A personal account of the development of modern biological research in Portugal.

PubMed

De Sousa, Maria

2009-01-01

Portugal celebrated in 2006 its first 20 years of the formal introduction of the practice of external evaluation of research proposals in the national funding system. Accounts of changes in numbers of publications, citations, numbers of research projects funded and budget figures can be found in Government Reports (www.oces.mctes.pt.). An offshoot of the decisive and firm implementation of that practice in what was to become the Health Sciences was that the area became an attractor for young researchers in the basic biological sciences, namely, molecular, cellular and developmental biology. Reciprocally, the entry of basic biological scientists into medically oriented groups totally changed the landscape, the soil, the seeding, the cross-fertilization and the flowering of biomedical research in the country. This paper is a personal account of the experience of a scientist who was asked by the then President of the National Research Council, Jose Mariano Gago to co-ordinate the introduction of external evaluation of research projects and research institutes in the Health Sciences in Portugal between 1986 and 1997.

New experimental research stand SVICKA neutron field analysis using neutron activation detector technique

NASA Astrophysics Data System (ADS)

Varmuza, Jan; Katovsky, Karel; Zeman, Miroslav; Stastny, Ondrej; Haysak, Ivan; Holomb, Robert

2018-04-01

Knowledge of neutron energy spectra is very important because neutrons with various energies have a different material impact or a biological tissue impact. This paper presents basic results of the neutron flux distribution inside the new experimental research stand SVICKA which is located at Brno University of Technology in Brno, Czech Republic. The experiment also focused on the investigation of the sandwich biological shielding quality that protects staff against radiation effects. The set of indium activation detectors was used to the investigation of neutron flux distribution. The results of the measurement provide basic information about the neutron flux distribution inside all irradiation channels and no damage or cracks are present in the experimental research stand biological shielding.

[Progress in synthetic biology of "973 Funding Program" in China].

PubMed

Chen, Guoqiang; Wang, Ying

2015-06-01

This paper reviews progresses made in China from 2011 in areas of "Synthetic Biology" supported by State Basic Research 973 Program. Till the end of 2014, 9 "synthetic biology" projects have been initiated with emphasis on "microbial manufactures" with the 973 Funding Program. Combined with the very recent launch of one project on "mammalian cell synthetic biology" and another on "plant synthetic biology", Chinese "synthetic biology" research reflects its focus on "manufactures" while not giving up efforts on "synthetic biology" of complex systems.

Ludwig von Bertalanffy's organismic view on the theory of evolution.

PubMed

Drack, Manfred

2015-03-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. © 2015 Wiley Periodicals, Inc.

Bibliometric analysis of original molecular biology research in anaesthesia.

PubMed

Schreiber, K; Girard, T; Kindler, C H

2004-10-01

Molecular biology has expanded the horizons of anaesthesia during the last 20 years and has led to an increase of basic science articles that are published in the specialised anaesthetic journals or originate in anaesthetic institutions. We searched for and analysed the specific features, such as year of publication, publishing journal, and country of origin, of all such molecular biology articles stored in the MEDLINE database during the period 1986-2002. We identified 1265 original articles that used molecular biology techniques; 223 (18%) of these articles were published in anaesthetic journals and 1042 (82%) articles in 556 other biomedical journals. While in the late 1980s only a few molecular biology articles were published each year by anaesthetic institutions, worldwide this number reached approximately 200 basic science articles by the end of 2002. The USA clearly dominates the field of anaesthesia with respect to molecular biology research with 839 (66%) such articles.

Why Flies? Inexpensive Public Engagement Exercises to Explain the Value of Basic Biomedical Research on "Drosophila melanogaster"

ERIC Educational Resources Information Center

Pulver, Stefan R.; Cognigni, Paola; Denholm, Barry; Fabre, Caroline; Gu, Wendy X. W.; Linneweber, Gerit; Prieto-Godino, Lucia; Urbancic, Vasja; Zwart, Maarten; Miguel-Aliaga, Irene

2011-01-01

Invertebrate model organisms are powerful systems for uncovering conserved principles of animal biology. Despite widespread use in scientific communities, invertebrate research is often severely undervalued by laypeople. Here, we present a set of simple, inexpensive public outreach exercises aimed at explaining to the public why basic research on…

Sex and the Biology Teacher

ERIC Educational Resources Information Center

Keller, Dolores Elaine

1972-01-01

Summarizes evidence that mammals are basically female, with masculine characteristics being imposed by hormonal changes in embryos or post-natally. Advocates the removal of male-dominant terminology in biological research and teaching. (AL)

78 FR 10186 - Center For Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-13

... Committee: Center for Scientific Review Special Emphasis Panel; RFA: EY 13-001 Basic Behavioral Research on... Panel; Fellowships: Cell Biology, Developmental Biology and Bioengineering. Date: March 7, 2013. Time: 8...

The poverty-related neglected diseases: Why basic research matters.

PubMed

Hotez, Peter J

2017-11-01

Together, malaria and the neglected tropical diseases (NTDs) kill more than 800,000 people annually, while creating long-term disability in millions more. International support for mass drug administration, bed nets, and other preventive measures has resulted in huge public health gains, while support for translational research is leading to the development of some new neglected disease drugs, diagnostics, and vaccines. However, funding for basic science research has not kept up, such that we are missing opportunities to create a more innovative pipeline of control tools for parasitic and related diseases. There is an urgent need to expand basic science approaches for neglected diseases, especially in the areas of systems biology and immunology; ecology, evolution, and mathematical biology; functional and comparative OMICs; gene editing; expanded use of model organisms; and a new single-cell combinatorial indexing RNA sequencing approach. The world's poor deserve access to innovation for neglected diseases. It should be considered a fundamental human right.

Gravitational biology on the space station

NASA Technical Reports Server (NTRS)

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.

The next generation of training for Arabidopsis researchers: bioinformatics and quantitative biology

USDA-ARS?s Scientific Manuscript database

It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (P...

Biological imaging with coherent Raman scattering microscopy: a tutorial

PubMed Central

Alfonso-García, Alba; Mittal, Richa; Lee, Eun Seong; Potma, Eric O.

2014-01-01

Abstract. Coherent Raman scattering (CRS) microscopy is gaining acceptance as a valuable addition to the imaging toolset of biological researchers. Optimal use of this label-free imaging technique benefits from a basic understanding of the physical principles and technical merits of the CRS microscope. This tutorial offers qualitative explanations of the principles behind CRS microscopy and provides information about the applicability of this nonlinear optical imaging approach for biological research. PMID:24615671

Water Resources Research October 1, 1979 - September 30, 1980: Summary statements of research activities by the Water Resources Division

USGS Publications Warehouse

,

1981-01-01

Research in the WRD had its beginnings in the late 1950's when the "core research" line item was added to the Congressional budget. Since this time the Federal program has grown from a "basic sciences" program to one that includes a broad spectrum of basic and applied scientific investigations. Water resources research in WRD includes the study of water in all its phases and uses the basic sciences of mathematics, chemistry, physics, biology, geology and engineering to gain a fundamental understanding of the processes that affect the movement of water and its chemical constituents through hydrologic systems. The basic knowledge and methodologies derived from water resources research are applicable not only to the solution of current problems associated with the Nation's water resources, but also to anticipated hydrologic issues.

Learning Biology through Research Papers: A Stimulus for Question-Asking by High-School Students

ERIC Educational Resources Information Center

Brill, Gilat; Yarden, Anat

2003-01-01

Question-asking is a basic skill, required for the development of scientific thinking. However, the way in which science lessons are conducted does not usually stimulate question-asking by students. To make students more familiar with the scientific inquiry process, we developed a curriculum in developmental biology based on research papers…

Influence of Previous Knowledge, Language Skills and Domain-Specific Interest on Observation Competency

ERIC Educational Resources Information Center

Kohlhauf, Lucia; Rutke, Ulrike; Neuhaus, Birgit

2011-01-01

Many epoch-making biological discoveries (e.g. Darwinian Theory) were based upon observations. Nevertheless, observation is often regarded as "just looking" rather than a basic scientific skill. As observation is one of the main research methods in biological sciences, it must be considered as an independent research method and systematic practice…

malERA: An updated research agenda for basic science and enabling technologies in malaria elimination and eradication

PubMed Central

2017-01-01

Basic science holds enormous power for revealing the biological mechanisms of disease and, in turn, paving the way toward new, effective interventions. Recognizing this power, the 2011 Research Agenda for Malaria Eradication included key priorities in fundamental research that, if attained, could help accelerate progress toward disease elimination and eradication. The Malaria Eradication Research Agenda (malERA) Consultative Panel on Basic Science and Enabling Technologies reviewed the progress, continuing challenges, and major opportunities for future research. The recommendations come from a literature of published and unpublished materials and the deliberations of the malERA Refresh Consultative Panel. These areas span multiple aspects of the Plasmodium life cycle in both the human host and the Anopheles vector and include critical, unanswered questions about parasite transmission, human infection in the liver, asexual-stage biology, and malaria persistence. We believe an integrated approach encompassing human immunology, parasitology, and entomology, and harnessing new and emerging biomedical technologies offers the best path toward addressing these questions and, ultimately, lowering the worldwide burden of malaria. PMID:29190277

Introduction to Oxidative Stress in Biomedical and Biological Research

PubMed Central

Breitenbach, Michael; Eckl, Peter

2015-01-01

Oxidative stress is now a well-researched area with thousands of new articles appearing every year. We want to give the reader here an overview of the topics in biomedical and basic oxidative stress research which are covered by the authors of this thematic issue. We also want to give the newcomer a short introduction into some of the basic concepts, definitions and analytical procedures used in this field. PMID:26117854

Model Organisms Fact Sheet: Using Model Organisms to Study Health and Disease

MedlinePlus

... NIGMS use research organisms to explore the basic biology and chemistry of life. Scientists decide which organism ... controls allow for more precise understanding of the biological factors being studied and provide greater certainty about ...

Cancer Biology

ERIC Educational Resources Information Center

Dominiecki, Mary E.

2004-01-01

University of Colorado's Virtual Student Fellowship available at and developed by Bakemeier, Richard F. This website is designed to give students applying for a fellowship an overview of basic topics in biology and how they are used by cancer researchers to develop new treatments.

Drosophila Genetic Resource and Stock Center; The National BioResource Project.

PubMed

Yamamoto, Masa-Toshi

2010-01-01

The fruit fly, Drosophila melanogaster, is not categorized as a laboratory animal, but it is recognised as one of the most important model organisms for basic biology, life science, and biomedical research. This tiny fly continues to occupy a core place in genetics and genomic approaches to studies of biology and medicine. The basic principles of genetics, including the variations of phenotypes, mutations, genetic linkage, meiotic chromosome segregation, chromosome aberrations, recombination, and precise mapping of genes by genetic as well as cytological means, were all derived from studies of Drosophila. Recombinant DNA technology was developed in the 1970s and Drosophila DNA was the first among multicellular organisms to be cloned. It provided a detailed characterization of genes in combination of classical cytogenetic data. Drosophila thus became the pioneering model organism for various fields of life science research into multicellular organisms. Here, I briefly describe the history of Drosophila research and provide a few examples of the application of the abundant genetic resources of Drosophila to basic biology and medical investigations. A Japanese national project, the National BioResource Project (NBRP) for collection, maintainance, and provision of Drosophila resources, that is well known and admired by researchers in other countries as an important project, is also briefly described.

Thin film bioreactors in space

NASA Technical Reports Server (NTRS)

Hughes-Fulford, M.; Scheld, H. W.

1989-01-01

Studies from the Skylab, SL-3 and D-1 missions have demonstrated that biological organisms grown in microgravity have changes in basic cellular functions such as DNA, mRNA and protein synthesis, cytoskeleton synthesis, glucose utilization, and cellular differentiation. Since microgravity could affect prokaryotic and eukaryotic cells at a subcellular and molecular level, space offers an opportunity to learn more about basic biological systems with one inmportant variable removed. The thin film bioreactor will facilitate the handling of fluids in microgravity, under constant temperature and will allow multiple samples of cells to be grown with variable conditions. Studies on cell cultures grown in microgravity would make it possible to identify and quantify changes in basic biological function in microgravity which are needed to develop new applications of orbital research and future biotechnology.

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Neural Development Section (NDS) headed by Dr. Lino Tessarollo has an open postdoctoral fellow position. The candidate should have a background in neurobiology and basic expertise in molecular biology, cell biology, immunoistochemistry and biochemistry.  Experience in confocal analysis is desired. The NDS study the biology of neurotrophin and Trk receptors function by

Ludwig von Bertalanffy's Organismic View on the Theory of Evolution

PubMed Central

Drack, Manfred

2015-01-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 77–90, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:25727202

Microfluidic tools for cell biological research

PubMed Central

Velve-Casquillas, Guilhem; Le Berre, Maël; Piel, Matthieu; Tran, Phong T.

2010-01-01

Summary Microfluidic technology is creating powerful tools for cell biologists to control the complete cellular microenvironment, leading to new questions and new discoveries. We review here the basic concepts and methodologies in designing microfluidic devices, and their diverse cell biological applications. PMID:21152269

Training Under-Represented Students in Biological Research at Fisk University

NASA Technical Reports Server (NTRS)

Gunasekaran, Muthukumaran

1999-01-01

The objectives of our training and research project in biology at Fisk are to motivate and train our African-American undergraduate and graduate students by (a) teaching the basic principles and applications of different biological, biochemical and biophysical research techniques; (b) providing a "hands on experience" with laboratory instrumentation (c) requiring the students to participate in the proposed research project entitled "Cyanobacterial Bioreactors for Oxygen and Ammonia Production under "CELSS" Conditions" to gain confidence in independently conducting experiments and (d) providing training in scientific data collection and presentation to peers in scientific conferences or meetings.

Middle/High School Students in the Research Laboratory: A Summer Internship Program Emphasizing the Interdisciplinary Nature of Biology

ERIC Educational Resources Information Center

McMiller, Tracee; Lee, Tameshia; Saroop, Ria; Green, Tyra; Johnson, Casonya M.

2006-01-01

We describe an eight-week summer Young Scientist in Training (YSIT) internship program involving middle and high school students. This program exposed students to current basic research in molecular genetics, while introducing or reinforcing principles of the scientific method and demonstrating the uses of mathematics and chemistry in biology. For…

Brain-Based Research & Language Teaching.

ERIC Educational Resources Information Center

Christison, MaryAnn

2002-01-01

Introduces brain-based teaching and learning. Reviews basic biological facts about the human brain and discusses seven principles based on recent research that have practical benefits for English-as-a-Foreign-Language teachers. (Author/VWL)

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

ERIC Educational Resources Information Center

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…

The Second Annual Symposium of the NASA Specialized Center of Research and Training (NSCORT) in Gravitational Biology.

PubMed

Spooner, B S

1993-04-01

The second annual meeting of the NSCORT in Gravitational Biology was held at Kansas State University on September 29-October 1, 1992. Symposium presentations at the meeting included ones on basic gravitational cellular and developmental biology, spaceflight hardware for biological studies, studies on Space Shuttle, and special talks on Space Station Freedom and on life support systems.

The Second Annual Symposium of the NASA Specialized Center of Research and Training (NSCORT) in Gravitational Biology

NASA Technical Reports Server (NTRS)

Spooner, B. S.

1993-01-01

The second annual meeting of the NSCORT in Gravitational Biology was held at Kansas State University on September 29-October 1, 1992. Symposium presentations at the meeting included ones on basic gravitational cellular and developmental biology, spaceflight hardware for biological studies, studies on Space Shuttle, and special talks on Space Station Freedom and on life support systems.

Initiatives in biological research in Indian psychiatry

PubMed Central

Shrivatava, Amresh

2010-01-01

Biological psychiatry is an exploratory science for mental health. These biological changes provide some explicit insight into the complex area of ‘brain-mind and behavior’. One major achievement of research in biological field is the finding to explain how biological factors cause changes in behavior. In India, we have a clear history of initiatives in research from a biological perspective, which goes back to 1958. In the last 61 years, this field has seen significant evolution, precision and effective utilization of contemporary technological advances. It is a matter of great pride to see that in spite of difficult times in terms of challenges of practice and services, administration, resource, funding and manpower the zest for research was very forthcoming. There was neither dedicated time nor any funding for conducting research. It came from the intellectual insight of our fore fathers in the field of mental health to gradually grow to the state of strategic education in research, training in research, international research collaborations and setting up of internationally accredited centers. During difficult economic conditions in the past, the hypothesis tested and conclusions derived have not been so important. It is more important how it was done, how it was made possible and how robust traditions were established. Almost an entire spectrum of biological research has been touched upon by Indian researchers. Some of these are electroconvulsive therapy, biological markers, neurocognition, neuroimaging, neuroendocrine, neurochemistry, electrophysiology and genetics. A lot has been published given the limited space in the Indian Journal of Psychiatry and other medical journals published in India. A large body of biological research conducted on Indian patients has also been published in International literature (which I prefer to call non-Indian journals). Newer research questions in biological psychiatry, keeping with trend of international standards are currently being investigated by the younger generation with great enthusiasm. What we have achieved so far is the foundation work in last 60 years. Our main challenge in development of biological psychiatry research in India remains resources in terms of manpower, funding and dedicated time for research psychiatrists. Developing basic sciences laboratories, discrete research questions, high quality methodology, and logistical support are some of the essentials. In the present time the culture of research has changed. It is specific and evidence-based. We have time-tested examples of International collaborative research. We need to get more resources, develop education, collaboration and effective leadership. In times to come, India will provide international leadership in basic and clinical biological psychiatry. There is hope. PMID:21836666

The Graduate Training Programme "Molecular Imaging for the Analysis of Gene and Protein Expression": A Case Study with an Insight into the Participation of Universities of Applied Sciences

ERIC Educational Resources Information Center

Hafner, Mathias

2008-01-01

Cell biology and molecular imaging technologies have made enormous progress in basic research. However, the transfer of this knowledge to the pharmaceutical drug discovery process, or even therapeutic improvements for disorders such as neuronal diseases, is still in its infancy. This transfer needs scientists who can integrate basic research with…

Research Associate | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). KEY ROLES/RESPONSIBILITIES - Research Associate III Dr. Zbigniew Dauter is the head investigator of the Synchrotron Radiation Research Section (SRRS) of CCR’s Macromolecular Crystallography Laboratory. The Synchrotron Radiation Research Section is located at Argonne National Laboratory, Argonne, Illinois; this is the site of the largest U.S. synchrotron facility. The SRRS uses X-ray diffraction technique to solve crystal structures of various proteins and nucleic acids of biological and medical relevance. The section is also specializing in analyzing crystal structures at extremely high resolution and accuracy and in developing methods of effective diffraction data collection and in using weak anomalous dispersion effects to solve structures of macromolecules. The areas of expertise are: Structural and molecular biology Macromolecular crystallography Diffraction data collection Dr. Dauter requires research support in these areas, and the individual will engage in the purification and preparation of samples, crystallize proteins using various techniques, and derivatize them with heavy atoms/anomalous scatterers, and establish conditions for cryogenic freezing. Individual will also participate in diffraction data collection at the Advanced Photon Source. In addition, the candidate will perform spectroscopic and chromatographic analyses of protein and nucleic acid samples in the context of their purity, oligomeric state and photophysical properties.

APPLICATION OF GENOMIC AND PROTEOMIC INDICATORS TO CHARACTERIZE EXPOSURE OF AQUATIC ORGANISMS TO ENVIRONMENTAL CONTAMINANTS

EPA Science Inventory

Advances in molecular biological methods are continually being brought to bear on human health research, from a basic understanding of systems biology to identification of toxicity pathways for environmental stressors and to correlations of molecular indicators with physiological...

An Undergraduate Course to Bridge the Gap between Textbooks and Scientific Research

ERIC Educational Resources Information Center

Wiegant, Fred; Scager, Karin; Boonstra, Johannes

2011-01-01

This article reports on a one-semester Advanced Cell Biology course that endeavors to bridge the gap between gaining basic textbook knowledge about cell biology and learning to think and work as a researcher. The key elements of this course are 1) learning to work with primary articles in order to get acquainted with the field of choice, to learn…

Current, Short Term, Future and Star Wars Research Projects for Ornamental Crops

USDA-ARS?s Scientific Manuscript database

The USDA-ARS Greenhouse Production Research Group is involved in fundamental and developmental plant research aimed at developing tools for early stress detection and efficient agrochemical utilization for protected horticulture crops. The group conducts basic plant biology research with the goal o...

Biophysics at the Boundaries: The Next Problem Sets

NASA Astrophysics Data System (ADS)

Skolnick, Malcolm

2009-03-01

The interface between physics and biology is one of the fastest growing subfields of physics. As knowledge of such topics as cellular processes and complex ecological systems advances, researchers have found that progress in understanding these and other systems requires application of more quantitative approaches. Today, there is a growing demand for quantitative and computational skills in biological research and the commercialization of that research. The fragmented teaching of science in our universities still leaves biology outside the quantitative and mathematical culture that is the foundation of physics. This is particularly inopportune at a time when the needs for quantitative thinking about biological systems are exploding. More physicists should be encouraged to become active in research and development in the growing application fields of biophysics including molecular genetics, biomedical imaging, tissue generation and regeneration, drug development, prosthetics, neural and brain function, kinetics of nonequilibrium open biological systems, metabolic networks, biological transport processes, large-scale biochemical networks and stochastic processes in biochemical systems to name a few. In addition to moving into basic research in these areas, there is increasing opportunity for physicists in industry beginning with entrepreneurial roles in taking research results out of the laboratory and in the industries who perfect and market the inventions and developments that physicists produce. In this talk we will identify and discuss emerging opportunities for physicists in biophysical and biotechnological pursuits ranging from basic research through development of applications and commercialization of results. This will include discussion of the roles of physicists in non-traditional areas apart from academia such as patent law, financial analysis and regulatory science and the problem sets assigned in education and training that will enable future biophysicists to fill these roles.

CSBB: synthetic biology research at Newcastle University.

PubMed

Goñi-Moreno, Angel; Wipat, Anil; Krasnogor, Natalio

2017-06-15

The Centre for Synthetic Biology and the Bioeconomy (CSBB) brings together a far-reaching multidisciplinary community across all Newcastle University's faculties - Medical Sciences, Science, Agriculture and Engineering, and Humanities, Arts and Social Sciences. The CSBB focuses on many different areas of Synthetic Biology, including bioprocessing, computational design and in vivo computation, as well as improving understanding of basic molecular machinery. Such breadth is supported by major national and international research funding, a range of industrial partners in the North East of England and beyond, as well as a large number of doctoral and post-doctoral researchers. The CSBB trains the next generation of scientists through a 1-year MSc in Synthetic Biology. © 2017 The Author(s).

Driving forces of biomedical science education and research in state-of-the arts academic medical centres: the United States as example.

PubMed

John, T A

2011-06-01

Basic science departments in academic medical centres are influenced by changes that are commonly directed at medical education and financial gain. Some of such changes may have been detrimental to or may have enhanced basic science education. They may have determined basic science research focus or basic science research methods. However, there is lack of research on the educational process in the basic sciences including training of PhD's while there is ample research on medical education pertaining to training of medical doctors. The author here identifies, from university websites and available literature, some forces that have driven teaching and research focus and methods in state-of-the-arts academic medical centres in recent times with a view of seeing through their possible influences on basic science education and research, using the United States of America as an example. The "forces" are: Changes in medical schools; Medical educational philosophies: problem based learning, evidence based medicine, cyberlearning and self-directed learning; Shifting impressions of the value of basic sciences in medical schools; Research trends in Basic Sciences: role of antivivisectionists, alternative experimentations, explosion of molecular and cell biology; Technological advancements; Commercialization of research; and Funding agencies. The author encourages African leaders in academia to pay attention to such forces as the leadership seeks to raise African Universities as centres of knowledge that have a major role in acquiring, preserving, imparting, and utilizing knowledge.

Concepts for the clinical use of stem cells in equine medicine

PubMed Central

Koch, Thomas G.; Berg, Lise C.; Betts, Dean H.

2008-01-01

Stem cells from various tissues hold great promise for their therapeutic use in horses, but so far efficacy or proof-of-principle has not been established. The basic characteristics and properties of various equine stem cells remain largely unknown, despite their increasingly widespread experimental and empirical commercial use. A better understanding of equine stem cell biology and concepts is needed in order to develop and evaluate rational clinical applications in the horse. Controlled, well-designed studies of the basic biologic characteristics and properties of these cells are needed to move this new equine research field forward. Stem cell research in the horse has exciting equine specific and comparative perspectives that will most likely benefit the health of horses and, potentially, humans. PMID:19119371

Quantum dots in bio-imaging: Revolution by the small

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

Arya, Harinder; Kaul, Zeenia; Wadhwa, Renu

2005-04-22

Visual analysis of biomolecules is an integral avenue of basic and applied biological research. It has been widely carried out by tagging of nucleotides and proteins with traditional fluorophores that are limited in their application by features such as photobleaching, spectral overlaps, and operational difficulties. Quantum dots (QDs) are emerging as a superior alternative and are poised to change the world of bio-imaging and further its applications in basic and applied biology. The interdisciplinary field of nanobiotechnology is experiencing a revolution and QDs as an enabling technology have become a harbinger of this hybrid field. Within a decade, research onmore » QDs has evolved from being a pure science subject to the one with high-end commercial applications.« less

Synthetic biology: An emerging research field in China

PubMed Central

Pei, Lei; Schmidt, Markus; Wei, Wei

2011-01-01

Synthetic biology is considered as an emerging research field that will bring new opportunities to biotechnology. There is an expectation that synthetic biology will not only enhance knowledge in basic science, but will also have great potential for practical applications. Synthetic biology is still in an early developmental stage in China. We provide here a review of current Chinese research activities in synthetic biology and its different subfields, such as research on genetic circuits, minimal genomes, chemical synthetic biology, protocells and DNA synthesis, using literature reviews and personal communications with Chinese researchers. To meet the increasing demand for a sustainable development, research on genetic circuits to harness biomass is the most pursed research within Chinese researchers. The environmental concerns are driven force of research on the genetic circuits for bioremediation. The research on minimal genomes is carried on identifying the smallest number of genomes needed for engineering minimal cell factories and research on chemical synthetic biology is focused on artificial proteins and expanded genetic code. The research on protocells is more in combination with the research on molecular-scale motors. The research on DNA synthesis and its commercialisation are also reviewed. As for the perspective on potential future Chinese R&D activities, it will be discussed based on the research capacity and governmental policy. PMID:21729747

Fundamentals of microfluidic cell culture in controlled microenvironments†

PubMed Central

Young, Edmond W. K.; Beebe, David J.

2010-01-01

Microfluidics has the potential to revolutionize the way we approach cell biology research. The dimensions of microfluidic channels are well suited to the physical scale of biological cells, and the many advantages of microfluidics make it an attractive platform for new techniques in biology. One of the key benefits of microfluidics for basic biology is the ability to control parameters of the cell microenvironment at relevant length and time scales. Considerable progress has been made in the design and use of novel microfluidic devices for culturing cells and for subsequent treatment and analysis. With the recent pace of scientific discovery, it is becoming increasingly important to evaluate existing tools and techniques, and to synthesize fundamental concepts that would further improve the efficiency of biological research at the microscale. This tutorial review integrates fundamental principles from cell biology and local microenvironments with cell culture techniques and concepts in microfluidics. Culturing cells in microscale environments requires knowledge of multiple disciplines including physics, biochemistry, and engineering. We discuss basic concepts related to the physical and biochemical microenvironments of the cell, physicochemical properties of that microenvironment, cell culture techniques, and practical knowledge of microfluidic device design and operation. We also discuss the most recent advances in microfluidic cell culture and their implications on the future of the field. The goal is to guide new and interested researchers to the important areas and challenges facing the scientific community as we strive toward full integration of microfluidics with biology. PMID:20179823

[Biological research and security institutes].

PubMed

Darsie, G; Falczuk, A J; Bergmann, I E

2006-04-01

The threat of using biological material for ago-bioterrorist ends has risen in recent years, which means that research and diagnostic laboratories, biological agent banks and other institutions authorised to carry out scientific activities have had to implement biosafety and biosecurity measures to counter the threat, while carrying out activities to help prevent and monitor the accidental or intentional introduction of exotic animal diseases. This article briefly sets outthe basic components of biosafety and biosecurity, as well as recommendations on organisational strategies to consider in laboratories that support agro-bioterrorist surveillance and prevention programs.

A research agenda for helminth diseases of humans: basic research and enabling technologies to support control and elimination of helminthiases.

PubMed

Lustigman, Sara; Geldhof, Peter; Grant, Warwick N; Osei-Atweneboana, Mike Y; Sripa, Banchob; Basáñez, María-Gloria

2012-01-01

Successful and sustainable intervention against human helminthiases depends on optimal utilisation of available control measures and development of new tools and strategies, as well as an understanding of the evolutionary implications of prolonged intervention on parasite populations and those of their hosts and vectors. This will depend largely on updated knowledge of relevant and fundamental parasite biology. There is a need, therefore, to exploit and apply new knowledge and techniques in order to make significant and novel gains in combating helminthiases and supporting the sustainability of current and successful mass drug administration (MDA) programmes. Among the fields of basic research that are likely to yield improved control tools, the Disease Reference Group on Helminth Infections (DRG4) has identified four broad areas that stand out as central to the development of the next generation of helminth control measures: 1) parasite genetics, genomics, and functional genomics; 2) parasite immunology; 3) (vertebrate) host-parasite interactions and immunopathology; and 4) (invertebrate) host-parasite interactions and transmission biology. The DRG4 was established in 2009 by the Special Programme for Research and Training in Tropical Diseases (TDR). The Group was given the mandate to undertake a comprehensive review of recent advances in helminthiases research in order to identify notable gaps and highlight priority areas. This paper summarises recent advances and discusses challenges in the investigation of the fundamental biology of those helminth parasites under the DRG4 Group's remit according to the identified priorities, and presents a research and development agenda for basic parasite research and enabling technologies that will help support control and elimination efforts against human helminthiases.

Federal Research and Development Funding: FY2010

DTIC Science & Technology

2009-09-23

Budget activities 6.4 and 6.5 focus on the development of specific weapon systems or components (e.g., the Joint Strike Fighter or missile defense systems...more than the request for chemical and biological basic research and would provide $10 million in the Infrastructure and Geophysical Division for...40 40 Chemical and Biological 208 200 207 222 207 Command, Control, and Interoperability 57 75 80 81 83 Explosives 78 96 121 121 121 Human

Echinococcus as a model system: biology and epidemiology.

PubMed

Thompson, R C A; Jenkins, D J

2014-10-15

The introduction of Echinococcus to Australia over 200 years ago and its establishment in sheep rearing areas of the country inflicted a serious medical and economic burden on the country. This resulted in an investment in both basic and applied research aimed at learning more about the biology and life cycle of Echinococcus. This research served to illustrate the uniqueness of the parasite in terms of developmental biology and ecology, and the value of Echinococcus as a model system in a broad range of research, from fundamental biology to theoretical control systems. These studies formed the foundation for an international, diverse and ongoing research effort on the hydatid organisms encompassing stem cell biology, gene regulation, strain variation, wildlife diseases and models of transmission dynamics. We describe the development, nature and diversity of this research, and how it was initiated in Australia but subsequently has stimulated much international and collaborative research on Echinococcus. Copyright © 2014 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

An introduction to the molecular basics of aryl hydrocarbon receptor biology.

PubMed

Abel, Josef; Haarmann-Stemmann, Thomas

2010-11-01

Depending on their chemical structure and properties, environmental chemicals and other xenobiotics that enter the cell can affect cellular function by either nonselective binding to cellular macromolecules or by interference with cellular receptors, which would initiate a more defined cell biological response. One of these intracellular chemosensor molecules is the aryl hydrocarbon receptor (AhR), a transcription factor of the bHLH/PAS family that is known to mediate the biochemical and toxic effects of dioxins, polyaromatic hydrocarbons and related compounds. Numerous investigations have revealed that the AhR is not only a master regulator of drug metabolism activated by anthropogenic chemicals, but is also triggered by natural and endogenous ligands and can influence cell biological endpoints such as growth and differentiation. Cutting-edge research has identified new intriguing functions of the AhR, such as during proteasomal degradation of steroid hormone receptors, the cellular UVB stress response and the differentiation of certain T-cell subsets. In this review we provide both a survey of the fundamental basics of AhR biology and an insight into new functional aspects of AhR signaling to further stimulate research on this intriguing transcription factor at the interface between toxicology, cell biology and immunology.

Scientific innovation's two Valleys of Death: how blood and tissue banks can help to bridge the gap.

PubMed

Thompson, Sean D A

2014-12-01

Most biomedical basic research in the United States takes place at universities and research institutes and is funded by federal grants. Basic research is awarded billions of federal dollars every year, enabling new discoveries and greater understanding of the fundamental science that makes new innovations and therapies possible. However, when basic research yields an invention of practical use and the research evolves from basic to applied, the playing field changes. Pre-technology licensing federal dollars all but disappear, and innovations rely predominantly on private funding to support the full path from bench to bedside. It is along this path that the scientific advance faces two Valleys of Death. These sometimes insurmountable development stages are the product of the innovation's inherent financial, business and investment risks. Well-planned and executed in vivo studies using quality biological materials demonstrating proof-of-concept is often the key to bridging these gaps, and blood and tissue banks offer unique services and resources to enable this process.

Scientific Innovation's Two Valleys of Death: How Blood and Tissue Banks Can Help to Bridge the Gap

PubMed Central

Thompson, Sean D.A.

2014-01-01

Abstract Most biomedical basic research in the United States takes place at universities and research institutes and is funded by federal grants. Basic research is awarded billions of federal dollars every year, enabling new discoveries and greater understanding of the fundamental science that makes new innovations and therapies possible. However, when basic research yields an invention of practical use and the research evolves from basic to applied, the playing field changes. Pre-technology licensing federal dollars all but disappear, and innovations rely predominantly on private funding to support the full path from bench to bedside. It is along this path that the scientific advance faces two Valleys of Death. These sometimes insurmountable development stages are the product of the innovation’s inherent financial, business and investment risks. Well-planned and executed in vivo studies using quality biological materials demonstrating proof-of-concept is often the key to bridging these gaps, and blood and tissue banks offer unique services and resources to enable this process. PMID:25457967

Secretary | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research programs in basic or applied molecular biology, immunology, retrovirology, cancer biology, or human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick national Laboratory for Cancer Research (FNLCR). The BSP Office provides procurement and logistical assistance in support of the research activities of the Center for Cancer Research.KEY ROLES/RESPONSIBILITIES The Secretary III will: Provide heavy-volume procurement support to a large customer base of laboratory staff, both Leidos Biomed and CCR (gov’t), using blanket orders, purchase requisitions, credit card, and online warehouse system Data entry into appropriate financial system component (CostPoint, Cor360), status checks on orders, maintenance of orders log, reconciliation of credit card transactions, maintenance of electronic filing systems Providing logistical support for the facilitation of travel packages (both pre-travel and post travel) for Leidos Biomed employees, as well as the coordination of seminar speakers and subsequent reimbursements Composing and answering emails/correspondence Communicating with all levels of personnel, both verbally and in writing, to gather and clearly convey information

Flow Cytometry Technician | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). KEY ROLES/RESPONSIBILITIES The Flow Cytometry Core (Flow Core) of the Cancer and Inflammation Program (CIP) is a service core which supports the research efforts of the CCR by providing expertise in the field of flow cytometry (using analyzers and sorters) with the goal of gaining a more thorough understanding of the biology of cancer and cancer cells. The Flow Core provides service to 12-15 CIP laboratories and more than 22 non-CIP laboratories. Flow core staff provide technical advice on the experimental design of applications, which include immunological phenotyping, cell function assays, and cell cycle analysis. Work is performed per customer requirements, and no independent research is involved. The Flow Cytometry Technician will be responsible for: Monitor performance of and maintain high dimensional flow cytometer analyzers and cell sorters Operate high dimensional flow cytometer analyzers and cell sorters Monitoring lab supply levels and order lab supplies, perform various record keeping responsibilities Assist in the training of scientific end users on the use of flow cytometry in their research, as well as how to operate and troubleshoot the bench-top analyzer instruments Experience with sterile technique and tissue culture

Research, the lifeline of medicine.

PubMed

Kornberg, A

1976-05-27

Advances in medicine spring from discoveries in physics, chemistry and biology. Among key contributions to the diagnosis, treatment and prevention of cardiovascular and pulmonary diseases, a recent Comroe-Dripps analysis shows two thirds to have been basic rather than applied research. Without a firm foundation in basic knowledge innovations perceived as advances prove hollow and collapse. Strong social, economic and political pressures now threaten acquisition of basic knowledge. Scientists feel driven to undertake excessively complex problems and gamble against the historical record that science generally progresses by tackling discrete and well defined questions. Regardless of circumstances, professional standards require the physician and scientist to be creative and enlarge the fund of knowledge.

Student- and faculty-reported importance of science prerequisites for osteopathic medical school: a survey-based study.

PubMed

Binstock, Judith; Junsanto-Bahri, Tipsuda

2014-04-01

The relevance of current standard medical school science prerequisites is being reexamined. (1) To identify which science prerequisites are perceived to best prepare osteopathic medical students for their basic science and osteopathic manipulative medicine (OMM) coursework and (2) to determine whether science prerequisites for osteopathic medical school should be modified. Preclinical osteopathic medical students and their basic science and OMM faculty from 3 colleges of osteopathic medicine were surveyed about the importance of specific science concepts, laboratories, and research techniques to medical school coursework. Participants chose responses on a 5-point scale, with 1 indicating "strongly disagree" or "not important" and 5 indicating "strongly agree" or "extremely important." Participants were also surveryed on possible prerequisite modifications. Student responses (N=264) to the general statement regarding prerequisites were "neutral" for basic science coursework and "disagree" for OMM coursework, with mean (standard deviation [SD]) scores of 3.37 (1.1) and 2.68 (1.2), respectively. Faculty responses (N=49) were similar, with mean (SD) scores of 3.18 (1.1) for basic science coursework and 2.67 (1.2) for OMM coursework. Student mean (SD) scores were highest for general biology for basic science coursework (3.93 [1.1]) and physics for OMM coursework (2.5 [1.1]). Student mean (SD) scores were lowest for physics for basic science coursework (1.79 [1.2]) and organic chemistry for OMM coursework (1.2 [0.7]). Both basic science and OMM faculty rated general biology highest in importance (mean [SD] scores, 3.73 [0.9] and 4.22 [1.0], respectively). Students and faculty rated biochemistry high in importance for basic science coursework (mean [SD] scores of 3.66 [1.2] and 3.32 [1.2], respectively). For basic science coursework, students and faculty rated most laboratories as "important," with the highest mean (SD) ratings for general anatomy (students, 3.66 [1.5]; faculty, 3.72 [1.1]) and physiology (students, 3.56 [1.7]; faculty, 3.61 [1.1]). For their OMM coursework, students rated only general anatomy and physiology laboratories as "important" (mean [SD] scores, 3.22 [1.8] and 2.61 [1.6], respectively), whereas OMM faculty rated all laboratories as "important" (mean scores, >3). Both student and faculty respondents rated research techniques higher in importance for basic science coursework than for OMM coursework. For prerequisite modifications, all respondents indicated "no change" for biology and "reduce content" for organic chemistry and physics. All respondents favored adding physiology and biochemistry as prerequisites. General biology and laboratory were the only standard prerequisites rated as "important." Research techniques were rated as "important" for basic science coursework only. Physiology and biochemistry were identified as possible additions to prerequisites. It may be necessary for colleges of osteopathic medicine to modify science prerequisites to reflect information that is pertinent to their curricula.

Information resources at the National Center for Biotechnology Information.

PubMed Central

Woodsmall, R M; Benson, D A

1993-01-01

The National Center for Biotechnology Information (NCBI), part of the National Library of Medicine, was established in 1988 to perform basic research in the field of computational molecular biology as well as build and distribute molecular biology databases. The basic research has led to new algorithms and analysis tools for interpreting genomic data and has been instrumental in the discovery of human disease genes for neurofibromatosis and Kallmann syndrome. The principal database responsibility is the National Institutes of Health (NIH) genetic sequence database, GenBank. NCBI, in collaboration with international partners, builds, distributes, and provides online and CD-ROM access to over 112,000 DNA sequences. Another major program is the integration of multiple sequences databases and related bibliographic information and the development of network-based retrieval systems for Internet access. PMID:8374583

Senior Computational Scientist | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). The Cancer & Inflammation Program (CIP), Basic Science Program, HLA Immunogenetics Section, under the leadership of Dr. Mary Carrington, studies the influence of human leukocyte antigens (HLA) and specific KIR/HLA genotypes on risk of and outcomes to infection, cancer, autoimmune disease, and maternal-fetal disease. Recent studies have focused on the impact of HLA gene expression in disease, the molecular mechanism regulating expression levels, and the functional basis for the effect of differential expression on disease outcome. The lab’s further focus is on the genetic basis for resistance/susceptibility to disease conferred by immunogenetic variation. KEY ROLES/RESPONSIBILITIES The Senior Computational Scientist will provide research support to the CIP-BSP-HLA Immunogenetics Section performing bio-statistical design, analysis and reporting of research projects conducted in the lab. This individual will be involved in the implementation of statistical models and data preparation. Successful candidate should have 5 or more years of competent, innovative biostatistics/bioinformatics research experience, beyond doctoral training Considerable experience with statistical software, such as SAS, R and S-Plus Sound knowledge, and demonstrated experience of theoretical and applied statistics Write program code to analyze data using statistical analysis software Contribute to the interpretation and publication of research results

Is basic science disappearing from medicine? The decline of biomedical research in the medical literature.

PubMed

Steinberg, Benjamin E; Goldenberg, Neil M; Fairn, Gregory D; Kuebler, Wolfgang M; Slutsky, Arthur S; Lee, Warren L

2016-02-01

Explosive growth in our understanding of genomics and molecular biology have fueled calls for the pursuit of personalized medicine, the notion of harnessing biologic variability to provide patient-specific care. This vision will necessitate a deep understanding of the underlying pathophysiology in each patient. Medical journals play a pivotal role in the education of trainees and clinicians, yet we suspected that the amount of basic science in the top medical journals has been in decline. We conducted an automated search strategy in PubMed to identify basic science articles and calculated the proportion of articles dealing with basic science in the highest impact journals for 8 different medical specialties from 1994 to 2013. We observed a steep decline (40-60%) in such articles over time in almost all of the journals examined. This rapid decline in basic science from medical journals is likely to affect practitioners' understanding of and interest in the basic mechanisms of disease and therapy. In this Life Sciences Forum, we discuss why this decline may be occurring and what it means for the future of science and medicine. © FASEB.

Federal Research and Development Funding: FY2010

DTIC Science & Technology

2009-07-15

6.5 focus on the development of specific weapon systems or components (e.g., the Joint Strike Fighter or missile defense systems), for which an...separate item in FY2009. The House bill would provide $15 million more than the request for chemical and biological basic research and would provide $10...Maritime 25 33 40 40 40 Chemical and Biological 208 200 207 222 207 Command, Control, and Interoperability 57 75 80 81 83 Explosives 78 96 121

Centro de Biologia Molecular "Severo Ochoa": a center for basic research into Alzheimer's disease.

PubMed

Avila, Jesus; Hernandez, Felix; Wandosell, Francisco; Lucas, Jose J; Esteban, Jose A; Ledesma, M Dolores; Bullido, Maria J

2010-01-01

One important aspect of studies carried out at the Center for Molecular Biology "Severo Ochoa" is focused on basic aspects of Alzheimer's disease, mainly the search for suitable therapeutic targets for this disorder. Several groups at the Center are involved in these studies, and, in this spotlight, the work they are carrying out will be described.

A decade of molecular cell biology: achievements and challenges.

PubMed

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.

A decade of molecular cell biology: achievements and challenges

PubMed Central

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

2012-01-01

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. PMID:21941276

NCI 1st International Workshop on the Biology, Prevention, and Treatment of Relapse After Allogeneic Hematopoietic Stem Cell Transplantation: Summary and Recommendations from the Organizing Committee

PubMed Central

Bishop, Michael R.; Alyea, Edwin P.; Cairo, Mitchell S.; Falkenburg, J.H. Frederik; June, Carl H.; Kröger, Nicolaus; Little, Richard F.; Miller, Jeffrey S.; Pavletic, Steven Z.; Porter, David L.; Riddell, Stanley R.; van Besien, Koen; Wayne, Alan S.; Weisdorf, Daniel J.; Wu, Roy S.; Giralt, Sergio

2011-01-01

The First International Workshop on The Biology, Prevention, and Treatment of Relapse After Allogeneic Hematopoietic Stem Cell Transplantation was organized and convened to identify, prioritize, and coordinate future research activities related to relapse after allogeneic hematopoietic stem cell transplantation (alloHSCT). Each of the Workshop’s six working committees have published individual reports of ongoing basic, translational and clinical research and recommended areas for future research related to the areas of relapse biology, epidemiology, prevention and treatment. This document summarizes each of the committees’ recommendations and suggests three major initiatives for a coordinated research effort to address the problem of relapse after alloHSCT. The first is the need to establish multi-center correlative and clinical trials networks for basic/translational, epidemiological, and clinical research. Second, there is a need for a network of biorepositories for the collection of samples pre- and post-alloHSCT to aid in laboratory and clinical studies. Third, there should be further refinement, implementation, and study of the proposed Workshop disease-specific response and relapse definitions and the recommendations for monitoring of minimal residual disease. These recommendations, in coordination with ongoing research initiatives and transplant organizations, provide a research framework to rapidly and efficiently address the significant problem of relapse following alloHSCT. PMID:21224011

Brain Chemistry and Behaviour: An Update on Neuroscience Research and Its Implications for Understanding Drug Addiction

ERIC Educational Resources Information Center

Robinson, Emma S. J.

2011-01-01

Psychiatric disorders such as drug addiction represent one of the biggest challenges to society. This article reviews clinical and basic science research to illustrate how developments in research methodology have enabled neuroscientists to understand more about the brain mechanisms involved in addiction biology. Treating addiction represents a…

Increasing both the public health potential of basic research and the scientist satisfaction. An international survey of bio-scientists.

PubMed

Sorrentino, Carmen; Boggio, Andrea; Confalonieri, Stefano; Hemenway, David; Scita, Giorgio; Ballabeni, Andrea

2016-01-01

Basic scientific research generates knowledge that has intrinsic value which is independent of future applications. Basic research may also lead to practical benefits, such as a new drug or diagnostic method. Building on our previous study of basic biomedical and biological researchers at Harvard, we present findings from a new survey of similar scientists from three countries. The goal of this study was to design policies to enhance both the public health potential and the work satisfaction and test scientists' attitudes towards these factors. The present survey asked about the scientists' motivations, goals and perspectives along with their attitudes concerning  policies designed to increase both the practical (i.e. public health) benefits of basic research as well as their own personal satisfaction. Close to 900 basic investigators responded to the survey; results corroborate the main findings from the previous survey of Harvard scientists. In addition, we find that most bioscientists disfavor present policies that require a discussion of the public health potential of their proposals in grants but generally favor softer policies aimed at increasing the quality of work and the potential practical benefits of basic research. In particular, bioscientists are generally supportive of those policies entailing the organization of more meetings between scientists and the general public, the organization of more academic discussion about the role of scientists in the society, and the implementation of a "basic bibliography" for each new approved drug.

Increasing both the public health potential of basic research and the scientist satisfaction. An international survey of bio-scientists

PubMed Central

Sorrentino, Carmen; Boggio, Andrea; Confalonieri, Stefano; Hemenway, David; Scita, Giorgio; Ballabeni, Andrea

2016-01-01

Basic scientific research generates knowledge that has intrinsic value which is independent of future applications. Basic research may also lead to practical benefits, such as a new drug or diagnostic method. Building on our previous study of basic biomedical and biological researchers at Harvard, we present findings from a new survey of similar scientists from three countries. The goal of this study was to design policies to enhance both the public health potential and the work satisfaction and test scientists’ attitudes towards these factors. The present survey asked about the scientists’ motivations, goals and perspectives along with their attitudes concerning  policies designed to increase both the practical (i.e. public health) benefits of basic research as well as their own personal satisfaction. Close to 900 basic investigators responded to the survey; results corroborate the main findings from the previous survey of Harvard scientists. In addition, we find that most bioscientists disfavor present policies that require a discussion of the public health potential of their proposals in grants but generally favor softer policies aimed at increasing the quality of work and the potential practical benefits of basic research. In particular, bioscientists are generally supportive of those policies entailing the organization of more meetings between scientists and the general public, the organization of more academic discussion about the role of scientists in the society, and the implementation of a “basic bibliography” for each new approved drug. PMID:27347372

A Transparent Window into Biology: A Primer on Caenorhabditis elegans.

PubMed

Corsi, Ann K; Wightman, Bruce; Chalfie, Martin

2015-06-01

A little over 50 years ago, Sydney Brenner had the foresight to develop the nematode (round worm) Caenorhabditis elegans as a genetic model for understanding questions of developmental biology and neurobiology. Over time, research on C. elegans has expanded to explore a wealth of diverse areas in modern biology including studies of the basic functions and interactions of eukaryotic cells, host-parasite interactions, and evolution. C. elegans has also become an important organism in which to study processes that go awry in human diseases. This primer introduces the organism and the many features that make it an outstanding experimental system, including its small size, rapid life cycle, transparency, and well-annotated genome. We survey the basic anatomical features, common technical approaches, and important discoveries in C. elegans research. Key to studying C. elegans has been the ability to address biological problems genetically, using both forward and reverse genetics, both at the level of the entire organism and at the level of the single, identified cell. These possibilities make C. elegans useful not only in research laboratories, but also in the classroom where it can be used to excite students who actually can see what is happening inside live cells and tissues. Copyright © 2015 Corsi, Wightman, and Chalfie.

Basic energy sciences: Summary of accomplishments

NASA Astrophysics Data System (ADS)

1990-05-01

For more than four decades, the Department of Energy, including its predecessor agencies, has supported a program of basic research in nuclear- and energy related sciences, known as Basic Energy Sciences. The purpose of the program is to explore fundamental phenomena, create scientific knowledge, and provide unique user facilities necessary for conducting basic research. Its technical interests span the range of scientific disciplines: physical and biological sciences, geological sciences, engineering, mathematics, and computer sciences. Its products and facilities are essential to technology development in many of the more applied areas of the Department's energy, science, and national defense missions. The accomplishments of Basic Energy Sciences research are numerous and significant. Not only have they contributed to Departmental missions, but have aided significantly the development of technologies which now serve modern society daily in business, industry, science, and medicine. In a series of stories, this report highlights 22 accomplishments, selected because of their particularly noteworthy contributions to modern society. A full accounting of all the accomplishments would be voluminous. Detailed documentation of the research results can be found in many thousands of articles published in peer-reviewed technical literature.

Basic Energy Sciences: Summary of Accomplishments

DOE R&D Accomplishments Database

1990-05-01

For more than four decades, the Department of Energy, including its predecessor agencies, has supported a program of basic research in nuclear- and energy-related sciences, known as Basic Energy Sciences. The purpose of the program is to explore fundamental phenomena, create scientific knowledge, and provide unique user'' facilities necessary for conducting basic research. Its technical interests span the range of scientific disciplines: physical and biological sciences, geological sciences, engineering, mathematics, and computer sciences. Its products and facilities are essential to technology development in many of the more applied areas of the Department's energy, science, and national defense missions. The accomplishments of Basic Energy Sciences research are numerous and significant. Not only have they contributed to Departmental missions, but have aided significantly the development of technologies which now serve modern society daily in business, industry, science, and medicine. In a series of stories, this report highlights 22 accomplishments, selected because of their particularly noteworthy contributions to modern society. A full accounting of all the accomplishments would be voluminous. Detailed documentation of the research results can be found in many thousands of articles published in peer-reviewed technical literature.

Using RNAi in C. "elegans" to Demonstrate Gene Knockdown Phenotypes in the Undergraduate Biology Lab Setting

ERIC Educational Resources Information Center

Roy, Nicole M.

2013-01-01

RNA interference (RNAi) is a powerful technology used to knock down genes in basic research and medicine. In 2006 RNAi technology using "Caenorhabditis elegans" ("C. elegans") was awarded the Nobel Prize in medicine and thus students graduating in the biological sciences should have experience with this technology. However,…

The Crossroads between Biology and Mathematics: The Scientific Method as the Basics of Scientific Literacy

ERIC Educational Resources Information Center

Karsai, Istvan; Kampis, George

2010-01-01

Biology is changing and becoming more quantitative. Research is creating new challenges that need to be addressed in education as well. New educational initiatives focus on combining laboratory procedures with mathematical skills, yet it seems that most curricula center on a single relationship between scientific knowledge and scientific method:…

Freshwater Ecosystem Research in Water Quality Management

ERIC Educational Resources Information Center

Ferris, James J.; And Others

1974-01-01

Describes the use of modeling techniques to contribute to the basic knowledge of ecologic science, and in solving problems of biological production, resource-use planning and management, and environmental quality. (JR)

Synthetic biology expands chemical control of microorganisms.

PubMed

Ford, Tyler J; Silver, Pamela A

2015-10-01

The tools of synthetic biology allow researchers to change the ways engineered organisms respond to chemical stimuli. Decades of basic biology research and new efforts in computational protein and RNA design have led to the development of small molecule sensors that can be used to alter organism function. These new functions leap beyond the natural propensities of the engineered organisms. They can range from simple fluorescence or growth reporting to pathogen killing, and can involve metabolic coordination among multiple cells or organisms. Herein, we discuss how synthetic biology alters microorganisms' responses to chemical stimuli resulting in the development of microbes as toxicity sensors, disease treatments, and chemical factories. Copyright © 2015 Elsevier Ltd. All rights reserved.

Integrating the dimensions of sex and gender into basic life sciences research: methodologic and ethical issues.

PubMed

Holdcroft, Anita

2007-01-01

The research process -- from study design and selecting a species and its husbandry, through the experiment, analysis, peer review, and publication -- is rarely subject to questions about sex or gender differences in mainstream life sciences research. However, the impact of sex and gender on these processes is important in explaining biological variations and presentation of symptoms and diseases. This review aims to challenge assumptions and to develop opportunities to mainstream sex and gender in basic scientific research. Questions about the mechanisms of sex and gender effects were reviewed in relation to biological, environmental, social, and psychological interactions. Gender variations, in respect to aging, socializing, and reproduction, that are present in human populations but are rarely featured in laboratory research were considered to more effectively translate animal research into clinical health care. Methodologic approaches to address the present lack of a gender dimension in research include actively reducing variations through attention to physical factors, biological rhythms, and experimental design. In addition, through genomic and acute nongenomic activity, hormones may compound effects through multiple small sex differences that occur during the course of an acute pathologic event. Furthermore, the many exogenous sex steroid hormones and their congeners used in medicine (eg, in contraception and cancer therapies) may add to these effects. The studies reviewed provide evidence that sex and gender are determinants of many outcomes in life science research. To embed the gender dimension into basic scientific research, a broad approach -- gender mainstreaming -- is warranted. One example is the use of review boards (eg, animal ethical review boards and journal peer-review boards) in which gender-related standardized questions can be asked about study design and analysis. A more fundamental approach is to question the relevance of present-day laboratory models to design methods to best represent the age-related changes, comorbidity, and variations experienced by each sex in clinical medicine.

Introducing basic molecular biology to Turkish rural and urban primary school children via hands-on PCR and gel electrophoresis activities.

PubMed

Selli, Cigdem; Yıldırım, Gokce; Kaymak, Aysegul; Karacicek, Bilge; Ogut, Deniz; Gungor, Turkan; Erem, Erdem; Ege, Mehmet; Bümen, Nilay; Tosun, Metiner

2014-01-01

This study includes the results of a 2-day education project titled "Molecular Biology Laboratory Summer School, MoBiLYO." The project was held at a University Research Center by scientists from Department of Pharmacology and graduate students. The project was composed of introductory lectures, model construction, DNA isolation, polymerase chain reaction (PCR), and gel electrophoresis. The participants were 13-year-old eighth-graders attending primary schools affiliated with Ministry of National Education in urban and rural areas of Izmir, Turkey. The purpose of this study was to introduce basic molecular biology concepts through individually performed experiments such as PCR and gel electrophoresis integrated with creative drama. The students were assessed at the beginning and the end of each project day via mini-tests, experimental and presentation skills evaluation forms. Data showed that students' knowledge about DNA structure and basic molecular biology techniques significantly increased. On the basis of experimental and presentational skills, there was no significant difference between kids from urban and rural schools or between public and boarding public schools, whereas the average score of girls was significantly higher than that of boys. In conclusion, individually performed experiments integrated with creative drama significantly increased students' perception of complex experimental procedures on basic molecular biology concepts. Data suggests that integration of these concepts into the science and technology curriculum of Turkish primary education may support the recruitment of future scientists who can handle rapidly developing genomic techniques that will affect our everyday life. © 2014 by The International Union of Biochemistry and Molecular Biology.

Translating Alcohol Research

PubMed Central

Batman, Angela M.; Miles, Michael F.

2015-01-01

Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of streamlining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD. PMID:26259085

Translating Alcohol Research: Opportunities and Challenges.

PubMed

Batman, Angela M; Miles, Michael F

2015-01-01

Alcohol use disorder (AUD) and its sequelae impose a major burden on the public health of the United States, and adequate long-term control of this disorder has not been achieved. Molecular and behavioral basic science research findings are providing the groundwork for understanding the mechanisms underlying AUD and have identified multiple candidate targets for ongoing clinical trials. However, the translation of basic research or clinical findings into improved therapeutic approaches for AUD must become more efficient. Translational research is a multistage process of stream-lining the movement of basic biomedical research findings into clinical research and then to the clinical target populations. This process demands efficient bidirectional communication across basic, applied, and clinical science as well as with clinical practitioners. Ongoing work suggests rapid progress is being made with an evolving translational framework within the alcohol research field. This is helped by multiple interdisciplinary collaborative research structures that have been developed to advance translational work on AUD. Moreover, the integration of systems biology approaches with collaborative clinical studies may yield novel insights for future translational success. Finally, appreciation of genetic variation in pharmacological or behavioral treatment responses and optimal communication from bench to bedside and back may strengthen the success of translational research applications to AUD.

78 FR 12072 - Center for Scientific Review; Notice of Closed Meetings

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-21

... unwarranted invasion of personal privacy. Name of Committee: AIDS and Related Research Integrated Review Group... Emphasis Panel; PAR Panel: Cancer Health Disparities/Diversity in Basic Cancer Research. Date: March 18-19... for Scientific Review Special Emphasis Panel; Small Business: Orthopedic and Skeletal Biology. Date...

Proteogenomics | Office of Cancer Clinical Proteomics Research

Cancer.gov

Proteogenomics, or the integration of proteomics with genomics and transcriptomics, is an emerging approach that promises to advance basic, translational and clinical research.  By combining genomic and proteomic information, leading scientists are gaining new insights due to a more complete and unified understanding of complex biological processes.

New Policy Options Through Technology.

ERIC Educational Resources Information Center

Schmitt, Harrison

1981-01-01

The author discusses past contributions technology has made to society and ways it will contribute to society's future. Included in these areas are basic biological research, laser technology, information systems, and space technologies. (CT)

Life Sciences Space Station planning document: A reference payload for the Life Sciences Research Facility

NASA Technical Reports Server (NTRS)

1986-01-01

The Space Station, projected for construction in the early 1990s, will be an orbiting, low-gravity, permanently manned facility providing unprecedented opportunities for scientific research. Facilities for Life Sciences research will include a pressurized research laboratory, attached payloads, and platforms which will allow investigators to perform experiments in the crucial areas of Space Medicine, Space Biology, Exobiology, Biospherics and Controlled Ecological Life Support System (CELSS). These studies are designed to determine the consequences of long-term exposure to space conditions, with particular emphasis on assuring the permanent presence of humans in space. The applied and basic research to be performed, using humans, animals, and plants, will increase our understanding of the effects of the space environment on basic life processes. Facilities being planned for remote observations from platforms and attached payloads of biologically important elements and compounds in space and on other planets (Exobiology) will permit exploration of the relationship between the evolution of life and the universe. Space-based, global scale observations of terrestrial biology (Biospherics) will provide data critical for understanding and ultimately managing changes in the Earth's ecosystem. The life sciences community is encouraged to participate in the research potential the Space Station facilities will make possible. This document provides the range and scope of typical life sciences experiments which could be performed within a pressurized laboratory module on Space Station.

Biological research on a Space Station

NASA Technical Reports Server (NTRS)

Krikorian, A. D.; Johnson, Catherine C.

1990-01-01

A Space Station can provide reliable, long duration access to ug environments for basic and applied biological research. The uniqueness of access to near-weightless environments to probe fundamental questions of significance to gravitational and Space biologists can be exploited from many vantage points. Access to centrifuge facilities that can provide 1 g and hypo-g controls will permit identification of gravity-dependent or primary effects. Understanding secondary effects of the ug environment as well will allow a fuller exploitation of the Space environment.

Introduction to Modern Methods in Light Microscopy.

PubMed

Ryan, Joel; Gerhold, Abby R; Boudreau, Vincent; Smith, Lydia; Maddox, Paul S

2017-01-01

For centuries, light microscopy has been a key method in biological research, from the early work of Robert Hooke describing biological organisms as cells, to the latest in live-cell and single-molecule systems. Here, we introduce some of the key concepts related to the development and implementation of modern microscopy techniques. We briefly discuss the basics of optics in the microscope, super-resolution imaging, quantitative image analysis, live-cell imaging, and provide an outlook on active research areas pertaining to light microscopy.

Synthetic Biology and the Translational Imperative.

PubMed

Heidari Feidt, Raheleh; Ienca, Marcello; Elger, Bernice Simone; Folcher, Marc

2017-12-18

Advances at the interface between the biological sciences and engineering are giving rise to emerging research fields such as synthetic biology. Harnessing the potential of synthetic biology requires timely and adequate translation into clinical practice. However, the translational research enterprise is currently facing fundamental obstacles that slow down the transition of scientific discoveries from the laboratory to the patient bedside. These obstacles including scarce financial resources and deficiency of organizational and logistic settings are widely discussed as primary impediments to translational research. In addition, a number of socio-ethical considerations inherent in translational research need to be addressed. As the translational capacity of synthetic biology is tightly linked to its social acceptance and ethical approval, ethical limitations may-together with financial and organizational problems-be co-determinants of suboptimal translation. Therefore, an early assessment of such limitations will contribute to proactively favor successful translation and prevent the promising potential of synthetic biology from remaining under-expressed. Through the discussion of two case-specific inventions in synthetic biology and their associated ethical implications, we illustrate the socio-ethical challenges ahead in the process of implementing synthetic biology into clinical practice. Since reducing the translational lag is essential for delivering the benefits of basic biomedical research to society at large and promoting global health, we advocate a moral obligation to accelerating translational research: the "translational imperative."

New measurements for hadrontherapy and space radiation: biology

NASA Technical Reports Server (NTRS)

Blakely, E. A.

2001-01-01

The dual goals of optimizing clinical efficacy of hadrontherapy and determining radiation risk estimates for space research have intersected to a common focus for investigation of the biological effects of charged particles. This paper briefly highlights recent international progress at accelerator facilities engaged in both biological and clinical studies of the effects of particle beams, primarily protons, carbon and iron ions. Basic mechanisms of molecular, cellular and tissue responses continue under investigation for radiations with a range of ionization densities. Late normal tissue effects, including the risk of cancer in particular, are of importance for both research fields. International cooperation has enhanced the rate of progress as evidenced by recent publications. Specific areas of biomedical research related to the biological radiotoxicity of critical organs (especially the central nervous system), individual radiosensitivities to radiation carcinogenesis, and the analysis of effects in mixed radiation fields still require more research. Recommendations for addressing these issues are made.

The NASA Materials Science Research Program - It's New Strategic Goals and Plans

NASA Technical Reports Server (NTRS)

Schlagheck, Ronald A.

2003-01-01

In 2001, the NASA created a separate science enterprise, the Office of Biological and Physical Research (OBPR), to perform strategical and fundamental research bringing together physics, chemistry, biology, and engineering to solve problems needed for future agency mission goals. The Materials Science Program is one of basic research disciplines within this new Enterprise's Division of Physical Sciences Research. The Materials Science Program participates to utilize effective use of International Space Station (ISS) experimental facilities, target new scientific and technology questions, and transfer results for Earth benefits. The program has recently pursued new investigative research in areas necessary to expand NASA knowledge base for exploration of the universe, some of which will need access to the microgravity of space. The program has a wide variety of traditional ground and flight based research related types of basic science related to materials crystallization, fundamental processing, and properties characterization in order to obtain basic understanding of various phenomena effects and relationships to the structures, processing, and properties of materials. A summary of the types and sources for this research is presented and those experiments planned for the space. Areas to help expand the science basis for NASA future missions are described. An overview of the program is given including the scope of the current and future NASA Research Announcements with emphasis on new materials science initiatives. A description of the planned flight experiments to be conducted on the International Space Station program along with the planned facility class Materials Science Research Rack (MSRR) and Microgravity Glovebox (MSG) type investigations.

Centers of Excellence on Environmental Health Disparities Research

EPA Pesticide Factsheets

collaborative effort that encourages basic, biological, clinical, epidemiological, behavioral, and/or social scientific investigations of disease conditions that are known to be a significant burden in low socioeconomic and health disparate populations

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

Hules, John

This 1998 annual report from the National Scientific Energy Research Computing Center (NERSC) presents the year in review of the following categories: Computational Science; Computer Science and Applied Mathematics; and Systems and Services. Also presented are science highlights in the following categories: Basic Energy Sciences; Biological and Environmental Research; Fusion Energy Sciences; High Energy and Nuclear Physics; and Advanced Scientific Computing Research and Other Projects.

Inter- and Transdisciplinary Work: Connecting Research on Hormones with Problems of Educational Practice

ERIC Educational Resources Information Center

Rappolt-Schlichtmann, Gabrielle; Watamura, Sarah E.

2010-01-01

More than ever before, leaders within the field of education are looking to research on basic processes to inform and improve educational practices. Success requires building a reciprocal relationship between the field of education and research on learning and development, similar to what exists between biology and medicine. Key to this effort is…

NCI-CPTAC DREAM Proteogenomics Challenge (Registration Now Open) | Office of Cancer Clinical Proteomics Research

Cancer.gov

Proteogenomics, integration of proteomics, genomics, and transcriptomics, is an emerging approach that promises to advance basic, translational and clinical research.  By combining genomic and proteomic information, leading scientists are gaining new insights due to a more complete and unified understanding of complex biological processes.

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

PubMed

Zheng, Jie; Harris, Marcelline R; Masci, Anna Maria; Lin, Yu; Hero, Alfred; Smith, Barry; He, Yongqun

2016-09-14

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. The terms in OBCS including 'data collection', 'data transformation in statistics', 'data visualization', 'statistical data analysis', and 'drawing a conclusion based on data', cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. Currently, OBCS comprehends 878 terms, representing 20 BFO classes, 403 OBI classes, 229 OBCS specific classes, and 122 classes imported from ten other OBO ontologies. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. Other ongoing projects using OBCS for statistical data processing are also discussed. The OBCS source code and documentation are available at: https://github.com/obcs/obcs . The Ontology of Biological and Clinical Statistics (OBCS) is a community-based open source ontology in the domain of biological and clinical statistics. OBCS is a timely ontology that represents statistics-related terms and their relations in a rigorous fashion, facilitates standard data analysis and integration, and supports reproducible biological and clinical research.

Introducing Basic Molecular Biology to Turkish Rural and Urban Primary School Children via Hands-on PCR and Gel Electrophoresis Activities

ERIC Educational Resources Information Center

Selli, Cigdem; Yildirim, Gokce; Kaymak, Aysegul; Karacicek, Bilge; Ogut, Deniz; Gungor, Turkan; Erem, Erdem; Ege, Mehmet; Bümen, Nilay; Tosun, Metiner

2014-01-01

This study includes the results of a 2-day education project titled "Molecular Biology Laboratory Summer School, MoBiLYO." The project was held at a University Research Center by scientists from Department of Pharmacology and graduate students. The project was composed of introductory lectures, model construction, DNA isolation,…

Muscle Satellite Cells: Exploring the Basic Biology to Rule Them.

PubMed

Almeida, Camila F; Fernandes, Stephanie A; Ribeiro Junior, Antonio F; Keith Okamoto, Oswaldo; Vainzof, Mariz

2016-01-01

Adult skeletal muscle is a postmitotic tissue with an enormous capacity to regenerate upon injury. This is accomplished by resident stem cells, named satellite cells, which were identified more than 50 years ago. Since their discovery, many researchers have been concentrating efforts to answer questions about their origin and role in muscle development, the way they contribute to muscle regeneration, and their potential to cell-based therapies. Satellite cells are maintained in a quiescent state and upon requirement are activated, proliferating, and fusing with other cells to form or repair myofibers. In addition, they are able to self-renew and replenish the stem pool. Every phase of satellite cell activity is highly regulated and orchestrated by many molecules and signaling pathways; the elucidation of players and mechanisms involved in satellite cell biology is of extreme importance, being the first step to expose the crucial points that could be modulated to extract the optimal response from these cells in therapeutic strategies. Here, we review the basic aspects about satellite cells biology and briefly discuss recent findings about therapeutic attempts, trying to raise questions about how basic biology could provide a solid scaffold to more successful use of these cells in clinics.

The opportunities for space biology research on the Space Station

NASA Technical Reports Server (NTRS)

Ballard, Rodney W.; Souza, Kenneth A.

1987-01-01

The life sciences research facilities for the Space Station are being designed to accommodate both animal and plant specimens for long durations studies. This will enable research on how living systems adapt to microgravity, how gravity has shaped and affected life on earth, and further the understanding of basic biological phenomena. This would include multigeneration experiments on the effects of microgravity on the reproduction, development, growth, physiology, behavior, and aging of organisms. To achieve these research goals, a modular habitat system and on-board variable gravity centrifuges, capable of holding various animal, plant, cells and tissues, is proposed for the science laboratory.

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Contribution of NIH funding to new drug approvals 2010–2016

PubMed Central

Beierlein, Jennifer M.; Khanuja, Navleen Surjit; McNamee, Laura M.; Ledley, Fred D.

2018-01-01

This work examines the contribution of NIH funding to published research associated with 210 new molecular entities (NMEs) approved by the Food and Drug Administration from 2010–2016. We identified >2 million publications in PubMed related to the 210 NMEs (n = 131,092) or their 151 known biological targets (n = 1,966,281). Of these, >600,000 (29%) were associated with NIH-funded projects in RePORTER. This funding included >200,000 fiscal years of NIH project support (1985–2016) and project costs >$100 billion (2000–2016), representing ∼20% of the NIH budget over this period. NIH funding contributed to every one of the NMEs approved from 2010–2016 and was focused primarily on the drug targets rather than on the NMEs themselves. There were 84 first-in-class products approved in this interval, associated with >$64 billion of NIH-funded projects. The percentage of fiscal years of project funding identified through target searches, but not drug searches, was greater for NMEs discovered through targeted screening than through phenotypic methods (95% versus 82%). For targeted NMEs, funding related to targets preceded funding related to the NMEs, consistent with the expectation that basic research provides validated targets for targeted screening. This analysis, which captures basic research on biological targets as well as applied research on NMEs, suggests that the NIH contribution to research associated with new drug approvals is greater than previously appreciated and highlights the risk of reducing federal funding for basic biomedical research. PMID:29440428

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

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

NONE

1996-04-01

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

Research Associate | Center for Cancer Research

Cancer.gov

The Basic Science Program (BSP) at the Frederick National Laboratory for Cancer Research (FNLCR) pursues independent, multidisciplinary research programs in basic or applied molecular biology, immunology, retrovirology, cancer biology or human genetics. As part of the BSP, the Microbiome and Genetics Core (the Core) characterizes microbiomes by next-generation sequencing to determine their composition and variation, as influenced by immune, genetic, and host health factors. The Core provides support across a spectrum of processes, from nucleic acid isolation through bioinformatics and statistical analysis. KEY ROLES/RESPONSIBILITIES The Research Associate II will provide support in the areas of automated isolation, preparation, PCR and sequencing of DNA on next generation platforms (Illumina MiSeq and NextSeq). An opportunity exists to join the Core’s team of highly trained experimentalists and bioinformaticians working to characterize microbiome samples. The following represent requirements of the position: A minimum of five (5) years related of biomedical experience. Experience with high-throughput nucleic acid (DNA/RNA) extraction. Experience in performing PCR amplification (including quantitative real-time PCR). Experience or familiarity with robotic liquid handling protocols (especially on the Eppendorf epMotion 5073 or 5075 platforms). Experience in operating and maintaining benchtop Illumina sequencers (MiSeq and NextSeq). Ability to evaluate experimental quality and to troubleshoot molecular biology protocols. Experience with sample tracking, inventory management and biobanking. Ability to operate and communicate effectively in a team-oriented work environment.

Microgravity: A New Tool for Basic and Applied Research in Space

NASA Technical Reports Server (NTRS)

1985-01-01

This brochure highlights selected aspects of the NASA Microgravity Science and Applications program. So that we can expand our understanding and control of physical processes, this program supports basic and applied research in electronic materials, metals, glasses and ceramics, biological materials, combustion and fluids and chemicals. NASA facilities that provide weightless environments on the ground, in the air, and in space are available to U.S. and foreign investigators representing the academic and industrial communities. After a brief history of microgravity research, the text explains the advantages and methods of performing microgravity research. Illustrations follow of equipment used and experiments preformed aboard the Shuttle and of prospects for future research. The brochure concludes be describing the program goals and the opportunities for participation.

Oral biology in middle age: a history of the University at Buffalo Oral Biology PhD Program.

PubMed

Scannapieco, F A

2014-05-01

In 1960, the first Department of Oral Biology in the United States dedicated to the conduct of research, graduate biomedical research education, and the provision of basic oral science education for the DDS curriculum was established at the University at Buffalo. In 1963, the Department organized the first PhD Program in Oral Biology in the United States. This PhD program has produced a large cadre of oral health researchers, many of whom have gone on to make major contributions to dental research and education. This article provides a brief history of the program, the context within which the program was organized and developed, and a description of some of the many faculty, students, and fellows associated with the program. Additionally, to celebrate the 50th anniversary of this program, a symposium, entitled "The Oral Microbiome, Immunity and Chronic Disease", was held on June 12-14, 2013, in Buffalo, New York. The proceedings are published online in Advances in Dental Research (2014, Vol. 26).

Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics

PubMed Central

Bourgard, Catarina; Albrecht, Letusa; Kayano, Ana C. A. V.; Sunnerhagen, Per; Costa, Fabio T. M.

2018-01-01

During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research. PMID:29473024

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Driving Discovery | Division of Cancer Prevention

Cancer.gov

Progress against cancer depends on many types of research—including basic, translational, and clinical—across different research areas, from the biology of cancer cells to studies of large populations. Regardless of the research type or area, supporting the best science and the best scientists is of paramount importance to NCI. Learn more about driving progress against cancer.

Design and construction of functional AAV vectors.

PubMed

Gray, John T; Zolotukhin, Serge

2011-01-01

Using the basic principles of molecular biology and laboratory techniques presented in this chapter, researchers should be able to create a wide variety of AAV vectors for both clinical and basic research applications. Basic vector design concepts are covered for both protein coding gene expression and small non-coding RNA gene expression cassettes. AAV plasmid vector backbones (available via AddGene) are described, along with critical sequence details for a variety of modular expression components that can be inserted as needed for specific applications. Protocols are provided for assembling the various DNA components into AAV vector plasmids in Escherichia coli, as well as for transferring these vector sequences into baculovirus genomes for large-scale production of AAV in the insect cell production system.

Making Science Work.

ERIC Educational Resources Information Center

Thomas, Lewis

1981-01-01

Presents a viewpoint concerning the impact of recent scientific advances on society. Discusses biological discoveries, space exploration, computer technology, development of new astronomical theories, the behavioral sciences, and basic research. Challenges to keeping science current with technological advancement are also discussed. (DS)

Controlling complexity: the clinical relevance of mouse complex genetics

PubMed Central

Schughart, Klaus; Libert, Claude; Kas, Martien J

2013-01-01

Experimental animal models are essential to obtain basic knowledge of the underlying biological mechanisms in human diseases. Here, we review major contributions to biomedical research and discoveries that were obtained in the mouse model by using forward genetics approaches and that provided key insights into the biology of human diseases and paved the way for the development of novel therapeutic approaches. PMID:23632795

Update on zinc biology.

PubMed

Solomons, Noel W

2013-01-01

Zinc has become a prominent nutrient of clinical and public health interest in the new millennium. Functions and actions for zinc emerge as increasingly ubiquitous in mammalian anatomy, physiology and metabolism. There is undoubtedly an underpinning in fundamental biology for all of the aspects of zinc in human health (clinical and epidemiological) in pediatric and public health practice. Unfortunately, basic science research may not have achieved a full understanding as yet. As a complement to the applied themes in the companion articles, a selection of recent advances in the domains homeostatic regulation and transport of zinc is presented; they are integrated, in turn, with findings on genetic expression, intracellular signaling, immunity and host defense, and bone growth. The elements include ionic zinc, zinc transporters, metallothioneins, zinc metalloenzymes and zinc finger proteins. In emerging basic research, we find some plausible mechanistic explanations for delayed linear growth with zinc deficiency and increased infectious disease resistance with zinc supplementation. Copyright © 2013 S. Karger AG, Basel.

Integrating population genetics and conservation biology in the era of genomics.

PubMed

Ouborg, N Joop

2010-02-23

As one of the final activities of the ESF-CONGEN Networking programme, a conference entitled 'Integrating Population Genetics and Conservation Biology' was held at Trondheim, Norway, from 23 to 26 May 2009. Conference speakers and poster presenters gave a display of the state-of-the-art developments in the field of conservation genetics. Over the five-year running period of the successful ESF-CONGEN Networking programme, much progress has been made in theoretical approaches, basic research on inbreeding depression and other genetic processes associated with habitat fragmentation and conservation issues, and with applying principles of conservation genetics in the conservation of many species. Future perspectives were also discussed in the conference, and it was concluded that conservation genetics is evolving into conservation genomics, while at the same time basic and applied research on threatened species and populations from a population genetic point of view continues to be emphasized.

When cloud computing meets bioinformatics: a review.

PubMed

Zhou, Shuigeng; Liao, Ruiqi; Guan, Jihong

2013-10-01

In the past decades, with the rapid development of high-throughput technologies, biology research has generated an unprecedented amount of data. In order to store and process such a great amount of data, cloud computing and MapReduce were applied to many fields of bioinformatics. In this paper, we first introduce the basic concepts of cloud computing and MapReduce, and their applications in bioinformatics. We then highlight some problems challenging the applications of cloud computing and MapReduce to bioinformatics. Finally, we give a brief guideline for using cloud computing in biology research.

A review of the biology and literature of the Gulf Coast Toad (Incilius nebulifer), native to Mexico and the United States.

PubMed

Mendelson, Joseph R Iii; Kinsey, Chase T; Murphy, James B

2015-06-24

The Gulf Coast Toad (Incilius nebulifer) is an abundant and widespread species within its range in the United States and Mexico, so it appears on many faunal checklists and is considered in diverse kinds of research. We review the basic biology, distribution, and published history of this species, identifying only those records and publications referable to I. nebulifer, to help researchers identify published works pertaining to I. nebulfer rather than I. valliceps, with which it formerly was considered to be conspecific.

An Introductory "How-to" Guide for Incorporating Microbiome Research into Integrative and Comparative Biology.

PubMed

Kohl, Kevin D

2017-10-01

Research on host-associated microbial communities has grown rapidly. Despite the great body of work, inclusion of microbiota-related questions into integrative and comparative biology is still lagging behind other disciplines. The purpose of this paper is to offer an introduction into the basic tools and techniques of host-microbe research. Specifically, what considerations should be made before embarking on such projects (types of samples, types of controls)? How is microbiome data analyzed and integrated with data measured from the hosts? How can researchers experimentally manipulate the microbiome? With this information, integrative and comparative biologists should be able to include host-microbe studies into their research and push the boundaries of both fields. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Revisiting the NIH Taskforce on the Research needs of Eosinophil-Associated Diseases (RE-TREAD).

PubMed

Khoury, Paneez; Akuthota, Praveen; Ackerman, Steven J; Arron, Joseph R; Bochner, Bruce S; Collins, Margaret H; Kahn, Jean-Emmanuel; Fulkerson, Patricia C; Gleich, Gerald J; Gopal-Srivastava, Rashmi; Jacobsen, Elizabeth A; Leiferman, Kristen M; Francesca, Levi-Schaffer; Mathur, Sameer K; Minnicozzi, Michael; Prussin, Calman; Rothenberg, Marc E; Roufosse, Florence; Sable, Kathleen; Simon, Dagmar; Simon, Hans-Uwe; Spencer, Lisa A; Steinfeld, Jonathan; Wardlaw, Andrew J; Wechsler, Michael E; Weller, Peter F; Klion, Amy D

2018-04-19

Eosinophil-associated diseases (EADs) are rare, heterogeneous disorders characterized by the presence of eosinophils in tissues and/or peripheral blood resulting in immunopathology. The heterogeneity of tissue involvement, lack of sufficient animal models, technical challenges in working with eosinophils, and lack of standardized histopathologic approaches have hampered progress in basic research. Additionally, clinical trials and drug development for rare EADs are limited by the lack of primary and surrogate endpoints, biomarkers, and validated patient-reported outcomes. Researchers with expertise in eosinophil biology and eosinophil-related diseases reviewed the state of current eosinophil research, resources, progress, and unmet needs in the field since the 2012 meeting of the NIH Taskforce on the Research of Eosinophil-Associated Diseases (TREAD). RE-TREAD focused on gaps in basic science, translational, and clinical research on eosinophils and eosinophil-related pathogenesis. Improved recapitulation of human eosinophil biology and pathogenesis in murine models was felt to be of importance. Characterization of eosinophil phenotypes, the role of eosinophil subsets in tissues, identification of biomarkers of eosinophil activation and tissue load, and a better understanding of the role of eosinophils in human disease were prioritized. Finally, an unmet need for tools for use in clinical trials was emphasized. Histopathologic scoring, patient- and clinician-reported outcomes, and appropriate coding were deemed of paramount importance for research collaborations, drug development, and approval by regulatory agencies. Further exploration of the eosinophil genome, epigenome, and proteome was also encouraged. Although progress has been made since 2012, unmet needs in eosinophil research remain a priority. ©2018 Society for Leukocyte Biology.

The 12th International Workshops on Opportunistic Protists (IWOP-12)

PubMed Central

Weiss, Louis M.; Cushion, Melanie T.; Didier, Elizabeth; Xiao, Lihua; Marciano-Cabral, Francine; Sinai, Anthony P.; Matos, Olga; Calderon, Enrique J.; Kaneshiro, Edna S.

2013-01-01

The 12th International Workshops on Opportunistic Protists (IWOP-12) was held in August 2012 in Tarrytown, New York. The objectives of the IWOP meetings are to: (1) serve as a forum for exchange of new information among active researchers concerning the basic biology, molecular genetics, immunology, biochemistry, pathogenesis, drug development, therapy, and epidemiology of these immunodeficiency-associated pathogenic eukaryotic microorganisms that are seen in patients with AIDS and (2) foster the entry of new and young investigators into these underserved research areas. The IWOP meeting focuses on opportunistic protists, e.g. the free-living amoebae, Pneumocystis, Cryptosporidium, Toxoplasma, the Microsporidia, and kinetoplastid flagellates. This conference represents the major conference that brings together research groups working on these opportunistic pathogens. Slow but steady progress is being achieved on understanding the biology of these pathogenic organisms, their involvement in disease causation in both immune-deficient and immune-competent hosts, and is providing critical insights into these emerging and reemerging pathogens. This IWOP meeting demonstrated the importance of newly developed genomic level information for many of these pathogens and how analysis of such large data sets is providing key insights into the basic biology of these organisms. A great concern is the loss of scientific expertise and diversity in the research community due to the ongoing decline in research funding. This loss of researchers is due to the small size of many of these research communities and a lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms. PMID:23560871

Encouraging minority undergraduates to choose science careers: career paths survey results.

PubMed

Villarejo, Merna; Barlow, Amy E L; Kogan, Deborah; Veazey, Brian D; Sweeney, Jennifer K

2008-01-01

To explore the reasons for the dearth of minorities in Ph.D.-level biomedical research and identify opportunities to increase minority participation, we surveyed high-achieving alumni of an undergraduate biology enrichment program for underrepresented minorities. Respondents were asked to describe their career paths and to reflect on the influences that guided their career choices. We particularly probed for attitudes and experiences that influenced students to pursue a research career, as well as factors relevant to their choice between medicine (the dominant career choice) and basic science. In agreement with earlier studies, alumni strongly endorsed supplemental instruction as a mechanism for achieving excellence in basic science courses. Undergraduate research was seen as broadening by many and was transformative for half of the alumni who ultimately decided to pursue Ph.D.s in biomedical research. That group had expressed no interest in research careers at college entry and credits their undergraduate research experience with putting them on track toward a research career. A policy implication of these results is that making undergraduate research opportunities widely available to biology students (including "premed" students) in the context of a structured educational enrichment program should increase the number of minority students who choose to pursue biomedical Ph.D.s.

A new era in science at Washington University, St. Louis: Viktor Hamburger's zoology department in the 1940's.

PubMed

Carson, H L

2001-04-01

In the early 1940s, the administration of the College of Arts and Sciences at Washington University, St. Louis was firmly in the hands of classical scholars who were not inclined to promote the development of modern research on scientific subjects. Funds supporting research in biology favored the School of Medicine and the Missouri Botanical Garden. Viktor Hamburger arrived at Washington University in 1935. At about the time he became the Acting Chairman of Zoology in 1942, research work in the biological departments began a dramatic surge that has continued to this day. For 65 years under his counsel and leadership, basic biology has thrived at this fine institution. As an early faculty recruit, I recount here a few personal recollections from those formative years.

Life sciences and environmental sciences

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

Not Available

1992-02-01

The DOE laboratories play a unique role in bringing multidisciplinary talents -- in biology, physics, chemistry, computer sciences, and engineering -- to bear on major problems in the life and environmental sciences. Specifically, the laboratories utilize these talents to fulfill OHER's mission of exploring and mitigating the health and environmental effects of energy use, and of developing health and medical applications of nuclear energy-related phenomena. At Lawrence Berkeley Laboratory (LBL) support of this mission is evident across the spectrum of OHER-sponsored research, especially in the broad areas of genomics, structural biology, basic cell and molecular biology, carcinogenesis, energy and environment,more » applications to biotechnology, and molecular, nuclear and radiation medicine. These research areas are briefly described.« less

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

PubMed

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.

An emerging synthesis between community ecology and evolutionary biology.

PubMed

Johnson, Marc T J; Stinchcombe, John R

2007-05-01

A synthesis between community ecology and evolutionary biology is emerging that identifies how genetic variation and evolution within one species can shape the ecological properties of entire communities and, in turn, how community context can govern evolutionary processes and patterns. This synthesis incorporates research on the ecology and evolution within communities over short timescales (community genetics and diffuse coevolution), as well as macroevolutionary timescales (community phylogenetics and co-diversification of communities). As we discuss here, preliminary evidence supports the hypothesis that there is a dynamic interplay between ecology and evolution within communities, yet researchers have not yet demonstrated convincingly whether, and under what circumstances, it is important for biologists to bridge community ecology and evolutionary biology. Answering this question will have important implications for both basic and applied problems in biology.

Computer Science Research Funding: How Much Is Too Little?

DTIC Science & Technology

2009-06-01

Bioinformatics Parallel computing Computational biology Principles of programming Computational neuroscience Real-time and embedded systems Scientific...National Security Agency ( NSA ) • Missile Defense Agency (MDA) and others The various research programs have been coordinated through the DDR&E...DOD funding included only DARPA and OSD programs. FY07 and FY08 PBR funding included DARPA, NSA , some of the Services’ basic and applied research

Workshop summary. Biomedical and Space-Related Research with Heavy Ions at the BEVALAC

NASA Technical Reports Server (NTRS)

Schimmerling, W.; Curtis, S. B.

1989-01-01

The authors provide an overview of papers presented at a workshop on Biomedical and Space-Related Research with Heavy Ions at the BEVALAC at Lawrence Berkeley Laboratory. Goals of the meeting were to determine the critical experiments using heavy ions as probes in radiation physics, radiation chemistry, macromolecular and cellular biology, evolution science, basic neurophysiology, and medical therapies; how beam lines and facilities at Lawrence Berkeley Laboratory can be improved for these experiments; and implications in priorities and funding for national policy. Workshop topics included physics and facilities, cellular and molecular biology, tissue radiobiology, and the future of heavy ion research.

Recent progress in structural biology: lessons from our research history.

PubMed

Nitta, Ryo; Imasaki, Tsuyoshi; Nitta, Eriko

2018-05-16

The recent 'resolution revolution' in structural analyses of cryo-electron microscopy (cryo-EM) has drastically changed the research strategy for structural biology. In addition to X-ray crystallography and nuclear magnetic resonance spectroscopy, cryo-EM has achieved the structural analysis of biological molecules at near-atomic resolution, resulting in the Nobel Prize in Chemistry 2017. The effect of this revolution has spread within the biology and medical science fields affecting everything from basic research to pharmaceutical development by visualizing atomic structure. As we have used cryo-EM as well as X-ray crystallography since 2000 to elucidate the molecular mechanisms of the fundamental phenomena in the cell, here we review our research history and summarize our findings. In the first half of the review, we describe the structural mechanisms of microtubule-based motility of molecular motor kinesin by using a joint cryo-EM and X-ray crystallography method. In the latter half, we summarize our structural studies on transcriptional regulation by X-ray crystallography of in vitro reconstitution of a multi-protein complex.

Establishing Research and Management Priorities for Invasive Water Primroses (Ludwigia spp.)

DTIC Science & Technology

2016-02-01

among the most aggressive aquatic invasive plant invaders in the world. These aquatic Ludwigia species can impart severe ecological , economic, and...global trade and projected climate change. This technical report presents an overview of the biology and ecology of these invasive plant species, along...primrose species, like other invasive plants , must be grounded in basic knowledge of the biology and ecology of the species and their responses to

Sandalwood: basic biology, tissue culture, and genetic transformation.

PubMed

Teixeira da Silva, Jaime A; Kher, Mafatlal M; Soner, Deepak; Page, Tony; Zhang, Xinhua; Nataraj, M; Ma, Guohua

2016-04-01

Sustainable resource preservation of Santalum species that yield commercially important forest products is needed. This review provides an understanding of their basic biology, propagation, hemi-parasitic nature, reproductive biology, and biotechnology. Many species of the genus Santalum (Santalaceae) have been exploited unremittingly for centuries, resulting in the extinction of one and the threatened status of three other species. This reduction in biodiversity of sandalwood has resulted from the commercial exploitation of its oil-rich fragrant heartwood. In a bid to conserve the remaining germplasm, biotechnology provides a feasible, and effective, means of propagating members of this genus. This review provides a detailed understanding of the biological mechanisms underlying the success or failure of traditional propagation, including a synopsis of the process of hemi-parasitism in S. album, and of the suitability of host plants to sustain the growth of seedlings and plants under forestry production. For the mass production of economically important metabolites, and to improve uniformity of essential oils, the use of clonal material of similar genetic background for cultivation is important. This review summarizes traditional methods of sandalwood production with complementary and more advanced in vitro technologies to provide a basis for researchers, conservationists and industry to implement sustainable programs of research and development for this revered genus.

Underdetermination in evidence-based medicine.

PubMed

Chin-Yee, Benjamin H

2014-12-01

This article explores the philosophical implications of evidence-based medicine's (EBM's) epistemology in terms of the problem of underdetermination of theory by evidence as expounded by the Duhem-Quine thesis. EBM hierarchies of evidence privilege clinical research over basic science, exacerbating the problem of underdetermination. Because of severe underdetermination, EBM is unable to meaningfully test core medical beliefs that form the basis of our understanding of disease and therapeutics. As a result, EBM adopts an epistemic attitude that is sceptical of explanations from the basic biological sciences, and is relegated to a view of disease at a population level. EBM's epistemic attitude provides a limited research heuristic by preventing the development of a theoretical framework required for understanding disease mechanism and integrating knowledge to develop new therapies. Medical epistemology should remain pluralistic and include complementary approaches of basic science and clinical research, thus avoiding the limited epistemic attitude entailed by EBM hierarchies. © 2014 John Wiley & Sons, Ltd.

Why we need more basic biology research, not less.

PubMed

Botstein, David

2012-11-01

Much of the spectacular progress in biomedical science over the last half-century is the direct consequence of the work of thousands of basic scientists whose primary goal was understanding of the fundamental working of living things. Despite this, many politicians, funders, and even scientists have come to believe that the pace of successful applications to medical diagnosis and therapy is limited by our willingness to focus directly on human health, rather than a continuing deficit of understanding. By this theory, curiosity-driven research, aimed at understanding, is no longer important or even useful. What is advocated instead is "translational" research aimed directly at treating disease. I believe this idea to be deeply mistaken. Recent history suggests instead that what we have learned in the last 50 years is only the beginning. The way forward is to invest more in basic science, not less.

The Plant Protoplast: A Useful Tool for Plant Research and Student Instruction

ERIC Educational Resources Information Center

Wagner, George J.; And Others

1978-01-01

A plant protoplast is basically a plant cell that lacks a cell wall. This article outlines some of the ways in which protoplasts may be used to advance understanding of plant cell biology in research and student instruction. Topics include high efficiency experimental virus infection, organelle isolation, and osmotic effects. (Author/MA)

Contribution of NIH funding to new drug approvals 2010-2016.

PubMed

Galkina Cleary, Ekaterina; Beierlein, Jennifer M; Khanuja, Navleen Surjit; McNamee, Laura M; Ledley, Fred D

2018-03-06

This work examines the contribution of NIH funding to published research associated with 210 new molecular entities (NMEs) approved by the Food and Drug Administration from 2010-2016. We identified >2 million publications in PubMed related to the 210 NMEs ( n = 131,092) or their 151 known biological targets ( n = 1,966,281). Of these, >600,000 (29%) were associated with NIH-funded projects in RePORTER. This funding included >200,000 fiscal years of NIH project support (1985-2016) and project costs >$100 billion (2000-2016), representing ∼20% of the NIH budget over this period. NIH funding contributed to every one of the NMEs approved from 2010-2016 and was focused primarily on the drug targets rather than on the NMEs themselves. There were 84 first-in-class products approved in this interval, associated with >$64 billion of NIH-funded projects. The percentage of fiscal years of project funding identified through target searches, but not drug searches, was greater for NMEs discovered through targeted screening than through phenotypic methods (95% versus 82%). For targeted NMEs, funding related to targets preceded funding related to the NMEs, consistent with the expectation that basic research provides validated targets for targeted screening. This analysis, which captures basic research on biological targets as well as applied research on NMEs, suggests that the NIH contribution to research associated with new drug approvals is greater than previously appreciated and highlights the risk of reducing federal funding for basic biomedical research. Copyright © 2018 the Author(s). Published by PNAS.

[Organization of clinical research: in a large scale department for cardiothoracic surgery].

PubMed

Sarikouch, S; Schilling, T; Haverich, A

2010-04-01

Translation of basic research results into routine patient care is delayed in parts by lack of institutionalization in clinical research. In this article the research structure and organization of our Department of Cardiac, Thoracic, Transplantation and Vascular Surgery are described.Basic research, separately directed, is accomplished in the Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO) and within the scope of the Excellence cluster "REBIRTH--from Regenerative Biology to Reconstructive Therapy".Clinical research is directed by heads of the subdepartments of our institution (valve and coronary surgery, aortic surgery, surgical electrophysiology, vascular surgery, thoracic surgery, cardiac assist systems, thoracic transplantation, intensive care and pediatric heart surgery).A separate subdepartment for clinical research is responsible for study coordination and accompanies clinical studies from study design and patient screening to publication. This subdepartment also serves as a constant contact to sponsors and superordinated research organizations within the Hannover Medical School.

Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry

PubMed Central

Harris, D. Calvin; Jewett, Michael C.

2014-01-01

Just as synthetic organic chemistry once revolutionized the ability of chemists to build molecules (including those that did not exist in nature) following a basic set of design rules, cell-free synthetic biology is beginning to provide an improved toolbox and faster process for not only harnessing but also expanding the chemistry of life. At the interface between chemistry and biology, research in cell-free synthetic systems is proceeding in two different directions: using synthetic biology for synthetic chemistry and using synthetic chemistry to reprogram or mimic biology. In the coming years, the impact of advances inspired by these approaches will make possible the synthesis of non-biological polymers having new backbone compositions, new chemical properties, new structures, and new functions. PMID:22483202

Basic design of MRM assays for peptide quantification.

PubMed

James, Andrew; Jorgensen, Claus

2010-01-01

With the recent availability and accessibility of mass spectrometry for basic and clinical research, the requirement for stable, sensitive, and reproducible assays to specifically detect proteins of interest has increased. Multiple reaction monitoring (MRM) or selective reaction monitoring (SRM) is a highly selective, sensitive, and robust assay to monitor the presence and amount of biomolecules. Until recently, MRM was typically used for the detection of drugs and other biomolecules from body fluids. With increased focus on biomarkers and systems biology approaches, researchers in the proteomics field have taken advantage of this approach. In this chapter, we will introduce the reader to the basic principle of designing and optimizing an MRM workflow. We provide examples of MRM workflows for standard proteomic samples and provide suggestions for the reader who is interested in using MRM for quantification.

Cleft Palate-Craniofacial Journal 50th anniversary editorial board commentary: anatomy, basic sciences, and genetics--then and now.

PubMed

Mooney, Mark P; Cooper, Gregory M; Marazita, Mary L

2014-05-01

To celebrate the 50th year of the Cleft Palate-Craniofacial Journal we look back to where we started in 1964 and where we are now, and we speculate about directions for the future in a "Then and Now" editorial series. This editorial examines changing trends and perspectives in anatomical, basic science, and genetic studies published in this 50-year interval. In volume 1 there were 45 total papers, seven (16%) of which were peer-reviewed basic science and genetic articles published: four in anatomy, three in craniofacial biology, and none in genetics. In contrast, in volume 50, of 113 articles there were 47 (42%) peer-reviewed basic science and genetic articles published: 30 in anatomy, five in craniofacial biology, and 12 in genetics. Topical analysis of published manuscripts then and now reveal that similar topics in anatomy and craniofacial biology are still being researched today (e.g., phenotypic variability, optimal timing of surgery, presurgical orthopedics, bone grafting); whereas, most of the more recent papers use advanced technology to address old questions. In contrast, genetic publications have clearly increased in frequency during the last 50 years, which parallels advances in the field during this time. However, all of us have noticed that the more "cutting-edge" papers in these areas are not being submitted for publication to the journal, but instead to discipline-specific journals. Concerted efforts are therefore indicated to attract and publish these cutting-edge papers in order to keep the Cleft Palate-Craniofacial Journal in the forefront of orofacial cleft and craniofacial anomaly research and to provide a valuable service to American Cleft Palate-Craniofacial Association members.

Organic synthesis toward small-molecule probes and drugs

PubMed Central

Schreiber, Stuart L.

2011-01-01

“Organic synthesis” is a compound-creating activity often focused on biologically active small molecules. This special issue of PNAS explores innovations and trends in the field that are enabling the synthesis of new types of small-molecule probes and drugs. This perspective article frames the research described in the special issue but also explores how these modern capabilities can both foster a new and more extensive view of basic research in the academy and promote the linkage of life-science research to the discovery of novel types of small-molecule therapeutics [Schreiber SL (2009) Chem Bio Chem 10:26–29]. This new view of basic research aims to bridge the chasm between basic scientific discoveries in life sciences and new drugs that treat the root cause of human disease—recently referred to as the “valley of death” for drug discovery. This perspective article describes new roles that modern organic chemistry will need to play in overcoming this challenge. PMID:21464328

Critical Need for Family-Based, Quasi-Experimental Designs in Integrating Genetic and Social Science Research

PubMed Central

Lahey, Benjamin B.; Turkheimer, Eric; Lichtenstein, Paul

2013-01-01

Researchers have identified environmental risks that predict subsequent psychological and medical problems. Based on these correlational findings, researchers have developed and tested complex developmental models and have examined biological moderating factors (e.g., gene–environment interactions). In this context, we stress the critical need for researchers to use family-based, quasi-experimental designs when trying to integrate genetic and social science research involving environmental variables because these designs rigorously examine causal inferences by testing competing hypotheses. We argue that sibling comparison, offspring of twins or siblings, in vitro fertilization designs, and other genetically informed approaches play a unique role in bridging gaps between basic biological and social science research. We use studies on maternal smoking during pregnancy to exemplify these principles. PMID:23927516

Critical need for family-based, quasi-experimental designs in integrating genetic and social science research.

PubMed

D'Onofrio, Brian M; Lahey, Benjamin B; Turkheimer, Eric; Lichtenstein, Paul

2013-10-01

Researchers have identified environmental risks that predict subsequent psychological and medical problems. Based on these correlational findings, researchers have developed and tested complex developmental models and have examined biological moderating factors (e.g., gene-environment interactions). In this context, we stress the critical need for researchers to use family-based, quasi-experimental designs when trying to integrate genetic and social science research involving environmental variables because these designs rigorously examine causal inferences by testing competing hypotheses. We argue that sibling comparison, offspring of twins or siblings, in vitro fertilization designs, and other genetically informed approaches play a unique role in bridging gaps between basic biological and social science research. We use studies on maternal smoking during pregnancy to exemplify these principles.

Population Disparities in Mental Health: Insights From Cultural Neuroscience

PubMed Central

Blizinsky, Katherine D.

2013-01-01

By 2050, nearly 1 in 5 Americans (19%) will be an immigrant, including Hispanics, Blacks, and Asians, compared to the 1 in 8 (12%) in 2005. They will vary in the extent to which they are at risk for mental health disorders. Given this increase in cultural diversity within the United States and costly population health disparities across cultural groups, it is essential to develop a more comprehensive understanding of how culture affects basic psychological and biological mechanisms. We examine these basic mechanisms that underlie population disparities in mental health through cultural neuroscience. We discuss the challenges to and opportunities for cultural neuroscience research to determine sociocultural and biological factors that confer risk for and resilience to mental health disorders across the globe. PMID:23927543

Population disparities in mental health: insights from cultural neuroscience.

PubMed

Chiao, Joan Y; Blizinsky, Katherine D

2013-10-01

By 2050, nearly 1 in 5 Americans (19%) will be an immigrant, including Hispanics, Blacks, and Asians, compared to the 1 in 8 (12%) in 2005. They will vary in the extent to which they are at risk for mental health disorders. Given this increase in cultural diversity within the United States and costly population health disparities across cultural groups, it is essential to develop a more comprehensive understanding of how culture affects basic psychological and biological mechanisms. We examine these basic mechanisms that underlie population disparities in mental health through cultural neuroscience. We discuss the challenges to and opportunities for cultural neuroscience research to determine sociocultural and biological factors that confer risk for and resilience to mental health disorders across the globe.

Machine learning for Big Data analytics in plants.

PubMed

Ma, Chuang; Zhang, Hao Helen; Wang, Xiangfeng

2014-12-01

Rapid advances in high-throughput genomic technology have enabled biology to enter the era of 'Big Data' (large datasets). The plant science community not only needs to build its own Big-Data-compatible parallel computing and data management infrastructures, but also to seek novel analytical paradigms to extract information from the overwhelming amounts of data. Machine learning offers promising computational and analytical solutions for the integrative analysis of large, heterogeneous and unstructured datasets on the Big-Data scale, and is gradually gaining popularity in biology. This review introduces the basic concepts and procedures of machine-learning applications and envisages how machine learning could interface with Big Data technology to facilitate basic research and biotechnology in the plant sciences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fundamental Biological Research on the International Space Station

NASA Technical Reports Server (NTRS)

Souza, K. A.; Yost, Bruce; Fletcher, L.; Dalton, Bonnie P. (Technical Monitor)

2000-01-01

The fundamental Biology Program of NASA's Life Sciences Division is chartered with enabling and sponsoring research on the International Space Station (ISS) in order to understand the effects of the space flight environment, particularly microgravity, on living systems. To accomplish this goal, NASA Ames Research Center (ARC) has been tasked with managing the development of a number of biological habitats, along with their support systems infrastructure. This integrated suite of habitats and support systems is being designed to support research requirements identified by the scientific community. As such, it will support investigations using cells and tissues, avian eggs, insects, plants, aquatic organisms and rodents. Studies following organisms through complete life cycles and over multiple generations will eventually be possible. As an adjunct to the development of these basic habitats, specific analytical and monitoring technologies are being targeted for maturation to complete the research cycle by transferring existing or emerging analytical techniques, sensors, and processes from the laboratory bench to the ISS research platform.

Nucleic acids-based tools for ballast water surveillance, monitoring, and research

EPA Science Inventory

Understanding the risks of biological invasion posed by ballast water—whether in the context of compliance testing, routine monitoring, or basic research—is fundamentally an exercise in biodiversity assessment, and as such should take advantage of the best tools avail...

In search of a metatheory for cognitive development (or, Piaget is dead and I don't feel so good myself).

PubMed

Bjorklund, D F

1997-02-01

With the waning of influence of Piaget's theory and the shortcomings of information-processing perspectives of cognitive growth, cognitive developmentalists lack a common set of broad, overarching principles and assumptions--a metatheory--to guide their research. Developmental biology is suggested as metatheory for cognitive development. Although it is important for developmentalists to understand proximal biological causes (e.g., brain development), most important for such a metatheory is an evolutionary perspective. Some basic principles of evolutionary psychology are introduced, and examples of contemporary research and theory consistent with these ideas are provided.

A scientific role for Space Station Freedom: Research at the cellular level

NASA Technical Reports Server (NTRS)

Johnson, Terry C.; Brady, John N.

1993-01-01

The scientific importance of Space Station Freedom is discussed in light of the valuable information that can be gained in cellular and developmental biology with regard to the microgravity environment on the cellular cytoskeleton, cellular responses to extracellular signal molecules, morphology, events associated with cell division, and cellular physiology. Examples of studies in basic cell biology, as well as their potential importance to concerns for future enabling strategies, are presented.

Rich in life but poor in data: the known knowns and known unknowns of modelling how soil biology drives soil structure

NASA Astrophysics Data System (ADS)

Hallett, Paul; Ogden, Mike

2015-04-01

Soil biology has a fascinating capacity to manipulate pore structure by altering or overcoming hydrological and mechanical properties of soil. Many have postulated, quite rightly, that this capacity of soil biology to 'engineer' its habitat drives its diversity, improves competitiveness and increases resilience to external stresses. A large body of observational research has quantified pore structure evolution accompanied by the growth of organisms in soil. Specific compounds that are exuded by organisms or the biological structures they create have been isolated and found to correlate well with observed changes to pore structure or soil stability. This presentation will provide an overview of basic mechanical and hydrological properties of soil that are affected by biology, and consider missing data that are essential to model how they impact soil structure evolution. Major knowledge gaps that prevent progress will be identified and suggestions will be made of how research in this area should progress. We call for more research to gain a process based understanding of structure formation by biology, to complement observational studies of soil structure before and after imposed biological activity. Significant advancement has already been made in modelling soil stabilisation by plant roots, by combining data on root biomechanics, root-soil interactions and soil mechanical properties. Approaches for this work were developed from earlier materials science and geotechnical engineering research, and the same ethos should be adopted to model the impacts of other biological compounds. Fungal hyphae likely reinforce soils in a similar way to plant roots, with successful biomechanical measurements of these micron diameter structures achieved with micromechanical test frames. Extending root reinforcement models to fungi would not be a straightforward exercise, however, as interparticle bonding and changes to pore water caused by fungal exudates could have a major impact on structure formation and stability. Biological exudates from fungi, bacteria or roots have been found to decrease surface tension and increase viscosity of pore water, with observed impacts to soil strength and water retention. Modelling approaches developed in granular mechanics and geotechnical engineering could be built upon to incorporate biological transformations of hydrological and mechanical properties of soil. With new testing approaches, adapted from materials science, pore scale hydromechanical impacts from biological exudates can be quantified. The research can be complemented with model organisms with differences in biological structures (e.g. root hair mutants), exudation or other properties. Coupled with technological advances that provide 4D imaging of soil structure at relatively rapid capture rates, the potential opportunities to disentangle and model how biology drives soil structure evolution and stability are vast. By quantifying basic soil hydrological and mechanical processes that are driven by soil biology, unknown unknowns may also emerge, providing new insight into how soils function.

The 12th International Workshops on Opportunistic Protists (IWOP-12).

PubMed

Weiss, Louis M; Cushion, Melanie T; Didier, Elizabeth; Xiao, Lihua; Marciano-Cabral, Francine; Sinai, Anthony P; Matos, Olga; Calderon, Enrique J; Kaneshiro, Edna S

2013-01-01

The 12th International Workshops on Opportunistic Protists (IWOP-12) was held in August 2012 in Tarrytown, New York. The objectives of the IWOP meetings are to: (1) serve as a forum for exchange of new information among active researchers concerning the basic biology, molecular genetics, immunology, biochemistry, pathogenesis, drug development, therapy, and epidemiology of these immunodeficiency-associated pathogenic eukaryotic microorganisms that are seen in patients with AIDS and (2) foster the entry of new and young investigators into these underserved research areas. The IWOP meeting focuses on opportunistic protists, e.g. the free-living amoebae, Pneumocystis, Cryptosporidium, Toxoplasma, the Microsporidia, and kinetoplastid flagellates. This conference represents the major conference that brings together research groups working on these opportunistic pathogens. Slow but steady progress is being achieved on understanding the biology of these pathogenic organisms, their involvement in disease causation in both immune-deficient and immune-competent hosts, and is providing critical insights into these emerging and reemerging pathogens. This IWOP meeting demonstrated the importance of newly developed genomic level information for many of these pathogens and how analysis of such large data sets is providing key insights into the basic biology of these organisms. A great concern is the loss of scientific expertise and diversity in the research community due to the ongoing decline in research funding. This loss of researchers is due to the small size of many of these research communities and a lack of appreciation by the larger scientific community concerning the state of art and challenges faced by researchers working on these organisms. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

'Fish matters': the relevance of fish skin biology to investigative dermatology.

PubMed

Rakers, Sebastian; Gebert, Marina; Uppalapati, Sai; Meyer, Wilfried; Maderson, Paul; Sell, Anne F; Kruse, Charli; Paus, Ralf

2010-04-01

Fish skin is a multi-purpose tissue that serves numerous vital functions including chemical and physical protection, sensory activity, behavioural purposes or hormone metabolism. Further, it is an important first-line defense system against pathogens, as fish are continuously exposed to multiple microbial challenges in their aquatic habitat. Fish skin excels in highly developed antimicrobial features, many of which have been preserved throughout evolution, and infection defense principles employed by piscine skin are still operative in human skin. This review argues that it is both rewarding and important for investigative dermatologists to revive their interest in fish skin biology, as it provides insights into numerous fundamental issues that are of major relevance to mammalian skin. The basic molecular insights provided by zebrafish in vivo-genomics for genetic, regeneration and melanoma research, the complex antimicrobial defense systems of fish skin and the molecular controls of melanocyte stem cells are just some of the fascinating examples that illustrate the multiple potential uses of fish skin models in investigative dermatology. We synthesize the essentials of fish skin biology and highlight selected aspects that are of particular comparative interest to basic and clinically applied human skin research.

Stress biology and aging mechanisms: toward understanding the deep connection between adaptation to stress and longevity.

PubMed

Epel, Elissa S; Lithgow, Gordon J

2014-06-01

The rate of biological aging is modulated in part by genes interacting with stressor exposures. Basic research has shown that exposure to short-term stress can strengthen cellular responses to stress ("hormetic stress"). Hormetic stress promotes longevity in part through enhanced activity of molecular chaperones and other defense mechanisms. In contrast, prolonged exposure to stress can overwhelm compensatory responses ("toxic stress") and shorten lifespan. One key question is whether the stressors that are well understood in basic models of aging can help us understand psychological stressors and human health. The psychological stress response promotes regulatory changes important in aging (e.g., increases in stress hormones, inflammation, oxidative stress, insulin). The negative effects of severe stress are well documented in humans. Potential positive effects of acute stress (stress resistance) are less studied, especially at the cellular level. Can stress resistance slow the rate of aging in humans, as it does in model organisms? If so, how can we promote stress resistance in humans? We urge a new research agenda embracing the continuum from cellular stress to psychological stress, using basic and human research in tandem. This will require interdisciplinary novel approaches that hold much promise for understanding and intervening in human chronic disease. © The Author 2014. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Arctic research in the classroom: A teacher's experiences translated into data driven lesson plans

NASA Astrophysics Data System (ADS)

Kendrick, E. O.; Deegan, L.

2011-12-01

Incorporating research into high school science classrooms can promote critical thinking skills and provide a link between students and the scientific community. Basic science concepts become more relevant to students when taught in the context of research. A vital component of incorporating current research into classroom lessons is involving high school teachers in authentic research. The National Science Foundation sponsored Research Experience for Teachers (RET) program has inspired me to bring research to my classroom, communicate the importance of research in the classroom to other teachers and create lasting connections between students and the research community. Through my experiences as an RET at Toolik Field Station in Alaska, I have created several hands-on lessons and laboratory activities that are based on current arctic research and climate change. Each lesson uses arctic research as a theme for exemplifying basic biology concepts as well as increasing awareness of current topics such as climate change. For instance, data collected on the Kuparuk River will be incorporated into classroom activities that teach concepts such as primary production, trophic levels in a food chain and nutrient cycling within an ecosystem. Students will not only understand the biological concepts but also recognize the ecological implications of the research being conducted in the arctic. By using my experience in arctic research as a template, my students will gain a deeper understanding of the scientific process. I hope to create a crucial link of information between the science community and science education in public schools.

Toward University Modeling Instruction—Biology: Adapting Curricular Frameworks from Physics to Biology

PubMed Central

Manthey, Seth; Brewe, Eric

2013-01-01

University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence. PMID:23737628

Toward university modeling instruction--biology: adapting curricular frameworks from physics to biology.

PubMed

Manthey, Seth; Brewe, Eric

2013-06-01

University Modeling Instruction (UMI) is an approach to curriculum and pedagogy that focuses instruction on engaging students in building, validating, and deploying scientific models. Modeling Instruction has been successfully implemented in both high school and university physics courses. Studies within the physics education research (PER) community have identified UMI's positive impacts on learning gains, equity, attitudinal shifts, and self-efficacy. While the success of this pedagogical approach has been recognized within the physics community, the use of models and modeling practices is still being developed for biology. Drawing from the existing research on UMI in physics, we describe the theoretical foundations of UMI and how UMI can be adapted to include an emphasis on models and modeling for undergraduate introductory biology courses. In particular, we discuss our ongoing work to develop a framework for the first semester of a two-semester introductory biology course sequence by identifying the essential basic models for an introductory biology course sequence.

Life sciences research on the space station: An introduction

NASA Technical Reports Server (NTRS)

1985-01-01

The Space Station will provide an orbiting, low gravity, permanently manned facility for scientific research, starting in the 1990s. The facilities for life sciences research are being designed to allow scientific investigators to perform research in Space Medicine and Space Biology, to study the consequences of long-term exposure to space conditions, and to allow for the permanent presence of humans in space. This research, using humans, animals, and plants, will provide an understanding of the effects of the space environment on the basic processes of life. In addition, facilities are being planned for remote observations to study biologically important elements and compounds in space and on other planets (exobiology), and Earth observations to study global ecology. The life sciences community is encouraged to plan for participation in scientific research that will be made possible by the Space Station research facility.

Histochemistry in biology and medicine: a message from the citing journals.

PubMed

Pellicciari, Carlo

2015-12-23

Especially in recent years, biomedical research has taken advantage of the progress in several disciplines, among which microscopy and histochemistry. To assess the influence of histochemistry in the biomedical field, the articles published during the period 2011-2015 have been selected from different databases and grouped by subject categories: as expected, biological and biomedical studies where histochemistry has been used as a major experimental approach include a wide of basic and applied researches on both humans and other animal or plant organisms. To better understand the impact of histochemical publications onto the different biological and medical disciplines, it was useful to look at the journals where the articles published in a multidisciplinary journal of histochemistry have been cited: it was observed that, in the five-years period considered, 20% only of the citations were in histochemical periodicals, the remaining ones being in journals of Cell & Tissue biology,  general and experimental Medicine, Oncology, Biochemistry & Molecular biology, Neurobiology, Anatomy & Morphology, Pharmacology & Toxicology, Reproductive biology, Veterinary sciences, Physiology, Endocrinology, Tissue engineering & Biomaterials,  as well as in multidisciplinary journals.It is easy to foresee that also in the future the histochemical journals will be an attended forum for basic and applied scientists in the biomedical field. It will be crucial that these journals be open to an audience as varied as possible, publishing articles on the application of refined techniques to very different experimental models: this will stimulate non-histochemist scientists to approach histochemistry whose application horizon could expand to novel and possibly exclusive subjects.

Histochemistry in Biology and Medicine: A Message From the Citing Journals

PubMed Central

2015-01-01

Especially in recent years, biomedical research has taken advantage of the progress in several disciplines, among which microscopy and histochemistry. To assess the influence of histochemistry in the biomedical field, the articles published during the period 2011-2015 have been selected from different databases and grouped by subject categories. As expected, biological and biomedical studies where histochemistry has been used as a major experimental approach include a wide range of basic and applied researches on both humans and other animal or plant organisms. To better understand the impact of histochemical publications onto the different biological and medical disciplines, it was useful to look at the journals where the articles published in a multidisciplinary journal of histochemistry have been cited: it was observed that, in the five-years period considered, 20% only of the citations were in histochemical periodicals, the remaining ones being in journals of Cell & Tissue biology, general and experimental Medicine, Oncology, Biochemistry & Molecular biology, Neurobiology, Anatomy & Morphology, Pharmacology & Toxicology, Reproductive biology, Veterinary sciences, Physiology, Endocrinology, Tissue engineering & Biomaterials, as well as in multidisciplinary journals. It is easy to foresee that also in the future the histochemical journals will be an attended forum for basic and applied scientists in the biomedical field. It will be crucial that these journals be open to an audience as varied as possible, publishing articles on the application of refined techniques to very different experimental models: this will stimulate non-histochemist scientists to approach histochemistry whose application horizon could expand to novel and possibly exclusive subjects. PMID:26708189

Housing and maintenance of Ambystoma mexicanum, the Mexican axolotl.

PubMed

Farkas, Johanna E; Monaghan, James R

2015-01-01

The aim of this paper is to assemble a significant amount of information on Ambystoma mexicanum, the axolotl salamander, to assist in the basic knowledge needed to raise, breed, and study most aspects of axolotl biology. It is important to understand the basic biology of the axolotl in order to make informed decisions on their proper care and use in experiments. Therefore, we will provide necessary information to the non-herpetologist that will assist in their study of this unique and fascinating animal. We also aim to provide a resource on the general anatomy, behavior, and experimental tips specific to the Mexican axolotl that will be of use to most axolotl laboratories. Axolotls have been actively researched since the 1860s, giving testament to their relatively straightforward maintenance and their versatility as an animal model for development and regeneration. Interest in using the axolotl in laboratory research has grown tremendously over the past decade, so dedicated resources to support the study of this species are needed and encouraged.

Interview: from Down's syndrome to basic epigenetics and back again.

PubMed

Lawrence, Jeanne; Telfer, Caroline

2013-12-01

Dr Jeanne Lawrence talks to Caroline Telfer, Commissioning Editor. Dr Jeanne Lawrence is an internationally recognized leader in the study of chromosome regulation by noncoding RNA and nuclear and genome organization. Her research bridges fundamental questions about genome regulation with clinical implications of recent advances in epigenetics. Her interest in chromosome structure and regulation has been a theme throughout her career and she has been honored for her work developing sensitive FISH technology for the detection of single copy genes, as well as RNAs. Her laboratory's publications include the initial demonstration of cell type-specific gene organization with nuclear subdomains; the novel biology of a noncoding RNA, XIST, which coats a whole X-chromosome to induce its silencing; and a new architectural role for a large noncoding RNA to scaffold a nuclear body. Her laboratory's work on epigenetic chromosome regulation in stem cells led to recent studies regarding unanticipated roles of repeat sequences in normal chromosome regulation and deregulation in cancer. Most recently, her laboratory has demonstrated a new approach to translate the basic mechanism of X-chromosome inactivation to correct a chromosomal dosage imbalance in patient-derived cells with trisomy 21 (Down's syndrome). Dr Lawrence has received awards from numerous agencies, including a Research Career Development Award from the National Center for Human Genome Research, career awards from the American Society of Cell Biology, the German Society for Biochemistry, the Muscular Dystrophy Association and a John Merck Fund Translational Research Award. She has served on the NIH National Advisory Council for Human Genome Research, numerous study sections and is currently a monitoring editor for the Journal of Cell Biology. Dr Lawrence has a BA in Biology and Music from Stephens College (MO, USA), a MS in Human Genetics and Genetic Counseling from Rutgers University (NJ, USA) and a PhD in Developmental Biology from Brown University (RI, USA). She is currently a Professor and Interim Chair of the Department of Cell and Developmental Biology at the University of Massachusetts Medical School (MA, USA).

Middle/high school students in the research laboratory: A summer internship program emphasizing the interdisciplinary nature of biology.

PubMed

McMiller, Tracee; Lee, Tameshia; Saroop, Ria; Green, Tyra; Johnson, Casonya M

2006-03-01

We describe an eight-week summer Young Scientist in Training (YSIT) internship program involving middle and high school students. This program exposed students to current basic research in molecular genetics, while introducing or reinforcing principles of the scientific method and demonstrating the uses of mathematics and chemistry in biology. For the laboratory-based program, selected students from Baltimore City Schools working in groups of three were teamed with undergraduate research assistants at Morgan State University. Teams were assigned a project that was indirectly related to our laboratory research on the characterization of gene expression in Caenorhabditis elegans. At the end of the program, teams prepared posters detailing their accomplishments, and presented their findings to parents and faculty members during a mini-symposium. The posters were also submitted to the respective schools and the interns were offered a presentation of their research at local high school science fairs. Copyright © 2006 International Union of Biochemistry and Molecular Biology, Inc.

Summary of the International Conference on Arabidopsis Research 2011, June 22-25, 2011

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

Meyers, Blake C

2012-07-15

This project provided participant support for the gathering of plant biologists at the International Conferences on Arabidopsis Research (ICAR) in 2011. Arabidopsis thaliana, the reference flowering plant, has been intensely studied over the last 20 years and has proven to be an ideal model for studying nearly all aspects of plant biology. The success of this research field has been greatly facilitated by the openness and collegiality of the community fostered through multiple international forums including the ICAR. Advances in basic and applied plant biology are featured at the meeting, which is the primary gathering point for this strongly integratedmore » international community. The ICAR convenes plant researchers, allows discussion and dissemination of the latest research in plant biology, and facilitates dialog among those that may be separated by geography, career stage, and culture. This project focused on facilitating access by early career scientists that have reduced access to attend major meetings.« less

Assessment of knowledge of participants on basic molecular biology techniques after 5-day intensive molecular biology training workshops in Nigeria.

PubMed

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

2017-07-08

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 Medical Research (NIMR), to improve the knowledge and skills of laboratory personnel and academics in health, research, and educational facilities. Five-day molecular biology workshops were conducted annually between 2011 and 2014, with participants drawn from health, research facilities, and the academia. The courses consisted of theoretical and practical sessions. The impact of the workshops on knowledge and skill acquisition was evaluated by pre- and post-tests which consisted of 25 multiple choice and other questions. Sixty-five participants took part in the workshops. The mean knowledge of molecular biology as evaluated by the pre- and post-test assessments were 8.4 (95% CI 7.6-9.1) and 13.0 (95 CI 11.9-14.1), respectively. The mean post-test score was significantly greater than the mean pre-test score (p < 0.0001). The five-day molecular biology workshop significantly increased the knowledge and skills of participants in molecular biology techniques. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(4):313-317, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

Soil bed reactor work of the Environmental Research Lab. of the University of Arizona in support of the research and development of Biosphere 2

NASA Technical Reports Server (NTRS)

Frye, Robert

1990-01-01

Research at the Environmental Research Lab in support of Biosphere 2 was both basic and applied in nature. One aspect of the applied research involved the use of biological reactors for the scrubbing of trace atmospheric organic contaminants. The research involved a quantitative study of the efficiency of operation of Soil Bed Reactors (SBR) and the optimal operating conditions for contaminant removal. The basic configuration of a SBR is that air is moved through a living soil that supports a population of plants. Upon exposure to the soil, contaminants are either passively adsorbed onto the surface of soil particles, chemically transformed in the soil to usable compounds that are taken up by the plants or microbes as a metabolic energy source and converted to CO2 and water.

Laboratory for Energy-Related Health Research: Annual report, fiscal year 1987

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

Abell, D.L.

1989-04-01

The laboratory's research objective is to provide new knowledge for an improved understanding of the potential bioenvironmental and occupational health problems associated with energy utilization. Our purpose is to contribute to the safe and healthful development of energy resources for the benefit of mankind. This research encompasses several areas of basic investigation that relate to toxicological and biomedical problems associated with potentially toxic chemical and radioactive substances and ionizing radiation, with particular emphasis on carcinogenicity. Studies of systemic injury and nuclear-medical diagnostic and therapeutic methods are also involved. This program is interdisciplinary; it involves physics, chemistry, environmental engineering, biophysics andmore » biochemistry, cellular and molecular biology, physiology, immunology, toxicology, both human and veterinary medicine, nuclear medicine, pathology, hematology, radiation biology, reproductive biology, oncology, biomathematics, and computer science. The principal themes of the research at LEHR center around the biology, radiobiology, and health status of the skeleton and its blood-forming constituents; the toxicology and properties of airborne materials; the beagle as an experimental animal model; carcinogenesis; and the scaling of the results from laboratory animal studies to man for appropriate assessment of risk.« less

Invited Review Article: Current State of Research on Biological Effects of Terahertz Radiation

NASA Astrophysics Data System (ADS)

Wilmink, Gerald J.; Grundt, Jessica E.

2011-10-01

Terahertz (THz) imaging and sensing technologies are increasingly being used in a host of medical, military, and security applications. For example, THz systems are now being tested at international airports for security screening purposes, at major medical centers for cancer and burn diagnosis, and at border patrol checkpoints for identification of concealed explosives, drugs, and weapons. Recent advances in THz applications have stimulated renewed interest regarding the biological effects associated with this frequency range. Biological effects studies are a valuable type of basic science research because they serve to enhance our fundamental understanding of the mechanisms that govern THz interactions with biological systems. Such studies are also important because they often times lay the foundation for the development of future applications. In addition, from a practical standpoint, THz biological effects research is also necessary for accurate health hazard evaluation, the development of empirically-based safety standards, and for the safe use of THz systems. Given the importance and timeliness of THz bioeffects data, the purpose of this review is twofold. First, to provide readers with a common reference, which contains the necessary background concepts in biophysics and THz technology, that are required to both conduct and evaluate THz biological research. Second, to provide a critical review of the scientific literature.

Cell biology, biophysics, and mechanobiology: From the basics to Clinics.

PubMed

Zeng, Y

2017-04-29

Cell biology, biomechanics and biophysics are the key subjects that guide our understanding in diverse areas of tissue growth, development, remodeling and homeostasis. Novel discoveries such as molecular mechanism, and mechanobiological mechanism in cell biology, biomechanics and biophysics play essential roles in our understanding of the pathogenesis of various human diseases, as well as in designing the treatment of these diseases. In addition, studies in these areas will also facilitate early diagnostics of human diseases, such as cardiovascular diseases and cancer. In this special issue, we collected 10 original research articles and 1 review...

The biology of cancer: what do oncology nurses really need to know.

PubMed

Eggert, Julie

2011-02-01

To describe the impact of genetics and genomics on the biology of cancer and the implications for patient care. Pubmed; CINAHL. Cancer research in genetics/genomics has identified new mechanisms influencing personalized risk assessment/management, early detection, cancer treatment, and long-term screening/surveillance. Understanding the basics of genetics/genomics on the biology of cancer will facilitate patient education and care delivery, including the administration and monitoring of genetically targeted therapies whose toxicities may in part be mediated by the molecular pathways targeted by the specific agent. Copyright © 2011 Elsevier Inc. All rights reserved.

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

PubMed Central

Mulder, Nicola J.; Christoffels, Alan; de Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Ché S.; Snoep, Jacky L.; Tastan Bishop, Özlem; Tiffin, Nicki

2016-01-01

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt. PMID:26845152

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt.

PubMed

Mulder, Nicola J; Christoffels, Alan; de Oliveira, Tulio; Gamieldien, Junaid; Hazelhurst, Scott; Joubert, Fourie; Kumuthini, Judit; Pillay, Ché S; Snoep, Jacky L; Tastan Bishop, Özlem; Tiffin, Nicki

2016-02-01

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.

Postdoctoral Fellow | Center for Cancer Research

Cancer.gov

The Neural Development Section (NDS) headed by Dr. Lino Tessarollo has an open postdoctoral fellow position. The candidate should have a background in neurobiology and basic expertise in molecular biology, cell biology, immunoistochemistry and biochemistry.  Experience in confocal analysis is desired. The NDS study the biology of neurotrophin and Trk receptors function by using both in vitro and in vivo approaches. Our group makes extensive use of engineered mouse models and cell culture models. The current research emphasis is on understanding the molecular mechanisms by which activated trk receptor function. Specifically, we are dissecting the molecular mechanism responsible for modulating Trk receptors activity, including their interaction with specific scaffold proteins and proteins leading to de-activation of Trk signaling. Moreover, we are attempting to identify new signaling pathways activated by truncated Trk receptors.

Synergy of understanding dermatologic disease and epidermal biology.

PubMed

Stanley, John R

2012-02-01

Dermatologic disease, although seldom life threatening, can be extremely disfiguring and interfere with the quality of life. In addition, as opposed to other organs, just the aging of skin and its adnexal structure the hair follicle can result in cosmetic concerns that affect most of us. The articles in this dermatology Review Series demonstrate recent progress in understanding the cell biology and molecular pathophysiology of the epidermis and hair follicles, which harbor keratinocyte and melanocyte stem cells. They reveal a dynamic relationship between research and clinical care: knowledge of dermatologic disease has facilitated the understanding of the biology of the epidermis and, in turn, progress in basic science has informed our understanding of disease. This type of synergy is a profound strength of clinical research of the type that the JCI is dedicated to publishing.

The Emergence of Geroscience as an Interdisciplinary Approach to the Enhancement of Health Span and Life Span

PubMed Central

Sierra, Felipe

2016-01-01

Research on the biology of aging has accelerated rapidly in the last two decades. It is now at the point where translation of the findings into useful approaches to improve the health of the elderly population seems possible. In trying to fill that gap, a new field termed geroscience will be articulated here that attempts to identify the biological underpinnings for the age-dependency of most chronic diseases. Herein, I will review the major conceptual issues leading to the formulation of geroscience as a field, as well as give examples of current areas of inquiry in which basic aging biology research could lead to therapeutic approaches to address age-related chronic diseases, not one at a time, but most of them in unison. PMID:26931460

2011 Vascular Research Initiatives Conference: basic foundations of translational research in vascular disease.

PubMed

Ziegler, Kenneth R; Dardik, Alan

2011-07-01

The Vascular Research Initiatives Conference (VRIC) is an annual conference organized by the Society for Vascular Surgery (SVS). The 2011 VRIC was held in Chicago (IL, USA) to precede and coincide with the first day of the meeting of the Council on Arteriosclerosis, Thrombosis and Vascular Biology (ATVB) of the American Heart Association. The event is designed to present world class vascular research results, encourage collaboration between vascular surgeons and basic scientists in related disciplines, as well as to stimulate interest in research among aspiring academic vascular surgeons. The 2011 VRIC featured plenary sessions addressing peripheral arterial disease, vascular endothelium and thrombosis, aneurysms, and stem cells and tissue engineering. Recipients of the SVS partner grants with the National Institutes of Health K08 awardees presented their progress reports, and keynote addresses were given by Linda Graham and Frank LoGerfo.

Cell biology: at the center of modern biomedicine.

PubMed

Budde, Priya Prakash; Williams, Elizabeth H; Misteli, Tom

2012-10-01

How does basic cell biology contribute to biomedicine? A new series of Features in JCB provides a cross section of compelling examples of how basic cell biology findings can lead to therapeutics. These articles highlight the fruitful, essential, and increasingly prominent bridge that exists between cell biology and the clinic.

Expression and Purification of Recombinant Human Basic Fibroblast Growth Factor Fusion Proteins and Their Uses in Human Stem Cell Culture.

PubMed

Imsoonthornruksa, Sumeth; Pruksananonda, Kamthorn; Parnpai, Rangsun; Rungsiwiwut, Ruttachuk; Ketudat-Cairns, Mariena

2015-01-01

To reduce the cost of cytokines and growth factors in stem cell research, a simple method for the production of soluble and biological active human basic fibroblast growth factor (hbFGF) fusion protein in Escherichia coli was established. Under optimal conditions, approximately 60-80 mg of >95% pure hbFGF fusion proteins (Trx-6xHis-hbFGF and 6xHis-hbFGF) were obtained from 1 liter of culture broth. The purified hbFGF proteins, both with and without the fusion tags, were biologically active, which was confirmed by their ability to stimulate proliferation of NIH3T3 cells. The fusion proteins also have the ability to support several culture passages of undifferentiated human embryonic stem cells and induce pluripotent stem cells. This paper describes a low-cost and uncomplicated method for the production and purification of biologically active hbFGF fusion proteins. © 2015 S. Karger AG, Basel.

Opportunities and challenges of current electrophysiology research: a plea to establish 'translational electrophysiology' curricula.

PubMed

Lau, Dennis H; Volders, Paul G A; Kohl, Peter; Prinzen, Frits W; Zaza, Antonio; Kääb, Stefan; Oto, Ali; Schotten, Ulrich

2015-05-01

Cardiac electrophysiology has evolved into an important subspecialty in cardiovascular medicine. This is in part due to the significant advances made in our understanding and treatment of heart rhythm disorders following more than a century of scientific discoveries and research. More recently, the rapid development of technology in cellular electrophysiology, molecular biology, genetics, computer modelling, and imaging have led to the exponential growth of knowledge in basic cardiac electrophysiology. The paradigm of evidence-based medicine has led to a more comprehensive decision-making process and most likely to improved outcomes in many patients. However, implementing relevant basic research knowledge in a system of evidence-based medicine appears to be challenging. Furthermore, the current economic climate and the restricted nature of research funding call for improved efficiency of translation from basic discoveries to healthcare delivery. Here, we aim to (i) appraise the broad challenges of translational research in cardiac electrophysiology, (ii) highlight the need for improved strategies in the training of translational electrophysiologists, and (iii) discuss steps towards building a favourable translational research environment and culture. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2015. For permissions please email: journals.permissions@oup.com.

Making evolutionary biology a basic science for medicine

PubMed Central

Nesse, Randolph M.; Bergstrom, Carl T.; Ellison, Peter T.; Flier, Jeffrey S.; Gluckman, Peter; Govindaraju, Diddahally R.; Niethammer, Dietrich; Omenn, Gilbert S.; Perlman, Robert L.; Schwartz, Mark D.; Thomas, Mark G.; Stearns, Stephen C.; Valle, David

2010-01-01

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease. PMID:19918069

Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

PubMed

Nesse, Randolph M; Bergstrom, Carl T; Ellison, Peter T; Flier, Jeffrey S; Gluckman, Peter; Govindaraju, Diddahally R; Niethammer, Dietrich; Omenn, Gilbert S; Perlman, Robert L; Schwartz, Mark D; Thomas, Mark G; Stearns, Stephen C; Valle, David

2010-01-26

New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and when and how they should learn it. Our general conclusion is that evolutionary biology is a crucial basic science for medicine. In addition to looking at established evolutionary methods and topics, such as population genetics and pathogen evolution, we highlight questions about why natural selection leaves bodies vulnerable to disease. Knowledge about evolution provides physicians with an integrative framework that links otherwise disparate bits of knowledge. It replaces the prevalent view of bodies as machines with a biological view of bodies shaped by evolutionary processes. Like other basic sciences, evolutionary biology needs to be taught both before and during medical school. Most introductory biology courses are insufficient to establish competency in evolutionary biology. Premedical students need evolution courses, possibly ones that emphasize medically relevant aspects. In medical school, evolutionary biology should be taught as one of the basic medical sciences. This will require a course that reviews basic principles and specific medical applications, followed by an integrated presentation of evolutionary aspects that apply to each disease and organ system. Evolutionary biology is not just another topic vying for inclusion in the curriculum; it is an essential foundation for a biological understanding of health and disease.

Knowledge, Expectations, and Inductive Reasoning within Conceptual Hierarchies

ERIC Educational Resources Information Center

Coley, John D.; Hayes, Brett; Lawson, Christopher; Moloney, Michelle

2004-01-01

Previous research (e.g. "Cognition" 64 (1997) 73) suggests that the privileged level for inductive inference in a folk biological conceptual hierarchy does not correspond to the ''basic'' level (i.e. the level at which concepts are both informative and distinct). To further explore inductive inference within conceptual hierarchies, we examine…

An organismal view of dendrochronology

Treesearch

Kevin T. Smith

2008-01-01

An organism is the most basic unit of independent life. The tree-ring record is defined by organismal processes. Dendrochronology contributes to investigations far removed from organismal biology, e.g., archeology, climatology, disturbance ecology, etc. The increasing integration of dendrochronology into a diverse research community suggests an opportunity for a brief...

Fundulus as the Premier Teleost Model in Environmental Biology: Opportunities for New Insights Using Genomics

EPA Science Inventory

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an ex...

Laboratory Safety in the Biology Lab.

ERIC Educational Resources Information Center

Ritch, Donna; Rank, Jane

2001-01-01

Reports on a research project to determine if students possess and comprehend basic safety knowledge. Shows a significant increase in the amount of safety knowledge gained when students are exposed to various topics in laboratory safety and are held accountable for learning the information as required in a laboratory safety course. (Author/MM)

Wilderness and well-being: Complexity, time, and psychological growth

Treesearch

Joar Vitterso

2002-01-01

This paper presents the argument for interdisciplinary wilderness research. The idea of interdisciplinarity is grounded in theories of emotion and psychological growth that are compatible with basic knowledge in other scientific disciplines, and in particular with concepts related to evolution. Considering humans as biological knowledge systems, designed by natural...

Independent Gene Discovery and Testing

ERIC Educational Resources Information Center

Palsule, Vrushalee; Coric, Dijana; Delancy, Russell; Dunham, Heather; Melancon, Caleb; Thompson, Dennis; Toms, Jamie; White, Ashley; Shultz, Jeffry

2010-01-01

A clear understanding of basic gene structure is critical when teaching molecular genetics, the central dogma and the biological sciences. We sought to create a gene-based teaching project to improve students' understanding of gene structure and to integrate this into a research project that can be implemented by instructors at the secondary level…

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

NASA Astrophysics Data System (ADS)

Susanti, R.; Anwar, Y.; Ermayanti

2018-04-01

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

Inhalation Toxicology Research Institute annual report, October 1, 1994--September 30, 1995

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

Bice, D.E.; Hahn, F.F.; Hoover, M.D.

1995-12-01

The mission of the Inhalation Toxicology Research Institute (ITRI) is to conduct basic and applied research to improve the understanding of the nature and magnitude of the human health impacts of inhaling airborne materials in the home, workplace, and general environment. Institute research programs have a strong basic science orientation with emphasis on the nature and behavior of airborne materials, the fundamental biology of the respiratory tract, the fate of inhaled materials and the mechanisms by which they cause disease, and the means by which data produced in the laboratory can be used to estimate risks to human health. Disordersmore » of the respiratory tract continue to be a major health concern, and inhaled toxicants are thought to contribute substantially to respiratory morbidity. As the largest laboratory dedicated to the study of basic inhalation toxicology, ITRI provides a national resource of specialized facilities, personnel, and educational activities serving the needs of government, academia, and industry. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.« less

TMS-EEG: From basic research to clinical applications

NASA Astrophysics Data System (ADS)

Hernandez-Pavon, Julio C.; Sarvas, Jukka; Ilmoniemi, Risto J.

2014-11-01

Transcranial magnetic stimulation (TMS) combined with electroencephalography (EEG) is a powerful technique for non-invasively studying cortical excitability and connectivity. The combination of TMS and EEG has widely been used to perform basic research and recently has gained importance in different clinical applications. In this paper, we will describe the physical and biological principles of TMS-EEG and different applications in basic research and clinical applications. We will present methods based on independent component analysis (ICA) for studying the TMS-evoked EEG responses. These methods have the capability to remove and suppress large artifacts, making it feasible, for instance, to study language areas with TMS-EEG. We will discuss the different applications and limitations of TMS and TMS-EEG in clinical applications. Potential applications of TMS are presented, for instance in neurosurgical planning, depression and other neurological disorders. Advantages and disadvantages of TMS-EEG and its variants such as repetitive TMS (rTMS) are discussed in comparison to other brain stimulation and neuroimaging techniques. Finally, challenges that researchers face when using this technique will be summarized.

Genetics as a modernization program: biological research at the Kaiser Wilhelm Institutes and the political economy of the Nazi State.

PubMed

Gausemeier, Bernd

2010-01-01

During the Third Reich, the biological institutes of the Kaiser Wilhelm Society (KWG, Kaiser-Wilhelm-Gesellschaft) underwent a substantial reorganization and modernization. This paper discusses the development of projects in the fields of biochemical genetics, virus research, radiation genetics, and plant genetics that were initiated in those years. These cases exemplify, on the one hand, the political conditions for biological research in the Nazi state. They highlight how leading scientists advanced their projects by building close ties with politicians and science-funding organizations and companies. On the other hand, the study examines how the contents of research were shaped by, and how they contributed to, the aims and needs of the political economy of the Nazi system. This paper therefore aims not only to highlight basic aspects of scientific development under Nazism, but also to provide general insights into the structure of the Third Reich and the dynamics of its war economy.

The molecular biology of soft-tissue sarcomas and current trends in therapy.

PubMed

Quesada, Jorge; Amato, Robert

2012-01-01

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.

SH2 Domain-Based FRET Biosensor for Measuring BCR-ABL Activity in Living CML Cells.

PubMed

Fujioka, Mari; Asano, Yumi; Nakada, Shigeyuki; Ohba, Yusuke

2017-01-01

Fluorescent proteins (FPs) displaying distinct spectra have shed their light on a wide range of biological functions. Moreover, sophisticated biosensors engineered to contain single or multiple FPs, including Förster resonance energy transfer (FRET)-based biosensors, spatiotemporally reveal the molecular mechanisms underlying a variety of pathophysiological processes. However, their usefulness for applied life sciences has yet to be fully explored. Recently, our research group has begun to expand the potential of FPs from basic biological research to the clinic. Here, we describe a method to evaluate the responsiveness of leukemia cells from patients to tyrosine kinase inhibitors using a biosensor based on FP technology and the principle of FRET. Upon phosphorylation of the tyrosine residue of the biosensor, binding of the SH2 domain to phosphotyrosine induces conformational change of the biosensor and brings the donor and acceptor FPs into close proximity. Therefore, kinase activity and response to kinase inhibitors can be monitored by an increase and a decrease in FRET efficiency, respectively. As in basic research, this biosensor resolves hitherto arduous tasks and may provide innovative technological advances in clinical laboratory examinations. State-of-the-art detection devices that enable such innovation are also introduced.

Thirty-sixth Lauriston S. Taylor Lecture on radiation protection and measurements--from the field to the laboratory and back: the what ifs, wows, and who cares of radiation biology.

PubMed

Brooks, Antone L

2013-11-01

My scientific journey started at the University of Utah chasing fallout. It was on everything, in everything, and was distributed throughout the ecosystem. This resulted in radiation doses to humans and caused me great concern. From this concern I asked the question, "Are there health effects from these radiation doses and levels of radioactive contamination?" I have invested my scientific career trying to address this basic question. While conducting research, I got acquainted with many of the What ifs of radiation biology. The major What if in my research was, "What if we have underestimated the radiation risk for internally-deposited radioactive material?" While conducting research to address this important question, many other What ifs came up related to dose, dose rate, and dose distribution. I also encountered a large number of Wows. One of the first was when I went from conducting environmental fallout studies to research in a controlled laboratory. The activity in fallout was expressed as pCi L⁻¹, whereas it was necessary to inject laboratory animals with μCi g⁻¹ body weight to induce measurable biological changes, chromosome aberrations, and cancer. Wow! That is seven to nine orders of magnitude above the activity levels found in the environment. Other Wows have made it necessary for the field of radiation biology to make important paradigm shifts. For example, one shift involved changing from "hit theory" to total tissue responses as the result of bystander effects. Finally, Who cares? While working at U.S. Department of Energy headquarters and serving on many scientific committees, I found that science does not drive regulatory and funding decisions. Public perception and politics seem to be major driving forces. If scientific data suggested that risk had been underestimated, everyone cared. When science suggested that risk had been overestimated, no one cared. This result-dependent Who cares? was demonstrated as we tried to generate interactions by holding meetings with individuals involved in basic low-dose research, regulators, and the news media. As the scientists presented their "exciting data" that suggested that risk was overestimated, many of the regulators simply said, "We cannot use such data." The newspaper people said, "It is not possible to get such information by my editors." In spite of these difficulties, research results from basic science must be made available and considered by members of the public as well as by those that make regulatory recommendations. Public outreach of the data is critical and must continue to be a future focus to address properly the question of, "Who cares?" My journey in science, like many of yours, has been a mixture of chasing money, beatings, and the joys of unique and interesting research results. Perhaps through our experiences, we can improve research environments, funding, and use of the valuable information that is generated. Scientists that study at all levels of biological organization, from the environment to the laboratory and human epidemiology, must share expertise and data to address the What Ifs, Wows, and Who Cares of radiation biology.

Federal Research and Development Funding: FY2017

DTIC Science & Technology

2016-06-24

facilities and equipment; does not include physical assets for R&D such as R&D equipment and facilities or routine product testing, quality control...multiagency R&D initiative to advance understanding and control of matter at the nanoscale, where the physical , chemical, and biological properties of...nuclear programs that dated back to the Manhattan Project. Today, DOE conducts basic scientific research in areas ranging from nuclear physics to the

The Meduza experiment: An orbital complex ten weeks in flight

NASA Technical Reports Server (NTRS)

Ovcharov, V.

1979-01-01

The newspaper article discusses the contribution of space research to understanding the origin of life on Earth. Part of this basic research involves studying amino acids, ribonucleic acid and DNA molecules subjected to cosmic radiation. The results from the Meduza experiment are not all analyzed as yet. The article also discusses the psychological changes in cosmonauts as evidenced by their attitude towards biology experiments in space.

On the future contents of a small journal of histochemistry.

PubMed

Pellicciari, C

2012-12-10

In the last three years, more than 70,000 scientific articles have been published in peer reviewed journals on the application of histochemistry in the biomedical field: most of them did not appear in strictly histochemical journals, but in others dealing with cell and molecular biology, medicine or biotechnology. This proves that histochemistry is still an active and innovative discipline with relevance in basic and applied biological research, but also demonstrates that especially the small histochemical Journals should likely reconsider their scopes and strategies to preserve their authorship. A review of the last three years volumes of the European Journal of Histochemistry, taken as an example of a long-time established small Journal, confirmed that the published articles were widely heterogeneous in their topics and experimental models, as in this Journal's tradition. This strongly suggests that a Journal of histochemistry should keep its role as a forum open to an audience as broad as possible, publishing papers on cell and tissue biology in a wide variety of models. This will improve knowledge of the basic mechanisms of development and differentiation, while helping to increase the number of potential authors since scientists who generally do not use histochemistry in their research will find hints for the applications of histochemical techniques to novel still unexplored subjects.

On the future contents of a small journal of histochemistry

PubMed Central

Pellicciari, C.

2012-01-01

In the last three years, more than 70,000 scientific articles have been published in peer reviewed journals on the application of histochemistry in the biomedical field: most of them did not appear in strictly histochemical journals, but in others dealing with cell and molecular biology, medicine or biotechnology. This proves that histochemistry is still an active and innovative discipline with relevance in basic and applied biological research, but also demonstrates that especially the small histochemical journals should likely reconsider their scopes and strategies to preserve their authorship. A review of the last three years volumes of the European Journal of Histochemistry, taken as an example of a long-time established small journal, confirmed that the published articles were widely heterogeneous in their topics and experimental models, as in this journal's tradition. This strongly suggests that a journal of histochemistry should keep its role as a forum open to an audience as broad as possible, publishing papers on cell and tissue biology in a wide variety of models. This will improve knowledge of the basic mechanisms of development and differentiation, while helping to increase the number of potential authors since scientists who generally do not use histochemistry in their research will find hints for the applications of histochemical techniques to novel still unexplored subjects. PMID:23361247

From high dilutions to digital biology: the physical nature of the biological signal.

PubMed

Thomas, Yolène

2015-10-01

The memory of water was a radical idea that arose in the laboratory of Jacques Benveniste in the late 1980s. Twenty-five years have passed and yet the often angry debate on its merits continues despite the increasing number of scientists who have reported confirmation of the basic results. One working hypothesis was that molecules can communicate with each other, exchanging information without being in physical contact and that at least some biological functions can be mimicked by certain energetic modes characteristics of a given molecule. These considerations informed exploratory research which led to the speculation that biological signaling might be transmissible by electromagnetic means. Around 1991, the transfer of specific molecular signals to sensitive biological systems was achieved using an amplifier and electromagnetic coils. In 1995, a more sophisticated procedure was established to record, digitize and replay these signals using a multimedia computer. From a physical and chemical perspective, these experiments pose a riddle, since it is not clear what mechanism can sustain such 'water memory' of the exposure to molecular signals. From a biological perspective, the puzzle is what nature of imprinted effect (water structure) can impact biological function. A parallel can be drawn between this debate on the memory of water, which presumes that the action of molecules is mediated by an electromagnetic phenomenon, and the often acrimonious debate on the transmission of nerve influxes via synaptic transfer of specific molecules, neurotransmitters. The latter debate began in 1921 with the first experiments by Loewi and was still active in 1949, 28 years later. A strong reluctance to accept research that questions basic aspects of long-accepted biochemical paradigms is to be expected. In this paper we will provide a brief summary of experiments relating to the memory of water: the earlier work on high dilutions (HD) and then the experiments, which followed and continue today, on digital biology. Copyright © 2015 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

[Interferon. An overview of the state of basic research with special regard to interferon-gamma].

PubMed

Günther, G; Otto, B

1993-02-01

Interferons / An overview on the state of basic research with special regard to interferon-gamma Interferons are multifunctional glycoproteins with a broad range of antiviral, antiproliferative and immunoregulatory effects on the target cell. This review deals with the basics as well as with more recent developments in interferon research. A historic overview of 35 years of interferon research since the discovery of interferons by Isaacs and Lindenmann in 1957 introduces the most important milestones in this field and appreciates the work of the participating researchers. A brief description of the classification of interferons based on different tissue sources, different antigenic properties and different induction behaviour is made. The main part of this review focuses on human interferon-gamma. We discuss recent work on the structure-function relationship of interferon-gamma. The interferon-gamma receptor and its role in signal transduction is another part of this paper. The structure and length of the C-terminal region of interferon-gamma seems to be important for receptor binding and expression of biological activities. A conservative estimate is that the family of IFN-activated genes numbers 15-20 in most cells.

An Undergraduate Course to Bridge the Gap between Textbooks and Scientific Research

PubMed Central

Wiegant, Fred; Scager, Karin; Boonstra, Johannes

2011-01-01

This article reports on a one-semester Advanced Cell Biology course that endeavors to bridge the gap between gaining basic textbook knowledge about cell biology and learning to think and work as a researcher. The key elements of this course are 1) learning to work with primary articles in order to get acquainted with the field of choice, to learn scientific reasoning, and to identify gaps in our current knowledge that represent opportunities for further research; 2) formulating a research project with fellow students; 3) gaining thorough knowledge of relevant methodology and technologies used within the field of cell biology; 4) developing cooperation and leadership skills; and 5) presenting and defending research projects before a jury of experts. The course activities were student centered and focused on designing a genuine research program. Our 5-yr experience with this course demonstrates that 1) undergraduate students are capable of delivering high-quality research designs that meet professional standards, and 2) the authenticity of the learning environment in this course strongly engages students to become self-directed and critical thinkers. We hope to provide colleagues with an example of a course that encourages and stimulates students to develop essential research thinking skills. PMID:21364103

An undergraduate course to bridge the gap between textbooks and scientific research.

PubMed

Wiegant, Fred; Scager, Karin; Boonstra, Johannes

2011-01-01

This article reports on a one-semester Advanced Cell Biology course that endeavors to bridge the gap between gaining basic textbook knowledge about cell biology and learning to think and work as a researcher. The key elements of this course are 1) learning to work with primary articles in order to get acquainted with the field of choice, to learn scientific reasoning, and to identify gaps in our current knowledge that represent opportunities for further research; 2) formulating a research project with fellow students; 3) gaining thorough knowledge of relevant methodology and technologies used within the field of cell biology; 4) developing cooperation and leadership skills; and 5) presenting and defending research projects before a jury of experts. The course activities were student centered and focused on designing a genuine research program. Our 5-yr experience with this course demonstrates that 1) undergraduate students are capable of delivering high-quality research designs that meet professional standards, and 2) the authenticity of the learning environment in this course strongly engages students to become self-directed and critical thinkers. We hope to provide colleagues with an example of a course that encourages and stimulates students to develop essential research thinking skills.

Tissue engineering and regenerative medicine in applied research: a year in review of 2014.

PubMed

Lin, Xunxun; Huang, Jia; Shi, Yuan; Liu, Wei

2015-04-01

Tissue engineering and regenerative medicine (TERM) remains to be one of the fastest growing fields, which covers a wide scope of topics of both basic and applied biological researches. This overview article summarized the advancements in applied researches of TERM area, including stem cell-mediated tissue regeneration, material science, and TERM clinical trial. These achievements demonstrated the great potential of clinical regenerative therapy of tissue/organ disease or defect through stem cells and tissue engineering approaches.

Research and Operational Support for the Study of Militarily Relevant Infectious Diseases of Interest to the United States Army and the Royal Thai Army

DTIC Science & Technology

2007-01-01

sporozoites from P. vivax specimens obtained from throughout the world . These sporozoites could then be used in a variety of experimental models (i.e., we...maintenance of a center for excellence focused on the basic biology and epidemiology of malaria. 31 2. To assess emerging febrile diseases along...classical and state- of -the-art technologies as possible to the above multi-faceted research. Clinical research included mobile epidemiology team able to

TRANSAUTOPHAGY: European network for multidisciplinary research and translation of autophagy knowledge.

PubMed

Casas, Caty; Codogno, Patrice; Pinti, Marcello; Batoko, Henri; Morán, María; Proikas-Cezanne, Tassula; Reggiori, Fulvio; Sirko, Agnieszka; Soengas, María S; Velasco, Guillermo; Lafont, Frank; Lane, Jon; Faure, Mathias; Cossarizza, Andrea

2016-01-01

A collaborative consortium, named "TRANSAUTOPHAGY," has been created among European research groups, comprising more than 150 scientists from 21 countries studying diverse branches of basic and translational autophagy. The consortium was approved in the framework of the Horizon 2020 Program in November 2015 as a COST Action of the European Union (COST means: CO-operation in Science and Technology), and will be sponsored for 4 years. TRANSAUTOPHAGY will form an interdisciplinary platform for basic and translational researchers, enterprises and stakeholders of diverse disciplines (including nanotechnology, bioinformatics, physics, chemistry, biology and various medical disciplines). TRANSAUTOPHAGY will establish 5 different thematic working groups, formulated to cooperate in research projects, share ideas, and results through workshops, meetings and short term exchanges of personnel (among other initiatives). TRANSAUTOPHAGY aims to generate breakthrough multidisciplinary knowledge about autophagy regulation, and to boost translation of this knowledge into biomedical and biotechnological applications.

TRANSAUTOPHAGY: European network for multidisciplinary research and translation of autophagy knowledge

PubMed Central

Casas, Caty; Codogno, Patrice; Pinti, Marcello; Batoko, Henri; Morán, María; Proikas-Cezanne, Tassula; Reggiori, Fulvio; Sirko, Agnieszka; Soengas, María S; Velasco, Guillermo; Lafont, Frank; Lane, Jon; Faure, Mathias; Cossarizza, Andrea

2016-01-01

abstract A collaborative consortium, named “TRANSAUTOPHAGY,” has been created among European research groups, comprising more than 150 scientists from 21 countries studying diverse branches of basic and translational autophagy. The consortium was approved in the framework of the Horizon 2020 Program in November 2015 as a COST Action of the European Union (COST means: CO-operation in Science and Technology), and will be sponsored for 4 years. TRANSAUTOPHAGY will form an interdisciplinary platform for basic and translational researchers, enterprises and stakeholders of diverse disciplines (including nanotechnology, bioinformatics, physics, chemistry, biology and various medical disciplines). TRANSAUTOPHAGY will establish 5 different thematic working groups, formulated to cooperate in research projects, share ideas, and results through workshops, meetings and short term exchanges of personnel (among other initiatives). TRANSAUTOPHAGY aims to generate breakthrough multidisciplinary knowledge about autophagy regulation, and to boost translation of this knowledge into biomedical and biotechnological applications. PMID:27046256

An investigation of bacterial protein interactions as a primary research project in a sophomore-level molecular biology course.

PubMed

Cardinale, Jean A

2011-01-01

Longer term research activities that may be incorporated in undergraduate courses are a powerful tool for promoting student interest and learning, developing cognitive process skills, and allowing undergraduates to experience real research activities in which they may not otherwise have the opportunity to participate. The challenge to doing so in lower-level courses is that students may have not fully grasped the scientific concepts needed to undertake such research endeavors, and that they may be discouraged if activities are perceived to be too challenging. The paper describes how a bacterial protein:protein interaction detection system was adapted and incorporated into the laboratory component of a sophomore-level Molecular Cell Biology course. The project was designed to address multiple learning objectives connecting course content to the laboratory activities, as well as teach basic molecular biology laboratory skills and procedures in the context of a primary research activity. Pre- and posttesting and student surveys both suggest that the laboratory curriculum resulted in significant learning gains, as well as being well received and valued by the students.

Chromatin regulation at the frontier of synthetic biology.

PubMed

Keung, Albert J; Joung, J Keith; Khalil, Ahmad S; Collins, James J

2015-03-01

As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.

Chromatin regulation at the frontier of synthetic biology

PubMed Central

Keung, Albert J.; Joung, J. Keith; Khalil, Ahmad S.; Collins, James J.

2016-01-01

As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including `epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication. PMID:25668787

Undergraduate basic science preparation for dental school.

PubMed

Humphrey, Sue P; Mathews, Robert E; Kaplan, Alan L; Beeman, Cynthia S

2002-11-01

In the Institute of Medicines report Dental Education at the Crossroads, it was suggested that dental schools across the country move toward integrated basic science education for dental and medical students in their curricula. To do so, dental school admission requirements and recommendations must be closely reviewed to ensure that students are adequately prepared for this coursework. The purpose of our study was twofold: 1) to identify student dentists' perceptions of their predental preparation as it relates to course content, and 2) to track student dentists' undergraduate basic science course preparation and relate that to DAT performance, basic science course performance in dental school, and Part I and Part II National Board performance. In the first part of the research, a total of ninety student dentists (forty-five from each class) from the entering classes of 1996 and 1997 were asked to respond to a survey. The survey instrument was distributed to each class of students after each completed the largest basic science class given in their second-year curriculum. The survey investigated the area of undergraduate major, a checklist of courses completed in their undergraduate preparation, the relevance of the undergraduate classes to the block basic science courses, and the strength of requiring or recommending the listed undergraduate courses as a part of admission to dental school. Results of the survey, using frequency analysis, indicate that students felt that the following classes should be required, not recommended, for admission to dental school: Microbiology 70 percent, Biochemistry 54.4 percent, Immunology 57.78 percent, Anatomy 50 percent, Physiology 58.89 percent, and Cell Biology 50 percent. The second part of the research involved anonymously tracking undergraduate basic science preparation of the same students with DAT scores, the grade received in a representative large basic science course, and Part I and Part II National Board performance. Using T-test analysis correlations, results indicate that having completed multiple undergraduate basic science courses (as reported by AADSAS BCP hours) did not significantly (p < .05) enhance student performance in any of these parameters. Based on these results, we conclude that student dentists with undergraduate preparation in science and nonscience majors can successfully negotiate the dental school curriculum, even though the students themselves would increase admission requirements to include more basic science courses than commonly required. Basically, the students' recommendations for required undergraduate basic science courses would replicate the standard basic science coursework found in most dental schools: anatomy, histology, biochemistry, microbiology, physiology, and immunology plus the universal foundation course of biology.

Breast Cancer Subtypes: Morphologic and Biologic Characterization

PubMed Central

2016-01-01

Advances in basic science, technology and translational research have created a revolution in breast cancer diagnosis and therapy. Researchers' discoveries of genes defining variability in response to therapy and heterogeneity in clinical presentations and tumor biology are the foundation of the path to personalized medicine. The success of personalized breast cancer care depends on access to pertinent clinical information and risk factors, optimal imaging findings, well-established morphologic features, and traditional and contemporary prognostic/predictive testing. The integration of these entities provides an opportunity to identify patients who can benefit from specific therapies, and demonstrates the link between breast cancer subtypes and their association with different tumor biology. It is critical to recognize specific types of breast cancer in individual patients and design optimal personalized therapy. This article will highlight the roles of morphologic features and established tumor biomarkers on patient outcome. PMID:26756229

Multi-walled carbon nanotubes and metallic nanoparticles and their application in biomedicine.

PubMed

Rojas-Chapana, Jose A; Giersig, Michael

2006-02-01

Interdisciplinary research has become a matter of paramount importance for novel applications of nanomaterials in biology and medicine. As such, many disciplines-physics, chemistry, microbiology, cell biology, and material science-all contribute to the design, synthesis and fabrication of functional and biocompatible devices at the nanometer scale. Since the most areas of cell biology and biomedicine deal with functional entities such as DNA and proteins, mimicry of these structures and function in the nanosize range offers exciting opportunities for the development of biosensors, biochips, and bioplatforms. In this report we highlight the potential benefits and challenges that arise in the manufacture of biocompatible nanoparticles and nano-networks that can be coupled with biological objects. Among the challenges facing us are those concerned with making the necessary advances in enabling affordability, innovation, and quality of manufactured nanodevices for rapid progress in the emerging field of bio-nanotechnology. The convergence of nanotechnology and biomedicine makes nanoscale research highly promising for new discoveries that can cost-effectively accelerate progress in moving from basic research to practical prototypes and products.

A Pharmacology-Based Enrichment Program for Undergraduates Promotes Interest in Science

PubMed Central

Godin, Elizabeth A.; Wormington, Stephanie V.; Perez, Tony; Barger, Michael M.; Snyder, Kate E.; Richman, Laura Smart; Schwartz-Bloom, Rochelle; Linnenbrink-Garcia, Lisa

2015-01-01

There is a strong need to increase the number of undergraduate students who pursue careers in science to provide the “fuel” that will power a science and technology–driven U.S. economy. Prior research suggests that both evidence-based teaching methods and early undergraduate research experiences may help to increase retention rates in the sciences. In this study, we examined the effect of a program that included 1) a Summer enrichment 2-wk minicourse and 2) an authentic Fall research course, both of which were designed specifically to support students' science motivation. Undergraduates who participated in the pharmacology-based enrichment program significantly improved their knowledge of basic biology and chemistry concepts; reported high levels of science motivation; and were likely to major in a biological, chemical, or biomedical field. Additionally, program participants who decided to major in biology or chemistry were significantly more likely to choose a pharmacology concentration than those majoring in biology or chemistry who did not participate in the enrichment program. Thus, by supporting students' science motivation, we can increase the number of students who are interested in science and science careers. PMID:26538389

Faking It Won't Make It in Science

ERIC Educational Resources Information Center

Cavanagh, Sean

2004-01-01

For years, educators and researchers have seen teachers at all grade levels attempt to upgrade their grasp of physics, chemistry, and biology, from basic theories to complex material. Now, the pressure on schools and instructors to improve science instruction is likely to intensify, with approaching federal requirements on states to test students…

Students' Bibliographic Research: Competition Enhances Results.

ERIC Educational Resources Information Center

Engel, Nora; And Others

1996-01-01

Describes an approach to a course about the basics of genetics and molecular biology that utilizes a contest that involves students in accessing information about a topic such as sex determination, neural development, and gene therapy. The general objective of the approach is to inspire students to become familiar with the scientific literature.…

Generation and characterization of the Western Regional Research Center brachypodium T-DNA insertional mutant collection

USDA-ARS?s Scientific Manuscript database

The model grass Brachypodium distachyon (Brachypodium) is an excellent system for studying the basic biology underlying traits relevant to the use of grasses as food, forage and energy crops. To add to the growing collection of Brachypodium resources available to plant scientists, we further optim...

Production of germline ablated male pigs via Crispr/Cas editing of the NANOS2 gene

USDA-ARS?s Scientific Manuscript database

The availability of alternative models to flies, worms, and mice for studying germ cell biology is important for translating findings to higher order mammals. In this context, investigations in pigs and other livestock species can also serve to find applications for both basic biomedical research ...

Training the Intellect Versus Development of the Child.

ERIC Educational Resources Information Center

Zigler, Edward

In a speech before the American Educational Research Association, the author asserts that childhood education theory is going through one of its periodic over-reactions to new findings. The result is the present overemphasis on environmentally caused cognitive development. Yet a very basic biological law is the law of human variability. The…

78 FR 65343 - Center for Scientific Review; Amended Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-31

...; Amended Notice of Meeting Notice is hereby given of a change in the meeting of the Center for Scientific Review Special Emphasis Panel, Revision Applications for Basic, Social and Behavioral Research on the Social, Cultural, Biological and Psychological Mechanisms of Stigma, October 20, 2013, 6:00 p.m. to...

What Type of Faculty and Training Are Required for a Successful Basic Sciences Program?

ERIC Educational Resources Information Center

Adams, Anthony

1992-01-01

Science education for optometry must go beyond therapeutic patient management to more preparation for biologically based care. Optometry faculty should be involved in research driven by specific patient problems and should prepare professionals to address patient quality-of-life and daily living needs. Interdisciplinary collaboration is needed.…

Plasma medicine—current state of research and medical application

NASA Astrophysics Data System (ADS)

Weltmann, K.-D.; von Woedtke, Th

2017-01-01

Plasma medicine means the direct application of cold atmospheric plasma (CAP) on or in the human body for therapeutic purposes. Further, the field interacts strongly with results gained for biological decontamination. Experimental research as well as first practical application is realized using two basic principles of CAP sources: dielectric barrier discharges (DBD) and atmospheric pressure plasma jets (APPJ). Originating from the fundamental insights that the biological effects of CAP are most probably caused by changes of the liquid environment of cells, and are dominated by reactive oxygen and nitrogen species (ROS, RNS), basic mechanisms of biological plasma activity are identified. It was demonstrated that there is no increased risk of cold plasma application and, above all, there are no indications for genotoxic effects. The most important biological effects of cold atmospheric pressure plasma were identified: (1) inactivation of a broad spectrum of microorganisms including multidrug resistant ones; (2) stimulation of cell proliferation and tissue regeneration with lower plasma treatment intensity (treatment time); (3) inactivation of cells by initialization of programmed cell death (apoptosis) with higher plasma treatment intensity (treatment time). In recent years, the main focus of clinical applications was in the field of wound healing and treatment of infective skin diseases. First CAP sources are CE-certified as medical devices now which is the main precondition to start the introduction of plasma medicine into clinical reality. Plasma application in dentistry and, above all, CAP use for cancer treatment are becoming more and more important research fields in plasma medicine. A further in-depth knowledge of control and adaptation of plasma parameters and plasma geometries is needed to obtain suitable and reliable plasma sources for the different therapeutic indications and to open up new fields of medical application.

Cornelia de Lange syndrome: further delineation of phenotype, cohesin biology and educational focus, 5th Biennial Scientific and Educational Symposium abstracts.

PubMed

Kline, Antonie D; Calof, Anne L; Schaaf, Cheri A; Krantz, Ian D; Jyonouchi, Soma; Yokomori, Kyoko; Gauze, Maria; Carrico, Cheri S; Woodman, Julie; Gerton, Jennifer L; Vega, Hugo; Levin, Alex V; Shirahige, Katsuhiko; Champion, Michele; Goodban, Marjorie T; O'Connor, Julia T; Pipan, Mary; Horsfield, Julia; Deardorff, Matthew A; Ishman, Stacey L; Dorsett, Dale

2014-06-01

Cornelia de Lange syndrome (CdLS) is the prototype for the cohesinopathy disorders that have mutations in genes associated with the cohesin subunit in all cells. Roberts syndrome is the next most common cohesinopathy. In addition to the developmental implications of cohesin biology, there is much translational and basic research, with progress towards potential treatment for these conditions. Clinically, there are many issues in CdLS faced by the individual, parents and caretakers, professionals, and schools. The following abstracts are presentations from the 5th Cornelia de Lange Syndrome Scientific and Educational Symposium on June 20-21, 2012, in conjunction with the Cornelia de Lange Syndrome Foundation National Meeting, Lincolnshire, IL. The research committee of the CdLS Foundation organizes the meeting, reviews and accepts abstracts and subsequently disseminates the information to the families. In addition to the basic science and clinical discussions, there were educationally-focused talks related to practical aspects of management at home and in school. AMA CME credits were provided by Greater Baltimore Medical Center, Baltimore, MD. © 2014 Wiley Periodicals, Inc.

Fundamental ecology is fundamental.

PubMed

Courchamp, Franck; Dunne, Jennifer A; Le Maho, Yvon; May, Robert M; Thébaud, Christophe; Hochberg, Michael E

2015-01-01

The primary reasons for conducting fundamental research are satisfying curiosity, acquiring knowledge, and achieving understanding. Here we develop why we believe it is essential to promote basic ecological research, despite increased impetus for ecologists to conduct and present their research in the light of potential applications. This includes the understanding of our environment, for intellectual, economical, social, and political reasons, and as a major source of innovation. We contend that we should focus less on short-term, objective-driven research and more on creativity and exploratory analyses, quantitatively estimate the benefits of fundamental research for society, and better explain the nature and importance of fundamental ecology to students, politicians, decision makers, and the general public. Our perspective and underlying arguments should also apply to evolutionary biology and to many of the other biological and physical sciences. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Flow Cytometry Scientist | Center for Cancer Research

Cancer.gov

PROGRAM DESCRIPTION The Basic Science Program (BSP) pursues independent, multidisciplinary research in basic and applied molecular biology, immunology, retrovirology, cancer biology, and human genetics. Research efforts and support are an integral part of the Center for Cancer Research (CCR) at the Frederick National Laboratory for Cancer Research (FNLCR). KEY ROLES/RESPONSIBILITIES The Flow Cytometry Core (Flow Core) in the Cancer and Inflammation Program (CIP) is a service core which supports the research efforts of the CCR by providing expertise in the field of flow cytometry (using analyzers and sorters) with the goal of gaining a more thorough understanding of the biology of the immune system, cancer, and inflammation processes. The Flow Core provides service to 12-15 CIP laboratories and more than 22 non-CIP laboratories. Flow core staff provide technical advice on the experimental design of applications, which include immunological phenotyping, cell function assays, and cell cycle analysis. Work is performed per customer requirements, and no independent research is involved. The Flow Cytometry Scientist will be responsible for: Daily management of the Flow Cytometry Core, to include the supervision and guidance of technical staff members Monitor performance of and maintain high dimensional flow cytometer analyzers and cell sorters Operate high dimensional flow cytometer analyzers and cell sorters Provide scientific expertise to the user community and facilitate the development of cutting edge technologies Interact with Flow Core users and customers, and provide technical and scientific advice, and guidance regarding their experiments, including possible collaborations Train staff and scientific end users on the use of flow cytometry in their research, as well as teach them how to operate and troubleshoot the bench-top analyzer instruments Prepare and deliver lectures, as well as one-on-one training sessions, with customers/users Ensure that protocols are up-to-date, and appropriately adhered to Experience with sterile technique and tissue culture

Marine biosurfaces research program

NASA Astrophysics Data System (ADS)

The Office of Naval Research (ONR) of the U.S. Navy is starting a basic research program to address the initial events that control colonization of surfaces by organisms in marine environments. The program “arises from the Navy's need to understand and ultimately control biofouling and biocorrosion in marine environments,” according to a Navy announcement.The program, “Biological Processes Controlling Surface Modification in the Marine Environment,” will emphasize the application of in situ techniques and modern molecular biological, biochemical, and biophysical approaches; it will also encourage the development of interdisciplinary projects. Specific areas of interest include sensing and response to environmental surface (physiology/physical chemistry), factors controlling movement to and retention at surfaces (behavior/hydrodynamics), genetic regulation of attachment (molecular genetics), and mechanisms of attachment (biochemistry/surface chemistry).

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

PubMed Central

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

2017-01-01

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

Self-Organization of Stem Cell Colonies and of Early Mammalian Embryos: Recent Experiments Shed New Light on the Role of Autonomy vs. External Instructions in Basic Body Plan Development

PubMed Central

Denker, Hans-Werner

2016-01-01

“Organoids”, i.e., complex structures that can develop when pluripotent or multipotent stem cells are maintained in three-dimensional cultures, have become a new area of interest in stem cell research. Hopes have grown that when focussing experimentally on the mechanisms behind this type of in vitro morphogenesis, research aiming at tissue and organ replacements can be boosted. Processes leading to the formation of organoids in vitro are now often addressed as self-organization, a term referring to the formation of complex tissue architecture in groups of cells without depending on specific instruction provided by other cells or tissues. The present article focuses on recent reports using the term self-organization in the context of studies on embryogenesis, specifically addressing pattern formation processes in human blastocysts attaching in vitro, or in colonies of pluripotent stem cells (“gastruloids”). These morphogenetic processes are of particular interest because, during development in vivo, they lead to basic body plan formation and individuation. Since improved methodologies like those employed by the cited authors became available, early embryonic pattern formation/self-organization appears to evolve now as a research topic of its own. This review discusses concepts concerning the involved mechanisms, focussing on autonomy of basic body plan development vs. dependence on external signals, as possibly provided by implantation in the uterus, and it addresses biological differences between an early mammalian embryo, e.g., a morula, and a cluster of pluripotent stem cells. It is concluded that, apart from being of considerable biological interest, the described type of research needs to be contemplated carefully with regard to ethical implications when performed with human cells. PMID:27792143

Self-Organization of Stem Cell Colonies and of Early Mammalian Embryos: Recent Experiments Shed New Light on the Role of Autonomy vs. External Instructions in Basic Body Plan Development.

PubMed

Denker, Hans-Werner

2016-10-25

" Organoids ", i.e., complex structures that can develop when pluripotent or multipotent stem cells are maintained in three-dimensional cultures, have become a new area of interest in stem cell research. Hopes have grown that when focussing experimentally on the mechanisms behind this type of in vitro morphogenesis, research aiming at tissue and organ replacements can be boosted. Processes leading to the formation of organoids in vitro are now often addressed as self-organization , a term referring to the formation of complex tissue architecture in groups of cells without depending on specific instruction provided by other cells or tissues. The present article focuses on recent reports using the term self-organization in the context of studies on embryogenesis , specifically addressing pattern formation processes in human blastocysts attaching in vitro, or in colonies of pluripotent stem cells (" gastruloids "). These morphogenetic processes are of particular interest because, during development in vivo, they lead to basic body plan formation and individuation. Since improved methodologies like those employed by the cited authors became available, early embryonic pattern formation/self-organization appears to evolve now as a research topic of its own. This review discusses concepts concerning the involved mechanisms, focussing on autonomy of basic body plan development vs. dependence on external signals, as possibly provided by implantation in the uterus, and it addresses biological differences between an early mammalian embryo, e.g., a morula, and a cluster of pluripotent stem cells. It is concluded that, apart from being of considerable biological interest, the described type of research needs to be contemplated carefully with regard to ethical implications when performed with human cells.

A sense of life: computational and experimental investigations with models of biochemical and evolutionary processes.

PubMed

Mishra, Bud; Daruwala, Raoul-Sam; Zhou, Yi; Ugel, Nadia; Policriti, Alberto; Antoniotti, Marco; Paxia, Salvatore; Rejali, Marc; Rudra, Archisman; Cherepinsky, Vera; Silver, Naomi; Casey, William; Piazza, Carla; Simeoni, Marta; Barbano, Paolo; Spivak, Marina; Feng, Jiawu; Gill, Ofer; Venkatesh, Mysore; Cheng, Fang; Sun, Bing; Ioniata, Iuliana; Anantharaman, Thomas; Hubbard, E Jane Albert; Pnueli, Amir; Harel, David; Chandru, Vijay; Hariharan, Ramesh; Wigler, Michael; Park, Frank; Lin, Shih-Chieh; Lazebnik, Yuri; Winkler, Franz; Cantor, Charles R; Carbone, Alessandra; Gromov, Mikhael

2003-01-01

We collaborate in a research program aimed at creating a rigorous framework, experimental infrastructure, and computational environment for understanding, experimenting with, manipulating, and modifying a diverse set of fundamental biological processes at multiple scales and spatio-temporal modes. The novelty of our research is based on an approach that (i) requires coevolution of experimental science and theoretical techniques and (ii) exploits a certain universality in biology guided by a parsimonious model of evolutionary mechanisms operating at the genomic level and manifesting at the proteomic, transcriptomic, phylogenic, and other higher levels. Our current program in "systems biology" endeavors to marry large-scale biological experiments with the tools to ponder and reason about large, complex, and subtle natural systems. To achieve this ambitious goal, ideas and concepts are combined from many different fields: biological experimentation, applied mathematical modeling, computational reasoning schemes, and large-scale numerical and symbolic simulations. From a biological viewpoint, the basic issues are many: (i) understanding common and shared structural motifs among biological processes; (ii) modeling biological noise due to interactions among a small number of key molecules or loss of synchrony; (iii) explaining the robustness of these systems in spite of such noise; and (iv) cataloging multistatic behavior and adaptation exhibited by many biological processes.

Regenerative patterning in Swarm Robots: mutual benefits of research in robotics and stem cell biology.

PubMed

Rubenstein, Michael; Sai, Ying; Chuong, Cheng-Ming; Shen, Wei-Min

2009-01-01

This paper presents a novel perspective of Robotic Stem Cells (RSCs), defined as the basic non-biological elements with stem cell like properties that can self-reorganize to repair damage to their swarming organization. Self here means that the elements can autonomously decide and execute their actions without requiring any preset triggers, commands, or help from external sources. We develop this concept for two purposes. One is to develop a new theory for self-organization and self-assembly of multi-robots systems that can detect and recover from unforeseen errors or attacks. This self-healing and self-regeneration is used to minimize the compromise of overall function for the robot team. The other is to decipher the basic algorithms of regenerative behaviors in multi-cellular animal models, so that we can understand the fundamental principles used in the regeneration of biological systems. RSCs are envisioned to be basic building elements for future systems that are capable of self-organization, self-assembly, self-healing and self-regeneration. We first discuss the essential features of biological stem cells for such a purpose, and then propose the functional requirements of robotic stem cells with properties equivalent to gene controller, program selector and executor. We show that RSCs are a novel robotic model for scalable self-organization and self-healing in computer simulations and physical implementation. As our understanding of stem cells advances, we expect that future robots will be more versatile, resilient and complex, and such new robotic systems may also demand and inspire new knowledge from stem cell biology and related fields, such as artificial intelligence and tissue engineering.

Regenerative patterning in Swarm Robots: mutual benefits of research in robotics and stem cell biology

PubMed Central

RUBENSTEIN, MICHAEL; SAI, YING; CHUONG, CHENG-MING; SHEN, WEI-MIN

2010-01-01

This paper presents a novel perspective of Robotic Stem Cells (RSCs), defined as the basic non-biological elements with stem cell like properties that can self-reorganize to repair damage to their swarming organization. “Self” here means that the elements can autonomously decide and execute their actions without requiring any preset triggers, commands, or help from external sources. We develop this concept for two purposes. One is to develop a new theory for self-organization and self-assembly of multi-robots systems that can detect and recover from unforeseen errors or attacks. This self-healing and self-regeneration is used to minimize the compromise of overall function for the robot team. The other is to decipher the basic algorithms of regenerative behaviors in multi-cellular animal models, so that we can understand the fundamental principles used in the regeneration of biological systems. RSCs are envisioned to be basic building elements for future systems that are capable of self-organization, self-assembly, self-healing and self-regeneration. We first discuss the essential features of biological stem cells for such a purpose, and then propose the functional requirements of robotic stem cells with properties equivalent to gene controller, program selector and executor. We show that RSCs are a novel robotic model for scalable self-organization and self-healing in computer simulations and physical implementation. As our understanding of stem cells advances, we expect that future robots will be more versatile, resilient and complex, and such new robotic systems may also demand and inspire new knowledge from stem cell biology and related fields, such as artificial intelligence and tissue engineering. PMID:19557691

A unique large-scale undergraduate research experience in molecular systems biology for non-mathematics majors.

PubMed

Kappler, Ulrike; Rowland, Susan L; Pedwell, Rhianna K

2017-05-01

Systems biology is frequently taught with an emphasis on mathematical modeling approaches. This focus effectively excludes most biology, biochemistry, and molecular biology students, who are not mathematics majors. The mathematical focus can also present a misleading picture of systems biology, which is a multi-disciplinary pursuit requiring collaboration between biochemists, bioinformaticians, and mathematicians. This article describes an authentic large-scale undergraduate research experience (ALURE) in systems biology that incorporates proteomics, bacterial genomics, and bioinformatics in the one exercise. This project is designed to engage students who have a basic grounding in protein chemistry and metabolism and no mathematical modeling skills. The pedagogy around the research experience is designed to help students attack complex datasets and use their emergent metabolic knowledge to make meaning from large amounts of raw data. On completing the ALURE, participants reported a significant increase in their confidence around analyzing large datasets, while the majority of the cohort reported good or great gains in a variety of skills including "analysing data for patterns" and "conducting database or internet searches." An environmental scan shows that this ALURE is the only undergraduate-level system-biology research project offered on a large-scale in Australia; this speaks to the perceived difficulty of implementing such an opportunity for students. We argue however, that based on the student feedback, allowing undergraduate students to complete a systems-biology project is both feasible and desirable, even if the students are not maths and computing majors. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(3):235-248, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

Molecular communication among biological nanomachines: a layered architecture and research issues.

PubMed

Nakano, Tadashi; Suda, Tatsuya; Okaie, Yutaka; Moore, Michael J; Vasilakos, Athanasios V

2014-09-01

Molecular communication is an emerging communication paradigm for biological nanomachines. It allows biological nanomachines to communicate through exchanging molecules in an aqueous environment and to perform collaborative tasks through integrating functionalities of individual biological nanomachines. This paper develops the layered architecture of molecular communication and describes research issues that molecular communication faces at each layer of the architecture. Specifically, this paper applies a layered architecture approach, traditionally used in communication networks, to molecular communication, decomposes complex molecular communication functionality into a set of manageable layers, identifies basic functionalities of each layer, and develops a descriptive model consisting of key components of the layer for each layer. This paper also discusses open research issues that need to be addressed at each layer. In addition, this paper provides an example design of targeted drug delivery, a nanomedical application, to illustrate how the layered architecture helps design an application of molecular communication. The primary contribution of this paper is to provide an in-depth architectural view of molecular communication. Establishing a layered architecture of molecular communication helps organize various research issues and design concerns into layers that are relatively independent of each other, and thus accelerates research in each layer and facilitates the design and development of applications of molecular communication.

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2017-06-01

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

IBPRO – a novel short-duration teaching course in advanced physics and biology underlying cancer radiotherapy

PubMed Central

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

2017-01-01

This article provides a summary and status report of the ongoing advanced education program IBPRO – Integrated course in Biology and Physics of Radiation Oncology. IBPRO is a five-year program funded by NCI. It addresses the recognized deficiency in the number of mentors available who have the required knowledge and skill to provide the teaching and training that is required for future radiation oncologists and researchers in radiation sciences. Each year, IBPRO brings together 50 attendees typically at assistant professor level and upwards, who are already qualified/certified radiation oncologists, medical physicists or biologists. These attendees receive keynote lectures and activities based on active learning strategies, merging together the clinical, biological and physics underpinnings of radiation oncology, at the forefront of the field. This experience is aimed at increasing collaborations, raising the level and amount of basic and applied research undertaken in radiation oncology, and enabling attendees to confidently become involved in the future teaching and training of researchers and radiation oncologists. PMID:28328309

Activity-based protein profiling: from enzyme chemistry to proteomic chemistry.

PubMed

Cravatt, Benjamin F; Wright, Aaron T; Kozarich, John W

2008-01-01

Genome sequencing projects have provided researchers with a complete inventory of the predicted proteins produced by eukaryotic and prokaryotic organisms. Assignment of functions to these proteins represents one of the principal challenges for the field of proteomics. Activity-based protein profiling (ABPP) has emerged as a powerful chemical proteomic strategy to characterize enzyme function directly in native biological systems on a global scale. Here, we review the basic technology of ABPP, the enzyme classes addressable by this method, and the biological discoveries attributable to its application.

The Biotechnology Facility for International Space Station.

PubMed

Goodwin, Thomas; Lundquist, Charles; Tuxhorn, Jennifer; Hurlbert, Katy

2004-03-01

The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput.

Update on the genomics and basic biology of Brachypodium: International Brachypodium Initiative (IBI).

PubMed

Catalan, Pilar; Chalhoub, Boulos; Chochois, Vincent; Garvin, David F; Hasterok, Robert; Manzaneda, Antonio J; Mur, Luis A J; Pecchioni, Nicola; Rasmussen, Søren K; Vogel, John P; Voxeur, Aline

2014-07-01

The scientific presentations at the First International Brachypodium Conference (abstracts available at http://www.brachy2013.unimore.it) are evidence of the widespread adoption of Brachypodium distachyon as a model system. Furthermore, the wide range of topics presented (genome evolution, roots, abiotic and biotic stress, comparative genomics, natural diversity, and cell walls) demonstrates that the Brachypodium research community has achieved a critical mass of tools and has transitioned from resource development to addressing biological questions, particularly those unique to grasses. Copyright © 2014 Elsevier Ltd. All rights reserved.

Genomic instability and bystander effects: a paradigm shift in radiation biology?

NASA Technical Reports Server (NTRS)

Morgan, William F.

2002-01-01

A basic paradigm in radiobiology is that, following exposure to ionizing radiation, the deposition of energy in the cell nucleus and the resulting damage to DNA, the principal target, are responsible for the radiation's deleterious biological effects. Findings in two rapidly expanding fields of research--radiation-induced genomic instability and bystander effects--have caused us to reevaluate these central tenets. In this article, the potential influence of induced genomic instability and bystander effects on cellular injury after exposure to low-level radiation will be reviewed.

The Biotechnology Facility for International Space Station

NASA Technical Reports Server (NTRS)

Goodwin, Thomas; Lundquist, Charles; Tuxhorn, Jennifer; Hurlbert, Katy

2004-01-01

The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput.

Connecting biology and organic chemistry introductory laboratory courses through a collaborative research project.

PubMed

Boltax, Ariana L; Armanious, Stephanie; Kosinski-Collins, Melissa S; Pontrello, Jason K

2015-01-01

Modern research often requires collaboration of experts in fields, such as math, chemistry, biology, physics, and computer science to develop unique solutions to common problems. Traditional introductory undergraduate laboratory curricula in the sciences often do not emphasize connections possible between the various disciplines. We designed an interdisciplinary, medically relevant, project intended to help students see connections between chemistry and biology. Second term organic chemistry laboratory students designed and synthesized potential polymer inhibitors or inducers of polyglutamine protein aggregation. The use of novel target compounds added the uncertainty of scientific research to the project. Biology laboratory students then tested the novel potential pharmaceuticals in Huntington's disease model assays, using in vitro polyglutamine peptide aggregation and in vivo lethality studies in Drosophila. Students read articles from the primary literature describing the system from both chemical and biological perspectives. Assessment revealed that students emerged from both courses with a deeper understanding of the interdisciplinary nature of biology and chemistry and a heightened interest in basic research. The design of this collaborative project for introductory biology and organic chemistry labs demonstrated how the local interests and expertise at a university can be drawn from to create an effective way to integrate these introductory courses. Rather than simply presenting a series of experiments to be replicated, we hope that our efforts will inspire other scientists to think about how some aspect of authentic work can be brought into their own courses, and we also welcome additional collaborations to extend the scope of the scientific exploration. © 2015 The International Union of Biochemistry and Molecular Biology.

Autonomous biological system-an unique method of conducting long duration space flight experiments for pharmaceutical and gravitational biology research

NASA Astrophysics Data System (ADS)

Anderson, G. A.; MacCallum, T. K.; Poynter, J. E.; Klaus, D., Dr.

1998-01-01

Paragon Space Development Corporation (SDC) has developed an Autonomous Biological System (ABS) that can be flown in space to provide for long term growth and breeding of aquatic plants, animals, microbes and algae. The system functions autonomously and in isolation from the spacecraft life support systems and with no mandatory crew time required for function or observation. The ABS can also be used for long term plant and animal life support and breeding on a free flyer space craft. The ABS units are a research tool for both pharmaceutical and basic space biological sciences. Development flights in May of 1996 and September, 1996 through January, 1997 were largely successful, showing both that the hardware and life systems are performing with beneficial results, though some surprises were still found. The two space flights, plus the current flight now on Mir, are expected to result in both a scientific and commercially usable system for breeding and propagation of animals and plants in space.

Fungal biology and agriculture: revisiting the field

USGS Publications Warehouse

Yarden, O.; Ebbole, D.J.; Freeman, S.; Rodriguez, R.J.; Dickman, M. B.

2003-01-01

Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.

Single cell biology beyond the era of antibodies: relevance, challenges, and promises in biomedical research.

PubMed

Abraham, Parvin; Maliekal, Tessy Thomas

2017-04-01

Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems. Even though microfluidics and microraft array are newer techniques exploited for single cell biology, fluorescence-activated cell sorting (FACS) remains the gold standard technique for isolation of cells for many biomedical applications, like stem cell therapy. Here, we present a comprehensive and comparative account of some of the probes that are useful in FACS. Further, we illustrate how these techniques could be applied in biomedical research. It is postulated that intracellular molecular markers like nucleostemin (GNL3), alkaline phosphatase (ALPL) and HIRA can be used for improving the outcome of cardiac as well as bone regeneration. Another field that could utilize intracellular markers is diagnostics, and we propose the use of specific peptide nucleic acid probes (PNPs) against certain miRNAs for cancer surgical margin prediction. The newer techniques for single cell biology, based on intracellular molecules, will immensely enhance the repertoire of possible markers for the isolation of cell types useful in biomedical research.

Membrane Fluidity Changes, A Basic Mechanism of Interaction of Gravity with Cells?

NASA Astrophysics Data System (ADS)

Kohn, Florian; Hauslage, Jens; Hanke, Wolfgang

2017-10-01

All life on earth has been established under conditions of stable gravity of 1g. Nevertheless, in numerous experiments the direct gravity dependence of biological processes has been shown on all levels of organization, from single molecules to humans. According to the underlying mechanisms a variety of questions, especially about gravity sensation of single cells without specialized organelles or structures for gravity sensing is being still open. Biological cell membranes are complex structures containing mainly lipids and proteins. Functional aspects of such membranes are usually attributed to membrane integral proteins. This is also correct for the gravity dependence of cells and organisms which is well accepted since long for a wide range of biological systems. However, it is as well established that parameters of the lipid matrix are directly modifying the function of proteins. Thus, the question must be asked, whether, and how far plain lipid membranes are affected by gravity directly. In principle it can be said that up to recently no real basic mechanism for gravity perception in single cells has been presented or verified. However, it now has been shown that as a basic membrane parameter, membrane fluidity, is significantly dependent on gravity. This finding might deliver a real basic mechanism for gravity perception of living organisms on all scales. In this review we summarize older and more recent results to demonstrate that the finding of membrane fluidity being gravity dependent is consistent with a variety of published laboratory experiments. We additionally point out to the consequences of these recent results for research in the field life science under space condition.

Basic autonomy as a fundamental step in the synthesis of life.

PubMed

Ruiz-Mirazo, Kepa; Moreno, Alvaro

2004-01-01

In the search for the primary roots of autonomy (a pivotal concept in Varela's comprehensive understanding of living beings), the theory of autopoiesis provided an explicit criterion to define minimal life in universal terms, and was taken as a guideline in the research program for the artificial synthesis of biological systems. Acknowledging the invaluable contribution of the autopoietic school to present biological thinking, we offer an alternative way of conceiving the most basic forms of autonomy. We give a bottom-up account of the origins of "self-production" (or self-construction, as we propose to call it), pointing out which are the minimal material and energetic requirements for the constitution of basic autonomous systems. This account is, indeed, committed to the project of developing a general theory of biology, but well grounded in the universal laws of physics and chemistry. We consider that the autopoietic theory was formulated in highly abstract terms and, in order to advance in the implementation of minimal autonomous systems (and, at the same time, make major progress in exploring the origins of life), a more specific characterization of minimal autonomous systems is required. Such a characterization will not be drawn from a review of the autopoietic criteria and terminology (à la Fleischaker) but demands a whole reformulation of the question: a proper naturalization of the concept of autonomy. Finally, we also discuss why basic autonomy, according to our account, is necessary but not sufficient for life, in contrast with Varela's idea that autopoiesis was a necessary and sufficient condition for it.

How to Design a Genetic Mating Scheme: A Basic Training Package for Drosophila Genetics

PubMed Central

Roote, John; Prokop, Andreas

2013-01-01

Drosophila melanogaster is a powerful model organism for biological research. The essential and common instrument of fly research is genetics, the art of applying Mendelian rules in the specific context of Drosophila with its unique classical genetic tools and the breadth of modern genetic tools and strategies brought in by molecular biology, transgenic technologies and the use of recombinases. Training newcomers to fly genetics is a complex and time-consuming task but too important to be left to chance. Surprisingly, suitable training resources for beginners currently are not available. Here we provide a training package for basic Drosophila genetics, designed to ensure that basic knowledge on all key areas is covered while reducing the time invested by trainers. First, a manual introduces to fly history, rationale for mating schemes, fly handling, Mendelian rules in fly, markers and balancers, mating scheme design, and transgenic technologies. Its self-study is followed by a practical training session on gender and marker selection, introducing real flies under the dissecting microscope. Next, through self-study of a PowerPoint presentation, trainees are guided step-by-step through a mating scheme. Finally, to consolidate knowledge, trainees are asked to design similar mating schemes reflecting routine tasks in a fly laboratory. This exercise requires individual feedback but also provides unique opportunities for trainers to spot weaknesses and strengths of each trainee and take remedial action. This training package is being successfully applied at the Manchester fly facility and may serve as a model for further training resources covering other aspects of fly research. PMID:23390611

A comprehensive crop genome research project: the Superhybrid Rice Genome Project in China.

PubMed

Yu, Jun; Wong, Gane Ka-Shu; Liu, Siqi; Wang, Jian; Yang, Huanming

2007-06-29

In May 2000, the Beijing Institute of Genomics formally announced the launch of a comprehensive crop genome research project on rice genomics, the Chinese Superhybrid Rice Genome Project. SRGP is not simply a sequencing project targeted to a single rice (Oryza sativa L.) genome, but a full-swing research effort with an ultimate goal of providing inclusive basic genomic information and molecular tools not only to understand biology of the rice, both as an important crop species and a model organism of cereals, but also to focus on a popular superhybrid rice landrace, LYP9. We have completed the first phase of SRGP and provide the rice research community with a finished genome sequence of an indica variety, 93-11 (the paternal cultivar of LYP9), together with ample data on subspecific (between subspecies) polymorphisms, transcriptomes and proteomes, useful for within-species comparative studies. In the second phase, we have acquired the genome sequence of the maternal cultivar, PA64S, together with the detailed catalogues of genes uniquely expressed in the parental cultivars and the hybrid as well as allele-specific markers that distinguish parental alleles. Although SRGP in China is not an open-ended research programme, it has been designed to pave a way for future plant genomics research and application, such as to interrogate fundamentals of plant biology, including genome duplication, polyploidy and hybrid vigour, as well as to provide genetic tools for crop breeding and to carry along a social burden-leading a fight against the world's hunger. It began with genomics, the newly developed and industry-scale research field, and from the world's most populous country. In this review, we summarize our scientific goals and noteworthy discoveries that exploit new territories of systematic investigations on basic and applied biology of rice and other major cereal crops.

An Introduction to Programming for Bioscientists: A Python-Based Primer

PubMed Central

Mura, Cameron

2016-01-01

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language’s usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a “variable,” the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences. PMID:27271528

An Introduction to Programming for Bioscientists: A Python-Based Primer.

PubMed

Ekmekci, Berk; McAnany, Charles E; Mura, Cameron

2016-06-01

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a "variable," the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.

Molecular and Cellular Biophysics

NASA Astrophysics Data System (ADS)

Jackson, Meyer B.

2006-01-01

Molecular and Cellular Biophysics provides advanced undergraduate and graduate students with a foundation in the basic concepts of biophysics. Students who have taken physical chemistry and calculus courses will find this book an accessible and valuable aid in learning how these concepts can be used in biological research. The text provides a rigorous treatment of the fundamental theories in biophysics and illustrates their application with examples. Conformational transitions of proteins are studied first using thermodynamics, and subsequently with kinetics. Allosteric theory is developed as the synthesis of conformational transitions and association reactions. Basic ideas of thermodynamics and kinetics are applied to topics such as protein folding, enzyme catalysis and ion channel permeation. These concepts are then used as the building blocks in a treatment of membrane excitability. Through these examples, students will gain an understanding of the general importance and broad applicability of biophysical principles to biological problems. Offers a unique synthesis of concepts across a wide range of biophysical topics Provides a rigorous theoretical treatment, alongside applications in biological systems Author has been teaching biophysics for nearly 25 years

On the search for design principles in biological systems.

PubMed

Poyatos, Juan F

2012-01-01

The search for basic concepts and underlying principles was at the core of the systems approach to science and technology. This approach was somehow abandoned in mainstream biology after its initial proposal, due to the rise and success of molecular biology. This situation has changed. The accumulated knowledge of decades of molecular studies in combination with new technological advances, while further highlighting the intricacies of natural systems, is also bringing back the quest-for-principles research program. Here, I present two lessons that I derived from my own quest: the importance of studying biological information processing to identify common principles in seemingly unrelated contexts and the adequacy of using known design principles at one level of biological organization as a valuable tool to help recognizing principles at an alternative one. These and additional lessons should contribute to the ultimate goal of establishing principles able to integrate the many scales of biological complexity.

The Effects of Instruction on College Nonmajors' Conceptions of Respiration and Photosynthesis. Research Series No. 164.

ERIC Educational Resources Information Center

Anderson, Charles W.; And Others

The processes of photosynthesis and respiration are basic to the understanding of many other aspects and functions of biological systems. Because of their curricular significance, these processes served as the focal point in an investigation of student conceptions and instructional effectiveness. In this study, students in a college nonscience…

Name that Gene: A Meaningful Computer-Based Genetics Classroom Activity that Incorporates Tolls Used by Real Research Scientists

ERIC Educational Resources Information Center

Wefer, Stephen H.

2003-01-01

"Name That Gene" is a simple classroom activity that incorporates bioinformatics (available biological information) into the classroom using "Basic Logical Alignment Search Tool (BLAST)." An excellent classroom activity involving bioinformatics and "BLAST" has been previously explored using sequences from bacteria, but it is tailored for college…

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

NASA Technical Reports Server (NTRS)

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.

Impact of Radiation Biology on Fundamental Insights in Biology

DOE R&D Accomplishments Database

Setlow, Richard B.

1982-07-27

Research supported by OHER [Office of Health and Environmental Research] and its predecessors has as one of its major goals an understanding of the effects of radiation at low doses and dose rates on biological systems, so as to predict their effects on humans. It is not possible to measure such effects directly. They must be predicted from basic knowledge on how radiation affects cellular components such as DNA and membranes and how cells react to such changes. What is the probability of radiation producing human mutations and what are the probabilities of radiation producing cancer? The end results of such studies are radiation exposure standards for workers and for the general population. An extension of these goals is setting standards for exposure to chemicals involved in various energy technologies. This latter problem is much more difficult because chemical dosimetry is a primitive state compared to radiation dosimetry.

Translational progress on tumor biomarkers

PubMed Central

Guo, Hongwei; Zhou, Xiaolin; Lu, Yi; Xie, Liye; Chen, Qian; Keller, Evan T; Liu, Qian; Zhou, Qinghua; Zhang, Jian

2015-01-01

There is an urgent need to apply basic research achievements to the clinic. In particular, mechanistic studies should be developed by bench researchers, depending upon clinical demands, in order to improve the survival and quality of life of cancer patients. To date, translational medicine has been addressed in cancer biology, particularly in the identification and characterization of novel tumor biomarkers. This review focuses on the recent achievements and clinical application prospects in tumor biomarkers based on translational medicine. PMID:26557902

The Emerging Field of Human Social Genomics

PubMed Central

Slavich, George M.; Cole, Steven W.

2013-01-01

Although we generally experience our bodies as being biologically stable across time and situations, an emerging field of research is demonstrating that external social conditions, especially our subjective perceptions of those conditions, can influence our most basic internal biological processes—namely, the expression of our genes. This research on human social genomics has begun to identify the types of genes that are subject to social-environmental regulation, the neural and molecular mechanisms that mediate the effects of social processes on gene expression, and the genetic polymorphisms that moderate individual differences in genomic sensitivity to social context. The molecular models resulting from this research provide new opportunities for understanding how social and genetic factors interact to shape complex behavioral phenotypes and susceptibility to disease. This research also sheds new light on the evolution of the human genome and challenges the fundamental belief that our molecular makeup is relatively stable and impermeable to social-environmental influence. PMID:23853742

Procurement of State-of-the-Art Research Equipment to Support Faculty Members Within the RNAi Therapeutics Institute

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

Terence Flotte, MD; Patricia McNulty

2010-06-29

This project funded the procurement of state-of-the-art research equipment to support world class faculty members within the RNAi Therapeutics Institute, a central program of the Advanced Therapeutics Cluster (ATC) project. The equipment purchased under this grant supports the RNA Therapeutics Institute (RTI) at the University of Massachusetts Medical School which seeks to build a community of scientists passionate about RNA. By uniting researchers studying the fundamental biology and mechanisms of cellular RNAs with those working to devise human therapies using or targeting nucleic acids, the RTI represents a new model for scientific exploration. By interweaving basic and applied nucleic acidmore » scientists with clinicians dedicated to finding new cures, our goal is to create a new paradigm for organizing molecular research that enables the rapid application of new biological discoveries to solutions for unmet challenges in human health.« less

Developmental Gene Regulation and Mechanisms of Evolution

NASA Technical Reports Server (NTRS)

1998-01-01

The Marine Biological Laboratory and the National Aeronautics and Space Administration have established a cooperative agreement with the formation of a Center for Advanced Studies 'in the Space Life Sciences (CASSLS) at the MBL. This Center serves as an interface between NASA and the basic science community, addressing issues of mutual interest. The Center for Advanced Studies 'in the Space Life Sciences provides a forum for scientists to think and discuss, often for the first time, the role that gravity and aspects of spaceflight may play 'in fundamental cellular and physiologic processes. In addition the Center will sponsor discussions on evolutionary biology. These interactions will inform the community of research opportunities that are of interest to NASA. This workshop is one of a series of symposia, workshops and seminars that will be held at the MBL to advise NASA on a wide variety of topics in the life sciences, including cell biology, developmental biology, mg evolutionary biology, molecular biology, neurobiology, plant biology and systems biology.

Dietary customs and food availability shape the preferences for basic tastes: A cross-cultural study among Polish, Tsimane' and Hadza societies.

PubMed

Sorokowska, Agnieszka; Pellegrino, Robert; Butovskaya, Marina; Marczak, Michalina; Niemczyk, Agnieszka; Huanca, Tomas; Sorokowski, Piotr

2017-09-01

Biological significance of food components suggests that preferences for basic tastes should be similar across cultures. On the other hand, cultural factors play an important role in diet and can consequently influence individual preference for food. To date, very few studies have compared basic tastes preferences among populations of very diverse environmental and cultural conditions, and research rather did not involve traditional populations for whom the biological significance of different food components might be the most pronounced. Hence, our study focused on basic taste preferences in three populations, covering a broad difference in diet due to environmental and cultural conditions, market availability, dietary habits and food acquirement: 1) a modern society (Poles, n = 200), 2) forager-horticulturalists from Amazon/Bolivia (Tsimane', n = 138), and 3) hunter-gatherers from Tanzania (Hadza, n = 85). The preferences for basic tastes were measured with sprays containing supra-threshold levels of sweet, sour, bitter, salty, and umami taste solutions. We observed several interesting differences between participating societies. We found that Tsimane' and Polish participants liked the sweet taste more than other tastes, while Hadza participants liked salty and sour tastes more than the remaining tastes. Further, Polish people found bitter taste particularly aversive, which was not observed in the traditional societies. Interestingly, no cross-cultural differences were observed for relative liking of umami taste - it was rated closely to neutral by members of all participating societies. Additionally, Hadza showed a pattern to like basic tastes that are more common to their current diet than societies with access to different food sources. These findings demonstrate the impact of diet and market availability on preference for basic tastes. Copyright © 2017 Elsevier Ltd. All rights reserved.

Chemical regulators of plant hormones and their applications in basic research and agriculture.

PubMed

Jiang, Kai; Asami, Tadao

2018-04-20

Plant hormones are small molecules that play versatile roles in regulating plant growth, development, and responses to the environment. Classic methodologies, including genetics, analytic chemistry, biochemistry, and molecular biology, have contributed to the progress in plant hormone studies. In addition, chemical regulators of plant hormone functions have been important in such studies. Today, synthetic chemicals, including plant growth regulators, are used to study and manipulate biological systems, collectively referred to as chemical biology. Here, we summarize the available chemical regulators and their contributions to plant hormone studies. We also pose questions that remain to be addressed in plant hormone studies and that might be solved with the help of chemical regulators.

Laboratory for Energy-Related Health Research annual report, fiscal year 1986

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

Abell, D.L.

1989-02-01

This report to the US Department of Energy summarizes research activities for the period from 1 October 1985--30 September 1986 at the Laboratory for Energy-related Health Research (LEHR) which is operated by the University of California, Davis. The laboratory's research objective is to provide new knowledge for an improved understanding of the potential bioenvironmental and occupational health problems associated with energy utilization to contribute to the safe and healthful development of energy resources for the benefit of mankind. This research encompasses several areas of basic investigation that relate to toxicological and biomedical problems associated with potentially toxic chemical and radioactivemore » substances and ionizing radiation, with particular emphasis on carcinogenicity. Studies of systemic injury and nuclear medical diagnostic and therapeutic methods are also involved. This is an interdisciplinary program spanning physics, chemistry, environmental engineering, biophysics and biochemistry, cellular and molecular biology, physiology, immunology, toxicology, both human and veterinary medicine, nuclear medicine, pathology, hematology, radiation biology, reproductive biology, oncology, biomathematics, and computer science. The principal themes of the research at LEHR center around the biology, radiobiology, and health status of the skeleton and its blood-forming constituents; the toxicology and properties of airborne materials; the beagle as an experimental animal model; carcinogenesis; and the scaling of the results from laboratory animal studies to man for appropriate assessment of risk.« less

Biology Division progress report for period of October 1, 1988--September 30, 1989

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

Not Available

1990-02-01

The Biology Division of the Oak Ridge National Laboratory is one component of the Department of Energy's intramural program in life sciences. With respect to experimental biology, the congressionally mandated mission of this Office is to study adverse health effects of energy production and utilization. Within this stated broad mission, common themes among the research programs of the Biology Division are interactions of animals, cells, and molecules with their respective environments. Investigations focus on genetic and somatic effects of radiation and chemicals. Goals include identification and quantification of these effects, elucidation of pathways by which the effects are expressed, assessmentmore » of risks associated with radiation and chemical exposures, and establishment of strategies for extrapolation of risk data from animals to humans. Concurrent basic studies in genetics, biochemistry, molecular biology, and cell biology illuminate normal life processes as prerequisites to comprehending mutagenic and carcinogenic effects of environmental agents. This Progress Report is intended to provide both broad perspectives of the Division's research programs and synopses of recent achievements. Readers are invited to contact individual principal investigators for more detailed information, including reprints of publications. 120 refs.« less

Introduction to metabolomics and its applications in ophthalmology

PubMed Central

Tan, S Z; Begley, P; Mullard, G; Hollywood, K A; Bishop, P N

2016-01-01

Metabolomics is the study of endogenous and exogenous metabolites in biological systems, which aims to provide comparative semi-quantitative information about all metabolites in the system. Metabolomics is an emerging and potentially powerful tool in ophthalmology research. It is therefore important for health professionals and researchers involved in the speciality to understand the basic principles of metabolomics experiments. This article provides an overview of the experimental workflow and examples of its use in ophthalmology research from the study of disease metabolism and pathogenesis to identification of biomarkers. PMID:26987591

Advancing pig cloning technologies towards application in regenerative medicine.

PubMed

Nagashima, H; Matsunari, H; Nakano, K; Watanabe, M; Umeyama, K; Nagaya, M

2012-08-01

Regenerative medicine is expected to make a significant contribution by development of novel therapeutic treatments for intractable diseases and for improving the quality of life of patients. Many advances in regenerative medicine, including basic and translational research, have been developed and tested in experimental animals; pigs have played an important role in various aspects of this work. The value of pigs as a model species is being enhanced by the generation of specially designed animals through cloning and genetic modifications, enabling more sophisticated research to be performed and thus accelerating the clinical application of regenerative medicine. This article reviews the significant aspects of the creation and application of cloned and genetically modified pigs in regenerative medicine research and considers the possible future directions of the technology. We also discuss the importance of reproductive biology as an interface between basic science and clinical medicine. © 2012 Blackwell Verlag GmbH.

Toxicogenomics and clinical toxicology: an example of the connection between basic and applied sciences.

PubMed

Ferrer-Dufol, Ana; Menao-Guillen, Sebastian

2009-04-10

The relationship between basic research and its potential clinical applications is often a difficult subject. Clinical toxicology has always been very dependent on experimental research whose usefulness has been impaired by the existence of huge differences in the toxicity expression of different substances, inter- and intra-species which make it difficult to predict clinical effects in humans. The new methods in molecular biology developed in the last decades are furnishing very useful tools to study some of the more relevant molecules implied in toxicokinetic and toxicodynamic processes. We aim to show some meaningful examples of how recent research developments with genes and proteins have clear applications to understand significant clinical matters, such as inter-individual variations in susceptibility to chemicals, and other phenomena related to the way some substances act to induce variations in the expression and functionality of these targets.

Systems biology solutions for biochemical production challenges.

PubMed

Hansen, Anne Sofie Lærke; Lennen, Rebecca M; Sonnenschein, Nikolaus; Herrgård, Markus J

2017-06-01

There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions. This additional complexity compared to basic science research requires pushing systems biology strategies to their limits and often spurs innovative developments that benefit fields outside metabolic engineering. Here we survey recent advanced applications of systems biology methods in engineering microbial production strains for biofuels and -chemicals. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Moonshot Science-Risks and Benefits.

PubMed

Casadevall, Arturo; Fang, Ferric C

2016-08-30

Ever since the successful Apollo 11 Moon landing in 1969, a "moonshot" has come to signify a bold effort to achieve a seemingly impossible task. The Obama administration recently called for a moonshot to cure cancer, an initiative that has elicited mixed responses from researchers who welcome additional funding but worry about raising expectations. We suggest that a successful moonshot requires a sufficient understanding of the basic science underlying a problem in question so that efforts can be focused on engineering a solution. Current gaps in our basic knowledge of cancer biology make the cancer moonshot a uniquely challenging endeavor. Nevertheless, history has shown that intensive research efforts have frequently yielded conceptual and technological breakthroughs with unanticipated benefits for society. We expect that this effort will be no different. Copyright © 2016 Casadevall and Fang.

The Discovery of Carboxyethylpyrroles (CEPs): Critical Insights into AMD, Autism, Cancer, and Wound Healing from Basic Research on the Chemistry of Oxidized Phospholipids

PubMed Central

Salomon, Robert G.; Hong, Li; Hollyfield, Joe G.

2011-01-01

Basic research, exploring the hypothesis that 2-(ω-carboxyethyl)pyrrole (CEP) modifications of proteins are generated nonenzymatically in vivo is delivering a bonanza of molecular mechanistic insights into age-related macular degeneration, autism, cancer, and wound healing. CEPs are produced through covalent modification of protein lysyl ε-amino groups by γ-hydroxyalkenal phospholipids that are formed by oxidative cleavage of docosahexaenate-containing phospholipids. Chemical synthesis of CEP-modified proteins and the production of highly specific antibodies that recognize them preceded and facilitated their detection in vivo and enabled exploration of their biological occurrence and activities. This investigational approach –from the chemistry of biomolecules to disease phenotype – is proving to be remarkably productive. PMID:21875030

Aquatic macroinvertebrates of the lower Missouri River

USGS Publications Warehouse

Poulton, Barry C.

2010-01-01

The U.S. Geological Survey (USGS) Columbia Environmental Research Center (CERC), in cooperation with the U.S. Environmental Protection Agency (USEPA), the U.S. Fish & Wildlife Service (USFWS), and the Missouri Department of Natural Resources (MDNR), has been conducting research on the aquatic macroinvertebrates of the lower Missouri River since the mid-1990s. This research was initiated in response to the need for comprehensive characterization of biological communities inhabiting aquatic habitats in large river systems that have historically been poorly studied. The USGS Status and Trends of Biological Resources Program provided partial funding for pilot studies that began in 1993 when the CERC was part of the USFWS. The purpose of this fact sheet is to provide stakeholders, scientists, management, and the general public with a basic summary of results from studies conducted by the CERC since that time period.

Research in Undergraduate Instruction: A Biotech Lab Project for Recombinant DNA Protein Expression in Bacteria

NASA Astrophysics Data System (ADS)

Brockman, Mark; Ordman, Alfred B.; Campbell, A. Malcolm

1996-06-01

In the sophomore-level Molecular Biology and Biotechnology course at Beloit College, students learn basic methods in molecular biology in the context of pursuing a semester-long original research project. We are exploring how DNA sequence affects expression levels of proteins. A DNA fragment encoding all or part of the guanylate monokinase (gmk) sequence is cloned into pSP73 and expressed in E. coli. A monoclonal antibody is made to gmk. The expression level of gmk is determined by SDS gel elctrophoresis, a Western blot, and an ELISA assay. Over four years, an increase in enrollment in the course from 9 to 34 students, the 85% of majors pursuing advanced degrees, and course evaluations all support the conclusion that involving students in research during undergraduate courses encourages them to pursue careers in science.

Current concept in neural regeneration research: NSCs isolation, characterization and transplantation in various neurodegenerative diseases and stroke: A review

PubMed Central

Vishwakarma, Sandeep K.; Bardia, Avinash; Tiwari, Santosh K.; Paspala, Syed A.B.; Khan, Aleem A.

2013-01-01

Since last few years, an impressive amount of data has been generated regarding the basic in vitro and in vivo biology of neural stem cells (NSCs) and there is much far hope for the success in cell replacement therapies for several human neurodegenerative diseases and stroke. The discovery of adult neurogenesis (the endogenous production of new neurons) in the mammalian brain more than 40 years ago has resulted in a wealth of knowledge about stem cells biology in neuroscience research. Various studies have done in search of a suitable source for NSCs which could be used in animal models to understand the basic and transplantation biology before treating to human. The difficulties in isolating pure population of NSCs limit the study of neural stem behavior and factors that regulate them. Several studies on human fetal brain and spinal cord derived NSCs in animal models have shown some interesting results for cell replacement therapies in many neurodegenerative diseases and stroke models. Also the methods and conditions used for in vitro culture of these cells provide an important base for their applicability and specificity in a definite target of the disease. Various important developments and modifications have been made in stem cells research which is needed to be more specified and enrolment in clinical studies using advanced approaches. This review explains about the current perspectives and suitable sources for NSCs isolation, characterization, in vitro proliferation and their use in cell replacement therapies for the treatment of various neurodegenerative diseases and strokes. PMID:25685495

Higher order thinking skills: using e-portfolio in project-based learning

NASA Astrophysics Data System (ADS)

Lukitasari, M.; Handhika, J.; Murtafiah, W.

2018-03-01

The purpose of this research is to describe students' higher-order thinking skills through project-based learning using e-portfolio. The method used in this research is descriptive qualitative method. The research instruments used were test, unstructured interview, and documentation. Research subjects were students of mathematics, physics and biology education department who take the Basics Physics course. The result shows that through project-based learning using e-portfolio the students’ ability to: analyze (medium category, N-Gain 0.67), evaluate (medium category, N-Gain 0.51), and create (medium Category, N-Gain 0.44) are improved.

Revisiting Preschoolers' Living Things Concept: A Microgenetic Analysis of Conceptual Change in Basic Biology

ERIC Educational Resources Information Center

Opfer, John E.; Siegler, Robert S.

2004-01-01

Many preschoolers know that plants and animals share basic biological properties, but this knowledge does not usually lead them to conclude that plants, like animals, are living things. To resolve this seeming paradox, we hypothesized that preschoolers largely base their judgments of life status on a biological property, capacity for teleological…

What makes for sound science?

PubMed

Costa, Fabrizio; Cramer, Grant; Finnegan, E Jean

2017-11-10

The inclusive threshold policy for publication in BMC journals including BMC Plant Biology means that editorial decisions are largely based on the soundness of the research presented rather than the novelty or potential impact of the work. Here we discuss what is required to ensure that research meets the requirement of scientific soundness. BMC Plant Biology and the other BCM-series journals ( https://www.biomedcentral.com/p/the-bmc-series-journals ) differ in policy from many other journals as they aim to provide a home for all publishable research. The inclusive threshold policy for publication means that editorial decisions are largely based on the soundness of the research presented rather than the novelty or potential impact of the work. The emphasis on scientific soundness ( http://blogs.biomedcentral.com/bmcseriesblog/2016/12/05/vital-importance-inclusive/ ) rather than novelty or impact is important because it means that manuscripts that may be judged to be of low impact due to the nature of the study as well as those reporting negative results or that largely replicate earlier studies, all of which can be difficult to publish elsewhere, are available to the research community. Here we discuss the importance of the soundness of research and provide some basic guidelines to assist authors to determine whether their research is appropriate for submission to BMC Plant Biology.Prior to a research article being sent out for review, the handling editor will first determine whether the research presented is scientifically valid. To be valid the research must address a question of biological significance using suitable methods and analyses, and must follow community-agreed standards relevant to the research field.

[Radar as imaging tool in ecology and conservation biology].

PubMed

Matyjasiak, Piotr

2017-01-01

Migrations and dispersal are among the most important ecological processes that shape ecosystems and influence our economy, health and safety. Movements of birds, bats and insects occur in a large spatial scale - regional, continental, or intercontinental. However, studies of these phenomena using classic methods are usually local. Breakthrough came with the development of radar technology, which enabled researchers to study animal movements in the atmosphere in a large spatial and temporal scale. The aim of this article was to present the radar imaging methods used in the research of aerial movements of birds, bats and insects. The types of radars used in research are described, and examples of the use of radar in basic research and in conservation biology are discussed. Radar visualizations are used in studies on the effect of meteorological conditions on bird migration, on spatial and temporal dynamics of movements of birds, bats and insects, and on the mechanism of orientation of migrating birds and insects. In conservation biology research radars are used in the monitoring of endangered species of birds and bats, to monitor bird activity at airports, as well as in assessing the impact of high constructions on flying birds and bats.

Island biology: looking towards the future

PubMed Central

Kueffer, Christoph; Drake, Donald R.; Fernández-Palacios, José María

2014-01-01

Oceanic islands are renowned for the profound scientific insights that their fascinating biotas have provided to biologists during the past two centuries. Research presented at Island Biology 2014—an international conference, held in Honolulu, Hawaii (7–11 July 2014), which attracted 253 presenters and 430 participants from at least 35 countries1—demonstrated that islands are reclaiming a leading role in ecology and evolution, especially for synthetic studies at the intersections of macroecology, evolution, community ecology and applied ecology. New dynamics in island biology are stimulated by four major developments. We are experiencing the emergence of a truly global and comprehensive island research community incorporating previously neglected islands and taxa. Macroecology and big-data analyses yield a wealth of global-scale synthetic studies and detailed multi-island comparisons, while other modern research approaches such as genomics, phylogenetic and functional ecology, and palaeoecology, are also dispersing to islands. And, increasingly tight collaborations between basic research and conservation management make islands places where new conservation solutions for the twenty-first century are being tested. Islands are home to a disproportionate share of the world's rare (and extinct) species, and there is an urgent need to develop increasingly collaborative and innovative research to address their conservation requirements. PMID:25339655

Directions in biomedical research: a plea for ideological pluralism.

PubMed

Malone, P Colm; Agutter, Paul S

2003-08-01

Feinstein [A.R. Feinstein, Am. J. Med. 107 (1999) 461] complained that 'basic medical science' has overwhelmed 'pathophysiological medical science' during the past half century, and 'destroyed the bridge between bedside and bench'. We agree that a 'drastic reorientation' will be necessary to correct the overemphasis and imbalance. Re-examining the roots of his problem, we believe that a plea to restore a balance between the 'status' (esteem) of 'large research' and 'small research' in medical science brings back into question the decision of academic physiologists to invoke the framework of Physics in/of 1847 [P.F. Cranefield, J. Hist. Med. Allied Sci. 12 (1957) 407] (together with an absolutist 'Prime Mover'/Metaphysic which Einstein would delete from Physics in 1905). The current 'imbalance' arose when that Cartesian 'Prime Mover' was NOT deleted from the Biological frame. Feinstein felt that the 'privileged status' (esteem) in which fund-giving bodies hold 'Small' researches compared to 'Large' should be cancelled. Once Biology replaces its Cartesian absolutism with a relativist framework, redress will follow naturally when living-material has regained the status of cause as well as effect. Descartes' 'Great Watchmaker' is a Dead God in Biology: a non-metaphysical Biological Perspective would restore balance between 'large' and 'small' investigations. ('Pluralism' implies that no scientific perspective would be second-rate in a relativist framework.)

Implementing Best Practices and Validation of Cryopreservation Techniques for Microorganisms

PubMed Central

Smith, David; Ryan, Matthew

2012-01-01

Authentic, well preserved living organisms are basic elements for research in the life sciences and biotechnology. They are grown and utilized in laboratories around the world and are key to many research programmes, industrial processes and training courses. They are vouchers for publications and must be available for confirmation of results, further study or reinvestigation when new technologies become available. These biological resources must be maintained without change in biological resource collections. In order to achieve best practice in the maintenance and provision of biological materials for industry, research and education the appropriate standards must be followed. Cryopreservation is often the best preservation method available to achieve these aims, allowing long term, stable storage of important microorganisms. To promulgate best practice the Organisation for Economic Development and Co-operation (OECD published the best practice guidelines for BRCs. The OECD best practice consolidated the efforts of the UK National Culture Collections, the European Common Access to Biological Resources and Information (CABRI) project consortium and the World Federation for Culture Collections. The paper discusses quality management options and reviews cryopreservation of fungi, describing how the reproducibility and quality of the technique is maintained in order to retain the full potential of fungi. PMID:22629202

Interfacing mathematics and biology: a discussion on training, research, collaboration, and funding.

PubMed

Miller, Laura A; Alben, Silas

2012-11-01

This article summarizes the discussion at a workshop on "Working at the Interface of Mathematics and Biology" at the 2012 Annual Meeting of the Society for Integrative and Comparative Biology. The goal of this workshop was to foster an ongoing discussion by the community on how to effectively train students from the biological, physical, engineering, and mathematical sciences to work at the intersection of these fields. One major point of discussion centered on how to be a successful interdisciplinary researcher in terms of where to publish, how to successfully write grants, and how to navigate evaluations for tenure and promotion. An emphasis was placed on the importance of developing strong multidisciplinary collaborations and clearly defining one's career trajectory to the home discipline. Another focus of the discussion was on the training of students and postdoctoral fellows in interdisciplinary work and helping these junior researchers to launch their careers. The group emphasized the need for the development of publicly available resources for biologists to learn basic tools for mathematical modeling and for mathematicians and engineers to see how their fields may be applied to current topics in the life sciences.

Making Basic Science Studies in Glaucoma More Clinically Relevant: The Need for a Consensus.

PubMed

Toris, Carol B; Gelfman, Claire; Whitlock, Andy; Sponsel, William E; Rowe-Rendleman, Cheryl L

2017-09-01

Glaucoma is a chronic, progressive, and debilitating optic neuropathy that causes retinal damage and visual defects. The pathophysiologic mechanisms of glaucoma remain ill-defined, and there is an indisputable need for contributions from basic science researchers in defining pathways for translational research. However, glaucoma researchers today face significant challenges due to the lack of a map of integrated pathways from bench to bedside and the lack of consensus statements to guide in choosing the right research questions, techniques, and model systems. Here, we present the case for the development of such maps and consensus statements, which are critical for faster development of the most efficacious glaucoma therapy. We underscore that interrogating the preclinical path of both successful and unsuccessful clinical programs is essential to defining future research. One aspect of this is evaluation of available preclinical research tools. To begin this process, we highlight the utility of currently available animal models for glaucoma and emphasize that there is a particular need for models of glaucoma with normal intraocular pressure. In addition, we outline a series of discoveries from cell-based, animal, and translational research that begin to reveal a map of glaucoma from cell biology to physiology to disease pathology. Completion of these maps requires input and consensus from the global glaucoma research community. This article sets the stage by outlining various approaches to such a consensus. Together, these efforts will help accelerate basic science research, leading to discoveries with significant clinical impact for people with glaucoma.

The Chemo-Biological Outreach of Nano-Biomaterials: Implications for Tissue Engineering and Regenerative Medicine.

PubMed

Kumar, Pradeep; Choonara, Yahya E; Khan, Riaz A; Pillay, Viness

2017-01-01

Nanobiomaterials can be defined as materials interacting with and influencing the biological microenvironment at a nanointerface. Recently the basic as well as applied research related to nanobiomaterials - a conjugation of nano-, material- and life-sciences - has immensely evolved for therapeutics and related biotechnology areas. The current overview focused on the potential of nanobiomaterial-based substrates towards the generation of biocompatible surfaces, tissue engineering architectures, and regenerative medicine. Emphasis was given to chemomolecular functionalization of nanobiomaterials, nanobiomaterial composites, and morphomechanically modified nanoarchetypes and their inherent chemo-biological interaction with the biological microenvironment. Additionally, recent developments in nanobiomaterial substrate design and structure, chemo-biological interface related bio-systems uses and further evolving applications in health care, therapeutics and nanomedicine were discussed herein. Furthermore, a special emphasis was placed on the nano-chemo-biological interactions inherent to various nanobiomaterial substrates in close vicinity with biological systems. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The neurosciences research program at MIT and the beginning of the modern field of neuroscience.

PubMed

Adelman, George

2010-01-15

The interdisciplinary field, "neuroscience," began at MIT in 1962 with the founding of the Neurosciences Research Program (NRP) by Francis O. Schmitt and a group of US and international scientists - physical, biological, medical, and behavioral - interested in understanding the brain basis of behavior and mind. They organized and held specialist meetings of basic topics in neuroscience, and the journal and book publications over the next 20 years, based on these meetings, helped establish the new field.

Optical Coherence Tomography: Basic Concepts and Applications in Neuroscience Research

PubMed Central

2017-01-01

Optical coherence tomography is a micrometer-scale imaging modality that permits label-free, cross-sectional imaging of biological tissue microstructure using tissue backscattering properties. After its invention in the 1990s, OCT is now being widely used in several branches of neuroscience as well as other fields of biomedical science. This review study reports an overview of OCT's applications in several branches or subbranches of neuroscience such as neuroimaging, neurology, neurosurgery, neuropathology, and neuroembryology. This study has briefly summarized the recent applications of OCT in neuroscience research, including a comparison, and provides a discussion of the remaining challenges and opportunities in addition to future directions. The chief aim of the review study is to draw the attention of a broad neuroscience community in order to maximize the applications of OCT in other branches of neuroscience too, and the study may also serve as a benchmark for future OCT-based neuroscience research. Despite some limitations, OCT proves to be a useful imaging tool in both basic and clinical neuroscience research. PMID:29214158

Basic Research Plan, February 2003

DTIC Science & Technology

2003-02-01

consistent. This effort includes the nitration , crystallization, and coating of CL–20. Under Army sponsor- ship, a process for the nitration of CL–20 has...actuators • Multiscale computational design of structural materials with embedded functionality • Materials with embedded electrical/magnetic/optical...the innovative use of biology to produce unique materials and processes of mili- tary relevance; to increase economic and environmental affordability

A Matter of Life and Death: Knowledge about the Body and Concept of Death in Adults with Intellectual Disabilities

ERIC Educational Resources Information Center

McEvoy, J.; Treacy, B.; Quigley, J.

2017-01-01

Background: An increased awareness of how people with intellectual disabilities (ID) understand death and dying is necessary in supporting life-long learning, post-bereavement support and planning end-of-life care. Previous research suggests that adults with ID have a limited or "patchy" understanding of the basic biological components…

A Bridge between Two Cultures: Uncovering the Chemistry Concepts Relevant to the Nursing Clinical Practice

ERIC Educational Resources Information Center

Brown, Corina E.; Henry, Melissa L. M.; Barbera, Jack; Hyslop, Richard M.

2012-01-01

This study focused on the undergraduate course that covers basic topics in general, organic, and biological (GOB) chemistry at a mid-sized state university in the western United States. The central objective of the research was to identify the main topics of GOB chemistry relevant to the clinical practice of nursing. The collection of data was…

Triatominae biochemistry goes to school: evaluation of a novel tool for teaching basic biochemical concepts of Chagas disease vectors.

PubMed

Cunha, Leonardo Rodrigues; Cudischevitch, Cecília de Oliveira; Carneiro, Alan Brito; Macedo, Gustavo Bartholomeu; Lannes, Denise; Silva-Neto, Mário Alberto Cardoso da

2014-01-01

We evaluate a new approach to teaching the basic biochemistry mechanisms that regulate the biology of Triatominae, major vectors of Trypanosoma cruzi, the causative agent of Chagas disease. We have designed and used a comic book, "Carlos Chagas: 100 years after a hero's discovery" containing scientific information obtained by seven distinguished contemporary Brazilian researchers working with Triatominaes. Students (22) in the seventh grade of a public elementary school received the comic book. The study was then followed up by the use of Concept Maps elaborated by the students. Six Concept Maps elaborated by the students before the introduction of the comic book received an average score of 7. Scores rose to an average of 45 after the introduction of the comic book. This result suggests that a more attractive content can greatly improve the knowledge and conceptual understanding among students not previously exposed to insect biochemistry. In conclusion, this study illustrates an alternative to current strategies of teaching about the transmission of neglected diseases. It also promotes the diffusion of the scientific knowledge produced by Brazilian researchers that may stimulate students to choose a scientific career. © 2014 The International Union of Biochemistry and Molecular Biology.

Longitudinal in vivo two-photon fluorescence imaging

PubMed Central

Crowe, Sarah E.; Ellis-Davies, Graham C.R.

2014-01-01

Fluorescence microscopy is an essential technique for the basic sciences, especially biomedical research. Since the invention of laser scanning confocal microscopy in 1980s, that enabled imaging both fixed and living biological tissue with three-dimensional precision, high-resolution fluorescence imaging has revolutionized biological research. Confocal microscopy, by its very nature, has one fundamental limitation. Due to the confocal pinhole, deep tissue fluorescence imaging is not practical. In contrast (no pun intended), two-photon fluorescence microscopy allows, in principle, the collection of all emitted photons from fluorophores in the imaged voxel, dramatically extending our ability to see deep into living tissue. Since the development of transgenic mice with genetically encoded fluorescent protein in neocortical cells in 2000, two-photon imaging has enabled the dynamics of individual synapses to be followed for up to two years. Since the initial landmark contributions to this field in 2002, the technique has been used to understand how neuronal structure are changed by experience, learning and memory and various diseases. Here we provide a basic summary of the crucial elements that are required for such studies, and discuss many applications of longitudinal two-photon fluorescence microscopy that have appeared since 2002. PMID:24214350

Biomedical text mining and its applications in cancer research.

PubMed

Zhu, Fei; Patumcharoenpol, Preecha; Zhang, Cheng; Yang, Yang; Chan, Jonathan; Meechai, Asawin; Vongsangnak, Wanwipa; Shen, Bairong

2013-04-01

Cancer is a malignant disease that has caused millions of human deaths. Its study has a long history of well over 100years. There have been an enormous number of publications on cancer research. This integrated but unstructured biomedical text is of great value for cancer diagnostics, treatment, and prevention. The immense body and rapid growth of biomedical text on cancer has led to the appearance of a large number of text mining techniques aimed at extracting novel knowledge from scientific text. Biomedical text mining on cancer research is computationally automatic and high-throughput in nature. However, it is error-prone due to the complexity of natural language processing. In this review, we introduce the basic concepts underlying text mining and examine some frequently used algorithms, tools, and data sets, as well as assessing how much these algorithms have been utilized. We then discuss the current state-of-the-art text mining applications in cancer research and we also provide some resources for cancer text mining. With the development of systems biology, researchers tend to understand complex biomedical systems from a systems biology viewpoint. Thus, the full utilization of text mining to facilitate cancer systems biology research is fast becoming a major concern. To address this issue, we describe the general workflow of text mining in cancer systems biology and each phase of the workflow. We hope that this review can (i) provide a useful overview of the current work of this field; (ii) help researchers to choose text mining tools and datasets; and (iii) highlight how to apply text mining to assist cancer systems biology research. Copyright © 2012 Elsevier Inc. All rights reserved.

Cell and molecular mechanics of biological materials

NASA Astrophysics Data System (ADS)

Bao, G.; Suresh, S.

2003-11-01

Living cells can sense mechanical forces and convert them into biological responses. Similarly, biological and biochemical signals are known to influence the abilities of cells to sense, generate and bear mechanical forces. Studies into the mechanics of single cells, subcellular components and biological molecules have rapidly evolved during the past decade with significant implications for biotechnology and human health. This progress has been facilitated by new capabilities for measuring forces and displacements with piconewton and nanometre resolutions, respectively, and by improvements in bio-imaging. Details of mechanical, chemical and biological interactions in cells remain elusive. However, the mechanical deformation of proteins and nucleic acids may provide key insights for understanding the changes in cellular structure, response and function under force, and offer new opportunities for the diagnosis and treatment of disease. This review discusses some basic features of the deformation of single cells and biomolecules, and examines opportunities for further research.

Behavioural science at work for Canada: National Research Council laboratories.

PubMed

Veitch, Jennifer A

2007-03-01

The National Research Council is Canada's principal research and development agency. Its 20 institutes are structured to address interdisciplinary problems for industrial sectors, and to provide the necessary scientific infrastructure, such as the national science library. Behavioural scientists are active in five institutes: Biological Sciences, Biodiagnostics, Aerospace, Information Technology, and Construction. Research topics include basic cellular neuroscience, brain function, human factors in the cockpit, human-computer interaction, emergency evacuation, and indoor environment effects on occupants. Working in collaboration with NRC colleagues and with researchers from universities and industry, NRC behavioural scientists develop knowledge, designs, and applications that put technology to work for people, designed with people in mind.

Journey of a molecular biologist.

PubMed

Nomura, Masayasu

2011-01-01

My journey into a research career began in fermentation biochemistry in an applied science department during the difficult post-World War II time in Japan. Subsequently, my desire to do research in basic science developed. I was fortunate to be a postdoctoral fellow in the United States during the early days of molecular biology. From 1957 to 1960, I worked with three pioneers of molecular biology, Sol Spiegelman, James Watson, and Seymour Benzer. These experiences helped me develop into a basic research scientist. My initial research projects at Osaka University, and subsequently at the University of Wisconsin, Madison, were on the mode of action of colicins as well as on mRNA and ribosomes. Following success in the reconstitution of ribosomal subunits, my efforts focused more on ribosomes, initially on the aspects of structure, function, and in vitro assembly, such as the construction of the 30S subunit assembly map. After this, my laboratory studied the regulation of the synthesis of ribosomes and ribosomal components in Escherichia coli. Our achievements included the discovery of translational feedback regulation of ribosomal protein synthesis and the identification of several repressor ribosomal proteins used in this regulation. In 1984, I moved to the University of California, Irvine, and initiated research on rRNA transcription by RNA polymerase I in the yeast Saccharomyces cerevisiae. The use of yeast genetics combined with biochemistry allowed us to identify genes uniquely involved in rRNA synthesis and to elucidate the mechanism of initiation of transcription. This essay is a reflection on my life as a research scientist.

The Ecology of a Keystone Seed Disperser, the Ant Rhytidoponera violacea

PubMed Central

Lubertazzi, Dave; Aliberti Lubertazzi, Maria A.; McCoy, Neil; Gove, Aaron D.; Majer, Jonathan D.; Dunn, Robert R.

2010-01-01

Rhytidoponera violacea (Forel) (Hymenoptera: Formicidae) is a keystone seed disperser in Kwongan heathl and habitats of southwestern Australia. Like many myrmecochorous ants, little is known about the basic biology of this species. In this study various aspects of the biology of R. violacea were examined and the researchers evaluated how these characteristics may influence seed dispersal. R. violacea nesting habits (relatively shallow nests), foraging behavior (scramble competitor and lax food selection criteria), and other life history characteristics complement their role as a mutualist that interacts with the seeds of many plant species. PMID:21067420

ProThera Biologics, Inc.: a novel immunomodulator and biomarker for life-threatening diseases.

PubMed

Lim, Yow-Pin

2013-02-01

ProThera Biologics is a development stage bio-therapeutics company in East Providence, Rhode Island. The company was founded in 2002 to focus on the critical role and commercial potential of Inter-alpha Inhibitor Proteins (IAIP) for treating acute life-threatening inflammatory diseases. The discovery research originated in the basic research laboratories of the co-founders, Yow-Pin Lim, MD, PhD, and Douglas C. Hixson, PhD, at Rhode Island Hospital, a Lifespan partner. The company is backed by the Slater Technology Fund and has received research grants from the Rhode Island State Science and Technology Council (RI STAC) as well as continuous funding from the National Institutes of Health (NIH), with several Phase I and II Small Business Innovation Research (SBIR) grants over the past 10 years. ProThera has developed a novel process to purify Inter-alpha Inhibitor Proteins from source material, and has conducted groundbreaking research into the usage of IAIP to fight systemic inflammation.

Chemogenomics: a discipline at the crossroad of high throughput technologies, biomarker research, combinatorial chemistry, genomics, cheminformatics, bioinformatics and artificial intelligence.

PubMed

Maréchal, Eric

2008-09-01

Chemogenomics is the study of the interaction of functional biological systems with exogenous small molecules, or in broader sense the study of the intersection of biological and chemical spaces. Chemogenomics requires expertises in biology, chemistry and computational sciences (bioinformatics, cheminformatics, large scale statistics and machine learning methods) but it is more than the simple apposition of each of these disciplines. Biological entities interacting with small molecules can be isolated proteins or more elaborate systems, from single cells to complete organisms. The biological space is therefore analyzed at various postgenomic levels (genomic, transcriptomic, proteomic or any phenotypic level). The space of small molecules is partially real, corresponding to commercial and academic collections of compounds, and partially virtual, corresponding to the chemical space possibly synthesizable. Synthetic chemistry has developed novel strategies allowing a physical exploration of this universe of possibilities. A major challenge of cheminformatics is to charter the virtual space of small molecules using realistic biological constraints (bioavailability, druggability, structural biological information). Chemogenomics is a descendent of conventional pharmaceutical approaches, since it involves the screening of chemolibraries for their effect on biological targets, and benefits from the advances in the corresponding enabling technologies and the introduction of new biological markers. Screening was originally motivated by the rigorous discovery of new drugs, neglecting and throwing away any molecule that would fail to meet the standards required for a therapeutic treatment. It is now the basis for the discovery of small molecules that might or might not be directly used as drugs, but which have an immense potential for basic research, as probes to explore an increasing number of biological phenomena. Concerns about the environmental impact of chemical industry open new fields of research for chemogenomics.

Analytical electron microscopy in the study of biological systems.

PubMed

Johnson, D E

1986-01-01

The AEM is a powerful tool in biological research, capable of providing information simply not available by other means. The use of a field emission STEM for this application can lead to a significant improvement in spatial resolution in most cases now allowed by the quality of the specimen preparation but perhaps ultimately limited by the effects of radiation damage. Increased elemental sensitivity is at least possible in selected cases with electron energy-loss spectrometry, but fundamental aspects of ELS will probably confine its role to that of a limited complement to EDS. The considerable margin for improvement in sensitivity of the basic analytical technique means that the search for technological improvement will continue. Fortunately, however, current technology can also continue to answer important biological questions.

The short-lived African turquoise killifish: an emerging experimental model for ageing

PubMed Central

Kim, Yumi; Nam, Hong Gil; Valenzano, Dario Riccardo

2016-01-01

ABSTRACT Human ageing is a fundamental biological process that leads to functional decay, increased risk for various diseases and, ultimately, death. Some of the basic biological mechanisms underlying human ageing are shared with other organisms; thus, animal models have been invaluable in providing key mechanistic and molecular insights into the common bases of biological ageing. In this Review, we briefly summarise the major applications of the most commonly used model organisms adopted in ageing research and highlight their relevance in understanding human ageing. We compare the strengths and limitations of different model organisms and discuss in detail an emerging ageing model, the short-lived African turquoise killifish. We review the recent progress made in using the turquoise killifish to study the biology of ageing and discuss potential future applications of this promising animal model. PMID:26839399

Advances in 3D cell culture technologies enabling tissue-like structures to be created in vitro.

PubMed

Knight, Eleanor; Przyborski, Stefan

2015-12-01

Research in mammalian cell biology often relies on developing in vitro models to enable the growth of cells in the laboratory to investigate a specific biological mechanism or process under different test conditions. The quality of such models and how they represent the behavior of cells in real tissues plays a critical role in the value of the data produced and how it is used. It is particularly important to recognize how the structure of a cell influences its function and how co-culture models can be used to more closely represent the structure of real tissue. In recent years, technologies have been developed to enhance the way in which researchers can grow cells and more readily create tissue-like structures. Here we identify the limitations of culturing mammalian cells by conventional methods on two-dimensional (2D) substrates and review the popular approaches currently available that enable the development of three-dimensional (3D) tissue models in vitro. There are now many ways in which the growth environment for cultured cells can be altered to encourage 3D cell growth. Approaches to 3D culture can be broadly categorized into scaffold-free or scaffold-based culture systems, with scaffolds made from either natural or synthetic materials. There is no one particular solution that currently satisfies all requirements and researchers must select the appropriate method in line with their needs. Using such technology in conjunction with other modern resources in cell biology (e.g. human stem cells) will provide new opportunities to create robust human tissue mimetics for use in basic research and drug discovery. Application of such models will contribute to advancing basic research, increasing the predictive accuracy of compounds, and reducing animal usage in biomedical science. © 2014 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.

JPRS Report, China, Handbook of Military Knowledge for Commanders

DTIC Science & Technology

1988-03-07

Chemical and Biological Weapons Chapter I Nuclear Weapons (178) A. Summary Statement on Nuclear Weapons (178) 1. Basic Principles of Nuclear...199) 1. Basic Principles of Protection Against Nuclear, Chemical and Biological Weapons* (199) 2. Maior Actions For Protection Against Nuclear...people’s bodies through the digestive tract. Skin contact. Biological warfare agents may enter the body directly through the skin , mucous membranes or

Challenges towards Revitalizing Hemp: A Multifaceted Crop.

PubMed

Schluttenhofer, Craig; Yuan, Ling

2017-11-01

Hemp has been an important crop throughout human history for food, fiber, and medicine. Despite significant progress made by the international research community, the basic biology of hemp plants remains insufficiently understood. Clear objectives are needed to guide future research. As a semi-domesticated plant, hemp has many desirable traits that require improvement, including eliminating seed shattering, enhancing the quantity and quality of stem fiber, and increasing the accumulation of phytocannabinoids. Methods to manipulate the sex of hemp plants will also be important for optimizing yields of seed, fiber, and cannabinoids. Currently, research into trait improvement is hindered by the lack of molecular techniques adapted to hemp. Here we review how addressing these limitations will help advance our knowledge of plant biology and enable us to fully domesticate and maximize the agronomic potential of this promising crop. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

BIOLOGICAL NETWORK EXPLORATION WITH CYTOSCAPE 3

PubMed Central

Su, Gang; Morris, John H.; Demchak, Barry; Bader, Gary D.

2014-01-01

Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and pathway construction. Cytoscape provides core functionality to load, visualize, search, filter and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the network, visualizing network associated data (attributes) and identifying clusters. It also highlights new features that benefit experienced users. PMID:25199793

Translating exercise biology into the Venezuelan medical education and health care system.

PubMed

Del Corral, Pedro

2007-09-01

In the absence of pharmacological agents, physical exercise was widely used by physicians in the late 19th century to treat a number of maladies. In the 1950's, epidemiological evidence suggested an association between physical activity and health, and increased interest in clinical exercise biology. By the 1990's, sufficient research data was accumulated on the benefits of exercise, such that North American medical associations, government agencies, and the World Health Organization have published guidelines on exercise for public and clinical populations. Despite this, leaders in medical education have remained reluctant to incorporate exercise biology into the core medical curriculum, or to systematically implement it in graduate medical education. This work reviews Venezuelan exercise biology literature, and its medical applications. Venezuelan scientists and clinicians have invested efforts in cardiopulmonary exercise testing, skeletal muscle adaptations to training and exercise cardiovascular pharmacology in patients, sedentary subjects and athletes. It is suggested here, that there is a need to develop education and research programs in basic and clinical exercise biology in the formal training of medical students, physicians in residency programs, and allied health care professionals. Tentative steps to initiate this process are proposed.

Healthy aging: The ultimate preventative medicine.

PubMed

Kaeberlein, Matt; Rabinovitch, Peter S; Martin, George M

2015-12-04

Age is the greatest risk factor for nearly every major cause of mortality in developed nations. Despite this, most biomedical research focuses on individual disease processes without much consideration for the relationships between aging and disease. Recent discoveries in the field of geroscience, which aims to explain biological mechanisms of aging, have provided insights into molecular processes that underlie biological aging and, perhaps more importantly, potential interventions to delay aging and promote healthy longevity. Here we describe some of these advances, along with efforts to move geroscience from the bench to the clinic. We also propose that greater emphasis should be placed on research into basic aging processes, because interventions that slow aging will have a greater effect on quality of life compared with disease-specific approaches. Copyright © 2015, American Association for the Advancement of Science.

Review of spectral imaging technology in biomedical engineering: achievements and challenges.

PubMed

Li, Qingli; He, Xiaofu; Wang, Yiting; Liu, Hongying; Xu, Dongrong; Guo, Fangmin

2013-10-01

Spectral imaging is a technology that integrates conventional imaging and spectroscopy to get both spatial and spectral information from an object. Although this technology was originally developed for remote sensing, it has been extended to the biomedical engineering field as a powerful analytical tool for biological and biomedical research. This review introduces the basics of spectral imaging, imaging methods, current equipment, and recent advances in biomedical applications. The performance and analytical capabilities of spectral imaging systems for biological and biomedical imaging are discussed. In particular, the current achievements and limitations of this technology in biomedical engineering are presented. The benefits and development trends of biomedical spectral imaging are highlighted to provide the reader with an insight into the current technological advances and its potential for biomedical research.

The Molecular Genetics of Autism Spectrum Disorders: Genomic Mechanisms, Neuroimmunopathology, and Clinical Implications

PubMed Central

Guerra, Daniel J.

2011-01-01

Autism spectrum disorders (ASDs) have become increasingly common in recent years. The discovery of single-nucleotide polymorphisms and accompanying copy number variations within the genome has increased our understanding of the architecture of the disease. These genetic and genomic alterations coupled with epigenetic phenomena have pointed to a neuroimmunopathological mechanism for ASD. Model animal studies, developmental biology, and affective neuroscience laid a foundation for dissecting the neural pathways impacted by these disease-generating mechanisms. The goal of current autism research is directed toward a systems biological approach to find the most basic genetic and environmental causes to this severe developmental disease. It is hoped that future genomic and neuroimmunological research will be directed toward finding the road toward prevention, treatment, and cure of ASD. PMID:22937247

Physics through the 1990s: Scientific interfaces and technological applications

NASA Technical Reports Server (NTRS)

1986-01-01

The volume examines the scientific interfaces and technological applications of physics. Twelve areas are dealt with: biological physics-biophysics, the brain, and theoretical biology; the physics-chemistry interface-instrumentation, surfaces, neutron and synchrotron radiation, polymers, organic electronic materials; materials science; geophysics-tectonics, the atmosphere and oceans, planets, drilling and seismic exploration, and remote sensing; computational physics-complex systems and applications in basic research; mathematics-field theory and chaos; microelectronics-integrated circuits, miniaturization, future trends; optical information technologies-fiber optics and photonics; instrumentation; physics applications to energy needs and the environment; national security-devices, weapons, and arms control; medical physics-radiology, ultrasonics, MNR, and photonics. An executive summary and many chapters contain recommendations regarding funding, education, industry participation, small-group university research and large facility programs, government agency programs, and computer database needs.

An age of enlightenment for cilia: The FASEB Summer Research Conference on the “Biology of Cilia and Flagella”

PubMed Central

Tran, Pamela V.; Lechtreck, Karl F.

2015-01-01

From July 19–24, 2015, 169 clinicians and basic scientists gathered in the vertiginous heights of Snowmass, Colorado (2,502 m) for the fourth FASEB summer research conference on the ‘Biology of Cilia and Flagella’. Organizers Maureen Barr (Rutgers University), Iain Drummond (Massachusetts General Hospital/Harvard Medical School), and Jagesh Shah (Brigham and Women’s Hospital/Harvard Medical School) assembled a program filled with new data and forward-thinking ideas documenting the ongoing growth of the field. Sixty oral presentations and 77 posters covered novel aspects of cilia structure, ciliogenesis, cilia motility, cilia-mediated signaling, and cilia-related disease. In this report, we summarize the meeting, highlight exciting developments and discuss open questions. PMID:26597000

[Seed geography: its concept and basic scientific issues].

PubMed

Yu, Shun-Li; Wang, Zong-Shuai; Zeren, Wangmu

2010-01-01

In this paper, a new concept 'seed geography' was provided, and its definition, research contents, and scientific issues were put forward. Seed geography is a newly developed interdisciplinary science from plant geography, seed ecology, and phytosociology, which studies the geographic variation patterns of seed biological traits as well as their relationships with environmental factors from macroscopic to microscopic, and the seed formation, development, and change trends. The main research contents would include geography of seed mass, geography of seed chemical components, geography of seed morphology, geography of seed cell biological characteristics, geography of seed physiological characteristics, geography of seed genetic characteristics, and geography of flower and fruit. To explore the scientific issues in seed geography would help us to better understand the long-term adaptation and evolution of seed characteristics to natural environments.

Innate and learned preferences for sweet taste during childhood.

PubMed

Ventura, Alison K; Mennella, Julie A

2011-07-01

In nature, carbohydrates are a source of energy often equated with sweetness, the detection of which is associated with powerful hedonic appeal. Intakes of processed carbohydrates in the form of added sugars and sugar-sweetened beverages have risen consistently among all age groups over the last two decades. In this review, we describe the biological underpinnings that drive the consumption of sweet-tasting foods among pediatric populations. Scientific literature suggests that children's liking for all that is sweet is not solely a product of modern-day technology and advertising but reflects their basic biology. In fact, heightened preference for sweet-tasting foods and beverages during childhood is universal and evident among infants and children around the world. The liking for sweet tastes during development may have ensured the acceptance of sweet-tasting foods, such as mother's milk and fruits. Moreover, recent research suggests that liking for sweets may be further promoted by the pain-reducing properties of sugars. An examination of the basic biology of sweet taste during childhood provides insight, as well as new perspectives, for how to modify children's preferences for and intakes of sweet foods to improve their diet quality.

Systems Biology Methods for Alzheimer's Disease Research Toward Molecular Signatures, Subtypes, and Stages and Precision Medicine: Application in Cohort Studies and Trials.

PubMed

Castrillo, Juan I; Lista, Simone; Hampel, Harald; Ritchie, Craig W

2018-01-01

Alzheimer's disease (AD) is a complex multifactorial disease, involving a combination of genomic, interactome, and environmental factors, with essential participation of (a) intrinsic genomic susceptibility and (b) a constant dynamic interplay between impaired pathways and central homeostatic networks of nerve cells. The proper investigation of the complexity of AD requires new holistic systems-level approaches, at both the experimental and computational level. Systems biology methods offer the potential to unveil new fundamental insights, basic mechanisms, and networks and their interplay. These may lead to the characterization of mechanism-based molecular signatures, and AD hallmarks at the earliest molecular and cellular levels (and beyond), for characterization of AD subtypes and stages, toward targeted interventions according to the evolving precision medicine paradigm. In this work, an update on advanced systems biology methods and strategies for holistic studies of multifactorial diseases-particularly AD-is presented. This includes next-generation genomics, neuroimaging and multi-omics methods, experimental and computational approaches, relevant disease models, and latest genome editing and single-cell technologies. Their progressive incorporation into basic research, cohort studies, and trials is beginning to provide novel insights into AD essential mechanisms, molecular signatures, and markers toward mechanism-based classification and staging, and tailored interventions. Selected methods which can be applied in cohort studies and trials, with the European Prevention of Alzheimer's Dementia (EPAD) project as a reference example, are presented and discussed.

Translating human biology (introduction to special issue).

PubMed

Brewis, Alexandra A; Mckenna, James J

2015-01-01

Introducing a special issue on "Translating Human Biology," we pose two basic questions: Is human biology addressing the most critical challenges facing our species? How can the processes of translating our science be improved and innovated? We analyze articles published in American Journal of Human Biology from 2004-2013, and find there is very little human biological consideration of issues related to most of the core human challenges such as water, energy, environmental degradation, or conflict. There is some focus on disease, and considerable focus on food/nutrition. We then introduce this special volume with reference to the following articles that provide exemplars for the process of how translation and concern for broader context and impacts can be integrated into research. Human biology has significant unmet potential to engage more fully in translation for the public good, through consideration of the topics we focus on, the processes of doing our science, and the way we present our domain expertise. © 2014 Wiley Periodicals, Inc.

Division of Energy Biosciences annual report and summaries of FY 1996 activities

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

NONE

1997-04-01

The mission of the Division of Energy Biosciences is to support research that advances the fundamental knowledge necessary for the future development of biotechnologies related to the Department of Energy`s mission. The departmental civilian objectives include effective and efficient energy production, energy conservation, environmental restoration, and waste management. The Energy Biosciences program emphasizes research in the microbiological and plant sciences, as these understudied areas offer numerous scientific opportunities to dramatically influence environmentally sensible energy production and conservation. The research supported is focused on the basic mechanism affecting plant productivity, conversion of biomass and other organic materials into fuels and chemicalsmore » by microbial systems, and the ability of biological systems to replace energy-intensive or pollutant-producing processes. The Division also addresses the increasing number of new opportunities arising at the interface of biology with other basic energy-related sciences such as biosynthesis of novel materials and the influence of soil organisms on geological processes. This report gives summaries on 225 projects on photosynthesis, membrane or ion transport, plant metabolism and biosynthesis, carbohydrate metabolism lipid metabolism, plant growth and development, plant genetic regulation and genetic mechanisms, plant cell wall development, lignin-polysaccharide breakdown, nitrogen fixation and plant-microbial symbiosis, mechanism for plant adaptation, fermentative microbial metabolism, one and two carbon microbial metabolism, extremophilic microbes, microbial respiration, nutrition and metal metabolism, and materials biosynthesis.« less

Active Hydrogenation Catalyst with a Structured, Peptide-Based Outer-Coordination Sphere

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

Jain, Avijita; Buchko, Garry W.; Reback, Matthew L.

2012-10-05

The synthesis, catalytic activity, and structural features of a rhodium-based hydrogenation catalyst containing a phosphine ligand coupled to a 14-residue peptide are reported. Both CD and NMR spectroscopy show that the peptide adopts a helical structure in 1:1:1 TFE/MeCN/H2O that is maintained when the peptide is attached to the ligand and when the ligand is attached to the metal complex. The metal complex hydrogenates aqueous solutions of 3-butenol to 1-butanol at 360 ± 50 turnovers/Rh/h at 294 K. This peptide- based catalyst represents a starting point for developing and characterizing a peptide-based outer-coordination sphere that can be used to introducemore » enzyme-like features into molecular catalysts. This work was funded by the US DOE Basic Energy Sciences, Chemical Sciences, Geoscience and Biosciences Division (AJ, JCL and WJS), the Office of Science Early Career Research Program through the Office of Basic Energy Sciences (GWB, MLR and WJS). Part of the research was conducted at the W.R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by U.S. Department of Energy’s Office of Biolog-ical and Environmental Research (BER) program located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for the U.S. Department of Energy.« less

The translational science training program at NIH: Introducing early career researchers to the science and operation of translation of basic research to medical interventions.

PubMed

Gilliland, C Taylor; Sittampalam, G Sitta; Wang, Philip Y; Ryan, Philip E

2017-01-02

Translational science is an emerging field that holds great promise to accelerate the development of novel medical interventions. As the field grows, so does the demand for highly trained biomedical scientists to fill the positions that are being created. Many graduate and postdoctorate training programs do not provide their trainees with sufficient education to take advantage of this growing employment sector. To help better prepare the trainees at the National Institutes of Health for possible careers in translation, we have created the Translational Science Training Program (TSTP). The TSTP is an intensive 2- to 3-day training program that introduces NIH postdoctoral trainees and graduate students to the science and operation of turning basic research discoveries into a medical therapeutic, device or diagnostic, and also exposes them to the variety of career options in translational science. Through a combination of classroom teaching from practicing experts in the various disciplines of translation and small group interactions with pre-clinical development teams, participants in the TSTP gain knowledge that will aid them in obtaining a career in translational science and building a network to make the transition to the field. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):13-24, 2017. © 2016 The International Union of Biochemistry and Molecular Biology.

An assessment of US microbiome research.

PubMed

Stulberg, Elizabeth; Fravel, Deborah; Proctor, Lita M; Murray, David M; LoTempio, Jonathan; Chrisey, Linda; Garland, Jay; Goodwin, Kelly; Graber, Joseph; Harris, M Camille; Jackson, Scott; Mishkind, Michael; Porterfield, D Marshall; Records, Angela

2016-01-11

Genome-enabled technologies have supported a dramatic increase in our ability to study microbial communities in environments and hosts. Taking stock of previously funded microbiome research can help to identify common themes, under-represented areas and research priorities to consider moving forward. To assess the status of US microbiome research, a team of government scientists conducted an analysis of federally funded microbiome research. Microbiomes were defined as host-, ecosystem- or habitat-associated communities of microorganisms, and microbiome research was defined as those studies that emphasize community-level analyses using 'omics technologies. Single pathogen, single strain and culture-based studies were not included, except symbiosis studies that served as models for more complex communities. Fourteen governmental organizations participated in the data call. The analysis examined three broad research themes, eight environments and eight microbial categories. Human microbiome research was larger than any other environment studied, and the basic biology research theme accounted for half of the total research activities. Computational biology and bioinformatics, reference databases and biorepositories, standardized protocols and high-throughput tools were commonly identified needs. Longitudinal and functional studies and interdisciplinary research were also identified as needs. This study has implications for the funding of future microbiome research, not only in the United States but beyond.

The Role of NG2 Glial Cells in ALS Pathogenesis

DTIC Science & Technology

2013-10-01

line of OPC differentiation from iPS cells. SHH, sonic hedgehog ; RA, retinoitic acid; bFGF, basic FGF; PDGF, platelet-derived growth factor; IGF...University School of Medicine, Baltimore, Maryland, USA. 3Department of Anatomy , Kitasato University School of Medicine, Sagamihara, Japan. 4Brain Science...6Present address: Shriners Hospital Pediatric Research Center, Department of Anatomy and Cell Biology, Temple University School of Medicine

AGENT-BASED MODELS IN EMPIRICAL SOCIAL RESEARCH*

PubMed Central

Bruch, Elizabeth; Atwell, Jon

2014-01-01

Agent-based modeling has become increasingly popular in recent years, but there is still no codified set of recommendations or practices for how to use these models within a program of empirical research. This article provides ideas and practical guidelines drawn from sociology, biology, computer science, epidemiology, and statistics. We first discuss the motivations for using agent-based models in both basic science and policy-oriented social research. Next, we provide an overview of methods and strategies for incorporating data on behavior and populations into agent-based models, and review techniques for validating and testing the sensitivity of agent-based models. We close with suggested directions for future research. PMID:25983351

The 'whole-animal approach' as a heuristic principle in neuroscience research.

PubMed

Serani-Merlo, Alejandro; Paz, Rodrigo; Castillo, Andrés

2005-01-01

Neuroscience embraces a heterogeneous group of disciplines. A conceptual framework that allows a better articulation of these different theoretical and experimental perspectives is needed. A 'whole-animal approach is proposed as a theoretical and hermeneutic tool. To illustrate the potential of this point of view, an overview of the research that has been performed in the extinction of fear-conditioned responses from Pavlov to the present is discussed. This is an example of how a whole-animal-based approach may help to organize and integrate basic and clinical neuroscience research. Our proposal is in agreement with recent statements calling for more integrative approaches in biological and neuropsychiatric research.

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

PubMed Central

Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S.

2011-01-01

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors. PMID:22046118

A first attempt to bring computational biology into advanced high school biology classrooms.

PubMed

Gallagher, Suzanne Renick; Coon, William; Donley, Kristin; Scott, Abby; Goldberg, Debra S

2011-10-01

Computer science has become ubiquitous in many areas of biological research, yet most high school and even college students are unaware of this. As a result, many college biology majors graduate without adequate computational skills for contemporary fields of biology. The absence of a computational element in secondary school biology classrooms is of growing concern to the computational biology community and biology teachers who would like to acquaint their students with updated approaches in the discipline. We present a first attempt to correct this absence by introducing a computational biology element to teach genetic evolution into advanced biology classes in two local high schools. Our primary goal was to show students how computation is used in biology and why a basic understanding of computation is necessary for research in many fields of biology. This curriculum is intended to be taught by a computational biologist who has worked with a high school advanced biology teacher to adapt the unit for his/her classroom, but a motivated high school teacher comfortable with mathematics and computing may be able to teach this alone. In this paper, we present our curriculum, which takes into consideration the constraints of the required curriculum, and discuss our experiences teaching it. We describe the successes and challenges we encountered while bringing this unit to high school students, discuss how we addressed these challenges, and make suggestions for future versions of this curriculum.We believe that our curriculum can be a valuable seed for further development of computational activities aimed at high school biology students. Further, our experiences may be of value to others teaching computational biology at this level. Our curriculum can be obtained at http://ecsite.cs.colorado.edu/?page_id=149#biology or by contacting the authors.

Instructional Quality Features in Videotaped Biology Lessons: Content-Independent Description of Characteristics

NASA Astrophysics Data System (ADS)

Dorfner, Tobias; Förtsch, Christian; Boone, William; Neuhaus, Birgit J.

2017-09-01

A number of studies on single instructional quality features have been reported for mathematics and science instruction. For summarizing single instructional quality features, researchers have created a model of three basic dimensions (classroom management, supportive climate, and cognitive activation) of instructional quality mainly through observing mathematics instruction. Considering this model as valid for all subjects and as usable for describing instruction, we used it in this study which aimed to analyze characteristics of instructional quality in biology lessons of high-achieving and low-achieving classes, independently of content. Therefore, we used the data of three different previous video studies of biology instruction conducted in Germany. From each video study, we selected three high-achieving and three low-achieving classes (N = 18 teachers; 35 videos) for our multiple-case study, in which conspicuous characteristics of instructional quality features were qualitatively identified and qualitatively analyzed. The amount of these characteristics was counted in a quantitative way in all the videos. The characteristics we found could be categorized using the model of three basic dimensions of instructional quality despite some subject-specific differences for biology instruction. Our results revealed that many more characteristics were observable in high-achieving classes than in low-achieving classes. Thus, we believe that this model could be used to describe biology instruction independently of the content. We also make the claims about the qualities for biology instruction—working with concentration in a content-structured environment, getting challenged in higher order thinking, and getting praised for performance—that could have positive influence on students' achievement.

Basic principles of molecular effects of irradiation.

PubMed

Selzer, Edgar; Hebar, Alexandra

2012-02-01

In order to understand the consequences of radiation a thorough understanding of the radiobiological mechanisms of the molecular up to the clinical level is of importance. Radiobiology therefore combines the basic principles of physics as well as biology and medicine and is concerned with the action of radiation from the subcellular level up to the living organism. Topics of interest and relevance are covered in much more broadness as is possible in the short following article in the literature to which the interested reader is referred to. Classical books in this field were written by Steel et al. (1989) as well as by Hall (1994). Topics usually covered by radiobiological reviews are the classification of different types of radiation, cell cycle dependency of radiation effects, types of radiation damage and cell death, dose response curves, measurement of radiation damage, the oxygen effect, relative biological effectiveness, the influence of dose rate, and several other important research areas. This short overview will concentrate on a subset of radiobiological topics of high importance and relative novelty.

Biological characters of bats in relation to natural reservoir of emerging viruses.

PubMed

Omatsu, Tsutomu; Watanabe, Shumpei; Akashi, Hiroomi; Yoshikawa, Yasuhiro

2007-09-01

Many investigators focused on bats (Chiroptera) for their specific character, i.e. echolocation system, phylogenic tree, food practice and unique reproduction. However, most of basic information about the vital functions related to anti-viral activity has been unclear. For evaluating some animals as a natural reservoir or host of infectious pathogens, it is necessary that not only their immune system but also their biology, the environment of their living, food habits and physiological features should be clarified and they should be analyzed from these multi-view points. The majority of current studies on infectious diseases have been conducted for the elucidation of viral virulence using experimental animals or viral gene function in vitro, but in a few case, researchers focused on wild animal itself. In this paper, we described basic information about bats as follows; genetic background, character of the immunological factors, histological character of immune organs, the physiological function and sensitivity of bat cells to viral infection.

The new biology: beyond the Modern Synthesis

PubMed Central

Rose, Michael R; Oakley, Todd H

2007-01-01

Background The last third of the 20th Century featured an accumulation of research findings that severely challenged the assumptions of the "Modern Synthesis" which provided the foundations for most biological research during that century. The foundations of that "Modernist" biology had thus largely crumbled by the start of the 21st Century. This in turn raises the question of foundations for biology in the 21st Century. Conclusion Like the physical sciences in the first half of the 20th Century, biology at the start of the 21st Century is achieving a substantive maturity of theory, experimental tools, and fundamental findings thanks to relatively secure foundations in genomics. Genomics has also forced biologists to connect evolutionary and molecular biology, because these formerly Balkanized disciplines have been brought together as actors on the genomic stage. Biologists are now addressing the evolution of genetic systems using more than the concepts of population biology alone, and the problems of cell biology using more than the tools of biochemistry and molecular biology alone. It is becoming increasingly clear that solutions to such basic problems as aging, sex, development, and genome size potentially involve elements of biological science at every level of organization, from molecule to population. The new biology knits together genomics, bioinformatics, evolutionary genetics, and other such general-purpose tools to supply novel explanations for the paradoxes that undermined Modernist biology. Open Peer Reviewers This article was reviewed by W.F. Doolittle, E.V. Koonin, and J.M. Logsdon. For the full reviews, please go to the Reviewers' Comments section. PMID:18036242

The Development of a Post-Baccalaureate Certificate Program in Molecular Diagnostics

PubMed Central

Williams, Gail S.; Brown, Judith D.; Keagle, Martha B.

2000-01-01

A post-baccalaureate certificate program in diagnostic molecular sciences was created in 1995 by the Diagnostic Genetic Sciences Program in the School of Allied Health at the University of Connecticut. The required on-campus lecture and laboratory courses include basic laboratory techniques, health care issues, cell biology, immunology, human genetics, research, management, and molecular diagnostic techniques and laboratory in molecular diagnostics. These courses precede a 6-month, full-time practicum at an affiliated full-service molecular laboratory. The practicum includes amplification and blotting methods, a research project, and a choice of specialized electives including DNA sequencing, mutagenesis, in situ hybridization methods, or molecular diagnostic applications in microbiology. Graduates of the program are immediately eligible to sit for the National Credentialing Agency examination in molecular biology to obtain the credential Clinical Laboratory Specialist in Molecular Biology (CLSp(MB). This description of the University of Connecticut program may assist other laboratory science programs in creating similar curricula. PMID:11232107

Kirlian Photography as a Teaching Tool of Physics

NASA Astrophysics Data System (ADS)

Terrel, Andy; Thacker, Beth Ann, , Dr.

2002-10-01

There are a number of groups across the country working on redesigning introductory physics courses by incorporating physics education research, modeling, and making the courses appeal to students in broader fields. We spent the summer exploring Kirlian photography, a subject that can be understood by students with a basic comprehension of electrostatics but is still questioned by many people in other fields. Kirlian photography's applications have captivated alternative medicine but still requires research from both physics and biology to understand if it has potential as medical tool. We used a simple setup to reproduce the physics that has been done to see if it could be used in an educational setting. I will demonstrate how Kirlian photography can be explained by physics but also how the topic still needs research to completely understand its possible biological applications. By incorporating such a topic into a curriculum, one is able to teach students to explore supposed supernatural phenomena scientifically and to promote research among undergraduate students.

Biomarkers--a pot of gold or a can of worms?: Meeting report from the 2nd World Congress on Biomarkers & Clinical Research, 2011, Baltimore, USA.

PubMed

Weber, Georg F; Warren, Jeremy; Shoma, Hitoshi; Chen, Tao; Halim, Abdel; Chakravarty, Geetika

2012-08-01

Biomarkers are biological agents used as indicators of biological states. In clinical applications, biomarkers reflect the presence, severity, or progression of disease states. They may also predict risk or responsiveness of a disease to a given treatment. There has been increasingly intense research interest in biomarkers, yet their translation into routine clinical use is lagging. To stimulate communication and cross-fertilization, the 2nd World Congress on Biomarkers & Clinical Research was held in Baltimore, MD, USA in 2011. The symposium covered a broad range of basic and applied biomarker research with the intent to facilitate bench-to-bedside developments. Sessions discussed DNA-based, proteomic, and blood-borne markers. The presentations covered biomarkers for cancer, other various diseases, and toxicological agents. Other topics included biomarker data assimilation, validation, standardization and quality control, as well as molecular imaging and informatics. New high-throughput assays, model systems and emerging technologies give reasons to hope for further rapid progress in the field.

Comparative Biology of Aging

PubMed Central

2009-01-01

Virtually, all research on basic mechanisms of aging has used species that are short lived and thus demonstrably unsuccessful at combating basic aging processes. A novel comparative approach would use a diversity of populations and species, focusing on those with particularly long, healthy lives, seeking the causative mechanisms that distinguish them from shorter lived relatives. Species of interest from this perspective include the naked mole rat, a mouse-size rodent that lives up to 30 years in the laboratory, and the little brown bat, which lives up to 34 years in the wild. Comparisons among dogs of different sizes, which differ by more than 50% in health span might also prove rewarding, as might novel species chosen because of their similarity to humans in certain key traits. Primates, because of their sophisticated cognitive ability, are a group of special value, and small, short-lived primates like the common marmoset might prove especially beneficial. Cell repositories and tissue banks from key species, as well as genomic and analytic tools optimized for comparative studies, would make valuable contributions to a new comparative approach to basic aging research. PMID:19223603

The principle of safety evaluation in medicinal drug - how can toxicology contribute to drug discovery and development as a multidisciplinary science?

PubMed

Horii, Ikuo

2016-01-01

Pharmaceutical (drug) safety assessment covers a diverse science-field in the drug discovery and development including the post-approval and post-marketing phases in order to evaluate safety and risk management. The principle in toxicological science is to be placed on both of pure and applied sciences that are derived from past/present scientific knowledge and coming new science and technology. In general, adverse drug reactions are presented as "biological responses to foreign substances." This is the basic concept of thinking about the manifestation of adverse drug reactions. Whether or not toxic expressions are extensions of the pharmacological effect, adverse drug reactions as seen from molecular targets are captured in the category of "on-target" or "off-target", and are normally expressed as a biological defense reaction. Accordingly, reactions induced by pharmaceuticals can be broadly said to be defensive reactions. Recent molecular biological conception is in line with the new, remarkable scientific and technological developments in the medical and pharmaceutical areas, and the viewpoints in the field of toxicology have shown that they are approaching toward the same direction as well. This paper refers to the basic concept of pharmaceutical toxicology, the differences for safety assessment in each stage of drug discovery and development, regulatory submission, and the concept of scientific considerations for risk assessment and management from the viewpoint of "how can multidisciplinary toxicology contribute to innovative drug discovery and development?" And also realistic translational research from preclinical to clinical application is required to have a significant risk management in post market by utilizing whole scientific data derived from basic and applied scientific research works. In addition, the significance for employing the systems toxicology based on AOP (Adverse Outcome Pathway) analysis is introduced, and coming challenges on precision medicine are to be addressed for the new aspect of efficacy and safety evaluation.

The making of the Women in Biology forum (WiB) at Bioclues.

PubMed

Singhania, Reeta Rani; Madduru, Dhatri; Pappu, Pranathi; Panchangam, Sameera; Suravajhala, Renuka; Chandrasekharan, Mohanalatha

2014-01-01

The Women in Biology forum (WiB) of Bioclues (India) began in 2009 to promote and support women pursuing careers in bioinformatics and computational biology. WiB was formed in order to help women scientists deprived of basic research, boost the prominence of women scientists particularly from developing countries, and bridge the gender gap to innovation. WiB has also served as a platform to highlight the work of established female scientists in these fields. Several award-winning women researchers have shared their experiences and provided valuable suggestions to WiB. Headed by Mohanalatha Chandrasekharan and supported by Dr. Reeta Rani Singhania and Renuka Suravajhala, WiB has seen major progress in the last couple of years particularly in the two avenues Mentoring and Research, off the four avenues in Bioclues: Mentoring, Outreach, Research and Entrepreneurship (MORE). In line with the Bioclues vision for bioinformatics in India, the WiB Journal Club (JoC) recognizes women scientists working on functional genomics and bioinformatics, and provides scientific mentorship and support for project design and hypothesis formulation. As a part of Bioclues, WiB members practice the group's open-desk policy and its belief that all members are free to express their own thoughts and opinions. The WiB forum appreciates suggestions and welcomes scientists from around the world to be a part of their mission to encourage women to pursue computational biology and bioinformatics.

Division of Biological and Medical Research annual report 1978

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

Rosenthal, M.W.

1978-01-01

The research during 1978 in the Division of Biological and Medical Research, Argonne National Laboratory, is summarized. Studies related to nuclear energy include responses of beagles to continuous low-level /sup 60/Co gamma radiation, and development of leukemic indicators; comparison of lifetime effects in mice of low-level neutron and /sup 60/Co gamma radiation; genetic effects of high LET radiations; and metabolic and therapeutic studies of heavy metals. Studies of nonnuclear energy sources deal with characterization and toxicological evaluation of effluents of fluidized bed combustion and coal gasification; electrical storage systems; electric fields associated with energy transmission; and development of population projectionmore » models and assessment of human risk. Basic research studies include fundamental structural and biophysical investigations; circadian rhythms; mutagenesis in bacteria and mammalian cells; cell killing, damage, and repair in mammalian cells; carcinogenesis and cocarcinogenesis; the use of liposomes as biological carriers; and studies of environmental influences on life-span, physiological performance, and circadian cycles. In the area of medical development, proteins in urine and tissues of normal and diseased humans are analyzed, and advanced analytical procedures for use of stable isotopes in clinical research and diagnosis are developed and applied. The final sections of the report cover support facilities, educational activities, the seminar program, staff talks, and staff publications.« less

Trends in Type of Original Psoriasis Publications by Decade, 1960 to 2010.

PubMed

Sako, Eric; Famenini, Shannon; Wu, Jashin J

2016-01-01

Research investigating psoriasis has spanned decades, and as our understanding of the disease has evolved, the focus of publications has changed. We sought to characterize the trends in original psoriasis-related research from 1960 to 2010 chronologically by decade. A literature review was performed using the keyword psoriasis in the MEDLINE database. All original psoriasis-related articles published at the beginning of each decade were searched and categorized by study type and topic. Number of articles per topic. A total of 869 original psoriasis-related articles were found. The number of publications increased 18 fold over 5 decades. The immunology and pathogenesis of psoriasis was the most frequently researched topic (36%), and retrospective studies were the most common study type (37%). Recent highly published topics included biologic therapy, genetics, and psoriasis-associated cardiovascular disease. Original psoriasis-related publications have grown substantially since 1960. Basic science research into the immunology and pathogenesis has been and continues to be the mainstay of psoriasis research. Recent research trends suggest the focus has expanded to topics such as psoriasis-associated cardiovascular disease, genetics, and biologic therapy.

Application of phase-trafficking methods to natural products research.

PubMed

Araya, Juan J; Montenegro, Gloria; Mitscher, Lester A; Timmermann, Barbara N

2010-09-24

A novel simultaneous phase-trafficking approach using spatially separated solid-supported reagents for rapid separation of neutral, basic, and acidic compounds from organic plant extracts with minimum labor is reported. Acidic and basic ion-exchange resins were physically separated into individual sacks ("tea bags") for trapping basic and acidic compounds, respectively, leaving behind in solution neutral components of the natural mixtures. Trapped compounds were then recovered from solid phase by appropriate suspension in acidic or basic solutions. The feasibility of the proposed separation protocol was demonstrated and optimized with an "artificial mixture" of model compounds. In addition, the utility of this methodology was illustrated with the successful separation of the alkaloid skytanthine from Skytanthus acutus Meyen and the main catechins and caffeine from Camellia sinensis L. (Kuntze). This novel approach offers multiple advantages over traditional extraction methods, as it is not labor intensive, makes use of only small quantities of solvents, produces fractions in adequate quantities for biological assays, and can be easily adapted to field conditions for bioprospecting activities.

Application of Phase-Trafficking Methods to Natural Products Research

PubMed Central

Araya, Juan J.; Montenegro, Gloria; Mitscher, Lester A.; Timmermann, Barbara N.

2010-01-01

A novel simultaneous phase-trafficking approach using spatially separated solid-supported reagents (SSR) for rapid separation of neutral, basic, and acidic compounds from organic plant extracts with minimum labor is reported. Acidic and basic ion exchange resins were physically separated into individual sacks (“teabags”) for trapping basic and acidic compounds respectively, leaving behind in solution neutral components of the natural mixtures. Trapped compounds were then recovered from solid phase by appropriate suspension in acidic or basic solutions. The feasibility of the proposed separation protocol was demonstrated and optimized with an “artificial mixture” of model compounds. In addition, the utility of this methodology was illustrated with the successful separation of the alkaloid skytanthine from Skytanthus acutus Meyen and the main catechins and caffeine from Camellia sinensis L. (Kuntze). This novel approach offers multiple advantages over traditional extraction methods, as it is not labor intensive, makes use of only small quantities of solvents, produces fractions in adequate quantities for biological assays, and can be easily adapted to field conditions for bioprospecting activities. PMID:20704309

Mesenchymal Stem Cells in Lipogems, a Reverse Story: from Clinical Practice to Basic Science.

PubMed

Tremolada, Carlo; Ricordi, Camillo; Caplan, Arnold I; Ventura, Carlo

2016-01-01

The idea that basic science should be the starting point for modern clinical approaches has been consolidated over the years, and emerged as the cornerstone of Molecular Medicine. Nevertheless, there is increasing concern over the low efficiency and inherent costs related to the translation of achievements from the bench to the bedside. These burdens are also perceived with respect to the effectiveness of translating basic discoveries in stem cell biology to the newly developing field of advanced cell therapy or Regenerative Medicine. As an alternative paradigm, past and recent history in Medical Science provides remarkable reverse stories in which clinical observations at the patient's bedside have fed major advances in basic research which, in turn, led to consistent progression in clinical practice. Within this context, we discuss our recently developed method and device, which forms the core of a system (Lipogems) for processing of human adipose tissue solely with the aid of mild mechanical forces to yield a microfractured tissue product.

Challenges and Practices in Building and Implementing Biosafety and Biosecurity Programs to Enable Basic and Translational Research with Select Agents.

PubMed

Jonsson, Colleen B; Cole, Kelly Stefano; Roy, Chad J; Perlin, David S; Byrne, Gerald

2013-04-29

Select agent research in the United States must meet federally-mandated biological surety guidelines and rules which are comprised of two main components: biosecurity and biosafety. Biosecurity is the process employed for ensuring biological agents are properly safeguarded against theft, loss, diversion, unauthorized access or use/release. Biosafety is those processes that ensure that operations with such agents are conducted in a safe, secure and reliable manner. As such, a biological surety program is generally concerned with biological agents that present high risk for adverse medical and/or agricultural consequences upon release outside of proper containment. The U.S. Regional and National Biocontainment Laboratories (RBL, NBL) represent expertise in this type of research, and are actively engaged in the development of programs to address these critical needs and federal requirements. While this comprises an ongoing activity for the RBLs, NBLs and other facilities that handle select agents as new guidelines and regulations are implemented, the present article is written with the goal of presenting a simplified yet comprehensive review of these requirements. Herein, we discuss the requirements and the various activities that the RBL/NBL programs have implemented to achieve these metrics set forth by various agencies within the U.S. Federal government.

Challenges and Practices in Building and Implementing Biosafety and Biosecurity Programs to Enable Basic and Translational Research with Select Agents

PubMed Central

Jonsson, Colleen B.; Cole, Kelly Stefano; Roy, Chad J.; Perlin, David S.; Byrne, Gerald

2014-01-01

Select agent research in the United States must meet federally-mandated biological surety guidelines and rules which are comprised of two main components: biosecurity and biosafety. Biosecurity is the process employed for ensuring biological agents are properly safeguarded against theft, loss, diversion, unauthorized access or use/release. Biosafety is those processes that ensure that operations with such agents are conducted in a safe, secure and reliable manner. As such, a biological surety program is generally concerned with biological agents that present high risk for adverse medical and/or agricultural consequences upon release outside of proper containment. The U.S. Regional and National Biocontainment Laboratories (RBL, NBL) represent expertise in this type of research, and are actively engaged in the development of programs to address these critical needs and federal requirements. While this comprises an ongoing activity for the RBLs, NBLs and other facilities that handle select agents as new guidelines and regulations are implemented, the present article is written with the goal of presenting a simplified yet comprehensive review of these requirements. Herein, we discuss the requirements and the various activities that the RBL/NBL programs have implemented to achieve these metrics set forth by various agencies within the U.S. Federal government. PMID:24900945

Bioinstrumentation: Tools for Understanding Life.

ERIC Educational Resources Information Center

Wandersee, James H., Ed.; And Others

This book was written to help introductory biology teachers gain a basic understanding of contemporary bioinstrumentation and the uses to which it is put in the laboratory. It includes topics that are most basic to understanding the nature of biology. The book is divided into five sections: (1) "Separation and Identification" that includes…

Paul Polani and the development of medical genetics

PubMed Central

Harper, Peter S.

2007-01-01

Paul Polani (1914-2006) was one of the key figures internationally in the beginnings and development of medical genetics. Best remembered scientifically for his highly original work on the basis of human sex chromosome disorders, notably Turner syndrome, he pioneered the application of basic biological research to clinical genetic problems. The unit that he founded in 1960, at Guys Hospital, London, provided an unparalleled model for combined research and service in medical genetics across a wide range of laboratory areas and helped to establish medical genetics as a specific discipline. PMID:17066298

Considerations and recent advances in neuroscience.

PubMed

Gorman, Adrienne M; Doyle, Karen M

2009-02-01

Neuroscience is a rapidly developing area of science which has benefitted from the blurring of interdisciplinary boundaries. This was apparent in the range of papers presented at this year's Neuroscience Ireland Conference, held in Galway during August 2008. The event was attended by academics, postdoctoral and postgraduate researchers, scientists from industry and clinicians. The themes of this year's conference, neurodegeneration, neuroregeneration, pain, glial cell biology and psychopharmacology, were chosen for their reflection of areas of strength in neuroscience within Ireland. In addition to basic science, translational research also featured strongly.

Continuation of Crosscutting Technology Development at Cast

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

Yoon, Roe-Hoan

2012-03-31

This Final Technical Report describes progress made on the sub-projects awarded in the Cooperative Agreement DE-FC26-05NT42457: Continuation of Crosscutting Technology Development at Center for Advanced Separation Technologies (CAST). The final reports for each sub-project are attached in the appendix. Much of the research to be conducted with Cooperative Agreement funds will be longer-term, high-risk, basic research and will be carried out in five broad areas: a) Solid-solid separation b) Solid-liquid separation c) Chemical/Biological Extraction d) Modeling and Control, and e) Environmental Control.

Basic research in homeopathy and ultra-high dilutions: what progress is being made?

PubMed

Betti, Lucietta; Trebbi, Grazia; Olioso, Debora; Marzotto, Marta; Bellavite, Paolo

2013-04-01

This report summarises the latest research developments in the field of high dilutions and homeopathy, as presented at the GIRI symposium of the leading international organisation of scientists in this field, in Florence, Italy in September 2012. The scientific community's early scepticism concerning the possible biological and pharmacological activity of highly diluted solutions, is giving way to a more open-minded attitude that no longer obstructs critical and experimental investigations in this emerging field of biomedicine. Copyright © 2013. Published by Elsevier Ltd.. All rights reserved.

A series of enzymology-based experiments designed to mimic an applied research project.

PubMed

Boyce, Angela; Walsh, Gary

2005-11-01

Four mini-practicals are described in which the effects of temperature and pH on phytase activity are assessed, as well as the enzyme's thermostability and the effect upon stability of simulated digestive tract conditions. Phytase is routinely incorporated into monogastric animal feed to ameliorate the negative nutritional and environmental consequences of its substrate, dietary phytic acid. In addition to illustrating selected basic concepts in enzymology, the combined experiments allow the students to determine the suitability of the test phytase for inclusion in animal feed. As such the practical mimics an applied research project and is particularly suited to biotechnology students undertaking courses in basic biochemistry. Students may be segregated into groups of 4, with each team member charged with undertaking one of the mini-experiments. In this way students are given individual responsibility and learn to work as part of an integrated research grouping. Copyright © 2005 International Union of Biochemistry and Molecular Biology, Inc.

Introduction to the Special Section on Epigenetics.

PubMed

Lester, Barry M; Conradt, Elisabeth; Marsit, Carmen

2016-01-01

Epigenetics provides the opportunity to revolutionize our understanding of the role of genetics and the environment in explaining human behavior, although the use of epigenetics to study human behavior is just beginning. In this introduction, the authors present the basics of epigenetics in a way that is designed to make this exciting field accessible to a wide readership. The authors describe the history of human behavioral epigenetic research in the context of other disciplines and graphically illustrate the burgeoning of research in the application of epigenetic methods and principles to the study of human behavior. The role of epigenetics in normal embryonic development and the influence of biological and environmental factors altering behavior through epigenetic mechanisms and developmental programming are discussed. Some basic approaches to the study of epigenetics are reviewed. The authors conclude with a discussion of challenges and opportunities, including intervention, as the field of human behavioral epigenetics continue to grow. © 2016 The Authors. Child Development © 2016 Society for Research in Child Development, Inc.

Electrophoresis experiments in microgravity

NASA Technical Reports Server (NTRS)

Snyder, Robert S.; Rhodes, Percy H.

1991-01-01

The use of the microgravity environment to separate and purify biological cells and proteins has been a major activity since the beginning of the NASA Microgravity Science and Applications program. Purified populations of cells are needed for research, transplantation and analysis of specific cell constituents. Protein purification is a necessary step in research areas such as genetic engineering where the new protein has to be separated from the variety of other proteins synthesized from the microorganism. Sufficient data are available from the results of past electrophoresis experiments in space to show that these experiments were designed with incomplete knowledge of the fluid dynamics of the process including electrohydrodynamics. However, electrophoresis is still an important separation tool in the laboratory and thermal convection does limit its performance. Thus, there is a justification for electrophoresis but the emphasis of future space experiments must be directed toward basic research with model experiments to understand the microgravity environment and fluid analysis to test the basic principles of the process.

The biobank for the molecular classification of kidney disease: research translation and precision medicine in nephrology.

PubMed

Muruve, Daniel A; Mann, Michelle C; Chapman, Kevin; Wong, Josee F; Ravani, Pietro; Page, Stacey A; Benediktsson, Hallgrimur

2017-07-26

Advances in technology and the ability to interrogate disease pathogenesis using systems biology approaches are exploding. As exemplified by the substantial progress in the personalized diagnosis and treatment of cancer, the application of systems biology to enable precision medicine in other disciplines such as Nephrology is well underway. Infrastructure that permits the integration of clinical data, patient biospecimens and advanced technologies is required for institutions to contribute to, and benefit from research in molecular disease classification and to devise specific and patient-oriented treatments. We describe the establishment of the Biobank for the Molecular Classification of Kidney Disease (BMCKD) at the University of Calgary, Alberta, Canada. The BMCKD consists of a fully equipped wet laboratory, an information technology infrastructure, and a formal operational, ethical and legal framework for banking human biospecimens and storing clinical data. The BMCKD first consolidated a large retrospective cohort of kidney biopsy specimens to create a population-based renal pathology database and tissue inventory of glomerular and other kidney diseases. The BMCKD will continue to prospectively bank all kidney biopsies performed in Southern Alberta. The BMCKD is equipped to perform molecular, clinical and epidemiologic studies in renal pathology. The BMCKD also developed formal biobanking procedures for human specimens such as blood, urine and nucleic acids collected for basic and clinical research studies or for advanced diagnostic technologies in clinical care. The BMCKD is guided by standard operating procedures, an ethics framework and legal agreements with stakeholders that include researchers, data custodians and patients. The design and structure of the BMCKD permits its inclusion in a wide variety of research and clinical activities. The BMCKD is a core multidisciplinary facility that will bridge basic and clinical research and integrate precision medicine into renal pathology and nephrology.

Technology base for microgravity horticulture

NASA Technical Reports Server (NTRS)

Sauer, R. L.; Magnuson, J. W.; Scruby, R. R.; Scheld, H. W.

1987-01-01

Advanced microgravity plant biology research and life support system development for the spacecraft environment are critically hampered by the lack of a technology base. This inadequacy stems primarily from the fact that microgravity results in a lack of convective currents and phase separation as compared to the one gravity environment. A program plan is being initiated to develop this technology base. This program will provide an iterative flight development effort that will be closely integrated with both basic science investigations and advanced life support system development efforts incorporating biological processes. The critical considerations include optimum illumination methods, root aeration, root and shoot support, and heat rejection and gas exchange in the plant canopy.

The short-lived African turquoise killifish: an emerging experimental model for ageing.

PubMed

Kim, Yumi; Nam, Hong Gil; Valenzano, Dario Riccardo

2016-02-01

Human ageing is a fundamental biological process that leads to functional decay, increased risk for various diseases and, ultimately, death. Some of the basic biological mechanisms underlying human ageing are shared with other organisms; thus, animal models have been invaluable in providing key mechanistic and molecular insights into the common bases of biological ageing. In this Review, we briefly summarise the major applications of the most commonly used model organisms adopted in ageing research and highlight their relevance in understanding human ageing. We compare the strengths and limitations of different model organisms and discuss in detail an emerging ageing model, the short-lived African turquoise killifish. We review the recent progress made in using the turquoise killifish to study the biology of ageing and discuss potential future applications of this promising animal model. © 2016. Published by The Company of Biologists Ltd.

The Biology of Aging and Cancer: Frailty, Inflammation, and Immunity.

PubMed

Zhang, Xinwen; Meng, Xin; Chen, Yiyin; Leng, Sean X; Zhang, Haiyan

The majority of patients with common malignancies are older adults. Intrinsic complex biological changes of aging along with inflammation, immunosenescence, age-associated chronic diseases, and extrinsic environmental and psychosocial factors have significant impact on not only development and behavior of individual malignancies, but also physiologic reserve and vulnerability of older patients who suffer from them. As a result, clinical practice of geriatric oncology demands integration of careful geriatric assessment and management. This article provides an overview of basic biology of aging and its relationship with cancer. After a brief introduction about the definition and mechanisms of aging, as well as age-related biological and physiological changes, the discussion mainly focuses on recent development and insights into the relationship of frailty, inflammation, and immunity with cancer, highlighting how the new knowledge can help further improve assessment and treatment of older patients with malignancies and promote cancer research.

A Trait-Based Approach to Advance Coral Reef Science.

PubMed

Madin, Joshua S; Hoogenboom, Mia O; Connolly, Sean R; Darling, Emily S; Falster, Daniel S; Huang, Danwei; Keith, Sally A; Mizerek, Toni; Pandolfi, John M; Putnam, Hollie M; Baird, Andrew H

2016-06-01

Coral reefs are biologically diverse and ecologically complex ecosystems constructed by stony corals. Despite decades of research, basic coral population biology and community ecology questions remain. Quantifying trait variation among species can help resolve these questions, but progress has been hampered by a paucity of trait data for the many, often rare, species and by a reliance on nonquantitative approaches. Therefore, we propose filling data gaps by prioritizing traits that are easy to measure, estimating key traits for species with missing data, and identifying 'supertraits' that capture a large amount of variation for a range of biological and ecological processes. Such an approach can accelerate our understanding of coral ecology and our ability to protect critically threatened global ecosystems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cancer biology and genomics: translating discoveries, transforming pathology.

PubMed

Ladanyi, Marc; Hogendoorn, Pancras C W

2011-01-01

Advances in our understanding of cancer biology and discoveries emerging from cancer genomics are being translated into real clinical benefits for patients with cancer. The 2011 Journal of Pathology Annual Review Issue provides a snapshot of recent rapid progress on multiple fronts in the war on cancer or, more precisely, the wars on cancers. Indeed, perhaps the most notable recent shift is reflected by the sharp increase in understanding the biology of multiple specific cancers and using these new insights to inform rationally targeted therapies, with often striking successes. These recent developments, as reviewed in this issue, show how the long-term investments in basic cancer research are finally beginning to bear fruit. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

A biosafety level 2 virology lab for biotechnology undergraduates.

PubMed

Matza-Porges, Sigal; Nathan, Dafna

2017-11-01

Medical, industrial, and basic research relies heavily on the use of viruses and vectors. Therefore, it is important that bioscience undergraduates learn the practicalities of handling viruses. Teaching practical virology in a student laboratory setup presents safety challenges, however. The aim of this article is to describe the design and implementation of a virology laboratory, with emphasis on student safety, for biotechnology undergraduates. Cell culture techniques, animal virus infection, quantification, and identification are taught at a biosafety level 2 for a diverse group of undergraduates ranging from 20 to 50 students per group. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(6):537-543, 2017. © 2017 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

An off-the-shelf, authentic, and versatile undergraduate molecular biology practical course.

PubMed

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 is a versatile workbench, adaptable to different degree subjects, and can be easily modified to undertake novel research as part of its teaching activities. Course activities include DNA extraction, RFLP, PCR, DNA sequencing, gel electrophoresis, and transformation, alongside a range of basic microbiology techniques. Students particularly appreciated the relevance of the practical to professional practice and the authenticity of the experimental work. © 2015 The International Union of Biochemistry and Molecular Biology.

Connective tissue growth factor (CTGF) from basics to clinics.

PubMed

Ramazani, Yasaman; Knops, Noël; Elmonem, Mohamed A; Nguyen, Tri Q; Arcolino, Fanny Oliveira; van den Heuvel, Lambert; Levtchenko, Elena; Kuypers, Dirk; Goldschmeding, Roel

2018-03-21

Connective tissue growth factor, also known as CCN2, is a cysteine-rich matricellular protein involved in the control of biological processes, such as cell proliferation, differentiation, adhesion and angiogenesis, as well as multiple pathologies, such as tumor development and tissue fibrosis. Here, we describe the molecular and biological characteristics of CTGF, its regulation and various functions in the spectrum of development and regeneration to fibrosis. We further outline the preclinical and clinical studies concerning compounds targeting CTGF in various pathologies with the focus on heart, lung, liver, kidney and solid organ transplantation. Finally, we address the advances and pitfalls of translational fibrosis research and provide suggestions to move towards a better management of fibrosis. Copyright © 2017 International Society of Matrix Biology. Published by Elsevier B.V. All rights reserved.

JPRS Report, Science & Technology. Europe: Economic Competitiveness

DTIC Science & Technology

1991-01-28

development: funding of R&D contracts subcontracted to external parties by companies with less than 1000 employees. • Technically oriented company... Analysis Using Molecular Biology," which it has been sponsoring since 1985. As of 1991, the program will receive a total of DM25 Million in...For instance, the five Dutch multinationals—Shell, Philips, Unilever , Akzo, DSM—earmark about 20 percent of their R&D budget to basic research

Why are sex and gender important to basic physiology and translational and individualized medicine?

PubMed

Miller, Virginia M

2014-03-01

Sex refers to biological differences between men and women. Although sex is a fundamental aspect of human physiology that splits the population in two approximately equal halves, this essential biological variable is rarely considered in the design of basic physiological studies, in translating findings from basic science to clinical research, or in developing personalized medical strategies. Contrary to sex, gender refers to social and cultural factors related to being a man or a woman in a particular historical and cultural context. Unfortunately, gender is often used incorrectly by scientists and clinical investigators as synonymous with sex. This article clarifies the definition of sex and gender and reviews evidence showing how sex and gender interact with each other to influence etiology, presentation of disease, and treatment outcomes. In addition, strategies to improve the inclusion of female and male human beings in preclinical and clinical studies will be presented, and the importance of embedding concepts of sex and gender into postgraduate and medical curricula will be discussed. Also, provided is a list of resources for educators. In the history of medical concepts, physiologists have provided pivotal contributions to understanding health and disease processes. In the future, physiologists should provide the evidence for advancing personalized medicine and for reducing sex and gender disparities in health care.

Why are sex and gender important to basic physiology and translational and individualized medicine?

PubMed Central

2014-01-01

Sex refers to biological differences between men and women. Although sex is a fundamental aspect of human physiology that splits the population in two approximately equal halves, this essential biological variable is rarely considered in the design of basic physiological studies, in translating findings from basic science to clinical research, or in developing personalized medical strategies. Contrary to sex, gender refers to social and cultural factors related to being a man or a woman in a particular historical and cultural context. Unfortunately, gender is often used incorrectly by scientists and clinical investigators as synonymous with sex. This article clarifies the definition of sex and gender and reviews evidence showing how sex and gender interact with each other to influence etiology, presentation of disease, and treatment outcomes. In addition, strategies to improve the inclusion of female and male human beings in preclinical and clinical studies will be presented, and the importance of embedding concepts of sex and gender into postgraduate and medical curricula will be discussed. Also, provided is a list of resources for educators. In the history of medical concepts, physiologists have provided pivotal contributions to understanding health and disease processes. In the future, physiologists should provide the evidence for advancing personalized medicine and for reducing sex and gender disparities in health care. PMID:24414073

Malaria vaccines: looking back and lessons learnt

PubMed Central

Lorenz, Veronique; Karanis, Panagiotis

2011-01-01

The current status of malaria vaccine approaches has the background of a long and arduous path of malaria disease control and vaccine development. Here, we critically review with regard to unilateral interventional approaches and highlight the impact of socioeconomic elements of malaria endemicity. The necessity of re-energizing basic research of malaria life-cycle and Plasmodium developmental biology to provide the basis for promising and cost-effective vaccine approaches and to reach eradication goals is more urgent than previously believed. We closely analyse the flaws of various vaccine approaches, outline future directions and challenges that still face us and conclude that the focus of the field must be shifted to the basic research efforts including findings on the skin stage of infection. We also reflect on economic factors of vaccine development and the impact of public perception when it comes to vaccine uptake. PMID:23569729

Fungal genome sequencing: basic biology to biotechnology.

PubMed

Sharma, Krishna Kant

2016-08-01

The genome sequences provide a first glimpse into the genomic basis of the biological diversity of filamentous fungi and yeast. The genome sequence of the budding yeast, Saccharomyces cerevisiae, with a small genome size, unicellular growth, and rich history of genetic and molecular analyses was a milestone of early genomics in the 1990s. The subsequent completion of fission yeast, Schizosaccharomyces pombe and genetic model, Neurospora crassa initiated a revolution in the genomics of the fungal kingdom. In due course of time, a substantial number of fungal genomes have been sequenced and publicly released, representing the widest sampling of genomes from any eukaryotic kingdom. An ambitious genome-sequencing program provides a wealth of data on metabolic diversity within the fungal kingdom, thereby enhancing research into medical science, agriculture science, ecology, bioremediation, bioenergy, and the biotechnology industry. Fungal genomics have higher potential to positively affect human health, environmental health, and the planet's stored energy. With a significant increase in sequenced fungal genomes, the known diversity of genes encoding organic acids, antibiotics, enzymes, and their pathways has increased exponentially. Currently, over a hundred fungal genome sequences are publicly available; however, no inclusive review has been published. This review is an initiative to address the significance of the fungal genome-sequencing program and provides the road map for basic and applied research.

Reporting Experiments in Homeopathic Basic Research (REHBaR).

PubMed

Stock-Schröer, Beate

2015-10-01

The aim of this study was to develop a criteria catalogue serving as a guideline for authors to improve quality of Reporting Experiments in Homeopathic Basic Research (REHBaR). Main focus was in the field of biochemical and biological experiments. So far, there was no guideline for scientists and authors available, unlike criteria catalogues common in clinical research. A Delphi Process was conducted among experts who published experimental work within the last five years in this field. The process included a total of five rounds, three rounds of adjusting and phrasing plus two consensus conferences. A checklist of 23 items was achieved, augmented with detailed examples how to handle each item while compiling a publication. Background, objectives and possible hypotheses are necessary to be given in the part 'introduction'. The section 'materials and methods' is the most important part, where a detailed description of chosen controls, object of investigation, experimental setup, replication, parameters, intervention, allocation, blinding, and statistical methods is mandatory. In the 'results' section sufficient details on analysed data, descriptive as well as inferential are needed. Moreover, authors should discuss their results and interpret them in the context of current evidence. REHBaR was compiled for authors when preparing their manuscripts, and to be used by scientific journals in the reviewing process. Reporting experiments in basic research in homeopathy is an important issue to state the quality and validity of gained results. A guideline for REHBaR seemed to be the first step to come to a commitment what information is necessary to be given in a paper. More than that, the catalogue can serve as a statement what the standards in good basic research should be. Copyright © 2015 The Faculty of Homeopathy. Published by Elsevier Ltd. All rights reserved.

Inhalation Toxicology Research Institute. Annual report, October 1, 1995--September 30, 1996

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

Bice, D.E.; Hahn, F.F.; Henderson, R.F.

1996-12-01

The Inhalation Toxicology Research Institute (ITRI) is a Government-owned facility leased and operated by the Lovelace Biomedical and Environmental Research Institute (LBERI) as a private, nonprofit research and testing laboratory. LBERI is an operating subsidiary of the Lovelace Respiratory Research Institute. Through September 30, 1996, ITRI was a Federally Funded Research and Development Center operated by Lovelace for the US Department of Energy (DOE) as a {open_quotes}Single Program Laboratory{close_quotes} within the DOE Office of Health and Environmental Research, Office of Energy Research. Work for DOE continues in the privatized ITRI facility under a Cooperative Agreement. At the time of publication,more » approximately 70% of the Institute`s research is funded by DOE, and the remainder is funded by a variety of Federal agency, trade association, individual industry, and university customers. The principal mission of ITRI is to conduct basic and applied research to improve our understanding of the nature and magnitude of the human health impacts of inhaling airborne materials in the home, workplace, and general environment. Institute research programs have a strong basic science orientation with emphasis on the nature and behavior of airborne materials, the fundamental biology of the respiratory tract, the fate of inhaled materials and the mechanisms by which they cause disease, and the means by which data produced in the laboratory can be used to estimate risks to human health. Disorders of the respiratory tract continue to be a major health concern, and inhaled toxicants are thought to contribute substantially to respiratory morbidity. As the country`s largest facility dedicated to the study of basic inhalation toxicology, ITRI provides a national resource of specialized facilities, personnel, and educational activities serving the needs of government, academia, and industry.« less

Tenure Track Investigator | Center for Cancer Research

Cancer.gov

The Neuro-Oncology Branch (NOB), Center for Cancer Research (CCR) of the National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (HHS), Bethesda, MD, is actively recruiting for a tenure-track principal investigator to work in the area of immunology and/or immunotherapy.  The NOB Immunology/Immunotherapy Investigator will be tasked with forming and leading an independent research program.  This position will build the basic immunology program in the NOB and complement ongoing and planned translational research and clinical trials evaluating the effects of immunotherapy in patients with primary brain tumors.  This program will be able to access biospecimens generated from ongoing and planned immunotherapy protocols within the NOB, thus creating an opportunity to perform correlative studies to interrogate the complex biology of immunologic response, toxicity, and treatment resistance.  Demonstrated expertise in scientific inquiries in immunotherapy and/or immunology are essential, but prior work in brain tumors is not required.  This is an exciting opportunity to join a growing trans-institutional research team that promotes and supports collaborations across the basic, translational, and clinical research spectrum to develop novel therapeutics for individuals with primary central nervous system malignancies that will globally influence the field.

A Researcher's Guide to Mass Spectrometry-Based Proteomics

PubMed Central

Savaryn, John P.; Toby, Timothy K.; Kelleher, Neil L.

2016-01-01

Mass spectrometry (MS) is widely recognized as a powerful analytical tool for molecular research. MS is used by researchers around the globe to identify, quantify, and characterize biomolecules like proteins from any number of biological conditions or sample types. As instrumentation has advanced, and with the coupling of liquid chromatography (LC) for high-throughput LC-MS/MS, a proteomics experiment measuring hundreds to thousands of proteins/protein groups is now commonplace. While expert practitioners who best understand the operation of LC-MS systems tend to have strong backgrounds in physics and engineering, consumers of proteomics data and technology are not exposed to the physio-chemical principles underlying the information they seek. Since articles and reviews tend not to focus on bridging this divide, our goal here is to span this gap and translate MS ion physics into language intuitive to the general reader active in basic or applied biomedical research. Here, we visually describe what happens to ions as they enter and move around inside a mass spectrometer. We describe basic MS principles, including electric current, ion optics, ion traps, quadrupole mass filters, and Orbitrap FT-analyzers. PMID:27553853

History and perspectives of medical research at the Albert Schweitzer Hospital in Lambaréné, Gabon.

PubMed

Ramharter, Michael; Adegnika, Ayola A; Agnandji, Selidji T; Matsiegui, Pierre Blaise; Grobusch, Martin P; Winkler, Stefan; Graninger, Wolfgang; Krishna, Sanjeev; Yazdanbakhsh, Maria; Mordmüller, Benjamin; Lell, Bertrand; Missinou, Michel A; Mavoungou, Elie; Issifou, Saadou; Kremsner, Peter G

2007-01-01

In 1913 Albert Schweitzer founded one of the first modern hospitals in Africa dedicated to the health of the local population. The Albert Schweitzer Hospital is located in Lambaréné, a small town in Gabon. In 1981 a research department--the Medical Research Unit--was established with the aim to perform research in the field of infectious diseases ( www.lambarene.org ). The main focus lies on clinical research on malaria and other parasitic diseases. Studies on the molecular biology and immunology of parasitic diseases are fostered since the inauguration of a novel building dedicated for basic science. A training program in clinical research in tropical diseases for African scientists has been set up recently.

The NASA Materials Science Research Program: It's New Strategic Goals and Opportunities

NASA Technical Reports Server (NTRS)

Schlagheck, Ronald A.; Stagg, Elizabeth

2004-01-01

In the past year, the NASA s Office of Biological and Physical Research (OBPR) has formulated a long term plan to perform strategical and fundamental research bringing together physics, chemistry, biology, and engineering to solve problems needed for current and future agency mission goals. Materials Science is one of basic disciplines within the Enterprise s Division of Physical Sciences Research. The Materials Science Program participates to utilize effective use of International Space Station (ISS) and various world class ground laboratory facilities to solve new scientific and technology questions and transfer these results for public and agency benefits. The program has recently targeted new investigative research in strategic areas necessary to expand NASA knowledge base for exploration of the universe and some of these experiments will need access to the microgravity of space. The program is implementing a wide variety of traditional ground and flight based research related types of fundamental science related to materials crystallization, fundamental processing, and properties characterization in order to obtain basic understanding of various phenomena effects and relationships to the structures, processing, and properties of materials. , In addition new initiatives in radiation protection, materials for propulsion and In-space fabrication and repair focus on research helping the agency solve problems needed for future transportation into the solar system. A summary of the types and sources for this research is presented including those experiments planned for a low gravity environment. Areas to help expand the science basis for NASA future missions are described. An overview of the program is given including the scope of the current and future NASA Research Announcements with emphasis on new materials science initiatives. A description of the planned flight experiments to be conducted on the International Space Station program along with the planned facility class Materials Science Research Rack (MSRR) and Microgravity Glovebox (MSG) type investigations. Some initial results from the first three materials experiments are given.

Imaging and the new biology: What's wrong with this picture?

NASA Astrophysics Data System (ADS)

Vannier, Michael W.

2004-05-01

The Human Genome has been defined, giving us one part of the equation that stems from the central dogma of molecular biology. Despite this awesome scientific achievement, the correspondence between genomics and imaging is weak, since we cannot predict an organism's phenotype from even perfect knowledge of its genetic complement. Biological knowledge comes in several forms, and the genome is perhaps the best known and most completely understood type. Imaging creates another form of biological information, providing the ability to study morphology, growth and development, metabolic processes, and diseases in vitro and in vivo at many levels of scale. The principal challenge in biomedical imaging for the future lies in the need to reconcile the data provided by one or multiple modalities with other forms of biological knowledge, most importantly the genome, proteome, physiome, and other "-ome's." To date, the imaging science community has not set a high priority on the unification of their results with genomics, proteomics, and physiological functions in most published work. Images are relatively isolated from other forms of biological data, impairing our ability to conceive and address many fundamental questions in research and clinical practice. This presentation will explain the challenge of biological knowledge integration in basic research and clinical applications from the standpoint of imaging and image processing. The impediments to progress, isolation of the imaging community, and mainstream of new and future biological science will be identified, so the critical and immediate need for change can be highlighted.

Yeast Genomics for Bread, Beer, Biology, Bucks and Breath

NASA Astrophysics Data System (ADS)

Sakharkar, Kishore R.; Sakharkar, Meena K.

The rapid advances and scale up of projects in DNA sequencing dur ing the past two decades have produced complete genome sequences of several eukaryotic species. The versatile genetic malleability of the yeast, and the high degree of conservation between its cellular processes and those of human cells have made it a model of choice for pioneering research in molecular and cell biology. The complete sequence of yeast genome has proven to be extremely useful as a reference towards the sequences of human and for providing systems to explore key gene functions. Yeast has been a ‘legendary model’ for new technologies and gaining new biological insights into basic biological sciences and biotechnology. This chapter describes the awesome power of yeast genetics, genomics and proteomics in understanding of biological function. The applications of yeast as a screening tool to the field of drug discovery and development are highlighted and the traditional importance of yeast for bakers and brewers is discussed.

Versatile and on-demand biologics co-production in yeast.

PubMed

Cao, Jicong; Perez-Pinera, Pablo; Lowenhaupt, Ky; Wu, Ming-Ru; Purcell, Oliver; de la Fuente-Nunez, Cesar; Lu, Timothy K

2018-01-08

Current limitations to on-demand drug manufacturing can be addressed by technologies that streamline manufacturing processes. Combining the production of two or more drugs into a single batch could not only be useful for research, clinical studies, and urgent therapies but also effective when combination therapies are needed or where resources are scarce. Here we propose strategies to concurrently produce multiple biologics from yeast in single batches by multiplexing strain development, cell culture, separation, and purification. We demonstrate proof-of-concept for three biologics co-production strategies: (i) inducible expression of multiple biologics and control over the ratio between biologic drugs produced together; (ii) consolidated bioprocessing; and (iii) co-expression and co-purification of a mixture of two monoclonal antibodies. We then use these basic strategies to produce drug mixtures as well as to separate drugs. These strategies offer a diverse array of options for on-demand, flexible, low-cost, and decentralized biomanufacturing applications without the need for specialized equipment.

Life Sciences Research in the Centrifuge Accommodation Module of the International Space Station

NASA Technical Reports Server (NTRS)

Dalton, Bonnie P.; Plaut, Karen; Meeker, Gabrielle B.; Sun, Sid (Technical Monitor)

2000-01-01

The Centrifuge Accommodation Module (CAM) will be the home of the fundamental biology research facilities on the International Space Station (ISS). These facilities are being built by the Biological Research Project (BRP), whose goal is to oversee development of a wide variety of habitats and host systems to support life sciences research on the ISS. The habitats and host systems are designed to provide life support for a variety of specimens including cells, bacteria, yeast, plants, fish, rodents, eggs (e.g., quail), and insects. Each habitat contains specimen chambers that allow for easy manipulation of specimens and alteration of sample numbers. All habitats are capable of sustaining life support for 90 days and have automated as well as full telescience capabilities for sending habitat parameters data to investigator homesite laboratories. The habitats provide all basic life support capabilities including temperature control, humidity monitoring and control, waste management, food, media and water delivery as well as adjustable lighting. All habitats will have either an internal centrifuge or are fitted to the 2.5-meter diameter centrifuge allowing for variable centrifugation up to 2 g. Specimen chambers are removable so that the specimens can be handled in the life sciences glovebox. Laboratory support equipment is provided for handling the specimens. This includes a compound and dissecting microscope with advanced video imaging, mass measuring devices, refrigerated centrifuge for processing biological samples, pH meter, fixation and complete cryogenic storage capabilities. The research capabilities provided by the fundamental biology facilities will allow for flexibility and efficiency for long term research on the International Space Station.

[Progress of researches on mechanism of acupuncture therapy underlying improvement of acute cerebral hemorrhage].

PubMed

Wang, Fan; Wang, Hai-qiao; Dong, Gui-rong

2011-04-01

In the present paper, the authors review the progress of researches on the mechanism of acupuncture therapy underlying improvement of acute cerebral hemorrhage from experimental studies and research methods. The effects of acupuncture intervention mainly involve (1) lessening inflammatory reactions, (2) reducing impairment of free radicals and excitatory amino acids on cerebral neurons, (3) balancing release of vascular bioactive substances to increase regional cerebral blood flow, and (4) promoting repair and regeneration of the neural tissue, etc. In regard to the research methods, many new biological techniques such as biological molecular approaches, neuro-cellular chemical methods, reverse transcription-polymerase chain reaction (RT-PCR) or quantitative real time-PCR, situ hybridization, western blotting, electron microscope, etc., have been extensively applied to researches on the underlying mechanism of acupuncture therapy for cerebral infarction. In addition, the authors also pointed out that in spite of achieving some bigger progresses in experimental studies, most of the results basically reflect static, isolated and regional changes rather than dynamic and whole body changes. For this reason, more vivo research techniques and noninvasive research methods are highly recommended to be used in the future research on the underlying mechanisms of acupuncture therapy for acute cerebral ischemia.

The Wetland and Aquatic Research Center strategic science plan

USGS Publications Warehouse

,

2017-02-02

IntroductionThe U.S. Geological Survey (USGS) Wetland and Aquatic Research Center (WARC) has two primary locations (Gainesville, Florida, and Lafayette, Louisiana) and field stations throughout the southeastern United States and Caribbean. WARC’s roots are in U.S. Fish and Wildlife Service (USFWS) and National Park Service research units that were brought into the USGS as the Biological Research Division in 1996. Founded in 2015, WARC was created from the merger of two long-standing USGS biology science Centers—the Southeast Ecological Science Center and the National Wetlands Research Center—to bring together expertise in biology, ecology, landscape science, geospatial applications, and decision support in order to address issues nationally and internationally. WARC scientists apply their expertise to a variety of wetland and aquatic research and monitoring issues that require coordinated, integrated efforts to better understand natural environments. By increasing basic understanding of the biology of important species and broader ecological and physiological processes, this research provides information to policymakers and aids managers in their stewardship of natural resources and in regulatory functions.This strategic science plan (SSP) was developed to guide WARC research during the next 5–10 years in support of Department of the Interior (DOI) partnering bureaus such as the USFWS, the National Park Service, and the Bureau of Ocean Energy Management, as well as other Federal, State, and local natural resource management agencies. The SSP demonstrates the alignment of the WARC goals with the USGS mission areas, associated programs, and other DOI initiatives. The SSP is necessary for workforce planning and, as such, will be used as a guide for future needs for personnel. The SSP also will be instrumental in developing internal funding priorities and in promoting WARC’s capabilities to both external cooperators and other groups within the USGS.

Strategies for structuring interdisciplinary education in Systems Biology: an European perspective

PubMed Central

Cvijovic, Marija; Höfer, Thomas; Aćimović, Jure; Alberghina, Lilia; Almaas, Eivind; Besozzi, Daniela; Blomberg, Anders; Bretschneider, Till; Cascante, Marta; Collin, Olivier; de Atauri, Pedro; Depner, Cornelia; Dickinson, Robert; Dobrzynski, Maciej; Fleck, Christian; Garcia-Ojalvo, Jordi; Gonze, Didier; Hahn, Jens; Hess, Heide Marie; Hollmann, Susanne; Krantz, Marcus; Kummer, Ursula; Lundh, Torbjörn; Martial, Gifta; dos Santos, Vítor Martins; Mauer-Oberthür, Angela; Regierer, Babette; Skene, Barbara; Stalidzans, Egils; Stelling, Jörg; Teusink, Bas; Workman, Christopher T; Hohmann, Stefan

2016-01-01

Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii) a description of possible career paths for students who undergo such an education, (iv) conditions that should improve the recruitment of students to such programmes and (v) mechanisms for collaboration and excellence spreading among education professionals. With the growing interest of industry in applying Systems Biology approaches in their fields, a concerted action between academia and industry is needed to build this expertise. Here we present a reflection of the European situation and expertise, where most of the challenges we discuss are universal, anticipating that our suggestions will be useful internationally. We believe that one of the overriding goals of any Systems Biology education should be a student’s ability to phrase and communicate research questions in such a manner that they can be solved by the integration of experiments and modelling, as well as to communicate and collaborate productively across different experimental and theoretical disciplines in research and development. PMID:28725471

The 24th Annual Prostate Cancer Foundation scientific retreat report.

PubMed

Miyahira, Andrea K; Soule, Howard R

2018-05-15

The 24th Annual Prostate Cancer Foundation (PCF) Scientific Retreat was held from October 5-7, 2017, at the Omni Shoreham Hotel in Washington, DC. The PCF Scientific Retreat is a scientific conference that specifically focuses on cutting edge research deemed to have significant promise for accelerating advances in prostate cancer biology and treatment. Themes highlighted at this year's meeting included: (i) new understandings in prostate cancer biology and disease progression; (ii) new mechanisms and treatment targets in advanced prostate cancer; (iii) advances in precision medicine genomics, germline genetics, and selection of targeted therapies; (iv) PSMA-targeted agents for PET imaging and radionuclide therapy; (v) approaches for improving the efficacy of immunotherapy in prostate cancer; (vi) applications of 3D Genomics in prostate cancer research; and (vii) potential applications of artificial intelligence in prostate cancer. This article reviews the research presented at the PCF Scientific Retreat, in order to improve understanding of the current state of prostate cancer research, encourage discourse and exchange of novel ideas, and stimulate new basic, translational, and clinical research that will ultimately improve the lives of patients. © 2018 Wiley Periodicals, Inc.

Can cancer researchers accurately judge whether preclinical reports will reproduce?

PubMed Central

Mandel, David R.; Kimmelman, Jonathan

2017-01-01

There is vigorous debate about the reproducibility of research findings in cancer biology. Whether scientists can accurately assess which experiments will reproduce original findings is important to determining the pace at which science self-corrects. We collected forecasts from basic and preclinical cancer researchers on the first 6 replication studies conducted by the Reproducibility Project: Cancer Biology (RP:CB) to assess the accuracy of expert judgments on specific replication outcomes. On average, researchers forecasted a 75% probability of replicating the statistical significance and a 50% probability of replicating the effect size, yet none of these studies successfully replicated on either criterion (for the 5 studies with results reported). Accuracy was related to expertise: experts with higher h-indices were more accurate, whereas experts with more topic-specific expertise were less accurate. Our findings suggest that experts, especially those with specialized knowledge, were overconfident about the RP:CB replicating individual experiments within published reports; researcher optimism likely reflects a combination of overestimating the validity of original studies and underestimating the difficulties of repeating their methodologies. PMID:28662052

Assessment of programs in space biology and medicine

NASA Technical Reports Server (NTRS)

1991-01-01

Over the past 30 or more years, the National Research Council Space Studies Board and its various committees have published hundreds of recommendations concerning life sciences research. Several particularly noteworthy themes appear consistently: (1) Balance - the need for a well-balanced research program in terms of ground versus flight, basic versus clinical, and internal versus extramural; (2) Excellence - because of the extremely limited number of flight opportunities (as well as their associated relative costs), the need for absolute excellence in the research that is conducted, in terms of topic, protocol, and investigator, and (3) Facilities - the single most important facility for life sciences research in space, an on-board, variable force centrifuge. In this first assessment report, the Committee on Space Biology and Medicine emphasizes that these long-standing themes remain as essential today as when first articulated. On the brink of the twenty-first century, the nation is contemplating the goal of human space exploration; consequently, the themes bear repeating. Each is a critical component of what will be necessary to successfully achieve such a goal.

Frequency and Type of Conflicts of Interest in the Peer Review of Basic Biomedical Research Funding Applications: Self-Reporting Versus Manual Detection.

PubMed

Gallo, Stephen A; Lemaster, Michael; Glisson, Scott R

2016-02-01

Despite the presumed frequency of conflicts of interest in scientific peer review, there is a paucity of data in the literature reporting on the frequency and type of conflicts that occur, particularly with regard to the peer review of basic science applications. To address this gap, the American Institute of Biological Sciences (AIBS) conducted a retrospective analysis of conflict of interest data from the peer review of 282 biomedical research applications via several onsite review panels. The overall conflicted-ness of these panels was significantly lower than that reported for regulatory review. In addition, the majority of identified conflicts were institutional or collaborative in nature. No direct financial conflicts were identified, although this is likely due to the relatively basic science nature of the research. It was also found that 65 % of identified conflicts were manually detected by AIBS staff searching reviewer CVs and application documents, with the remaining 35 % resulting from self-reporting. The lack of self-reporting may be in part attributed to a lack of perceived risk of the conflict. This result indicates that many potential conflicts go unreported in peer review, underscoring the importance of improving detection methods and standardizing the reporting of reviewer and applicant conflict of interest information.

Bioinformatics by Example: From Sequence to Target

NASA Astrophysics Data System (ADS)

Kossida, Sophia; Tahri, Nadia; Daizadeh, Iraj

2002-12-01

With the completion of the human genome, and the imminent completion of other large-scale sequencing and structure-determination projects, computer-assisted bioscience is aimed to become the new paradigm for conducting basic and applied research. The presence of these additional bioinformatics tools stirs great anxiety for experimental researchers (as well as for pedagogues), since they are now faced with a wider and deeper knowledge of differing disciplines (biology, chemistry, physics, mathematics, and computer science). This review targets those individuals who are interested in using computational methods in their teaching or research. By analyzing a real-life, pharmaceutical, multicomponent, target-based example the reader will experience this fascinating new discipline.

Contradictory results in interferon research

NASA Technical Reports Server (NTRS)

Sonnenfeld, G.

1984-01-01

Several reports on immunologically related interferon research, both in the areas of basic science and clinical research, are briefly reviewed, and it is noted that in many cases the results obtained are contradictory. It is argued, however, that the contradictory results are not surprising since interferon is a biological response modifier and has been known to produce opposite results even when the same interferon prepartion is used. It is emphasized that dosage, timing, route, and other experimental conditions are essential factors in planning immunological studies with interferon. Careful planning of future experiments with interferon should be required to prevent the possible generation of effects that are opposite to those expected.

An eye for discovery

PubMed Central

Stahl, Andreas; Smith, Lois E.H.

2010-01-01

Vision research has often led to significant advances in our understanding of biology. There has also been particular success in translating basic research in the eye into breakthrough clinical therapies that mark important milestones for ophthalmology and also for medical research. Anti-VEGF therapy for age-related macular degeneration was named as one of the top ten science advancements of the year 2006. Only two years later, successful transfer of the RPE65 gene into retinal pigment epithelium of patients with Leber congenital amaurosis was noted as one of the most important clinical applications of gene therapy. The articles in this Review series outline current developments in vision research and highlight its continued importance in ophthalmology and medicine. PMID:20811156

[The need for experiments using primates from a scientific point of view].

PubMed

Kaup, F J

2007-03-01

Concerning the public discussion on animal experiments using primates, various research fields are demonstrated where non-human primates are necessary for certain scientific reasons at this time. Non-human Primates are used in Germany mainly in regulatory toxicology and pharmaceutical safety studies.A small amount is disposed in different fields of biological or biomedical basic research. This includes in particular neurosciences and infection research. 2006 New and Old World monkeys were needed in Germany in 2005. No chimpanzees are used anymore as laboratory animals in Germany since many years. Several examples are presented to demonstrate that certain research fields need non-human primates as laboratory animals in the foreseeable future.

The Human Ageing Genomic Resources: online databases and tools for biogerontologists

PubMed Central

de Magalhães, João Pedro; Budovsky, Arie; Lehmann, Gilad; Costa, Joana; Li, Yang; Fraifeld, Vadim; Church, George M.

2009-01-01

Summary Ageing is a complex, challenging phenomenon that will require multiple, interdisciplinary approaches to unravel its puzzles. To assist basic research on ageing, we developed the Human Ageing Genomic Resources (HAGR). This work provides an overview of the databases and tools in HAGR and describes how the gerontology research community can employ them. Several recent changes and improvements to HAGR are also presented. The two centrepieces in HAGR are GenAge and AnAge. GenAge is a gene database featuring genes associated with ageing and longevity in model organisms, a curated database of genes potentially associated with human ageing, and a list of genes tested for their association with human longevity. A myriad of biological data and information is included for hundreds of genes, making GenAge a reference for research that reflects our current understanding of the genetic basis of ageing. GenAge can also serve as a platform for the systems biology of ageing, and tools for the visualization of protein-protein interactions are also included. AnAge is a database of ageing in animals, featuring over 4,000 species, primarily assembled as a resource for comparative and evolutionary studies of ageing. Longevity records, developmental and reproductive traits, taxonomic information, basic metabolic characteristics, and key observations related to ageing are included in AnAge. Software is also available to aid researchers in the form of Perl modules to automate numerous tasks and as an SPSS script to analyse demographic mortality data. The Human Ageing Genomic Resources are available online at http://genomics.senescence.info. PMID:18986374

Understanding and protecting the world's biodiversity: the role and legacy of the SCAR programme "Evolution and Biodiversity in the Antarctic".

PubMed

di Prisco, Guido; Convey, Peter; Gutt, Julian; Cowan, Don; Conlan, Kathleen; Verde, Cinzia

2012-12-01

Current global changes are prompting scientists and governments to consider the risk of extinction of species inhabiting environments influenced by ice. Concerted, multidisciplinary, international programmes aimed at understanding life processes, evolution and adaptations in the Polar Regions will help to counteract such an event by protecting polar life and ecosystems. There is a long tradition of international scientific cooperation in Antarctica that provides a strong foundation for such approaches. While basic understanding is emerging, we still largely lack predictive biological models, and need to achieve further integration amongst biological and non-biological disciplines. The ongoing SCAR Science Research Programme, "Evolution and Biodiversity in the Antarctic (EBA)" has successfully carried out its crucial role of providing an overarching umbrella for SCAR research in Life Sciences. Now is the time for aiming to progress beyond this important role, and the Antarctic biology community is proposing two programmes, focussed on distinct but complementary aspects of polar biology and working across marine, freshwater and terrestrial environments: "State of the Antarctic Ecosystem (AntEco)", and "Antarctic Thresholds--Ecosystem Resilience and Adaptation (AnT-ERA)". These programmes are the legacy of EBA, and they are key to understanding and protect Antarctic biodiversity. Copyright © 2012 Elsevier B.V. All rights reserved.

The nuclear envelope from basic biology to therapy.

PubMed

Worman, Howard J; Foisner, Roland

2010-02-01

The nuclear envelope has long been a focus of basic research for a highly specialized group of cell biologists. More recently, an expanding group of scientists and physicians have developed a keen interest in the nuclear envelope since mutations in the genes encoding lamins and associated proteins have been shown to cause a diverse range of human diseases often called laminopathies or nuclear envelopathies. Most of these diseases have tissue-selective phenotypes, suggesting that the nuclear envelope must function in cell-type- and developmental-stage-specific processes such as chromatin organization, regulation of gene expression, controlled nucleocytoplasmic transport and response to stress in metazoans. On 22-23 April 2009, Professor Christopher Hutchison organized the 4th British Nuclear Envelope Disease and Chromatin Organization meeting at the College of St Hild and St Bede at Durham University, sponsored by the Biochemical Society. In attendance were investigators with one common interest, the nuclear envelope, but with diverse expertise and training in animal and plant cell biology, genetics, developmental biology and medicine. We were each honoured to be keynote speakers. This issue of Biochemical Society Transactions contains papers written by some of the presenters at this scientifically exciting meeting, held in a bucolic setting where the food was tasty and the wine flowed freely. Perhaps at the end of this excellent meeting more questions were raised than answered, which will stimulate future research. However, what became clear is that the nuclear envelope is a cellular structure with critical functions in addition to its traditional role as a barrier separating the nuclear and cytoplasmic compartments in interphase eukaryotic cells.

Human hair follicle organ culture: theory, application and perspectives.

PubMed

Langan, Ewan A; Philpott, Michael P; Kloepper, Jennifer E; Paus, Ralf

2015-12-01

For almost a quarter of a century, ex vivo studies of human scalp hair follicles (HFs) have permitted major advances in hair research, spanning diverse fields such as chronobiology, endocrinology, immunology, metabolism, mitochondrial biology, neurobiology, pharmacology, pigmentation and stem cell biology. Despite this, a comprehensive methodological guide to serum-free human HF organ culture (HFOC) that facilitates the selection and analysis of standard HF biological parameters and points out both research opportunities and pitfalls to newcomers to the field is still lacking. The current methods review aims to close an important gap in the literature and attempts to promote standardisation of human HFOC. We provide basic information outlining the establishment of HFOC through to detailed descriptions of the analysis of standard read-out parameters alongside practical examples. The guide closes by pointing out how serum-free HFOC can be utilised optimally to obtain previously inaccessible insights into human HF biology and pathology that are of interest to experimental dermatologists, geneticists, developmental biologists and (neuro-) endocrinologists alike and by highlighting novel applications of the model, including gene silencing and gene expression profiling of defined, laser capture-microdissected HF compartments. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Coordinating an IPLS class with a biology curriculum: NEXUS/Physics

NASA Astrophysics Data System (ADS)

Redish, Edward

2014-03-01

A multi-disciplinary team of scientists has been reinventing the Introductory Physics for Life Scientists (IPLS) course at the University of Maryland. We focus on physics that connects elements common to the curriculum for all life scientists - molecular and cellular biology - with building general scientific competencies, such as mathematical modeling, reasoning from core principles, and multi-representation translation. The prerequisites for the class include calculus, chemistry, and biology. In addition to building the basic ideas of the Newtonian framework, electric currents, and optics, our prerequisites allow us to include topics such as atomic interactions and chemical bonding, random motion and diffusion, thermodynamics (including entropy and free energy), and spectroscopy. Our chemical bonding unit helps students link the view of energy developed in traditional macroscopic physics with the idea of chemical bonding as a source of energy presented in their chemistry and biology classes. Education research has played a central role in our design, as has a strong collaboration between our Discipline-Based Education and the Biophysics Research groups. These elements permit us to combine modern pedagogy with cutting-edge insights into the physics of living systems. Supported in part by a grant from HHMI and the US NSF grant #1122818/.

Significance of biological resource collection and tumor tissue bank creation.

PubMed

Yu, Ying-Yan; Zhu, Zheng-Gang

2010-01-15

Progress in the molecular oncology of gastrointestinal carcinomas depends on high quality cancer tissues for research. Recent acceleration on new technological platforms as well as the "omics" revolution increases the demands on tissues and peripheral blood for research at the DNA, mRNA and protein levels. Tissue bank creation emerges as a priority. Tumor tissue banks are facilities that are organized to collect, store and distribute samples of tumor and normal tissue for further use in basic and translational cancer research. The samples are generally obtained immediately after excision, prior to fixation, to ensure optimal preservation of proteins and nucleic acids. It is possible for surgeons or pathologists to collect fresh tissue prospectively during their routine dissection procedures. Most tissue banks are "project-driven" tumor banks, which are specialized collections of tumor samples on which their research is based. Systematic collection of all available tumor tissue is much rarer. High quality tissue banks need the collaboration of clinicians and basic scientists, but also the informed consent of patients and ethical approval. Through the standard operation procedure, snap frozen fresh tissue collection, storage and quality control for cryopreserved tissues are the pivotal factors on tissue bank construction and maintaining. The purpose of the tissue bank creation is enhancing the quality and speed on both the basic and translational research on gastrointestinal cancer. The quality assurance and quality control are handled based on reviewing HE staining slides or touch imprint cytology by pathologists.

Stress and reproductive failure: past notions, present insights and future directions

PubMed Central

Sheps, Sam; Clara Arck, Petra

2008-01-01

Problem Maternal stress perception is frequently alleged as a cause of infertility, miscarriages, late pregnancy complications or impaired fetal development. The purpose of the present review is to critically assess the biological and epidemiological evidence that considers the plausibility of a stress link to human reproductive failure. Methods All epidemiological studies published between 1980 and 2007 that tested the link between stress exposure and impaired reproductive success in humans were identified. Study outcomes were evaluated on the basis of how associations were predicted, tested and integrated with theories of etiology arising from recent scientific developments in the basic sciences. Further, published evidence arising from basic science research has been assessed in order to provide a mechanistic concept and biological evidence for the link between stress perception and reproductive success. Results Biological evidence points to an immune–endocrine disequilibrium in response to stress and describes a hierarchy of biological mediators involved in a stress trigger to reproductive failure. Epidemiological evidence presents positive correlations between various pregnancy failure outcomes with pre-conception negative life events and elevated daily urinary cortisol. Strikingly, a relatively new conceptual approach integrating the two strands of evidence suggests the programming of stress susceptibility in mother and fetus via a so-called pregnancy stress syndrome. Conclusions An increasing specificity of knowledge is available about the types and impact of biological and social pathways involved in maternal stress responses. The present evidence is sufficient to warrant a reconsideration of conventional views on the etiology of reproductive failure. Physicians and patients will benefit from the adaptation of this integrated evidence to daily clinical practice. PMID:18274890

How biological background assumptions influence scientific risk evaluation of stacked genetically modified plants: an analysis of research hypotheses and argumentations.

PubMed

Rocca, Elena; Andersen, Fredrik

2017-08-14

Scientific risk evaluations are constructed by specific evidence, value judgements and biological background assumptions. The latter are the framework-setting suppositions we apply in order to understand some new phenomenon. That background assumptions co-determine choice of methodology, data interpretation, and choice of relevant evidence is an uncontroversial claim in modern basic science. Furthermore, it is commonly accepted that, unless explicated, disagreements in background assumptions can lead to misunderstanding as well as miscommunication. Here, we extend the discussion on background assumptions from basic science to the debate over genetically modified (GM) plants risk assessment. In this realm, while the different political, social and economic values are often mentioned, the identity and role of background assumptions at play are rarely examined. We use an example from the debate over risk assessment of stacked genetically modified plants (GM stacks), obtained by applying conventional breeding techniques to GM plants. There are two main regulatory practices of GM stacks: (i) regulate as conventional hybrids and (ii) regulate as new GM plants. We analyzed eight papers representative of these positions and found that, in all cases, additional premises are needed to reach the stated conclusions. We suggest that these premises play the role of biological background assumptions and argue that the most effective way toward a unified framework for risk analysis and regulation of GM stacks is by explicating and examining the biological background assumptions of each position. Once explicated, it is possible to either evaluate which background assumptions best reflect contemporary biological knowledge, or to apply Douglas' 'inductive risk' argument.

Synthetic biology: applying biological circuits beyond novel therapies.

PubMed

Dobrin, Anton; Saxena, Pratik; Fussenegger, Martin

2016-04-18

Synthetic biology, an engineering, circuit-driven approach to biology, has developed whole new classes of therapeutics. Unfortunately, these advances have thus far been undercapitalized upon by basic researchers. As discussed herein, using synthetic circuits, one can undertake exhaustive investigations of the endogenous circuitry found in nature, develop novel detectors and better temporally and spatially controlled inducers. One could detect changes in DNA, RNA, protein or even transient signaling events, in cell-based systems, in live mice, and in humans. Synthetic biology has also developed inducible systems that can be induced chemically, optically or using radio waves. This induction has been re-wired to lead to changes in gene expression, RNA stability and splicing, protein stability and splicing, and signaling via endogenous pathways. Beyond simple detectors and inducible systems, one can combine these modalities and develop novel signal integration circuits that can react to a very precise pre-programmed set of conditions or even to multiple sets of precise conditions. In this review, we highlight some tools that were developed in which these circuits were combined such that the detection of a particular event automatically triggered a specific output. Furthermore, using novel circuit-design strategies, circuits have been developed that can integrate multiple inputs together in Boolean logic gates composed of up to 6 inputs. We highlight the tools available and what has been developed thus far, and highlight how some clinical tools can be very useful in basic science. Most of the systems that are presented can be integrated together; and the possibilities far exceed the number of currently developed strategies.

Basic Research in Plasma Medicine - A Throughput Approach from Liquids to Cells

PubMed Central

Bekeschus, Sander; Schmidt, Anke; Niessner, Felix; Gerling, Torsten; Weltmann, Klaus-Dieter; Wende, Kristian

2017-01-01

In plasma medicine, ionized gases with temperatures close to that of vertebrate systems are applied to cells and tissues. Cold plasmas generate reactive species known to redox regulate biological processes in health and disease. Pre-clinical and clinical evidence points to beneficial effects of plasma treatment in the healing of chronic ulcer of the skin. Other emerging topics, such as plasma cancer treatment, are receiving increasing attention. Plasma medical research requires interdisciplinary expertise in physics, chemistry, and biomedicine. One goal of plasma research is to characterize plasma-treated cells in a variety of specific applications. This includes, for example, cell count and viability, cellular oxidation, mitochondrial activity, cytotoxicity and mode of cell death, cell cycle analysis, cell surface marker expression, and cytokine release. This study describes the essential equipment and workflows required for such research in plasma biomedicine. It describes the proper operation of an atmospheric pressure argon plasma jet, specifically monitoring its basic emission spectra and feed gas settings to modulate reactive species output. Using a high-precision xyz-table and computer software, the jet is hovered in millisecond-precision over the cavities of 96-well plates in micrometer-precision for maximal reproducibility. Downstream assays for liquid analysis of redox-active molecules are shown, and target cells are plasma-treated. Specifically, melanoma cells are analyzed in an efficient sequence of different consecutive assays but using the same cells: measurement of metabolic activity, total cell area, and surface marker expression of calreticulin, a molecule important for the immunogenic cell death of cancer cells. These assays retrieve content-rich biological information about plasma effects from a single plate. Altogether, this study describes the essential steps and protocols for plasma medical research. PMID:29286412

Basic Research in Plasma Medicine - A Throughput Approach from Liquids to Cells.

PubMed

Bekeschus, Sander; Schmidt, Anke; Niessner, Felix; Gerling, Torsten; Weltmann, Klaus-Dieter; Wende, Kristian

2017-11-17

In plasma medicine, ionized gases with temperatures close to that of vertebrate systems are applied to cells and tissues. Cold plasmas generate reactive species known to redox regulate biological processes in health and disease. Pre-clinical and clinical evidence points to beneficial effects of plasma treatment in the healing of chronic ulcer of the skin. Other emerging topics, such as plasma cancer treatment, are receiving increasing attention. Plasma medical research requires interdisciplinary expertise in physics, chemistry, and biomedicine. One goal of plasma research is to characterize plasma-treated cells in a variety of specific applications. This includes, for example, cell count and viability, cellular oxidation, mitochondrial activity, cytotoxicity and mode of cell death, cell cycle analysis, cell surface marker expression, and cytokine release. This study describes the essential equipment and workflows required for such research in plasma biomedicine. It describes the proper operation of an atmospheric pressure argon plasma jet, specifically monitoring its basic emission spectra and feed gas settings to modulate reactive species output. Using a high-precision xyz-table and computer software, the jet is hovered in millisecond-precision over the cavities of 96-well plates in micrometer-precision for maximal reproducibility. Downstream assays for liquid analysis of redox-active molecules are shown, and target cells are plasma-treated. Specifically, melanoma cells are analyzed in an efficient sequence of different consecutive assays but using the same cells: measurement of metabolic activity, total cell area, and surface marker expression of calreticulin, a molecule important for the immunogenic cell death of cancer cells. These assays retrieve content-rich biological information about plasma effects from a single plate. Altogether, this study describes the essential steps and protocols for plasma medical research.

Macro- and microscale fluid flow systems for endothelial cell biology.

PubMed

Young, Edmond W K; Simmons, Craig A

2010-01-21

Recent advances in microfluidics have brought forth new tools for studying flow-induced effects on mammalian cells, with important applications in cardiovascular, bone and cancer biology. The plethora of microscale systems developed to date demonstrate the flexibility of microfluidic designs, and showcase advantages of the microscale that are simply not available at the macroscale. However, the majority of these systems will likely not achieve widespread use in the biological laboratory due to their complexity and lack of user-friendliness. To gain widespread acceptance in the biological research community, microfluidics engineers must understand the needs of cell biologists, while biologists must be made aware of available technology. This review provides a critical evaluation of cell culture flow (CCF) systems used to study the effects of mechanical forces on endothelial cells (ECs) in vitro. To help understand the need for various designs of CCF systems, we first briefly summarize main properties of ECs and their native environments. Basic principles of various macro- and microscale systems are described and evaluated. New opportunities are uncovered for developing technologies that have potential to both improve efficiency of experimentation as well as answer important biological questions that otherwise cannot be tackled with existing systems. Finally, we discuss some of the unresolved issues related to microfluidic cell culture, suggest possible avenues of investigation that could resolve these issues, and provide an outlook for the future of microfluidics in biological research.

Measuring and Advancing Experimental Design Ability in an Introductory Course without Altering Existing Lab Curriculum.

PubMed

Shanks, Ryan A; Robertson, Chuck L; Haygood, Christian S; Herdliksa, Anna M; Herdliska, Heather R; Lloyd, Steven A

2017-01-01

Introductory biology courses provide an important opportunity to prepare students for future courses, yet existing cookbook labs, although important in their own way, fail to provide many of the advantages of semester-long research experiences. Engaging, authentic research experiences aid biology students in meeting many learning goals. Therefore, overlaying a research experience onto the existing lab structure allows faculty to overcome barriers involving curricular change. Here we propose a working model for this overlay design in an introductory biology course and detail a means to conduct this lab with minimal increases in student and faculty workloads. Furthermore, we conducted exploratory factor analysis of the Experimental Design Ability Test (EDAT) and uncovered two latent factors which provide valid means to assess this overlay model's ability to increase advanced experimental design abilities. In a pre-test/post-test design, we demonstrate significant increases in both basic and advanced experimental design abilities in an experimental and comparison group. We measured significantly higher gains in advanced experimental design understanding in students in the experimental group. We believe this overlay model and EDAT factor analysis contribute a novel means to conduct and assess the effectiveness of authentic research experiences in an introductory course without major changes to the course curriculum and with minimal increases in faculty and student workloads.

Physiologically based microenvironment for in vitro neural differentiation of adipose-derived stem cells.

PubMed

Graziano, Adriana Carol Eleonora; Avola, Rosanna; Perciavalle, Vincenzo; Nicoletti, Ferdinando; Cicala, Gianluca; Coco, Marinella; Cardile, Venera

2018-03-26

The limited capacity of nervous system to promote a spontaneous regeneration and the high rate of neurodegenerative diseases appearance are keys factors that stimulate researches both for defining the molecular mechanisms of pathophysiology and for evaluating putative strategies to induce neural tissue regeneration. In this latter aspect, the application of stem cells seems to be a promising approach, even if the control of their differentiation and the maintaining of a safe state of proliferation should be troubled. Here, we focus on adipose tissue-derived stem cells and we seek out the recent advances on the promotion of their neural differentiation, performing a critical integration of the basic biology and physiology of adipose tissue-derived stem cells with the functional modifications that the biophysical, biomechanical and biochemical microenvironment induces to cell phenotype. The pre-clinical studies showed that the neural differentiation by cell stimulation with growth factors benefits from the integration with biomaterials and biophysical interaction like microgravity. All these elements have been reported as furnisher of microenvironments with desirable biological, physical and mechanical properties. A critical review of current knowledge is here proposed, underscoring that a real advance toward a stable, safe and controllable adipose stem cells clinical application will derive from a synergic multidisciplinary approach that involves material engineer, basic cell biology, cell and tissue physiology.

The Nephrologist’s Tumor: Basic Biology and Management of Renal Cell Carcinoma

PubMed Central

Hu, Susie L.; Chang, Anthony; Perazella, Mark A.; Okusa, Mark D.; Jaimes, Edgar A.

2016-01-01

Kidney cancer, or renal cell carcinoma (RCC), is a disease of increasing incidence that is commonly seen in the general practice of nephrology. However, RCC is under-recognized by the nephrology community, such that its presence in curricula and research by this group is lacking. In the most common form of RCC, clear cell renal cell carcinoma (ccRCC), inactivation of the von Hippel–Lindau tumor suppressor is nearly universal; thus, the biology of ccRCC is characterized by activation of hypoxia-relevant pathways that lead to the associated paraneoplastic syndromes. Therefore, RCC is labeled the internist’s tumor. In light of this characterization and multiple other metabolic abnormalities recently associated with ccRCC, it can now be viewed as a metabolic disease. In this review, we discuss the basic biology, pathology, and approaches for treatment of RCC. It is important to distinguish between kidney confinement and distant spread of RCC, because this difference affects diagnostic and therapeutic approaches and patient survival, and it is important to recognize the key interplay between RCC, RCC therapy, and CKD. Better understanding of all aspects of this disease will lead to optimal patient care and more recognition of an increasingly prevalent nephrologic disease, which we now appropriately label the nephrologist’s tumor. PMID:26961346

Ligand-directed tosyl chemistry for in situ native protein labeling and engineering in living systems: from basic properties to applications.

PubMed

Tsukiji, Shinya; Hamachi, Itaru

2014-08-01

The ability to introduce any chemical probe to any endogenous target protein in its native environment, that is in cells and in vivo, is anticipated to provide various new exciting tools for biological and biomedical research. Although still at the prototype stage, the ligand-directed tosyl (LDT) chemistry is a novel type of affinity labeling technique that we developed for such a dream. This chemistry allows for modifying native proteins by various chemical probes with high specificity in various biological settings ranging from in vitro (in test tubes) to in living cells and in vivo. Since the first report, the list of proteins that are successfully labeled by the LDT chemistry has been increasing. A growing number of studies have demonstrated its utility to create semisynthetic proteins directly in cellular contexts. The in situ generated semisynthetic proteins are applicable for various types of analysis and imaging of intracellular biological processes. In this review, we summarize the basic properties of the LDT chemistry and its applications toward in situ engineering and analysis of native proteins in living systems. Current limitations and future challenges of this area are also described. Copyright © 2014 Elsevier Ltd. All rights reserved.

Synergy between medicinal chemistry and biological research.

PubMed

Moncada, Salvador; Coaker, Hannah

2014-09-01

Salvador Moncada studied medicine at the University of El Salvador (El Salvador) before coming to the UK in 1971 to work on a PhD with Professor John Vane at the Institute of Basic Medical Sciences, Royal College of Surgeons (UK). After a short period of research at the University of Honduras (Honduras), he joined the Wellcome Research Laboratories (UK) where he became Head of the Department of Prostaglandin Research and later, Director of Research. He returned to academic life in 1996 as founder and director of the Wolfson Institute for Biomedical Research at University College London (UK). Moncada played a role in the discovery of the mechanism of action of aspirin-like drugs and later led the teams which discover prostacyclin and identified nitric oxide as a biological mediator. In his role as a Director of Research of the Wellcome Laboratories, he oversaw the discovery and development of medicines for epilepsy, migraine, malaria and cancer. Currently, he is working on the regulation of cell proliferation as Director of the Institute of Cancer Sciences at the University of Manchester (UK). Moncada has won numerous awards from the international scientific community and in 2010, he received a knighthood from Her Majesty Queen Elizabeth II for his services to science.

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

PubMed

Turner, David P

2015-05-15

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

The genesis of craniofacial biology as a health science discipline.

PubMed

Sperber, G H; Sperber, S M

2014-06-01

The craniofacial complex encapsulates the brain and contains the organs for key functions of the body, including sight, hearing and balance, smell, taste, respiration and mastication. All these systems are intimately integrated within the head. The combination of these diverse systems into a new field was dictated by the dental profession's desire for a research branch of basic science devoted and attuned to its specific needs. The traditional subjects of genetics, embryology, anatomy, physiology, biochemistry, dental materials, odontology, molecular biology and palaeoanthropology pertaining to dentistry have been drawn together by many newly emerging technologies. These new technologies include gene sequencing, CAT scanning, MRI imaging, laser scanning, image analysis, ultrasonography, spectroscopy and visualosonics. A vibrant unitary discipline of investigation, craniofacial biology, has emerged that builds on the original concept of 'oral biology' that began in the 1960s. This paper reviews some of the developments that have led to the genesis of craniofacial biology as a fully-fledged health science discipline of significance in the advancement of clinical dental practice. Some of the key figures and milestones in craniofacial biology are identified. © 2014 Australian Dental Association.

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

NASA Astrophysics Data System (ADS)

Eftimie, Raluca

2015-03-01

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

Biomolecular Materials. Report of the January 13-15, 2002 Workshop

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

Alper, M. D.; Stupp, S. I.

2002-01-15

Twenty-two scientists from around the nation and the world met to discuss the way that the molecules, structures, processes and concepts of the biological world could be used or mimicked in designing novel materials, processes or devices of potential practical significance. The emphasis was on basic research, although the long-term goal is, in addition to increased knowledge, the development of applications to further the mission of the Department of Energy.

Fundulus as the Premier Teleost Model in Environmental Biology: Opportunities for New Insights Using Genomics

PubMed Central

Burnett, Karen G.; Bain, Lisa J.; Baldwin, William S.; Callard, Gloria V.; Cohen, Sarah; Di Giulio, Richard T.; Evans, David H.; Gómez-Chiarri, Marta; Hahn, Mark E.; Hoover, Cindi A.; Karchner, Sibel I.; Katoh, Fumi; MacLatchy, Deborah L.; Marshall, William S.; Meyer, Joel N.; Nacci, Diane E.; Oleksiak, Marjorie F.; Rees, Bernard B.; Singer, Thomas D.; Stegeman, John J.; Towle, David W.; Van Veld, Peter A.; Vogelbein, Wolfgang K.; Whitehead, Andrew; Winn, Richard N.; Crawford, Douglas L.

2007-01-01

A strong foundation of basic and applied research documents that the estuarine fish Fundulus heteroclitus and related species are unique laboratory and field models for understanding how individuals and populations interact with their environment. In this paper we summarize an extensive body of work examining the adaptive responses of Fundulus species to environmental conditions, and describe how this research has contributed importantly to our understanding of physiology, gene regulation, toxicology, and ecological and evolutionary genetics of teleosts and other vertebrates. These explorations have reached a critical juncture at which advancement is hindered by the lack of genomic resources for these species. We suggest that a more complete genomics toolbox for F. heteroclitus and related species will permit researchers to exploit the power of this model organism to rapidly advance our understanding of fundamental biological and pathological mechanisms among vertebrates, as well as ecological strategies and evolutionary processes common to all living organisms. PMID:18071578

Systems Approaches to Biology and Disease Enable Translational Systems Medicine

PubMed Central

Hood, Leroy; Tian, Qiang

2012-01-01

The development and application of systems strategies to biology and disease are transforming medical research and clinical practice in an unprecedented rate. In the foreseeable future, clinicians, medical researchers, and ultimately the consumers and patients will be increasingly equipped with a deluge of personal health information, e.g., whole genome sequences, molecular profiling of diseased tissues, and periodic multi-analyte blood testing of biomarker panels for disease and wellness. The convergence of these practices will enable accurate prediction of disease susceptibility and early diagnosis for actionable preventive schema and personalized treatment regimes tailored to each individual. It will also entail proactive participation from all major stakeholders in the health care system. We are at the dawn of predictive, preventive, personalized, and participatory (P4) medicine, the fully implementation of which requires marrying basic and clinical researches through advanced systems thinking and the employment of high-throughput technologies in genomics, proteomics, nanofluidics, single-cell analysis, and computation strategies in a highly-orchestrated discipline we termed translational systems medicine. PMID:23084773

Application of fluorescence resonance energy transfer in protein studies

PubMed Central

Ma, Linlin; Yang, Fan; Zheng, Jie

2014-01-01

Since the physical process of fluorescence resonance energy transfer (FRET) was elucidated more than six decades ago, this peculiar fluorescence phenomenon has turned into a powerful tool for biomedical research due to its compatibility in scale with biological molecules as well as rapid developments in novel fluorophores and optical detection techniques. A wide variety of FRET approaches have been devised, each with its own advantages and drawbacks. Especially in the last decade or so, we are witnessing a flourish of FRET applications in biological investigations, many of which exemplify clever experimental design and rigorous analysis. Here we review the current stage of FRET methods development with the main focus on its applications in protein studies in biological systems, by summarizing the basic components of FRET techniques, most established quantification methods, as well as potential pitfalls, illustrated by example applications. PMID:25368432

A new parallel DNA algorithm to solve the task scheduling problem based on inspired computational model.

PubMed

Wang, Zhaocai; Ji, Zuwen; Wang, Xiaoming; Wu, Tunhua; Huang, Wei

2017-12-01

As a promising approach to solve the computationally intractable problem, the method based on DNA computing is an emerging research area including mathematics, computer science and molecular biology. The task scheduling problem, as a well-known NP-complete problem, arranges n jobs to m individuals and finds the minimum execution time of last finished individual. In this paper, we use a biologically inspired computational model and describe a new parallel algorithm to solve the task scheduling problem by basic DNA molecular operations. In turn, we skillfully design flexible length DNA strands to represent elements of the allocation matrix, take appropriate biological experiment operations and get solutions of the task scheduling problem in proper length range with less than O(n 2 ) time complexity. Copyright © 2017. Published by Elsevier B.V.

[Precision medicine: new opportunities and challenges for molecular epidemiology].

PubMed

Song, Jing; Hu, Yonghua

2016-04-01

Since the completion of the Human Genome Project in 2003 and the announcement of the Precision Medicine Initiative by U.S. President Barack Obama in January 2015, human beings have initially completed the " three steps" of " genomics to biology, genomics to health as well as genomics to society". As a new inter-discipline, the emergence and development of precision medicine have relied on the support and promotion from biological science, basic medicine, clinical medicine, epidemiology, statistics, sociology and information science, etc. Meanwhile, molecular epidemiology is considered to be the core power to promote precision medical as a cross discipline of epidemiology and molecular biology. This article is based on the characteristics and research progress of medicine and molecular epidemiology respectively, focusing on the contribution and significance of molecular epidemiology to precision medicine, and exploring the possible opportunities and challenges in the future.

The detection and analysis of point processes in biological signals

NASA Technical Reports Server (NTRS)

Anderson, D. J.; Correia, M. J.

1977-01-01

A pragmatic approach to the detection and analysis of discrete events in biomedical signals is taken. Examples from both clinical and basic research are provided. Introductory sections discuss not only discrete events which are easily extracted from recordings by conventional threshold detectors but also events embedded in other information carrying signals. The primary considerations are factors governing event-time resolution and the effects limits to this resolution have on the subsequent analysis of the underlying process. The analysis portion describes tests for qualifying the records as stationary point processes and procedures for providing meaningful information about the biological signals under investigation. All of these procedures are designed to be implemented on laboratory computers of modest computational capacity.

Satellite Ocean Biology: Past, Present, Future

NASA Technical Reports Server (NTRS)

McClain, Charles R.

2012-01-01

Since 1978 when the first satellite ocean color proof-of-concept sensor, the Nimbus-7 Coastal Zone Color Scanner, was launched, much progress has been made in refining the basic measurement concept and expanding the research applications of global satellite time series of biological and optical properties such as chlorophyll-a concentrations. The seminar will review the fundamentals of satellite ocean color measurements (sensor design considerations, on-orbit calibration, atmospheric corrections, and bio-optical algorithms), scientific results from the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) and Moderate resolution Imaging Spectroradiometer (MODIS) missions, and the goals of future NASA missions such as PACE, the Aerosol, Cloud, Ecology (ACE), and Geostationary Coastal and Air Pollution Events (GeoCAPE) missions.

Effects of biological sex on the pathophysiology of the heart

PubMed Central

Fazal, Loubina; Azibani, Feriel; Vodovar, Nicolas; Cohen Solal, Alain; Delcayre, Claude; Samuel, Jane-Lise

2014-01-01

Cardiovascular diseases are the leading causes of death in men and women in industrialized countries. While the effects of biological sex on cardiovascular pathophysiology have long been known, the sex-specific mechanisms mediating these processes have been further elucidated over recent years. This review aims at analysing the sex-based differences in cardiac structure and function in adult mammals, and the sex-based differences in the main molecular mechanisms involved in the response of the heart to pathological situations. It emerged from this review that the sex-based difference is a variable that should be dealt with, not only in basic science or clinical research, but also with regards to therapeutic approaches. PMID:23763376

Urine: Waste product or biologically active tissue?

PubMed

2018-03-01

Historically, urine has been viewed primarily as a waste product with little biological role in the overall health of an individual. Increasingly, data suggest that urine plays a role in human health beyond waste excretion. For example, urine might act as an irritant and contribute to symptoms through interaction with-and potential compromise of-the urothelium. To explore the concept that urine may be a vehicle for agents with potential or occult bioactivity and to discuss existing evidence and novel research questions that may yield insight into such a role, the National Institute of Diabetes and Digestive and Kidney Disease invited experts in the fields of comparative evolutionary physiology, basic science, nephrology, urology, pediatrics, metabolomics, and proteomics (among others) to a Urinology Think Tank meeting on February 9, 2015. This report reflects ideas that evolved from this meeting and current literature, including the concept of urine quality, the biological, chemical, and physical characteristics of urine, including the microbiota, cells, exosomes, pH, metabolites, proteins, and specific gravity (among others). Additionally, the manuscript presents speculative, and hopefully testable, ideas about the functional roles of urine constituents in health and disease. Moving forward, there are several questions that need further understanding and pursuit. There were suggestions to consider actively using various animal models and their biological specimens to elaborate on basic mechanistic information regarding human bladder dysfunction. Published 2018. This article is a U.S. Government work and is in the public domain in the USA.

Time to tackle clonorchiasis in China

PubMed Central

2013-01-01

Recent publication of the global epidemiology of clonorchiasis and its relationship with cholangiocarcinoma in the journal of Infectious Diseases of Poverty has stressed the importance of Clonorchis sinensis infection. To further demonstrate its threat on public health, especially in China, comparisons between clonorchiasis and hepatitis B are made in terms of epidemiology, clinical symptoms and carcinogenicity, disability, as well as changing trends. Furthermore, major problems and prioritized researches are argued, from basic biology to intervention. Imbalance between the majority of infected population and the minority of researches in China urges for more work from Chinese scientists and international cooperation. PMID:23849773

OBPR Product Lines, Human Research Initiative, and Physics Roadmap for Exploration

NASA Technical Reports Server (NTRS)

Israelsson, Ulf

2004-01-01

The pace of change has increased at NASA. OBPR s focus is now on the Human interface as it relates to the new Exploration vision. The fundamental physics community must demonstrate how we can contribute. Many opportunities exist for physicists to participate in addressing NASA's cross-disciplinary exploration challenges: a) Physicists can contribute to elucidating basic operating principles for complex biological systems; b) Physics technologies can contribute to developing miniature sensors and systems required for manned missions to Mars. NASA Codes other than OBPR may be viable sources of funding for physics research.

Structural marsh management research priorities

USGS Publications Warehouse

Cahoon, Donald R.; Groat, Charles G.

1989-01-01

The paper presents a prioritized list of research issues related to structural marsh management developed by a multidisciplinary panel of regulatory agency representatives, landowners, and scientists. More than 75 issues were identified concerning landscape changes, influence on ecological processes (i.e., hydrologic, biologic, and edaphic factors), habitat quality, cumulative impacts, and management approach. These issues were prioritized and organized around six basic questions regulatory personnel must try to answer for each marsh management plan application. The six questions deal with the influence of marsh management on, in order of most immediate need, marsh loss and health, fisheries, wildlife, habitat change, water quality, and cumulative effects.

[Medical application of nano-materials].

PubMed

Jiang, Hui-qing; Chen, Yi-fei

2002-11-01

To review the research progress and medical application of nano-materials. The literature review and comprehensive analysis, methods were used in this study. The Nanotechnology is a typical crossing knowledge. It could be extensively applied in the fields of novel biomaterials, effective transmission of bioactive factor; the detection of functions for all vital organ systems, vascular circulation condition, the control of repair of burn trauma wounds will be monitored by the varied methods of nano technology combined with molecular biological engineering. The application of Nanotechnology will play important roles in clinical medicine, wound repair and basic research for the traditional Chinese medicine.

``What if we were in a test tube?'' Students' gendered meaning making during a biology lesson about the basic facts of the human genitals

NASA Astrophysics Data System (ADS)

Orlander, Auli Arvola

2014-06-01

This paper explores what happens in the encounters between presentations of "basic facts" about the human genitals and 15-year-old students during a biology lesson in a Swedish secondary school. In this paper, meaning making was approached as relational, context-dependent and continually transacted. For this reason the analysis was conducted through a series of close readings of situations where students interacted with each other and the teacher in opening up gaps about alternative ways of discussing gender. Drawing on Foucault's theories about the inclusion and exclusion of knowledge and the subsequent work of Butler and other feminist researchers, the paper illuminates what gendered relations remain tacit in the conversation. It then illustrates possible ways in which these tacit gendered meanings could be made overt and discussed with the students when making meaning about the human genitals. The paper also shows how the ways in which human genitals are transacted in the science classroom have importance for what kind of learning is made available to the students.

Recent advances in thermoregulation.

PubMed

Tansey, Etain A; Johnson, Christopher D

2015-09-01

Thermoregulation is the maintenance of a relatively constant core body temperature. Humans normally maintain a body temperature at 37°C, and maintenance of this relatively high temperature is critical to human survival. This concept is so important that control of thermoregulation is often the principal example cited when teaching physiological homeostasis. A basic understanding of the processes underpinning temperature regulation is necessary for all undergraduate students studying biology and biology-related disciplines, and a thorough understanding is necessary for those students in clinical training. Our aim in this review is to broadly present the thermoregulatory process taking into account current advances in this area. First, we summarize the basic concepts of thermoregulation and subsequently assess the physiological responses to heat and cold stress, including vasodilation and vasoconstriction, sweating, nonshivering thermogenesis, piloerection, shivering, and altered behavior. Current research is presented concerning the body's detection of thermal challenge, peripheral and central thermoregulatory control mechanisms, including brown adipose tissue in adult humans and temperature transduction by the relatively recently discovered transient receptor potential channels. Finally, we present an updated understanding of the neuroanatomic circuitry supporting thermoregulation. Copyright © 2015 The American Physiological Society.

Can stem cells really regenerate the human heart? Use your noggin, dickkopf! Lessons from developmental biology.

PubMed

Sommer, Paula

2013-06-01

The human heart is the first organ to develop and its development is fairly well characterised. In theory, the heart has the capacity to regenerate, as its cardiomyocytes may be capable of cell division and the adult heart contains a cardiac stem cell niche, presumably capable of differentiating into cardiomyocytes and other cardiac-associated cell types. However, as with most other organs, these mechanisms are not activated upon serious injury. Several experimental options to induce regeneration of the damaged heart tissue are available: activate the endogenous cardiomyocytes to divide, coax the endogenous population of stem cells to divide and differentiate, or add exogenous cell-based therapy to replace the lost cardiac tissue. This review is a summary of the recent research into all these avenues, discussing the reasons for the limited successes of clinical trials using stem cells after cardiac injury and explaining new advances in basic science. It concludes with a reiteration that chances of successful regeneration would be improved by understanding and implementing the basics of heart development and stem cell biology.

Recent advances in inkjet dispensing technologies: applications in drug discovery.

PubMed

Zhu, Xiangcheng; Zheng, Qiang; Yang, Hu; Cai, Jin; Huang, Lei; Duan, Yanwen; Xu, Zhinan; Cen, Peilin

2012-09-01

Inkjet dispensing technology is a promising fabrication methodology widely applied in drug discovery. The automated programmable characteristics and high-throughput efficiency makes this approach potentially very useful in miniaturizing the design patterns for assays and drug screening. Various custom-made inkjet dispensing systems as well as specialized bio-ink and substrates have been developed and applied to fulfill the increasing demands of basic drug discovery studies. The incorporation of other modern technologies has further exploited the potential of inkjet dispensing technology in drug discovery and development. This paper reviews and discusses the recent developments and practical applications of inkjet dispensing technology in several areas of drug discovery and development including fundamental assays of cells and proteins, microarrays, biosensors, tissue engineering, basic biological and pharmaceutical studies. Progression in a number of areas of research including biomaterials, inkjet mechanical systems and modern analytical techniques as well as the exploration and accumulation of profound biological knowledge has enabled different inkjet dispensing technologies to be developed and adapted for high-throughput pattern fabrication and miniaturization. This in turn presents a great opportunity to propel inkjet dispensing technology into drug discovery.

Furthering knowledge of seaweed growth and development to facilitate sustainable aquaculture.

PubMed

Charrier, Bénédicte; Abreu, Maria Helena; Araujo, Rita; Bruhn, Annette; Coates, Juliet C; De Clerck, Olivier; Katsaros, Christos; Robaina, Rafael R; Wichard, Thomas

2017-12-01

Macroalgae (seaweeds) are the subject of increasing interest for their potential as a source of valuable, sustainable biomass in the food, feed, chemical and pharmaceutical industries. Compared with microalgae, the pace of knowledge acquisition in seaweeds is slower despite the availability of whole-genome sequences and model organisms for the major seaweed groups. This is partly a consequence of specific hurdles related to the large size of these organisms and their slow growth. As a result, this basic scientific field is falling behind, despite the societal and economic importance of these organisms. Here, we argue that sustainable management of seaweed aquaculture requires fundamental understanding of the underlying biological mechanisms controlling macroalgal life cycles - from the production of germ cells to the growth and fertility of the adult organisms - using diverse approaches requiring a broad range of technological tools. This Viewpoint highlights several examples of basic research on macroalgal developmental biology that could enable the step-changes which are required to adequately meet the demands of the aquaculture sector. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Positron Emission Tomography: Principles, Technology, and Recent Developments

NASA Astrophysics Data System (ADS)

Ziegler, Sibylle I.

2005-04-01

Positron emission tomography (PET) is a nuclear medical imaging technique for quantitative measurement of physiologic parameters in vivo (an overview of principles and applications can be found in [P.E. Valk, et al., eds. Positron Emission Tomography. Basic Science and Clinical Practice. 2003, Springer: Heidelberg]), based on the detection of small amounts of posi-tron-emitter-labelled biologic molecules. Various radiotracers are available for neuro-logical, cardiological, and oncological applications in the clinic and in research proto-cols. This overview describes the basic principles, technology, and recent develop-ments in PET, followed by a section on the development of a tomograph with ava-lanche photodiodes dedicated for small animal imaging as an example of efforts in the domain of high resolution tomographs.

Deconstructing and Reconstructing Theory of Mind

PubMed Central

Schaafsma, Sara M.; Pfaff, Donald W.; Spunt, Robert P.; Adolphs, Ralph

2014-01-01

Usage of the term Theory of Mind (ToM) has exploded across fields ranging from developmental psychology to social neuroscience and psychiatry research. Yet its meaning is often vague and inconsistent, its biological bases are a subject of debate, and the methods used to study it are highly heterogeneous. Most critically, its original definition does not permit easy downward translation to more basic processes such as those studied by behavioral neuroscience, leaving the interpretation of neuroimaging results opaque. We argue for a reformulation of ToM through a systematic two-stage approach, beginning with a deconstruction of the construct into a comprehensive set of basic component processes, followed by a complementary reconstruction from which a scientifically tractable concept of ToM could be recovered. PMID:25496670

Central Dog-ma Disease Detectives: A Molecular Biology Inquiry Activity for Undergraduates

NASA Astrophysics Data System (ADS)

Quan, T. K.; Yuh, P.; Black, F.

2010-12-01

The Minority Access to Research Careers (MARC) and Minority Biomedical Research Support (MBRS) are programs at the University of California at Santa Cruz designed to support minority undergraduate students majoring in the sciences. Each summer MARC/MBRS sponsors a Summer Institute that involves week long "rotations" with different faculty mentors. In 2008, the Center for Adaptive Optics (CfAO) Professional Development Program (PDP) was responsible for overseeing one week of the Summer Institute, and designed it to be a Biomedical Short Course. As part of this short course, we designed a four-hour activity in which students collected their own data and explored relationships between the basic biomolecules DNA, RNA, and protein. The goal was to have the students use experimental data to support their explanation of the "Central Dogma" of molecular biology. Here we describe details of our activity and provide a post-teaching reflection on its success.

Advances in Decoding Breast Cancer Brain Metastasis

PubMed Central

Zhang, Chenyu; Yu, Dihua

2016-01-01

The past decade has witnessed impressive advances in cancer treatment ushered in by targeted and immunotherapies. However, with significantly prolonged survival, upon recurrence, more patients become inflicted by brain metastasis, which is mostly refractory to all currently available therapeutic regimens. Historically, brain metastasis is an understudied area in cancer research, partly due to the dearth of appropriate experimental models that closely simulate the special biological features of metastasis in the unique brain environment; and to the sophistication of techniques required to perform in-depth studies of the extremely complex and challenging brain metastasis. Yet, with increasing clinical demand for more effective treatment options, brain metastasis research has rapidly advanced in recent years. The present review spotlights the recent major progresses in basic and translational studies of brain metastasis with focuses on new animal models, novel imaging technologies, omics “big data” resources, and some new and exciting biological insights on brain metastasis. PMID:27873078

How the confocal laser scanning microscope entered biological research.

PubMed

Amos, W B; White, J G

2003-09-01

A history of the early development of the confocal laser scanning microscope in the MRC Laboratory of Molecular Biology in Cambridge is presented. The rapid uptake of this technology is explained by the wide use of fluorescence in the 80s. The key innovations were the scanning of the light beam over the specimen rather than vice-versa and a high magnification at the level of the detector, allowing the use of a macroscopic iris. These were followed by an achromatic all-reflective relay system, a non-confocal transmission detector and novel software for control and basic image processing. This design was commercialized successfully and has been produced and developed over 17 years, surviving challenges from alternative technologies, including solid-state scanning systems. Lessons are pointed out from the unusual nature of the original funding and research environment. Attention is drawn to the slow adoption of the instrument in diagnostic medicine, despite promising applications.

Evaluation of the Effects of Platelet-Rich Plasma (PRP) Therapy Involved in the Healing of Sports-Related Soft Tissue Injuries

PubMed Central

Middleton, Kellie K.; Barro, Victor; Muller, Bart; Terada, Satosha; Fu, Freddie H.

2012-01-01

Abstract Musculoskeletal injuries are the most common cause of severe long-term pain and physical disability, and affect hundreds of millions of people around the world. One of the most popular methods used to biologically enhance healing in the fields of orthopaedic surgery and sports medicine includes the use of autologous blood products, namely, platelet rich plasma (PRP). PRP is an autologous concentration of human platelets to supra-physiologic levels. At baseline levels, platelets function as a natural reservoir for growth factors including platelet-derived growth factor (PDGF), epidermal growth factor (EGF), transforming growth factor-beta 1 (TGF-β1), vascular endothelial growth factor (VEGF), basic fibroblast growth factor (FGF), hepatocyte growth factor (HGF), and insulin-like growth factor (IGF-I). PRP is commonly used in orthopaedic practice to augment healing in sports-related injuries of skeletal muscle, tendons, and ligaments. Despite its pervasive use, the clinical efficacy of PrP therapy and varying mechanisms of action have yet to be established. Basic science research has revealed that PRP exerts is effects through many downstream events secondary to release of growth factors and other bioactive factors from its alpha granules. These effects may vary depending on the location of injury and the concentration of important growth factors involved in various soft tissue healing responses. This review focuses on the effects of PrP and its associated bioactive factors as elucidated in basic science research. Current findings in PRP basic science research, which have shed light on its proposed mechanisms of action, have opened doors for future areas of PrP research. PMID:23576936

Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics

PubMed Central

Zhou, Tao; Zhou, Zuo-Min; Guo, Xue-Jiang

2013-01-01

Proteomics strategies have been widely used in the field of male reproduction, both in basic and clinical research. Bioinformatics methods are indispensable in proteomics-based studies and are used for data presentation, database construction and functional annotation. In the present review, we focus on the functional annotation of gene lists obtained through qualitative or quantitative methods, summarizing the common and male reproduction specialized proteomics databases. We introduce several integrated tools used to find the hidden biological significance from the data obtained. We further describe in detail the information on male reproduction derived from Gene Ontology analyses, pathway analyses and biomedical analyses. We provide an overview of bioinformatics annotations in spermatogenesis, from gene function to biological function and from biological function to clinical application. On the basis of recently published proteomics studies and associated data, we show that bioinformatics methods help us to discover drug targets for sperm motility and to scan for cancer-testis genes. In addition, we summarize the online resources relevant to male reproduction research for the exploration of the regulation of spermatogenesis. PMID:23852026

Applications of artificial neural networks in medical science.

PubMed

Patel, Jigneshkumar L; Goyal, Ramesh K

2007-09-01

Computer technology has been advanced tremendously and the interest has been increased for the potential use of 'Artificial Intelligence (AI)' in medicine and biological research. One of the most interesting and extensively studied branches of AI is the 'Artificial Neural Networks (ANNs)'. Basically, ANNs are the mathematical algorithms, generated by computers. ANNs learn from standard data and capture the knowledge contained in the data. Trained ANNs approach the functionality of small biological neural cluster in a very fundamental manner. They are the digitized model of biological brain and can detect complex nonlinear relationships between dependent as well as independent variables in a data where human brain may fail to detect. Nowadays, ANNs are widely used for medical applications in various disciplines of medicine especially in cardiology. ANNs have been extensively applied in diagnosis, electronic signal analysis, medical image analysis and radiology. ANNs have been used by many authors for modeling in medicine and clinical research. Applications of ANNs are increasing in pharmacoepidemiology and medical data mining. In this paper, authors have summarized various applications of ANNs in medical science.

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research

PubMed Central

Frank, Kiana L.; Alegado, Rosanna A.; Amend, Anthony S.; Arif, Mohammad; Bennett, Gordon M.; Jani, Andrea J.; Medeiros, Matthew C. I.; Mileyko, Yuriy; Nguyen, Nhu H.; Nigro, Olivia D.; Prisic, Sladjana; Shin, Sangwoo; Takagi, Daisuke; Wilson, Samuel T.; Yew, Joanne Y.

2018-01-01

ABSTRACT Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai‘i at Mānoa aims to fill this gap. We are united in our mutual interest in advancing a new paradigm for biology that incorporates our modern understanding of the importance of microorganisms. As our first concerted research effort, we will assess the diversity and function of microbes across an entire watershed on the island of Oahu, Hawai‘i. Due to its high ecological diversity across tractable areas of land and sea, Hawai‘i provides a model system for the study of complex microbial communities and the processes they mediate. Owing to our diverse expertise, we will leverage this study system to advance the field of biology. PMID:29556540

Computer literacy for life sciences: helping the digital-era biology undergraduates face today's research.

PubMed

Smolinski, Tomasz G

2010-01-01

Computer literacy plays a critical role in today's life sciences research. Without the ability to use computers to efficiently manipulate and analyze large amounts of data resulting from biological experiments and simulations, many of the pressing questions in the life sciences could not be answered. Today's undergraduates, despite the ubiquity of computers in their lives, seem to be largely unfamiliar with how computers are being used to pursue and answer such questions. This article describes an innovative undergraduate-level course, titled Computer Literacy for Life Sciences, that aims to teach students the basics of a computerized scientific research pursuit. The purpose of the course is for students to develop a hands-on working experience in using standard computer software tools as well as computer techniques and methodologies used in life sciences research. This paper provides a detailed description of the didactical tools and assessment methods used in and outside of the classroom as well as a discussion of the lessons learned during the first installment of the course taught at Emory University in fall semester 2009.

Compound facial expressions of emotion: from basic research to clinical applications

PubMed Central

Du, Shichuan; Martinez, Aleix M.

2015-01-01

Emotions are sometimes revealed through facial expressions. When these natural facial articulations involve the contraction of the same muscle groups in people of distinct cultural upbringings, this is taken as evidence of a biological origin of these emotions. While past research had identified facial expressions associated with a single internally felt category (eg, the facial expression of happiness when we feel joyful), we have recently studied facial expressions observed when people experience compound emotions (eg, the facial expression of happy surprise when we feel joyful in a surprised way, as, for example, at a surprise birthday party). Our research has identified 17 compound expressions consistently produced across cultures, suggesting that the number of facial expressions of emotion of biological origin is much larger than previously believed. The present paper provides an overview of these findings and shows evidence supporting the view that spontaneous expressions are produced using the same facial articulations previously identified in laboratory experiments. We also discuss the implications of our results in the study of psychopathologies, and consider several open research questions. PMID:26869845

Environmental Sciences Division: Summaries of research in FY 1996

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

NONE

This document describes the Fiscal Year 1996 activities and products of the Environmental Sciences Division, Office of Biological and Environmental Research, Office of Energy Research. The report is organized into four main sections. The introduction identifies the basic program structure, describes the programs of the Environmental Sciences Division, and provides the level of effort for each program area. The research areas and project descriptions section gives program contact information, and provides descriptions of individual research projects including: three-year funding history, research objective and approach used in each project, and results to date. Appendixes provide postal and e-mail addresses for principalmore » investigators and define acronyms used in the text. The indexes provide indexes of principal investigators, research institutions, and keywords for easy reference. Research projects are related to climatic change and remedial action.« less

Lesson plan profile of senior high school biology teachers in Subang

NASA Astrophysics Data System (ADS)

Rohayati, E.; Diana, S. W.; Priyandoko, D.

2018-05-01

Lesson plan have important role for biology teachers in teaching and learning process. The aim of this study was intended to gain an overview of lesson plan of biology teachers’ at Senior High Schools in Subang which were the members of biology teachers association in Subang. The research method was descriptive method. Data was collected from 30 biology teachers. The result of study showed that lesson plan profile in terms of subject’s identity had good category with 83.33 % of average score. Analysis on basic competence in fair category with 74.45 % of average score. The compatibility of method/strategy was in fair category with average score 72.22 %. The compatibility of instrument, media, and learning resources in fair category with 71.11 % of average score. Learning scenario was in good category with 77.00 % of average score. The compatibility of evaluation was in low category with 56.39 % of average score. It can be concluded that biology teachers in Subang were good enough in making lesson plan, however in terms of the compatibility of evaluation needed to be fixed. Furthermore, teachers’ training for biology teachers’ association was recommended to increasing teachers’ skill to be professional teachers.

Commentary: Prerequisite Knowledge

ERIC Educational Resources Information Center

Taylor, Ann T. S.

2013-01-01

Most biochemistry, genetics, cell biology, and molecular biology classes have extensive prerequisite or co-requisite requirements, often including introductory chemistry, introductory biology, and organic chemistry coursework. But what is the function of these prerequisites? While it seems logical that a basic understanding of biological and…

Lessons from Retinoblastoma: Implications for Cancer, Development, Evolution, and Regenerative Medicine.

PubMed

Dyer, Michael A

2016-10-01

Retinoblastoma is a rare childhood cancer of the developing retina, and studies on this orphan disease have led to fundamental discoveries in cancer biology. Retinoblastoma has also emerged as a model for translational research for pediatric solid tumors, which is particularly important as personalized medicine expands in oncology. Research on retinoblastomas has been combined with the exploration of retinal development and retinal degeneration to advance a new model of cell type-specific disease susceptibility termed 'cellular pliancy'. The concept can even be extended to species-specific regeneration. This review discusses the remarkable path of retinoblastoma research and how it has shaped the most current efforts in basic, translational, and clinical research in oncology and beyond. Copyright © 2016 Elsevier Ltd. All rights reserved.

Monitoring osseointegration and developing intelligent systems (Conference Presentation)

NASA Astrophysics Data System (ADS)

Salvino, Liming W.

2017-05-01

Effective monitoring of structural and biological systems is an extremely important research area that enables technology development for future intelligent devices, platforms, and systems. This presentation provides an overview of research efforts funded by the Office of Naval Research (ONR) to establish structural health monitoring (SHM) methodologies in the human domain. Basic science efforts are needed to utilize SHM sensing, data analysis, modeling, and algorithms to obtain the relevant physiological and biological information for human-specific health and performance conditions. This overview of current research efforts is based on the Monitoring Osseointegrated Prosthesis (MOIP) program. MOIP develops implantable and intelligent prosthetics that are directly anchored to the bone of residual limbs. Through real-time monitoring, sensing, and responding to osseointegration of bones and implants as well as interface conditions and environment, our research program aims to obtain individualized actionable information for implant failure identification, load estimation, infection mitigation and treatment, as well as healing assessment. Looking ahead to achieve ultimate goals of SHM, we seek to expand our research areas to cover monitoring human, biological and engineered systems, as well as human-machine interfaces. Examples of such include 1) brainwave monitoring and neurological control, 2) detecting and evaluating brain injuries, 3) monitoring and maximizing human-technological object teaming, and 4) closed-loop setups in which actions can be triggered automatically based on sensors, actuators, and data signatures. Finally, some ongoing and future collaborations across different disciplines for the development of knowledge automation and intelligent systems will be discussed.

Spontaneous ultraweak photon emission from biological systems and the endogenous light field.

PubMed

Schwabl, Herbert; Klima, Herbert

2005-04-01

Still one of the most astonishing biological electromagnetic phenomena is the ultraweak photon emission (UPE) from living systems. Organisms and tissues spontaneously emit measurable intensities of light, i.e. photons in the visible part of the electromagnetic spectrum (380-780 nm), in the range from 1 to 1,000 photons x s-1 x cm-2, depending on their condition and vitality. It is important not to confuse UPE from living systems with other biogenic light emitting processes such as bioluminescence or chemiluminescence. This article examines with basic considerations from physics on the quantum nature of photons the empirical phenomenon of UPE. This leads to the description of the non-thermal origin of this radiation. This is in good correspondence with the modern understanding of life phenomena as dissipative processes far from thermodynamic equilibrium. UPE also supports the understanding of life sustaining processes as basically driven by electromagnetic fields. The basic features of UPE, like intensity and spectral distribution, are known in principle for many experimental situations. The UPE of human leukocytes contributes to an endogenous light field of about 1011 photons x s-1 which can be influenced by certain factors. Further research is needed to reveal the statistical properties of UPE and in consequence to answer questions about the underlying mechanics of the biological system. In principle, statistical properties of UPE allow to reconstruct phase-space dynamics of the light emitting structures. Many open questions remain until a proper understanding of the electromagnetic interaction of the human organism can be achieved: which structures act as receptors and emitters for electromagnetic radiation? How is electromagnetic information received and processed within cells?

Ethics and methods for biological rhythm research on animals and human beings.

PubMed

Portaluppi, Francesco; Smolensky, Michael H; Touitou, Yvan

2010-10-01

This article updates the ethical standards and methods for the conduct of high-quality animal and human biological rhythm research, which should be especially useful for new investigators of the rhythms of life. The editors of Chronobiology International adhere to and endorse the Code of Conduct and Best Practice Guidelines of the Committee On Publication Ethics (COPE), which encourages communication of such updates at regular intervals in the journal. The journal accepts papers representing original work, no part of which was previously submitted for publication elsewhere, except as brief abstracts, as well as in-depth reviews. The majority of research papers published in Chronobiology International entails animal and human investigations. The editors and readers of the journal expect authors of submitted manuscripts to have made an important contribution to the research of biological rhythms and related phenomena using ethical methods/procedures and unbiased, accurate, and honest reporting of findings. Authors of scientific papers are required to declare all potential conflicts of interest. The journal and its editors endorse compliance of investigators to the Guide for the Care and Use of Laboratory Animals of the Institute for Laboratory Animal Research of the National Research Council, relating to the conduct of ethical research on laboratory and other animals, and the principles of the Declaration of Helsinki of the World Medical Association, relating to the conduct of ethical research on human beings. The peer review of manuscripts by Chronobiology International thus includes judgment as to whether or not the protocols and methods conform to ethical standards. Authors are expected to show mastery of the basic methods and procedures of biological rhythm research and proper statistical assessment of data, including the appropriate application of time series data analyses, as briefly reviewed in this article. The journal editors strive to consistently achieve high standards for the research of original and review papers reported in Chronobiology International, and current examples of expectations are presented herein.

Relevance of ancient Indian wisdom to modern mental health – A few examples

PubMed Central

Shamasundar, C.

2008-01-01

The ancient Indian concepts and paradigms relating to mental health are holistic and cover aspects that have been neglected by the modern mental health literature. The latter can borrow, study, and incorporate them in their text books to advantage. The current trend in mental health research is heavily biased in favour of biological aspects of psychological phenomena neglecting the basic entity, the mind. Correction of this partisan tilt is urgently needed. PMID:19742213

Edgewood Chemical Biological Center In-House Laboratory Independent Research Program Annual Report FY11

DTIC Science & Technology

2011-01-01

flow rates which were held constant from trial to trial by critical orifices, were checked with several different calibrated mass flow meters. None of...processes or products in mind”. ECBC views the ILIR program as a critical part of its efforts to ensure a high level of basic science, foster innovation in...missions. The ILIR program solicits innovative proposals from the Center’s principal investigators (PI) that correspond to ECBC’s critical core

[Nutrition sciences in the treatment of eating disorders].

PubMed

Haas, Verena; Boschmann, Michael

2015-01-01

Several studies provide evidence for the existence of a hypermetabolic state of biological origin in recently weight recovered patients with anorexia nervosa. It remains unclear if current nutritional rehabilitation strategies are consistent with the resulting high energy requirements. Further insight into specific pathophysiological characteristics of energetic efficiency in patients with anorexia nervosa will help us to provide evidence based nutritional guidance. Basic nutritional research in this field is urgently required. © Georg Thieme Verlag KG Stuttgart · New York.

Basic Research in the Mathematical Foundations of Stability Theory, Control Theory and Numerical Linear Algebra.

DTIC Science & Technology

1979-09-01

without determinantal divisors, Linear and Multilinear Algebra 7(1979), 107-109. 4. The use of integral operators in number theory (with C. Ryavec and...Gersgorin revisited, to appear in Letters in Linear Algebra. 15. A surprising determinantal inequality for real matrices (with C.R. Johnson), to appear in...Analysis: An Essay Concerning the Limitations of Some Mathematical Methods in the Social , Political and Biological Sciences, David Berlinski, MIT Press

Husbandry and care of quail

USGS Publications Warehouse

Ottinger, M.A.; Rattner, B.A.

1999-01-01

Both the Japanese and Bobwhite quail are important species for biomedical, toxicological and basic biological research. In view of their rapid maturation, high reproductive rate in captivity, and other physiological characteristics, these species have been and will continue to be used successfully as model avian species. This short reviews describes caging, environmental, and feed requirements for Japanese and Bobwhite quail maintained in captivity. Information on egg collection, incubation, care of young, handling, blood collection and common diseases are discussed.

Bridging the gap to therapeutic strategies based on connexin/pannexin biology.

PubMed

Naus, Christian C; Giaume, Christian

2016-11-29

A unique workshop was recently held focusing on enhancing collaborations leading to identify and update the development of therapeutic strategies targeting connexin/pannexin large pore channels. Basic scientists exploring the functions of these channels in various pathologies gathered together with leading pharma companies which are targeting gap junction proteins for specific therapeutic applications. This highlights how paths of discovery research can converge with therapeutic strategies in innovative ways to enhance target identification and validation.

Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research.

PubMed

Ke, Yonggang; Castro, Carlos; Choi, Jong Hyun

2018-06-04

Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.

CRISPR-Cas9: a promising tool for gene editing on induced pluripotent stem cells

PubMed Central

Kim, Eun Ji; Kang, Ki Ho; Ju, Ji Hyeon

2017-01-01

Recent advances in genome editing with programmable nucleases have opened up new avenues for multiple applications, from basic research to clinical therapy. The ease of use of the technology—and particularly clustered regularly interspaced short palindromic repeats (CRISPR)—will allow us to improve our understanding of genomic variation in disease processes via cellular and animal models. Here, we highlight the progress made in correcting gene mutations in monogenic hereditary disorders and discuss various CRISPR-associated applications, such as cancer research, synthetic biology, and gene therapy using induced pluripotent stem cells. The challenges, ethical issues, and future prospects of CRISPR-based systems for human research are also discussed. PMID:28049282

Defining a global research agenda for breast cancer

PubMed Central

Love, Richard R.

2008-01-01

In contrast to western high income nations, the incidence and mortality from breast cancer are increasing in most low and middle income countries worldwide. Current approaches to breast cancer control developed for populations of high income societies should not be directly transferred without evaluation. A relevant research agenda includes population differences in tumor biology and metabolization of systemic therapies; cultural and psychosocial issues; and operations in health care systems. Highest priority should be given to assessments of clinical downstaging and basic systemic treatment effectiveness in low and middle income populations. Partnerships of existing organizations in high income nations with those in low and middle income countries are currently the most feasible sources of research support. PMID:18837032

CRISPR-Cas9: a promising tool for gene editing on induced pluripotent stem cells.

PubMed

Kim, Eun Ji; Kang, Ki Ho; Ju, Ji Hyeon

2017-01-01

Recent advances in genome editing with programmable nucleases have opened up new avenues for multiple applications, from basic research to clinical therapy. The ease of use of the technology-and particularly clustered regularly interspaced short palindromic repeats (CRISPR)-will allow us to improve our understanding of genomic variation in disease processes via cellular and animal models. Here, we highlight the progress made in correcting gene mutations in monogenic hereditary disorders and discuss various CRISPR-associated applications, such as cancer research, synthetic biology, and gene therapy using induced pluripotent stem cells. The challenges, ethical issues, and future prospects of CRISPR-based systems for human research are also discussed.

Management of Anterior Cruciate Ligament Injury: What's In and What's Out?

PubMed Central

Raines, Benjamin Todd; Naclerio, Emily; Sherman, Seth L

2017-01-01

Sports medicine physicians have a keen clinical and research interest in the anterior cruciate ligament (ACL). The biomechanical, biologic, and clinical data researchers generate, help drive injury management and prevention practices globally. The current concepts in ACL injury and surgery are being shaped by technological advances, expansion in basic science research, resurging interest in ACL preservation, and expanding efforts regarding injury prevention. As new methods are being developed in this field, the primary goal of safely improving patient outcomes will be a unifying principle. With this review, we provide an overview of topics currently in controversy or debate, and we identify paradigm shifts in the understanding, management, and prevention of ACL tears. PMID:28966380

HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

PubMed

Forster, Samuel C; Browne, Hilary P; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Lawley, Trevor D

2016-01-04

The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Conceptual Foundations of Systems Biology Explaining Complex Cardiac Diseases.

PubMed

Louridas, George E; Lourida, Katerina G

2017-02-21

Systems biology is an important concept that connects molecular biology and genomics with computing science, mathematics and engineering. An endeavor is made in this paper to associate basic conceptual ideas of systems biology with clinical medicine. Complex cardiac diseases are clinical phenotypes generated by integration of genetic, molecular and environmental factors. Basic concepts of systems biology like network construction, modular thinking, biological constraints (downward biological direction) and emergence (upward biological direction) could be applied to clinical medicine. Especially, in the field of cardiology, these concepts can be used to explain complex clinical cardiac phenotypes like chronic heart failure and coronary artery disease. Cardiac diseases are biological complex entities which like other biological phenomena can be explained by a systems biology approach. The above powerful biological tools of systems biology can explain robustness growth and stability during disease process from modulation to phenotype. The purpose of the present review paper is to implement systems biology strategy and incorporate some conceptual issues raised by this approach into the clinical field of complex cardiac diseases. Cardiac disease process and progression can be addressed by the holistic realistic approach of systems biology in order to define in better terms earlier diagnosis and more effective therapy.

Before the long journey: Development of Soviet space biology and medicine

NASA Technical Reports Server (NTRS)

Gazenko, O. G.

1978-01-01

Academician O. Gazenko, Chief of the Institute of Biomedical Problems, USSR Ministry of Public Health, reviewed the short but intense history of Soviet research in space biology and medicine. The solid academic approach of the Soviet Academy of Sciences in giving a good start at the very beginning of the space age is stressed and key people and institutions who initiated these studies are named. The basic feature of the first period of space biology is seen as the search for answers to a few fundamental questions of survival in space. It is pointed out that the initiated investigations were replaced by refined, in-depth studies of the biological, biophysical, and biochemical processes in human organism in the space environment and the search for methods which should enable cosmonaut crews to live in space for several years during interplanetary journeys. Discussing the typical problems of this effort, Gazenko each time showed how they benefit medical science and practice in general.

Computational immunology--from bench to virtual reality.

PubMed

Chan, Cliburn; Kepler, Thomas B

2007-02-01

Drinking from a fire-hose is an old cliché for the experience of learning basic and clinical sciences in medical school, and the pipe has been growing fatter at an alarming rate. Of course, it does not stop when one graduates; if anything, both the researcher and clinician are flooded with even more information. Slightly embarrassingly, while modern science is very good at generating new information, our ability to weave multiple strands of data into a useful and coherent story lags quite far behind. Bioinformatics, systems biology and computational medicine have arisen in recent years to address just this challenge. This essay is an introduction to the problem of data synthesis and integration in biology and medicine, and how the relatively new art of biological simulation can provide a new kind of map for understanding physiology and pathology. The nascent field of computational immunology will be used for illustration, but similar trends are occurring broadly across all of biology and medicine.

Introduction to Single-Cell RNA Sequencing.

PubMed

Olsen, Thale Kristin; Baryawno, Ninib

2018-04-01

During the last decade, high-throughput sequencing methods have revolutionized the entire field of biology. The opportunity to study entire transcriptomes in great detail using RNA sequencing (RNA-seq) has fueled many important discoveries and is now a routine method in biomedical research. However, RNA-seq is typically performed in "bulk," and the data represent an average of gene expression patterns across thousands to millions of cells; this might obscure biologically relevant differences between cells. Single-cell RNA-seq (scRNA-seq) represents an approach to overcome this problem. By isolating single cells, capturing their transcripts, and generating sequencing libraries in which the transcripts are mapped to individual cells, scRNA-seq allows assessment of fundamental biological properties of cell populations and biological systems at unprecedented resolution. Here, we present the most common scRNA-seq protocols in use today and the basics of data analysis and discuss factors that are important to consider before planning and designing an scRNA-seq project. © 2018 by John Wiley & Sons, Inc. Copyright © 2018 John Wiley & Sons, Inc.

Ethical aspects of aging research.

PubMed

Seppet, Enn; Pääsuke, Mati; Conte, Maria; Capri, Miriam; Franceschi, Claudio

2011-12-01

During the last 50-60 years, due to development of medical care and hygienically safe living conditions, the average life span of European citizens has substantially increased, with a rapid growth of the population older than 65 years. This trend places ever-growing medical and economical burden on society, as many of the older subjects suffer from age-related diseases and frailty. Coping with these problems requires not only appropriate medical treatment and social support but also extensive research in many fields of aging-from biology to sociology, with involvement of older people as the research subjects. This work anticipates development and application of ethical standards suited to dynamic advances in aging research. The aim of this review is to update the knowledge in ethical requirements toward recruitment of older research subjects, obtaining of informed consent, collection of biological samples, and use of stem cells in preclinical and clinical settings. It is concluded that application of adequate ethical platform markedly facilitates recruitment of older persons for participation in research. Currently, the basic ethical concepts are subjected to extensive discussion, with participation of all interested parties, in order to guarantee successful research on problems of human aging, protect older people from undesired interference, and afford their benefits through supporting innovations in research, therapy, and care.

ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

PubMed

Zeng, Victor; Extavour, Cassandra G

2012-01-01

The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental biology, physiology, evolutionary biology, ecology, comparative genomics and phylogenomics. Database URL: asgard.rc.fas.harvard.edu.

Integrating writing into an introductory environmental science curriculum: Perspectives from biology and physics

NASA Astrophysics Data System (ADS)

Selkin, P. A.; Cline, E. T.; Beaufort, A.

2008-12-01

In the University of Washington, Tacoma's Environmental Science program, we are implementing a curriculum-wide, scaffolded strategy to teach scientific writing. Writing in an introductory science course is a powerful means to make students feel part of the scientific community, an important goal in our environmental science curriculum. Writing is already an important component of the UW Tacoma environmental science program at the upper levels: our approach is designed to prepare students for the writing-intensive junior- and senior-level seminars. The approach is currently being tested in introductory biology and physics before it is incorporated in the rest of the introductory environmental science curriculum. The centerpiece of our approach is a set of research and writing assignments woven throughout the biology and physics course sequences. The assignments progress in their degree of complexity and freedom through the sequence of introductory science courses. Each assignment is supported by a number of worksheets and short written exercises designed to teach writing and critical thought skills. The worksheets are focused on skills identified both by research in science writing and the instructors' experience with student writing. Students see the assignments as a way to personalize their understanding of basic science concepts, and to think critically about ideas that interest them. We find that these assignments provide a good way to assess student comprehension of some of the more difficult ideas in the basic sciences, as well as a means to engage students with the challenging concepts of introductory science courses. Our experience designing these courses can inform efforts to integrate writing throughout a geoscience or environmental science curriculum, as opposed to on a course-by-course basis.

Systems modelling methodology for the analysis of apoptosis signal transduction and cell death decisions.

PubMed

Rehm, Markus; Prehn, Jochen H M

2013-06-01

Systems biology and systems medicine, i.e. the application of systems biology in a clinical context, is becoming of increasing importance in biology, drug discovery and health care. Systems biology incorporates knowledge and methods that are applied in mathematics, physics and engineering, but may not be part of classical training in biology. We here provide an introduction to basic concepts and methods relevant to the construction and application of systems models for apoptosis research. We present the key methods relevant to the representation of biochemical processes in signal transduction models, with a particular reference to apoptotic processes. We demonstrate how such models enable a quantitative and temporal analysis of changes in molecular entities in response to an apoptosis-inducing stimulus, and provide information on cell survival and cell death decisions. We introduce methods for analyzing the spatial propagation of cell death signals, and discuss the concepts of sensitivity analyses that enable a prediction of network responses to disturbances of single or multiple parameters. Copyright © 2013 Elsevier Inc. All rights reserved.

Constructing Smart Protocells with Built-In DNA Computational Core to Eliminate Exogenous Challenge.

PubMed

Lyu, Yifan; Wu, Cuichen; Heinke, Charles; Han, Da; Cai, Ren; Teng, I-Ting; Liu, Yuan; Liu, Hui; Zhang, Xiaobing; Liu, Qiaoling; Tan, Weihong

2018-06-06

A DNA reaction network is like a biological algorithm that can respond to "molecular input signals", such as biological molecules, while the artificial cell is like a microrobot whose function is powered by the encapsulated DNA reaction network. In this work, we describe the feasibility of using a DNA reaction network as the computational core of a protocell, which will perform an artificial immune response in a concise way to eliminate a mimicked pathogenic challenge. Such a DNA reaction network (RN)-powered protocell can realize the connection of logical computation and biological recognition due to the natural programmability and biological properties of DNA. Thus, the biological input molecules can be easily involved in the molecular computation and the computation process can be spatially isolated and protected by artificial bilayer membrane. We believe the strategy proposed in the current paper, i.e., using DNA RN to power artificial cells, will lay the groundwork for understanding the basic design principles of DNA algorithm-based nanodevices which will, in turn, inspire the construction of artificial cells, or protocells, that will find a place in future biomedical research.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Nanobiotechnology: synthetic biology meets materials science.

PubMed

Jewett, Michael C; Patolsky, Fernando

2013-08-01

Nanotechnology, the area of science focused on the control of matter in the nanometer scale, allows ground-breaking changes of the fundamental properties of matter that are often radically different compared to those exhibited by the bulk counterparts. In view of the fact that dimensionality plays a key role in determining the qualities of matter, the realization of the great potential of nanotechnology has opened the door to other disciplines such as life sciences and medicine, where the merging between them offers exciting new applications, along with basic science research. The application of nanotechnology in life sciences, nanobiotechnology, is now having a profound impact on biological circuit design, bioproduction systems, synthetic biology, medical diagnostics, disease therapy and drug delivery. This special issue is dedicated to the overview of how we are learning to control biopolymers and biological machines at the molecular- and nanoscale. In addition, it covers far-reaching progress in the design and synthesis of nanoscale materials, thus enabling the construction of integrated systems in which the component blocks are comparable in size to the chemical and biological entities under investigation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Modularization of biochemical networks based on classification of Petri net t-invariants.

PubMed

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-02-08

Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied. We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in Saccharomyces cerevisiae) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability. We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.

Modularization of biochemical networks based on classification of Petri net t-invariants

PubMed Central

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-01-01

Background Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior. With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Methods Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied. Results We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in Saccharomyces cerevisiae) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability. Conclusion We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis. PMID:18257938

Basic Science Living Skills for Today's World. Teacher's Edition.

ERIC Educational Resources Information Center

Zellers (Robert W.) Educational Services, Johnstown, PA.

This document is a teacher's edition of a basic skills curriculum in science for adult basic education (ABE) students. The course consists of 25 lessons on basic science concepts, designed to give students a good understanding of the biological and physical sciences. Suggested activities and experiments that the student can do are also included.…

Network Analyses in Plant Pathogens.

PubMed

Botero, David; Alvarado, Camilo; Bernal, Adriana; Danies, Giovanna; Restrepo, Silvia

2018-01-01

Even in the age of big data in Biology, studying the connections between the biological processes and the molecular mechanisms behind them is a challenging task. Systems biology arose as a transversal discipline between biology, chemistry, computer science, mathematics, and physics to facilitate the elucidation of such connections. A scenario, where the application of systems biology constitutes a very powerful tool, is the study of interactions between hosts and pathogens using network approaches. Interactions between pathogenic bacteria and their hosts, both in agricultural and human health contexts are of great interest to researchers worldwide. Large amounts of data have been generated in the last few years within this area of research. However, studies have been relatively limited to simple interactions. This has left great amounts of data that remain to be utilized. Here, we review the main techniques in network analysis and their complementary experimental assays used to investigate bacterial-plant interactions. Other host-pathogen interactions are presented in those cases where few or no examples of plant pathogens exist. Furthermore, we present key results that have been obtained with these techniques and how these can help in the design of new strategies to control bacterial pathogens. The review comprises metabolic simulation, protein-protein interactions, regulatory control of gene expression, host-pathogen modeling, and genome evolution in bacteria. The aim of this review is to offer scientists working on plant-pathogen interactions basic concepts around network biology, as well as an array of techniques that will be useful for a better and more complete interpretation of their data.

Mechanisms of radiation interaction with DNA: Potential implications for radiation protection

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

Not Available

1988-01-01

The Office of Health and Environmental Research (OHER) of the US Department of Energy conducts a broad multidisciplinary research program which includes basic biophysics, biophysical chemistry, molecular and cellular biology as well as experimental animal studies and opportunistic human studies. This research is directed at understanding how low levels of radiation of various qualities produce the spectrum of biological effects that are seen for such exposures. This workshop was entitled ''Mechanisms of Radiation Interaction with DNA: Potential Implications for Radiation Protection.'' It ws jointly sponsored by the Department of Energy and the Commission of European Communities. The aim of themore » workshop was to review the base of knowledge in the area of mechanisms of radiation action at the DNA level, and to explore ways in which this information can be applied to the development of scientifically sound concepts and procedures for use in the field of radiation protection. The overview of research provided by this multidisciplinary group will be helpful to the Office in program planning. This report includes a summary of the presentations, extended abstracts, the meeting agenda, research recommendations, and a list of participants. Individual papers are processed separately for the data base.« less

Building dialogues between clinical and biomedical research through cross-species collaborations.

PubMed

Chao, Hsiao-Tuan; Liu, Lucy; Bellen, Hugo J

2017-10-01

Today, biomedical science is equipped with an impressive array of technologies and genetic resources that bolster our basic understanding of fundamental biology and enhance the practice of modern medicine by providing clinicians with a diverse toolkit to diagnose, prognosticate, and treat a plethora of conditions. Many significant advances in our understanding of disease mechanisms and therapeutic interventions have arisen from fruitful dialogues between clinicians and biomedical research scientists. However, the increasingly specialized scientific and medical disciplines, globalization of science and technology, and complex datasets often hinder the development of effective interdisciplinary collaborations between clinical medicine and biomedical research. The goal of this review is to provide examples of diverse strategies to enhance communication and collaboration across diverse disciplines. First, we discuss examples of efforts to foster interdisciplinary collaborations at institutional and multi-institutional levels. Second, we explore resources and tools for clinicians and research scientists to facilitate effective bi-directional dialogues. Third, we use our experiences in neurobiology and human genetics to highlight how communication between clinical medicine and biomedical research lead to effective implementation of cross-species model organism approaches to uncover the biological underpinnings of health and disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

Applying ecological and evolutionary theory to cancer: a long and winding road.

PubMed

Thomas, Frédéric; Fisher, Daniel; Fort, Philippe; Marie, Jean-Pierre; Daoust, Simon; Roche, Benjamin; Grunau, Christoph; Cosseau, Céline; Mitta, Guillaume; Baghdiguian, Stephen; Rousset, François; Lassus, Patrice; Assenat, Eric; Grégoire, Damien; Missé, Dorothée; Lorz, Alexander; Billy, Frédérique; Vainchenker, William; Delhommeau, François; Koscielny, Serge; Itzykson, Raphael; Tang, Ruoping; Fava, Fanny; Ballesta, Annabelle; Lepoutre, Thomas; Krasinska, Liliana; Dulic, Vjekoslav; Raynaud, Peggy; Blache, Philippe; Quittau-Prevostel, Corinne; Vignal, Emmanuel; Trauchessec, Hélène; Perthame, Benoit; Clairambault, Jean; Volpert, Vitali; Solary, Eric; Hibner, Urszula; Hochberg, Michael E

2013-01-01

Since the mid 1970s, cancer has been described as a process of Darwinian evolution, with somatic cellular selection and evolution being the fundamental processes leading to malignancy and its many manifestations (neoangiogenesis, evasion of the immune system, metastasis, and resistance to therapies). Historically, little attention has been placed on applications of evolutionary biology to understanding and controlling neoplastic progression and to prevent therapeutic failures. This is now beginning to change, and there is a growing international interest in the interface between cancer and evolutionary biology. The objective of this introduction is first to describe the basic ideas and concepts linking evolutionary biology to cancer. We then present four major fronts where the evolutionary perspective is most developed, namely laboratory and clinical models, mathematical models, databases, and techniques and assays. Finally, we discuss several of the most promising challenges and future prospects in this interdisciplinary research direction in the war against cancer.

Magnetic skyrmion-based artificial neuron device

NASA Astrophysics Data System (ADS)

Li, Sai; Kang, Wang; Huang, Yangqi; Zhang, Xichao; Zhou, Yan; Zhao, Weisheng

2017-08-01

Neuromorphic computing, inspired by the biological nervous system, has attracted considerable attention. Intensive research has been conducted in this field for developing artificial synapses and neurons, attempting to mimic the behaviors of biological synapses and neurons, which are two basic elements of a human brain. Recently, magnetic skyrmions have been investigated as promising candidates in neuromorphic computing design owing to their topologically protected particle-like behaviors, nanoscale size and low driving current density. In one of our previous studies, a skyrmion-based artificial synapse was proposed, with which both short-term plasticity and long-term potentiation functions have been demonstrated. In this work, we further report on a skyrmion-based artificial neuron by exploiting the tunable current-driven skyrmion motion dynamics, mimicking the leaky-integrate-fire function of a biological neuron. With a simple single-device implementation, this proposed artificial neuron may enable us to build a dense and energy-efficient spiking neuromorphic computing system.

Present and future breast cancer management--bench to bedside and back: a positioning paper of academia, regulatory authorities and pharmaceutical industry.

PubMed

Bartsch, R; Frings, S; Marty, M; Awada, A; Berghoff, A S; Conte, P; Dickin, S; Enzmann, H; Gnant, M; Hasmann, M; Hendriks, H R; Llombart, A; Massacesi, C; von Minckwitz, G; Penault-Llorca, F; Scaltriti, M; Yarden, Y; Zwierzina, H; Zielinski, C C

2014-04-01

Insights into tumour biology of breast cancer have led the path towards the introduction of targeted treatment approaches; still, breast cancer-related mortality remains relatively high. Efforts in the field of basic research revealed new druggable targets which now await validation within the context of clinical trials. Therefore, questions concerning the optimal design of future studies are becoming even more pertinent. Aspects such as the ideal end point, availability of predictive markers to identify the optimal cohort for drug testing, or potential mechanisms of resistance need to be resolved. An expert panel representing the academic community, the pharmaceutical industry, as well as European Regulatory Authorities met in Vienna, Austria, in November 2012, in order to discuss breast cancer biology, identification of novel biological targets and optimal drug development with the aim of treatment individualization. This article summarizes statements and perspectives provided by the meeting participants.

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

PubMed

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.

Precision medicine and drug development in Alzheimer's disease: The importance of sexual dimorphism and patient stratification.

PubMed

Hampel, Harald; Vergallo, Andrea; Giorgi, Filippo Sean; Kim, Seung Hyun; Depypere, Herman; Graziani, Manuela; Saidi, Amira; Nisticò, Robert; Lista, Simone

2018-06-12

Neurodegenerative diseases (ND) are among the leading causes of disability and mortality. Considerable sex differences exist in the occurrence of the various manifestations leading to cognitive decline. Alzheimer's disease (AD) exhibits substantial sexual dimorphisms and disproportionately affects women. Women have a higher life expectancy compared to men and, consequently, have more lifespan to develop AD. The emerging precision medicine and pharmacology concepts - taking into account the individual genetic and biological variability relevant for disease risk, prevention, detection, diagnosis, and treatment - are expected to substantially enhance our knowledge and management of AD. Stratifying the affected individuals by sex and gender is an important basic step towards personalization of scientific research, drug development, and care. We hypothesize that sex and gender differences, extending from genetic to psychosocial domains, are highly relevant for the understanding of AD pathophysiology, and for the conceptualization of basic/translational research and for clinical therapy trial design. Copyright © 2018 Elsevier Inc. All rights reserved.

Pro-tumorigenic roles of fibroblast activation protein in cancer: back to the basics.

PubMed

Puré, Ellen; Blomberg, Rachel

2018-05-03

Fibroblast activation protein (FAP) is a cell-surface serine protease that acts on various hormones and extracellular matrix components. FAP is highly upregulated in a wide variety of cancers, and is often used as a marker for pro-tumorigenic stroma. It has also been proposed as a molecular target of cancer therapies, and, especially in recent years, a great deal of research has gone into design and testing of diverse FAP-targeted treatments. Yet despite this growing field of research, our knowledge of FAP's basic biology and functional roles in various cancers has lagged behind its use as a tumor-stromal marker. In this review, we summarize and analyze recent advances in understanding the functions of FAP in cancer, most notably its prognostic value in various tumor types, cellular effects on various cell types, and potential as a therapeutic target. We highlight outstanding questions in the field, the answers to which could shape preclinical and clinical studies of FAP.

Revisiting the mitogenetic effect of ultra-weak photon emission

PubMed Central

Volodyaev, Ilya; Beloussov, Lev V.

2015-01-01

This paper reviews the 90 years long controversial history of the so-called “mitogenetic radiation,” the first case of non-chemical distant interactions, reported by Gurwitsch (1923). It was soon described as ultraweak UV, emitted by a number of biological systems, and stimulating mitosis in “competent” (in this sense) cells. In the following 20 years this phenomenon attracted enormous interest of the scientific community, and gave rise to more than 700 publications around the world. Yet, this wave of research vanished after several ostensibly disproving works in late 1930-s, and was not resumed later, regardless of quite serious grounds for that. The authors discuss separately two aspects of the problem: (1) do living organisms emit ultraweak radiation in the UV range (irrespective of whether it has any biological role), and (2) are there any real effects of this ultraweak photon emission (UPE) upon cell division and/or other biological functions? Analysis of the available data permits to conclude, that UV fraction of UPE should be regarded real, while its biological effects are difficult to reproduce. This causes a paradox. A number of presently known qualities of UPE were initially discovered (predicted?) by the “early workers” on the basis of biological effects. Yet the qualities they discovered were proved later (the UV component of UPE, the sources of UPE among biological systems, etc…), while the biological effect they used for UPE “detection” remains questionable. Importance of this area for basic biology and medicine, and potential usefulness of UPE as a non-invasive research method, invite scientists to attack this problem again, applying powerful research facilities of modern science. Yet, because of complexity and uncertainty of the problem, further progress in this area demands comprehensive examination of both positive and negative works, with particular attention to their methodical details. PMID:26441668

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

PubMed

Galperin, Michael Y; Rigden, Daniel J; Fernández-Suárez, Xosé M

2015-01-01

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.

PubMed

Iwayanagi, Takao; Miyamoto, Sei; Konno, Takeshi; Mizutani, Hisashi; Hirai, Tomohiro; Shigemoto, Yasumasa; Gojobori, Takashi; Sugawara, Hideaki

2012-09-01

The Targeted Proteins Research Program (TPRP) promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan is the phase II of structural biology project (2007-2011) following the Protein 3000 Project (2002-2006) in Japan. While the phase I Protein 3000 Project put partial emphasis on the construction and maintenance of pipelines for structural analyses, the TPRP is dedicated to revealing the structures and functions of the targeted proteins that have great importance in both basic research and industrial applications. To pursue this objective, 35 Targeted Proteins (TP) Projects selected in the three areas of fundamental biology, medicine and pharmacology, and food and environment are tightly collaborated with 10 Advanced Technology (AT) Projects in the four fields of protein production, structural analyses, chemical library and screening, and information platform. Here, the outlines and achievements of the 35 TP Projects are summarized in the system named TP Atlas. Progress in the diversified areas is described in the modules of Graphical Summary, General Summary, Tabular Summary, and Structure Gallery of the TP Atlas in the standard and unified format. Advances in TP Projects owing to novel technologies stemmed from AT Projects and collaborative research among TP Projects are illustrated as a hallmark of the Program. The TP Atlas can be accessed at http://net.genes.nig.ac.jp/tpatlas/index_e.html .

Measuring and Advancing Experimental Design Ability in an Introductory Course without Altering Existing Lab Curriculum†

PubMed Central

Shanks, Ryan A.; Robertson, Chuck L.; Haygood, Christian S.; Herdliksa, Anna M.; Herdliska, Heather R.; Lloyd, Steven A.

2017-01-01

Introductory biology courses provide an important opportunity to prepare students for future courses, yet existing cookbook labs, although important in their own way, fail to provide many of the advantages of semester-long research experiences. Engaging, authentic research experiences aid biology students in meeting many learning goals. Therefore, overlaying a research experience onto the existing lab structure allows faculty to overcome barriers involving curricular change. Here we propose a working model for this overlay design in an introductory biology course and detail a means to conduct this lab with minimal increases in student and faculty workloads. Furthermore, we conducted exploratory factor analysis of the Experimental Design Ability Test (EDAT) and uncovered two latent factors which provide valid means to assess this overlay model’s ability to increase advanced experimental design abilities. In a pre-test/post-test design, we demonstrate significant increases in both basic and advanced experimental design abilities in an experimental and comparison group. We measured significantly higher gains in advanced experimental design understanding in students in the experimental group. We believe this overlay model and EDAT factor analysis contribute a novel means to conduct and assess the effectiveness of authentic research experiences in an introductory course without major changes to the course curriculum and with minimal increases in faculty and student workloads. PMID:28904647

Biological Concepts. Student Manual. Biological Treatment Process Control.

ERIC Educational Resources Information Center

Carnegie, John W.

This manual contains the textual material for a three-lesson unit which introduces students to the basic concepts applicable to all biological treatment systems. The general topic areas addressed in the lessons are: (1) the microorganisms found in biological systems; (2) the factors that affect the growth and health of biological systems; and (3)…

Hormonal contraceptive use and women's risk of HIV acquisition: priorities emerging from recent data.

PubMed

Ralph, Lauren J; Gollub, Erica L; Jones, Heidi E

2015-12-01

Understanding whether hormonal contraception increases women's risk of HIV acquisition is a public health priority. This review summarizes recent epidemiologic and biologic data, and considers the implications of new evidence on research and programmatic efforts. Two secondary analyses of HIV prevention trials demonstrated increased HIV risk among depot medroxyprogesterone acetate (DMPA) users compared with nonhormonal/no method users and norethisterone enanthate (NET-EN) users. A study of women in serodiscordant partnerships found no significant association for DMPA or implants. Two meta-analyses found elevated risks of HIV among DMPA users compared with nonhormonal/no method users, with no association for NET-EN or combined oral contraceptive pills. In-vitro and animal model studies identified plausible biological mechanisms by which progestin exposure could increase risk of HIV, depending on the type and dose of progestin, but such mechanisms have not been definitively observed in humans. Recent epidemiologic and biologic evidence on hormonal contraception and HIV suggests a harmful profile for DMPA but not combined oral contraceptives. In limited data, NET-EN appears safer than DMPA. More research is needed on other progestin-based methods, especially implants and Sayana Press. Future priorities include updating modeling studies with new pooled estimates, continued basic science to understand biological mechanisms, expanding contraceptive choice, and identifying effective ways to promote dual method use.

From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

PubMed

Michelini, Flavia; Jalihal, Ameya P; Francia, Sofia; Meers, Chance; Neeb, Zachary T; Rossiello, Francesca; Gioia, Ubaldo; Aguado, Julio; Jones-Weinert, Corey; Luke, Brian; Biamonti, Giuseppe; Nowacki, Mariusz; Storici, Francesca; Carninci, Piero; Walter, Nils G; Fagagna, Fabrizio d'Adda di

2018-04-25

Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.

From genes to proteins to behavior: a laboratory project that enhances student understanding in cell and molecular biology.

PubMed

Aronson, Benjamin D; Silveira, Linda A

2009-01-01

In the laboratory, students can actively explore concepts and experience the nature of scientific research. We have devised a 5-wk laboratory project in our introductory college biology course whose aim was to improve understanding in five major concepts that are central to basic cellular, molecular biology, and genetics while teaching molecular biology techniques. The project was focused on the production of adenine in Saccharomyces cerevisiae and investigated the nature of mutant red colonies of this yeast. Students created red mutants from a wild-type strain, amplified the two genes capable of giving rise to the red phenotype, and then analyzed the nucleotide sequences. A quiz assessing student understanding in the five areas was given at the start and the end of the course. Analysis of the quiz showed significant improvement in each of the areas. These areas were taught in the laboratory and the classroom; therefore, students were surveyed to determine whether the laboratory played a role in their improved understanding of the five areas. Student survey data demonstrated that the laboratory did have an important role in their learning of the concepts. This project simulated steps in a research project and could be adapted for an advanced course in genetics.

BioMEMS and Lab-on-a-Chip Course Education at West Virginia University

PubMed Central

Liu, Yuxin

2011-01-01

With the rapid growth of Biological/Biomedical MicroElectroMechanical Systems (BioMEMS) and microfluidic-based lab-on-a-chip (LOC) technology to biological and biomedical research and applications, demands for educated and trained researchers and technicians in these fields are rapidly expanding. Universities are expected to develop educational plans to address these specialized needs in BioMEMS, microfluidic and LOC science and technology. A course entitled BioMEMS and Lab-on-a-Chip was taught recently at the senior undergraduate and graduate levels in the Department of Computer Science and Electrical Engineering at West Virginia University (WVU). The course focused on the basic principles and applications of BioMEMS and LOC technology to the areas of biomedicine, biology, and biotechnology. The course was well received and the enrolled students had diverse backgrounds in electrical engineering, material science, biology, mechanical engineering, and chemistry. Student feedback and a review of the course evaluations indicated that the course was effective in achieving its objectives. Student presentations at the end of the course were a highlight and a valuable experience for all involved. The course proved successful and will continue to be offered regularly. This paper provides an overview of the course as well as some development and future improvements. PMID:25586697

Enhancing Scientific Inquiry Literacy of Prospective Biology Teachers through Inquiry Lab Project in Microbiology

NASA Astrophysics Data System (ADS)

Kusnadi, K.; Rustaman, N. Y.; Redjeki, S.; Aryantha, I. N. P.

2017-09-01

The implementation of the inquiry laboratory based project to enhance scientific inquiry literacy of prospective biology teachers in Microbiology course has been done. The inquiry lab based project was designed by three stages were debriefing of basic microbiology lab skills, guided inquiry and free inquiry respectively. The Study was quasi experimental with control group pretest-posttest design. The subjects were prospective biology teachers consists of 80 students. The scientific inquiry literacy instrument refers to ScInqLiT by Wenning. The results showed that there was significant difference of scientific inquiry literacy posttest scores between experiment and control (α 0,05) and was obtained N-gain score was 0.49 (medium) to experiment and 0.24 (low) to control. Based on formative assessment showed that development of student’s scientific attitude, research and microbiology lab skills during conducting project were increased. Student’s research skills especially in identification of variables, constructing a hypothesis, communicating and concluding were increased. During implementation of inquiry project also showed that they carried out mind and hands-on and so collaborative group investigation lab activities. Our findings may aid in reforming higher-education, particularly in microbiology laboratory activities to better promote scientific inquiry literacy, scientific attitude, research and laboratory skills.

Stem cells in drug discovery, tissue engineering, and regenerative medicine: emerging opportunities and challenges.

PubMed

Nirmalanandhan, Victor Sanjit; Sittampalam, G Sitta

2009-08-01

Stem cells, irrespective of their origin, have emerged as valuable reagents or tools in human health in the past 2 decades. Initially, a research tool to study fundamental aspects of developmental biology is now the central focus of generating transgenic animals, drug discovery, and regenerative medicine to address degenerative diseases of multiple organ systems. This is because stem cells are pluripotent or multipotent cells that can recapitulate developmental paths to repair damaged tissues. However, it is becoming clear that stem cell therapy alone may not be adequate to reverse tissue and organ damage in degenerative diseases. Existing small-molecule drugs and biologicals may be needed as "molecular adjuvants" or enhancers of stem cells administered in therapy or adult stem cells in the diseased tissues. Hence, a combination of stem cell-based, high-throughput screening and 3D tissue engineering approaches is necessary to advance the next wave of tools in preclinical drug discovery. In this review, the authors have attempted to provide a basic account of various stem cells types, as well as their biology and signaling, in the context of research in regenerative medicine. An attempt is made to link stem cells as reagents, pharmacology, and tissue engineering as converging fields of research for the next decade.

The BIG Data Center: from deposition to integration to translation.

PubMed

2017-01-04

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Tissue repositories for research at Sheba Medical Center(SMC].

PubMed

Cohen, Yehudit; Barshack, Iris; Onn, Amir

2013-06-01

Cancer is the number one cause of death in both genders. Breakthroughs in the understanding of cancer biology, the identification of prognostic factors, and the development of new treatments are increasingly dependent on access to human cancer tissues with linked clinicopathological data. Access to human tumor samples and a large investment in translational research are needed to advance this research. The SMC tissue repositories provide researchers with biological materials, which are essential tools for cancer research. SMC tissue repositories for research aim to collect, document and preserve human biospecimens from patients with cancerous diseases. This is in order to provide the highest quality and well annotated biological biospecimens, used as essential tools to achieve the growing demands of scientific research needs. Such repositories are partners in acceLerating biomedical research and medical product development through clinical resources, in order to apply best options to the patients. Following Institutional Review Board approval and signing an Informed Consent Form, the tumor and tumor-free specimens are coLLected by a designated pathologist at the operating room only when there is a sufficient amount of the tumor, in excess of the routine needs. Blood samples are collected prior to the procedure. Other types of specimens collected include ascites fluid, pleural effusion, tissues for Optimal Cutting Temperature [OCT] and primary culture etc. Demographic, clinical, pathologicaL, and follow-up data are collected in a designated database. SMC has already established several organ or disease-specific tissue repositories within different departments. The foundation of tissue repositories requires the concentrated effort of a multidisciplinary team composed of paramedical, medical and scientific professionals. Research projects using these specimens facilitate the development of 'targeted therapy', accelerate basic research aimed at clarifying molecular mechanisms involved in cancer, and support the development of novel diagnostic tools.