presented. The past several years have seen rapid progress in the level of understanding of PA in particular, but the molecular literature regarding both PA and SEGA remains nebulous, ambiguous, and occasionally contradictory. In this review we provide a comprehensive discussion of the current understanding of the chromosomal, genomic, and epigenomic features of both PA and SEGA and provide a logical framework in which these data can be more readily understood.

From Molecular Biology to Biomedicine

International Nuclear Information System (INIS)

Salas, M.

2009-01-01

From Molecular Biology to Biomedicine. The well known molecular biologist Margarita Salas offered an informative conference at the CSN on progress in these areas since the discovery, more than half a century ago, of the structure of the molecule carrying genetic information, DNA, work that is having an enormous impact in areas such as biomedicine and foodstuff production. (Author)

Isotopes in molecular biology

International Nuclear Information System (INIS)

Goldfarb, P.S.G.

1988-01-01

The use of radioisotopes in molecular biology, with particular reference to the structure and functions of DNA, RNA and the cellular synthesis of proteins, is discussed. The use of labelled DNA and RNA in diagnostic techniques is presented. (U.K.)

Space Synthetic Biology (SSB)

Data.gov (United States)

National Aeronautics and Space Administration — This project focused on employing advanced biological engineering and bioelectrochemical reactor systems to increase life support loop closure and in situ resource...

Interactive analysis of systems biology molecular expression data

Directory of Open Access Journals (Sweden)

Prabhakar Sunil

2008-02-01

Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

Physics and the molecular revolution in plant biology: union needed for managing the future

Directory of Open Access Journals (Sweden)

Ulrich Lüttge

2016-10-01

Full Text Available The question was asked if there is still a prominent role of biophysics in plant biology in an age when molecular biology appears to be dominating. Mathematical formation of theory is essential in systems biology, and mathematics is more inherent in biophysics than in molecular biology. A survey is made identifying and briefly characterizing fields of plant biology where approaches of biophysics remain essential. In transport at membranes electrophysiology and thermodynamics are biophysical topics. Water is a special molecule. Its transport follows the physical laws of osmosis and gradients of water potential on the background of physics of hydraulic architecture. Photobiology needs understanding of the physics of electro-magnetic radiation of quantitative nature in photosynthesis and of qualitative nature in perception by the photo-sensors cryptochromes, phototropins and phytochrome in environmental responses and development. Biophysical oscillators can play a role in biological timing by the circadian clock. Integration in the self-organization of modules, such as roots, stems and leaves, for the emergence of whole plants as unitary organisms needs storage and transport of information where physical modes of signaling are essential with cross talks between electrical and hydraulic signals and with chemical signals. Examples are gravitropism and root-shoot interactions in water relations. All of these facets of plant biophysics overlie plant molecular biology and exchange with it. It is advocated that a union of approaches of plant molecular biology and biophysics needs to be cultivated. In many cases it is already operative. In bionics biophysics is producing output for practical applications linking biology with technology. Biomimetic engineering intrinsically uses physical approaches. An extreme biophysical perspective is looking out for life in space. Sustained and increased practice of biophysics with teaching and research deserves strong

GeneLab: NASA's Open Access, Collaborative Platform for Systems Biology and Space Medicine

Science.gov (United States)

Berrios, Daniel C.; Thompson, Terri G.; Fogle, Homer W.; Rask, Jon C.; Coughlan, Joseph C.

2015-01-01

NASA is investing in GeneLab1 (http:genelab.nasa.gov), a multi-year effort to maximize utilization of the limited resources to conduct biological and medical research in space, principally aboard the International Space Station (ISS). High-throughput genomic, transcriptomic, proteomic or other omics analyses from experiments conducted on the ISS will be stored in the GeneLab Data Systems (GLDS), an open-science information system that will also include a biocomputation platform with collaborative science capabilities, to enable the discovery and validation of molecular networks.

Assessment of Knowledge of Participants on Basic Molecular Biology Techniques after 5-Day Intensive Molecular Biology Training Workshops in Nigeria

Science.gov (United States)

Yisau, J. I.; Adagbada, A. O.; Bamidele, T.; Fowora, M.; Brai, B. I. C.; Adebesin, O.; Bamidele, M.; Fesobi, T.; Nwaokorie, F. O.; Ajayi, A.; Smith, S. I.

2017-01-01

The deployment of molecular biology techniques for diagnosis and research in Nigeria is faced with a number of challenges, including the cost of equipment and reagents coupled with the dearth of personnel skilled in the procedures and handling of equipment. Short molecular biology training workshops were conducted at the Nigerian Institute of…

Ordinary differential equations with applications in molecular biology.

Science.gov (United States)

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

Differential equations are of basic importance in molecular biology mathematics because many biological laws and relations appear mathematically in the form of a differential equation. In this article we presented some applications of mathematical models represented by ordinary differential equations in molecular biology. The vast majority of quantitative models in cell and molecular biology are formulated in terms of ordinary differential equations for the time evolution of concentrations of molecular species. Assuming that the diffusion in the cell is high enough to make the spatial distribution of molecules homogenous, these equations describe systems with many participating molecules of each kind. We propose an original mathematical model with small parameter for biological phospholipid pathway. All the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. If we reduce the size of the solution region the same small epsilon will result in a different condition number. It is clear that the solution for a smaller region is less difficult. We introduce the mathematical technique known as boundary function method for singular perturbation system. In this system, the small parameter is an asymptotic variable, different from the independent variable. In general, the solutions of such equations exhibit multiscale phenomena. Singularly perturbed problems form a special class of problems containing a small parameter which may tend to zero. Many molecular biology processes can be quantitatively characterized by ordinary differential equations. Mathematical cell biology is a very active and fast growing interdisciplinary area in which mathematical concepts, techniques, and models are applied to a variety of problems in developmental medicine and bioengineering. Among the different modeling approaches, ordinary differential equations (ODE) are particularly important and have led to significant advances

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.

Advancing cell biology through proteomics in space and time (PROSPECTS)

DEFF Research Database (Denmark)

Lamond, A.I.; Uhlen, M.; Horning, S.

2012-01-01

a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU......-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16...... quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how...

Evolution of egg coats: linking molecular biology and ecology.

Science.gov (United States)

Shu, Longfei; Suter, Marc J-F; Räsänen, Katja

2015-08-01

One central goal of evolutionary biology is to explain how biological diversity emerges and is maintained in nature. Given the complexity of the phenotype and the multifaceted nature of inheritance, modern evolutionary ecological studies rely heavily on the use of molecular tools. Here, we show how molecular tools help to gain insight into the role of egg coats (i.e. the extracellular structures surrounding eggs and embryos) in evolutionary diversification. Egg coats are maternally derived structures that have many biological functions from mediating fertilization to protecting the embryo from environmental hazards. They show great molecular, structural and functional diversity across species, but intraspecific variability and the role of ecology in egg coat evolution have largely been overlooked. Given that much of the variation that influences egg coat function is ultimately determined by their molecular phenotype, cutting-edge molecular tools (e.g. proteomics, glycomics and transcriptomics), combined with functional assays, are needed for rigorous inferences on their evolutionary ecology. Here, we identify key research areas and highlight emerging molecular techniques that can increase our understanding of the role of egg coats in the evolution of biological diversity, from adaptation to speciation. © 2015 John Wiley & Sons Ltd.

A National Comparison of Biochemistry and Molecular Biology Capstone Experiences

Science.gov (United States)

Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

2015-01-01

Recognizing the increasingly integrative nature of the molecular life sciences, the "American Society for Biochemistry and Molecular Biology" (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end,…

Teaching molecular genetics: Chapter 1--Background principles and methods of molecular biology.

NARCIS (Netherlands)

Knoers, N.V.A.M.; Monnens, L.A.H.

2006-01-01

In this first chapter of the series "Teaching molecular genetics," an introduction to molecular genetics is presented. We describe the structure of DNA and genes and explain in detail the central dogma of molecular biology, that is, the flow of genetic information from DNA via RNA to polypeptide

Chemoradiotherapy and molecular biology

International Nuclear Information System (INIS)

Hasegawa, Masatoshi; Mitsuhashi, Norio; Niibe, Hideo

2000-01-01

The current status of chemoradiotherapy was reviewed from the standpoint of molecular biology. Chemoradiotherapy was conducted to achieve systemic tumor control, to intensify the response to irradiation, and to reduce adverse reactions. The mechanisms of the efficacy of chemoradiotherapy were: modification of dose-response relationships, inhibition of tumor cell recovery from sublethal damage or potential lethal damage, effects on cell dynamics and the cell cycle, improvement of blood flow or reoxygenation, recruitment, improvement of drug uptake, increased cell damage. Cell death (necrosis and apoptosis) and cancer-related genes were described, as the essential points, because they are involved in the response to chemoradiotherapy. Cisplatin (platinum compound), 5-fluorouracil, etoposide, and taxoid (paclitaxel, docetaxel) were the principal anticancer agents used for chemoradiotherapy, and they enhanced the effects of irradiation. However, even when good responses or synergism between anticancer drug and radiotherapy was observed in in vitro studies, there was little therapeutic advantage clinically. Data from in vitro and in vivo studies should be collected and systemized, and ''molecular biology in chemotherapy'' that can be applied clinically may become established. (K.H.)

Systems biology for molecular life sciences and its impact in biomedicine.

Science.gov (United States)

Medina, Miguel Ángel

2013-03-01

Modern systems biology is already contributing to a radical transformation of molecular life sciences and biomedicine, and it is expected to have a real impact in the clinical setting in the next years. In this review, the emergence of systems biology is contextualized with a historic overview, and its present state is depicted. The present and expected future contribution of systems biology to the development of molecular medicine is underscored. Concerning the present situation, this review includes a reflection on the "inflation" of biological data and the urgent need for tools and procedures to make hidden information emerge. Descriptions of the impact of networks and models and the available resources and tools for applying them in systems biology approaches to molecular medicine are provided as well. The actual current impact of systems biology in molecular medicine is illustrated, reviewing two cases, namely, those of systems pharmacology and cancer systems biology. Finally, some of the expected contributions of systems biology to the immediate future of molecular medicine are commented.

Laboratory of Cell and Molecular Biology

Data.gov (United States)

Federal Laboratory Consortium — The Laboratory of Cell and Molecular Biology investigates the organization, compartmentalization, and biochemistry of eukaryotic cells and the pathology associated...

[Molecular Biology on the Mechanisms of Autism Spectrum Disorder for Clinical Psychiatrists].

Science.gov (United States)

Makinodan, Manabu

2015-01-01

While, in general, a certain number of clinical psychiatrists might not be familiar with molecular biology, the mechanisms of mental illnesses have been uncovered by molecular biology for decades. Among mental illnesses, even biological psychiatrists and neuroscientists have paid less attention to the biological treatment of autism spectrum disorder (ASD) than Alzheimer's disease and schizophrenia since ASD has been regarded as a developmental disorder that was seemingly untreatable. However, multifaceted methods of molecular biology have revealed the mechanisms that would lead to the medication of ASD. In this article, how molecular biology dissects the pathobiology of ASD is described in order to announce the possibilities of biological treatment for clinical psychiatrists.

Third international congress of plant molecular biology: Molecular biology of plant growth and development

Energy Technology Data Exchange (ETDEWEB)

Hallick, R.B. [ed.

1995-02-01

The Congress was held October 6-11, 1991 in Tucson with approximately 3000 scientists attending and over 300 oral presentations and 1800 posters. Plant molecular biology is one of the most rapidly developing areas of the biological sciences. Recent advances in the ability to isolate genes, to study their expression, and to create transgenic plants have had a major impact on our understanding of the many fundamental plant processes. In addition, new approaches have been created to improve plants for agricultural purposes. This is a book of presentation and posters from the conference.

A Diagnostic Assessment for Introductory Molecular and Cell Biology

Science.gov (United States)

Shi, Jia; Wood, William B.; Martin, Jennifer M.; Guild, Nancy A.; Vicens, Quentin; Knight, Jennifer K.

2010-01-01

We have developed and validated a tool for assessing understanding of a selection of fundamental concepts and basic knowledge in undergraduate introductory molecular and cell biology, focusing on areas in which students often have misconceptions. This multiple-choice Introductory Molecular and Cell Biology Assessment (IMCA) instrument is designed…

Synthetic biology: engineering molecular computers

CERN Multimedia

CERN. Geneva

2018-01-01

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

Molecular infection biology : interactions between microorganisms and cells

National Research Council Canada - National Science Library

Hacker, Jörg (Jörg Hinrich); Heesemann, Jurgen

2002-01-01

... and epidemiology of infectious diseases. Investigators, specialists, clinicians, and graduate students in biology, pharmacy, and medicine will find Molecular Infection Biology an invaluable addition to their professional libraries...

Commentary: Biochemistry and Molecular Biology Educators Launch National Network

Science.gov (United States)

Bailey, Cheryl; Bell, Ellis; Johnson, Margaret; Mattos, Carla; Sears, Duane; White, Harold B.

2010-01-01

The American Society of Biochemistry and Molecular Biology (ASBMB) has launched an National Science Foundation (NSF)-funded 5 year project to support biochemistry and molecular biology educators learning what and how students learn. As a part of this initiative, hundreds of life scientists will plan and develop a rich central resource for…

European activities in space radiation biology and exobiology

International Nuclear Information System (INIS)

Horneck, G.

1996-01-01

In view of the space station era, the European Space Agency has initiated a review and planning document for space life sciences. Radiation biology includes dosimetry of the radiation field and its modification by mass shielding, studies on the biological responses to radiation in space, on the potential impact of space flight environment on radiation effects, and assessing the radiation risks and establishing radiation protection guidelines. To reach a better understanding of the processes leading to the origin, evolution and distribution of life, exobiological activities include the exploration of the solar system, the collection and analysis of extraterrestrial samples and the utilization of space as a tool for testing the impact of space environment on organics and resistant life forms. (author)

Molecular biology applications to infectious diseases diagnostic

International Nuclear Information System (INIS)

2001-01-01

This project goes directed to the applications of the techniques of molecular biology in hepatitis virus.A great advance of these techniques it allows its application to the diagnose molecular and it becomes indispensable to have these fundamental tools in the field of the Health Public for the detection precocious, pursuit of the treatment, the one predicts and the evolution of the patient hepatitis bearing virus technical.Use of molecular biology to increase the handling and the control of the patients with hepatitis B and C and to detect an adult numbers of positive cases by means of the training and integration of all the countries participating.Implement the technique of PCR to identify the virus of the hepatitis B and C,implement quantification methods and genotipification for these virus

Molecular biology of Plasmodiophora brassicae

DEFF Research Database (Denmark)

Siemens, Johannes; Bulman, Simon; Rehn, Frank

2009-01-01

of several genes have been revealed, and the expression of those genes has been linked to development of clubroot to some extent. In addition, the sequence data have reinforced the inclusion of the plasmodiophorids within the Cercozoa. The recent successes in molecular biology have produced new approaches...

The order axiom and the biological space time

International Nuclear Information System (INIS)

Vu Huu Nhu

2014-01-01

This work focuses on the field of Biological Space - Time. In fact the conception of Biological Space - Time is connected with order character of sets. Because the illustration of order axioms is very important for searching order systems. In this work, the new form of order axioms has been illustrated in the form of (a,b) ≠ (b.a). It is a common form of Descartes product. Based on this we suggest the following formation of order lemma (a.b) ≠(b.a)↔ a Φ b. In this case Φ is an order relation. From the new form of order axiom, we determine the order system as follows: If S = (a,b) the set of two elements and the order axiom (a.b) ≠ (b.a) is satisfied. So that, in this case, S is called an order system. The life system are the most important order systems. We could illustrate the biological system as: S = (A, T, G, C). In this set, A, T, G, C are the elements of the genetic code and the order axiom is satisfied. As we know, for example, in genetic code: (AUG) ≠ (UGA) ≠ (UAG). The order biological system induces an order relation and it is the origin of the conception of Biological Space Time. The students of Physics and Biology could use this book as basic course for studies of Biological Space Time. (author)

Fundamental Space Biology-1: HHR and Incubator for ISS Space Life Sciences

Science.gov (United States)

Kirven-Brooks, M.; Fahlen, T.; Sato, K.; Reiss-Bubenheim, D.

The Space Station Biological Research Project (SSBRP) is developing an Incubator and a Habitat Holding Rack (HHR) to support life science experiments aboard the International Space Station (ISS). The HHR provides for cooling and power needs, and supports data transfer (including telemetry, commanding, video processing, Ethernet), video compression, and data and command storage). The Incubator is a habitat that provides for controlled temperature between +4 C and +45 C and air circulation. It has a set of connector ports for power, analog and digital sensors, and video pass-through to support experiment-unique hardware within the Incubator specimen chamber. The Incubator exchanges air with the ISS cabin. The Fundamental Space Biology-1 (FSB-1) Project will be delivering, the HHR and two Incubators to ISS. The two inaugural experiments to be conducted on ISS using this hardware will investigate the biological effects of the space environment on two model organisms, Saccharomyces cerevisiae (S. cerevisiae; yeast) and Caenorhabditis elegans (C. elegans; nematode). The {M}odel {Y}east {C}ultures {o}n {S}tation (MYCOS) experiment will support examination of the effect of microgravity and cosmic radiation on yeast biology. In the second series of experiments during the same increment, the effects of microgravity and space environment radiation on C. elegans will be examined. The {F}undamental Space Biology {I}ncubator {E}xperiment {R}esearch using {C}. {e}legans (FIERCE) study is designed to support a long duration, multi-generational study of nematodes. FIERCE on-orbit science operations will include video monitoring, sub-culturing and periodic fixation and freezing of samples. For both experiments, investigators will be solicited via an International Space Life Sciences Research Announcement. In the near future, the Centrifuge Accommodation Module will be delivered to ISS, which will house the SSBRP 2.5 m Centrifuge Rotor. The Incubator can be placed onto the Centrifuge

Molecular biology of pancreatic cancer: how useful is it in clinical practice?

Science.gov (United States)

Sakorafas, George H; Smyrniotis, Vasileios

2012-07-10

During the recent two decades dramatic advances of molecular biology allowed an in-depth understanding of pancreatic carcinogenesis. It is currently accepted that pancreatic cancer has a genetic component. The real challenge is now how these impressive advances could be used in clinical practice. To critically present currently available data regarding clinical application of molecular biology in pancreatic cancer. Reports about clinical implications of molecular biology in patients with pancreatic cancer were retrieved from PubMed. These reports were selected on the basis of their clinical relevance, and the data of their publication (preferentially within the last 5 years). Emphasis was placed on reports investigating diagnostic, prognostic, and therapeutic implications. Molecular biology can be used to identify individuals at high-risk for pancreatic cancer development. Intensive surveillance is indicated in these patients to detect pancreatic neoplasia ideally at a preinvasive stage, when curative resection is still possible. Molecular biology can also be used in the diagnosis of pancreatic cancer, with molecular analysis on samples of biologic material, such as serum or plasma, duodenal fluid or preferentially pure pancreatic juice, pancreatic cells or tissue, and stools. Molecular indices have also prognostic significance. Finally, molecular biology may have therapeutic implications by using various therapeutic approaches, such as antiangiogenic factors, purine synthesis inhibitors, matrix metalloproteinase inhibitors, factors modulating tumor-stroma interaction, inactivation of the hedgehog pathway, gene therapy, oncolytic viral therapy, immunotherapy (both passive as well as active) etc. Molecular biology may have important clinical implications in patients with pancreatic cancer and represents one of the most active areas on cancer research. Hopefully clinical applications of molecular biology in pancreatic cancer will expand in the future, improving the

National Aeronautics and Space Administration Biological Specimen Repository

Science.gov (United States)

McMonigal, Kathleen A.; Pietrzyk, Robert a.; Johnson, Mary Anne

2008-01-01

The National Aeronautics and Space Administration Biological Specimen Repository (Repository) is a storage bank that is used to maintain biological specimens over extended periods of time and under well-controlled conditions. Samples from the International Space Station (ISS), including blood and urine, will be collected, processed and archived during the preflight, inflight and postflight phases of ISS missions. This investigation has been developed to archive biosamples for use as a resource for future space flight related research. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can study space flight related changes and investigate physiological markers. The development of the National Aeronautics and Space Administration Biological Specimen Repository will allow for the collection, processing, storage, maintenance, and ethical distribution of biosamples to meet goals of scientific and programmatic relevance to the space program. Archiving of the biosamples will provide future research opportunities including investigating patterns of physiological changes, analysis of components unknown at this time or analyses performed by new methodologies.

Molecular biology - Part I: Techniques, terminology, and concepts

International Nuclear Information System (INIS)

Brown, J. Martin

1996-01-01

Purpose/Objective: One of the barriers to understanding modern molecular biology is the lack of a clear understanding of the relevant terminology, techniques, and concepts. This refresher course is intended to address these deficiencies starting from a basic level. The lecture will cover many of the common uses of recombinant DNA, including gene cloning and manipulation. The goal is to enable the nonspecialist to increase his or her understanding of molecular biology in order to more fully enjoy reading current publications and/or listening seminars. Radiation biologists trying to understand a little more molecular biology should also benefit. The following concepts will be among those explained and illustrated: restriction endonucleases, gel electrophoresis, gene cloning, use of vectors such as plasmids, bacteriophage, cosmids and viruses, cDNA and genomic libraries, Southern, Northern, and Western blotting, fluorescent in situ hybridization, polymerase chain reaction (PCR), gel retardation, and reporter gene assays

Biología molecular y cáncer de tiroides Molecular biology and thyroid cancer

Directory of Open Access Journals (Sweden)

Juan Cassola Santana

2010-12-01

Full Text Available Se realiza una revisión actualizada sobre aspectos de biología molecular que servirán de base al cirujano actuante para un mejor conocimiento del cáncer tiroideo. El objetivo radica en alertar a los cirujanos sobre las nuevas evaluaciones a las que podrán someterse los tumores de la tiroides, que implicarán cambios en toda la gama de conductas actuales en estos casos. Se señalan aspectos que sin duda cambiarán los conceptos que se manejan hoy día.A updating review is carry out on the features of molecular biology as a basis for acting surgeon to a better knowledge of thyroid cancer. The objective is to alert surgeons on the new assessments for this type of cancer, implicating changes in all the range of current behaviors in these cases. The features that will change the nowadays concepts in this respect.

2012 Gordon Research Conference, Plant molecular biology, July 15-20 2012

Energy Technology Data Exchange (ETDEWEB)

Sussman, Michael R. [Univ. of Wisconsin, Madison, WI (United States)

2013-07-20

The 2012 Gordon Conference on Plant Molecular Biology will present cutting-edge research on molecular aspects of plant growth and development, with particular emphasis on recent discoveries in molecular mechanisms involved with plant signaling systems. The Conference will feature a wide range of topics in plant molecular biology including hormone receptors and early events in hormone signaling, plant perception of and response to plant pathogen and symbionts, as well as technological and biological aspects of epigenomics particularly as it relates to signaling systems that regulate plant growth and development. Genomic approaches to plant signaling will be emphasized, including genomic profiling technologies for quantifying various biological subsystems, such as the epigenome, transcriptome, phosphorylome, and metabolome. The meeting will include an important session devoted to answering the question, "What are the biological and technological limits of plant breeding/genetics, and how can they be solved"?

Teaching molecular genetics: Chapter 1--Background principles and methods of molecular biology.

Science.gov (United States)

Knoers, Nine V A M; Monnens, Leo A H

2006-02-01

In this first chapter of the series "Teaching molecular genetics," an introduction to molecular genetics is presented. We describe the structure of DNA and genes and explain in detail the central dogma of molecular biology, that is, the flow of genetic information from DNA via RNA to polypeptide (protein). In addition, several basic and frequently used general molecular tools, such as restriction enzymes, Southern blotting, DNA amplification and sequencing are discussed, in order to lay the foundations for the forthcoming chapters.

Beneficial liaisons: radiobiology meets cellular and molecular biology

International Nuclear Information System (INIS)

Stevenson, Mary Ann; Coleman, C. Norman

1995-01-01

Purpose: The purpose of this course is to familiarize radiation oncologists with the concepts and terminology and molecular and cellular biology that are especially relevant to radiation oncology. The ability of radiation oncologists to remain current with the new discoveries of modern biology is essential to the development of improved therapeutic strategies and, importantly, to the proper balance between investment in technology and biology. Objective: This year, this Refresher Course is part of a three-part ''series'' including Drs. Martin Brown and Amato Giaccia. The objective is to provide continuing education for the academic and practicing radiation oncologist, physicist and biologist in the modern biologic concepts of cancer and its treatment. An effort will be made to relate these general concepts to the clinic by providing a broad view as to potential new biological treatments which might enhance the efficacy of radiation therapy. The specific focus of this Course will vary from year to year. Some of the classic radiation biology models which form the basis of clinical practice and laboratory research will be examined and 'newer' models will be presented which take into account the emerging knowledge of cellular and molecular biology. A few techniques in molecular and cellular biology will be described to the extent necessary to understand their basic concepts and their applicability. Aspects of radiation biology which will be covered include cell cycle, radiation-induced changes in the cellular phenotype, and considerations of the effect of the tumor microenvironment. It is not the expectation that the attendees will become experts in the particular subjects presented. Rather, it is the intent to increase their curiosity as to the new knowledge that is emerging and to demonstrate that these seemingly complicated areas can be understood and appreciated with a modicum of the effort

pGLO Mutagenesis: A Laboratory Procedure in Molecular Biology for Biology Students

Science.gov (United States)

Bassiri, Eby A.

2011-01-01

A five-session laboratory project was designed to familiarize or increase the laboratory proficiency of biology students and others with techniques and instruments commonly used in molecular biology research laboratories and industries. In this project, the EZ-Tn5 transposon is used to generate and screen a large number of cells transformed with…

The role and future of in-vitro isotopic techniques in molecular biology

International Nuclear Information System (INIS)

Dar, L.; Khan, B.K.

2004-01-01

In this review we discuss isotopic in-vitro molecular biology techniques, and their advantages and applications. Isotopic methods have helped to shape molecular biology since its early days. Despite the availability of non-isotopic alternatives, isotopic methods continue to be used in molecular biology due to certain advantages, especially related to sensitivity and cost-effectiveness. Numerous techniques involving the use of isotopes help in the characterization of genes, including the detection of single nucleotide polymorphisms (SNPs) or mutations. Other isotopic molecular methods are utilized to study the phenotypic expression of gene sequences and their mutation. Emerging branches of molecular biology like functional genomics and proteomics are extremely important for exploiting the rapidly growing data derived from whole genomic sequencing of human and microbial genomes. Recent molecular biology applications like the high-throughput array techniques are relevant in the context of both structural and functional genomics. In proteomics, stable isotope based technology has found applications in the analysis of protein structure and interactions. (author)

Biology relevant to space radiation

International Nuclear Information System (INIS)

Fry, R.J.M.

1997-01-01

There are only very limited data on the health effects to humans from the two major components of the radiations in space, namely protons and heavy ions. As a result, predictions of the accompanying effects must be based either on (1) data generated through studies of experimental systems exposed on earth at rates and fluences higher than those in space, or (2) extrapolations from studies of gamma and x rays. Better information is needed about the doses, dose rates, and the energy and LET spectra of the radiations at the organ level that are anticipated to be encountered during extended space missions. In particular, there is a need for better estimates of the relationship between radiation quality and biological effects. In the case of deterministic effects, it is the threshold that is important. The possibility of the occurrence of a large solar particle event (SPE) requires that such effects be considered during extended space missions. Analyses suggest, however, that it is feasible to provide sufficient shielding so as to reduce such effects to acceptable levels, particularly if the dose rates can be limited. If these analyses prove correct, the primary biological risks will be the stochastic effects (latent cancer induction). The contribution of one large SPE to the risk of stochastic effects while undesirable will not be large in comparison to the potential total dose on a mission of long duration

European Conference on Molecular Biology EMBO

CERN Multimedia

1967-01-01

European Conference on Molecular Biology, which eventually led to the setting up of EMBO, was held at CERN in April. Olivier Reverdin is adressing the delegates. Bernard Gregory is on the left and Willy Spuhler in the centre.

Molecular Biology and Prevention of Endometrial Cancer

National Research Council Canada - National Science Library

Maxwell, George L

2006-01-01

To increase our understanding of the molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive (OC) therapy. 1...

Molecular Biology and Prevention of Endometrial Cancer

National Research Council Canada - National Science Library

Maxwell, George

2003-01-01

To increase our understanding of the molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive therapy. Methods: 1...

Molecular Biology and Prevention of Endometrial Cancer

National Research Council Canada - National Science Library

Maxwell, George L

2004-01-01

To increase our understanding of the molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive therapy. Methods: 1...

Life sciences space biology project planning

Science.gov (United States)

Primeaux, G.; Newkirk, K.; Miller, L.; Lewis, G.; Michaud, R.

1988-01-01

The Life Sciences Space Biology (LSSB) research will explore the effect of microgravity on humans, including the physiological, clinical, and sociological implications of space flight and the readaptations upon return to earth. Physiological anomalies from past U.S. space flights will be used in planning the LSSB project.The planning effort integrates science and engineering. Other goals of the LSSB project include the provision of macroscopic view of the earth's biosphere, and the development of spinoff technology for application on earth.

Micropropagation, genetic engineering, and molecular biology of Populus

Science.gov (United States)

N. B. Klopfenstein; Y. W. Chun; M. -S. Kim; M. A. Ahuja; M. C. Dillon; R. C. Carman; L. G. Eskew

1997-01-01

Thirty-four Populus biotechnology chapters, written by 85 authors, are comprised in 5 sections: 1) in vitro culture (micropropagation, somatic embryogenesis, protoplasts, somaclonal variation, and germplasm preservation); 2) transformation and foreign gene expression; 3) molecular biology (molecular/genetic characterization); 4) biotic and abiotic resistance (disease,...

Frontiers of NMR in Molecular Biology

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-08-25

NMR spectroscopy is expanding the horizons of structural biology by determining the structures and describing the dynamics of blobular proteins in aqueous solution, as well as other classes of proteins including membrane proteins and the polypeptides that form the aggregates diagnostic of prion and amyloid diseases. Significant results are also emerging on DNA and RNA oligomers and their complexes with proteins. This meeting focused attention on key structural questions emanating from molecular biology and how NMR spectroscopy can be used to answer them.

Effects of space environment on biological characters of cultured rose seedlings

Science.gov (United States)

Min, L.; Huai, X.; Jinying, L.; Yi, P.; Chunhua, Z.

Cultured rose seedlings were carried into space by SHENZHOU-4 spacecraft and then used as the experimental material to investigate effects of the space environmental conditions on morphology cytology physiology and molecular biology of the seedlings After loaded on the space flight the plant s height number of leaves and fresh weight per seedling were all increased significantly compared to the ground controls The content of chlorophyll was basically unchanged In some cells the ultrastructural changes involved twist contraction and deformation of cell wall curvature and loose arrangement of lamellae of some chloroplasts and a significant increase in number of starch grains per chloroplast In addition the number of mitochondria increased but some mitochondrial outer membrane broke and some mitochondrial cristae disappeared The activities of the defense enzymes such as superoxide dismutase peroxidase and catalyse in rose leaves increased and the content of malondialdehyde decreased In the RAPD analysis with 40 10-mer primers 36 primers generated 148 DNA bands from both of the space flight treated seedlings and the ground controls and five primers amplified polymorphic products The rate of DNA variation was 6 34

Applications of space-electrophoresis in medicine. [for cellular separations in molecular biology

Science.gov (United States)

Bier, M.

1976-01-01

The nature of electrophoresis is reviewed and potential advances realizable in the field of biology and medicine from a space electrophoresis facility are examined. The ground-based applications of electrophoresis: (1) characterization of an ionized species; (2) determination of the quantitative composition of a complex mixture; and (3) isolation of the components of a mixture, separation achieved on the basis of the difference in transport rates is reviewed. The electrophoresis of living cells is considered, touching upon the following areas: the separation of T and B lymphocytes; the genetic influence on mouse lymphocyte mobilities; the abnormal production of specific and monoclonal immunoproteins; and the study of cancer. Schematic diagrams are presented of three types of electrophoresis apparatus: the column assembly for the static electrophoresis experiment on the Apollo-Soyuz mission, the continuous flow apparatus used in the same mission and a miniaturized electrophoresis apparatus.

Simple Calculation Programs for Biology Methods in Molecular ...

Indian Academy of Sciences (India)

First page Back Continue Last page Overview Graphics. Simple Calculation Programs for Biology Methods in Molecular Biology. GMAP: A program for mapping potential restriction sites. RE sites in ambiguous and non-ambiguous DNA sequence; Minimum number of silent mutations required for introducing a RE sites; Set ...

Invited Review Article: Advanced light microscopy for biological space research

Science.gov (United States)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; van Loon, Jack J. W. A.; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-10-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

Invited Review Article: Advanced light microscopy for biological space research

International Nuclear Information System (INIS)

De Vos, Winnok H.; Beghuin, Didier; Schwarz, Christian J.; Jones, David B.; Loon, Jack J. W. A. van; Bereiter-Hahn, Juergen; Stelzer, Ernst H. K.

2014-01-01

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy

Invited Review Article: Advanced light microscopy for biological space research

Energy Technology Data Exchange (ETDEWEB)

De Vos, Winnok H., E-mail: winnok.devos@uantwerpen.be [Laboratory of Cell Biology and Histology, Department of Veterinary Sciences, University of Antwerp, Antwerp (Belgium); Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, Ghent (Belgium); Beghuin, Didier [Lambda-X, Nivelles (Belgium); Schwarz, Christian J. [European Space Agency (ESA), ESTEC, TEC-MMG, Noordwijk (Netherlands); Jones, David B. [Institute for Experimental Orthopaedics and Biomechanics, Philipps University, Marburg (Germany); Loon, Jack J. W. A. van [Department of Oral and Maxillofacial Surgery/Oral Pathology, VU University Medical Center and Department of Oral Cell Biology, Academic Centre for Dentistry Amsterdam, Amsterdam (Netherlands); Bereiter-Hahn, Juergen; Stelzer, Ernst H. K. [Physical Biology, BMLS (FB15, IZN), Goethe University, Frankfurt am Main (Germany)

2014-10-15

As commercial space flights have become feasible and long-term extraterrestrial missions are planned, it is imperative that the impact of space travel and the space environment on human physiology be thoroughly characterized. Scrutinizing the effects of potentially detrimental factors such as ionizing radiation and microgravity at the cellular and tissue level demands adequate visualization technology. Advanced light microscopy (ALM) is the leading tool for non-destructive structural and functional investigation of static as well as dynamic biological systems. In recent years, technological developments and advances in photochemistry and genetic engineering have boosted all aspects of resolution, readout and throughput, rendering ALM ideally suited for biological space research. While various microscopy-based studies have addressed cellular response to space-related environmental stressors, biological endpoints have typically been determined only after the mission, leaving an experimental gap that is prone to bias results. An on-board, real-time microscopical monitoring device can bridge this gap. Breadboards and even fully operational microscope setups have been conceived, but they need to be rendered more compact and versatile. Most importantly, they must allow addressing the impact of gravity, or the lack thereof, on physiologically relevant biological systems in space and in ground-based simulations. In order to delineate the essential functionalities for such a system, we have reviewed the pending questions in space science, the relevant biological model systems, and the state-of-the art in ALM. Based on a rigorous trade-off, in which we recognize the relevance of multi-cellular systems and the cellular microenvironment, we propose a compact, but flexible concept for space-related cell biological research that is based on light sheet microscopy.

tRNA--the golden standard in molecular biology.

Science.gov (United States)

Barciszewska, Mirosława Z; Perrigue, Patrick M; Barciszewski, Jan

2016-01-01

Transfer RNAs (tRNAs) represent a major class of RNA molecules. Their primary function is to help decode a messenger RNA (mRNA) sequence in order to synthesize protein and thus ensures the precise translation of genetic information that is imprinted in DNA. The discovery of tRNA in the late 1950's provided critical insight into a genetic machinery when little was known about the central dogma of molecular biology. In 1965, Robert Holley determined the first nucleotide sequence of alanine transfer RNA (tRNA(Ala)) which earned him the 1968 Nobel Prize in Physiology or Medicine. Today, tRNA is one of the best described and characterized biological molecules. Here we review some of the key historical events in tRNA research which led to breakthrough discoveries and new developments in molecular biology.

The Central Dogma of Molecular Biology

Indian Academy of Sciences (India)

Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 3. The Central Dogma of Molecular Biology - A Retrospective after Fifty Years. Michel Morange. General Article Volume 14 Issue 3 March 2009 pp 236-247. Fulltext. Click here to view fulltext PDF. Permanent link:

Current dichotomy between traditional molecular biological and omic research in cancer biology and pharmacology.

Science.gov (United States)

Reinhold, William C

2015-12-10

There is currently a split within the cancer research community between traditional molecular biological hypothesis-driven and the more recent "omic" forms or research. While the molecular biological approach employs the tried and true single alteration-single response formulations of experimentation, the omic employs broad-based assay or sample collection approaches that generate large volumes of data. How to integrate the benefits of these two approaches in an efficient and productive fashion remains an outstanding issue. Ideally, one would merge the understandability, exactness, simplicity, and testability of the molecular biological approach, with the larger amounts of data, simultaneous consideration of multiple alterations, consideration of genes both of known interest along with the novel, cross-sample comparisons among cell lines and patient samples, and consideration of directed questions while simultaneously gaining exposure to the novel provided by the omic approach. While at the current time integration of the two disciplines remains problematic, attempts to do so are ongoing, and will be necessary for the understanding of the large cell line screens including the Developmental Therapeutics Program's NCI-60, the Broad Institute's Cancer Cell Line Encyclopedia, and the Wellcome Trust Sanger Institute's Cancer Genome Project, as well as the the Cancer Genome Atlas clinical samples project. Going forward there is significant benefit to be had from the integration of the molecular biological and the omic forms or research, with the desired goal being improved translational understanding and application.

Genetics and molecular biology of breast cancer

Energy Technology Data Exchange (ETDEWEB)

King, M.C. [California Univ., Berkeley, CA (United States); Lippman, M. [Georgetown Univ. Medical Center, Washington, DC (United States)] [comps.

1992-12-31

This volume contains the abstracts of oral presentations and poster sessions presented at the Cold Springs Harbor Meeting on Cancer Cells, this meeting entitled Genetics and Molecular Biology of Breast Cancer.

Barrett's esophagus: cancer and molecular biology

NARCIS (Netherlands)

Gibson, Michael K.; Dhaliwal, Arashinder S.; Clemons, Nicholas J.; Phillips, Wayne A.; Dvorak, Katerina; Tong, Daniel; Law, Simon; Pirchi, E. Daniel; Räsänen, Jari; Krasna, Mark J.; Parikh, Kaushal; Krishnadath, Kausilia K.; Chen, Yu; Griffiths, Leonard; Colleypriest, Benjamin J.; Farrant, J. Mark; Tosh, David; Das, Kiron M.; Bajpai, Manisha

2013-01-01

The following paper on the molecular biology of Barrett's esophagus (BE) includes commentaries on signaling pathways central to the development of BE including Hh, NF-κB, and IL-6/STAT3; surgical approaches for esophagectomy and classification of lesions by appropriate therapy; the debate over the

Bioenergetics molecular biology, biochemistry, and pathology

CERN Document Server

Ozawa, Takayuki

1990-01-01

The emergence of the Biochemical Sciences is underlined by the FAOB symposium in Seoul and highlighted by this Satellite meeting on the "New Bioenergetics. " Classical mitochondrial electron transfer and energy coupling is now complemented by the emerging molecular biology of the respiratory chain which is studied hand in hand with the recognition of mitochondrial disease as a major and emerging study in the basic and clinical medical sciences. Thus, this symposium has achieved an important balance of the fundamental and applied aspects of bioenergetics in the modern setting of molecular biology and mitochondrial disease. At the same time, the symposium takes note not only of the emerging excellence of Biochemical Studies in the Orient and indeed in Korea itself, but also retrospectively enjoys the history of electron transport and energy conservation as represented by the triumvirate ofYagi, King and Slater. Many thanks are due Drs. Kim and Ozawa for their elegant organization of this meeting and its juxtapo...

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.

[The molecular biology of epithelial ovarian cancer].

Science.gov (United States)

Leary, Alexandra; Pautier, Patricia; Tazi, Youssef; Morice, Philippe; Duvillard, Pierre; Gouy, Sébastien; Uzan, Catherine; Gauthier, Hélène; Balleyguier, Corinne; Lhommé, Catherine

2012-12-01

Epithelial ovarian cancer frequently presents at an advanced stage where the cornerstone of management remains surgery and platinum-based chemotherapy. Unfortunately, despite sometimes dramatic initial responses, advanced ovarian cancer almost invariably relapses. Little progress has been made in the identification of effective targeted-therapies for ovarian cancer. The majority of clinical trials investigating novel agents have been negative and the only approved targeted-therapy is bevacizumab, for which reliable predictive biomarkers still elude us. Ovarian cancer is treated as a uniform disease. Yet, biological studies have highlighted the heterogeneity of this malignancy with marked differences in histology, oncogenesis, prognosis, chemo-responsiveness, and molecular profile. Recent high throughput molecular analyses have identified a huge number of genomic/phenotypic alterations. Broadly speaking, high grade serous carcinomas (type II) display significant genomic instability and numerous amplifications and losses; low grade (type I) tumors are genomically stable but display frequent mutations. Importantly, many of these genomic alterations relate to known oncogenes for which targeted-therapies are available or in development. There is today a real potential for personalized medicine in ovarian cancer. We will review the current literature regarding the molecular characterization of epithelial ovarian cancer and discuss the biological rationale for a number of targeted strategies. In order to translate these biological advances into meaningful clinical improvements for our patients, it is imperative to incorporate translational research in ovarian cancer trials, a number of strategies will be proposed such as the acquisition of quality tumor samples, including sequential pre- and post-treatment biopsies, the potential of liquid biopsies, and novel trial designs more adapted to the molecular era of ovarian cancer research.

The molecular biology of ilarviruses.

Science.gov (United States)

Pallas, Vicente; Aparicio, Frederic; Herranz, Mari C; Sanchez-Navarro, Jesus A; Scott, Simon W

2013-01-01

Ilarviruses were among the first 16 groups of plant viruses approved by ICTV. Like Alfalfa mosaic virus (AMV), bromoviruses, and cucumoviruses they are isometric viruses and possess a single-stranded, tripartite RNA genome. However, unlike these other three groups, ilarviruses were recognized as being recalcitrant subjects for research (their ready lability is reflected in the sigla used to create the group name) and were renowned as unpromising subjects for the production of antisera. However, it was recognized that they shared properties with AMV when the phenomenon of genome activation, in which the coat protein (CP) of the virus is required to be present to initiate infection, was demonstrated to cross group boundaries. The CP of AMV could activate the genome of an ilarvirus and vice versa. Development of the molecular information for ilarviruses lagged behind the knowledge available for the more extensively studied AMV, bromoviruses, and cucumoviruses. In the past 20 years, genomic data for most known ilarviruses have been developed facilitating their detection and allowing the factors involved in the molecular biology of the genus to be investigated. Much information has been obtained using Prunus necrotic ringspot virus and the more extensively studied AMV. A relationship between some ilarviruses and the cucumoviruses has been defined with the recognition that members of both genera encode a 2b protein involved in RNA silencing and long distance viral movement. Here, we present a review of the current knowledge of both the taxonomy and the molecular biology of this genus of agronomically and horticulturally important viruses. Copyright © 2013 Elsevier Inc. All rights reserved.

Space Biology and Medicine. Volume I; Space and Its Exploration

Science.gov (United States)

Nicogossian, Arnauld E.; Mohler, Stanley R.; Gazenko, Oleg G.; Grigoryev, Anatoliy I.

1993-01-01

and a path to our common future. But for humanity to embark on this path, we need to understand ourselves in a new environment. As such, an understanding of the biological consequences of and opportunities in space flight is essential. In this, the first volume of a joint U.S./Russian series on space biology and medicine, we describe the current status of our understanding of space and present general information that will prove useful when reading subsequent volumes. Since we are witnesses to the beginning of a new era of interplanetary travel, a significant portion of the first volume will concentrate on the physical and ecological conditions that exist in near and outer space, as well as heavenly bodies from the smallest ones to the giant planets and stars. While space exploration is a comparatively recent endeavor, its foundations were laid much more than 30 years ago, and its history has been an eventful one. In the first part of this volume, Rauschenbach, Sokolskiy, and Gurjian address the "Historical Aspects of Space Exploration" from its beginnings to a present-day view of the events of the space age. The nature of space itself and its features is the focus of the second section of the volume. In the first chapter of the part, "Stars and Interstellar Space," the origin and evolution of stars, and the nature of the portions of space most distant from Earth are described by Galeev and Marochnik. In Chapter 2, Pisarenko, Logachev, and Kurt in "The Sun and Interplanetary Space" bring us to the vicinity of our own solar system and provide a description and discussion of the nearest star and its influence on the space environment that our Earth and the other planets inhabit. In our solar system there are many fascinating objects, remnants of the formation of a rather ordinary star in a rather obscure portion of the galaxy. Historical accident has caused us to be much more curious (and knowledgeable) about "The Inner Planets of the Solar System" than about any of

[Progress in molecular biology of a semi-mangrove, Millettia pinnata].

Science.gov (United States)

Huang, Jianzi; Zhang, Wanke; Huang, Rongfeng; Zheng, Yizhi

2015-04-01

Millettia pinnata L. is a leguminous tree with great potential in biodiesel applications and also a typical semi-mangrove. In this review, we presented several aspects about the recent research progress in molecular biology of M. pinnata. We descrived several types of molecular markers used to assess the genetic diversity and phylogeny of this species, genome and transcriptome analyses based on high-throughput sequencing platform accomplished for this species, and several gene and genomic sequences of this species isolated for further research. Finally, based on the current research progress, we proposed some orientations for future molecular biology research on M. pinnata.

Systematic Representation of Molecular Biology Knowledge.

Science.gov (United States)

Fisher, Kathleen M.

A small set of relationships has been identified which appears to be sufficient for describing all molecular and cellular reactions and structures discussed in an introductory biology course. A precise definition has been developed for each relationship. These 20 relationships are of four types: (1) analytical; (2) spatial; (3) temporal; and (4)…

Molecular biology of potyviruses.

Science.gov (United States)

Revers, Frédéric; García, Juan Antonio

2015-01-01

Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses. © 2015 Elsevier Inc. All rights reserved.

A decade of molecular cell biology: achievements and challenges.

Science.gov (United States)

Akhtar, Asifa; Fuchs, Elaine; Mitchison, Tim; Shaw, Reuben J; St Johnston, Daniel; Strasser, Andreas; Taylor, Susan; Walczak, Claire; Zerial, Marino

2011-09-23

Nature Reviews Molecular Cell Biology celebrated its 10-year anniversary during this past year with a series of specially commissioned articles. To complement this, here we have asked researchers from across the field for their insights into how molecular cell biology research has evolved during this past decade, the key concepts that have emerged and the most promising interfaces that have developed. Their comments highlight the broad impact that particular advances have had, some of the basic understanding that we still require, and the collaborative approaches that will be essential for driving the field forward.

Grete Kellenberger-Gujer: Molecular biology research pioneer.

Science.gov (United States)

Citi, Sandra; Berg, Douglas E

2016-01-01

Grete Kellenberger-Gujer was a Swiss molecular biologist who pioneered fundamental studies of bacteriophage in the mid-20(th) century at the University of Geneva. Her life and career stories are reviewed here, focusing on her fundamental contributions to our early understanding of phage biology via her insightful analyses of phenomena such as the lysogenic state of a temperate phage (λ), genetic recombination, radiation's in vivo consequences, and DNA restriction-modification; on her creative personality and interactions with peers; and how her academic advancement was affected by gender, societal conditions and cultural attitudes of the time. Her story is important scientifically, putting into perspective features of the scientific community from just before the molecular biology era started through its early years, and also sociologically, in illustrating the numerous "glass ceilings" that, especially then, often hampered the advancement of creative women.

Digital learning material for experimental design and model building in molecular biology

NARCIS (Netherlands)

Aegerter-Wilmsen, T.

2005-01-01

Designing experimental approaches is a major cognitive skill in molecular biology research, and building models, including quantitative ones, is a cognitive skill which is rapidly gaining importance. Since molecular biology education at university level is aimed at educating future researchers, we

Synthetic biology assemblies for sustainable space exploration

Data.gov (United States)

National Aeronautics and Space Administration — The work utilized synthetic biology to create sustainable food production processes by developing technology to efficiently convert inedible crop waste to...

Information theory in molecular biology

OpenAIRE

Adami, Christoph

2004-01-01

This article introduces the physics of information in the context of molecular biology and genomics. Entropy and information, the two central concepts of Shannon's theory of information and communication, are often confused with each other but play transparent roles when applied to statistical ensembles (i.e., identically prepared sets) of symbolic sequences. Such an approach can distinguish between entropy and information in genes, predict the secondary structure of ribozymes, and detect the...

The extracellular matrix of plants: Molecular, cellular and developmental biology

Energy Technology Data Exchange (ETDEWEB)

NONE

1996-12-31

A symposium entitled ``The Extracellular Matrix of Plants: Molecular, Cellular and Developmental Biology was held in Tamarron, Colorado, March 15--21, 1996. The following topics were explored in addresses by 43 speakers: structure and biochemistry of cell walls; biochemistry, molecular biology and biosynthesis of lignin; secretory pathway and synthesis of glycoproteins; biosynthesis of matrix polysaccharides, callose and cellulose; role of the extracellular matrix in plant growth and development; plant cell walls in symbiosis and pathogenesis.

Gravitational biology and space life sciences: Current status and ...

Indian Academy of Sciences (India)

Gravitational and space biology organizations and journals. American Institute of ... of Scientific Unions (now the International Council for. Science). COSPAR ... Greek Aerospace Medical Association & Space Research. (GASMA). Provides ...

A Systems Biology Analysis Unfolds the Molecular Pathways and Networks of Two Proteobacteria in Spaceflight and Simulated Microgravity Conditions.

Science.gov (United States)

Roy, Raktim; Shilpa, P Phani; Bagh, Sangram

2016-09-01

Bacteria are important organisms for space missions due to their increased pathogenesis in microgravity that poses risks to the health of astronauts and for projected synthetic biology applications at the space station. We understand little about the effect, at the molecular systems level, of microgravity on bacteria, despite their significant incidence. In this study, we proposed a systems biology pipeline and performed an analysis on published gene expression data sets from multiple seminal studies on Pseudomonas aeruginosa and Salmonella enterica serovar Typhimurium under spaceflight and simulated microgravity conditions. By applying gene set enrichment analysis on the global gene expression data, we directly identified a large number of new, statistically significant cellular and metabolic pathways involved in response to microgravity. Alteration of metabolic pathways in microgravity has rarely been reported before, whereas in this analysis metabolic pathways are prevalent. Several of those pathways were found to be common across studies and species, indicating a common cellular response in microgravity. We clustered genes based on their expression patterns using consensus non-negative matrix factorization. The genes from different mathematically stable clusters showed protein-protein association networks with distinct biological functions, suggesting the plausible functional or regulatory network motifs in response to microgravity. The newly identified pathways and networks showed connection with increased survival of pathogens within macrophages, virulence, and antibiotic resistance in microgravity. Our work establishes a systems biology pipeline and provides an integrated insight into the effect of microgravity at the molecular systems level. Systems biology-Microgravity-Pathways and networks-Bacteria. Astrobiology 16, 677-689.

Molecular Biology and Prevention of Endometrial Cancer. Addendum

National Research Council Canada - National Science Library

Maxwell, George L

2008-01-01

Objective: To increase our understanding of the molecular aberrations associated with endometrial carcinogenesis and the biologic mechanisms underlying the protective effect of oral contraceptive (OC) therapy. Methods: 1...

Connecting Biology to Electronics: Molecular Communication via Redox Modality.

Science.gov (United States)

Liu, Yi; Li, Jinyang; Tschirhart, Tanya; Terrell, Jessica L; Kim, Eunkyoung; Tsao, Chen-Yu; Kelly, Deanna L; Bentley, William E; Payne, Gregory F

2017-12-01

Biology and electronics are both expert at for accessing, analyzing, and responding to information. Biology uses ions, small molecules, and macromolecules to receive, analyze, store, and transmit information, whereas electronic devices receive input in the form of electromagnetic radiation, process the information using electrons, and then transmit output as electromagnetic waves. Generating the capabilities to connect biology-electronic modalities offers exciting opportunities to shape the future of biosensors, point-of-care medicine, and wearable/implantable devices. Redox reactions offer unique opportunities for bio-device communication that spans the molecular modalities of biology and electrical modality of devices. Here, an approach to search for redox information through an interactive electrochemical probing that is analogous to sonar is adopted. The capabilities of this approach to access global chemical information as well as information of specific redox-active chemical entities are illustrated using recent examples. An example of the use of synthetic biology to recognize external molecular information, process this information through intracellular signal transduction pathways, and generate output responses that can be detected by electrical modalities is also provided. Finally, exciting results in the use of redox reactions to actuate biology are provided to illustrate that synthetic biology offers the potential to guide biological response through electrical cues. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Space Synthetic Biology Project

Science.gov (United States)

Howard, David; Roman, Monsi; Mansell, James (Matt)

2015-01-01

Synthetic biology is an effort to make genetic engineering more useful by standardizing sections of genetic code. By standardizing genetic components, biological engineering will become much more similar to traditional fields of engineering, in which well-defined components and subsystems are readily available in markets. Specifications of the behavior of those components and subsystems can be used to model a system which incorporates them. Then, the behavior of the novel system can be simulated and optimized. Finally, the components and subsystems can be purchased and assembled to create the optimized system, which most often will exhibit behavior similar to that indicated by the model. The Space Synthetic Biology project began in 2012 as a multi-Center effort. The purpose of this project was to harness Synthetic Biology principals to enable NASA's missions. A central target for application was to Environmental Control & Life Support (ECLS). Engineers from NASA Marshall Space Flight Center's (MSFC's) ECLS Systems Development Branch (ES62) were brought into the project to contribute expertise in operational ECLS systems. Project lead scientists chose to pursue the development of bioelectrochemical technologies to spacecraft life support. Therefore, the ECLS element of the project became essentially an effort to develop a bioelectrochemical ECLS subsystem. Bioelectrochemical systems exploit the ability of many microorganisms to drive their metabolisms by direct or indirect utilization of electrical potential gradients. Whereas many microorganisms are capable of deriving the energy required for the processes of interest (such as carbon dioxide (CO2) fixation) from sunlight, it is believed that subsystems utilizing electrotrophs will exhibit smaller mass, volume, and power requirements than those that derive their energy from sunlight. In the first 2 years of the project, MSFC personnel conducted modeling, simulation, and conceptual design efforts to assist the

Recommendations for accreditation of laboratories in molecular biology of hematologic malignancies.

Science.gov (United States)

Flandrin-Gresta, Pascale; Cornillet, Pascale; Hayette, Sandrine; Gachard, Nathalie; Tondeur, Sylvie; Mauté, Carole; Cayuela, Jean-Michel

2015-01-01

Over recent years, the development of molecular biology techniques has improved the hematological diseases diagnostic and follow-up. Consequently, these techniques are largely used in the biological screening of these diseases; therefore the Hemato-oncology molecular diagnostics laboratories must be actively involved in the accreditation process according the ISO 15189 standard. The French group of molecular biologists (GBMHM) provides requirements for the implementation of quality assurance for the medical molecular laboratories. This guideline states the recommendations for the pre-analytical, analytical (methods validation procedures, quality controls, reagents), and post-analytical conditions. In addition, herein we state a strategy for the internal quality control management. These recommendations will be regularly updated.

Molecular knots in biology and chemistry

International Nuclear Information System (INIS)

Lim, Nicole C H; Jackson, Sophie E

2015-01-01

Knots and entanglements are ubiquitous. Beyond their aesthetic appeal, these fascinating topological entities can be either useful or cumbersome. In recent decades, the importance and prevalence of molecular knots have been increasingly recognised by scientists from different disciplines. In this review, we provide an overview on the various molecular knots found in naturally occurring biological systems (DNA, RNA and proteins), and those created by synthetic chemists. We discuss the current knowledge in these fields, including recent developments in experimental and, in some cases, computational studies which are beginning to shed light into the complex interplay between the structure, formation and properties of these topologically intricate molecules. (paper)

Molecular Biology of Pancreatic Cancer: How Useful Is It in Clinical Practice?

OpenAIRE

George H Sakorafas; Vasileios Smyrniotis

2012-01-01

Context During the recent two decades dramatic advances of molecular biology allowed an in-depth understanding of pancreatic carcinogenesis. It is currently accepted that pancreatic cancer has a genetic component. The real challenge is now how these impressive advances could be used in clinical practice. Objective To critically present currently available data regarding clinical application of molecular biology in pancreatic cancer. Methods Reports about clinical implications of molecular bio...

Space Biology Model Organism Research on the Deep Space Gateway to Pioneer Discovery and Advance Human Space Exploration

Science.gov (United States)

Sato, K. Y.; Tomko, D. L.; Levine, H. G.; Quincy, C. D.; Rayl, N. A.; Sowa, M. B.; Taylor, E. M.; Sun, S. C.; Kundrot, C. E.

2018-02-01

Model organisms are foundational for conducting physiological and systems biology research to define how life responds to the deep space environment. The organisms, areas of research, and Deep Space Gateway capabilities needed will be presented.

Genomic Signal Processing: Predicting Basic Molecular Biological Principles

Science.gov (United States)

Alter, Orly

2005-03-01

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

Molecular and biological interactions in colorectal cancer

NARCIS (Netherlands)

Heer, Pieter de

2007-01-01

The current thesis discusses the use of molecular and biological tumor markers to predict clinical outcome. By studying several key processes in the develepment of cancer as regulation of cell motility (non-receptor protein tyrosin adesion kinases, FAK, Src and paxillin, Apoptosis (caspase-3

Can molecular cell biology explain chromosome motions?

Directory of Open Access Journals (Sweden)

Gagliardi L

2011-05-01

Full Text Available Abstract Background Mitotic chromosome motions have recently been correlated with electrostatic forces, but a lingering "molecular cell biology" paradigm persists, proposing binding and release proteins or molecular geometries for force generation. Results Pole-facing kinetochore plates manifest positive charges and interact with negatively charged microtubule ends providing the motive force for poleward chromosome motions by classical electrostatics. This conceptual scheme explains dynamic tracking/coupling of kinetochores to microtubules and the simultaneous depolymerization of kinetochore microtubules as poleward force is generated. Conclusion We question here why cells would prefer complex molecular mechanisms to move chromosomes when direct electrostatic interactions between known bound charge distributions can accomplish the same task much more simply.

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

The technology for biology in space lags far behind the gold standard for biological experiments on Earth. To remedy this disparity, the Rothschild lab works on proof of concept, prototyping, and developing of new sensors and devices to further the capabilities of biology research on satellites. One such device is the PowerCell Payload System. One goal for synthetic biology in aiding space travel and colonization is to genetically engineer living cells to produce biochemicals in space. However, such farming in space presupposes bacteria retain their functionality post-launch, bombarded by radiation, and without the 1G of Earth. Our questions is, does a co-culture of cyanobacteria and protein-synthesizing bacteria produce Earth-like yields of target proteins? Is the yield sensitive to variable gravitational forces? To answer these questions, a PowerCell Payload System will spend 1 year aboard the German Aerospace Center's Euglena and Combined Regenerative Organic-food Production In Space (Eu:CROPIS) mission satellite. The PowerCell system is a pair of two 48-well microfluidic cards, each well seeded with bacteria. The system integrates fluidic, thermal, optical, electronic, and control systems to germinate bacteria spores, then measure the protein synthesized for comparison to parallel experiments conducted on the Earth. In developing the PowerCell Payload, we gained insight into the shortcomings of biology experiments on satellites. To address these issues, we have started three new prototyping projects: 1) The development of an extremely stable and radiation resistant cell-free system, allowing for the construction of proteins utilizing only cell components instead of living cells. This can be lyophilized on a substrate, like paper. (2) Using paper as a microfluidic platform that is flexible, stable, cheap, and wicking. The capillary action eliminates the need for pumps, reducing volume, mass, and potential failing points. Electrodes can be printed on the paper to

Plant synthetic biology for molecular engineering of signalling and development.

Science.gov (United States)

Nemhauser, Jennifer L; Torii, Keiko U

2016-03-02

Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.

Molecular biology approaches in bioadhesion research

Directory of Open Access Journals (Sweden)

Marcelo Rodrigues

2014-07-01

Full Text Available The use of molecular biology tools in the field of bioadhesion is still in its infancy. For new research groups who are considering taking a molecular approach, the techniques presented here are essential to unravelling the sequence of a gene, its expression and its biological function. Here we provide an outline for addressing adhesion-related genes in diverse organisms. We show how to gradually narrow down the number of candidate transcripts that are involved in adhesion by (1 generating a transcriptome and a differentially expressed cDNA list enriched for adhesion-related transcripts, (2 setting up a BLAST search facility, (3 perform an in situ hybridization screen, and (4 functional analyses of selected genes by using RNA interference knock-down. Furthermore, latest developments in genome-editing are presented as new tools to study gene function. By using this iterative multi-technologies approach, the identification, isolation, expression and function of adhesion-related genes can be studied in most organisms. These tools will improve our understanding of the diversity of molecules used for adhesion in different organisms and these findings will help to develop innovative bio-inspired adhesives.

Modeling human risk: Cell & molecular biology in context

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-06-01

It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response.

Applications of neutron scattering in molecular biological research

International Nuclear Information System (INIS)

Nierhaus, K.H.

1984-01-01

The study of the molecular structure of biological materials by neutron scattering is described. As example the results of the study of the components of a ribosome of Escherichia coli are presented. (HSI) [de

Time scale of diffusion in molecular and cellular biology

International Nuclear Information System (INIS)

Holcman, D; Schuss, Z

2014-01-01

Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function. (topical review)

Time scale of diffusion in molecular and cellular biology

Science.gov (United States)

Holcman, D.; Schuss, Z.

2014-05-01

Diffusion is the driver of critical biological processes in cellular and molecular biology. The diverse temporal scales of cellular function are determined by vastly diverse spatial scales in most biophysical processes. The latter are due, among others, to small binding sites inside or on the cell membrane or to narrow passages between large cellular compartments. The great disparity in scales is at the root of the difficulty in quantifying cell function from molecular dynamics and from simulations. The coarse-grained time scale of cellular function is determined from molecular diffusion by the mean first passage time of molecular Brownian motion to a small targets or through narrow passages. The narrow escape theory (NET) concerns this issue. The NET is ubiquitous in molecular and cellular biology and is manifested, among others, in chemical reactions, in the calculation of the effective diffusion coefficient of receptors diffusing on a neuronal cell membrane strewn with obstacles, in the quantification of the early steps of viral trafficking, in the regulation of diffusion between the mother and daughter cells during cell division, and many other cases. Brownian trajectories can represent the motion of a molecule, a protein, an ion in solution, a receptor in a cell or on its membrane, and many other biochemical processes. The small target can represent a binding site or an ionic channel, a hidden active site embedded in a complex protein structure, a receptor for a neurotransmitter on the membrane of a neuron, and so on. The mean time to attach to a receptor or activator determines diffusion fluxes that are key regulators of cell function. This review describes physical models of various subcellular microdomains, in which the NET coarse-grains the molecular scale to a higher cellular-level, thus clarifying the role of cell geometry in determining subcellular function.

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

The early years of molecular biology: personal recollections.

Science.gov (United States)

Holliday, Robin

2003-05-01

The early years of molecular biology were characterized by a strong interaction between theory and experiment. This included the elucidation of the structure of DNA itself; genetic fine structure, recombination and repair; DNA replication; template-directed protein synthesis; the universality of the triplet genetic code, and the co-linearity of the DNA sequence of structural genes and the sequence of amino acids in proteins. The principle of co-linearity was later modified when split genes were discovered. It is suggested that accurate splicing of gene transcripts might also be template directed. In 1958 Crick proposed a 'central dogma' of molecular biology stating that information could not be transmitted from proteins to DNA. Nevertheless, proteins can chemically modify DNA, and this is now known to have strong effects on gene expression.

A comparative cellular and molecular biology of longevity database.

Science.gov (United States)

Stuart, Jeffrey A; Liang, Ping; Luo, Xuemei; Page, Melissa M; Gallagher, Emily J; Christoff, Casey A; Robb, Ellen L

2013-10-01

Discovering key cellular and molecular traits that promote longevity is a major goal of aging and longevity research. One experimental strategy is to determine which traits have been selected during the evolution of longevity in naturally long-lived animal species. This comparative approach has been applied to lifespan research for nearly four decades, yielding hundreds of datasets describing aspects of cell and molecular biology hypothesized to relate to animal longevity. Here, we introduce a Comparative Cellular and Molecular Biology of Longevity Database, available at ( http://genomics.brocku.ca/ccmbl/ ), as a compendium of comparative cell and molecular data presented in the context of longevity. This open access database will facilitate the meta-analysis of amalgamated datasets using standardized maximum lifespan (MLSP) data (from AnAge). The first edition contains over 800 data records describing experimental measurements of cellular stress resistance, reactive oxygen species metabolism, membrane composition, protein homeostasis, and genome homeostasis as they relate to vertebrate species MLSP. The purpose of this review is to introduce the database and briefly demonstrate its use in the meta-analysis of combined datasets.

Cold Spring Harbor symposia on quantitative biology: Volume 51, Molecular biology of /ital Homo sapiens/

International Nuclear Information System (INIS)

1986-01-01

This volume is the second part of a collection of papers submitted by the participants to the 1986 Cold Spring Harbor Symposium on Quantitative Biology entitled Molecular Biology of /ital Homo sapiens/. The 49 papers included in this volume are grouped by subject into receptors, human cancer genes, and gene therapy. (DT)

2012 Gordon Research Conference on Cellular and Molecular Fungal Biology, Final Progress Report

Energy Technology Data Exchange (ETDEWEB)

Berman, Judith [Univ. of Minnesota, Minneapolis, MN (United States)

2012-06-22

The Gordon Research Conference on Cellular and Molecular Fungal Biology was held at Holderness School, Holderness New Hampshire, June 17 - 22, 2012. The 2012 Gordon Conference on Cellular and Molecular Fungal Biology (CMFB) will present the latest, cutting-edge research on the exciting and growing field of molecular and cellular aspects of fungal biology. Topics will range from yeast to filamentous fungi, from model systems to economically important organisms, and from saprophytes and commensals to pathogens of plants and animals. The CMFB conference will feature a wide range of topics including systems biology, cell biology and morphogenesis, organismal interactions, genome organisation and regulation, pathogenesis, energy metabolism, biomass production and population genomics. The Conference was well-attended with 136 participants. Gordon Research Conferences does not permit publication of meeting proceedings.

Generative Mechanistic Explanation Building in Undergraduate Molecular and Cellular Biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-01-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among…

Systems theoretic analysis of the central dogma of molecular biology: some recent results.

Science.gov (United States)

Gao, Rui; Yu, Juanyi; Zhang, Mingjun; Tarn, Tzyh-Jong; Li, Jr-Shin

2010-03-01

This paper extends our early study on a mathematical formulation of the central dogma of molecular biology, and focuses discussions on recent insights obtained by employing advanced systems theoretic analysis. The goal of this paper is to mathematically represent and interpret the genetic information flow at the molecular level, and explore the fundamental principle of molecular biology at the system level. Specifically, group theory was employed to interpret concepts and properties of gene mutation, and predict backbone torsion angle along the peptide chain. Finite state machine theory was extensively applied to interpret key concepts and analyze the processes related to DNA hybridization. Using the proposed model, we have transferred the character-based model in molecular biology to a sophisticated mathematical model for calculation and interpretation.

Gregory Bateson's relevance to current molecular biology

DEFF Research Database (Denmark)

Bruni, Luis Emilio

2008-01-01

in a developmental pathway. Being a central figure in the development of cybernetic theory he collaborated with a range of researchers from the life sciences who were innovating their own disciplines by introducing cybernetic concepts in their particular fields and disciplines. In the light of this, it should...... not come as a surprise today to realize how the general ideas that he was postulating for the study of communication systems in biology fit so well with the astonishing findings of current molecular biology, for example in the field of cellular signal transduction networks. I guess this is the case due...

Bacteriophages: The viruses for all seasons of molecular biology

Directory of Open Access Journals (Sweden)

Karam Jim D

2005-03-01

Full Text Available Abstract Bacteriophage research continues to break new ground in our understanding of the basic molecular mechanisms of gene action and biological structure. The abundance of bacteriophages in nature and the diversity of their genomes are two reasons why phage research brims with excitement. The pages of Virology Journal will reflect the excitement of the "New Phage Biology."

Fundamental Approaches in Molecular Biology for Communication Sciences and Disorders

Science.gov (United States)

Bartlett, Rebecca S.; Jette, Marie E.; King, Suzanne N.; Schaser, Allison; Thibeault, Susan L.

2012-01-01

Purpose: This contemporary tutorial will introduce general principles of molecular biology, common deoxyribonucleic acid (DNA), ribonucleic acid (RNA), and protein assays and their relevance in the field of communication sciences and disorders. Method: Over the past 2 decades, knowledge of the molecular pathophysiology of human disease has…

2011 Archaea: Ecology, Metabolism, & Molecular Biology

Energy Technology Data Exchange (ETDEWEB)

Keneth Stedman

2011-08-05

Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

Cellular and Molecular Biological Approaches to Interpreting Ancient Biomarkers

Science.gov (United States)

Newman, Dianne K.; Neubauer, Cajetan; Ricci, Jessica N.; Wu, Chia-Hung; Pearson, Ann

2016-06-01

Our ability to read the molecular fossil record has advanced significantly in the past decade. Improvements in biomarker sampling and quantification methods, expansion of molecular sequence databases, and the application of genetic and cellular biological tools to problems in biomarker research have enabled much of this progress. By way of example, we review how attempts to understand the biological function of 2-methylhopanoids in modern bacteria have changed our interpretation of what their molecular fossils tell us about the early history of life. They were once thought to be biomarkers of cyanobacteria and hence the evolution of oxygenic photosynthesis, but we now believe that 2-methylhopanoid biosynthetic capacity originated in the Alphaproteobacteria, that 2-methylhopanoids are regulated in response to stress, and that hopanoid 2-methylation enhances membrane rigidity. We present a new interpretation of 2-methylhopanes that bridges the gap between studies of the functions of 2-methylhopanoids and their patterns of occurrence in the rock record.

Quantitative computational models of molecular self-assembly in systems biology.

Science.gov (United States)

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Permeating disciplines: Overcoming barriers between molecular simulations and classical structure-function approaches in biological ion transport.

Science.gov (United States)

Howard, Rebecca J; Carnevale, Vincenzo; Delemotte, Lucie; Hellmich, Ute A; Rothberg, Brad S

2018-04-01

Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment. Here, we seek to provide contemporary context, concrete examples, and a look to the future for bridging disciplinary gaps in biological ion transport. This article is part of a Special Issue entitled: Beyond the Structure-Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain. Copyright © 2017 Elsevier B.V. All rights reserved.

Molecular radiation biology: Future aspects

International Nuclear Information System (INIS)

Hagen, U.

1990-01-01

Future aspects of molecular radiation biology may be envisaged by looking for unsolved problems and ways to analyse them. Considering the endpoints of cellular radiation effects as cell inactivation, chromosome aberrations, mutation and transformation, the type of DNA damage in the irradiated cell and the mechanisms of DNA repair as excision repair, recombination repair and mutagenic repair are essential topics. At present, great efforts are made to identify, to clone and to sequence genes involved in the control of repair of DNA damage and to study their regulation. There are close relationships between DNA repair genes isolated from various organisms, which promises fast progress for the molecular analysis of repair processes in mammalian cells. More knowledge is necessary regarding the function of the gene products, i.e. enzymes and proteins involved in DNA repair. Effort should be made to analyse the enzymatic reactions, leading to an altered nucleotide sequence, encountered as a point mutation. Mislead mismatch repair and modulation of DNA polymerase might be possible mechanisms. (orig.)

Molecular biology of gastric cancer.

Science.gov (United States)

Cervantes, A; Rodríguez Braun, E; Pérez Fidalgo, A; Chirivella González, I

2007-04-01

Despite its decreasing incidence overall, gastric cancer is still a challenging disease. Therapy is based mainly upon surgical resection when the tumour remains localised in the stomach. Conventional chemotherapy may play a role in treating micrometastatic disease and is effective as palliative therapy for recurrent or advanced disease. However, the knowledge of molecular pathways implicated in gastric cancer pathogenesis is still in its infancy and the contribution of molecular biology to the development of new targeted therapies in gastric cancer is far behind other more common cancers such as breast, colon or lung. This review will focus first on the difference of two well defined types of gastric cancer: intestinal and diffuse. A discussion of the cell of origin of gastric cancer with some intriguing data implicating bone marrow derived cells will follow, and a comprehensive review of different genetic alterations detected in gastric cancer, underlining those that may have clinical, therapeutic or prognostic implications.

A comprehensive study into the molecular methodology and molecular biology of methanogenic Archaea

DEFF Research Database (Denmark)

Lange, M.; Ahring, Birgitte Kiær

2001-01-01

Methanogens belong to the kingdom of Euryarchaeota in the domain of Archaea. The Archaea differ from Bacteria in many aspects important to molecular work. Among these are cell wall composition, their sensitivity to antibiotics, their translation and transcription machinery, and their very strict ...... procedures. Efficient genetic manipulation systems, including shuttle and integration vector systems, have appeared for mesophilic, but not for thermophilic species within the last few years and will have a major impact on future investigations of methanogenic molecular biology....

Crucible: A System for Space Synthetic Biology Experiments

Data.gov (United States)

National Aeronautics and Space Administration — The goal of this project is to expand the capability and methodologies in experimental extreme biology as a step towards Martian ecopoiesis. The objectives in...

Generative mechanistic explanation building in undergraduate molecular and cellular biology

Science.gov (United States)

Southard, Katelyn M.; Espindola, Melissa R.; Zaepfel, Samantha D.; Bolger, Molly S.

2017-09-01

When conducting scientific research, experts in molecular and cellular biology (MCB) use specific reasoning strategies to construct mechanistic explanations for the underlying causal features of molecular phenomena. We explored how undergraduate students applied this scientific practice in MCB. Drawing from studies of explanation building among scientists, we created and applied a theoretical framework to explore the strategies students use to construct explanations for 'novel' biological phenomena. Specifically, we explored how students navigated the multi-level nature of complex biological systems using generative mechanistic reasoning. Interviews were conducted with introductory and upper-division biology students at a large public university in the United States. Results of qualitative coding revealed key features of students' explanation building. Students used modular thinking to consider the functional subdivisions of the system, which they 'filled in' to varying degrees with mechanistic elements. They also hypothesised the involvement of mechanistic entities and instantiated abstract schema to adapt their explanations to unfamiliar biological contexts. Finally, we explored the flexible thinking that students used to hypothesise the impact of mutations on multi-leveled biological systems. Results revealed a number of ways that students drew mechanistic connections between molecules, functional modules (sets of molecules with an emergent function), cells, tissues, organisms and populations.

Practices and exploration on competition of molecular biological detection technology among students in food quality and safety major.

Science.gov (United States)

Chang, Yaning; Peng, Yuke; Li, Pengfei; Zhuang, Yingping

2017-07-08

With the increasing importance in the application of the molecular biological detection technology in the field of food safety, strengthening education in molecular biology experimental techniques is more necessary for the culture of the students in food quality and safety major. However, molecular biology experiments are not always in curricula of Food quality and safety Majors. This paper introduced a project "competition of molecular biological detection technology for food safety among undergraduate sophomore students in food quality and safety major", students participating in this project needed to learn the fundamental molecular biology experimental techniques such as the principles of molecular biology experiments and genome extraction, PCR and agarose gel electrophoresis analysis, and then design the experiments in groups to identify the meat species in pork and beef products using molecular biological methods. The students should complete the experimental report after basic experiments, write essays and make a presentation after the end of the designed experiments. This project aims to provide another way for food quality and safety majors to improve their knowledge of molecular biology, especially experimental technology, and enhances them to understand the scientific research activities as well as give them a chance to learn how to write a professional thesis. In addition, in line with the principle of an open laboratory, the project is also open to students in other majors in East China University of Science and Technology, in order to enhance students in other majors to understand the fields of molecular biology and food safety. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):343-350, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

A national comparison of biochemistry and molecular biology capstone experiences.

Science.gov (United States)

Aguanno, Ann; Mertz, Pamela; Martin, Debra; Bell, Ellis

2015-01-01

Recognizing the increasingly integrative nature of the molecular life sciences, the American Society for Biochemistry and Molecular Biology (ASBMB) recommends that Biochemistry and Molecular Biology (BMB) programs develop curricula based on concepts, content, topics, and expected student outcomes, rather than courses. To that end, ASBMB conducted a series of regional workshops to build a BMB Concept Inventory containing validated assessment tools, based on foundational and discipline-specific knowledge and essential skills, for the community to use. A culminating activity, which integrates the educational experience, is often part of undergraduate molecular life science programs. These "capstone" experiences are commonly defined as an attempt to measure student ability to synthesize and integrate acquired knowledge. However, the format, implementation, and approach to outcome assessment of these experiences are quite varied across the nation. Here we report the results of a nation-wide survey on BMB capstone experiences and discuss this in the context of published reports about capstones and the findings of the workshops driving the development of the BMB Concept Inventory. Both the survey results and the published reports reveal that, although capstone practices do vary, certain formats for the experience are used more frequently and similarities in learning objectives were identified. The use of rubrics to measure student learning is also regularly reported, but details about these assessment instruments are sparse in the literature and were not a focus of our survey. Finally, we outline commonalities in the current practice of capstones and suggest the next steps needed to elucidate best practices. © 2015 The International Union of Biochemistry and Molecular Biology.

Using a Computer Animation to Teach High School Molecular Biology

Science.gov (United States)

Rotbain, Yosi; Marbach-Ad, Gili; Stavy, Ruth

2008-01-01

We present an active way to use a computer animation in secondary molecular genetics class. For this purpose we developed an activity booklet that helps students to work interactively with a computer animation which deals with abstract concepts and processes in molecular biology. The achievements of the experimental group were compared with those…

Humans in Space: Summarizing the Medico-Biological Results of the Space Shuttle Program

Science.gov (United States)

Risin, Diana; Stepaniak, P. C.; Grounds, D. J.

2011-01-01

As we celebrate the 50th anniversary of Gagarin's flight that opened the era of Humans in Space we also commemorate the 30th anniversary of the Space Shuttle Program (SSP) which was triumphantly completed by the flight of STS-135 on July 21, 2011. These were great milestones in the history of Human Space Exploration. Many important questions regarding the ability of humans to adapt and function in space were answered for the past 50 years and many lessons have been learned. Significant contribution to answering these questions was made by the SSP. To ensure the availability of the Shuttle Program experiences to the international space community NASA has made a decision to summarize the medico-biological results of the SSP in a fundamental edition that is scheduled to be completed by the end of 2011 beginning 2012. The goal of this edition is to define the normal responses of the major physiological systems to short-duration space flights and provide a comprehensive source of information for planning, ensuring successful operational activities and for management of potential medical problems that might arise during future long-term space missions. The book includes the following sections: 1. History of Shuttle Biomedical Research and Operations; 2. Medical Operations Overview Systems, Monitoring, and Care; 3. Biomedical Research Overview; 4. System-specific Adaptations/Responses, Issues, and Countermeasures; 5. Multisystem Issues and Countermeasures. In addition, selected operational documents will be presented in the appendices. The chapters are written by well-recognized experts in appropriate fields, peer reviewed, and edited by physicians and scientists with extensive expertise in space medical operations and space-related biomedical research. As Space Exploration continues the major question whether humans are capable of adapting to long term presence and adequate functioning in space habitats remains to be answered We expect that the comprehensive review of

Editorial: Molecular Organization of Membranes: Where Biology Meets Biophysics

Czech Academy of Sciences Publication Activity Database

Cebecauer, Marek; Holowka, D.

2017-01-01

Roč. 5, č. 113 (2017), s. 1-3 ISSN 2296-634X Institutional support: RVO:61388955 Keywords : nanodomains * membrane properties * cell membrane Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology

Molecular imaging of prostate cancer: translating molecular biology approaches into the clinical realm.

Science.gov (United States)

Vargas, Hebert Alberto; Grimm, Jan; F Donati, Olivio; Sala, Evis; Hricak, Hedvig

2015-05-01

The epidemiology of prostate cancer has dramatically changed since the introduction of prostate-specific antigen (PSA) screening in the 1980's. Most prostate cancers today are detected at early stages of the disease and are considered 'indolent'; however, some patients' prostate cancers demonstrate a more aggressive behaviour which leads to rapid progression and death. Increasing understanding of the biology underlying the heterogeneity that characterises this disease has led to a continuously evolving role of imaging in the management of prostate cancer. Functional and metabolic imaging techniques are gaining importance as the impact on the therapeutic paradigm has shifted from structural tumour detection alone to distinguishing patients with indolent tumours that can be managed conservatively (e.g., by active surveillance) from patients with more aggressive tumours that may require definitive treatment with surgery or radiation. In this review, we discuss advanced imaging techniques that allow direct visualisation of molecular interactions relevant to prostate cancer and their potential for translation to the clinical setting in the near future. The potential use of imaging to follow molecular events during drug therapy as well as the use of imaging agents for therapeutic purposes will also be discussed. • Advanced imaging techniques allow direct visualisation of molecular interactions in prostate cancer. • MRI/PET, optical and Cerenkov imaging facilitate the translation of molecular biology. • Multiple compounds targeting PSMA expression are currently undergoing clinical translation. • Other targets (e.g., PSA, prostate-stem cell antigen, GRPR) are in development.

Proceedings of the symposium on molecular biology and radiation protection

International Nuclear Information System (INIS)

Marko, A.M.

1996-02-01

The symposium on molecular biology and radiation protection was organized in sessions with the following titles: Radiation protection and the human genome; Molecular changes in DNA induced by radiation; Incidence of genetic changes - pre-existing, spontaneous and radiation-induced; Research directions and ethical implications. The ten papers in the symposium have been abstracted individually

Proceedings of the symposium on molecular biology and radiation protection

Energy Technology Data Exchange (ETDEWEB)

Marko, A M [Atomic Energy Control Board, Ottawa, ON (Canada). Advisory Committee on Radiological Protection; Myers, D K; Atchison, R J [Atomic Energy Control Board, Ottawa, ON (Canada). Advisory Committee on Radiological Protection. Secretariat; Gentner, N E [Atomic Energy of Canada Ltd., Chalk River, ON (Canada)

1996-02-01

The symposium on molecular biology and radiation protection was organized in sessions with the following titles: Radiation protection and the human genome; Molecular changes in DNA induced by radiation; Incidence of genetic changes - pre-existing, spontaneous and radiation-induced; Research directions and ethical implications. The ten papers in the symposium have been abstracted individually.

[Molecular Biology for Surgical Treatment of Lung Cancer].

Science.gov (United States)

Suda, Kenichi; Mitsudomi, Tetsuya

2017-01-01

Progress in lung cancer research achieved during the last 10 years was summarized. These include identification of novel driver mutations and application of targeted therapies, resistance mechanisms to targeted therapies, and immunotherapy with immune checkpoint inhibitors. Molecular biology also affects the field of surgical treatment. Several molecular markers have been reported to predict benign/ malignant or stable/growing tumors, although far from clinical application. In perioperative period, there is a possibility of atrial natriuretic peptide to prevent cancer metastasis. As adjuvant settings, although biomarker-based cytotoxic therapies failed to show clinical efficacy, several trials are ongoing employing molecular targeted agents (EGFR-TKI or ALK-TKI) or immune checkpoint inhibitors. In clinical practice, mutational information is sometimes used to distinguish 2nd primary tumors from pulmonary metastases of previous cancers. Surgery also has important role for oligo-progressive disease during molecular targeted therapies.

On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

Energy Technology Data Exchange (ETDEWEB)

Giampaolo, Alessia Di [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Mazza, Fernando [Department of Health Sciences, Univ. of L’Aquila, 67010 L’Aquila (Italy); Daidone, Isabella [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Amicosante, Gianfranco; Perilli, Mariagrazia [Dipartimento di Scienze Cliniche Applicate e Biotecnologiche, Università degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy); Aschi, Massimiliano, E-mail: massimiliano.aschi@univaq.it [Dipartimento di Scienze Fisiche e Chimiche, Universita’ degli Studi di l’Aquila, Via Vetoio snc, 67100 Coppito (AQ) (Italy)

2013-07-12

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment.

On the structural affinity of macromolecules with different biological properties: Molecular dynamics simulations of a series of TEM-1 mutants

International Nuclear Information System (INIS)

Giampaolo, Alessia Di; Mazza, Fernando; Daidone, Isabella; Amicosante, Gianfranco; Perilli, Mariagrazia; Aschi, Massimiliano

2013-01-01

Highlights: •We have performed molecular dynamics simulations of TEM-1 mutants. •Mutations effects on the mechanical properties are considered. •Mutants do not significantly alter the average enzymes structure. •Mutants produce sharp alterations in enzyme conformational repertoire. •Mutants also produce changes in the active site volume. -- Abstract: Molecular Dynamics simulations have been carried out in order to provide a molecular rationalization of the biological and thermodynamic differences observed for a class of TEM β-lactamases. In particular we have considered the TEM-1(wt), the single point mutants TEM-40 and TEM-19 representative of IRT and ESBL classes respectively, and TEM-1 mutant M182T, TEM-32 and TEM-20 which differ from the first three for the additional of M182T mutation. Results indicate that most of the thermodynamic, and probably biological behaviour of these systems arise from subtle effects which, starting from the alterations of the local interactions, produce drastic modifications of the conformational space spanned by the enzymes. The present study suggests that systems showing essentially the same secondary and tertiary structure may differentiate their chemical–biological activity essentially (and probably exclusively) on the basis of the thermal fluctuations occurring in their physiological environment

Modeling human risk: Cell ampersand molecular biology in context

International Nuclear Information System (INIS)

1997-06-01

It is anticipated that early in the next century manned missions into outer space will occur, with a mission to Mars scheduled between 2015 and 2020. However, before such missions can be undertaken, a realistic estimation of the potential risks to the flight crews is required. One of the uncertainties remaining in this risk estimation is that posed by the effects of exposure to the radiation environment of outer space. Although the composition of this environment is fairly well understood, the biological effects arising from exposure to it are not. The reasons for this are three-fold: (1) A small but highly significant component of the radiation spectrum in outer space consists of highly charged, high energy (HZE) particles which are not routinely experienced on earth, and for which there are insufficient data on biological effects; (2) Most studies on the biological effects of radiation to date have been high-dose, high dose-rate, whereas in space, with the exception of solar particle events, radiation exposures will be low-dose, low dose-rate; (3) Although it has been established that the virtual absence of gravity in space has a profound effect on human physiology, it is not clear whether these effects will act synergistically with those of radiation exposure. A select panel will evaluate the utilizing experiments and models to accurately predict the risks associated with exposure to HZE particles. Topics of research include cellular and tissue response, health effects associated with radiation damage, model animal systems, and critical markers of Radiation response

Molecular basis sets - a general similarity-based approach for representing chemical spaces.

Science.gov (United States)

Raghavendra, Akshay S; Maggiora, Gerald M

2007-01-01

A new method, based on generalized Fourier analysis, is described that utilizes the concept of "molecular basis sets" to represent chemical space within an abstract vector space. The basis vectors in this space are abstract molecular vectors. Inner products among the basis vectors are determined using an ansatz that associates molecular similarities between pairs of molecules with their corresponding inner products. Moreover, the fact that similarities between pairs of molecules are, in essentially all cases, nonzero implies that the abstract molecular basis vectors are nonorthogonal, but since the similarity of a molecule with itself is unity, the molecular vectors are normalized to unity. A symmetric orthogonalization procedure, which optimally preserves the character of the original set of molecular basis vectors, is used to construct appropriate orthonormal basis sets. Molecules can then be represented, in general, by sets of orthonormal "molecule-like" basis vectors within a proper Euclidean vector space. However, the dimension of the space can become quite large. Thus, the work presented here assesses the effect of basis set size on a number of properties including the average squared error and average norm of molecular vectors represented in the space-the results clearly show the expected reduction in average squared error and increase in average norm as the basis set size is increased. Several distance-based statistics are also considered. These include the distribution of distances and their differences with respect to basis sets of differing size and several comparative distance measures such as Spearman rank correlation and Kruscal stress. All of the measures show that, even though the dimension can be high, the chemical spaces they represent, nonetheless, behave in a well-controlled and reasonable manner. Other abstract vector spaces analogous to that described here can also be constructed providing that the appropriate inner products can be directly

Space Biology Meets Astrobiology: Critical Synergies and Concerns

Science.gov (United States)

Boston, Penelope J.; Kirven-Brooks, Melissa

2016-01-01

The broad fields of space biology and astrobiology share much in common in terms of science questions, approaches, and goals. However, historical circumstances and funding agency practices have frequently resulted in a wide separation between the two related areas. Is this a good thing? We believe that it is not, and that much is to be gained in each field from sharing ideas, resources, and perhaps projects between investigators traditionally working in one discipline or the other. Some of the strengths that the Space Biology community offers include sophistication and experience in flying experiments on space missions. In turn, Astrobiology has focused heavily on ground-based and field research. Challenging physical and chemical conditions experienced in space and on other planets partially overlap, and much can be gleaned from the body of work of each community along these topical lines. A combination of these areas of expertise and experience could result in major advances to all involved. When possible, avoiding having to reinvent methods or approaches already used by a sister community can result in greater efficiencies of resource use. We will discuss some case studies where we believe there are significant overlaps including adaptation to a variety of environmental stresses, extremophiles as potential flight organisms, microfluidics as applied to planetary environment simulations, and others.

Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell.

Science.gov (United States)

Cordova, Caio M M; Hoeltgebaum, Daniela L; Machado, Laís D P N; Santos, Larissa Dos

2016-01-01

Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology.

STRUCTURAL BIOLOGY AND MOLECULAR MEDICINE RESEARCH PROGRAM (LSBMM)

International Nuclear Information System (INIS)

Eisenberg, David S.

2008-01-01

The UCLA-DOE Institute of Genomics and Proteomics is an organized research unit of the University of California, sponsored by the Department of Energy through the mechanism of a Cooperative Agreement. Today the Institute consists of 10 Principal Investigators and 7 Associate Members, developing and applying technologies to promote the biological and environmental missions of the Department of Energy, and 5 Core Technology Centers to sustain this work. The focus is on understanding genomes, pathways and molecular machines in organisms of interest to DOE, with special emphasis on developing enabling technologies. Since it was founded in 1947, the UCLA-DOE Institute has adapted its mission to the research needs of DOE and its progenitor agencies as these research needs have changed. The Institute started as the AEC Laboratory of Nuclear Medicine, directed by Stafford Warren, who later became the founding Dean of the UCLA School of Medicine. In this sense, the entire UCLA medical center grew out of the precursor of our Institute. In 1963, the mission of the Institute was expanded into environmental studies by Director Ray Lunt. I became the third director in 1993, and in close consultation with David Galas and John Wooley of DOE, shifted the mission of the Institute towards genomics and proteomics. Since 1993, the Principal Investigators and Core Technology Centers are entirely new, and the Institute has separated from its former division concerned with PET imaging. The UCLA-DOE Institute shares the space of Boyer Hall with the Molecular Biology Institute, and assumes responsibility for the operation of the main core facilities. Fig. 1 gives the organizational chart of the Institute. Some of the benefits to the public of research carried out at the UCLA-DOE Institute include the following: The development of publicly accessible, web-based databases, including the Database of Protein Interactions, and the ProLinks database of genomicly inferred protein function linkages

Molecular biology applications to infectious diseases diagnostic; Aplicaciones de la Biologica Molecular al diagnostico de enfermedades infecciosas

Energy Technology Data Exchange (ETDEWEB)

NONE

2001-07-01

This project goes directed to the applications of the techniques of molecular biology in hepatitis virus.A great advance of these techniques it allows its application to the diagnose molecular and it becomes indispensable to have these fundamental tools in the field of the Health Public for the detection precocious, pursuit of the treatment, the one predicts and the evolution of the patient hepatitis bearing virus technical.Use of molecular biology to increase the handling and the control of the patients with hepatitis B and C and to detect an adult numbers of positive cases by means of the training and integration of all the countries participating.Implement the technique of PCR to identify the virus of the hepatitis B and C,implement quantification methods and genotipification for these virus.

Delivery of Biologics Across the Blood-Brain Barrier with Molecular Trojan Horse Technology.

Science.gov (United States)

Pardridge, William M

2017-12-01

Biologics are potential new therapeutics for many diseases of the central nervous system. Biologics include recombinant lysosomal enzymes, neurotrophins, decoy receptors, and therapeutic antibodies. These are large molecule drugs that do not cross the blood-brain barrier (BBB). All classes of biologics have been tested, without success, in clinical trials of brain disease over the last 25 years. In none of these past clinical trials was the biologic re-engineered to enable transport across the BBB. If the biologic does not cross the BBB, the drug cannot reach the target site in brain, and success in a clinical trial is not expected. Biologics can be re-engineered for BBB transport with the use of molecular Trojan horse technology. A BBB molecular Trojan horse is a monoclonal antibody (MAb) against an endogenous BBB receptor transporter, such as the insulin receptor or transferrin receptor. The receptor-specific MAb penetrates the brain via transport on the endogenous BBB receptor. The MAb acts as a molecular Trojan horse to deliver across the BBB the biologic pharmaceutical that is genetically fused to the MAb. The lead Trojan horse is a MAb against the human insulin receptor (HIR), and HIRMAb-derived fusion proteins have entered clinical trials for the treatment of brain disease.

International Conference on Intelligent Systems for Molecular Biology (ISMB)

Energy Technology Data Exchange (ETDEWEB)

Goldberg, Debra; Hibbs, Matthew; Kall, Lukas; Komandurglayavilli, Ravikumar; Mahony, Shaun; Marinescu, Voichita; Mayrose, Itay; Minin, Vladimir; Neeman, Yossef; Nimrod, Guy; Novotny, Marian; Opiyo, Stephen; Portugaly, Elon; Sadka, Tali; Sakabe, Noboru; Sarkar, Indra; Schaub, Marc; Shafer, Paul; Shmygelska, Olena; Singer, Gregory; Song, Yun; Soumyaroop, Bhattacharya; Stadler, Michael; Strope, Pooja; Su, Rong; Tabach, Yuval; Tae, Hongseok; Taylor, Todd; Terribilini, Michael; Thomas, Asha; Tran, Nam; Tseng, Tsai-Tien; Vashist, Akshay; Vijaya, Parthiban; Wang, Kai; Wang, Ting; Wei, Lai; Woo, Yong; Wu, Chunlei; Yamanishi, Yoshihiro; Yan, Changhui; Yang, Jack; Yang, Mary; Ye, Ping; Zhang, Miao

2009-12-29

The Intelligent Systems for Molecular Biology (ISMB) conference has provided a general forum for disseminating the latest developments in bioinformatics on an annual basis for the past 13 years. ISMB is a multidisciplinary conference that brings together scientists from computer science, molecular biology, mathematics and statistics. The goal of the ISMB meeting is to bring together biologists and computational scientists in a focus on actual biological problems, i.e., not simply theoretical calculations. The combined focus on "intelligent systems" and actual biological data makes ISMB a unique and highly important meeting, and 13 years of experience in holding the conference has resulted in a consistently well organized, well attended, and highly respected annual conference. The ISMB 2005 meeting was held June 25-29, 2005 at the Renaissance Center in Detroit, Michigan. The meeting attracted over 1,730 attendees. The science presented was exceptional, and in the course of the five-day meeting, 56 scientific papers, 710 posters, 47 Oral Abstracts, 76 Software demonstrations, and 14 tutorials were presented. The attendees represented a broad spectrum of backgrounds with 7% from commercial companies, over 28% qualifying for student registration, and 41 countries were represented at the conference, emphasizing its important international aspect. The ISMB conference is especially important because the cultures of computer science and biology are so disparate. ISMB, as a full-scale technical conference with refereed proceedings that have been indexed by both MEDLINE and Current Contents since 1996, bridges this cultural gap.

Just Working with the Cellular Machine: A High School Game for Teaching Molecular Biology

Science.gov (United States)

Cardoso, Fernanda Serpa; Dumpel, Renata; Gomes da Silva, Luisa B.; Rodrigues, Carlos R.; Santos, Dilvani O.; Cabral, Lucio Mendes; Castro, Helena C.

2008-01-01

Molecular biology is a difficult comprehension subject due to its high complexity, thus requiring new teaching approaches. Herein, we developed an interdisciplinary board game involving the human immune system response against a bacterial infection for teaching molecular biology at high school. Initially, we created a database with several…

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.

Screens as light biological variable in microgravitational space environment.

Science.gov (United States)

Schlacht, S.; Masali, M.

Foreword The ability of the biological organisms to orient themselves and to synchronize on the variations of the solar rhythms is a fundamental aspect in the planning of the human habitat above all when habitat is confined in the Space the planetary and in satellite outer space settlements In order to simulate the experience of the astronauts in long duration missions one of the dominant characteristics of the Space confined habitats is the absence of the earthlings solar cycles references The Sun is the main references and guidelines of the biological compass and timepiece The organism functions are influenced from the variation of the light in the round of the 24 hours the human circadian rhythms In these habitats it is therefore necessary to reproduce the color and intensity of the solar light variations along the arc of the day according to defined scientific programs assuring a better performance of the human organism subsubsection Multilayer Foldable Screens as biological environmental variable In the project Multilayer Foldable Screens are the monitors posed in the ceiling of an Outer Space habitat and are made of liquid crystals and covered with Kevlar they stand for a modulate and flexible structure for different arrangements and different visions Screens work sout s on all the solar light frequencies and display the images that the subject needs They are characterized from the emission of an environmental light that restores the earthly solar cycle for intensity and color temperature to irradiate

Importancia de la biología molecular para la Fisioterapia moderna Importance of molecular biology for the modern Physical Therapy

Directory of Open Access Journals (Sweden)

Carolina Ramírez Ramírez

2011-12-01

Full Text Available Para que el cuerpo de conocimiento de una profesión crezca y se fortalezca debe estar al día con los avances científicos y tecnológicos que surgen continuamente para incluirlos en el repertorio de recursos que usa para la investigación de problemas específicos de su saber. Recientemente el desciframiento del código genético y la secuenciación del genoma humano creó la base para el surgimiento de metodologías y técnicas en el área de la biología molecular, las cuales permitieron profundizar en el conocimiento de la estructura y función de los tejidos humanos y también mejoraron el entendimiento de los mecanismos por los cuales actúan formas de intervención usadas cotidianamente por profesionales en salud. La Fisioterapia utiliza modalidades físicas que interactúan con los tejidos corporales, por ello la biología molecular permite un mejor entendimiento de los efectos que las dichas modalidades generan en el tejido sobre el cual son aplicadas. Por tanto el objetivo de este artículo es reflexionar sobre la necesidad de que el Fisioterapeuta se apropie del conocimiento en ésta área de las ciencias básicas, usarlo como herramienta para la solución de preguntas relevantes de su quehacer clínico y así contribuir de manera efectiva con la generación de nuevo conocimiento que promueva la práctica basada en la evidencia y fomente el crecimiento de la profesión. Salud UIS 2011; 43 (3: 317-320A profession can be improved through the development and application of scientific and technological advances around the issues relating to their expertise. Recently, the deciphering of the genetic code and human genome sequencing creates the basis for the development of methodologies and techniques of molecular biology. These resources have allowed a deeper understanding of the human tissue structure and function, and intervention mechanisms used by health professionals. Physiotherapy uses physical modalities affecting the tissues of the

A discussion of molecular biology methods for protein engineering

CSIR Research Space (South Africa)

Zawaira, A

2011-09-01

Full Text Available A number of molecular biology techniques are available to generate variants from a particular start gene for eventual protein expression. The authors discuss the basic principles of these methods in a repertoire that may be used to achieve...

Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

Directory of Open Access Journals (Sweden)

Jiyoung Kang

2012-01-01

Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

Biodiversity: molecular biological domains, symbiosis and kingdom origins

Science.gov (United States)

Margulis, L.

1992-01-01

The number of extant species of organisms is estimated to be from fewer than 3 to more than 30 x 10(6) (May, 1992). Molecular biology, comparative genetics and ultrastructural analyses provide new insights into evolutionary relationships between these species, including increasingly precise ideas of how species and higher taxa have evolved from common ancestors. Accumulation of random mutations and large macromolecular sequence change in all organisms since the Proterozoic Eon has been importantly supplemented by acquisition of inherited genomes ('symbiogenesis'). Karyotypic alterations (polyploidization and karyotypic fissioning) have been added to these other mechanisms of species origin in plants and animals during the Phanerozoic Eon. The new evolution concepts (coupled with current rapid rates of species extinction and ignorance of the extent of biodiversity) prompted this analysis of the field of systematic biology and its role in the reorganization of extant species into higher taxa. Two superkingdoms (= Domains: Prokaryotae and Eukaryotae) and five kingdoms (Monera = Procaryotae or Bacteria; Protoctista: algae, amoebae, ciliates, foraminifera, oomycetes, slime molds, etc.; Mychota: 'true' fungi; Plantae: one phylum (division) of bryophytes and nine phyla of tracheophytes; and Animalia) are recognized. Two subkingdoms comprise the monera: the great diverse lineages are Archaebacteria and Eubacteria. The criteria for classification using molecular, ultrastructural and genetic data for this scheme are mentioned. For the first time since the nineteenth century, logical, technical definitions for each group are given with their time of appearance as inferred from the fossil record in the primary scientific literature. This classification scheme, which most closely reflects the evolutionary history, molecular biology, genetics and ultrastructure of extant life, requires changes in social organization of biologists, many of whom as botanists and zoologists, still

2009 Archaea: Ecology, Metabolism & Molecular Biology GRC

Energy Technology Data Exchange (ETDEWEB)

Furlow, Julie Maupin- [Univ. of Florida, Gainesville, FL (United States)

2009-07-26

Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.

Nutritional education from Molecular and Cellular Biology

Directory of Open Access Journals (Sweden)

Zaida Ramona Betancourt Betancourt

2014-12-01

Full Text Available The nutritional education is current topic, constituting a necessity in the contemporary world, given mainly by the contribution that it makes in maintaining the human health under good conditions. Starting from this problem, it is presented this article whose objective is: to show the potential ities that the discipline Cellular and Molecular Biology offers, for the treatment of these contents, since this discipline is worked in the second semester of first year and first semester of in the formation of professors of the Biology - Geography and Bio logy - C hemistry careers which can contribute to the development of knowledge, habits and abilities that allows them to appropriate of responsible behaviours for the achievement of correct nutritional habits.

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

Tangible Models and Haptic Representations Aid Learning of Molecular Biology Concepts

Science.gov (United States)

Johannes, Kristen; Powers, Jacklyn; Couper, Lisa; Silberglitt, Matt; Davenport, Jodi

2016-01-01

Can novel 3D models help students develop a deeper understanding of core concepts in molecular biology? We adapted 3D molecular models, developed by scientists, for use in high school science classrooms. The models accurately represent the structural and functional properties of complex DNA and Virus molecules, and provide visual and haptic…

Bragg Curve, Biological Bragg Curve and Biological Issues in Space Radiation Protection with Shielding

Science.gov (United States)

Honglu, Wu; Cucinotta, F.A.; Durante, M.; Lin, Z.; Rusek, A.

2006-01-01

The space environment consists of a varying field of radiation particles including high-energy ions, with spacecraft shielding material providing the major protection to astronauts from harmful exposure. Unlike low-LET gamma or X-rays, the presence of shielding does not always reduce the radiation risks for energetic charged particle exposure. Since the dose delivered by the charged particle increases sharply as the particle approaches the end of its range, a position known as the Bragg peak, the Bragg curve does not necessarily represent the biological damage along the particle traversal since biological effects are influenced by the track structure of both primary and secondary particles. Therefore, the biological Bragg curve is dependent on the energy and the type of the primary particle, and may vary for different biological endpoints. To achieve a Bragg curve distribution, we exposed cells to energetic heavy ions with the beam geometry parallel to a monolayer of fibroblasts. Qualitative analyses of gamma-H2AX fluorescence, a known marker of DSBs, indicated increased clustering of DNA damage before the Bragg peak, enhanced homogenous distribution at the peak, and provided visual evidence of high linear energy transfer (LET) particle traversal of cells beyond the Bragg peak. A quantitative biological response curve generated for micronuclei (MN) induction across the Bragg curve did not reveal an increased yield of MN at the location of the Bragg peak. However, the ratio of mono-to bi-nucleated cells, which indicates inhibition in cell progression, increased at the Bragg peak location. These results, along with other biological concerns, show that space radiation protection with shielding can be a complicated issue.

Practices and Exploration on Competition of Molecular Biological Detection Technology among Students in Food Quality and Safety Major

Science.gov (United States)

Chang, Yaning; Peng, Yuke; Li, Pengfei; Zhuang, Yingping

2017-01-01

With the increasing importance in the application of the molecular biological detection technology in the field of food safety, strengthening education in molecular biology experimental techniques is more necessary for the culture of the students in food quality and safety major. However, molecular biology experiments are not always in curricula…

Molecular biology and its applications in orthodontics and oral and maxillofacial surgery

NARCIS (Netherlands)

Ren, Yjin

2005-01-01

: Molecular biology is an exciting, rapidly expanding field, which has enabled enormously greater understanding of the biology of diseases and malfunctions in many fields. It chiefly concerns itself with understanding the interactions between the various systems of a cell, including the

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

Science.gov (United States)

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

2013-01-01

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

Life sciences payloads analyses and technical program planning studies. [project planning of space missions of space shuttles in aerospace medicine and space biology

Science.gov (United States)

1976-01-01

Contractural requirements, project planning, equipment specifications, and technical data for space shuttle biological experiment payloads are presented. Topics discussed are: (1) urine collection and processing on the space shuttle, (2) space processing of biochemical and biomedical materials, (3) mission simulations, and (4) biomedical equipment.

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.

Effects of space environment on biological characteristics of melanoma B16 cells

International Nuclear Information System (INIS)

Geng Chuanying; Xiang Qing; Xu Mei; Li Hongyan; Xu Bo; Fang Qing; Tang Jingtian; Guo Yupeng

2006-01-01

Objective: To examine the effects of space environment on biological characteristics of melanoma B16 Cells. Methods: B16 cells were carried to the space (in orbit for 8 days, circle the earth 286 times) by the 20th Chinese recoverable satellite, and then harvested and monocloned. 110 strains of space B16 cells were obtained in total. Ten strains of space B16 cells were selected and its morphological changes were examined with the phasecontrast microscope. Flow cytometry and MTT assay were carried out to evaluate the cell cycle and cell viability. Results Morphological changes were observed in the space cells, and melainin granules on the surface in some cells. It was demonstrated by MTF assay that space cells viability varied muti- directionally. It was showed by flow cytometry analysis that G1 phase of space cells was prolonged, S phase shortened. Conclusion: Space environment may change the biological characteristics of melanoma B16 cells. (authors)

Molecular biology III - Oncogenes and tumor suppressor genes

International Nuclear Information System (INIS)

Giaccia, Amato J.

1996-01-01

Purpose: The purpose of this course is to introduce to radiation oncologists the basic concepts of tumorigenesis, building on the information that will be presented in the first and second part of this series of lectures. Objective: Our objective is to increase the current understanding of radiation oncologists with the process of tumorigenesis, especially focusing on genes that are altered in many tumor types that are potential candidates for novel molecular strategies. As strategies to treat cancer of cancer are becoming more sophisticated, it will be important for both the practitioner and academician to develop a basic understanding of the function of cancer 'genes'. This will be the third in a series of refresher courses that are meant to address recent advances in Cancer Biology in a way that both clinicians without previous knowledge of molecular biology or experienced researchers will find interesting. The lecture will begin with a basic overview of tumorigenesis; methods of detecting chromosome/DNA alterations, approaches used to isolate oncogenes and tumor suppressor genes, and their role in cell killing by apoptosis. Special attention will be given to oncogenes and tumor suppressor genes that are modulated by ionizing radiation and the tumor microenvironment. We will relate the biology of oncogenes and tumor suppressor genes to basic aspects of radiation biology that would be important in clinical practice. Finally, we will review recent studies on the prognostic significance of p53 mutations and apoptosis in tumor specimens. The main point of this lecture is to relate both researcher and clinician what are the therapeutic ramifications of oncogene and tumor suppressor gene mutations found in human neoptasia

Egyptian Journal of Biochemistry and Molecular Biology - Vol 32, No ...

African Journals Online (AJOL)

The Egyptian Journal of Biochemistry and Molecular Biology. ... Therapeutic Impacts of Almond Oil and Olive Oil on Cholesterol Dynamics and ... Multidrug Resistance Proteins in Pancreatic Carcinoma · EMAIL FULL TEXT EMAIL FULL TEXT

Script, code, information: how to differentiate analogies in the "prehistory" of molecular biology.

Science.gov (United States)

Kogge, Werner

2012-01-01

The remarkable fact that twentieth-century molecular biology developed its conceptual system on the basis of sign-like terms has been the object of numerous studies and debates. Throughout these, the assumption is made that this vocabulary's emergence should be seen in the historical context of mathematical communication theory and cybernetics. This paper, in contrast, sets out the need for a more differentiated view: whereas the success of the terms "code" and "information" would probably be unthinkable outside that historical context, general semiotic and especially scriptural concepts arose far earlier in the "prehistory" of molecular biology, and in close association with biological research and phenomena. This distinction, established through a reconstruction of conceptual developments between 1870 and 1950, makes it possible to separate off a critique of the reductive implications of particular information-based concepts from the use of semiotic and scriptural concepts, which is fundamental to molecular biology. Gene-centrism and determinism are not implications of semiotic and scriptural analogies, but arose only when the vocabulary of information was superimposed upon them.

The contribution of neutron scattering to molecular biology

International Nuclear Information System (INIS)

Stuhrmann, H.B.

1983-01-01

About half of the atoms of living cells are hydrogens, and nearly all biological applications of neutron scattering rely on the well-known difference in the scattering lengths of the proton and the deuteron. This introduces us to a wide variety of biological problems, which are related with hydrogen in water, proteins, nucleic acids and lipids. Neutron scattering gives an answer to both structural and dynamical aspects of the system in question. With deuterium labelled samples unambiguous information about molecular structure and motion becomes accessible. The architecture of viruses, cell membranes and gene expressing molecules has become a lot clearer with neutron scattering. (author)

Historical parallels of biological space experiments from Soyuz, Salyut and Mir to Shenzhou flights

Science.gov (United States)

Nechitailo, Galina S.; Kondyurin, Alexey

2016-07-01

Human exploitation of space is a great achievement of our civilization. After the first space flights a development of artificial biological environment in space systems is a second big step. First successful biological experiments on a board of space station were performed on Salyut and Mir stations in 70-90th of last century such as - first long time cultivation of plants in space (wheat, linen, lettuce, crepis); - first flowers in space (Arabidopsis); - first harvesting of seeds in space (Arabidopsis); - first harvesting of roots (radish); - first full life cycle from seeds to seeds in space (wheat), Guinness recorded; - first tissue culture experiments (Panax ginseng L, Crocus sativus L, Stevia rebaundiana B; - first tree growing in space for 2 years (Limonia acidissima), Guinness recorded. As a new wave, the modern experiments on a board of Shenzhou Chinese space ships are performed with plants and tissue culture. The space flight experiments are now focused on applications of the space biology results to Earth technologies. In particular, the tomato seeds exposed 6 years in space are used in pharmacy industry in more then 10 pharmaceutical products. Tissue culture experiments are performed on the board of Shenzhou spaceship for creation of new bioproducts including Space Panax ginseng, Space Spirulina, Space Stetatin, Space Tomato and others products with unique properties. Space investments come back.

Dissecting the Molecular Mechanisms of Neurodegenerative Diseases through Network Biology

Directory of Open Access Journals (Sweden)

Jose A. Santiago

2017-05-01

Full Text Available Neurodegenerative diseases are rarely caused by a mutation in a single gene but rather influenced by a combination of genetic, epigenetic and environmental factors. Emerging high-throughput technologies such as RNA sequencing have been instrumental in deciphering the molecular landscape of neurodegenerative diseases, however, the interpretation of such large amounts of data remains a challenge. Network biology has become a powerful platform to integrate multiple omics data to comprehensively explore the molecular networks in the context of health and disease. In this review article, we highlight recent advances in network biology approaches with an emphasis in brain-networks that have provided insights into the molecular mechanisms leading to the most prevalent neurodegenerative diseases including Alzheimer’s (AD, Parkinson’s (PD and Huntington’s diseases (HD. We discuss how integrative approaches using multi-omics data from different tissues have been valuable for identifying biomarkers and therapeutic targets. In addition, we discuss the challenges the field of network medicine faces toward the translation of network-based findings into clinically actionable tools for personalized medicine applications.

Naumovozyma castellii: an alternative model for budding yeast molecular biology.

Science.gov (United States)

Karademir Andersson, Ahu; Cohn, Marita

2017-03-01

Naumovozyma castellii (Saccharomyces castellii) is a member of the budding yeast family Saccharomycetaceae. It has been extensively used as a model organism for telomere biology research and has gained increasing interest as a budding yeast model for functional analyses owing to its amenability to genetic modifications. Owing to the suitable phylogenetic distance to S. cerevisiae, the whole genome sequence of N. castellii has provided unique data for comparative genomic studies, and it played a key role in the establishment of the timing of the whole genome duplication and the evolutionary events that took place in the subsequent genomic evolution of the Saccharomyces lineage. Here we summarize the historical background of its establishment as a laboratory yeast species, and the development of genetic and molecular tools and strains. We review the research performed on N. castellii, focusing on areas where it has significantly contributed to the discovery of new features of molecular biology and to the advancement of our understanding of molecular evolution. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Future directions for radiological physics: An interface with molecular biology

International Nuclear Information System (INIS)

Braby, L.A.

1987-01-01

Recent experiments with low energy x-rays and fast molecular ions have shown that the products of the interaction of several ionizations within a few nanometers dominate radiation effects. However, the authors still can only make assumptions about the physical and chemical nature of this initial damage. Enzymatic repair of DNA damage is another key factor, but they have little idea of what governs the success or failure (misrepair) of these processes. Unresolved problems like these dictate the future direction of radiological physics. Molecular biology techniques are being applied to determine molecular alterations which result in observed damage. Interpretation of these experiments will require new data on the physics of energy transfer to macromolecules and the stochastics of energy deposition in time. Future studies will attempt to identify the initial damage, before biological processes have amplified it. This will require a detailed understanding of the role of chromatin structure in governing gene expression, the transport of energy within macromolecules, the transport of ions and radicals in the semiordered environment near DNA strands, and many other physical characteristics within the living cell

How phenotypic plasticity made its way into molecular biology

Indian Academy of Sciences (India)

2009-08-03

Aug 3, 2009 ... Phenotypic plasticity has been fashionable in recent years. It has never been absent from the studies of evolutionary biologists, although the availability of stable animal models has limited its role. Although opposed by the reductionist and deterministic approach of molecular biology, phenotypic plasticity ...

Implications of molecular heterogeneity for the cooperativity of biological macromolecules.

Science.gov (United States)

Solomatin, Sergey V; Greenfeld, Max; Herschlag, Daniel

2011-06-01

Cooperativity, a universal property of biological macromolecules, is typically characterized by a Hill slope, which can provide fundamental information about binding sites and interactions. We demonstrate, through simulations and single-molecule FRET (smFRET) experiments, that molecular heterogeneity lowers bulk cooperativity from the intrinsic value for the individual molecules. As heterogeneity is common in smFRET experiments, appreciation of its influence on fundamental measures of cooperativity is critical for deriving accurate molecular models.

GeneLab Phase 2: Integrated Search Data Federation of Space Biology Experimental Data

Science.gov (United States)

Tran, P. B.; Berrios, D. C.; Gurram, M. M.; Hashim, J. C. M.; Raghunandan, S.; Lin, S. Y.; Le, T. Q.; Heher, D. M.; Thai, H. T.; Welch, J. D.;

Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth.

Science.gov (United States)

Karouia, Fathi; Peyvan, Kianoosh; Pohorille, Andrew

2017-11-15

Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis. Published by Elsevier Inc.

US and Russian Cooperation in Space Biology and Medicine

Science.gov (United States)

Sawin, C.F.; Hanson, S.I.; House, N.G.; Pestov, I.D.

2009-01-01

This slide presentation concerns the 5th volume of a joint publication that describes the cooperation between the United States and Russia in research into space biology and medicine. Each of the chapters is briefly summarized.

Third workshop on heavy charged particles in biology and medicine

International Nuclear Information System (INIS)

Kraft, G.; Grundinger, U.

1987-07-01

The book of abstracts contains 67 papers presented at the workshop. Main topics are: Physics, chemistry, DNA, cell biology, cellular and molecular repair, space biology, tumor and tissue biology, predictive assays, cancer therapy, and new projects. Separate entries in the database are prepared for all of these papers. (MG)

Epidemiology and Molecular Biology of Head and Neck Cancer.

Science.gov (United States)

Jou, Adriana; Hess, Jochen

2017-01-01

Head and neck cancer is a common and aggressive malignancy with a high morbidity and mortality profile. Although the large majority of cases resemble head and neck squamous cell carcinoma (HNSCC), the current classification based on anatomic site and tumor stage fails to capture the high level of biologic heterogeneity, and appropriate clinical management remains a major challenge. Hence, a better understanding of the molecular biology of HNSCC is urgently needed to support biomarker development and personalized care for patients. This review focuses on recent findings based on integrative genomics analysis and multi-scale modeling approaches and how they are beginning to provide more sophisticated clues as to the biological and clinical diversity of HNSCC. © 2017 S. Karger GmbH, Freiburg.

In vitro studies. Contribution of radioactive marking to molecular biology development

International Nuclear Information System (INIS)

Sentenac, A.

1997-01-01

The spectacular and rapid development of molecular biology is essentially related to the utilization of marked molecules which leads to quantitative and qualitative information; the use of radioactive tracers allowed for the observation of the biosynthesis of biological polymers, and thus, for example, the formation of DNA, RNA or proteins. A historical review of the great discoveries in this field, is presented

Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

Science.gov (United States)

Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

2014-01-01

Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

How diverse are diversity assessment methods? A comparative analysis and benchmarking of molecular descriptor space.

Science.gov (United States)

Koutsoukas, Alexios; Paricharak, Shardul; Galloway, Warren R J D; Spring, David R; Ijzerman, Adriaan P; Glen, Robert C; Marcus, David; Bender, Andreas

2014-01-27

Chemical diversity is a widely applied approach to select structurally diverse subsets of molecules, often with the objective of maximizing the number of hits in biological screening. While many methods exist in the area, few systematic comparisons using current descriptors in particular with the objective of assessing diversity in bioactivity space have been published, and this shortage is what the current study is aiming to address. In this work, 13 widely used molecular descriptors were compared, including fingerprint-based descriptors (ECFP4, FCFP4, MACCS keys), pharmacophore-based descriptors (TAT, TAD, TGT, TGD, GpiDAPH3), shape-based descriptors (rapid overlay of chemical structures (ROCS) and principal moments of inertia (PMI)), a connectivity-matrix-based descriptor (BCUT), physicochemical-property-based descriptors (prop2D), and a more recently introduced molecular descriptor type (namely, "Bayes Affinity Fingerprints"). We assessed both the similar behavior of the descriptors in assessing the diversity of chemical libraries, and their ability to select compounds from libraries that are diverse in bioactivity space, which is a property of much practical relevance in screening library design. This is particularly evident, given that many future targets to be screened are not known in advance, but that the library should still maximize the likelihood of containing bioactive matter also for future screening campaigns. Overall, our results showed that descriptors based on atom topology (i.e., fingerprint-based descriptors and pharmacophore-based descriptors) correlate well in rank-ordering compounds, both within and between descriptor types. On the other hand, shape-based descriptors such as ROCS and PMI showed weak correlation with the other descriptors utilized in this study, demonstrating significantly different behavior. We then applied eight of the molecular descriptors compared in this study to sample a diverse subset of sample compounds (4%) from an

Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

Science.gov (United States)

Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

1993-01-01

This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

Multispectral optical tweezers for molecular diagnostics of single biological cells

Science.gov (United States)

Butler, Corey; Fardad, Shima; Sincore, Alex; Vangheluwe, Marie; Baudelet, Matthieu; Richardson, Martin

2012-03-01

Optical trapping of single biological cells has become an established technique for controlling and studying fundamental behavior of single cells with their environment without having "many-body" interference. The development of such an instrument for optical diagnostics (including Raman and fluorescence for molecular diagnostics) via laser spectroscopy with either the "trapping" beam or secondary beams is still in progress. This paper shows the development of modular multi-spectral imaging optical tweezers combining Raman and Fluorescence diagnostics of biological cells.

Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

Science.gov (United States)

Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

2018-01-01

Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

Multiwire proportional chambers in the devices for molecular biology constructed at JINR

Energy Technology Data Exchange (ETDEWEB)

Anisimov, Y S; Chernenko, S P; Ivanov, A B; Peshekhonov, V D; Skvaril, J; Zanevsky, Y V [Joint Inst. for Nuclear Research, Dubna (USSR). Lab. of High Energy; Kheiker, D M [Joint Inst. for Nuclear Research, Dubna (USSR). Lab. of High Energy; AN SSSR, Moscow. Inst. Kristallografii)

1980-10-01

The automation of measuring processes in molecular biology is a current problem. In order to solve this problem, conventionally used methods should be changed for an up-to-date technique which allows the processes of data measurement and analysis to be automated. Toward this end two-coordinate proportional chambers (MWPCs) are coming widely into use. The use of MWPCs in devices for radiochromatography and x-ray diffractrometry is discussed in this paper. A new device consisting of proportional chambers has been constructed for an automated analysis of thin layer radiochromatograms. The device enables one to localize radioactive zones (labelled with /sup 3/H, /sup 14/C, /sup 32/P), to identify radionuclides and to measure their activities. The device has a high sensitivity (5 pCi for tritium), a small dead time, good space resolution (in the case of /sup 3/H zones spaced 1-2 mm apart are separated) and high reproducibility. For x-ray diffractometry of single crystals, a high counting rate device has been constructed on the basis of a MWPC with a total number of channels amounting to 350 x 200 = 70,000. The dead time of the device is about 0.6 ..mu..s which allows to detect 3 x 10/sup 5/ events/s at counting losses of no more than 20%. The quantum efficiency (Cu K..cap alpha..) is about 73%. The X and Y space resolution (fwhm) is equal to 1 mm and 1.7 mm, respectively.

Molecular biology of the lung cancer

International Nuclear Information System (INIS)

Panov, S.Z.

2005-01-01

Background. Lung cancer is one of the most common malignant diseases and leading cause of cancer death worldwide. The advances in molecular biology and genetics, including the modern microarray technology and rapid sequencing techniques, have enabled a remarkable progress into elucidating the lung cancer ethiopathogenesis. Numerous studies suggest that more than 20 different genetic and epigenetic alterations are accumulating during the pathogenesis of clinically evident pulmonary cancers as a clonal, multistep process. Thus far, the most investigated alterations are the inactivational mutations and losses of tumour suppressor genes and the overexpression of growth-promoting oncogenes. More recently, the acquired epigenetic inactivation of tumour suppressor genes by promoter hypermethylation has been recognized. The early clonal genetic abnormalities that occur in preneoplastic bronchial epithelium damaged by smoking or other carcinogenes are being identified. The molecular distinctions between small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), as well as between tumors with different clinical outcomes have been described. These investigations lead to the h allmarks of lung cancer . Conclusions. It is realistic to expect that the molecular and cell culture-based investigations will lead to discoveries of new clinical applications with the potential to provide new avenues for early diagnosis, risk assessment, prevention, and most important, new more effective treatment approaches for the lung cancer patients. (author)

Frontiers in nuclear medicine symposium: Nuclear medicine & molecular biology

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-04-01

This document contains the abstracts from the American College of Nuclear Physicians 1993 Fall Meeting entitled, `Frontiers in Nuclear Medicine Symposium: Nuclear Medicine and Molecular Biology`. This meeting was sponsored by the US DOE, Office of Health and Environmental Research, Office of Energy Research. The program chairman was Richard C. Reba, M.D.

Biology, Bionomics and Molecular Biology of Anopheles sinensis Wiedemann 1828 (Diptera: Culicidae), Main Malaria Vector in China.

Science.gov (United States)

Feng, Xinyu; Zhang, Shaosen; Huang, Fang; Zhang, Li; Feng, Jun; Xia, Zhigui; Zhou, Hejun; Hu, Wei; Zhou, Shuisen

2017-01-01

China has set a goal to eliminate all malaria in the country by 2020, but it is unclear if current understanding of malaria vectors and transmission is sufficient to achieve this objective. Anopheles sinensis is the most widespread malaria vector specie in China, which is also responsible for vivax malaria outbreak in central China. We reviewed literature from 1954 to 2016 on An. sinensis with emphasis on biology, bionomics, and molecular biology. A total of 538 references were relevant and included. An. sienesis occurs in 29 Chinese provinces. Temperature can affect most life-history parameters. Most An. sinensis are zoophilic, but sometimes they are facultatively anthropophilic. Sporozoite analysis demonstrated An. sinensis efficacy on Plasmodium vivax transmission. An. sinensis was not stringently refractory to P. falciparum under experimental conditions, however, sporozoite was not found in salivary glands of field collected An. sinensis . The literature on An. sienesis biology and bionomics was abundant, but molecular studies, such as gene functions and mechanisms, were limited. Only 12 molecules (genes, proteins or enzymes) have been studied. In addition, there were considerable untapped omics resources for potential vector control tools. Existing information on An. sienesis could serve as a baseline for advanced research on biology, bionomics and genetics relevant to vector control strategies.

A Comprehensive Experiment for Molecular Biology: Determination of Single Nucleotide Polymorphism in Human REV3 Gene Using PCR-RFLP

Science.gov (United States)

Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

2017-01-01

Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of…

A comprehensive experiment for molecular biology: Determination of single nucleotide polymorphism in human REV3 gene using PCR-RFLP.

Science.gov (United States)

Zhang, Xu; Shao, Meng; Gao, Lu; Zhao, Yuanyuan; Sun, Zixuan; Zhou, Liping; Yan, Yongmin; Shao, Qixiang; Xu, Wenrong; Qian, Hui

2017-07-08

Laboratory exercise is helpful for medical students to understand the basic principles of molecular biology and to learn about the practical applications of molecular biology. We have designed a lab course on molecular biology about the determination of single nucleotide polymorphism (SNP) in human REV3 gene, the product of which is a subunit of DNA polymerase ζ and SNPs in this gene are associated with altered susceptibility to cancer. This newly designed experiment is composed of three parts, including genomic DNA extraction, gene amplification by PCR, and genotyping by RFLP. By combining these activities, the students are not only able to learn a series of biotechniques in molecular biology, but also acquire the ability to link the learned knowledge with practical applications. This comprehensive experiment will help the medical students improve the conceptual understanding of SNP and the technical understanding of SNP detection. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):299-304, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

The biochemistry and molecular biology of xenobiotic polymer degradation by microorganisms.

Science.gov (United States)

Kawai, Fusako

2010-01-01

Research on microbial degradation of xenobiotic polymers has been underway for more than 40 years. It has exploited a new field not only in applied microbiology but also in environmental microbiology, and has greatly contributed to polymer science by initiating the design of biodegradable polymers. Owing to the development of analytical tools and technology, molecular biological and biochemical advances have made it possible to prospect for degrading microorganisms in the environment and to determine the mechanisms involved in biodegradation when xenobiotic polymers are introduced into the environment and are exposed to microbial attack. In this review, the molecular biological and biochemical aspects of the microbial degradation of xenobiotic polymers are summarized, and possible applications of potent microorganisms, enzymes, and genes in environmental biotechnology are suggested.

Frontiers in mathematical biology

CERN Document Server

1994-01-01

Volume 100, which is the final volume of the LNBM series serves to commemorate the acievements in two decades of this influential collection of books in mathematical biology. The contributions, by the leading mathematical biologists, survey the state of the art in the subject, and offer speculative, philosophical and critical analyses of the key issues confronting the field. The papers address fundamental issues in cell and molecular biology, organismal biology, evolutionary biology, population ecology, community and ecosystem ecology, and applied biology, plus the explicit and implicit mathematical challenges. Cross-cuttting issues involve the problem of variation among units in nonlinear systems, and the related problems of the interactions among phenomena across scales of space, time and organizational complexity.

Structural insight into RNA recognition motifs: versatile molecular Lego building blocks for biological systems.

Science.gov (United States)

Muto, Yutaka; Yokoyama, Shigeyuki

2012-01-01

'RNA recognition motifs (RRMs)' are common domain-folds composed of 80-90 amino-acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. Copyright © 2012 John Wiley & Sons, Ltd.

Barrett's esophagus: cancer and molecular biology.

Science.gov (United States)

Gibson, Michael K; Dhaliwal, Arashinder S; Clemons, Nicholas J; Phillips, Wayne A; Dvorak, Katerina; Tong, Daniel; Law, Simon; Pirchi, E Daniel; Räsänen, Jari; Krasna, Mark J; Parikh, Kaushal; Krishnadath, Kausilia K; Chen, Yu; Griffiths, Leonard; Colleypriest, Benjamin J; Farrant, J Mark; Tosh, David; Das, Kiron M; Bajpai, Manisha

2013-10-01

The following paper on the molecular biology of Barrett's esophagus (BE) includes commentaries on signaling pathways central to the development of BE including Hh, NF-κB, and IL-6/STAT3; surgical approaches for esophagectomy and classification of lesions by appropriate therapy; the debate over the merits of minimally invasive esophagectomy versus open surgery; outcomes for patients with pharyngolaryngoesophagectomy; the applications of neoadjuvant chemotherapy and chemoradiotherapy; animal models examining the surgical models of BE and esophageal adenocarcinoma; the roles of various morphogens and Cdx2 in BE; and the use of in vitro BE models for chemoprevention studies. © 2013 New York Academy of Sciences.

Genetics and molecular biology of hypotension

Science.gov (United States)

Robertson, D.

1994-01-01

Major strides in the molecular biology of essential hypertension are currently underway. This has tended to obscure the fact that a number of inherited disorders associated with low blood pressure exist and that these diseases may have milder and underrecognized phenotypes that contribute importantly to blood pressure variation in the general population. This review highlights some of the gene products that, if abnormal, could cause hypotension in some individuals. Diseases due to abnormalities in the catecholamine enzymes are discussed in detail. It is likely that genetic abnormalities with hypotensive phenotypes will be as interesting and diverse as those that give rise to hypertensive disorders.

Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

OpenAIRE

Jacobs, Nicole L.; Albertson, R. Craig; Wiles, Jason R.

2011-01-01

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the ...

Cells from icons to symbols: molecularizing cell biology in the 1980s.

Science.gov (United States)

Serpente, Norberto

2011-12-01

Over centuries cells have been the target of optical and electronic microscopes as well as others technologies, with distinctive types of visual output. Whilst optical technologies produce images 'evident to the eye', the electronic and especially the molecular create images that are more elusive to conceptualization and assessment. My study applies the semiotic approach to the production of images in cell biology to capture the shift from microscopic images to non-traditional visual technologies around 1980. Here I argue that the visual shift that coincides with the growing dominance of molecular biology involves a change from iconic to symbolic forms. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do…

The diverse and expanding role of mass spectrometry in structural and molecular biology.

Science.gov (United States)

Lössl, Philip; van de Waterbeemd, Michiel; Heck, Albert Jr

2016-12-15

The emergence of proteomics has led to major technological advances in mass spectrometry (MS). These advancements not only benefitted MS-based high-throughput proteomics but also increased the impact of mass spectrometry on the field of structural and molecular biology. Here, we review how state-of-the-art MS methods, including native MS, top-down protein sequencing, cross-linking-MS, and hydrogen-deuterium exchange-MS, nowadays enable the characterization of biomolecular structures, functions, and interactions. In particular, we focus on the role of mass spectrometry in integrated structural and molecular biology investigations of biological macromolecular complexes and cellular machineries, highlighting work on CRISPR-Cas systems and eukaryotic transcription complexes. © 2016 The Authors. Published under the terms of the CC BY NC ND 4.0 license.

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

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.

Semester-long inquiry-based molecular biology laboratory: Transcriptional regulation in yeast.

Science.gov (United States)

Oelkers, Peter M

2017-03-04

A single semester molecular biology laboratory has been developed in which students design and execute a project examining transcriptional regulation in Saccharomyces cerevisiae. Three weeks of planning are allocated to developing a hypothesis through literature searches and use of bioinformatics. Common experimental plans address a cell process and how three genes that encode for proteins involved in that process are transcriptionally regulated in response to changing environmental conditions. Planning includes designing oligonucleotides to amplify the putative promoters of the three genes of interest. After the PCR, each product is cloned proximal to β-galactosidase in a yeast reporter plasmid. Techniques used include agarose electrophoresis, extraction of DNA from agarose, plasmid purification from bacteria, restriction digestion, ligation, and bacterial transformation. This promoter/reporter plasmid is then transformed into yeast. Transformed yeast are cultured in conditions prescribed in the experimental design, lysed and β-galactosidase activity is measured. The course provides an independent research experience in a group setting. Notebooks are maintained on-line with regular feedback. Projects culminate with the presentation of a poster worth 60% of the grade. Over the last three years, about 65% of students met expectations for experimental design, data acquisition, and analysis. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(2):145-151, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Molecular biological aspects of acquired bullous diseases

DEFF Research Database (Denmark)

Dabelsteen, Erik

1998-01-01

Bullous diseases of the oral mucosa and skin were originally classified on the basis of clinical and histological criteria. The discovery of autoantibodies in some of these patients and the introduction of molecular biology have resulted in a new understanding of the pathological mechanisms of many...... of the bullous lesions. In this article, updated topics of the immune-mediated bullous lesions which involve oral mucosa and skin are reviewed. Pemphigus antigens, which are desmosomal-associated proteins and belong to the cadherin superfamily of cell adhesion proteins, have been isolated, and their genes have...

High molecular weight DNA assembly in vivo for synthetic biology applications.

Science.gov (United States)

Juhas, Mario; Ajioka, James W

2017-05-01

DNA assembly is the key technology of the emerging interdisciplinary field of synthetic biology. While the assembly of smaller DNA fragments is usually performed in vitro, high molecular weight DNA molecules are assembled in vivo via homologous recombination in the host cell. Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae are the main hosts used for DNA assembly in vivo. Progress in DNA assembly over the last few years has paved the way for the construction of whole genomes. This review provides an update on recent synthetic biology advances with particular emphasis on high molecular weight DNA assembly in vivo in E. coli, B. subtilis and S. cerevisiae. Special attention is paid to the assembly of whole genomes, such as those of the first synthetic cell, synthetic yeast and minimal genomes.

[Molecular biology, darwinism and nomogenesis].

Science.gov (United States)

Vol'kenshteĭn, M V

1987-01-01

The theory of nomogenesis put forward by L. S. Berg in 1922 is discussed. It is shown that side by side with some erroneous anti-darwinian ideas the theory contains a series of important suggestions which anticipate the further development of the synthetic theory of evolution. Berg has foreseen the development of molecular biology. Thus he was the fore-teller of our branch of science. The theory of nomogenesis emphasized the limitations of natural selection which determine the directionality of evolution. Berg treated the speciation as a kind of phase transition. Even the most conscientious critics of Berg have misrepresented the real sense of his works. It is totally groundless to treat nomogenesis as an idealistic of Lamarkian theory. Berg was superior to his critics. However the enthusiasm about nomogenesis in our time shows the inability to separate "the grains from weeds".

Modeling Dispersion of Chemical-Biological Agents in Three Dimensional Living Space

International Nuclear Information System (INIS)

William S. Winters

2002-01-01

This report documents a series of calculations designed to demonstrate Sandia's capability in modeling the dispersal of chemical and biological agents in complex three-dimensional spaces. The transport of particles representing biological agents is modeled in a single room and in several connected rooms. The influence of particle size, particle weight and injection method are studied

molecular biology approach to the search for novel hiv proteases ...

African Journals Online (AJOL)

... which could be tested in the animal models of HIV infection before subjection to clinical trials. Optimistically, the magic HIV therapeutics may be hidden in such insects and may require the application of molecular biology techniques to unravel. KEY WORDS: Antiretroviral drugs, malaria, proteases, restriction enzymes, ...

Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

International Nuclear Information System (INIS)

Watson, J.D.; Siniscalco, M.

1986-01-01

This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

Abstracts of the 27. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

International Nuclear Information System (INIS)

1998-01-01

This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology

Abstracts of the 26. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

International Nuclear Information System (INIS)

1997-01-01

This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology

Parallel computing and molecular dynamics of biological membranes

International Nuclear Information System (INIS)

La Penna, G.; Letardi, S.; Minicozzi, V.; Morante, S.; Rossi, G.C.; Salina, G.

1998-01-01

In this talk I discuss the general question of the portability of molecular dynamics codes for diffusive systems on parallel computers of the APE family. The intrinsic single precision of the today available platforms does not seem to affect the numerical accuracy of the simulations, while the absence of integer addressing from CPU to individual nodes puts strong constraints on possible programming strategies. Liquids can be satisfactorily simulated using the ''systolic'' method. For more complex systems, like the biological ones at which we are ultimately interested in, the ''domain decomposition'' approach is best suited to beat the quadratic growth of the inter-molecular computational time with the number of atoms of the system. The promising perspectives of using this strategy for extensive simulations of lipid bilayers are briefly reviewed. (orig.)

The molecular biology and diagnostics of Chlamydia trachomatis

DEFF Research Database (Denmark)

Birkelund, Svend

1992-01-01

The rapid development of biotechnological methods provides the potential of dissecting the molecular structure of microorganisms. In this review the molecular biology of chlamydia is described. The genus Chlamydia contains three species C. trachomatis, C. psittaci, and C. pneumonia which all...... are important human pathogens. Chlamydia is obligate intracellular bacteria with a unique biphasic life cycle. The extracellularly chlamydial elementary bodies (EB) are small, metabolic inactive, infectious particles with a tight outer cell membrane. After internalization into host cells the chlamydial...... of chlamydia have not yet been found. The adhesin(s) is unknown, and no factor of importance for the inhibition of fusion between phagosome and host cell lysosomes has been described. A protein similar to the mip gene product of Legionella pneumofila may be a possible candidate for a pathogenicity factor...

Combining Radiation Epidemiology With Molecular Biology-Changing From Health Risk Estimates to Therapeutic Intervention.

Science.gov (United States)

Abend, Michael; Port, Matthias

2016-08-01

The authors herein summarize six presentations dedicated to the key session "molecular radiation epidemiology" of the ConRad meeting 2015. These presentations were chosen in order to highlight the promise when combining conventional radiation epidemiology with molecular biology. Conventional radiation epidemiology uses dose estimates for risk predictions on health. However, combined with molecular biology, dose-dependent bioindicators of effect hold the promise to improve clinical diagnostics and to provide target molecules for potential therapeutic intervention. One out of the six presentations exemplified the use of radiation-induced molecular changes as biomarkers of exposure by measuring stabile chromosomal translocations. The remaining five presentations focused on molecular changes used as bioindicators of the effect. These bioindicators of the effect could be used for diagnostic purposes on colon cancers (genomic instability), thyroid cancer (CLIP2), or head and neck squamous cell cancers. Therapeutic implications of gene expression changes were examined in Chernobyl thyroid cancer victims and Mayak workers.

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

Science.gov (United States)

Kudoh, Hiroshi

2016-04-01

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

Haemoprotozoa: Making biological sense of molecular phylogenies

Directory of Open Access Journals (Sweden)

Peter O'Donoghue

2017-12-01

Full Text Available A range of protistan parasites occur in the blood of vertebrates and are transmitted by haematophagous invertebrate vectors. Some 48 genera are recognized in bood primarily on the basis of parasite morphology and host specificity; including extracellular kinetoplastids (trypanosomatids and intracellular apicomplexa (haemogregarines, haemococcidia, haemosporidia and piroplasms. Gene sequences are available for a growing number of species and molecular phylogenies often link parasite and host or vector evolution. This review endeavours to reconcile molecular clades with biological characters. Four major trypanosomatid clades have been associated with site of development in the vector: salivarian or stercorarian for Trypanosoma, and supra- or peri-pylorian for Leishmania. Four haemogregarine clades have been associated with acarine vectors (Hepatozoon A and B, Karyolysus, Hemolivia and another two with leeches (Dactylosoma, Haemogregarina sensu stricto. Two haemococcidian clades (Lankesterella, Schellackia using leeches and mosquitoes (as paratenic hosts! were paraphyletic with monoxenous enteric coccidia. Two major haemosporidian clades have been associated with mosquito vectors (Plasmodium from mammals, Plasmodium from birds and lizards, two with midges (Hepatocystis from bats, Parahaemoproteus from birds and two with louse-flies and black-flies (Haemoproteus and Leucocytozoon from birds. Three major piroplasm clades were recognized: one associated with transovarian transmission in ticks (Babesia sensu stricto; one with pre-erythrocytic schizogony in vertebrates (Theileria/Cytauxzoon; and one with neither (Babesia sensu lato. Broad comparative studies with allied groups suggest that trypanosomatids and haemogregarines evolved first in aquatic and then terrestrial environments, as evidenced by extant lineages in invertebrates and their radiation in vertebrates. In contrast, haemosporidia and haemococcidia are thought to have evolved first in

A Model of How Different Biology Experts Explain Molecular and Cellular Mechanisms

Science.gov (United States)

Trujillo, Caleb M.; Anderson, Trevor R.; Pelaez, Nancy J.

2015-01-01

Constructing explanations is an essential skill for all science learners. The goal of this project was to model the key components of expert explanation of molecular and cellular mechanisms. As such, we asked: What is an appropriate model of the components of explanation used by biology experts to explain molecular and cellular mechanisms? Do explanations made by experts from different biology subdisciplines at a university support the validity of this model? Guided by the modeling framework of R. S. Justi and J. K. Gilbert, the validity of an initial model was tested by asking seven biologists to explain a molecular mechanism of their choice. Data were collected from interviews, artifacts, and drawings, and then subjected to thematic analysis. We found that biologists explained the specific activities and organization of entities of the mechanism. In addition, they contextualized explanations according to their biological and social significance; integrated explanations with methods, instruments, and measurements; and used analogies and narrated stories. The derived methods, analogies, context, and how themes informed the development of our final MACH model of mechanistic explanations. Future research will test the potential of the MACH model as a guiding framework for instruction to enhance the quality of student explanations. PMID:25999313

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

Science.gov (United States)

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

1998-01-01

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

Conservation Biological Control of Pests in the Molecular Era: New Opportunities to Address Old Constraints

Science.gov (United States)

Gurr, Geoff M.; You, Minsheng

2016-01-01

Biological control has long been considered a potential alternative to pesticidal strategies for pest management but its impact and level of use globally remain modest and inconsistent. A rapidly expanding range of molecular – particularly DNA-related – techniques is currently revolutionizing many life sciences. This review identifies a series of constraints on the development and uptake of conservation biological control and considers the contemporary and likely future influence of molecular methods on these constraints. Molecular approaches are now often used to complement morphological taxonomic methods for the identification and study of biological control agents including microbes. A succession of molecular techniques has been applied to ‘who eats whom’ questions in food-web ecology. Polymerase chain reaction (PCR) approaches have largely superseded immunological approaches such as enzyme-linked immunosorbent assay (ELISA) and now – in turn – are being overtaken by next generation sequencing (NGS)-based approaches that offer unparalleled power at a rapidly diminishing cost. There is scope also to use molecular techniques to manipulate biological control agents, which will be accelerated with the advent of gene editing tools, the CRISPR/Cas9 system in particular. Gene editing tools also offer unparalleled power to both elucidate and manipulate plant defense mechanisms including those that involve natural enemy attraction to attacked plants. Rapid advances in technology will allow the development of still more novel pest management options for which uptake is likely to be limited chiefly by regulatory hurdles. PMID:26793225

Molecular biology of Homo sapiens: Abstracts of papers presented at the 51st Cold Spring Harbor symposium on quantitative biology

Energy Technology Data Exchange (ETDEWEB)

Watson, J.D.; Siniscalco, M.

1986-01-01

This volume contains abstracts of papers presented at the 51st Cold Springs Harbor Symposium on Quantitative Biology. The topic for this meeting was the ''Molecular Biology of Homo sapiens.'' Sessions were entitled Human Gene Map, Human Cancer Genes, Genetic Diagnosis, Human Evolution, Drugs Made Off Human Genes, Receptors, and Gene Therapy. (DT)

Biological and Medical Experiments on the Space Shuttle, 1981 - 1985

Science.gov (United States)

Halstead, Thora W. (Editor); Dufour, Patricia A. (Editor)

1986-01-01

This volume is the first in a planned series of reports intended to provide a comprehensive record of all the biological and medical experiments and samples flown on the Space Shuttle. Experiments described have been conducted over a five-year period, beginning with the first plant studies conducted on STS-2 in November 1981, and extending through STS 61-C, the last mission to fly before the tragic Challenger accident of January 1986. Experiments were sponsored within NASA not only by the Life Sciences Division of the Office of Space Science and Applications, but also by the Shuttle Student Involvement Program (SSIP) and the Get Away Special (GAS) Program. Independent medical studies were conducted as well on the Shuttle crew under the auspices of the Space Biomedical Research Institute at Johnson Space Center. In addition, cooperative agreements between NASA and foreign government agencies led to a number of independent experiments and also paved the way for the joint US/ESA Spacelab 1 mission and the German (DFVLR) Spacelab D-1. Experiments included: (1) medically oriented studies of the crew aimed at identifying, preventing, or treating health problems due to space travel; (2) projects to study morphological, physiological, or behavioral effects of microgravity on animals and plants; (3) studies of the effects of microgravity on cells and tissues; and (4) radiation experiments monitoring the spacecraft environment with chemical or biological dosimeters or testing radiation effects on simple organisms and seeds.

Mapping molecular orientational distributions for biological sample in 3D (Conference Presentation)

Science.gov (United States)

HE, Wei; Ferrand, Patrick; Richter, Benjamin; Bastmeyer, Martin; Brasselet, Sophie

2016-04-01

Measuring molecular orientation properties is very appealing for scientists in molecular and cell biology, as well as biomedical research. Orientational organization at the molecular scale is indeed an important brick to cells and tissues morphology, mechanics, functions and pathologies. Recent work has shown that polarized fluorescence imaging, based on excitation polarization tuning in the sample plane, is able to probe molecular orientational order in biological samples; however this applies only to information in 2D, projected in the sample plane. To surpass this limitation, we extended this approach to excitation polarization tuning in 3D. The principle is based on the decomposition of any arbitrary 3D linear excitation in a polarization along the longitudinal z-axis, and a polarization in the transverse xy-sample plane. We designed an interferometer with one arm generating radial polarization light (thus producing longitudinal polarization under high numerical aperture focusing), the other arm controlling a linear polarization in the transverse plane. The amplitude ratio between the two arms can vary so as to get any linear polarized excitation in 3D at the focus of a high NA objective. This technique has been characterized by polarimetry imaging at the back focal plane of the focusing objective, and modeled theoretically. 3D polarized fluorescence microscopy is demonstrated on actin stress fibers in non-flat cells suspended on synthetic polymer structures forming supporting pillars, for which heterogeneous actin orientational order could be identified. This technique shows a great potential in structural investigations in 3D biological systems, such as cell spheroids and tissues.

Doctoral conceptual thresholds in cellular and molecular biology

Science.gov (United States)

Feldon, David F.; Rates, Christopher; Sun, Chongning

2017-12-01

In the biological sciences, very little is known about the mechanisms by which doctoral students acquire the skills they need to become independent scientists. In the postsecondary biology education literature, identification of specific skills and effective methods for helping students to acquire them are limited to undergraduate education. To establish a foundation from which to investigate the developmental trajectory of biologists' research skills, it is necessary to identify those skills which are integral to doctoral study and distinct from skills acquired earlier in students' educational pathways. In this context, the current study engages the framework of threshold concepts to identify candidate skills that are both obstacles and significant opportunities for developing proficiency in conducting research. Such threshold concepts are typically characterised as transformative, integrative, irreversible, and challenging. The results from interviews and focus groups with current and former doctoral students in cellular and molecular biology suggest two such threshold concepts relevant to their subfield: the first is an ability to effectively engage primary research literature from the biological sciences in a way that is critical without dismissing the value of its contributions. The second is the ability to conceptualise appropriate control conditions necessary to design and interpret the results of experiments in an efficient and effective manner for research in the biological sciences as a discipline. Implications for prioritising and sequencing graduate training experiences are discussed on the basis of the identified thresholds.

Molecular biology in marine science: Scientific questions, technological approaches, and practical implications

Energy Technology Data Exchange (ETDEWEB)

NONE

1994-12-31

This report describes molecular techniques that could be invaluable in addressing process-oriented problems in the ocean sciences that have perplexed oceanographers for decades, such as understanding the basis for biogeochemical processes, recruitment processes, upper-ocean dynamics, biological impacts of global warming, and ecological impacts of human activities. The coupling of highly sophisticated methods, such as satellite remote sensing, which permits synoptic monitoring of chemical, physical, and biological parameters over large areas, with the power of modern molecular tools for ``ground truthing`` at small scales could allow scientists to address questions about marine organisms and the ocean in which they live that could not be answered previously. Clearly, the marine sciences are on the threshold of an exciting new frontier of scientific discovery and economic opportunity.

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.

Molecular quantum control landscapes in von Neumann time-frequency phase space

Science.gov (United States)

Ruetzel, Stefan; Stolzenberger, Christoph; Fechner, Susanne; Dimler, Frank; Brixner, Tobias; Tannor, David J.

2010-10-01

Recently we introduced the von Neumann representation as a joint time-frequency description for femtosecond laser pulses and suggested its use as a basis for pulse shaping experiments. Here we use the von Neumann basis to represent multidimensional molecular control landscapes, providing insight into the molecular dynamics. We present three kinds of time-frequency phase space scanning procedures based on the von Neumann formalism: variation of intensity, time-frequency phase space position, and/or the relative phase of single subpulses. The shaped pulses produced are characterized via Fourier-transform spectral interferometry. Quantum control is demonstrated on the laser dye IR140 elucidating a time-frequency pump-dump mechanism.

Günter Blobel: Pioneer of molecular cell biology (1936-2018).

Science.gov (United States)

2018-04-02

Günter Blobel was a scientific colossus who dedicated his career to understanding the mechanisms for protein sorting to membrane organelles. His monumental contributions established research paradigms for major arenas of molecular cell biology. For this work, he received many accolades, including the Nobel Prize in Medicine or Physiology in 1999. He was a scientist of extreme passion and a nurturing mentor for generations of researchers, imbuing them with his deep love of cell biology and galvanizing them to continue his scientific legacy. Günter passed away on February 18, 2018, at the age of 81. © 2018 Rockefeller University Press.

The All Terrain Bio nano Gear for Space Radiation Detection System

International Nuclear Information System (INIS)

Ummat, Ajay; Mavroidis, Constantinos

2007-01-01

This paper discusses about the relevance of detecting space radiations which are very harmful and pose numerous health issues for astronauts. There are many ways to detect radiations, but we present a non-invasive way of detecting them in real-time while an astronaut is in the mission. All Terrain Bio-nano (ATB) gear system is one such concept where we propose to detect various levels of space radiations depending on their intensity and warn the astronaut of probable biological damage. A basic framework for radiation detection system which utilizes bio-nano machines is discussed. This radiation detection system is termed as 'radiation-responsive molecular assembly' (RMA) for the detection of space radiations. Our objective is to create a device which could detect space radiations by creating an environment equivalent to human cells within its structure and bio-chemically sensing the effects induced therein. For creating such an environment and further bio-chemically sensing space radiations bio-nano systems could be potentially used. These bio-nano systems could interact with radiations and signal based on the intensity of the radiations their relative biological effectiveness. Based on the energy and kind of radiation encountered, a matrix of signals has to be created which corresponds to a particular biological effect. The key advantage of such a design is its ability to interact with the radiation at e molecular scale; characterize its intensity based on energy deposition and relate it to the relative biological effectiveness based on the correspondence established through molecular structures and bond strengths of the bio-nano system

Massively Parallel, Molecular Analysis Platform Developed Using a CMOS Integrated Circuit With Biological Nanopores

Science.gov (United States)

Roever, Stefan

2012-01-01

A massively parallel, low cost molecular analysis platform will dramatically change the nature of protein, molecular and genomics research, DNA sequencing, and ultimately, molecular diagnostics. An integrated circuit (IC) with 264 sensors was fabricated using standard CMOS semiconductor processing technology. Each of these sensors is individually controlled with precision analog circuitry and is capable of single molecule measurements. Under electronic and software control, the IC was used to demonstrate the feasibility of creating and detecting lipid bilayers and biological nanopores using wild type α-hemolysin. The ability to dynamically create bilayers over each of the sensors will greatly accelerate pore development and pore mutation analysis. In addition, the noise performance of the IC was measured to be 30fA(rms). With this noise performance, single base detection of DNA was demonstrated using α-hemolysin. The data shows that a single molecule, electrical detection platform using biological nanopores can be operationalized and can ultimately scale to millions of sensors. Such a massively parallel platform will revolutionize molecular analysis and will completely change the field of molecular diagnostics in the future.

Synthetic Biology as an Enabling Technology for Space Exploration

Science.gov (United States)

Rothschild, Lynn J.

2016-01-01

Human exploration off planet is severely limited by the cost of launching materials into space and by re-supply. Thus materials brought from Earth must be light, stable and reliable at destination. Using traditional approaches, a lunar or Mars base would require either transporting a hefty store of metals or heavy manufacturing equipment and construction materials for in situ extraction; both would severely limit any other mission objectives. Long-term human space presence requires periodic replenishment, adding a massive cost overhead. Even robotic missions often sacrifice science goals for heavy radiation and thermal protection. Biology has the potential to solve these problems because life can replicate and repair itself, and perform a wide variety of chemical reactions including making food, fuel and materials. Synthetic biology enhances and expands life's evolved repertoire. Using organisms as feedstock, additive manufacturing through bioprinting will make possible the dream of producing bespoke tools, food, smart fabrics and even replacement organs on demand. This new approach and the resulting novel products will enable human exploration and settlement on Mars, while providing new manufacturing approaches for life on Earth.

Introducing Molecular Biology to Environmental Engineers through Development of a New Course.

Science.gov (United States)

Oerther, Daniel B.

2002-01-01

Introduces a molecular biology course designed for environmental engineering majors using 16S ribosomal ribonucleic acid-targeted technology that allows students to identify and study microorganisms in bioreactor environments. (Contains 17 references.) (YDS)

2010 Plant Molecular Biology Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Michael Sussman

2010-07-23

The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2010 conference will continue in that tradition. Emerging concerns about food security have inspired a program with three main themes: (1) genomics, natural variation and breeding to understand adaptation and crop improvement, (2) hormonal cross talk, and (3) plant/microbe interactions. There are also sessions on epigenetics and proteomics/metabolomics. Thus this conference will bring together a range of disciplines, will foster the exchange of ideas and enable participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner. In particular, this conference plays a key role in enabling students and postdocs (the next generation of research leaders) to mingle with pioneers in multiple areas of plant science.

Abstracts of the 30. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

International Nuclear Information System (INIS)

2001-01-01

Several aspects concerning biochemistry and molecular biology of either animals, plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques

Semester-Long Inquiry-Based Molecular Biology Laboratory: Transcriptional Regulation in Yeast

Science.gov (United States)

Oelkers, Peter M.

2017-01-01

A single semester molecular biology laboratory has been developed in which students design and execute a project examining transcriptional regulation in "Saccharomyces cerevisiae." Three weeks of planning are allocated to developing a hypothesis through literature searches and use of bioinformatics. Common experimental plans address a…

Landing in the future: Biological experiments on Earth and in space orbit

Science.gov (United States)

Pokrovskiy, A.

1980-01-01

The development of an Earth biosatellite to duplicate the parameters of pressure, temperature, humidity and others in a space environment onboard Cosmos-1129 is discussed. Effects of a space environment on fruit flies, dogs, laboratory rats in procreation, behavior, stress, biorhythm, body composition, gravitation preference, and cell cultures are examined. The space environment for agricultural products is also studied. The effects of heavy nuclei of galactic space radiation on biological objects inside and outside the satellite is studied, and methods of electrostatic protection are developed.

Landing in the future: Biological experiments on Earth and in space orbit

Science.gov (United States)

Pokrovskiy, A.

1980-09-01

The development of an Earth biosatellite to duplicate the parameters of pressure, temperature, humidity and others in a space environment onboard Cosmos-1129 is discussed. Effects of a space environment on fruit flies, dogs, laboratory rats in procreation, behavior, stress, biorhythm, body composition, gravitation preference, and cell cultures are examined. The space environment for agricultural products is also studied. The effects of heavy nuclei of galactic space radiation on biological objects inside and outside the satellite is studied, and methods of electrostatic protection are developed.

Molecular structure descriptors in the computer-aided design of biologically active compounds

International Nuclear Information System (INIS)

Raevsky, Oleg A

1999-01-01

The current state of description of molecular structure in computer-aided molecular design of biologically active compounds by means of descriptors is analysed. The information contents of descriptors increases in the following sequence: element-level descriptors-structural formulae descriptors-electronic structure descriptors-molecular shape descriptors-intermolecular interaction descriptors. Each subsequent class of descriptors normally covers information contained in the previous-level ones. It is emphasised that it is practically impossible to describe all the features of a molecular structure in terms of any single class of descriptors. It is recommended to optimise the number of descriptors used by means of appropriate statistical procedures and characteristics of structure-property models based on these descriptors. The bibliography includes 371 references.

Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

Science.gov (United States)

Wagner, James M; Alper, Hal S

2016-04-01

Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

Abstracts of the 28. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

International Nuclear Information System (INIS)

1999-01-01

Biochemistry, genetic and molecular biology aspects of either animals (including man), plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioenzymatic assay, radioreceptor assay) and nuclear magnetic resonance are the most applied techniques

Biological effects of space radiation on human cells. History, advances and outcomes

International Nuclear Information System (INIS)

Maalouf, M.; Foray, N.; Durante, M.

2011-01-01

Exposure to radiation is one of the main concerns for space exploration by humans. By focusing deliberately on the works performed on human cells, we endeavored to review, decade by decade, the technological developments and conceptual advances of space radiation biology. Despite considerable efforts, the cancer and the toxicity risks remain to be quantified: the nature and the frequency of secondary heavy ions need to be better characterized in order to estimate their contribution to the dose and to the final biological response; the diversity of radiation history of each astronaut and the impact of individual susceptibility make very difficult any epidemiological analysis for estimating hazards specifically due to space radiation exposure. Cytogenetic data undoubtedly revealed that space radiation exposure produce significant damage in cells. However, our knowledge of the basic mechanisms specific to low-dose, to repeated doses and to adaptive response is still poor. The application of new radiobiological techniques, like immunofluorescence, and the use of human tissue models different from blood, like skin fibroblasts, may help in clarifying all the above items. (author)

A Self-Assisting Protein Folding Model for Teaching Structural Molecular Biology.

Science.gov (United States)

Davenport, Jodi; Pique, Michael; Getzoff, Elizabeth; Huntoon, Jon; Gardner, Adam; Olson, Arthur

2017-04-04

Structural molecular biology is now becoming part of high school science curriculum thus posing a challenge for teachers who need to convey three-dimensional (3D) structures with conventional text and pictures. In many cases even interactive computer graphics does not go far enough to address these challenges. We have developed a flexible model of the polypeptide backbone using 3D printing technology. With this model we have produced a polypeptide assembly kit to create an idealized model of the Triosephosphate isomerase mutase enzyme (TIM), which forms a structure known as TIM barrel. This kit has been used in a laboratory practical where students perform a step-by-step investigation into the nature of protein folding, starting with the handedness of amino acids to the formation of secondary and tertiary structure. Based on the classroom evidence we collected, we conclude that these models are valuable and inexpensive resource for teaching structural molecular biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Role of Molecular Biology in the Biomonitoring of Human Exposure to Chemicals

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Balam Muñoz

2010-11-01

Full Text Available Exposure to different substances in an occupational environment is of utmost concern to global agencies such as the World Health Organization and the International Labour Organization. Interest in improving work health conditions, particularly of those employees exposed to noxious chemicals, has increased considerably and has stimulated the search for new, more specific and selective tests. Recently, the field of molecular biology has been indicated as an alternative technique for monitoring personnel while evaluating work-related pathologies. Originally, occupational exposure to environmental toxicants was assessed using biochemical techniques to determine the presence of higher concentrations of toxic compounds in blood, urine, or other fluids or tissues; results were used to evaluate potential health risk. However, this approach only estimates the presence of a noxious chemical and its effects, but does not prevent or diminish the risk. Molecular biology methods have become very useful in occupational medicine to provide more accurate and opportune diagnostics. In this review, we discuss the role of the following common techniques: (1 Use of cell cultures; (2 evaluation of gene expression; (3 the “omic” sciences (genomics, transcriptomics, proteomics and metabolomics and (4 bioinformatics. We suggest that molecular biology has many applications in occupational health where the data can be applied to general environmental conditions.

Building bridges between cellular and molecular structural biology.

Science.gov (United States)

Patwardhan, Ardan; Brandt, Robert; Butcher, Sarah J; Collinson, Lucy; Gault, David; Grünewald, Kay; Hecksel, Corey; Huiskonen, Juha T; Iudin, Andrii; Jones, Martin L; Korir, Paul K; Koster, Abraham J; Lagerstedt, Ingvar; Lawson, Catherine L; Mastronarde, David; McCormick, Matthew; Parkinson, Helen; Rosenthal, Peter B; Saalfeld, Stephan; Saibil, Helen R; Sarntivijai, Sirarat; Solanes Valero, Irene; Subramaniam, Sriram; Swedlow, Jason R; Tudose, Ilinca; Winn, Martyn; Kleywegt, Gerard J

2017-07-06

The integration of cellular and molecular structural data is key to understanding the function of macromolecular assemblies and complexes in their in vivo context. Here we report on the outcomes of a workshop that discussed how to integrate structural data from a range of public archives. The workshop identified two main priorities: the development of tools and file formats to support segmentation (that is, the decomposition of a three-dimensional volume into regions that can be associated with defined objects), and the development of tools to support the annotation of biological structures.

Molecular biological features of male germ cell differentiation

Science.gov (United States)

HIROSE, MIKA; TOKUHIRO, KEIZO; TAINAKA, HITOSHI; MIYAGAWA, YASUSHI; TSUJIMURA, AKIRA; OKUYAMA, AKIHIKO; NISHIMUNE, YOSHITAKE

2007-01-01

Somatic cell differentiation is required throughout the life of a multicellular organism to maintain homeostasis. In contrast, germ cells have only one specific function; to preserve the species by conveying the parental genes to the next generation. Recent studies of the development and molecular biology of the male germ cell have identified many genes, or isoforms, that are specifically expressed in the male germ cell. In the present review, we consider the unique features of male germ cell differentiation. (Reprod Med Biol 2007; 6: 1–9) PMID:29699260

Abstracts of the 29. annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

International Nuclear Information System (INIS)

2000-01-01

Several aspects concerning biochemistry and molecular biology of either animals (including man), plants and microorganisms are studied. Topics such as cell membrane structures (including receptors), enzymatic assays, biological pathways, structural chemical analysis, metabolism, biological functions are focused. The use of radiolabelled compounds (radioassay, radioenzymatic assay, radioreceptor assay and nuclear magnetic resonance are the most applied techniques

Correlativity study on MRI morphologic features, pathology, and molecular biology of breast cancer

International Nuclear Information System (INIS)

Chen Rong; Gong Shuigen; Zhang Weiguo; Chen Jinhua; He Shuangwu; Liu Baohua; Li Zengpeng

2004-01-01

Objective: To investigate the correlation among MRI morphologic features, pathology, and molecular biology of breast cancer. Methods: MR scanning was performed in 78 patients with breast cancer before operation and MRI morphologic features of breast cancer were analyzed. The mastectomy specimens of the breast neoplasm were stained with immunohistochemistry, and the expression of estrogen receptor (ER), progesterone receptor (PR), C-erbB-2, p53, and the distribution of microvessel density (MVD) was measured. The pathologic results were compared with MRI features. Results: Among the 80 breast cancers, ER positive expression was positively correlated with the spiculate margin of breast cancer (P 0.05). Among the 41 breast cancers with dynamic MR scans, there was positive correlation between the spatial distribution of contrast agent and MVD (P<0.01). Conclusion: There exists some correlation among MRI morphologic features, pathology, and molecular biology factors in breast cancer to certain extent. The biologic behavior and prognosis of the breast cancer can be assessed according to MRI features

The Physics of Proteins An Introduction to Biological Physics and Molecular Biophysics

CERN Document Server

Frauenfelder, Hans; Chan, Winnie S

2010-01-01

Physics and the life sciences have established new connections within the past few decades, resulting in biological physics as an established subfield with strong groups working in many physics departments. These interactions between physics and biology form a two-way street with physics providing new tools and concepts for understanding life, while biological systems can yield new insights into the physics of complex systems. To address the challenges of this interdisciplinary area, The Physics of Proteins: An Introduction to Biological Physics and Molecular Biophysics is divided into three interconnected sections. In Parts I and II, early chapters introduce the terminology and describe the main biological systems that physicists will encounter. Similarities between biomolecules, glasses, and solids are stressed with an emphasis on the fundamental concepts of living systems. The central section (Parts III and IV) delves into the dynamics of complex systems. A main theme is the realization that biological sys...

Adrenocortical carcinoma: the dawn of a new era of genomic and molecular biology analysis.

Science.gov (United States)

Armignacco, R; Cantini, G; Canu, L; Poli, G; Ercolino, T; Mannelli, M; Luconi, M

2018-05-01

Over the last decade, the development of novel and high penetrance genomic approaches to analyze biological samples has provided very new insights in the comprehension of the molecular biology and genetics of tumors. The use of these techniques, consisting of exome sequencing, transcriptome, miRNome, chromosome alteration, genome, and epigenome analysis, has also been successfully applied to adrenocortical carcinoma (ACC). In fact, the analysis of large cohorts of patients allowed the stratification of ACC with different patterns of molecular alterations, associated with different outcomes, thus providing a novel molecular classification of the malignancy to be associated with the classical pathological analysis. Improving our knowledge about ACC molecular features will result not only in a better diagnostic and prognostic accuracy, but also in the identification of more specific therapeutic targets for the development of more effective pharmacological anti-cancer approaches. In particular, the specific molecular alteration profiles identified in ACC may represent targetable events by the use of already developed or newly designed drugs enabling a better and more efficacious management of the ACC patient in the context of new frontiers of personalized precision medicine.

New approaches in mathematical biology: Information theory and molecular machines

International Nuclear Information System (INIS)

Schneider, T.

1995-01-01

My research uses classical information theory to study genetic systems. Information theory was founded by Claude Shannon in the 1940's and has had an enormous impact on communications engineering and computer sciences. Shannon found a way to measure information. This measure can be used to precisely characterize the sequence conservation at nucleic-acid binding sites. The resulting methods, by completely replacing the use of ''consensus sequences'', provide better models for molecular biologists. An excess of conservation led us to do experimental work on bacteriophage T7 promoters and the F plasmid IncD repeats. The wonderful fidelity of telephone communications and compact disk (CD) music can be traced directly to Shannon's channel capacity theorem. When rederived for molecular biology, this theorem explains the surprising precision of many molecular events. Through connections with the Second Law of Thermodyanmics and Maxwell's Demon, this approach also has implications for the development of technology at the molecular level. Discussions of these topics are held on the internet news group bionet.info-theo. (author). (Abstract only)

bcl::Cluster : A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System.

Science.gov (United States)

Alexander, Nathan; Woetzel, Nils; Meiler, Jens

2011-02-01

Clustering algorithms are used as data analysis tools in a wide variety of applications in Biology. Clustering has become especially important in protein structure prediction and virtual high throughput screening methods. In protein structure prediction, clustering is used to structure the conformational space of thousands of protein models. In virtual high throughput screening, databases with millions of drug-like molecules are organized by structural similarity, e.g. common scaffolds. The tree-like dendrogram structure obtained from hierarchical clustering can provide a qualitative overview of the results, which is important for focusing detailed analysis. However, in practice it is difficult to relate specific components of the dendrogram directly back to the objects of which it is comprised and to display all desired information within the two dimensions of the dendrogram. The current work presents a hierarchical agglomerative clustering method termed bcl::Cluster. bcl::Cluster utilizes the Pymol Molecular Graphics System to graphically depict dendrograms in three dimensions. This allows simultaneous display of relevant biological molecules as well as additional information about the clusters and the members comprising them.

Three-dimensional labeling program for elucidation of the geometric properties of biological particles in three-dimensional space.

Science.gov (United States)

Nomura, A; Yamazaki, Y; Tsuji, T; Kawasaki, Y; Tanaka, S

1996-09-15

For all biological particles such as cells or cellular organelles, there are three-dimensional coordinates representing the centroid or center of gravity. These coordinates and other numerical parameters such as volume, fluorescence intensity, surface area, and shape are referred to in this paper as geometric properties, which may provide critical information for the clarification of in situ mechanisms of molecular and cellular functions in living organisms. We have established a method for the elucidation of these properties, designated the three-dimensional labeling program (3DLP). Algorithms of 3DLP are so simple that this method can be carried out through the use of software combinations in image analysis on a personal computer. To evaluate 3DLP, it was applied to a 32-cell-stage sea urchin embryo, double stained with FITC for cellular protein of blastomeres and propidium iodide for nuclear DNA. A stack of optical serial section images was obtained by confocal laser scanning microscopy. The method was found effective for determining geometric properties and should prove applicable to the study of many different kinds of biological particles in three-dimensional space.

Recent advances in biological effect and molecular mechanism of arabidopsis thaliana irradiated by ion beams

International Nuclear Information System (INIS)

Wu Dali; Hou Suiwen; Li Wenjian

2008-01-01

Newly research progresses were summarized in effect of ion beams on seed surface, biological effect, growth, development, gravitropism and so on. Furthermore, mutation molecular mechanism of Arabidopsis thaliana was discussed, for example, alteration of DNA bases, DNA damage, chromosomal recombination, characteristics of mutant transmissibility, etc. Meanwhile, the achievements of transfer- ring extraneous gene to Arabidopsis thaliana by ion beams were reviewed in the paper. At last, the future prospective are also discussed here in mutation molecular mechanism and the potential application of biological effect of heavy ion beams. (authors)

Research Applications of Proteolytic Enzymes in Molecular Biology

Directory of Open Access Journals (Sweden)

József Tőzsér

2013-11-01

Full Text Available Proteolytic enzymes (also termed peptidases, proteases and proteinases are capable of hydrolyzing peptide bonds in proteins. They can be found in all living organisms, from viruses to animals and humans. Proteolytic enzymes have great medical and pharmaceutical importance due to their key role in biological processes and in the life-cycle of many pathogens. Proteases are extensively applied enzymes in several sectors of industry and biotechnology, furthermore, numerous research applications require their use, including production of Klenow fragments, peptide synthesis, digestion of unwanted proteins during nucleic acid purification, cell culturing and tissue dissociation, preparation of recombinant antibody fragments for research, diagnostics and therapy, exploration of the structure-function relationships by structural studies, removal of affinity tags from fusion proteins in recombinant protein techniques, peptide sequencing and proteolytic digestion of proteins in proteomics. The aim of this paper is to review the molecular biological aspects of proteolytic enzymes and summarize their applications in the life sciences.

Features of Knowledge Building in Biology: Understanding Undergraduate Students' Ideas about Molecular Mechanisms.

Science.gov (United States)

Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S

2016-01-01

Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. © 2016 K. Southard et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Molecular gyroscopes and biological effects of weak extremely low-frequency magnetic fields

International Nuclear Information System (INIS)

Binhi, V.N.; Savin, A.V.

2002-01-01

Extremely low-frequency magnetic fields are known to affect biological systems. In many cases, biological effects display 'windows' in biologically effective parameters of the magnetic fields: most dramatic is the fact that the relatively intense magnetic fields sometimes do not cause appreciable effect, while smaller fields of the order of 10-100 μT do. Linear resonant physical processes do not explain the frequency windows in this case. Amplitude window phenomena suggest a nonlinear physical mechanism. Such a nonlinear mechanism has been proposed recently to explain those 'windows'. It considers the quantum-interference effects on the protein-bound substrate ions. Magnetic fields cause an interference of ion quantum states and change the probability of ion-protein dissociation. This ion-interference mechanism predicts specific magnetic-field frequency and amplitude windows within which the biological effects occur. It agrees with a lot of experiments. However, according to the mechanism, the lifetime Γ -1 of ion quantum states within a protein cavity should be of unrealistic value, more than 0.01 s for frequency band 10-100 Hz. In this paper, a biophysical mechanism has been proposed, which (i) retains the attractive features of the ion interference mechanism, i.e., predicts physical characteristics that might be experimentally examined and (ii) uses the principles of gyroscopic motion and removes the necessity to postulate large lifetimes. The mechanism considers the dynamics of the density matrix of the molecular groups, which are attached to the walls of protein cavities by two covalent bonds, i.e., molecular gyroscopes. Numerical computations have shown almost free rotations of the molecular gyroscopes. The relaxation time due to van der Waals forces was about 0.01 s for the cavity size of 28 Aa

Hamiltonian flow over saddles for exploring molecular phase space structures

Science.gov (United States)

Farantos, Stavros C.

2018-03-01

Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

Stochastic narrow escape in molecular and cellular biology analysis and applications

CERN Document Server

Holcman, David

2015-01-01

This book covers recent developments in the non-standard asymptotics of the mathematical narrow escape problem in stochastic theory, as well as applications of the narrow escape problem in cell biology. The first part of the book concentrates on mathematical methods, including advanced asymptotic methods in partial equations, and is aimed primarily at applied mathematicians and theoretical physicists who are interested in biological applications. The second part of the book is intended for computational biologists, theoretical chemists, biochemists, biophysicists, and physiologists. It includes a summary of output formulas from the mathematical portion of the book and concentrates on their applications in modeling specific problems in theoretical molecular and cellular biology. Critical biological processes, such as synaptic plasticity and transmission, activation of genes by transcription factors, or double-strained DNA break repair, are controlled by diffusion in structures that have both large and small sp...

On the shoulders of giants: Molecular Biology in Public Health

Directory of Open Access Journals (Sweden)

Carmine Melino

2005-03-01

Full Text Available

We accepted with great pleasure the invitation by professor Walter Ricciardi,our friend and colleague, to write an editorial in order to introduce this special issue dedicated to Molecular Biology in Hygiene. We are delighted for two connected reasons.

First, Carmine,as a former professor of Hygiene,has passed his concepts of Hygiene on to his family and, despite significant difficulties, keeps working on the problems of preventive medicine in the work environment and in geriatrics. Second, Gerry, raised in an environment of hygienists, has dedicated all his professional efforts to Molecular Biology. As these two distinct experiences have constantly mixed within our family over time, we appreciate the promiscuous intermingling of these two disciplines in this thematic issue.

The result is a useful common effort aiming at understanding the problems of diseases in the work environment and in the human environment in general.

These problems have a profound social meaning, for which it is necessary to create an essential collaboration with scientific research.

This is the only way to benefit human society.

Design of a Comprehensive Biochemistry and Molecular Biology Experiment: Phase Variation Caused by Recombinational Regulation of Bacterial Gene Expression

Science.gov (United States)

Sheng, Xiumei; Xu, Shungao; Lu, Renyun; Isaac, Dadzie; Zhang, Xueyi; Zhang, Haifang; Wang, Huifang; Qiao, Zheng; Huang, Xinxiang

2014-01-01

Scientific experiments are indispensable parts of Biochemistry and Molecular Biology. In this study, a comprehensive Biochemistry and Molecular Biology experiment about "Salmonella enterica" serovar Typhi Flagellar phase variation has been designed. It consisted of three parts, namely, inducement of bacterial Flagellar phase variation,…

Origins Space Telescope: Tracing Dark Molecular Gas in the Milky Way

Science.gov (United States)

Narayanan, Desika; Li, Qi; Krumholz, Mark; Dave, Romeel; Origins Space Telescope Science and Technology Definition Team

2018-01-01

We present theoretical models for quantifying the fraction of CO-dark molecular gas in galaxies. To do this, we combine novel thermal, chemical, and radiative equilibrium calculations with high-resolution cosmological zoom galaxy formation models. We discuss how this dark molecular gas will be uncovered by the Origins Space Telescope, one of the four science and technology definition studies of NASA Headquarters for the 2020 Astronomy and Astrophysics Decadal survey.

OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.

Science.gov (United States)

Zhou, Guangyan; Xia, Jianguo

2018-06-07

Biological networks play increasingly important roles in omics data integration and systems biology. Over the past decade, many excellent tools have been developed to support creation, analysis and visualization of biological networks. However, important limitations remain: most tools are standalone programs, the majority of them focus on protein-protein interaction (PPI) or metabolic networks, and visualizations often suffer from 'hairball' effects when networks become large. To help address these limitations, we developed OmicsNet - a novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space. Users can upload one or multiple lists of molecules of interest (genes/proteins, microRNAs, transcription factors or metabolites) to create and merge different types of biological networks. The 3D network visualization system was implemented using the powerful Web Graphics Library (WebGL) technology that works natively in most major browsers. OmicsNet supports force-directed layout, multi-layered perspective layout, as well as spherical layout to help visualize and navigate complex networks. A rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis. OmicsNet is freely available at http://www.omicsnet.ca.

Molecular biological factors in the diagnosis of cervical intraepithelial neoplasias

Directory of Open Access Journals (Sweden)

Yu. N. Ponomareva

2010-01-01

Full Text Available The authors have made a complex analysis of the molecular biological factors associated with cervical intraepithelial neoplasia. They have revealed that infection by oncogenic human papillomavirus types is associated with suppressed apoptosis and enhanced cellular proliferative activity, which can be effectively used in the diagnosis and prediction of cervical neoplasias to optimize management tac- tics and to improve the results of treatment.

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

International Nuclear Information System (INIS)

McMahon, S.

2016-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

2016-06-15

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

Using Active Learning in a Studio Classroom to Teach Molecular Biology

Science.gov (United States)

Nogaj, Luiza A.

2013-01-01

This article describes the conversion of a lecture-based molecular biology course into an active learning environment in a studio classroom. Specific assignments and activities are provided as examples. The goal of these activities is to involve students in collaborative learning, teach them how to participate in the learning process, and give…

The isolated Leptospira Spp. Identification by molecular biological techniques

Directory of Open Access Journals (Sweden)

Duangjai Suwancharoen

2017-01-01

Full Text Available Leptospirosis is a zoonotic disease caused by the bacteria of Leptospira spp. Identification of this bacterium relies on serotyping and genotyping. Data base for animal causative serovars in Thailand is limited. As the unknown serovars are found in the laboratory, they need to be sent overseas for referent identification. To reduce the cost, this research intended to develop a leptospiral identification method which is user–friendly and able to classify efficiently. Ten Leptospira isolations were cultured from urine samples. They were identified by three molecular biological techniques, including Pulsed-Field Gel Electrophoresis (PFGE, Variable Number Tandem Repeat (VNTR and Multilocus Sequence Typing (MLST. These methods were developed and compared to find the most suitable one for leptospiral identification. VNTR was found to be inappropriate since it could not identify the agents and it did not show the PCR product. PFGE and MLST gave the same results of the unknown 1 and 2 which were L.weilii sv Samin st Samin. Unknown 4 showed different results by each technique. Unknown 5 to 10 were likely to be L.meyeri sv Ranarum st ICF and Leptonema illini sv Illini st 3055 by PFGE but MLST could not identify the serovar. However, molecular biological technique for Leptospira identification should be done by several methods in order to confirm the result of each other.

Simulations on the Teaching of Molecular Biology: Experience’s Report

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A.L.S. Silva

2013-05-01

Full Text Available INTRODUCTION: The comprehension of techniques used in Molecular Biology neither always is easy.Therefore, the objective of this work was to apply simulations in Molecular Biology for graduating students of a Pharmacy course froma private educational institution, to allow them to practice the apparent difficult protocols. MATERIALS AND METHODS: Three groups of students (50 each were evaluated. Two of them were submitted to different simulatory activities,such as: a visiting the virtual laboratory of Utah University (USA to understand gel electrophoresis and polymerasechain reaction (PCR techniques, b extracting DNA from oral mucosa by means of a homemade protocol, c investigating simulatory paternity tests, d proposing their own microarrays by painting them on paper and then interpreted the results according to the colors, e designing primers (small fragments of DNA to PCR with the free software Primer3 and testing them in silico PCR. The third group of students was only submitted to oral theoretical classes about all these themes. The progress of the understanding was qualitatively evaluated and compared by the analysis of questionnaires. RESULTS AND DISCUSSION: The groups submitted to the virtual classes were responsive during the development of activities and had a better performance in the examinations than the group that had only theoretical classes, showing better comprehension about the themes. Their greatest difficult was the limitation in the English language to interact with the websites (they often asked about an alternative site in Portuguese. CONCLUSION: The didactical sequence involving exercises in websites by using freeware and recreational activities in classroom with graduating students of Pharmacy proved to be an effective tool in the learning of some of the techniques in Molecular Biology, mainly when a lab and some equipment are not available to perform practical activities

MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

Directory of Open Access Journals (Sweden)

Xia Xuhua

2005-03-01

Full Text Available Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

A guide on instrument of biochemistry and molecular biology

International Nuclear Information System (INIS)

1995-10-01

This book is about instrument on biochemistry and molecular biology, which consists of six chapters. It deals with introduction of advanced bio-instrument, common utilization and maintain, explanation of each instrument like capillary electrophoresis, interactive laser cytometer, personal computer and software, an electron microscope and DNA/RNS synthesis instrument, large equipment and special system like information system and network, analysis system for genome and large spectro graph, outside donation, examples for common utilization and appendix on data like application form for use.

Special conference of the American Association for Cancer Research on molecular imaging in cancer: linking biology, function, and clinical applications in vivo.

Science.gov (United States)

Luker, Gary D

2002-04-01

The AACR Special Conference on Molecular Imaging in Cancer: Linking Biology, Function, and Clinical Applications In Vivo, was held January 23-27, 2002, at the Contemporary Hotel, Walt Disney World, Orlando, FL. Co-Chairs David Piwnica-Worms, Patricia Price and Thomas Meade brought together researchers with diverse expertise in molecular biology, gene therapy, chemistry, engineering, pharmacology, and imaging to accelerate progress in developing and applying technologies for imaging specific cellular and molecular signals in living animals and humans. The format of the conference was the presentation of research that focused on basic and translational biology of cancer and current state-of-the-art techniques for molecular imaging in animal models and humans. This report summarizes the special conference on molecular imaging, highlighting the interfaces of molecular biology with animal models, instrumentation, chemistry, and pharmacology that are essential to convert the dreams and promise of molecular imaging into improved understanding, diagnosis, and management of cancer.

DAE-BRNS life sciences symposium on molecular biology of stress response and its applications

International Nuclear Information System (INIS)

2005-01-01

The world of living organisms is full of challenges from their surroundings and these organisms learn to adapt themselves to the changes - some transient and some permanent - in these surroundings. The demands on adaptability to stress are very strong for extremophiles that live in harsh conditions such as cold or hot temperatures, salinity and hyperbaric habitats. The stress could be biotic (e.g. infection or parasitism) or abiotic (e.g. temperature, light, salinity, heavy metals etc.) Evolutionarily living organisms have developed different shapes, coloration, habits etc. to survive in their habitats. The molecular mechanisms of these biological adaptations have become clearer only in recent years from the studies on the biological responses of an organism to stresses during its life time. Such responses are characterized by activation of certain genes and synthesis of proteins and metabolites, which facilitate amelioration of the stress. The molecular biology (biochemistry and genetics) of stress response is being constantly unravelled thanks to the availability of highly sensitive and high throughput techniques and a plethora of extremophilic experimental systems such as archaebacteria, radio resistant bacteria and midges, plants surviving in cold etc. An interesting outcome of this voluminous research has been the knowledge that responses to a group of stresses share common mechanisms, at least in part. This reflects the biologically conservationist trend among otherwise diverse organisms and stresses. In this symposium several papers and posters in the area of molecular biology of stress are presented in addition to some very interesting and promising-to-be informative and stimulating plenary lectures and invited talks from highly reputed scientists. The papers relevant to INIS are indexed separately

Using whole mount in situ hybridization to link molecular and organismal biology.

Science.gov (United States)

Jacobs, Nicole L; Albertson, R Craig; Wiles, Jason R

2011-03-31

Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the embryology and gross anatomy of several organisms representing various chordate taxa primarily via traditional dissections and the use of models. The final portion of the course involved an innovative approach to teaching anatomy through observation of vertebrate development employing molecular techniques in which WISH was performed on zebrafish embryos. A heterozygous fibroblast growth factor 8 a (fgf8a) mutant line, ace, was used. Due to Mendelian inheritance, ace intercrosses produced wild type, heterozygous, and homozygous ace/fgf8a mutants in a 1:2:1 ratio. RNA probes with known expression patterns in the midline and in developing anatomical structures such as the heart, somites, tailbud, myotome, and brain were used. WISH was performed using zebrafish at the 13 somite and prim-6 stages, with students performing the staining reaction in class. The study of zebrafish embryos at different stages of development gave students the ability to observe how these anatomical structures changed over ontogeny. In addition, some ace/fgf8a mutants displayed improper heart looping, and defects in somite and brain development. The students in this lab observed the normal development of various organ systems using both external anatomy as well as gene expression patterns. They also identified and described embryos displaying improper anatomical development and gene expression (i.e., putative mutants). For instructors at institutions that do not already own the necessary equipment or where

Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

Science.gov (United States)

Black, Michael W.; Tuan, Alice; Jonasson, Erin

2008-01-01

The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

Using Biocatalysis to Integrate Organic Chemistry into a Molecular Biology Laboratory Course

Science.gov (United States)

Beers, Mande; Archer, Crystal; Feske, Brent D.; Mateer, Scott C.

2012-01-01

Current cutting-edge biomedical investigation requires that the researcher have an operational understanding of several diverse disciplines. Biocatalysis is a field of science that operates at the crossroads of organic chemistry, biochemistry, microbiology, and molecular biology, and provides an excellent model for interdisciplinary research. We…

Forty Years of Ebolavirus Molecular Biology: Understanding a Novel Disease Agent Through the Development and Application of New Technologies.

Science.gov (United States)

Groseth, Allison; Hoenen, Thomas

2017-01-01

Molecular biology is a broad discipline that seeks to understand biological phenomena at a molecular level, and achieves this through the study of DNA, RNA, proteins, and/or other macromolecules (e.g., those involved in the modification of these substrates). Consequently, it relies on the availability of a wide variety of methods that deal with the collection, preservation, inactivation, separation, manipulation, imaging, and analysis of these molecules. As such the state of the art in the field of ebolavirus molecular biology research (and that of all other viruses) is largely intertwined with, if not driven by, advancements in the technical methodologies available for these kinds of studies. Here we review of the current state of our knowledge regarding ebolavirus biology and emphasize the associated methods that made these discoveries possible.

Technical and operational assessment of molecular nanotechnology for space operations

Science.gov (United States)

McKendree, Thomas Lawrence

2001-07-01

This study assesses the performance of conventional technology and three levels of molecular nanotechnology (MNT) for space operations. The measures of effectiveness are technical performance parameters for five space transportation architectures, and the total logistics cost for an evaluation scenario with mining, market and factory locations on the Moon, Mars and asteroids. On these measures of effectiveness, improvements of 2--4 orders of magnitude are seen in chemical rockets, solar electric ion engines, solar sail accelerations (but not transit times), and in structural masses for planetary skyhooks and towers. Improvements in tether performance and logistics costs are nearer to 1 order of magnitude. Appendices suggest additional improvements may be possible in space mining, closed-environment life support, flexible operations, and with other space transportation architectures. In order to assess logistics cost, this research extends the facility location problem of location theory to orbital space. This extension supports optimal siting of a single facility serving circular, coplanar orbits, locations in elliptic planetary and moon orbits, and heuristic siting of multiple facilities. It focuses on conventional rocket transportation, and on high performance rockets supplying at least 1 m/s2 acceleration and 500,000 m/s exhaust velocity. Mathematica implementations are provided in appendices. Simple MNT allows diamond and buckytube construction. The main benefits are in chemical rocket performance, solar panel specific power, solar electric ion engine performance, and skyhook and tower structural masses. Complex MNT allows very small machinery, permitting large increases in solar panel specific power, which enables solar electric ion engines that are high performance rockets, and thus reduces total logistics costs an order of magnitude. Most Advance MNT allows molecular manufacturing, which enables self-repair, provides at least marginal improvements in nearly

Biosensors for Real-Time Monitoring of Radiation-Induced Biologic Effects in Space

Science.gov (United States)

Baker, James R.; Balogh, Lajos; Majoros, Istvan; Keszler, Balazs; Myc, Andrzej; Kukowska-Latallo, Jolanta; Norris, Theodore; delaiglesia, Felix; Beeson, Nicholas W. (Compiler)

2002-01-01

This work seeks to develop cellular biosensors based on dendritic polymers. Nanoscale polymer structures less than 20 nm in diameter will be used as the basis of the biosensors. The structures will be designed to target into specific cells of an astronaut and be able to monitor health issues such as exposure to radiation. Multiple components can be assembled on the polymers including target directors, analytical devices (such as molecular probes), and reporting agents. The reporting will be accomplished through fluorescence signal monitoring, with the use of multispectral analysis for signal interpretation. These nanosensors could facilitate the success and increase the safety of extended space flight. The design and assembly of these devices has been pioneered at the Center for Biologic Nanotechnology in the University of Michigan. This period, synthesis of the test-bed biosensors continued. Studies were performed on the candidate fluorescent dyes to determine which might be suitable for the biosensor under development. Development continued on producing an artificial capillary bed as a tool for the use in the production of the fluorescence signal monitor. Work was also done on the in vitro multispectral analysis system, which uses the robotic microscope.

Centre for Cellular and Molecular Biology to breed vultures for Parsis

African Journals Online (AJOL)

Hyderabad – Parsis worried about the growing pile of bodies in their 'Towers of Silence' can take heart. The Centre for Cellular and Molecular Biology. (CCMB) has decided to take up, on an express basis, the job of breeding vultures, which can later be transported to various parts of the country. Though the problem of ...

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.

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.

Space Biology and Medicine. Volume 4; Health, Performance, and Safety of Space Crews

Science.gov (United States)

Dietlein, Lawrence F. (Editor); Pestov, Igor D. (Editor)

2004-01-01

Volume IV is devoted to examining the medical and associated organizational measures used to maintain the health of space crews and to support their performance before, during, and after space flight. These measures, collectively known as the medical flight support system, are important contributors to the safety and success of space flight. The contributions of space hardware and the spacecraft environment to flight safety and mission success are covered in previous volumes of the Space Biology and Medicine series. In Volume IV, we address means of improving the reliability of people who are required to function in the unfamiliar environment of space flight as well as the importance of those who support the crew. Please note that the extensive collaboration between Russian and American teams for this volume of work resulted in a timeframe of publication longer than originally anticipated. Therefore, new research or insights may have emerged since the authors composed their chapters and references. This volume includes a list of authors' names and addresses should readers seek specifics on new information. At least three groups of factors act to perturb human physiological homeostasis during space flight. All have significant influence on health, psychological, and emotional status, tolerance, and work capacity. The first and most important of these factors is weightlessness, the most specific and radical change in the ambient environment; it causes a variety of functional and structural changes in human physiology. The second group of factors precludes the constraints associated with living in the sealed, confined environment of spacecraft. Although these factors are not unique to space flight, the limitations they entail in terms of an uncomfortable environment can diminish the well-being and performance of crewmembers in space. The third group of factors includes the occupational and social factors associated with the difficult, critical nature of the

Primary Molecular Disorders and Secondary Biological Adaptations in Bartter Syndrome

Science.gov (United States)

Deschênes, Georges; Fila, Marc

2011-01-01

Bartter syndrome is a hereditary disorder that has been characterized by the association of hypokalemia, alkalosis, and the hypertrophy of the juxtaglomerular complex with secondary hyperaldosteronism and normal blood pressure. By contrast, the genetic causes of Bartter syndrome primarily affect molecular structures directly involved in the sodium reabsorption at the level of the Henle loop. The ensuing urinary sodium wasting and chronic sodium depletion are responsible for the contraction of the extracellular volume, the activation of the renin-aldosterone axis, the secretion of prostaglandins, and the biological adaptations of downstream tubular segments, meaning the distal convoluted tubule and the collecting duct. These secondary biological adaptations lead to hypokalemia and alkalosis, illustrating a close integration of the solutes regulation in the tubular structures. PMID:21941653

Primary Molecular Disorders and Secondary Biological Adaptations in Bartter Syndrome

Directory of Open Access Journals (Sweden)

Georges Deschênes

2011-01-01

Full Text Available Bartter syndrome is a hereditary disorder that has been characterized by the association of hypokalemia, alkalosis, and the hypertrophy of the juxtaglomerular complex with secondary hyperaldosteronism and normal blood pressure. By contrast, the genetic causes of Bartter syndrome primarily affect molecular structures directly involved in the sodium reabsorption at the level of the Henle loop. The ensuing urinary sodium wasting and chronic sodium depletion are responsible for the contraction of the extracellular volume, the activation of the renin-aldosterone axis, the secretion of prostaglandins, and the biological adaptations of downstream tubular segments, meaning the distal convoluted tubule and the collecting duct. These secondary biological adaptations lead to hypokalemia and alkalosis, illustrating a close integration of the solutes regulation in the tubular structures.

Molecular Biology and Infection of Hepatitis E Virus

Directory of Open Access Journals (Sweden)

Yuchen Nan

2016-09-01

Full Text Available Hepatitis E virus (HEV is a viral pathogen transmitted primarily via fecal-oral route. In humans, HEV mainly causes acute hepatitis and is responsible for large outbreaks of hepatitis across the world. The case fatality rate of HEV-induced hepatitis ranges from 0.5 to 3% in young adults and up to 30% in infected pregnant women. HEV strains infecting humans are classified into four genotypes. HEV strains from genotype 3 and 4 are zoonotic, whereas those from genotype 1 and 2 have no known animal reservoirs. Recently, notable progress has been accomplished for better understanding of HEV biology and infection, such as chronic HEV infection, in vitro cell culture system, quasi-enveloped HEV virions, functions of the HEV proteins, mechanism of HEV antagonizing host innate immunity, HEV pathogenesis and vaccine development. However, further investigation on the cross-species HEV infection, host tropism, vaccine efficacy and HEV-specific antiviral strategy is still needed. This review mainly focuses on molecular biology and infection of HEV and offers perspective new insight of this enigmatic virus.

Molpher: a software framework for systematic chemical space exploration

Czech Academy of Sciences Publication Activity Database

Hoksza, D.; Škoda, P.; Voršilák, M.; Svozil, Daniel

2014-01-01

Roč. 6, č. 1 (2014) ISSN 1758-2946 R&D Projects: GA TA ČR TA02010212; GA ČR(CZ) GAP202/11/0968; GA ČR(CZ) GP14-29032P Keywords : Chemical space exploration * De-novo design * In silico ligand design * Chemical biology tools Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.547, year: 2014

Molecular insights into the biology of Greater Sage-Grouse

Science.gov (United States)

Oyler-McCance, Sara J.; Quinn, Thomas W.

2011-01-01

Recent research on Greater Sage-Grouse (Centrocercus urophasianus) genetics has revealed some important findings. First, multiple paternity in broods is more prevalent than previously thought, and leks do not comprise kin groups. Second, the Greater Sage-Grouse is genetically distinct from the congeneric Gunnison sage-grouse (C. minimus). Third, the Lyon-Mono population in the Mono Basin, spanning the border between Nevada and California, has unique genetic characteristics. Fourth, the previous delineation of western (C. u. phaios) and eastern Greater Sage-Grouse (C. u. urophasianus) is not supported genetically. Fifth, two isolated populations in Washington show indications that genetic diversity has been lost due to population declines and isolation. This chapter examines the use of molecular genetics to understand the biology of Greater Sage-Grouse for the conservation and management of this species and put it into the context of avian ecology based on selected molecular studies.

Progress in nucleic acid research and molecular biology

International Nuclear Information System (INIS)

Cohn, W.E.; Moldave, K.

1988-01-01

Complementary Use of Chemical Modification and Site-Directed Mutagenesis to Probe Structure-Activity Relationships in Enzymes. Mechanisms of the Antiviral Action of Inteferons. Modulation of Cellular Genes by Oncogenes. DNA Damage Produced by Ionizing Radiation in Mammalian Cells: Identities, Mechanisms of Formation, and Reparability. Human Ferritin Gene Expression. Molecular Biology of the Insulin Receptor. Cap-Binding Proteins of Eukaryotic Messenger RNA: Functions in Initiation and Control of Translation. Physical Monitoring of Meiotic and Mitotic Recombination in Yeast. Early Signals Underlying the Induction of the c-fos and c-myc Genes in Quiescent Fibroblasts: Studies with Bombesin and Other Growth Factors. Each chapter includes references

Effect of buffer at nanoscale molecular recognition interfaces - electrostatic binding of biological polyanions.

Science.gov (United States)

Rodrigo, Ana C; Laurini, Erik; Vieira, Vânia M P; Pricl, Sabrina; Smith, David K

2017-10-19

We investigate the impact of an over-looked component on molecular recognition in water-buffer. The binding of a cationic dye to biological polyanion heparin is shown by isothermal calorimetry to depend on buffer (Tris-HCl > HEPES > PBS). The heparin binding of self-assembled multivalent (SAMul) cationic micelles is even more buffer dependent. Multivalent electrostatic molecular recognition is buffer dependent as a result of competitive interactions between the cationic binding interface and anions present in the buffer.

Biological and Physical Space Research Laboratory 2002 Science Review

Science.gov (United States)

Curreri, P. A. (Editor); Robinson, M. B. (Editor); Murphy, K. L. (Editor)

2003-01-01

With the International Space Station Program approaching core complete, our NASA Headquarters sponsor, the new Code U Enterprise, Biological and Physical Research, is shifting its research emphasis from purely fundamental microgravity and biological sciences to strategic research aimed at enabling human missions beyond Earth orbit. Although we anticipate supporting microgravity research on the ISS for some time to come, our laboratory has been vigorously engaged in developing these new strategic research areas.This Technical Memorandum documents the internal science research at our laboratory as presented in a review to Dr. Ann Whitaker, MSFC Science Director, in July 2002. These presentations have been revised and updated as appropriate for this report. It provides a snapshot of the internal science capability of our laboratory as an aid to other NASA organizations and the external scientific community.

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

DEFF Research Database (Denmark)

Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

2008-01-01

is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology......Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

Dictionary of microbiology and molecular biology. 2nd ed

Energy Technology Data Exchange (ETDEWEB)

Singleton, P.; Sainsbury, D.

1988-01-01

A newly revised edition of the standard reference for microbiology and molecular biology. Includes a multitude of new terms and designations which, although widely used in the literature, are seldom defined outside the book or paper in which they first appeared. Also accounts for the changes in the meanings of older terms brought about by advances in knowledge. Definition of all terms reflects their actual usage in current journals and texts, and also given (where appropriate) are former meanings, alternative meanings, and synonyms. Includes terms from such fields as mycology, protozoology, virology, etc.

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.

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.

Metabolism in time and space – exploring the frontier of developmental biology

Czech Academy of Sciences Publication Activity Database

Krejčí, Alena; Tennessen, J. M.

2017-01-01

Roč. 144, č. 18 (2017), s. 3193-3198 ISSN 0950-1991 Institutional support: RVO:60077344 Keywords : metabolism * mitochondria * aerobic glycolysis Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Genetics and heredity (medical genetics to be 3) Impact factor: 5.843, year: 2016 http://dev.biologists.org/content/144/18/3193

Features of Knowledge Building in Biology: Understanding Undergraduate Students’ Ideas about Molecular Mechanisms

Science.gov (United States)

Southard, Katelyn; Wince, Tyler; Meddleton, Shanice; Bolger, Molly S.

2016-01-01

Research has suggested that teaching and learning in molecular and cellular biology (MCB) is difficult. We used a new lens to understand undergraduate reasoning about molecular mechanisms: the knowledge-integration approach to conceptual change. Knowledge integration is the dynamic process by which learners acquire new ideas, develop connections between ideas, and reorganize and restructure prior knowledge. Semistructured, clinical think-aloud interviews were conducted with introductory and upper-division MCB students. Interviews included a written conceptual assessment, a concept-mapping activity, and an opportunity to explain the biomechanisms of DNA replication, transcription, and translation. Student reasoning patterns were explored through mixed-method analyses. Results suggested that students must sort mechanistic entities into appropriate mental categories that reflect the nature of MCB mechanisms and that conflation between these categories is common. We also showed how connections between molecular mechanisms and their biological roles are part of building an integrated knowledge network as students develop expertise. We observed differences in the nature of connections between ideas related to different forms of reasoning. Finally, we provide a tentative model for MCB knowledge integration and suggest its implications for undergraduate learning. PMID:26931398

Intravascular near-infrared fluorescence molecular imaging of atherosclerosis: toward coronary arterial visualization of biologically high-risk plaques

Science.gov (United States)

Calfon, Marcella A.; Vinegoni, Claudio; Ntziachristos, Vasilis; Jaffer, Farouc A.

2010-01-01

New imaging methods are urgently needed to identify high-risk atherosclerotic lesions prior to the onset of myocardial infarction, stroke, and ischemic limbs. Molecular imaging offers a new approach to visualize key biological features that characterize high-risk plaques associated with cardiovascular events. While substantial progress has been realized in clinical molecular imaging of plaques in larger arterial vessels (carotid, aorta, iliac), there remains a compelling, unmet need to develop molecular imaging strategies targeted to high-risk plaques in human coronary arteries. We present recent developments in intravascular near-IR fluorescence catheter-based strategies for in vivo detection of plaque inflammation in coronary-sized arteries. In particular, the biological, light transmission, imaging agent, and engineering principles that underlie a new intravascular near-IR fluorescence sensing method are discussed. Intravascular near-IR fluorescence catheters appear highly translatable to the cardiac catheterization laboratory, and thus may offer a new in vivo method to detect high-risk coronary plaques and to assess novel atherosclerosis biologics.

Abstracts of the 26. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 26. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

Energy Technology Data Exchange (ETDEWEB)

NONE

1997-07-01

This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology.

Abstracts of the 27. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology; Resumos da 27. reuniao anual da Sociedade Brasileira de Bioquimica e Biologia Molecular

Energy Technology Data Exchange (ETDEWEB)

NONE

1998-07-01

This meeting was about biochemistry and molecular biology. It was discussed topics related to bio energetic, channels, transports, biotechnology, metabolism, cellular biology, immunology, toxicology, photobiology and pharmacology.

Molecular pathology and prostate cancer therapeutics: from biology to bedside.

Science.gov (United States)

Rodrigues, Daniel Nava; Butler, Lisa M; Estelles, David Lorente; de Bono, Johann S

2014-01-01

Prostate cancer (PCa) is the second most commonly diagnosed malignancy in men and has an extremely heterogeneous clinical behaviour. The vast majority of PCas are hormonally driven diseases in which androgen signalling plays a central role. The realization that castration-resistant prostate cancer (CRPC) continues to rely on androgen signalling prompted the development of new, effective androgen blocking agents. As the understanding of the molecular biology of PCas evolves, it is hoped that stratification of prostate tumours into distinct molecular entities, each with its own set of vulnerabilities, will be a feasible goal. Around half of PCas harbour rearrangements involving a member of the ETS transcription factor family. Tumours without this rearrangement include SPOP mutant as well as SPINK1-over-expressing subtypes. As the number of targeted therapy agents increases, it is crucial to determine which patients will benefit from these interventions and molecular pathology will be key in this respect. In addition to directly targeting cells, therapies that modify the tumour microenvironment have also been successful in prolonging the lives of PCa patients. Understanding the molecular aspects of PCa therapeutics will allow pathologists to provide core recommendations for patient management. Copyright © 2013 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

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

Science.gov (United States)

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

2013-01-01

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

Beyond a pedagogical tool: 30 years of Molecular biology of the cell.

Science.gov (United States)

Serpente, Norberto

2013-02-01

In 1983, a bulky and profusely illustrated textbook on molecular and cell biology began to inhabit the shelves of university libraries worldwide. The effect of capturing the eyes and souls of biologists was immediate as the book provided them with a new and invigorating outlook on what cells are and what they do.

An Off-the-Shelf, Authentic, and Versatile Undergraduate Molecular Biology Practical Course

Science.gov (United States)

Whitworth, David E.

2015-01-01

We provide a prepackaged molecular biology course, which has a broad context and is scalable to large numbers of students. It is provided complete with technical setup guidance, a reliable assessment regime, and can be readily implemented without any development necessary. Framed as a forensic examination of blue/white cloning plasmids, the course…

Interactomes to Biological Phase Space: a call to begin thinking at a new level in computational biology.

Energy Technology Data Exchange (ETDEWEB)

Davidson, George S.; Brown, William Michael

2007-09-01

Techniques for high throughput determinations of interactomes, together with high resolution protein collocalizations maps within organelles and through membranes will soon create a vast resource. With these data, biological descriptions, akin to the high dimensional phase spaces familiar to physicists, will become possible. These descriptions will capture sufficient information to make possible realistic, system-level models of cells. The descriptions and the computational models they enable will require powerful computing techniques. This report is offered as a call to the computational biology community to begin thinking at this scale and as a challenge to develop the required algorithms and codes to make use of the new data.3

Molecular biology and riddle of cancer: the ‘Tom & Jerry’ show

Directory of Open Access Journals (Sweden)

Md. Al Mamun

2011-11-01

Full Text Available From the conventional Bird’s eye, cancer initiation and metastasis are generally intended to be understood beneath the light of classical clonal genetic, epigenetic and cancer stem cell model. But inspite decades of investigation, molecular biology has shown hard success to give Eagle’s eye in unraveling the riddle of cancer. And it seems, tiring Tom runs in vague behind naughty Jerry.

Using novel descriptor accounting for ligand-receptor interactions to define and visually explore biologically relevant chemical space.

Science.gov (United States)

Rabal, Obdulia; Oyarzabal, Julen

2012-05-25

The definition and pragmatic implementation of biologically relevant chemical space is critical in addressing navigation strategies in the overlapping regions where chemistry and therapeutically relevant targets reside and, therefore, also key to performing an efficient drug discovery project. Here, we describe the development and implementation of a simple and robust method for representing biologically relevant chemical space as a general reference according to current knowledge, independently of any reference space, and analyzing chemical structures accordingly. Underlying our method is the generation of a novel descriptor (LiRIf) that converts structural information into a one-dimensional string accounting for the plausible ligand-receptor interactions as well as for topological information. Capitalizing on ligand-receptor interactions as a descriptor enables the clustering, profiling, and comparison of libraries of compounds from a chemical biology and medicinal chemistry perspective. In addition, as a case study, R-groups analysis is performed to identify the most populated ligand-receptor interactions according to different target families (GPCR, kinases, etc.), as well as to evaluate the coverage of biologically relevant chemical space by structures annotated in different databases (ChEMBL, Glida, etc.).

Retracted: Molecular Characterization and Biological Activity of Interferon-α in Indian Peafowl (Pavo cristatus).

Science.gov (United States)

Zhao, Hongjing; Wang, Yu; Liu, Juanjuan; Shao, Yizhi; Li, Jinglun; Chai, Hongliang; Xing, Mingwei

2017-08-07

DNA and Cell Biology (DNA&CB) is officially retracting the paper by Zhao H, Wang Y, Liu J, Shao Y, Li J, Chai H, Xing M, entitled, "Molecular Characterization and Biological activity of Interferon-α in Indian Peafowl (Pavo cristatus)," [Epub ahead of print]; 2017, DOI: 10.1089/dna.2017.3798. The Editor-in-Chief of DNA&CB, Dr. Carol Shoshkes Reiss, was alerted to a discrepancy between the findings in the article by Zhao et al., and those of others, about the absence of expression of ISG15 in chickens. Dr. Reiss requested from the authors a clarification in their observations and inquired about the failure to include relevant citations in the reference section of the paper. Based on the response from the authors, it appeared that they did not have the confidence in the data as they were not able to repeat the experiments, and were also unsure of the molecular probes that were used in the study. Therefore, the Editor has determined that the paper should be officially retracted from DNA and Cell Biology.

The Design and Transformation of Biofundamentals: A Nonsurvey Introductory Evolutionary and Molecular Biology Course.

Science.gov (United States)

Klymkowsky, Michael W; Rentsch, Jeremy D; Begovic, Emina; Cooper, Melanie M

2016-01-01

Many introductory biology courses amount to superficial surveys of disconnected topics. Often, foundational observations and the concepts derived from them and students' ability to use these ideas appropriately are overlooked, leading to unrealistic expectations and unrecognized learning obstacles. The result can be a focus on memorization at the expense of the development of a meaningful framework within which to consider biological phenomena. About a decade ago, we began a reconsideration of what an introductory course should present to students and the skills they need to master. The original Web-based course's design presaged many of the recommendations of the Vision and Change report; in particular, a focus on social evolutionary mechanisms, stochastic (evolutionary and molecular) processes, and core ideas (cellular continuity, evolutionary homology, molecular interactions, coupled chemical reactions, and molecular machines). Inspired by insights from the Chemistry, Life, the Universe & Everything general chemistry project, we transformed the original Web version into a (freely available) book with a more unified narrative flow and a set of formative assessments delivered through the beSocratic system. We outline how student responses to course materials are guiding future course modifications, in particular a more concerted effort at helping students to construct logical, empirically based arguments, explanations, and models. © 2016 M. W. Klymkowsky et al. CBE—Life Sciences Education © 2016 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Investigating Viruses during the Transformation of Molecular Biology.

Science.gov (United States)

Moss, Bernard

2017-03-10

This Reflections article describes my early work on viral enzymes and the discovery of mRNA capping, how my training in medicine and biochemistry merged as I evolved into a virologist, the development of viruses as vaccine vectors, and how scientific and technological developments during the 1970s and beyond set the stage for the interrogation of nearly every step in the reproductive cycle of vaccinia virus (VACV), a large DNA virus with about 200 genes. The reader may view this article as a work in progress, because I remain actively engaged in research at the National Institutes of Health (NIH) notwithstanding 50 memorable years there. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The molecular genetics of the telomere biology disorders.

Science.gov (United States)

Bertuch, Alison A

2016-08-02

The importance of telomere function for human health is exemplified by a collection of Mendelian disorders referred to as the telomere biology disorders (TBDs), telomeropathies, or syndromes of telomere shortening. Collectively, the TBDs cover a spectrum of conditions from multisystem disease presenting in infancy to isolated disease presentations in adulthood, most notably idiopathic pulmonary fibrosis. Eleven genes have been found mutated in the TBDs to date, each of which is linked to some aspect of telomere maintenance. This review summarizes the molecular defects that result from mutations in these genes, highlighting recent advances, including the addition of PARN to the TBD gene family and the discovery of heterozygous mutations in RTEL1 as a cause of familial pulmonary fibrosis.

Diagnosis and management of differentiated thyroid cancer using molecular biology.

Science.gov (United States)

Witt, Robert L; Ferris, Robert L; Pribitkin, Edmund A; Sherman, Steven I; Steward, David L; Nikiforov, Yuri E

2013-04-01

To define molecular biology in clinical practice for diagnosis, surgical management, and prognostication of differentiated thyroid cancer. Ovid Medline 2006-2012 Manuscripts with clinical correlates. Papillary thyroid carcinomas harbor point mutations of the BRAF and RAS genes or RET/PTC rearrangements, all of which activate the mitogen-activated protein kinase pathway. These mutually exclusive mutations are found in 70% of PTC. BRAF mutation is found in 45% of papillary thyroid cancer and is highly specific. Follicular carcinomas are known to harbor RAS mutation or PAX8/PPARγ rearrangement. These mutations are also mutually exclusive and identified in 70% of follicular carcinomas. Molecular classifiers measure the expression of a large number of genes on a microarray chip providing a substantial negative predictive value pending further validation. 1) 20% to 30% of cytologically classified Follicular Neoplasms and Follicular Lesion of Undetermined Significance collectively are malignant on final pathology. Approximately 70% to 80% of thyroid lobectomies performed solely for diagnostic purposes are benign. Molecular alteration testing may reduce the number of unnecessary thyroid procedures, 2) may reduce the number of completion thyroidectomies, and 3) may lead to more individualized operative and postoperative management. Molecular testing for BRAF, RAS, RET/PTC, and PAX8/PPARγ for follicular lesion of undetermined significance and follicular neoplasm improve specificity, whereas molecular classifiers may add negative predictive value to fine needle aspiration diagnosis. Copyright © 2013 The American Laryngological, Rhinological, and Otological Society, Inc.

Biological effects of space-induced mutation on robinia pseudoacacia

International Nuclear Information System (INIS)

Yuan Cunquan; Li Yun; Lu Chao; Yang Min; Zhang Yuyao

2010-01-01

Dry seeds of Robinia pseudoacacia were carried by Shijian No.8 breeding satellite for mutagenesis and the biological effect of space-induced mutation was studied. The parameters of Robinia pseudoacacia such as plant height, stem base, branch number, knot spacing, length of thorn and chlorophyll content were analyzed, and, at the same time, the genetic diversity was tested by SSR marker. The results showed that the plant height and stem base of 2-year-old seedlings which derived from space mutagenesis were 22.0% and 24.1% lower than those of control, and 3-year-old seedlings were 13.1% and 22.4% lower than those of control, respectively. While the inhibiting effect of plant height became undermined in the following growth years. However, the inhibiting effect in stem base existed all the time,the length of thorn of branch and stem were 15.6% and 28.6% shorter than the control,respectively. Compared with the control,the variation of the length of thorn from stem was extremely significant. The variation of chlorophyll a content from space mutagenesis compared with control was not remarkable, while the total chlorophyll and chlorophyll b contents were 18.7% and 9.7% lower than those of control, respectively, and the difference between space mutagenesis and control was significant. While the chlorophyll a/b was 25.6% higher than that of control, but the difference was not significant. The coefficient of variation of the relative traits was increased by the space mutagenesis. The extensively population genome mutation after space-induction were not detected by SSR (Simple Sequence Repeats). (authors)

Theories and models on the biological of cells in space

Science.gov (United States)

Todd, P.; Klaus, D. M.

1996-01-01

A wide variety of observations on cells in space, admittedly made under constraining and unnatural conditions in may cases, have led to experimental results that were surprising or unexpected. Reproducibility, freedom from artifacts, and plausibility must be considered in all cases, even when results are not surprising. The papers in symposium on 'Theories and Models on the Biology of Cells in Space' are dedicated to the subject of the plausibility of cellular responses to gravity -- inertial accelerations between 0 and 9.8 m/sq s and higher. The mechanical phenomena inside the cell, the gravitactic locomotion of single eukaryotic and prokaryotic cells, and the effects of inertial unloading on cellular physiology are addressed in theoretical and experimental studies.

[Etiologic diagnosis in meningitis and encephalitis molecular biology techniques].

Science.gov (United States)

Conca, Natalia; Santolaya, María Elena; Farfan, Mauricio J; Cofré, Fernanda; Vergara, Alejandra; Salazar, Liliana; Torres, Juan Pablo

2016-01-01

The aetiological study of infections of the central nervous system has traditionally been performed using bacterial cultures and, more recently, using polymerase chain reaction (PCR) for herpes simplex virus (HSV). Bacterial cultures may not have good performance, especially in the context of patients who have received antibiotics prior to sampling, and a request for HSV only by PCR reduces the information to only one aetiological agent. The aim of this study is to determine the infectious causes of meningitis and encephalitis, using traditional microbiology and molecular biology to improve the aetiological diagnosis of these diseases. A prospective study was conducted on 19 patients with suspected meningitis, admitted to the Luis Calvo Mackenna Hospital in Santiago, Chile, from March 1, 2011 to March 30, 2012. After obtaining informed consent, the CSF samples underwent cytochemical study, conventional culture, multiplex PCR for the major producing bacterial meningitis (N. meningitidis, S. pneumoniae, H. influenzae), real-time single PCR for HSV-1 and 2, VZV, EBV, CMV, HHV-6 and enterovirus. Clinical and epidemiological data were also collected from the clinical records. Of the 19 patients analysed, 2 were diagnosed by conventional methods and 7 by adding molecular biology (increase to 37%). Three patients had meningitis due to S. pneumoniae, one due to Enterobacter cloacae, 2 patients meningoencephalitis HSV-1, and one VZV meningitis. The addition of PCR to conventional diagnostic methods in CNS infections increases the probability of finding the causal agent. This allows a more adequate, timely and rational management of the disease. Copyright © 2014. Publicado por Elsevier España, S.L.U.

Micro/nanofabricated environments for synthetic biology.

Science.gov (United States)

Collier, C Patrick; Simpson, Michael L

2011-08-01

A better understanding of how confinement, crowding and reduced dimensionality modulate reactivity and reaction dynamics will aid in the rational and systematic discovery of functionality in complex biological systems. Artificial microfabricated and nanofabricated structures have helped elucidate the effects of nanoscale spatial confinement and segregation on biological behavior, particularly when integrated with microfluidics, through precise control in both space and time of diffusible signals and binding interactions. Examples of nanostructured interfaces for synthetic biology include the development of cell-like compartments for encapsulating biochemical reactions, nanostructured environments for fundamental studies of diffusion, molecular transport and biochemical reaction kinetics, and regulation of biomolecular interactions as functions of microfabricated and nanofabricated topological constraints. Copyright © 2011 Elsevier Ltd. All rights reserved.

Sclerotinia sclerotiorum (Lib.) de Bary: biology and molecular traits of a cosmopolitan pathogen

NARCIS (Netherlands)

Bolton, M.D.; Thomma, B.P.H.J.; Nelson, B.D.

2006-01-01

Sclerotinia sclerotiorum (Lib.) de Bary is a necrotrophic fungal pathogen causing disease in a wide range of plants. This review summarizes current knowledge of mechanisms employed by the fungus to parasitize its host with emphasis on biology, physiology and molecular aspects of pathogenicity. In

Hidden Markov models and other machine learning approaches in computational molecular biology

Energy Technology Data Exchange (ETDEWEB)

Baldi, P. [California Inst. of Tech., Pasadena, CA (United States)

1995-12-31

This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. Computational tools are increasingly needed to process the massive amounts of data, to organize and classify sequences, to detect weak similarities, to separate coding from non-coding regions, and reconstruct the underlying evolutionary history. The fundamental problem in machine learning is the same as in scientific reasoning in general, as well as statistical modeling: to come up with a good model for the data. In this tutorial four classes of models are reviewed. They are: Hidden Markov models; artificial Neural Networks; Belief Networks; and Stochastic Grammars. When dealing with DNA and protein primary sequences, Hidden Markov models are one of the most flexible and powerful alignments and data base searches. In this tutorial, attention is focused on the theory of Hidden Markov Models, and how to apply them to problems in molecular biology.

Application of Molecular Adsorber Coatings in Chamber A for the James Webb Space Telescope

Science.gov (United States)

Abraham, Nithin S.

2017-01-01

As a coating made of highly porous zeolite materials, the Molecular Adsorber Coating (MAC) was developed to capture outgassed molecular contaminants, such as hydrocarbons and silicones. For spaceflight applications, the adsorptive capabilities of the coating can alleviate on-orbit outgassing concerns on or near sensitive surfaces and instruments within the spacecraft. Similarly, this sprayable paint technology has proven to be significantly beneficial for ground-based space applications, in particular, for vacuum chamber environments. This presentation describes the application of the MAC technology for the James Webb Space Telescope (JWST) at NASA Johnson Space Center (JSC). The coating was used as a mitigation tool to entrap outgassed contaminants, specifically silicone-based diffusion pump oil, from within JSCs cryogenic optical vacuum chamber test facility called Chamber A. This presentation summarizes the background, fabrication, installation, chemical analysis test results, and future plans for the MAC technology, which was effectively used to protect the JWST test equipment from vacuum chamber contamination. As a coating made of highly porous zeolite materials, the Molecular Adsorber Coating (MAC) was developed to capture outgassed molecular contaminants, such as hydrocarbons and silicones. For spaceflight applications, the adsorptive capabilities of the coating can alleviate on-orbit outgassing concerns on or near sensitive surfaces and instruments within the spacecraft. Similarly, this sprayable paint technology has proven to be significantly beneficial for ground-based space applications, in particular, for vacuum chamber environments. This presentation describes the application of the MAC technology for the James Webb Space Telescope (JWST) at NASA Johnson Space Center (JSC). The coating was used as a mitigation tool to entrap outgassed contaminants, specifically silicone-based diffusion pump oil, from within JSCs cryogenic optical vacuum chamber test

Molecular docking.

Science.gov (United States)

Morris, Garrett M; Lim-Wilby, Marguerita

2008-01-01

Molecular docking is a key tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the predominant binding mode(s) of a ligand with a protein of known three-dimensional structure. Successful docking methods search high-dimensional spaces effectively and use a scoring function that correctly ranks candidate dockings. Docking can be used to perform virtual screening on large libraries of compounds, rank the results, and propose structural hypotheses of how the ligands inhibit the target, which is invaluable in lead optimization. The setting up of the input structures for the docking is just as important as the docking itself, and analyzing the results of stochastic search methods can sometimes be unclear. This chapter discusses the background and theory of molecular docking software, and covers the usage of some of the most-cited docking software.

Protein signatures using electrostatic molecular surfaces in harmonic space

Directory of Open Access Journals (Sweden)

C. Sofia Carvalho

2013-10-01

Full Text Available We developed a novel method based on the Fourier analysis of protein molecular surfaces to speed up the analysis of the vast structural data generated in the post-genomic era. This method computes the power spectrum of surfaces of the molecular electrostatic potential, whose three-dimensional coordinates have been either experimentally or theoretically determined. Thus we achieve a reduction of the initial three-dimensional information on the molecular surface to the one-dimensional information on pairs of points at a fixed scale apart. Consequently, the similarity search in our method is computationally less demanding and significantly faster than shape comparison methods. As proof of principle, we applied our method to a training set of viral proteins that are involved in major diseases such as Hepatitis C, Dengue fever, Yellow fever, Bovine viral diarrhea and West Nile fever. The training set contains proteins of four different protein families, as well as a mammalian representative enzyme. We found that the power spectrum successfully assigns a unique signature to each protein included in our training set, thus providing a direct probe of functional similarity among proteins. The results agree with established biological data from conventional structural biochemistry analyses.

Infusing Bioinformatics and Research-Like Experience into a Molecular Biology Laboratory Course

Science.gov (United States)

Nogaj, Luiza A.

2014-01-01

A nine-week laboratory project designed for a sophomore level molecular biology course is described. Small groups of students (3-4 per group) choose a tumor suppressor gene (TSG) or an oncogene for this project. Each group researches the role of their TSG/oncogene from primary literature articles and uses bioinformatics engines to find the gene…

Intraductal papillary-mucinous neoplasia of the pancreas: Histopathology and molecular biology

OpenAIRE

Verbeke, Caroline S

2010-01-01

Intraductal papillary-mucinous neoplasm (IPMN) of the pancreas is a clinically and morphologically distinctive precursor lesion of pancreatic cancer, characterized by gradual progression through a sequence of neoplastic changes. Based on the nature of the constituting neoplastic epithelium, degree of dysplasia and location within the pancreatic duct system, IPMNs are divided in several types which differ in their biological properties and clinical outcome. Molecular analysis and recent animal...

Biología y regulación molecular de la micorriza arbuscular

Directory of Open Access Journals (Sweden)

S. Guzmán-González

2005-01-01

Full Text Available Las micorrizas arbusculares son asociaciones simbióticas formadas entre un amplio rango de especies de plantas y hongos del orden Glomales. El hongo coloniza el apoplasto y células corticales de la raíz. El desarrollo de esta asociación, altamente compatible, requiere de la diferenciación celular y molecular coordinada de ambos simbiontes, para formar una interface especializada en la cual ocurre la transferencia bidireccional de nutrimentos. Esta revisión resume los resultados obtenidos con el uso de técnicas de biología molecular en el entendimiento del desarrollo de la simbiosis micorrízica arbuscular.

Biochemistry and Molecular Biology of Flaviviruses.

Science.gov (United States)

Barrows, Nicholas J; Campos, Rafael K; Liao, Kuo-Chieh; Prasanth, K Reddisiva; Soto-Acosta, Ruben; Yeh, Shih-Chia; Schott-Lerner, Geraldine; Pompon, Julien; Sessions, October M; Bradrick, Shelton S; Garcia-Blanco, Mariano A

2018-04-25

Flaviviruses, such as dengue, Japanese encephalitis, tick-borne encephalitis, West Nile, yellow fever, and Zika viruses, are critically important human pathogens that sicken a staggeringly high number of humans every year. Most of these pathogens are transmitted by mosquitos, and not surprisingly, as the earth warms and human populations grow and move, their geographic reach is increasing. Flaviviruses are simple RNA-protein machines that carry out protein synthesis, genome replication, and virion packaging in close association with cellular lipid membranes. In this review, we examine the molecular biology of flaviviruses touching on the structure and function of viral components and how these interact with host factors. The latter are functionally divided into pro-viral and antiviral factors, both of which, not surprisingly, include many RNA binding proteins. In the interface between the virus and the hosts we highlight the role of a noncoding RNA produced by flaviviruses to impair antiviral host immune responses. Throughout the review, we highlight areas of intense investigation, or a need for it, and potential targets and tools to consider in the important battle against pathogenic flaviviruses.

Oligometastatic prostate cancer: shaping the definition with molecular imaging and an improved understanding of tumor biology.

Science.gov (United States)

Joice, Gregory A; Rowe, Steven P; Pienta, Kenneth J; Gorin, Michael A

2017-11-01

The aim of this review is to discuss how novel imaging modalities and molecular markers are shaping the definition of oligometastatic prostate cancer. To effectively classify a patient as having oligometastatic prostate cancer, diagnostic tests must be sensitive enough to detect subtle sites of metastatic disease. Conventional imaging modalities can readily detect widespread polymetastatic disease but do not have the sensitivity necessary to reliably classify patients as oligometastatic. Molecular imaging using both metabolic- and molecularly-targeted radiotracers has demonstrated great promise in aiding in our ability to define the oligometastatic state. Perhaps the most promising data to date have been generated with radiotracers targeting prostate-specific membrane antigen. In addition, early studies are beginning to define biologic markers in the oligometastatic state that may be indicative of disease with minimal metastatic potential. Recent developments in molecular imaging have allowed for improved detection of metastatic prostate cancer allowing for more accurate staging of patients with oligometastatic disease. Future development of biologic markers may assist in defining the oligometastatic state and determining prognosis.

Pragmatic turn in biology: From biological molecules to genetic content operators.

Science.gov (United States)

Witzany, Guenther

2014-08-26

Erwin Schrödinger's question "What is life?" received the answer for decades of "physics + chemistry". The concepts of Alain Turing and John von Neumann introduced a third term: "information". This led to the understanding of nucleic acid sequences as a natural code. Manfred Eigen adapted the concept of Hammings "sequence space". Similar to Hilbert space, in which every ontological entity could be defined by an unequivocal point in a mathematical axiomatic system, in the abstract "sequence space" concept each point represents a unique syntactic structure and the value of their separation represents their dissimilarity. In this concept molecular features of the genetic code evolve by means of self-organisation of matter. Biological selection determines the fittest types among varieties of replication errors of quasi-species. The quasi-species concept dominated evolution theory for many decades. In contrast to this, recent empirical data on the evolution of DNA and its forerunners, the RNA-world and viruses indicate cooperative agent-based interactions. Group behaviour of quasi-species consortia constitute de novo and arrange available genetic content for adaptational purposes within real-life contexts that determine epigenetic markings. This review focuses on some fundamental changes in biology, discarding its traditional status as a subdiscipline of physics and chemistry.

Integr8: enhanced inter-operability of European molecular biology databases.

Science.gov (United States)

Kersey, P J; Morris, L; Hermjakob, H; Apweiler, R

2003-01-01

The increasing production of molecular biology data in the post-genomic era, and the proliferation of databases that store it, require the development of an integrative layer in database services to facilitate the synthesis of related information. The solution of this problem is made more difficult by the absence of universal identifiers for biological entities, and the breadth and variety of available data. Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented as an n-tier system using a modern object-oriented programming language (Java). An object-relational mapping tool, OJB, is being used to specify the interface between the upper layers and an underlying relational database. The European Bioinformatics Institute is launching the Integr8 project. Integr8 will be an automatically populated database in which we will maintain stable identifiers for biological entities, describe their relationships with each other (in accordance with the central dogma of biology), and store equivalences between identified entities in the source databases. Only core data will be stored in Integr8, with web links to the source databases providing further information. Integr8 will provide the integrative layer of the next generation of bioinformatics services from the EBI. Web-based interfaces will be developed to offer gene-centric views of the integrated data, presenting (where known) the links between genome, proteome and phenotype.

The Molecular Biology of Soft-Tissue Sarcomas and Current Trends in Therapy

Directory of Open Access Journals (Sweden)

Jorge Quesada

2012-01-01

Full Text Available Basic research in sarcoma models has been fundamental in the discovery of scientific milestones leading to a better understanding of the molecular biology of cancer. Yet, clinical research in sarcoma has lagged behind other cancers because of the multiple clinical and pathological entities that characterize sarcomas and their rarity. Sarcomas encompass a very heterogeneous group of tumors with diverse pathological and clinical overlapping characteristics. Molecular testing has been fundamental in the identification and better definition of more specific entities among this vast array of malignancies. A group of sarcomas are distinguished by specific molecular aberrations such as somatic mutations, intergene deletions, gene amplifications, reciprocal translocations, and complex karyotypes. These and other discoveries have led to a better understanding of the growth signals and the molecular pathways involved in the development of these tumors. These findings are leading to treatment strategies currently under intense investigation. Disruption of the growth signals is being targeted with antagonistic antibodies, tyrosine kinase inhibitors, and inhibitors of several downstream molecules in diverse molecular pathways. Preliminary clinical trials, supported by solid basic research and strong preclinical evidence, promises a new era in the clinical management of these broad spectrum of malignant tumors.

Transmission electron microscopy in molecular structural biology: A historical survey.

Science.gov (United States)

Harris, J Robin

2015-09-01

In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

Current status of molecular biological techniques for plant breeding in the Republic of Korea

Energy Technology Data Exchange (ETDEWEB)

Sohn, Seong-Han; Lee, Si-Myung; Park, Bum-Seok; Yun, In-Sun; Goo, Doe-Hoe; Kim, Seok-Dong [Rural Development Administration, National Institute of Agricultural Science and Technology, Suwon (Korea)

2002-02-01

Classical plant breeding has played an important role in developing new varieties in current agriculture. For decades, the technique of cross-pollination has been popular for breeding in cereal and horticultural crops to introduce special traits. However, recently the molecular techniques get widely accepted as an alternative tool in both introducing a useful trait for developing the new cultivars and investigating the characteristics of a trait in plant, like the identification of a gene. Using the advanced molecular technique, several genetically modified (GM) crops (e.g., Roundup Ready Soybean, YieldGard, LibertyLink etc.) became commercially cultivated and appeared in the global market since 1996. The GM crops, commercially available at the moment, could be regarded as successful achievements in history of crop breeding conferring the specific gene into economically valuable crops to make them better. Along with such achievements, on the other hand these new crops have also caused the controversial debate on the safety of GM crops as human consumption and environmental release as well. Nevertheless, molecular techniques are widespread and popular in both investigating the basic science of plant biology and breeding new varieties compared to their conventional counterparts. Thus, the Department of Bioresources at the National Institute of Agricultural Science and Technology (NIAST) has been using the molecular biological techniques as a complimentary tool for the improvement of crop varieties for almost two decades. (author)

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

Artificial microRNAs and their applications in plant molecular biology

Directory of Open Access Journals (Sweden)

Pérez-Quintero Álvaro Luis

2010-11-01

Full Text Available

Errant life, molecular biology, and biopower: Canguilhem, Jacob, and Foucault.

Science.gov (United States)

Talcott, Samuel

2014-01-01

This paper considers the theoretical circumstances that urged Michel Foucault to analyse modern societies in terms of biopower. Georges Canguilhem's account of the relations between science and the living forms an essential starting point for Foucault's own later explorations, though the challenges posed by the molecular revolution in biology and François Jacob's history of it allowed Foucault to extend and transform Canguilhem's philosophy of error. Using archival research into his 1955-1956 course on "Science and Error," I show that, for Canguilhem, it is inauthentic to treat a living being as an error, even if living things are capable of making errors in the domain of knowledge. The emergent molecular biology in the 1960s posed a grave challenge, however, since it suggested that individuals could indeed be errors of genetic reproduction. The paper discusses how Canguilhem and Foucault each responded to this by examining, among other texts, their respective reviews of Jacob's The Logic of the Living. For Canguilhem this was an opportunity to reaffirm the creativity of life in the living individual, which is not a thing to be evaluated, but the source of values. For Foucault, drawing on Jacob's work, this was the opportunity to develop a transformed account of valuation by posing biopower as the DNA of society. Despite their disagreements, the paper examines these three authors as different iterations of a historical epistemology attuned to errancy, error, and experimentation.

Molecular Sociology: Further Insights from Biological and Environmental Aspects

Directory of Open Access Journals (Sweden)

Ahed Jumah Mahmoud Al-Khatib

2015-11-01

Full Text Available The present study expanded our previous study in which features of molecular sociology were mentioned. In this study, we added the microbial dimensions in which it is thought that religiosity may be impacted by microbes that manipulate brains to create better conditions for their existence. This hypothesis is called “biomeme hypothesis”. We talked about other environmental impacts on human behaviors through three studies in which exposure to lead caused violent behaviors ending with arresting in prisons. By conclusion, the present study has expanded our horizon about interferences on various levels including biological and environmental impacts with our behaviors. Although we are convinced that behavior is a very diverse and complex phenomenon and cannot be understood within certain frame as either biologically or environmentally, but further new insights are possible to participate in better understanding of human behaviors. Many behaviors have their roots in religion, and we showed how religious rituals may be affected by some microbes that make to form a microenvironment within the host for microbial benefits.

Novel thrombopoietin mimetic peptides bind c-Mpl receptor: Synthesis, biological evaluation and molecular modeling.

Science.gov (United States)

Liu, Yaquan; Tian, Fang; Zhi, Dejuan; Wang, Haiqing; Zhao, Chunyan; Li, Hongyu

2017-02-01

Thrombopoietin (TPO) acts in promoting the proliferation of hematopoietic stem cells and by initiating specific maturation events in megakaryocytes. Now, TPO-mimetic peptides with amino acid sequences unrelated to TPO are of considerable pharmaceutical interest. In the present paper, four new TPO mimetic peptides that bind and activate c-Mpl receptor have been identified, synthesized and tested by Dual-Luciferase reporter gene assay for biological activities. The molecular modeling research was also approached to understand key molecular mechanisms and structural features responsible for peptide binding with c-Mpl receptor. The results presented that three of four mimetic peptides showed significant activities. In addition, the molecular modeling approaches proved hydrophobic interactions were the driven positive forces for binding behavior between peptides and c-Mpl receptor. TPO peptide residues in P7, P13 and P7' positions were identified by the analysis of hydrogen bonds and energy decompositions as the key ones for benefiting better biological activities. Our data suggested the synthesized peptides have considerable potential for the future development of stable and highly active TPO mimetic peptides. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molecular decompostition of anisotropic homogeneous mixed-norm spaces with applications to the boundedness of operators

DEFF Research Database (Denmark)

Cleanthous, Galatia; Georgiadis, Athanasios; Nielsen, Morten

2018-01-01

. Molecular decompositions for all the considered spaces are derived with the help of the algebra of almost diagonal operators. As an application, we obtain boundedness results on the considered spaces for Fourier multipliers and for pseudodifferential operators with suitable adapted homogeneous symbols using...

Right Versus Left Colon Cancer Biology: Integrating the Consensus Molecular Subtypes.

Science.gov (United States)

Lee, Michael S; Menter, David G; Kopetz, Scott

2017-03-01

Although clinical management of colon cancer generally has not accounted for the primary tumor site, left-sided and right-sided colon cancers harbor different clinical and biologic characteristics. Right-sided colon cancers are more likely to have genome-wide hypermethylation via the CpG island methylator phenotype (CIMP), hypermutated state via microsatellite instability, and BRAF mutation. There are also differential exposures to potential carcinogenic toxins and microbiota in the right and left colon. Gene expression analyses further shed light on distinct biologic subtypes of colorectal cancers (CRCs), with 4 consensus molecular subtypes (CMSs) identified. Importantly, these subtypes are differentially distributed between right- and left-sided CRCs, with greater proportions of the "microsatellite unstable/immune" CMS1 and the "metabolic" CMS3 subtypes found in right-sided colon cancers. This review summarizes important biologic distinctions between right- and left-sided CRCs that likely impact prognosis and may predict for differential responses to biologic therapy. Given the inferior prognosis of stage III-IV right-sided CRCs and emerging data suggesting that anti-epidermal growth factor receptor antibody therapy is associated with worse survival in right-sided stage IV CRCs compared with left-sided cancers, these biologic differences between right- and left-sided CRCs provide critical context and may provide opportunities to personalize therapy. Copyright © 2017 by the National Comprehensive Cancer Network.

The Value of Humans in the Biological Exploration of Space

Science.gov (United States)

Cockell, C. S.

2004-06-01

Regardless of the discovery of life on Mars, or of "no apparent life" on Mars, the questions that follow will provide a rich future for biological exploration. Extraordinary pattern recognition skills, decadal assimilation of data and experience, and rapid sample acquisition are just three of the characteristics that make humans the best means we have to explore the biological potential of Mars and other planetary surfaces. I make the case that instead of seeing robots as in conflict, or even in support, of human exploration activity, from the point of view of scientific data gathering and analysis, we should view humans as the most powerful robots we have, thus removing the separation that dogs discussions on the exploration of space. The narrow environmental requirements of humans, although imposing constraints on the life support systems required, is more than compensated for by their capabilities in biological exploration. I support this view with an example of the "Christmas present effect," a simple demonstration of human data and pattern recognition capabilities.

Molecular codes in biological and chemical reaction networks.

Directory of Open Access Journals (Sweden)

Dennis Görlich

Full Text Available Shannon's theory of communication has been very successfully applied for the analysis of biological information. However, the theory neglects semantic and pragmatic aspects and thus cannot directly be applied to distinguish between (bio- chemical systems able to process "meaningful" information from those that do not. Here, we present a formal method to assess a system's semantic capacity by analyzing a reaction network's capability to implement molecular codes. We analyzed models of chemical systems (martian atmosphere chemistry and various combustion chemistries, biochemical systems (gene expression, gene translation, and phosphorylation signaling cascades, an artificial chemistry, and random reaction networks. Our study suggests that different chemical systems possess different semantic capacities. No semantic capacity was found in the model of the martian atmosphere chemistry, the studied combustion chemistries, and highly connected random networks, i.e. with these chemistries molecular codes cannot be implemented. High semantic capacity was found in the studied biochemical systems and in random reaction networks where the number of second order reactions is twice the number of species. We conclude that our approach can be applied to evaluate the information processing capabilities of a chemical system and may thus be a useful tool to understand the origin and evolution of meaningful information, e.g. in the context of the origin of life.

Plant Molecular Biology 2008 Gordon Research Conference - July 13-18, 2008

Energy Technology Data Exchange (ETDEWEB)

Richard M. Amasino

2009-08-28

The Plant Molecular Biology Conference has traditionally covered a breadth of exciting topics and the 2008 conference will continue in that tradition. There will be sessions on metabolism; new methods to study genomes, proteomes and metabolomes; plant-microbe interactions; plant hormones; epigenetics. A new topic for the conference this year will be bioenergy. Thus this conference will bring together a range of disciplines to foster the exchange ideas and to permit the participants to learn of the latest developments and ideas in diverse areas of plant biology. The conference provides an excellent opportunity for individuals to discuss their research because additional speakers in each session will be selected from submitted abstracts. There will also be a poster session each day for a two-hour period prior to dinner.

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

Directory of Open Access Journals (Sweden)

Viroj Wiwanitkit

2008-06-01

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

Transition voltages of vacuum-spaced and molecular junctions with Ag and Pt electrodes

KAUST Repository

Wu, Kunlin; Bai, Meilin; Sanvito, Stefano; Hou, Shimin

2014-01-01

The transition voltage of vacuum-spaced and molecular junctions constructed with Ag and Pt electrodes is investigated by non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that, similarly

Insights into the immuno-molecular biology of Angiostrongylus vasorum through transcriptomics--prospects for new interventions.

Science.gov (United States)

Ansell, Brendan R E; Schnyder, Manuela; Deplazes, Peter; Korhonen, Pasi K; Young, Neil D; Hall, Ross S; Mangiola, Stefano; Boag, Peter R; Hofmann, Andreas; Sternberg, Paul W; Jex, Aaron R; Gasser, Robin B

2013-12-01

Angiostrongylus vasorum is a metastrongyloid nematode of dogs and other canids of major clinical importance in many countries. In order to gain first insights into the molecular biology of this worm, we conducted the first large-scale exploration of its transcriptome, and predicted essential molecules linked to metabolic and biological processes as well as host immune responses. We also predicted and prioritized drug targets and drug candidates. Following Illumina sequencing (RNA-seq), 52.3 million sequence reads representing adult A. vasorum were assembled and annotated. The assembly yielded 20,033 contigs, which encoded proteins with 11,505 homologues in Caenorhabditis elegans, and additional 2252 homologues in various other parasitic helminths for which curated data sets were publicly available. Functional annotation was achieved for 11,752 (58.6%) proteins predicted for A. vasorum, including peptidases (4.5%) and peptidase inhibitors (1.6%), protein kinases (1.7%), G protein-coupled receptors (GPCRs) (1.5%) and phosphatases (1.2%). Contigs encoding excretory/secretory and immuno-modulatory proteins represented some of the most highly transcribed molecules, and encoded enzymes that digest haemoglobin were conserved between A. vasorum and other blood-feeding nematodes. Using an essentiality-based approach, drug targets, including neurotransmitter receptors, an important chemosensory ion channel and cysteine proteinase-3 were predicted in A. vasorum, as were associated small molecular inhibitors/activators. Future transcriptomic analyses of all developmental stages of A. vasorum should facilitate deep explorations of the molecular biology of this important parasitic nematode and support the sequencing of its genome. These advances will provide a foundation for exploring immuno-molecular aspects of angiostrongylosis and have the potential to underpin the discovery of new methods of intervention. © 2013.

The impact of advances in human molecular biology on radiation genetic risk estimation in man

International Nuclear Information System (INIS)

Sankaranarayanan, K.

1996-01-01

This paper provides an overview of the conceptual framework, the data base, methods and assumptions used thus far to assess the genetic risks of exposure of human populations to ionising radiation. These are then re-examined in the contemporary context of the rapidly expanding knowledge of the molecular biology of human mendelian diseases. This re-examination reveals that (i) many of the assumptions used thus far in radiation genetic risk estimation may not be fully valid and (ii) the current genetic risk estimates are probably conservative, but provide an adequate margin of safety for radiological protection. The view is expressed that further advances in the field of genetic risk estimation will be largely driven by advances in the molecular biology of human genetic diseases. (author). 37 refs., 5 tabs

Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

Science.gov (United States)

Cramer, Patrick

2017-08-18

Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective. Copyright © 2017 Elsevier Ltd. All rights reserved.

Characterization of microbial communities in pest colonized books by molecular biology tools

OpenAIRE

Franco Palla

2011-01-01

This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR), sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of man...

Molecular and Biological Analysis of Potato virus M (PVM) Isolates from the Czech Republic

Czech Academy of Sciences Publication Activity Database

Plchová, Helena; Vaculík, Petr; Čeřovská, Noemi; Moravec, Tomáš; Dědič, P.

2015-01-01

Roč. 163, 11-12 (2015), s. 1031-1035 ISSN 0931-1785 R&D Projects: GA MŠk 1M06030 Institutional support: RVO:61389030 Keywords : Czech Republic * phylogeny * Potato virus M Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 0.945, year: 2015

Proceedings of the 3. international symposium on applied microbiology and molecular biology in oil systems: ISMOS 3

Energy Technology Data Exchange (ETDEWEB)

Rooijen, Gijs van; Caffrey, Sean M. [Genome Alberta (Canada); Lund Skovhus, Torben [DTI Oil and Gas (Denmark); Whitby, Corinne [University of Essex (United Kingdom)

2011-07-01

The 3rd international symposium on applied microbiology and molecular biology in oil systems was held in Calgary, Alberta, Canada, from June 13th to June 15th, 2011. This conference, organized by ISMOS TSC, gathered experts to discuss the application of microbial and molecular biology in the hydrocarbon sector. The conference was attended by key players from the oil and gas industry and provided them with the opportunity to learn about some of the latest technologies in areas such as the application of molecular microbiological methods for oil field systems, biodegradation of hydrocarbons in oil production, biofuels and downstream petroleum microbiology and challenges in biofuels and oil sands developments, and to network with their peers and share their expertise. 17 of the 31 papers presented during this conference have been catalogued separately for inclusion in this database.

Molecular biology of hyperthermophilic Archaea.

Science.gov (United States)

van der Oost, J; Ciaramella, M; Moracci, M; Pisani, F M; Rossi, M; de Vos, W M

1998-01-01

The sequences of a number of archaeal genomes have recently been completed, and many more are expected shortly. Consequently, the research of Archaea in general and hyperthermophiles in particular has entered a new phase, with many exciting discoveries to be expected. The wealth of sequence information has already led, and will continue to lead to the identification of many enzymes with unique properties, some of which have potential for industrial applications. Subsequent functional genomics will help reveal fundamental matters such as details concerning the genetic, biochemical and physiological adaptation of extremophiles, and hence give insight into their genomic evolution, polypeptide structure-function relations, and metabolic regulation. In order to optimally exploit many unique features that are now emerging, the development of genetic systems for hyperthermophilic Archaea is an absolute requirement. Such systems would allow the application of this class of Archaea as so-called "cell factories": (i) expression of certain archaeal enzymes for which no suitable conventional (mesophilic bacterial or eukaryal) systems are available, (ii) selection for thermostable variants of potentially interesting enzymes from mesophilic origin, and (iii) the development of in vivo production systems by metabolic engineering. An overview is given of recent insight in the molecular biology of hyperthermophilic Archaea, as well as of a number of promising developments that should result in the generation of suitable genetic systems in the near future.

Molecularly Imprinted Polymers for 5-Fluorouracil Release in Biological Fluids

Directory of Open Access Journals (Sweden)

Franco Alhaique

2007-04-01

Full Text Available The aim of this work was to investigate the possibility of employing Molecularly Imprinted Polymers (MIPs as a controlled release device for 5-fluorouracil (5-FU in biological fluids, especially gastrointestinal ones, compared to Non Imprinted Polymers (NIPs. MIPs were synthesized using methacrylic acid (MAA as functional monomer and ethylene glycol dimethacrylate (EGDMA as crosslinking agent. The capacity of the polymer to recognize and to bind the template selectively in both organic and aqueous media was evaluated. An in vitro release study was performed both in gastrointestinal and in plasma simulating fluids. The imprinted polymers bound much more 5-Fu than the corresponding non-imprinted ones and showed a controlled/sustained drug release, with MIPs release rate being indeed much more sustained than that obtained from NIPs. These polymers represent a potential valid system for drug delivery and this study indicates that the selective binding characteristic of molecularly imprinted polymers is promising for the preparation of novel controlled release drug dosage form.

Lessons learned from the design of chemical space networks and opportunities for new applications

Science.gov (United States)

Vogt, Martin; Stumpfe, Dagmar; Maggiora, Gerald M.; Bajorath, Jürgen

2016-03-01

The concept of chemical space is of fundamental relevance in chemical informatics and computer-aided drug discovery. In a series of articles published in the Journal of Computer- Aided Molecular Design, principles of chemical space design were evaluated, molecular networks proposed as an alternative to conventional coordinate-based chemical reference spaces, and different types of chemical space networks (CSNs) constructed and analyzed. Central to the generation of CSNs was the way in which molecular similarity relationships were assessed and a primary focal point was the network-based representation of biologically relevant chemical space. The design and comparison of CSNs based upon alternative similarity measures can be viewed as an evolutionary path with interesting lessons learned along the way. CSN design has matured to the point that such chemical space representations can be used in practice. In this contribution, highlights from the sequence of CSN design efforts are discussed in context, providing a perspective for future practical applications.

Lessons learned from the design of chemical space networks and opportunities for new applications.

Science.gov (United States)

Vogt, Martin; Stumpfe, Dagmar; Maggiora, Gerald M; Bajorath, Jürgen

2016-03-01

The concept of chemical space is of fundamental relevance in chemical informatics and computer-aided drug discovery. In a series of articles published in the Journal of Computer-Aided Molecular Design, principles of chemical space design were evaluated, molecular networks proposed as an alternative to conventional coordinate-based chemical reference spaces, and different types of chemical space networks (CSNs) constructed and analyzed. Central to the generation of CSNs was the way in which molecular similarity relationships were assessed and a primary focal point was the network-based representation of biologically relevant chemical space. The design and comparison of CSNs based upon alternative similarity measures can be viewed as an evolutionary path with interesting lessons learned along the way. CSN design has matured to the point that such chemical space representations can be used in practice. In this contribution, highlights from the sequence of CSN design efforts are discussed in context, providing a perspective for future practical applications.

Networks In Real Space: Characteristics and Analysis for Biology and Mechanics

Science.gov (United States)

Modes, Carl; Magnasco, Marcelo; Katifori, Eleni

Functional networks embedded in physical space play a crucial role in countless biological and physical systems, from the efficient dissemination of oxygen, blood sugars, and hormonal signals in vascular systems to the complex relaying of informational signals in the brain to the distribution of stress and strain in architecture or static sand piles. Unlike their more-studied abstract cousins, such as the hyperlinked internet, social networks, or economic and financial connections, these networks are both constrained by and intimately connected to the physicality of their real, embedding space. We report on the results of new computational and analytic approaches tailored to these physical networks with particular implications and insights for mammalian organ vasculature.

Extended phase-space methods for enhanced sampling in molecular simulations: a review

Directory of Open Access Journals (Sweden)

Hiroshi eFujisaki

2015-09-01

Full Text Available Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein and protein-DNA/RNA interactions. Straightforward applications however are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of the configuration space. Over the years, several techniques have been designed to overcome this problem and enhance space sampling. Here, we review a class of methods that rely on the idea of extending the set of dynamical variables of the system by adding extra ones associated to functions describing the process under study. In particular, we illustrate the Temperature Accelerated Molecular Dynamics (TAMD, Logarithmic Mean Force Dynamics (LogMFD, andMultiscale Enhanced Sampling (MSES algorithms. We also discuss combinations with techniques for searching reaction paths. We show the advantages presented by this approach and how it allows to quickly sample important regions of the free energy landscape via automatic exploration.

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

[Molecular biology of renal cancer: bases for genetic directed therapy in advanced disease].

Science.gov (United States)

Maroto Rey, José Pablo; Cillán Narvaez, Elena

2013-06-01

There has been expansion of therapeutic options in the management of metastatic renal cell carcinoma due to a better knowledge of the molecular biology of kidney cancers. There are different tumors grouped under the term renal cell carcinoma, being clear cell cancer the most frequent and accounting for 80% of kidney tumors. Mutations in the Von Hippel-Lindau gene can be identified in up to 80% of sporadic clear cell cancer, linking a genetically inheritable disease where vascular tumors are frequent, with renal cell cancer. Other histologic types present specific alterations in molecular pathways, like c-MET in papillary type I tumors, and Fumarase Hydratase in papillary type II tumors. Identification of the molecular alteration for a specific tumor may offer an opportunity for treatment selection based on biomarkers, and, in the future, for developing an engineering designed genetic treatment.

Biospheric Life Support - integrating biological regeneration into protection of humans in space.

Science.gov (United States)

Rocha, Mauricio; Iha, Koshun

2016-07-01

A biosphere stands for a set of biomes (regional biological communities) interacting in a materially closed (though energetically open) ecological system (CES). Earth's biosphere, the thin layer of life on the planet's surface, can be seen as a natural CES- where life "consumables" are regenerated/restored via biological, geological and chemical processes. In Life Sciences, artificial CESs- local ecosystems extracts with varying scales and degrees of closure, are considered convenient/representatives objects of study. For outer space, these concepts have been applied to the issue of life support- a significant consideration as long as distance from Earth increases. In the nineties, growing on the Russian expertise on biological life support, backed by a multidisciplinary science team, the famous Biosphere 2 appeared. That private project innovated, by assembling a set of Earth biomes samples- plus an organic ag one, inside a closed Mars base-like structure, next to 1.5 ha under glass, in Arizona, US. The crew of 8 inside completed their two years contract, though facing setbacks- the system failed, e.g., to produce enough food/air supplies. But their "failures"- if this word can be fairly applied to science endeavors, were as meaningful as their achievements for the future of life support systems (LSS) research. By this period, the Russians had accumulated experience in extended orbital stays, achieving biological outcomes inside their stations- e.g. complete wheat cycles. After reaching the Moon, the US administration decided to change national priorities, putting the space program as part of a "détente" policy, to relieve international tensions. Alongside the US space shuttle program, the Russians were invited to join the new International Space Station (ISS), bringing to that pragmatic project, also their physical/chemical LSS- top air/water regenerative technology at the time. Present US policy keeps the ISS operational, extending its service past its planned

Embryology meets molecular biology: Deciphering the apical ectodermal ridge.

Science.gov (United States)

Verheyden, Jamie M; Sun, Xin

2017-09-15

More than sixty years ago, while studying feather tracks on the shoulder of the chick embryo, Dr. John Saunders used Nile Blue dye to stain the tissue. There, he noticed a darkly stained line of cells that neatly rims the tip of the growing limb bud. Rather than ignoring this observation, he followed it up by removing this tissue and found that it led to a striking truncation of the limb skeletons. This landmark experiment marks the serendipitous discovery of the apical ectodermal ridge (AER), the quintessential embryonic structure that drives the outgrowth of the limb. Dr. Saunders continued to lead the limb field for the next fifty years, not just through his own work, but also by inspiring the next generation of researchers through his infectious love of science. Together, he and those who followed ushered in the discovery of fibroblast growth factor (FGF) as the AER molecule. The seamless marriage of embryology and molecular biology that led to the decoding of the AER serves as a shining example of how discoveries are made for the rest of the developmental biology field. Copyright © 2017 Elsevier Inc. All rights reserved.

Nacimiento y evolución de la bioquímica y la biología molecular en la Comunidad Valenciana (1963-2013)

OpenAIRE

CARBONELL GISBERT, JUAN

2013-01-01

Carbonell Gisbert, J. (2013). Nacimiento y evolución de la bioquímica y la biología molecular en la Comunidad Valenciana (1963-2013). SEBBM. Revista de la Sociedad Española de Bioquímica y Biología Molecular. 178:36-38. http://hdl.handle.net/10251/98796 S 36 38 178

Femtochemistry and femtobiology ultrafast dynamics in molecular science

CERN Document Server

Douhal, Abderrazzak

2002-01-01

This book contains important contributions from top international scientists on the-state-of-the-art of femtochemistry and femtobiology at the beginning of the new millennium. It consists of reviews and papers on ultrafast dynamics in molecular science.The coverage of topics highlights several important features of molecular science from the viewpoint of structure (space domain) and dynamics (time domain). First of all, the book presents the latest developments, such as experimental techniques for understanding ultrafast processes in gas, condensed and complex systems, including biological mol

What Skills Should Students of Undergraduate Biochemistry and Molecular Biology Programs Have upon Graduation?

Science.gov (United States)

White, Harold B.; Benore, Marilee A.; Sumter, Takita F.; Caldwell, Benjamin D.; Bell, Ellis

2013-01-01

Biochemistry and molecular biology (BMB) students should demonstrate proficiency in the foundational concepts of the discipline and possess the skills needed to practice as professionals. To ascertain the skills that should be required, groups of BMB educators met in several focused workshops to discuss the expectations with the ultimate goal of…

Automated Construction of Molecular Active Spaces from Atomic Valence Orbitals.

Science.gov (United States)

Sayfutyarova, Elvira R; Sun, Qiming; Chan, Garnet Kin-Lic; Knizia, Gerald

2017-09-12

We introduce the atomic valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multiconfiguration and multireference (MR) electronic structure calculations. Concretely, the technique constructs active molecular orbitals capable of describing all relevant electronic configurations emerging from a targeted set of atomic valence orbitals (e.g., the metal d orbitals in a coordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-reference wave function (such as from a Hartree-Fock or Kohn-Sham calculations) based on projectors to targeted atomic valence orbitals. We discuss the premises, theory, and implementation of the idea, and several of its variations are tested. To investigate the performance and accuracy, we calculate the excitation energies for various transition-metal complexes in typical application scenarios. Additionally, we follow the homolytic bond breaking process of a Fenton reaction along its reaction coordinate. While the described AVAS technique is not a universal solution to the active space problem, its premises are fulfilled in many application scenarios of transition-metal chemistry and bond dissociation processes. In these cases the technique makes MR calculations easier to execute, easier to reproduce by any user, and simplifies the determination of the appropriate size of the active space required for accurate results.

Program and abstracts of the 25. Annual meeting of the Brazilian Society on Biochemistry and Molecular Biology

International Nuclear Information System (INIS)

1996-01-01

The meeting was about biochemistry and molecular biology.In this meeting it was also discussed the following subjects: biotechnology, metabolism, enzymes, proteins, immunology, drugs and others related topics

Structural and Conformational Chemistry from Electrochemical Molecular Machines. Replicating Biological Functions. A Review.

Science.gov (United States)

Otero, Toribio F

2017-12-14

Each constitutive chain of a conducting polymer electrode acts as a reversible multi-step electrochemical molecular motor: reversible reactions drive reversible conformational movements of the chain. The reaction-driven cooperative actuation of those molecular machines generates, or destroys, inside the film the free volume required to lodge/expel balancing counterions and solvent: reactions drive reversible film volume variations, which basic structural components are here identified and quantified from electrochemical responses. The content of the reactive dense gel (chemical molecular machines, ions and water) mimics that of the intracellular matrix in living functional cells. Reaction-driven properties (composition-dependent properties) and devices replicate biological functions and organs. An emerging technological world of soft, wet, reaction-driven, multifunctional and biomimetic devices and the concomitant zoomorphic or anthropomorphic robots is presented. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular building blocks and their architecture in biologically/environmentally compatible soft matter chemical machinery.

Science.gov (United States)

Toyota, Taro; Banno, Taisuke; Nitta, Sachiko; Takinoue, Masahiro; Nomoto, Tomonori; Natsume, Yuno; Matsumura, Shuichi; Fujinami, Masanori

2014-01-01

This review briefly summarizes recent developments in the construction of biologically/environmentally compatible chemical machinery composed of soft matter. Since environmental and living systems are open systems, chemical machinery must continuously fulfill its functions not only through the influx and generation of molecules but also via the degradation and dissipation of molecules. If the degradation or dissipation of soft matter molecular building blocks and biomaterial molecules/polymers can be achieved, soft matter particles composed of them can be used to realize chemical machinery such as selfpropelled droplets, drug delivery carriers, tissue regeneration scaffolds, protocell models, cell-/tissuemarkers, and molecular computing systems.

Third Jesús Culebras Lecture: Molecular Biology and Clinical Nutrition; ¿where do we stand and where do we go?

OpenAIRE

Gil, Ángel

2013-01-01

Nutrition plays a fundamental role in the maintenance of health and the treatment of disease, and serves as the crossroads for many disciplines. Biochemistry and Molecular Biology represents a key brand of science to ascertain the mechanism of action of nutrients and other food bioactive compounds in health and disease. The aim of the present Jesús M. Culebras lecture is to consider the future of the relationships between Molecular Biology and Clinical Nutrition and to discuss the use of mole...

Molecular and cellular biology of cerebral arteriovenous malformations: a review of current concepts and future trends in treatment.

Science.gov (United States)

Rangel-Castilla, Leonardo; Russin, Jonathan J; Martinez-Del-Campo, Eduardo; Soriano-Baron, Hector; Spetzler, Robert F; Nakaji, Peter

2014-09-01

Arteriovenous malformations (AVMs) are classically described as congenital static lesions. However, in addition to rupturing, AVMs can undergo growth, remodeling, and regression. These phenomena are directly related to cellular, molecular, and physiological processes. Understanding these relationships is essential to direct future diagnostic and therapeutic strategies. The authors performed a search of the contemporary literature to review current information regarding the molecular and cellular biology of AVMs and how this biology will impact their potential future management. A PubMed search was performed using the key words "genetic," "molecular," "brain," "cerebral," "arteriovenous," "malformation," "rupture," "management," "embolization," and "radiosurgery." Only English-language papers were considered. The reference lists of all papers selected for full-text assessment were reviewed. Current concepts in genetic polymorphisms, growth factors, angiopoietins, apoptosis, endothelial cells, pathophysiology, clinical syndromes, medical treatment (including tetracycline and microRNA-18a), radiation therapy, endovascular embolization, and surgical treatment as they apply to AVMs are discussed. Understanding the complex cellular biology, physiology, hemodynamics, and flow-related phenomena of AVMs is critical for defining and predicting their behavior, developing novel drug treatments, and improving endovascular and surgical therapies.

Characterization of microbial communities in pest colonized books by molecular biology tools

Directory of Open Access Journals (Sweden)

Franco Palla

2011-08-01

Full Text Available This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR, sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods (in vitro culture and morphological analyses (OM, SEM, CLSM, in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.

Intraductal papillary-mucinous neoplasia of the pancreas: Histopathology and molecular biology.

Science.gov (United States)

Verbeke, Caroline S

2010-10-27

Intraductal papillary-mucinous neoplasm (IPMN) of the pancreas is a clinically and morphologically distinctive precursor lesion of pancreatic cancer, characterized by gradual progression through a sequence of neoplastic changes. Based on the nature of the constituting neoplastic epithelium, degree of dysplasia and location within the pancreatic duct system, IPMNs are divided in several types which differ in their biological properties and clinical outcome. Molecular analysis and recent animal studies suggest that IPMNs develop in the context of a field-defect and reveal their possible relationship with other neoplastic precursor lesions of pancreatic cancer.

Towards an identification of the pyrethroid pharmacophore. A molecular modelling study of some pyrethroid esters

DEFF Research Database (Denmark)

Byberg, J R; Jørgensen, Flemming Steen; Klemmensen, P D

1987-01-01

A molecular modelling and computer graphics study of a series of pyrethroid insecticides has been carried out. The three-dimensional arrangement of the groups essential for the biological activity (pharmacophore) has been identified for the acid and the alcohol moieties, respectively....... These pharmacophores are based on the relationship between molecular structure and biological activity for a number of pyrethroid esters. The pharmacophores, which describe the relative location in space of the unsaturated systems, the dimethyl groups and the ester moiety, may be useful in the design of novel...... compounds with pyrethroid activity....

Molecular genetics of glioblastomas: defining subtypes and understanding the biology.

Science.gov (United States)

Renault, Ilana Zalcberg; Golgher, Denise

2015-02-01

Despite comprehensive therapy, which includes surgery, radiotherapy, and chemotherapy, the prognosis of glioblastoma multiforme is very poor. Diagnosed individuals present an average of 12 to 18 months of life. This article provides an overview of the molecular genetics of these tumors. Despite the overwhelming amount of data available, so far little has been translated into real benefits for the patient. Because this is such a complex topic, the goal is to point out the main alterations in the biological pathways that lead to tumor formation, and how this can contribute to the development of better therapies and clinical care. Copyright © 2015 Elsevier Inc. All rights reserved.

Chapter 24: the coming of molecular biology and its impact on clinical neurology.

Science.gov (United States)

Smith, Christopher U M

2010-01-01

Although the chemical study of the nervous system dates back well into the 19th century, molecular biology and especially molecular neurobiology only began to be established in the second half of the 20th century. This chapter reviews their impact on clinical neuroscience during the 50 years since Watson and Crick published their seminal paper. After a short review of the part played by F.O. Schmitt in establishing molecular neuroscience the chapter outlines work that led to a detailed understanding of the biochemical structure and function of nerve cell membranes and their embedded channel proteins, receptors, and other molecules. The chapter then turns to the numerous pathologies that result from disorders of these elements: the various channel and gap-junction pathologies. The chapter continues with a discussion of some of the diseases caused by defective DNA, especially the trinucleotide repeat expansion diseases (TREDs) and ends with a short account of the development of molecular approaches to prion diseases, myasthenia gravis, and the neurodegenerative diseases of old age. Francis Bacon said long ago that "knowledge is power." The hope is that increasing molecular knowledge will help cure some of the human suffering seen in the neurological ward and clinic.

Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology (Final Report)

Science.gov (United States)

EPA announced the release of the final report, Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology. This report describes new approaches that are faster, less resource intensive, and more robust that can help ...

A Systems Biology Approach Reveals Converging Molecular Mechanisms that Link Different POPs to Common Metabolic Diseases.

Science.gov (United States)

Ruiz, Patricia; Perlina, Ally; Mumtaz, Moiz; Fowler, Bruce A

2016-07-01

A number of epidemiological studies have identified statistical associations between persistent organic pollutants (POPs) and metabolic diseases, but testable hypotheses regarding underlying molecular mechanisms to explain these linkages have not been published. We assessed the underlying mechanisms of POPs that have been associated with metabolic diseases; three well-known POPs [2,3,7,8-tetrachlorodibenzodioxin (TCDD), 2,2´,4,4´,5,5´-hexachlorobiphenyl (PCB 153), and 4,4´-dichlorodiphenyldichloroethylene (p,p´-DDE)] were studied. We used advanced database search tools to delineate testable hypotheses and to guide laboratory-based research studies into underlying mechanisms by which this POP mixture could produce or exacerbate metabolic diseases. For our searches, we used proprietary systems biology software (MetaCore™/MetaDrug™) to conduct advanced search queries for the underlying interactions database, followed by directional network construction to identify common mechanisms for these POPs within two or fewer interaction steps downstream of their primary targets. These common downstream pathways belong to various cytokine and chemokine families with experimentally well-documented causal associations with type 2 diabetes. Our systems biology approach allowed identification of converging pathways leading to activation of common downstream targets. To our knowledge, this is the first study to propose an integrated global set of step-by-step molecular mechanisms for a combination of three common POPs using a systems biology approach, which may link POP exposure to diseases. Experimental evaluation of the proposed pathways may lead to development of predictive biomarkers of the effects of POPs, which could translate into disease prevention and effective clinical treatment strategies. Ruiz P, Perlina A, Mumtaz M, Fowler BA. 2016. A systems biology approach reveals converging molecular mechanisms that link different POPs to common metabolic diseases. Environ

Intracellular antibody capture: A molecular biology approach to inhibitors of protein-protein interactions.

Science.gov (United States)

Zhang, Jing; Rabbitts, Terence H

2014-11-01

Many proteins of interest in basic biology, translational research studies and for clinical targeting in diseases reside inside the cell and function by interacting with other macromolecules. Protein complexes control basic processes such as development and cell division but also abnormal cell growth when mutations occur such as found in cancer. Interfering with protein-protein interactions is an important aspiration in both basic and disease biology but small molecule inhibitors have been difficult and expensive to isolate. Recently, we have adapted molecular biology techniques to develop a simple set of protocols for isolation of high affinity antibody fragments (in the form of single VH domains) that function within the reducing environment of higher organism cells and can bind to their target molecules. The method called Intracellular Antibody Capture (IAC) has been used to develop inhibitory anti-RAS and anti-LMO2 single domains that have been used for target validation of these antigens in pre-clinical cancer models and illustrate the efficacy of the IAC approach to generation of drug surrogates. Future use of inhibitory VH antibody fragments as drugs in their own right (we term these macrodrugs to distinguish them from small molecule drugs) requires their delivery to target cells in vivo but they can also be templates for small molecule drug development that emulate the binding sites of the antibody fragments. This article is part of a Special Issue entitled: Recent advances in molecular engineering of antibody. Copyright © 2014 Elsevier B.V. All rights reserved.

The molecular biology of prostate cancer: current understanding and clinical implications.

Science.gov (United States)

Gandhi, Jason; Afridi, Adil; Vatsia, Sohrab; Joshi, Gargi; Joshi, Gunjan; Kaplan, Steven A; Smith, Noel L; Khan, Sardar Ali

2018-04-01

With continuous progress over the past few decades in understanding diagnosis, treatment, and genetics, much has been learned about the prostate cancer-diagnosed genome. A comprehensive MEDLINE® and Google scholar literature search was conducted using keyword variations relating to the genetics of prostate cancer such as chromosomal alterations, androgen receptor, castration-resistant, inheritance, polymorphisms, oncogenes, metastasis, biomarkers, and immunotherapy. Traditionally, androgen receptors (AR) have been the focus of research. Recently, identification of recurrent chromosomal alterations that lead to either multiplication of regions (gain-of-function) or deletion of regions (loss-of-function) has opened the door to greater genetic accessibility. These chromosomal aberrations lead to variation in copy number and gene expression. Some of these chromosomal alterations are inherited, while others undergo somatic mutations during disease progression. Inherited gene mutations that make one susceptible to prostate cancer have been identified with familial-linked studies. Somatic genes that progress tumorigenesis have also been identified. Research on the molecular biology of prostate cancer has characterized these genes into tumor suppressor genes or oncogenes. Additionally, genome-wide assay studies have identified many high-risk single-nucleotide polymorphisms recurrent throughout the prostate cancer-diagnosed genome. Castration-resistant prostate cancer is the most aggressive form of prostate cancer, and its research has elucidated many types of mutations associated with AR itself, including enhanced expression and amplification, point mutations, and alternative splicing. Understanding the molecular biology of prostate cancer has permitted more accurate identification using advanced biomarkers and therapy for aggressive forms using immunotherapy. An age-related disease, prostate cancer commands profound attention. With increasing life expectancy and the

Identification of circulating prostate cancer cells: A challenge to the clinical implementation of molecular biology (Review)

NARCIS (Netherlands)

Schamhart, Denis H. J.; Maiazza, Ruth; Kurth, Karl-Heinz

2005-01-01

Conventional diagnosis of prostate cancer does not appear to be sensitive enough to differentiate pre-operatively between organ-confined and extracapsular disease. New technologies. arising from the field of molecular biology, have been introduced to improve diagnosis and their implementation into

Spaces of the possible: universal Darwinism and the wall between technological and biological innovation

Science.gov (United States)

Wagner, Andreas; Rosen, William

2014-01-01

Innovations in biological evolution and in technology have many common features. Some of them involve similar processes, such as trial and error and horizontal information transfer. Others describe analogous outcomes such as multiple independent origins of similar innovations. Yet others display similar temporal patterns such as episodic bursts of change separated by periods of stasis. We review nine such commonalities, and propose that the mathematical concept of a space of innovations, discoveries or designs can help explain them. This concept can also help demolish a persistent conceptual wall between technological and biological innovation. PMID:24850903

Preservation of pathological tissue specimens by freeze-drying for immunohistochemical staining and various molecular biological analyses.

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Matsuo, S; Sugiyama, T; Okuyama, T; Yoshikawa, K; Honda, K; Takahashi, R; Maeda, S

1999-05-01

Conditions of preserving DNA, RNA and protein in pathological specimens are of great importance as degradation of such macromolecules would critically affect results of molecular biological analysis. The feasibility of freeze-drying as a means of preserving pathological tissue samples for molecular analysis has previously been shown. In the present study, further tests on long-term storage conditions and analyses of freeze-dried samples by polymerase chain reaction (PCR), reverse transcriptase (RT)-PCR, western blotting and immunohistochemistry are reported. Rat chromosomal DNA of freeze-dried samples stored for 4 years showed slight degradation while RNA degradation was more prominently seen at an earlier stage of storage. However, these 4 year DNA and RNA samples were still able to serve as a template for some PCR and RT-PCR analyses, respectively. Overexpression of c-erbB-2 and p53 protein was demonstrated by western blotting and immunohistochemical staining using freeze-dried human breast cancer tissues. Although macromolecules in freeze-dried samples degrade to some extent during the preservation period, they should still be of value for certain molecular biological analyses and morphological examination; hence, providing more convenient and inexpensive ways of pathological tissue storage.

THE EVALUATION OF A TOOL FOR DISSEMINATION OF BIOTECHNOLOGY AND MOLECULAR BIOLOGY CONCEPTS IN FORMAL EDUCATION

Directory of Open Access Journals (Sweden)

F.M. Escanhoela

2007-05-01

Full Text Available Since 2003, the CBME Scientific Dissemination Coordination hasdeveloped a project related to the production and distribution of a scientificdissemination newspaper, called CBME InFORMAÇÃO, directed to high-schoolstudents and teachers. It is a quarterly publication and shows the concepts andadvances of studies in molecular biology and biotechnology. In order to evaluatethe newspaper, a research was accomplished in 2005. It involved 177 studentsfrom six high schools of São Carlos and region. In addition, opinions of fivescience teachers that worked with the newspaper in their classrooms, as well aseight Biology undergraduates were collected. The teachers received somequestionnaires that had to be answered by them and their students after a specifyactivity with the periodical – basically, the activities consisted of three stages:individual reading of the newspaper; formulation of questions by the teacher and,finally, group discussion on the chosen theme. The research confirmed theimportance of the use of the periodical as a tool in the formation of critical readersof facts related to the biotechnology and molecular biology, what should contributewith the citizenship development in the students. Moreover, it provided a possibilityto reorganize the periodical.

Biomarkers of Aging: From Function to Molecular Biology

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Karl-Heinz Wagner

2016-06-01

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

The Molecular Biology of Feline Immunodeficiency Virus (FIV

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Andrew M. L. Lever

2011-11-01

Full Text Available Feline immunodeficiency virus (FIV is widespread in feline populations and causes an AIDS-like illness in domestic cats. It is highly prevalent in several endangered feline species. In domestic cats FIV infection is a valuable small animal model for HIV infection. In recent years there has been a significant increase in interest in FIV, in part to exploit this, but also because of the potential it has as a human gene therapy vector. Though much less studied than HIV there are many parallels in the replication of the two viruses, but also important differences and, despite their likely common origin, the viruses have in some cases used alternative strategies to overcome similar problems. Recent advances in understanding the structure and function of FIV RNA and proteins and their interactions has enhanced our knowledge of FIV replication significantly, however, there are still many gaps. This review summarizes our current knowledge of FIV molecular biology and its similarities with, and differences from, other lentiviruses.

The molecular biology of feline immunodeficiency virus (FIV).

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Kenyon, Julia C; Lever, Andrew M L

2011-11-01

Feline immunodeficiency virus (FIV) is widespread in feline populations and causes an AIDS-like illness in domestic cats. It is highly prevalent in several endangered feline species. In domestic cats FIV infection is a valuable small animal model for HIV infection. In recent years there has been sa significant increase in interest in FIV, in part to exploit this, but also because of the potential it has as a human gene therapy vector. Though much less studied than HIV there are many parallels in the replication of the two viruses, but also important differences and, despite their likely common origin, the viruses have in some cases used alternative strategies to overcome similar problems. Recent advances in understanding the structure and function of FIV RNA and proteins and their interactions has enhanced our knowledge of FIV replication significantly, however, there are still many gaps. This review summarizes our current knowledge of FIV molecular biology and its similarities with, and differences from, other lentiviruses.

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

Science.gov (United States)

Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

2015-02-01

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

Science.gov (United States)

Ocak, S; Sos, M L; Thomas, R K; Massion, P P

2009-08-01

During the last decade, high-throughput technologies including genomic, epigenomic, transcriptomic and proteomic have been applied to further our understanding of the molecular pathogenesis of this heterogeneous disease, and to develop strategies that aim to improve the management of patients with lung cancer. Ultimately, these approaches should lead to sensitive, specific and noninvasive methods for early diagnosis, and facilitate the prediction of response to therapy and outcome, as well as the identification of potential novel therapeutic targets. Genomic studies were the first to move this field forward by providing novel insights into the molecular biology of lung cancer and by generating candidate biomarkers of disease progression. Lung carcinogenesis is driven by genetic and epigenetic alterations that cause aberrant gene function; however, the challenge remains to pinpoint the key regulatory control mechanisms and to distinguish driver from passenger alterations that may have a small but additive effect on cancer development. Epigenetic regulation by DNA methylation and histone modifications modulate chromatin structure and, in turn, either activate or silence gene expression. Proteomic approaches critically complement these molecular studies, as the phenotype of a cancer cell is determined by proteins and cannot be predicted by genomics or transcriptomics alone. The present article focuses on the technological platforms available and some proposed clinical applications. We illustrate herein how the "-omics" have revolutionised our approach to lung cancer biology and hold promise for personalised management of lung cancer.

Application of molecular biology of differentiated thyroid cancer for clinical prognostication.

Science.gov (United States)

Marotta, Vincenzo; Sciammarella, Concetta; Colao, Annamaria; Faggiano, Antongiulio

2016-11-01

Although cancer outcome results from the interplay between genetics and environment, researchers are making a great effort for applying molecular biology in the prognostication of differentiated thyroid cancer (DTC). Nevertheless, role of molecular characterisation in the prognostic setting of DTC is still nebulous. Among the most common and well-characterised genetic alterations related to DTC, including mutations of BRAF and RAS and RET rearrangements, BRAF V600E is the only mutation showing unequivocal association with clinical outcome. Unfortunately, its accuracy is strongly limited by low specificity. Recently, the introduction of next-generation sequencing techniques led to the identification of TERT promoter and TP53 mutations in DTC. These genetic abnormalities may identify a small subgroup of tumours with highly aggressive behaviour, thus improving specificity of molecular prognostication. Although knowledge of prognostic significance of TP53 mutations is still anecdotal, mutations of the TERT promoter have showed clear association with clinical outcome. Nevertheless, this genetic marker needs to be analysed according to a multigenetic model, as its prognostic effect becomes negligible when present in isolation. Given that any genetic alteration has demonstrated, taken alone, enough specificity, the co-occurrence of driving mutations is emerging as an independent genetic signature of aggressiveness, with possible future application in clinical practice. DTC prognostication may be empowered in the near future by non-tissue molecular prognosticators, including circulating BRAF V600E and miRNAs. Although promising, use of these markers needs to be refined by the technical sight, and the actual prognostic value is still yet to be validated. © 2016 Society for Endocrinology.

RT-PCR Protocols - Methods in Molecular Biology

Directory of Open Access Journals (Sweden)

Manuela Monti

2011-03-01

Full Text Available “The first record I have of it, is when I made a computer file which I usually did whenever I had an idea, that would have been on the Monday when I got back, and I called it Chain Reaction.POL, meaning polymerase. That was the identifier for it and later I called the thing the Polymerase Chain Reaction, which a lot of people thought was a dumb name for it, but it stuck, and it became PCR”. With these words the Nobel prize winner, Kary Mullis, explains how he named the PCR: one of the most important techniques ever invented and currently used in molecular biology. This book “RT-PCR Protocols” covers a wide range of aspects important for the setting of a PCR experiment for both beginners and advanced users. In my opinion the book is very well structured in three different sections. The first one describes the different technologies now available, like competitive RT-PCR, nested RT-PCR or RT-PCR for cloning. An important part regards the usage of PCR in single cell mouse embryos, stressing how important...........

Measurement issues associated with quantitative molecular biology analysis of complex food matrices for the detection of food fraud.

Science.gov (United States)

Burns, Malcolm; Wiseman, Gordon; Knight, Angus; Bramley, Peter; Foster, Lucy; Rollinson, Sophie; Damant, Andrew; Primrose, Sandy

2016-01-07

Following a report on a significant amount of horse DNA being detected in a beef burger product on sale to the public at a UK supermarket in early 2013, the Elliott report was published in 2014 and contained a list of recommendations for helping ensure food integrity. One of the recommendations included improving laboratory testing capacity and capability to ensure a harmonised approach for testing for food authenticity. Molecular biologists have developed exquisitely sensitive methods based on the polymerase chain reaction (PCR) or mass spectrometry for detecting the presence of particular nucleic acid or peptide/protein sequences. These methods have been shown to be specific and sensitive in terms of lower limits of applicability, but they are largely qualitative in nature. Historically, the conversion of these qualitative techniques into reliable quantitative methods has been beset with problems even when used on relatively simple sample matrices. When the methods are applied to complex sample matrices, as found in many foods, the problems are magnified resulting in a high measurement uncertainty associated with the result which may mean that the assay is not fit for purpose. However, recent advances in the technology and the understanding of molecular biology approaches have further given rise to the re-assessment of these methods for their quantitative potential. This review focuses on important issues for consideration when validating a molecular biology assay and the various factors that can impact on the measurement uncertainty of a result associated with molecular biology approaches used in detection of food fraud, with a particular focus on quantitative PCR-based and proteomics assays.

Automated Miniaturized Instrument for Space Biology Applications and the Monitoring of the Astronauts Health Onboard the ISS

Science.gov (United States)

Karouia, Fathi; Peyvan, Kia; Danley, David; Ricco, Antonio J.; Santos, Orlando; Pohorille, Andrew

2011-01-01

Human space travelers experience a unique environment that affects homeostasis and physiologic adaptation. The spacecraft environment subjects the traveler to noise, chemical and microbiological contaminants, increased radiation, and variable gravity forces. As humans prepare for long-duration missions to the International Space Station (ISS) and beyond, effective measures must be developed, verified and implemented to ensure mission success. Limited biomedical quantitative capabilities are currently available onboard the ISS. Therefore, the development of versatile instruments to perform space biological analysis and to monitor astronauts' health is needed. We are developing a fully automated, miniaturized system for measuring gene expression on small spacecraft in order to better understand the influence of the space environment on biological systems. This low-cost, low-power, multi-purpose instrument represents a major scientific and technological advancement by providing data on cellular metabolism and regulation. The current system will support growth of microorganisms, extract and purify the RNA, hybridize it to the array, read the expression levels of a large number of genes by microarray analysis, and transmit the measurements to Earth. The system will help discover how bacteria develop resistance to antibiotics and how pathogenic bacteria sometimes increase their virulence in space, facilitating the development of adequate countermeasures to decrease risks associated with human spaceflight. The current stand-alone technology could be used as an integrated platform onboard the ISS to perform similar genetic analyses on any biological systems from the tree of life. Additionally, with some modification the system could be implemented to perform real-time in-situ microbial monitoring of the ISS environment (air, surface and water samples) and the astronaut's microbiome using 16SrRNA microarray technology. Furthermore, the current system can be enhanced

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure.

Science.gov (United States)

Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

2016-05-17

Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

Science.gov (United States)

Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

2016-05-01

Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

Artificial intelligence in molecular biology: a review and assessment.

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Rawlings, C J; Fox, J P

1994-06-29

Over the past ten years, molecular biologists and computer scientists have experimented with various computational methods developed in artificial intelligence (AI). AI research has yielded a number of novel technologies, which are typified by an emphasis on symbolic (non-numerical) programming methods aimed at problems which are not amenable to classical algorithmic solutions. Prominent examples include knowledge-based and expert systems, qualitative simulation and artificial neural networks and other automated learning techniques. These methods have been applied to problems in data analysis, construction of advanced databases and modelling of biological systems. Practical results are now being obtained, notably in the recognition of active genes in genomic sequences, the assembly of physical and genetic maps and protein structure prediction. This paper outlines the principal methods, surveys the findings to date, and identifies the promising trends and current limitations.

Solid State Pathways towards Molecular Complexity in Space

Science.gov (United States)

Linnartz, Harold; Bossa, Jean-Baptiste; Bouwman, Jordy; Cuppen, Herma M.; Cuylle, Steven H.; van Dishoeck, Ewine F.; Fayolle, Edith C.; Fedoseev, Gleb; Fuchs, Guido W.; Ioppolo, Sergio; Isokoski, Karoliina; Lamberts, Thanja; Öberg, Karin I.; Romanzin, Claire; Tenenbaum, Emily; Zhen, Junfeng

2011-12-01

It has been a long standing problem in astrochemistry to explain how molecules can form in a highly dilute environment such as the interstellar medium. In the last decennium more and more evidence has been found that the observed mix of small and complex, stable and highly transient species in space is the cumulative result of gas phase and solid state reactions as well as gas-grain interactions. Solid state reactions on icy dust grains are specifically found to play an important role in the formation of the more complex ``organic'' compounds. In order to investigate the underlying physical and chemical processes detailed laboratory based experiments are needed that simulate surface reactions triggered by processes as different as thermal heating, photon (UV) irradiation and particle (atom, cosmic ray, electron) bombardment of interstellar ice analogues. Here, some of the latest research performed in the Sackler Laboratory for Astrophysics in Leiden, the Netherlands is reviewed. The focus is on hydrogenation, i.e., H-atom addition reactions and vacuum ultraviolet irradiation of interstellar ice analogues at astronomically relevant temperatures. It is shown that solid state processes are crucial in the chemical evolution of the interstellar medium, providing pathways towards molecular complexity in space.

Molecular ions in the laboratory and in space

Energy Technology Data Exchange (ETDEWEB)

McCarthy, Michael C. [Atomic and Molecular Physics Division, Harvard-Smithsonian Center for Astrophysics, Cambridge, Massachusetts, 02138 (United States)

2015-01-22

Molecular ions play a central role in the gas-phase chemistry of the interstellar medium; they also provide information on the physical conditions in astronomical sources (e.g., fractional ionization), and in some cases can be used to infer the abundance of nonpolar molecules such as N{sub 2} and CO{sub 2} which can not be observed in the radio band. During the past four years, the rotational spectra of six carbon-chain anions (C{sub 2}H{sup −}, C{sub 4}H{sup −}, C{sub 6}H{sup −}, C{sub 8}H{sup −}, CN{sup −}, C{sub 3}N{sup −}), NCO{sup −} and seven protonated species (HSCO{sup +}, HSCS{sup +}, cis- and trans-HOSO{sup +}, H{sub 2}NCO{sup +}, HNCOH{sup +}, and HNNO{sup +}) have been detected in our laboratory. On the basis of dedicated astronomical searches, all of the carbon-chain anions except C{sub 2}H{sup −} have now been identified in space. In addition to highlighting recent work on carbon-chain anions and protonated HSO{sub 2}{sup +}, efforts to better understand the distribution of anions in space using C{sub 6}H{sup −} as a tracer for negative charge are described.

Imaging modes of atomic force microscopy for application in molecular and cell biology.

Science.gov (United States)

Dufrêne, Yves F; Ando, Toshio; Garcia, Ricardo; Alsteens, David; Martinez-Martin, David; Engel, Andreas; Gerber, Christoph; Müller, Daniel J

2017-04-06

Atomic force microscopy (AFM) is a powerful, multifunctional imaging platform that allows biological samples, from single molecules to living cells, to be visualized and manipulated. Soon after the instrument was invented, it was recognized that in order to maximize the opportunities of AFM imaging in biology, various technological developments would be required to address certain limitations of the method. This has led to the creation of a range of new imaging modes, which continue to push the capabilities of the technique today. Here, we review the basic principles, advantages and limitations of the most common AFM bioimaging modes, including the popular contact and dynamic modes, as well as recently developed modes such as multiparametric, molecular recognition, multifrequency and high-speed imaging. For each of these modes, we discuss recent experiments that highlight their unique capabilities.

Development of a Semester-Long, Inquiry-Based Laboratory Course in Upper-Level Biochemistry and Molecular Biology

Science.gov (United States)

Murthy, Pushpalatha P. N.; Thompson, Martin; Hungwe, Kedmon

2014-01-01

A semester-long laboratory course was designed and implemented to familiarize students with modern biochemistry and molecular biology techniques. The designed format involved active student participation, evaluation of data, and critical thinking, and guided students to become independent researchers. The first part of the course focused on…

On The Development of Biophysical Models for Space Radiation Risk Assessment

Science.gov (United States)

Cucinotta, F. A.; Dicello, J. F.

1999-01-01

Experimental techniques in molecular biology are being applied to study biological risks from space radiation. The use of molecular assays presents a challenge to biophysical models which in the past have relied on descriptions of energy deposition and phenomenological treatments of repair. We describe a biochemical kinetics model of cell cycle control and DNA damage response proteins in order to model cellular responses to radiation exposures. Using models of cyclin-cdk, pRB, E2F's, p53, and GI inhibitors we show that simulations of cell cycle populations and GI arrest can be described by our biochemical approach. We consider radiation damaged DNA as a substrate for signal transduction processes and consider a dose and dose-rate reduction effectiveness factor (DDREF) for protein expression.

Characterization of Pathogenic Human MSH2 Missense Mutations Using Yeast as a Model System: A Laboratory Course in Molecular Biology

Science.gov (United States)

Gammie, Alison E.; Erdeniz, Naz

2004-01-01

This work describes the project for an advanced undergraduate laboratory course in cell and molecular biology. One objective of the course is to teach students a variety of cellular and molecular techniques while conducting original research. A second objective is to provide instruction in science writing and data presentation by requiring…

2010 CELL AND MOLECULAR FUNGAL BIOLOGY GORDON RESEARCH CONFERENCE, JUNE 13-18, 2010

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Michelle Momany

2010-06-18

The Cellular and Molecular Fungal Biology Conference provides a forum for presentation of the latest advances in fungal research with an emphasis on filamentous fungi. This open-registration scientific meeting brings together the leading scientists from academia, government and industry to discuss current research results and future directions at Holderness School, an outstanding venue for scientific interaction. A key objective of the conference is to foster interaction among scientists working on model fungi such as Saccharomyces cerevisiae, Schizosaccharomyces pombe, Neurospora crassa and Aspergillus nidulans and scientists working on a variety of filamentous fungi whose laboratory tractability is often inversely proportional to their medical, industrial or ecological importance. Sessions will be devoted to Systems Biology, Fungi and Cellulosic Biomass, Small RNAs, Population Genomics, Symbioses, Pathogenesis, Membrane Trafficking and Polarity, and Cytoskeleton and Motors. A session will also be devoted to hot topics picked from abstracts. The CMFB conference provides a unique opportunity to examine the breadth of fungal biology in a small meeting format that encourages in-depth discussion among the attendees.

Obstructive renal injury: from fluid mechanics to molecular cell biology.

Science.gov (United States)

Ucero, Alvaro C; Gonçalves, Sara; Benito-Martin, Alberto; Santamaría, Beatriz; Ramos, Adrian M; Berzal, Sergio; Ruiz-Ortega, Marta; Egido, Jesus; Ortiz, Alberto

2010-04-22

Urinary tract obstruction is a frequent cause of renal impairment. The physiopathology of obstructive nephropathy has long been viewed as a mere mechanical problem. However, recent advances in cell and systems biology have disclosed a complex physiopathology involving a high number of molecular mediators of injury that lead to cellular processes of apoptotic cell death, cell injury leading to inflammation and resultant fibrosis. Functional studies in animal models of ureteral obstruction using a variety of techniques that include genetically modified animals have disclosed an important role for the renin-angiotensin system, transforming growth factor-β1 (TGF-β1) and other mediators of inflammation in this process. In addition, high throughput techniques such as proteomics and transcriptomics have identified potential biomarkers that may guide clinical decision-making.

KRAS and BRAF Mutation Detection: Is Immunohistochemistry a Possible Alternative to Molecular Biology in Colorectal Cancer?

Directory of Open Access Journals (Sweden)

Nicolas Piton

2015-01-01

Full Text Available KRAS genotyping is mandatory in metastatic colorectal cancer treatment prior to undertaking antiepidermal growth factor receptor (EGFR monoclonal antibody therapy. BRAF V600E mutation is often present in colorectal carcinoma with CpG island methylator phenotype and microsatellite instability. Currently, KRAS and BRAF evaluation is based on molecular biology techniques such as SNaPshot or Sanger sequencing. As molecular testing is performed on formalin-fixed paraffin-embedded (FFPE samples, immunodetection would appear to be an attractive alternative for detecting mutations. Thus, our objective was to assess the validity of KRAS and BRAF immunodetection of mutations compared with the genotyping reference method in colorectal adenocarcinoma. KRAS and BRAF genotyping was assessed by SNaPshot. A rabbit anti-human KRAS polyclonal antibody was tested on 33 FFPE colorectal tumor samples with known KRAS status. Additionally, a mouse anti-human BRAF monoclonal antibody was tested on 30 FFPE tumor samples with known BRAF status. KRAS immunostaining demonstrated both poor sensitivity (27% and specificity (64% in detecting KRAS mutation. Conversely, BRAF immunohistochemistry showed perfect sensitivity (100% and specificity (100% in detecting V600E mutation. Although molecular biology remains the reference method for detecting KRAS mutation, immunohistochemistry could be an attractive method for detecting BRAF V600E mutation in colorectal cancer.

KRAS and BRAF Mutation Detection: Is Immunohistochemistry a Possible Alternative to Molecular Biology in Colorectal Cancer?

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Borrini, Francesco; Bolognese, Antonio; Lamy, Aude; Sabourin, Jean-Christophe

2015-01-01

KRAS genotyping is mandatory in metastatic colorectal cancer treatment prior to undertaking antiepidermal growth factor receptor (EGFR) monoclonal antibody therapy. BRAF V600E mutation is often present in colorectal carcinoma with CpG island methylator phenotype and microsatellite instability. Currently, KRAS and BRAF evaluation is based on molecular biology techniques such as SNaPshot or Sanger sequencing. As molecular testing is performed on formalin-fixed paraffin-embedded (FFPE) samples, immunodetection would appear to be an attractive alternative for detecting mutations. Thus, our objective was to assess the validity of KRAS and BRAF immunodetection of mutations compared with the genotyping reference method in colorectal adenocarcinoma. KRAS and BRAF genotyping was assessed by SNaPshot. A rabbit anti-human KRAS polyclonal antibody was tested on 33 FFPE colorectal tumor samples with known KRAS status. Additionally, a mouse anti-human BRAF monoclonal antibody was tested on 30 FFPE tumor samples with known BRAF status. KRAS immunostaining demonstrated both poor sensitivity (27%) and specificity (64%) in detecting KRAS mutation. Conversely, BRAF immunohistochemistry showed perfect sensitivity (100%) and specificity (100%) in detecting V600E mutation. Although molecular biology remains the reference method for detecting KRAS mutation, immunohistochemistry could be an attractive method for detecting BRAF V600E mutation in colorectal cancer. PMID:25983749

Churg-Strauss vasculitis and idiopathic hypereosinophyl syndrome: role of molecular biology in the differential diagnosis of hypereosinophyl syndrome

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A. d'Ascanio

2011-09-01

Full Text Available Objective: Hypereosinophilic syndromes are a heterogeneous group of uncommon disorders characterized by the presence of marked peripheral blood eosinophilia, tissue eosinophilia, or both, resulting in a wide variety of clinical manifestations, often without an identifiable cause. Churg-Strauss syndrome is a systemic vasculitis characterized by prominent peripheral eosinophilia, asthma and systemic involvement. The presence of mild to severe eosinophilia and systemic involvement raise the search of many trigger factor that need to be ruled out. Distinguishing CSS from idiopathic hypereosinophilic syndrome may be particularly challenging, especially in ANCA negative patients. Methods: The aim of the present study was to present a small case series of patients referred to a Rheumatology Unit for mild to severe eosinophilia and signs and symptoms of systemic involvement and to outline the clinical significance of molecular biology in the work-up of hypereosinophilia. Results: Eleven patients with moderate to severe peripheral eosinophylia, were referred to our Unit from 1996 to 2007. Female to male ratio was 7/4, mean age 40.54 (range 22-75. Three out of eleven patients resulted positive for molecular biology. The diagnosis of idiopathic hypereosinophylia was confirmed in one out of three on the basis of the clinical picture and bone marrow biopsy. Conclusions: Molecular biology may be useful in the screening and in the follow-up of a new hypereosinophylic patient.

Cell Culture in Microgravity: Opening the Door to Space Cell Biology

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Pellis, Neal R.; Dawson, David L. (Technical Monitor)

1999-01-01

Adaptational response of human cell populations to microgravity is investigated using simulation, short-term Shuttle experiments, and long-term microgravity. Simulation consists of a clinostatically-rotated cell culture system. The system is a horizontally-rotated cylinder completely filled with culture medium. Low speed rotation results in continuous-fall of the cells through the fluid medium. In this setting, cells: 1) aggregate, 2) propagate in three dimensions, 3) synthesize matrix, 4) differentiate, and 5) form sinusoids that facilitate mass transfer. Space cell culture is conducted in flight bioreactors and in static incubators. Cells grown in microgravity are: bovine cartilage, promyelocytic leukemia, kidney proximal tubule cells, adrenal medulla, breast and colon cancer, and endothelium. Cells were cultured in space to test specific hypotheses. Cartilage cells were used to determine structural differences in cartilage grown in space compared to ground-based bioreactors. Results from a 130-day experiment on Mir revealed that cartilage grown in space was substantially more compressible due to insufficient glycosaminoglycan in the matrix. Interestingly, earth-grown cartilage conformed better to the dimensions of the scaffolding material, while the Mir specimens were spherical. The other cell populations are currently being analyzed for cell surface properties, gene expression, and differentiation. Results suggest that some cells spontaneously differentiate in microgravity. Additionally, vast changes in gene expression may occur in response to microgravity. In conclusion, the transition to microgravity may constitute a physical perturbation in cells resulting in unique gene expressions, the consequences of which may be useful in tissue engineering, disease modeling, and space cell biology.

Biological Nanopores: Confined Spaces for Electrochemical Single-Molecule Analysis.

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Cao, Chan; Long, Yi-Tao

2018-02-20

Nanopore sensing is developing into a powerful single-molecule approach to investigate the features of biomolecules that are not accessible by studying ensemble systems. When a target molecule is transported through a nanopore, the ions occupying the pore are excluded, resulting in an electrical signal from the intermittent ionic blockade event. By statistical analysis of the amplitudes, duration, frequencies, and shapes of the blockade events, many properties of the target molecule can be obtained in real time at the single-molecule level, including its size, conformation, structure, charge, geometry, and interactions with other molecules. With the development of the use of α-hemolysin to characterize individual polynucleotides, nanopore technology has attracted a wide range of research interest in the fields of biology, physics, chemistry, and nanoscience. As a powerful single-molecule analytical method, nanopore technology has been applied for the detection of various biomolecules, including oligonucleotides, peptides, oligosaccharides, organic molecules, and disease-related proteins. In this Account, we highlight recent developments of biological nanopores in DNA-based sensing and in studying the conformational structures of DNA and RNA. Furthermore, we introduce the application of biological nanopores to investigate the conformations of peptides affected by charge, length, and dipole moment and to study disease-related proteins' structures and aggregation transitions influenced by an inhibitor, a promoter, or an applied voltage. To improve the sensing ability of biological nanopores and further extend their application to a wider range of molecular sensing, we focus on exploring novel biological nanopores, such as aerolysin and Stable Protein 1. Aerolysin exhibits an especially high sensitivity for the detection of single oligonucleotides both in current separation and duration. Finally, to facilitate the use of nanopore measurements and statistical analysis

Integration of a zebrafish research project into a molecular biology course to support critical thinking and course content goals.

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Felzien, Lisa K

2016-11-12

Engaging undergraduates in research is essential for teaching them to think like scientists, and it has become a desired component of classroom and laboratory instruction. Research projects that span an entire semester expose students to a variety of concepts and techniques and allow students to use experiments to learn scientific principles, understand why specific techniques are applicable, critically analyze varied data, and examine how experimentation leads to acquiring knowledge. To provide an experience with these features, a semester long research project was integrated into a combined lecture and laboratory course, Molecular Biology. The project utilized the zebrafish model to examine gene expression during embryonic development and required students to develop and test hypotheses about the timing of expression of previously uncharacterized genes. The main goals for the project were to provide opportunities for students to develop critical thinking skills required for conducting research and to support the content goals of the course. To determine whether these goals were met, student performance on the steps of the project and related pre-test and post-test questions was examined. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):565-573, 2016. © 2016 The International Union of Biochemistry and Molecular Biology.

Proceedings of the FNCA workshop on plant mutation breeding 2001. Molecular biological techniques

International Nuclear Information System (INIS)

Kume, Tamikazu; Watanabe, Kazuo; Tano, Shigemitsu

2002-02-01

The FNCA (Forum for Nuclear Cooperation in Asia) Workshop on Plant Mutation Breeding was held on 20-24 August 2001 in Bangkok, Thailand. The Workshop was sponsored by the Ministry of Education, Culture, Sports, Science and Technology (MEXT). The Kasetsart University (KU), the Office of Atomic Energy for Peace (OAEP) and Department of Agriculture (DOA) acted as local host and the organizer with the cooperation of the Ministry of Agriculture, Forestry and Fisheries (MAFF) of Japan, the Japan Atomic Industrial Forum (JAIF) and Japan Atomic Energy Research Institute (JAERI). The Workshop was attended by two participants, a Project Leader and an expert on molecular biological techniques for plant mutation breeding, from each of the participating countries, i.e. China, Indonesia, Malaysia, the Philippines and Vietnam. One participant from the Republic of Korea, nine participants from Japan and thirteen participants from Thailand including three invited speakers attended the Workshop. Eleven papers including three invited papers on the current status of molecular biological techniques for plant mutation breeding were presented. Discussions were focused to further regional cooperation, to review and discuss results of past activities. The Medium-Term Plan of the project on the application of radiation and radioisotopes for agriculture in participating countries of Regional Nuclear Cooperation Activities (RNCA) was formulated and agreed. This proceeding compiles the invited and contributed papers that were submitted from the speakers. (author)

Molecular Force Spectroscopy on Cells

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Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

From gene to structure: Lactobacillus bulgaricus D-lactate dehydrogenase from yogurt as an integrated curriculum model for undergraduate molecular biology and biochemistry laboratory courses.

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