Advanced Biology [Sahuarita High School Career Curriculum Project.

ERIC Educational Resources Information Center

Christensen, Larry

This course in advanced biology is entitled "Advanced Genetics" and is one of a series of instructional guides prepared by teachers for the Sahuarita High School (Arizona) Career Curriculum Project. It consists of seven units of study, and 15 behavioral objectives relating to these units are stated. The topics covered include a review of genetics,…

Next-generation mammalian genetics toward organism-level systems biology.

PubMed

Susaki, Etsuo A; Ukai, Hideki; Ueda, Hiroki R

2017-01-01

Organism-level systems biology in mammals aims to identify, analyze, control, and design molecular and cellular networks executing various biological functions in mammals. In particular, system-level identification and analysis of molecular and cellular networks can be accelerated by next-generation mammalian genetics. Mammalian genetics without crossing, where all production and phenotyping studies of genome-edited animals are completed within a single generation drastically reduce the time, space, and effort of conducting the systems research. Next-generation mammalian genetics is based on recent technological advancements in genome editing and developmental engineering. The process begins with introduction of double-strand breaks into genomic DNA by using site-specific endonucleases, which results in highly efficient genome editing in mammalian zygotes or embryonic stem cells. By using nuclease-mediated genome editing in zygotes, or ~100% embryonic stem cell-derived mouse technology, whole-body knock-out and knock-in mice can be produced within a single generation. These emerging technologies allow us to produce multiple knock-out or knock-in strains in high-throughput manner. In this review, we discuss the basic concepts and related technologies as well as current challenges and future opportunities for next-generation mammalian genetics in organism-level systems biology.

Synthetic biology: advancing the design of diverse genetic systems

PubMed Central

Wang, Yen-Hsiang; Wei, Kathy Y.; Smolke, Christina D.

2013-01-01

A main objective of synthetic biology is to make the process of designing genetically-encoded biological systems more systematic, predictable, robust, scalable, and efficient. The examples of genetic systems in the field vary widely in terms of operating hosts, compositional approaches, and network complexity, ranging from a simple genetic switch to search-and-destroy systems. While significant advances in synthesis capabilities support the potential for the implementation of pathway- and genome-scale programs, several design challenges currently restrict the scale of systems that can be reasonably designed and implemented. Synthetic biology offers much promise in developing systems to address challenges faced in manufacturing, the environment and sustainability, and health and medicine, but the realization of this potential is currently limited by the diversity of available parts and effective design frameworks. As researchers make progress in bridging this design gap, advances in the field hint at ever more diverse applications for biological systems. PMID:23413816

Synthetic biology advances for pharmaceutical production

PubMed Central

Breitling, Rainer; Takano, Eriko

2015-01-01

Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems. PMID:25744872

The Use of Textbooks for Advanced-Level GCE Courses in Physics, Chemistry and Biology by Sixth-Form Students.

ERIC Educational Resources Information Center

Newton, D. P.

1984-01-01

A survey of sixth-form students to determine the level of A-level textbook use in physics, chemistry, and biology in English schools found that texts are used primarily after the lesson, at the student's discretion, and with great variations between students. Biology texts were used most, and physics texts used least. (MBR)

Advances in biologic augmentation for rotator cuff repair

PubMed Central

Patel, Sahishnu; Gualtieri, Anthony P.; Lu, Helen H.; Levine, William N.

2016-01-01

Rotator cuff tear is a very common shoulder injury that often necessitates surgical intervention for repair. Despite advances in surgical techniques for rotator cuff repair, there is a high incidence of failure after surgery because of poor healing capacity attributed to many factors. The complexity of tendon-to-bone integration inherently presents a challenge for repair because of a large biomechanical mismatch between the tendon and bone and insufficient regeneration of native tissue, leading to the formation of fibrovascular scar tissue. Therefore, various biological augmentation approaches have been investigated to improve rotator cuff repair healing. This review highlights recent advances in three fundamental approaches for biological augmentation for functional and integrative tendon–bone repair. First, the exploration, application, and delivery of growth factors to improve regeneration of native tissue is discussed. Second, applications of stem cell and other cell-based therapies to replenish damaged tissue for better healing is covered. Finally, this review will highlight the development and applications of compatible biomaterials to both better recapitulate the tendon–bone interface and improve delivery of biological factors for enhanced integrative repair. PMID:27750374

Tagging and Purifying Proteins to Teach Molecular Biology and Advanced Biochemistry

ERIC Educational Resources Information Center

Roecklein-Canfield, Jennifer A.; Lopilato, Jane

2004-01-01

Two distinct courses, "Molecular Biology" taught by the Biology Department and "Advanced Biochemistry" taught by the Chemistry Department, complement each other and, when taught in a coordinated and integrated way, can enhance student learning and understanding of complex material. "Molecular Biology" is a comprehensive lecture-based course with a…

Patient care in a biological safety level-4 (BSL-4) environment.

PubMed

Marklund, LeRoy A

2003-06-01

The greatest threats to America's public health include accidental importation of deadly diseases by international travelers and the release of biologic weapons by our adversaries. The greatest failure is unpreparedness because international travel and dispersion of biologic agents by our enemies are inevitable. An effective medical defense program is the recommended deterrent against these threats. The United States has a federal response plan in place that includes patient care and patient transport by using the highest level of biologic containment: BSL-4. The DoD has the capability to provide intensive care for victims infected with highly infectious yet unknown biologic agents in an environment that protects the caregiver while allowing scientists to study the characteristics of these new agents and assess the effectiveness of treatment. Army critical care nurses are vital in the biologic medical defense against unidentified infectious diseases, accidental occupational exposures, or intentional dispersion of weaponized biologic agents. Research that carefully advances healthcare using BSL-4 technology addresses the challenges of the human element of BSL-4 containment patient care, and BSL-4 patient transport enhances our nation's ability to address the emerging biologic threats we confront in the future.

Introduction to the Special Issue: Advances in island plant biology since Sherwin Carlquist's Island Biology

PubMed Central

Traveset, Anna; Fernández-Palacios, José María; Kueffer, Christoph; Bellingham, Peter J.; Morden, Clifford; Drake, Donald R.

2016-01-01

Sherwin Carlquist's seminal publications—in particular his classic Island Biology, published in 1974—formulated hypotheses specific to island biology that remain valuable today. This special issue brings together some of the most interesting contributions presented at the First Island Biology Symposium hosted in Honolulu on 7–11 July 2014. We compiled a total of 18 contributions that present data from multiple archipelagos across the world and from different disciplines within the plant sciences. In this introductory paper, we first provide a short overview of Carlquist's life and work and then summarize the main findings of the collated papers. A first group of papers deals with issues to which Carlquist notably contributed: long-distance dispersal, adaptive radiation and plant reproductive biology. The findings of such studies demonstrate the extent to which the field has advanced thanks to (i) the increasing availability and richness of island data, covering many taxonomic groups and islands; (ii) new information from the geosciences, phylogenetics and palaeoecology, which allows us a more realistic understanding of the geological and biological development of islands and their biotas; and (iii) the new theoretical and methodological advances that allow us to assess patterns of abundance, diversity and distribution of island biota over large spatial scales. Most other papers in the issue cover a range of topics related to plant conservation on islands, such as causes and consequences of mutualistic disruptions (due to pollinator or disperser losses, introduction of alien predators, etc.). Island biologists are increasingly considering reintroducing ecologically important species to suitable habitats within their historic range and to neighbouring islands with depauperate communities of vertebrate seed dispersers, and an instructive example is given here. Finally, contributions on ecological networks demonstrate the usefulness of this methodological tool to

Sarcomatoid renal cell carcinoma: Biology and treatment advances.

PubMed

Mouallem, Nemer El; Smith, Steven C; Paul, Asit K

2018-06-01

Sarcomatoid transformation in renal cell carcinoma, so called sacromatoid RCC (sRCC), is associated with an aggressive behavior and a poor prognosis. Current therapeutic approaches are largely ineffective. Recent studies looking into the genomic and molecular characterization of sRCCs have provided insights into the biology and pathogenesis of this entity. These advances in molecular signatures may help development of effective treatment strategies. We herein present a review of recent developments in the pathology, biology, and treatment modalities in sRCC. Copyright © 2017 Elsevier Inc. All rights reserved.

Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools.

PubMed

Siddiqui, Michael S; Thodey, Kate; Trenchard, Isis; Smolke, Christina D

2012-03-01

Secondary metabolites are an important source of high-value chemicals, many of which exhibit important pharmacological properties. These valuable natural products are often difficult to synthesize chemically and are commonly isolated through inefficient extractions from natural biological sources. As such, they are increasingly targeted for production by biosynthesis from engineered microorganisms. The budding yeast species Saccharomyces cerevisiae has proven to be a powerful microorganism for heterologous expression of biosynthetic pathways. S. cerevisiae's usefulness as a host organism is owed in large part to the wealth of knowledge accumulated over more than a century of intense scientific study. Yet many challenges are currently faced in engineering yeast strains for the biosynthesis of complex secondary metabolite production. However, synthetic biology is advancing the development of new tools for constructing, controlling, and optimizing complex metabolic pathways in yeast. Here, we review how the coupling between yeast biology and synthetic biology is advancing the use of S. cerevisiae as a microbial host for the construction of secondary metabolic pathways. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Bringing the Real World into the Biology Curriculum

ERIC Educational Resources Information Center

Lewis, Jenny

2006-01-01

This study followed a small but diverse group of biology teachers through the first two years of the pilot for a new Advanced Level Biology course--Salters-Nuffield Advanced Biology. SNAB aims to modernise A-level Biology using real world contexts and examples as the starting point, promoting conceptual understanding rather than factual recall,…

CAM Modalities Can Stimulate Advances in Theoretical Biology

PubMed Central

2005-01-01

Most complementary medicine is distinguished by not being supported by underlying theory accepted by Western science. However, for those who accept their validity, complementary and alternative medicine (CAM) modalities offer clues to understanding physiology and medicine more deeply. Ayurveda and vibrational medicine are stimulating new approaches to biological regulation. The new biophysics can be integrated to yield a single consistent theory, which may well underly much of CAM—a true ‘physics of physick’. The resulting theory seems to be a new, fundamental theory of health and etiology. It suggests that many CAM approaches to health care are scientifically in advance of those based on current Western biology. Such theories may well constitute the next steps in our scientific understanding of biology itself. If successfully developed, these ideas could result in a major paradigm shift in both biology and medicine, which will benefit all interested parties—consumers, health professionals, scientists, institutions and governments. PMID:15841271

Advanced high school biology in an era of rapid change: a summary of the biology panel report from the NRC Committee on Programs for Advanced Study of Mathematics and Science in American High Schools.

PubMed

Wood, William B

2002-01-01

A recently released National Research Council (NRC) report, Learning and Understanding: Improving Advanced Study of Mathematics and Science in U.S. High Schools, evaluated and recommended changes in the Advanced Placement (AP), International Baccalaureate (IB), and other advanced secondary school science programs. As part of this study, discipline-specific panels were formed to evaluate advanced programs in biology, chemistry, physics, and mathematics. Among the conclusions of the Content Panel for Biology were that AP courses in particular suffer from inadequate quality control as well as excessive pressure to fulfill their advanced placement function, which encourages teachers to attempt coverage of all areas of biology and emphasize memorization of facts rather than in-depth understanding. In this essay, the Panel's principal findings are discussed, with an emphasis on its recommendation that colleges and universities should be strongly discouraged from using performance on either the AP examination or the IB examination as the sole basis for automatic placement out of required introductory courses for biology majors and distribution requirements for nonmajors.

Advanced High School Biology in an Era of Rapid Change: A Summary of the Biology Panel Report from the NRC Committee on Programs for Advanced Study of Mathematics and Science in American High Schools

PubMed Central

2002-01-01

A recently released National Research Council (NRC) report, Learning and Understanding: Improving Advanced Study of Mathematics and Science in U.S. High Schools, evaluated and recommended changes in the Advanced Placement (AP), International Baccalaureate (IB), and other advanced secondary school science programs. As part of this study, discipline-specific panels were formed to evaluate advanced programs in biology, chemistry, physics, and mathematics. Among the conclusions of the Content Panel for Biology were that AP courses in particular suffer from inadequate quality control as well as excessive pressure to fulfill their advanced placement function, which encourages teachers to attempt coverage of all areas of biology and emphasize memorization of facts rather than in-depth understanding. In this essay, the Panel's principal findings are discussed, with an emphasis on its recommendation that colleges and universities should be strongly discouraged from using performance on either the AP examination or the IB examination as the sole basis for automatic placement out of required introductory courses for biology majors and distribution requirements for nonmajors. PMID:12669097

Advancing metabolic engineering through systems biology of industrial microorganisms.

PubMed

Dai, Zongjie; Nielsen, Jens

2015-12-01

Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

PubMed Central

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems. PMID:21850228

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

PubMed

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

Glycoengineering in CHO Cells: Advances in Systems Biology.

PubMed

Tejwani, Vijay; Andersen, Mikael R; Nam, Jong Hyun; Sharfstein, Susan T

2018-03-01

For several decades, glycoprotein biologics have been successfully produced from Chinese hamster ovary (CHO) cells. The therapeutic efficacy and potency of glycoprotein biologics are often dictated by their post-translational modifications, particularly glycosylation, which unlike protein synthesis, is a non-templated process. Consequently, both native and recombinant glycoprotein production generate heterogeneous mixtures containing variable amounts of different glycoforms. Stability, potency, plasma half-life, and immunogenicity of the glycoprotein biologic are directly influenced by the glycoforms. Recently, CHO cells have also been explored for production of therapeutic glycosaminoglycans (e.g., heparin), which presents similar challenges as producing glycoproteins biologics. Approaches to controlling heterogeneity in CHO cells and directing the biosynthetic process toward desired glycoforms are not well understood. A systems biology approach combining different technologies is needed for complete understanding of the molecular processes accounting for this variability and to open up new venues in cell line development. In this review, we describe several advances in genetic manipulation, modeling, and glycan and glycoprotein analysis that together will provide new strategies for glycoengineering of CHO cells with desired or enhanced glycosylation capabilities. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advanced composite applications for sub-micron biologically derived microstructures

NASA Technical Reports Server (NTRS)

Schnur, J. M.; Price, R. R.; Schoen, P. E.; Bonanventura, Joseph; Kirkpatrick, Douglas

1991-01-01

A major thrust of advanced material development is in the area of self-assembled ultra-fine particulate based composites (micro-composites). The application of biologically derived, self-assembled microstructures to form advanced composite materials is discussed. Hollow 0.5 micron diameter cylindrical shaped microcylinders self-assemble from diacetylenic lipids. These microstructures have a multiplicity of potential applications in the material sciences. Exploratory development is proceeding in application areas such as controlled release for drug delivery, wound repair, and biofouling as well as composites for electronic and magnetic applications, and high power microwave cathodes.

Advances in biologically inspired on/near sensor processing

NASA Astrophysics Data System (ADS)

McCarley, Paul L.

1999-07-01

As electro-optic sensors increase in size and frame rate, the data transfer and digital processing resource requirements also increase. In many missions, the spatial area of interest is but a small fraction of the available field of view. Choosing the right region of interest, however, is a challenge and still requires an enormous amount of downstream digital processing resources. In order to filter this ever-increasing amount of data, we look at how nature solves the problem. The Advanced Guidance Division of the Munitions Directorate, Air Force Research Laboratory at Elgin AFB, Florida, has been pursuing research in the are of advanced sensor and image processing concepts based on biologically inspired sensory information processing. A summary of two 'neuromorphic' processing efforts will be presented along with a seeker system concept utilizing this innovative technology. The Neuroseek program is developing a 256 X 256 2-color dual band IRFPA coupled to an optimized silicon CMOS read-out and processing integrated circuit that provides simultaneous full-frame imaging in MWIR/LWIR wavebands along with built-in biologically inspired sensor image processing functions. Concepts and requirements for future such efforts will also be discussed.

Synthetic biology advances and applications in the biotechnology industry: a perspective.

PubMed

Katz, Leonard; Chen, Yvonne Y; Gonzalez, Ramon; Peterson, Todd C; Zhao, Huimin; Baltz, Richard H

2018-06-18

Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.

Preparing Future Biology Faculty: An Advanced Professional Development Program for Graduate Students

ERIC Educational Resources Information Center

Lockwood, Stephanie A.; Miller, Amanda J.; Cromie, Meghan M.

2014-01-01

Formal professional development programs for biology graduate students interested in becoming faculty members have come far; however, programs that provide advanced teaching experience for seasoned graduate teaching assistants are scarce. We outline an advanced program that focuses on further training of graduate teaching assistants in pedagogy…

Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous catalytic ozonation and biological process.

PubMed

Zhuang, Haifeng; Han, Hongjun; Jia, Shengyong; Hou, Baolin; Zhao, Qian

2014-08-01

Advanced treatment of biologically pretreated coal gasification wastewater (CGW) was investigated employing heterogeneous catalytic ozonation integrated with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process. The results indicated that catalytic ozonation with the prepared catalyst (i.e. MnOx/SBAC, sewage sludge was converted into sludge based activated carbon (SBAC) which loaded manganese oxides) significantly enhanced performance of pollutants removal by generated hydroxyl radicals. The effluent of catalytic ozonation process was more biodegradable and less toxic than that in ozonation alone. Meanwhile, ANMBBR-BAF showed efficient capacity of pollutants removal in treatment of the effluent of catalytic ozonation at a shorter reaction time, allowing the discharge limits to be met. Therefore, the integrated process with efficient, economical and sustainable advantages was suitable for advanced treatment of real biologically pretreated CGW. Copyright © 2014 Elsevier Ltd. All rights reserved.

Teacher Assessment of University of London A-Level Biology Practical Notebooks--A Report on the First Operational Examination.

ERIC Educational Resources Information Center

Kingdon, J. M.; Hartley, D. J.

1982-01-01

Candidates taking University of London Advanced Level Biology Examination submit their practical/field-work notebooks for assessment (contributing 10 percent to final grade). Describes research undertaken during the first operation examination, reviewing assessment method and analyzing and discussing moderation techniques. Indicates assessment and…

Some Misconceptions in Meiosis Shown by Students Responding to an Advanced Level Practical Examination Question in Biology.

ERIC Educational Resources Information Center

Brown, C. R.

1990-01-01

Discussed are problems revealed in student responses to a practical task which formed part of an advanced level examination. The frequencies with which some misconceptions about cell reproduction and genetics occurred are presented. The nature of these misconceptions is analyzed and their implications discussed. (CW)

Advanced systems biology methods in drug discovery and translational biomedicine.

PubMed

Zou, Jun; Zheng, Ming-Wu; Li, Gen; Su, Zhi-Guang

2013-01-01

Systems biology is in an exponential development stage in recent years and has been widely utilized in biomedicine to better understand the molecular basis of human disease and the mechanism of drug action. Here, we discuss the fundamental concept of systems biology and its two computational methods that have been commonly used, that is, network analysis and dynamical modeling. The applications of systems biology in elucidating human disease are highlighted, consisting of human disease networks, treatment response prediction, investigation of disease mechanisms, and disease-associated gene prediction. In addition, important advances in drug discovery, to which systems biology makes significant contributions, are discussed, including drug-target networks, prediction of drug-target interactions, investigation of drug adverse effects, drug repositioning, and drug combination prediction. The systems biology methods and applications covered in this review provide a framework for addressing disease mechanism and approaching drug discovery, which will facilitate the translation of research findings into clinical benefits such as novel biomarkers and promising therapies.

Spatial transcriptomics: paving the way for tissue-level systems biology.

PubMed

Moor, Andreas E; Itzkovitz, Shalev

2017-08-01

The tissues in our bodies are complex systems composed of diverse cell types that often interact in highly structured repeating anatomical units. External gradients of morphogens, directional blood flow, as well as the secretion and absorption of materials by cells generate distinct microenvironments at different tissue coordinates. Such spatial heterogeneity enables optimized function through division of labor among cells. Unraveling the design principles that govern this spatial division of labor requires techniques to quantify the entire transcriptomes of cells while accounting for their spatial coordinates. In this review we describe how recent advances in spatial transcriptomics open the way for tissue-level systems biology. Copyright © 2017 Elsevier Ltd. All rights reserved.

Leveraging advances in biology to design biomaterials

NASA Astrophysics Data System (ADS)

Darnell, Max; Mooney, David J.

2017-12-01

Biomaterials have dramatically increased in functionality and complexity, allowing unprecedented control over the cells that interact with them. From these engineering advances arises the prospect of improved biomaterial-based therapies, yet practical constraints favour simplicity. Tools from the biology community are enabling high-resolution and high-throughput bioassays that, if incorporated into a biomaterial design framework, could help achieve unprecedented functionality while minimizing the complexity of designs by identifying the most important material parameters and biological outputs. However, to avoid data explosions and to effectively match the information content of an assay with the goal of the experiment, material screens and bioassays must be arranged in specific ways. By borrowing methods to design experiments and workflows from the bioprocess engineering community, we outline a framework for the incorporation of next-generation bioassays into biomaterials design to effectively optimize function while minimizing complexity. This framework can inspire biomaterials designs that maximize functionality and translatability.

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.

Advances in neuroscience and the biological and toxin weapons convention.

PubMed

Dando, Malcolm

2011-01-01

This paper investigates the potential threat to the prohibition of the hostile misuse of the life sciences embodied in the Biological and Toxin Weapons Convention from the rapid advances in the field of neuroscience. The paper describes how the implications of advances in science and technology are considered at the Five Year Review Conferences of the Convention and how State Parties have developed their appreciations since the First Review Conference in 1980. The ongoing advances in neurosciences are then assessed and their implications for the Convention examined. It is concluded that State Parties should consider a much more regular and systematic review system for such relevant advances in science and technology when they meet at the Seventh Review Conference in late 2011, and that neuroscientists should be much more informed and engaged in these processes of protecting their work from malign misuse.

PARPs and ADP-ribosylation: recent advances linking molecular functions to biological outcomes

PubMed Central

Gupte, Rebecca; Liu, Ziying; Kraus, W. Lee

2017-01-01

The discovery of poly(ADP-ribose) >50 years ago opened a new field, leading the way for the discovery of the poly(ADP-ribose) polymerase (PARP) family of enzymes and the ADP-ribosylation reactions that they catalyze. Although the field was initially focused primarily on the biochemistry and molecular biology of PARP-1 in DNA damage detection and repair, the mechanistic and functional understanding of the role of PARPs in different biological processes has grown considerably of late. This has been accompanied by a shift of focus from enzymology to a search for substrates as well as the first attempts to determine the functional consequences of site-specific ADP-ribosylation on those substrates. Supporting these advances is a host of methodological approaches from chemical biology, proteomics, genomics, cell biology, and genetics that have propelled new discoveries in the field. New findings on the diverse roles of PARPs in chromatin regulation, transcription, RNA biology, and DNA repair have been complemented by recent advances that link ADP-ribosylation to stress responses, metabolism, viral infections, and cancer. These studies have begun to reveal the promising ways in which PARPs may be targeted therapeutically for the treatment of disease. In this review, we discuss these topics and relate them to the future directions of the field. PMID:28202539

Advances in Neuroscience and the Biological and Toxin Weapons Convention

PubMed Central

Dando, Malcolm

2011-01-01

This paper investigates the potential threat to the prohibition of the hostile misuse of the life sciences embodied in the Biological and Toxin Weapons Convention from the rapid advances in the field of neuroscience. The paper describes how the implications of advances in science and technology are considered at the Five Year Review Conferences of the Convention and how State Parties have developed their appreciations since the First Review Conference in 1980. The ongoing advances in neurosciences are then assessed and their implications for the Convention examined. It is concluded that State Parties should consider a much more regular and systematic review system for such relevant advances in science and technology when they meet at the Seventh Review Conference in late 2011, and that neuroscientists should be much more informed and engaged in these processes of protecting their work from malign misuse. PMID:21350673

Recent Advances in the Chemical Biology of Nitroxyl (HNO) Detection and Generation

PubMed Central

Miao, Zhengrui; King, S. Bruce

2016-01-01

Nitroxyl or azanone (HNO) represents the redox-related (one electron reduced and protonated) relative of the well-known biological signaling molecule nitric oxide (NO). Despite the close structural similarity to NO, defined biological roles and endogenous formation of HNO remain unclear due to the high reactivity of HNO with itself, soft nucleophiles and transition metals. While significant work has been accomplished in terms of the physiology, biology and chemistry of HNO, important and clarifying work regarding HNO detection and formation has occurred within the last 10 years. This review summarizes advances in the areas of HNO detection and donation and their application to normal and pathological biology. Such chemical biological tools allow a deeper understanding of biological HNO formation and the role that HNO plays in a variety of physiological systems. PMID:27108951

ATP: A Coherent View for School Advanced Level Studies in Biology.

ERIC Educational Resources Information Center

Gayford, Chris

1986-01-01

Discusses how instruction of biological concepts as ATP cellular energetics is related to fundamental physical science understandings. Reviews areas of common misconceptions and confusions. Summarizes results of a study which investigated students' knowledge and perception of difficulty associated with the topic of energy and ATP. (ML)

Advances in the Biology and Chemistry of Sialic Acids

PubMed Central

Chen, Xi; Varki, Ajit

2010-01-01

Sialic acids are a subset of nonulosonic acids, which are nine-carbon alpha-keto aldonic acids. Natural existing sialic acid-containing structures are presented in different sialic acid forms, various sialyl linkages, and on diverse underlying glycans. They play important roles in biological, pathological, and immunological processes. Sialobiology has been a challenging and yet attractive research area. Recent advances in chemical and chemoenzymatic synthesis as well as large-scale E. coli cell-based production have provided a large library of sialoside standards and derivatives in amounts sufficient for structure-activity relationship studies. Sialoglycan microarrays provide an efficient platform for quick identification of preferred ligands for sialic acid-binding proteins. Future research on sialic acid will continue to be at the interface of chemistry and biology. Research efforts will not only lead to a better understanding of the biological and pathological importance of sialic acids and their diversity, but could also lead to the development of therapeutics. PMID:20020717

Advancing the science of forest hydrology A challenge to agricultural and biological engineers

Treesearch

Devendra Amatya; Wayne Skaggs; Carl Trettin

2009-01-01

For more than a century, agricultural and biological engineers have provided major advances in science, engineering, and technology to increase food and fiber production to meet the demands of a rapidly growing global population. The land base for these technological advances has originated largely from forested lands, which have experienced dramatic declines over the...

Using Advance Organizers to Enhance Students' Motivation in Learning Biology

ERIC Educational Resources Information Center

Shihusa, Hudson; Keraro, Fred N.

2009-01-01

This study investigated the effect of using advance organizers on students' motivation to learn biology. The research design used was quasi-experimental design where the non-randomised Solomon Four group was adopted. The focus was on the topic pollution. The sample comprised of 166 form three (third grade in the secondary school cycle) students in…

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

Book review: Advances in reintroduction biology of Australian and New Zealand fauna

USGS Publications Warehouse

Muths, Erin L.

2016-01-01

Review info: Advances in Reintroduction Biology of Australian and New Zealand Fauna. Doug P. Armstrong, Matthew W. Hayward, Dorian Moro, and Philip J. Seddon, editors. 2015. ISBN 978-1486303014. 320 pp.

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

PubMed

Dogrusoz, U; Erson, E Z; Giral, E; Demir, E; Babur, O; Cetintas, A; Colak, R

2006-02-01

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

The Emory Chemical Biology Discovery Center: leveraging academic innovation to advance novel targets through HTS and beyond.

PubMed

Johns, Margaret A; Meyerkord-Belton, Cheryl L; Du, Yuhong; Fu, Haian

2014-03-01

The Emory Chemical Biology Discovery Center (ECBDC) aims to accelerate high throughput biology and translation of biomedical research discoveries into therapeutic targets and future medicines by providing high throughput research platforms to scientific collaborators worldwide. ECBDC research is focused at the interface of chemistry and biology, seeking to fundamentally advance understanding of disease-related biology with its HTS/HCS platforms and chemical tools, ultimately supporting drug discovery. Established HTS/HCS capabilities, university setting, and expertise in diverse assay formats, including protein-protein interaction interrogation, have enabled the ECBDC to contribute to national chemical biology efforts, empower translational research, and serve as a training ground for young scientists. With these resources, the ECBDC is poised to leverage academic innovation to advance biology and therapeutic discovery.

Novel Advances in Shotgun Lipidomics for Biology and Medicine

PubMed Central

Wang, Miao; Wang, Chunyan; Han, Rowland H.; Han, Xianlin

2015-01-01

The field of lipidomics, as coined in 2003, has made profound advances and been rapidly expanded. The mass spectrometry-based strategies of this analytical methodology-oriented research discipline for lipid analysis are largely fallen into three categories: direct infusion-based shotgun lipidomics, liquid chromatography-mass spectrometry-based platforms, and matrix-assisted laser desorption/ionization mass spectrometry-based approaches (particularly in imagining lipid distribution in tissues or cells). This review focuses on shotgun lipidomics. After briefly introducing its fundamentals, the major materials of this article cover its recent advances. These include the novel methods of lipid extraction, novel shotgun lipidomics strategies for identification and quantification of previously hardly accessible lipid classes and molecular species including isomers, and novel tools for processing and interpretation of lipidomics data. Representative applications of advanced shotgun lipidomics for biological and biomedical research are also presented in this review. We believe that with these novel advances in shotgun lipidomics, this approach for lipid analysis should become more comprehensive and high throughput, thereby greatly accelerating the lipidomics field to substantiate the aberrant lipid metabolism, signaling, trafficking, and homeostasis under pathological conditions and their underpinning biochemical mechanisms. PMID:26703190

Information Literacy in Biology Education: An Example from an Advanced Cell Biology Course

PubMed Central

2005-01-01

Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information literacy instruction and then proceed to select, update, and write about a current research topic in an upper-level cell biology course is described. Students research the chosen topic using paper and electronic resources, generate a list of relevant articles, prepare abstracts based on papers read, and, finally, prepare a “state-of-the-art” paper on the topic. This approach, which extends over most of one semester, has resulted in a number of well-researched and well-written papers that incorporate some of the latest research in cell biology. The steps in this project have also led to students who are prepared to address future projects on new and complex topics. The project is part of an undergraduate course in cell biology, but parts of the assignments can be modified to fit a variety of subject areas and levels. PMID:16341261

Kant on biological teleology: Towards a two-level interpretation.

PubMed

Quarfood, Marcel

2006-12-01

According to Kant's Critique of the power of judgment, teleological considerations are unavoidable for conceptualizing organisms. Does this mean that teleology is more than merely heuristic? Kant stresses the regulative status of teleological attributions, but sometimes he seems to treat teleology as a constitutive condition for biology. To clarify this issue, the concept of natural purpose and its role for biology are examined. I suggest that the concept serves an identificatory function: it singles out objects as natural purposes, whereby the special science of biology is constituted. This relative constitutivity of teleology is explicated by means of a distinction of levels: on the object level of biological science, teleology is taken as constitutive, though it is merely regulative on the philosophical meta level. This distinction also concerns the place of Aristotelian teleology in Kant: on the object level, the Aristotelian view is accepted, whereas on the meta level, an agnostic stance is taken concerning teleology.

Biological Soil Crust Web Site

Science.gov Websites

www.soilcrust.org Crust 101 Advanced Gallery References CCERS site Links Biological Soil Crusts Textbook Corrections Level of Development Index Biological soil crusts are the community of organisms , mosses, liverworts and lichens. A Field Guide to Biological Soil Crusts of Western U.S. Drylands: Common

Recent advances in food biopeptides: production, biological functionalities and therapeutic applications.

PubMed

Saadi, Sami; Saari, Nazamid; Anwar, Farooq; Abdul Hamid, Azizah; Ghazali, Hasanah Mohd

2015-01-01

The growing momentum of several common life-style diseases such as myocardial infarction, cardiovascular disorders, stroke, hypertension, diabetes, and atherosclerosis has become a serious global concern. Recent developments in the field of proteomics offering promising solutions to solving such health problems stimulates the uses of biopeptides as one of the therapeutic agents to alleviate disease-related risk factors. Functional peptides are typically produced from protein via enzymatic hydrolysis under in vitro or in vivo conditions using different kinds of proteolytic enzymes. An array of biological activities, including antioxidative, antihypertensive, antidiabetic and immunomodulating has been ascribed to different types of biopeptides derived from various food sources. In fact, biopeptides are nutritionally and functionally important for regulating some physiological functions in the body; however, these are yet to be extensively addressed with regard to their production through advance strategies, mechanisms of action and multiple biological functionalities. This review mainly focuses on recent biotechnological advances that are being made in the field of production in addition to covering the mode of action and biological activities, medicinal health functions and therapeutic applications of biopeptides. State-of-the-art strategies that can ameliorate the efficacy, bioavailability, and functionality of biopeptides along with their future prospects are likewise discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

A dedicated database system for handling multi-level data in systems biology.

PubMed

Pornputtapong, Natapol; Wanichthanarak, Kwanjeera; Nilsson, Avlant; Nookaew, Intawat; Nielsen, Jens

2014-01-01

Advances in high-throughput technologies have enabled extensive generation of multi-level omics data. These data are crucial for systems biology research, though they are complex, heterogeneous, highly dynamic, incomplete and distributed among public databases. This leads to difficulties in data accessibility and often results in errors when data are merged and integrated from varied resources. Therefore, integration and management of systems biological data remain very challenging. To overcome this, we designed and developed a dedicated database system that can serve and solve the vital issues in data management and hereby facilitate data integration, modeling and analysis in systems biology within a sole database. In addition, a yeast data repository was implemented as an integrated database environment which is operated by the database system. Two applications were implemented to demonstrate extensibility and utilization of the system. Both illustrate how the user can access the database via the web query function and implemented scripts. These scripts are specific for two sample cases: 1) Detecting the pheromone pathway in protein interaction networks; and 2) Finding metabolic reactions regulated by Snf1 kinase. In this study we present the design of database system which offers an extensible environment to efficiently capture the majority of biological entities and relations encountered in systems biology. Critical functions and control processes were designed and implemented to ensure consistent, efficient, secure and reliable transactions. The two sample cases on the yeast integrated data clearly demonstrate the value of a sole database environment for systems biology research.

Structural Biology for A-Level Students

ERIC Educational Resources Information Center

Philip, Judith

2013-01-01

The relationship between the structure and function of proteins is an important area in biochemistry. Pupils studying A-level Biology are introduced to the four levels of protein structure (primary, secondary, tertiary and quaternary) and how these can be used to describe the progressive folding of a chain of amino acid residues to a final,…

Advances in imaging secondary ion mass spectrometry for biological samples

DOE PAGES

Boxer, Steven G.; Kraft, Mary L.; Weber, Peter K.

2008-12-16

Imaging mass spectrometry combines the power of mass spectrometry to identify complex molecules based on mass with sample imaging. Recent advances in secondary ion mass spectrometry have improved sensitivity and spatial resolution, so that these methods have the potential to bridge between high-resolution structures obtained by X-ray crystallography and cyro-electron microscopy and ultrastructure visualized by conventional light microscopy. Following background information on the method and instrumentation, we address the key issue of sample preparation. Because mass spectrometry is performed in high vacuum, it is essential to preserve the lateral organization of the sample while removing bulk water, and this hasmore » been a major barrier for applications to biological systems. Furthermore, recent applications of imaging mass spectrometry to cell biology, microbial communities, and biosynthetic pathways are summarized briefly, and studies of biological membrane organization are described in greater depth.« less

Recent advances in the biological production of mannitol.

PubMed

Song, Seung Hoon; Vieille, Claire

2009-08-01

Mannitol is a fructose-derived, 6-carbon sugar alcohol that is widely found in bacteria, yeasts, fungi, and plants. Because of its desirable properties, mannitol has many applications in pharmaceutical products, in the food industry, and in medicine. The current mannitol chemical manufacturing process yields crystalline mannitol in yields below 20 mol% from 50% glucose/50% fructose syrups. Thus, microbial and enzymatic mannitol manufacturing methods have been actively investigated, in particular in the last 10 years. This review summarizes the most recent advances in biological mannitol production, including the development of bacterial-, yeast-, and enzyme-based transformations.

A theory of biological relativity: no privileged level of causation.

PubMed

Noble, Denis

2012-02-06

Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of 'biological relativity' and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.

A theory of biological relativity: no privileged level of causation

PubMed Central

Noble, Denis

2012-01-01

Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of ‘biological relativity’ and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined. PMID:23386960

Top-down models in biology: explanation and control of complex living systems above the molecular level.

PubMed

Pezzulo, Giovanni; Levin, Michael

2016-11-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. © 2016 The Author(s).

Top-down models in biology: explanation and control of complex living systems above the molecular level

PubMed Central

2016-01-01

It is widely assumed in developmental biology and bioengineering that optimal understanding and control of complex living systems follows from models of molecular events. The success of reductionism has overshadowed attempts at top-down models and control policies in biological systems. However, other fields, including physics, engineering and neuroscience, have successfully used the explanations and models at higher levels of organization, including least-action principles in physics and control-theoretic models in computational neuroscience. Exploiting the dynamic regulation of pattern formation in embryogenesis and regeneration requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. Here, we argue that top-down models of pattern homeostasis serve as proof of principle for extending the current paradigm beyond emergence and molecule-level rules. We define top-down control in a biological context, discuss the examples of how cognitive neuroscience and physics exploit these strategies, and illustrate areas in which they may offer significant advantages as complements to the mainstream paradigm. By targeting system controls at multiple levels of organization and demystifying goal-directed (cybernetic) processes, top-down strategies represent a roadmap for using the deep insights of other fields for transformative advances in regenerative medicine and systems bioengineering. PMID:27807271

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

PubMed

Gautier, Arnaud; Rodriguez, Raphaël

2017-05-18

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

New and unconventional approaches for advancing resolution in biological transmission electron microscopy by improving macromolecular specimen preparation and preservation.

PubMed

Massover, William H

2011-02-01

Resolution in transmission electron microscopy (TEM) now is limited by the properties of specimens, rather than by those of instrumentation. The long-standing difficulties in obtaining truly high-resolution structure from biological macromolecules with TEM demand the development, testing, and application of new ideas and unconventional approaches. This review concisely describes some new concepts and innovative methodologies for TEM that deal with unsolved problems in the preparation and preservation of macromolecular specimens. The selected topics include use of better support films, a more protective multi-component matrix surrounding specimens for cryo-TEM and negative staining, and, several quite different changes in microscopy and micrography that should decrease the effects of electron radiation damage; all these practical approaches are non-traditional, but have promise to advance resolution for specimens of biological macromolecules beyond its present level of 3-10 Å (0.3-1.0 nm). The result of achieving truly high resolution will be a fulfillment of the still unrealized potential of transmission electron microscopy for directly revealing the structure of biological macromolecules down to the atomic level. Published by Elsevier Ltd.

Multi-level and hybrid modelling approaches for systems biology.

PubMed

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

2017-01-01

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

Advances in Biological Science.

ERIC Educational Resources Information Center

Oppenheimer, Steven B.; And Others

1988-01-01

Reviews major developments in areas that are at the cutting edge of biological research. Areas include: human anti-cancer gene, recombinant DNA techniques for the detection of Huntington disease carriers, and marine biology. (CW)

IERL-RTP PROCEDURES MANUAL: LEVEL 1 ENVIRONMENTAL ASSESSMENT BIOLOGICAL TESTS

EPA Science Inventory

The manual gives revised procedures for Level 1 environmental assessment biological tests, and supersedes the first edition, EPA-600/7-77-043 (NTIS No. PB 268484), published in April 1977. The revised biological procedures complement the Level 1 chemical and physical procedures p...

Advanced nanoelectronic architectures for THz-based biological agent detection

NASA Astrophysics Data System (ADS)

Woolard, Dwight L.; Jensen, James O.

2009-02-01

The U.S. Army Research Office (ARO) and the U.S. Army Edgewood Chemical Biological Center (ECBC) jointly lead and support novel research programs that are advancing the state-of-the-art in nanoelectronic engineering in application areas that have relevance to national defense and security. One fundamental research area that is presently being emphasized by ARO and ECBC is the exploratory investigation of new bio-molecular architectural concepts that can be used to achieve rapid, reagent-less detection and discrimination of biological warfare (BW) agents, through the control of multi-photon and multi-wavelength processes at the nanoscale. This paper will overview an ARO/ECBC led multidisciplinary research program presently under the support of the U.S. Defense Threat Reduction Agency (DTRA) that seeks to develop new devices and nanoelectronic architectures that are effective for extracting THz signatures from target bio-molecules. Here, emphasis will be placed on the new nanosensor concepts and THz/Optical measurement methodologies for spectral-based sequencing/identification of genetic molecules.

Towards advanced biological detection using surface enhanced raman scattering (SERS)-based sensors

NASA Astrophysics Data System (ADS)

Hankus, Mikella E.; Stratis-Cullum, Dimitra N.; Pellegrino, Paul M.

2010-08-01

The Army has a need for an accurate, fast, reliable and robust means to identify and quantify defense related materials. Raman spectroscopy is a form of vibrational spectroscopy that is rapidly becoming a valuable tool for homeland defense applications, as it is well suited for the molecular identification of a variety of compounds, including explosives and chemical and biological hazards. To measure trace levels of these types of materials, surface enhanced Raman scattering (SERS), a specialized form of Raman scattering, can be employed. The SERS enhancements are produced on, or in close proximity to, a nanoscale roughened metal surface and are typically associated with increased local electromagnetic field strengths. However, before application of SERS in the field and in particular to biological and other hazard sensing applications, significant improvements in substrate performance are needed. In this work, we will report the use of several SERS substrate architectures (colloids, film-over-nanospheres (FONs) and commercially available substrates) for detecting and differentiating numerous endospore samples. The variance in spectra as obtained using different sensing architectures will also be discussed. Additionally, the feasibility of using a modified substrate architecture that is tailored with molecular recognition probe system for detecting biological samples will be explored. We will discuss the progress towards an advanced, hybrid molecular recognition with a SERS/Fluorescence nanoprobe system including the optimization, fabrication, and spectroscopic analysis of samples on a commercially available substrate. Additionally, the feasibility of using this single-step switching architecture for hazard material detection will also be explored.

An advanced web query interface for biological databases

PubMed Central

Latendresse, Mario; Karp, Peter D.

2010-01-01

Although most web-based biological databases (DBs) offer some type of web-based form to allow users to author DB queries, these query forms are quite restricted in the complexity of DB queries that they can formulate. They can typically query only one DB, and can query only a single type of object at a time (e.g. genes) with no possible interaction between the objects—that is, in SQL parlance, no joins are allowed between DB objects. Writing precise queries against biological DBs is usually left to a programmer skillful enough in complex DB query languages like SQL. We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough to be used by biologists. It supports queries containing multiple conditions, and connecting multiple object types without using the join concept, which is unintuitive to biologists. This interactive web interface is called the Structured Advanced Query Page (SAQP). Users interactively build up a wide range of query constructs. Interactive documentation within the SAQP describes the schema of the queried DBs. The SAQP is based on BioVelo, a query language based on list comprehension. The SAQP is part of the Pathway Tools software and is available as part of several bioinformatics web sites powered by Pathway Tools, including the BioCyc.org site that contains more than 500 Pathway/Genome DBs. PMID:20624715

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

PubMed

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

2016-09-01

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

Omics Advances in Ecotoxicology.

PubMed

Zhang, Xiaowei; Xia, Pu; Wang, Pingping; Yang, Jianghu; Baird, Donald J

2018-04-03

Toxic substances in the environment generate adverse effects at all levels of biological organization from the molecular level to community and ecosystem. Given this complexity, it is not surprising that ecotoxicologists have struggled to address the full consequences of toxic substance release at ecosystem level, due to the limits of observational and experimental tools to reveal the changes in deep structure at different levels of organization. -Omics technologies, consisting of genomics and ecogenomics, have the power to reveal, in unprecedented detail, the cellular processes of an individual or biodiversity of a community in response to environmental change with high sample/observation throughput. This represents a historic opportunity to transform the way we study toxic substances in ecosystems, through direct linkage of ecological effects with the systems biology of organisms. Three recent examples of -omics advance in the assessment of toxic substances are explored here: (1) the use of functional genomics in the discovery of novel molecular mechanisms of toxicity of chemicals in the environment; (2) the development of laboratory pipelines of dose-dependent, reduced transcriptomics to support high-throughput chemical testing at the biological pathway level; and (3) the use of eDNA metabarcoding approaches for assessing chemical effects on biological communities in mesocosm experiments and through direct observation in field monitoring. -Omics advances in ecotoxicological studies not only generate new knowledge regarding mechanisms of toxicity and environmental effect, improving the relevance and immediacy of laboratory toxicological assessment, but can provide a wholly new paradigm for ecotoxicology by linking ecological models to mechanism-based, systems biology approaches.

Advanced supersonic propulsion study. [with emphasis on noise level reduction

NASA Technical Reports Server (NTRS)

Sabatella, J. A. (Editor)

1974-01-01

A study was conducted to determine the promising propulsion systems for advanced supersonic transport application, and to identify the critical propulsion technology requirements. It is shown that noise constraints have a major effect on the selection of the various engine types and cycle parameters. Several promising advanced propulsion systems were identified which show the potential of achieving lower levels of sideline jet noise than the first generation supersonic transport systems. The non-afterburning turbojet engine, utilizing a very high level of jet suppression, shows the potential to achieve FAR 36 noise level. The duct-heating turbofan with a low level of jet suppression is the most attractive engine for noise levels from FAR 36 to FAR 36 minus 5 EPNdb, and some series/parallel variable cycle engines show the potential of achieving noise levels down to FAR 36 minus 10 EPNdb with moderate additional penalty. The study also shows that an advanced supersonic commercial transport would benefit appreciably from advanced propulsion technology. The critical propulsion technology needed for a viable supersonic propulsion system, and the required specific propulsion technology programs are outlined.

Choroid plexus papillomas: advances in molecular biology and understanding of tumorigenesis.

PubMed

Safaee, Michael; Oh, Michael C; Bloch, Orin; Sun, Matthew Z; Kaur, Gurvinder; Auguste, Kurtis I; Tihan, Tarik; Parsa, Andrew T

2013-03-01

Choroid plexus papillomas are rare, benign tumors originating from the choroid plexus. Although generally found within the ventricular system, they can arise ectopically in the brain parenchyma or disseminate throughout the neuraxis. We sought to review recent advances in our understanding of the molecular biology and oncogenic pathways associated with this disease. A comprehensive PubMed literature review was conducted to identify manuscripts discussing the clinical, molecular, and genetic features of choroid plexus papillomas. Articles concerning diagnosis, treatment, and long-term patient outcomes were also reviewed. The introduction of atypical choroid plexus papilloma as a distinct entity has increased the need for accurate histopathologic diagnosis. Advances in immunohistochemical staining have improved our ability to differentiate choroid plexus papillomas from other intracranial tumors or metastatic lesions using combinations of key markers and mitotic indices. Recent findings have implicated Notch3 signaling, the transcription factor TWIST1, platelet-derived growth factor receptor, and the tumor necrosis factor-related apoptosis-inducing ligand pathway in choroid plexus papilloma tumorigenesis. A combination of commonly occurring chromosomal duplications and deletions has also been identified. Surgical resection remains the standard of care, although chemotherapy and radiotherapy may be considered for recurrent or metastatic lesions. While generally considered benign, these tumors possess a complex biology that sheds insight into other choroid plexus tumors, particularly malignant choroid plexus carcinomas. Improving our understanding of the molecular biology, genetics, and oncogenic pathways associated with this tumor will allow for the development of targeted therapies and improved outcomes for patients with this disease.

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

PubMed

Maduraiveeran, Govindhan; Sasidharan, Manickam; Ganesan, Vellaichamy

2018-04-30

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

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

PubMed

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

2018-01-01

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

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

PubMed

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

2007-01-01

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

Zirconia nanocrystals as submicron level biological label

NASA Astrophysics Data System (ADS)

Smits, K.; Liepins, J.; Gavare, M.; Patmalnieks, A.; Gruduls, A.; Jankovica, D.

2012-08-01

Inorganic nanocrystals are of increasing interest for their usage in biology and pharmacology research. Our interest was to justify ZrO2 nanocrystal usage as submicron level biological label in baker's yeast Saccharomyces cerevisia culture. For the first time (to our knowledge) images with sub micro up-conversion luminescent particles in biologic media were made. A set of undoped as well as Er and Yb doped ZrO2 samples at different concentrations were prepared by sol-gel method. The up-conversion luminescence for free standing and for nanocrystals with baker's yeast cells was studied and the differences in up-conversion luminescence spectra were analyzed. In vivo toxic effects of ZrO2 nanocrystals were tested by co-cultivation with baker's yeast.

Biological processes for advancing lignocellulosic waste biorefinery by advocating circular economy.

PubMed

Liguori, Rossana; Faraco, Vincenza

2016-09-01

The actualization of a circular economy through the use of lignocellulosic wastes as renewable resources can lead to reduce the dependence from fossil-based resources and contribute to a sustainable waste management. The integrated biorefineries, exploiting the overall lignocellulosic waste components to generate fuels, chemicals and energy, are the pillar of the circular economy. The biological treatment is receiving great attention for the biorefinery development since it is considered an eco-friendly alternative to the physico-chemical strategies to increase the biobased product recovery from wastes and improve saccharification and fermentation yields. This paper reviews the last advances in the biological treatments aimed at upgrading lignocellulosic wastes, implementing the biorefinery concept and advocating circular economy. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparing Content in Selected GCE A Levels and Advanced GNVQs.

ERIC Educational Resources Information Center

Holding, Gordon; And Others

1996-01-01

In an action research project, four British further education colleges compared mandatory units of three Advanced General National Vocational Qualifications (GNVQs)--business, art and design, and health and social care--with related General Certificate of Education Advanced Level (GCE A-level) syllabuses. Activities included a detailed comparison…

Using the Principles of SoTL to Redesign an Advanced Evolutionary Biology Course

ERIC Educational Resources Information Center

deBraga, Michael; Boyd, Cleo; Abdulnour, Shahad

2015-01-01

A primary goal of university instruction is the students' demonstration of improved, highly developed critical thinking (CT) skills. However, how do faculty encourage CT and its potential concomitant increase in student workload without negatively impacting student perceptions of the course? In this investigation, an advanced biology course is…

Vermicomposting as an advanced biological treatment for industrial waste from the leather industry.

PubMed

Nunes, Ramom R; Bontempi, Rhaissa M; Mendonça, Giovane; Galetti, Gustavo; Rezende, Maria Olímpia O

2016-01-01

The leather industry (tanneries) generates high amounts of toxic wastes, including solid and liquid effluents that are rich in organic matter and mineral content. Vermicomposting was studied as an alternative method of treating the wastes from tanneries. Vermicompost was produced from the following tannery residues: tanned chips of wet-blue leather, sludge from a liquid residue treatment station, and a mixture of both. Five hundred earthworms (Eisenia fetida) were added to each barrel. During the following 135 days the following parameters were evaluated: pH, total organic carbon (TOC), organic matter (OM), cation exchange capacity (CEC), C:N ratio, and chromium content as Cr (III) and Cr (VI). The results for pH, TOC and OM contents showed decreases in their values during the composting process, whereas values for CEC and total nitrogen rose, indicating that the vermicompost reached maturity. For chromium, at 135 days, all values of Cr (VI) were below the detectable level. Therefore, the Cr (VI) content had probably been biologically transformed into Cr (III), confirming the use of this technique as an advanced biological treatment. The study reinforces the idea that vermicomposting could be introduced as an effective technology for the treatment of industrial tannery waste and the production of agricultural inputs.

Technological advancements for the detection of and protection against biological and chemical warfare agents.

PubMed

Eubanks, Lisa M; Dickerson, Tobin J; Janda, Kim D

2007-03-01

There is a growing need for technological advancements to combat agents of chemical and biological warfare, particularly in the context of the deliberate use of a chemical and/or biological warfare agent by a terrorist organization. In this tutorial review, we describe methods that have been developed both for the specific detection of biological and chemical warfare agents in a field setting, as well as potential therapeutic approaches for treating exposure to these toxic species. In particular, nerve agents are described as a typical chemical warfare agent, and the two potent biothreat agents, anthrax and botulinum neurotoxin, are used as illustrative examples of potent weapons for which countermeasures are urgently needed.

Big data mining powers fungal research: recent advances in fission yeast systems biology approaches.

PubMed

Wang, Zhe

2017-06-01

Biology research has entered into big data era. Systems biology approaches therefore become the powerful tools to obtain the whole landscape of how cell separate, grow, and resist the stresses. Fission yeast Schizosaccharomyces pombe is wonderful unicellular eukaryote model, especially studying its division and metabolism can facilitate to understanding the molecular mechanism of cancer and discovering anticancer agents. In this perspective, we discuss the recent advanced fission yeast systems biology tools, mainly focus on metabolomics profiling and metabolic modeling, protein-protein interactome and genetic interaction network, DNA sequencing and applications, and high-throughput phenotypic screening. We therefore hope this review can be useful for interested fungal researchers as well as bioformaticians.

PARTNERING WITH DOE TO APPLY ADVANCED BIOLOGICAL, ENVIRONMENTAL, AND COMPUTATIONAL SCIENCE TO ENVIRONMENTAL ISSUES

EPA Science Inventory

On February 18, 2004, the U.S. Environmental Protection Agency and Department of Energy signed a Memorandum of Understanding to expand the research collaboration of both agencies to advance biological, environmental, and computational sciences for protecting human health and the ...

Proteomics Improves the New Understanding of Honeybee Biology.

PubMed

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

2018-04-11

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

Biological intrusion of low-level-waste trench covers

NASA Astrophysics Data System (ADS)

Hakonson, T. E.; Gladney, E. S.

The long-term integrity of low-level waste shallow land burialsites is dependent on the interaction of physical, chemical, and biological factors that modify the waste containment system. The need to consider biological processes as being potentially important in reducing the integrity of waste burial site cover treatment is demonstrated. One approach to limiting biological intrusion through the waste cover is to apply a barrier within the profile to limit root and animal penetration with depth. Experiments in the Los Alamos Experimental Engineered Test Facility were initiated to develop and evaluate biological barriers that are effective in minimizing intrusion into waste trenches. The experiments that are described employ four different candidate barrier materials of geologic origin. Experimental variables that will be evaluated, in addition to barrier type, are barrier depth and sil overburden depth.

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

PubMed

Ioannou, L A; Li Puma, G; Fatta-Kassinos, D

2015-04-09

Winery wastewater is a major waste stream resulting from numerous cleaning operations that occur during the production stages of wine. The resulting effluent contains various organic and inorganic contaminants and its environmental impact is notable, mainly due to its high organic/inorganic load, the large volumes produced and its seasonal variability. Several processes for the treatment of winery wastewater are currently available, but the development of alternative treatment methods is necessary in order to (i) maximize the efficiency and flexibility of the treatment process to meet the discharge requirements for winery effluents, and (ii) decrease both the environmental footprint, as well as the investment/operational costs of the process. This review, presents the state-of-the-art of the processes currently applied and/or tested for the treatment of winery wastewater, which were divided into five categories: i.e., physicochemical, biological, membrane filtration and separation, advanced oxidation processes, and combined biological and advanced oxidation processes. The advantages and disadvantages, as well as the main parameters/factors affecting the efficiency of winery wastewater treatment are discussed. Both bench- and pilot/industrial-scale processes have been considered for this review. Copyright © 2014 Elsevier B.V. All rights reserved.

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

PubMed Central

Turner, David P.

2015-01-01

Low income, poor diet, obesity and a lack of exercise are inter-related lifestyle factors that can profoundly alter our biological 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 biological consequence of lifestyle that can directly impact tumor biology. Advanced glycation end-products (AGEs) 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 biological links with the socioeconomic and environmental risk factors that drive cancer disparity. Given the potential benefits of lifestyle changes and the potential biological role of AGEs in promoting cancer, opportunities exist for collaborations impacting basic, translational, epidemiological and cancer prevention initiatives. PMID:25920350

An intermediate-level course on Biological Physics

NASA Astrophysics Data System (ADS)

Nelson, Phil

2004-03-01

I describe both undergraduate and graduate 1-semester courses designed to give a survey of Biological Physics. The courses cover classical as well as recent topics. The undergraduate version requires calculus-based first-year physics as its prerequisite. With this level of assumed background, we can arrive at topics such as molecular motors, manipulation of single molecules, and the propagation of nerve impulses. Students majoring in physics, chemistry, biochemistry, and every engineering major (as well as a few in biology), end up taking this course. The graduate course covers the same material but includes exercises with symbolic mathematics packages and data modeling.

Advances in the analysis of biological samples using ionic liquids.

PubMed

Clark, Kevin D; Trujillo-Rodríguez, María J; Anderson, Jared L

2018-02-12

Ionic liquids are a class of solvents and materials that hold great promise in bioanalytical chemistry. Task-specific ionic liquids have recently been designed for the selective extraction, separation, and detection of proteins, peptides, nucleic acids, and other physiologically relevant analytes from complex biological samples. To facilitate rapid bioanalysis, ionic liquids have been integrated in miniaturized and automated procedures. Bioanalytical separations have also benefited from the modification of nonspecific magnetic materials with ionic liquids or the implementation of ionic liquids with inherent magnetic properties. Furthermore, the direct detection of the extracted molecules in the analytical instrument has been demonstrated with structurally tuned ionic liquids and magnetic ionic liquids, providing a significant advantage in the analysis of low-abundance analytes. This article gives an overview of these advances that involve the application of ionic liquids and derivatives in bioanalysis. Graphical abstract Ionic liquids, magnetic ionic liquids, and ionic liquid-based sorbents are increasing the speed, selectivity, and sensitivity in the analysis of biological samples.

Study of nanoscale structural biology using advanced particle beam microscopy

NASA Astrophysics Data System (ADS)

Boseman, Adam J.

This work investigates developmental and structural biology at the nanoscale using current advancements in particle beam microscopy. Typically the examination of micro- and nanoscale features is performed using scanning electron microscopy (SEM), but in order to decrease surface charging, and increase resolution, an obscuring conductive layer is applied to the sample surface. As magnification increases, this layer begins to limit the ability to identify nanoscale surface structures. A new technology, Helium Ion Microscopy (HIM), is used to examine uncoated surface structures on the cuticle of wild type and mutant fruit flies. Corneal nanostructures observed with HIM are further investigated by FIB/SEM to provide detailed three dimensional information about internal events occurring during early structural development. These techniques are also used to reconstruct a mosquito germarium in order to characterize unknown events in early oogenesis. Findings from these studies, and many more like them, will soon unravel many of the mysteries surrounding the world of developmental biology.

Robert J. Genco: Pioneer in Oral Science Advancement.

PubMed

Taubman, M A

2018-07-01

Professor Robert J. Genco made extraordinary research advances in immunology, periodontology, and microbiology research, pioneering major advances in oral science. In addition to his extraordinary research advancements in oral biology, his pioneering advances in oral science leadership at the local/university, national, and international levels are recognized worldwide, as are his educational advancements. In his era, he is truly the "father" of oral science.

Reassessing the Economic Value of Advanced Level Mathematics

ERIC Educational Resources Information Center

Adkins, Michael; Noyes, Andrew

2016-01-01

In the late 1990s, the economic return to Advanced level (A-level) mathematics was examined. The analysis was based upon a series of log-linear models of earnings in the 1958 National Child Development Survey (NCDS) and the National Survey of 1980 Graduates and Diplomates. The core finding was that A-level mathematics had a unique earnings premium…

Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

PubMed

Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

SLEPR: A Sample-Level Enrichment-Based Pathway Ranking Method — Seeking Biological Themes through Pathway-Level Consistency

PubMed Central

Yi, Ming; Stephens, Robert M.

2008-01-01

Analysis of microarray and other high throughput data often involves identification of genes consistently up or down-regulated across samples as the first step in extraction of biological meaning. This gene-level paradigm can be limited as a result of valid sample fluctuations and biological complexities. In this report, we describe a novel method, SLEPR, which eliminates this limitation by relying on pathway-level consistencies. Our method first selects the sample-level differentiated genes from each individual sample, capturing genes missed by other analysis methods, ascertains the enrichment levels of associated pathways from each of those lists, and then ranks annotated pathways based on the consistency of enrichment levels of individual samples from both sample classes. As a proof of concept, we have used this method to analyze three public microarray datasets with a direct comparison with the GSEA method, one of the most popular pathway-level analysis methods in the field. We found that our method was able to reproduce the earlier observations with significant improvements in depth of coverage for validated or expected biological themes, but also produced additional insights that make biological sense. This new method extends existing analyses approaches and facilitates integration of different types of HTP data. PMID:18818771

Recent biologic and genetic advances in neuroblastoma: Implications for diagnostic, risk stratification, and treatment strategies.

PubMed

Newman, Erika A; Nuchtern, Jed G

2016-10-01

Neuroblastoma is an embryonic cancer of neural crest cell lineage, accounting for up to 10% of all pediatric cancer. The clinical course is heterogeneous ranging from spontaneous regression in neonates to life-threatening metastatic disease in older children. Much of this clinical variance is thought to result from distinct pathologic characteristics that predict patient outcomes. Consequently, many research efforts have been focused on identifying the underlying biologic and genetic features of neuroblastoma tumors in order to more clearly define prognostic subgroups for treatment stratification. Recent technological advances have placed emphasis on the integration of genetic alterations and predictive biologic variables into targeted treatment approaches to improve patient survival outcomes. This review will focus on these recent advances and the implications they have on the diagnostic, staging, and treatment approaches in modern neuroblastoma clinical management. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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

2013-01-01

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

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.

Atom Probe Tomographic Analysis of Biological Systems Enabled by Advanced Specimen Preparation Approaches

NASA Astrophysics Data System (ADS)

Perea, D. E.; Evans, J. E.

2017-12-01

The ability to image biointerfaces over nanometer to micrometer length scales is fundamental to correlating biological composition and structure to physiological function, and is aided by a multimodal approach using advanced complementary microscopic and spectroscopic characterization techniques. Atom Probe Tomography (APT) is a rapidly expanding technique for atomic-scale three-dimensional structural and chemical analysis. However, the regular application of APT to soft biological materials is lacking in large part due to difficulties in specimen preparation and inabilities to yield meaningful tomographic reconstructions that produce atomic scale compositional distributions as no other technique currently can. Here we describe the atomic-scale tomographic analysis of biological materials using APT that is facilitated by an advanced focused ion beam based approach. A novel specimen preparation strategy is used in the analysis of horse spleen ferritin protein embedded in an organic polymer resin which provides chemical contrast to distinguish the inorganic-organic interface of the ferrihydrite mineral core and protein shell of the ferritin protein. One-dimensional composition profiles directly reveal an enhanced concentration of P and Na at the surface of the ferrihydrite mineral core. We will also describe the development of a unique multifunctional environmental transfer hub allowing controlled cryogenic transfer of specimens under vacuum pressure conditions between an Atom Probe and cryo-FIB/SEM. The utility of the environmental transfer hub is demonstrated through the acquisition of previously unavailable mass spectral analysis of an intact organometallic molecule made possible via controlled cryogenic transfer. The results demonstrate a viable application of APT analysis to study complex biological organic/inorganic interfaces relevant to energy and the environment. References D.E. Perea et al. An environmental transfer hub for multimodal atom probe tomography

Clinical and Biological Predictors of Plasma Levels of Soluble RAGE in Critically Ill Patients: Secondary Analysis of a Prospective Multicenter Observational Study.

PubMed

Pranal, Thibaut; Pereira, Bruno; Berthelin, Pauline; Roszyk, Laurence; Godet, Thomas; Chabanne, Russell; Eisenmann, Nathanael; Lautrette, Alexandre; Belville, Corinne; Blondonnet, Raiko; Cayot, Sophie; Gillart, Thierry; Skrzypczak, Yvan; Souweine, Bertrand; Bouvier, Damien; Blanchon, Loic; Sapin, Vincent; Constantin, Jean-Michel; Jabaudon, Matthieu

2018-01-01

Although soluble forms of the receptor for advanced glycation end products (RAGE) have been recently proposed as biomarkers in multiple acute or chronic diseases, few studies evaluated the influence of usual clinical and biological parameters, or of patient characteristics and comorbidities, on circulating levels of soluble RAGE in the intensive care unit (ICU) setting. To determine, among clinical and biological parameters that are usually recorded upon ICU admission, which variables, if any, could be associated with plasma levels of soluble RAGE. Data for this ancillary study were prospectively obtained from adult patients with at least one ARDS risk factor upon ICU admission enrolled in a large multicenter observational study. At ICU admission, plasma levels of total soluble RAGE (sRAGE) and endogenous secretory (es)RAGE were measured by duplicate ELISA and baseline patient characteristics, comorbidities, and usual clinical and biological indices were recorded. After univariate analyses, significant variables were used in multivariate, multidimensional analyses. 294 patients were included in this ancillary study, among whom 62% were admitted for medical reasons, including septic shock (11%), coma (11%), and pneumonia (6%). Although some variables were associated with plasma levels of RAGE soluble forms in univariate analysis, multidimensional analyses showed no significant association between admission parameters and baseline plasma sRAGE or esRAGE. We found no obvious association between circulating levels of soluble RAGE and clinical and biological indices that are usually recorded upon ICU admission. This trial is registered with NCT02070536.

Molecular cell biology and advanced microscopy: an interview with Joshua Z. Rappoport.

PubMed

Rappoport, Joshua Z

2018-05-01

Dr Joshua Z Rappoport, PhD, speaks to Nawsheen Boodhun, Managing Editor. Rappoport completed his bachelor's degree in Biology at Brown University (RI, USA). He then went on to earn a PhD from the Program in Mechanisms of Disease and Therapeutics at the Mount Sinai School of Medicine Graduate School of Biological Sciences of New York University (USA). Rappoport spent the early parts of his career working as a postdoctoral researcher at the Laboratory of Cellular Biophysics based in The Rockefeller University (NY, USA). He was subsequently recruited as a tenured faculty member to work as part of the School of Biosciences at the University of Birmingham (UK). 2014 marked the return of Rappoport to the USA, where he is currently a Research Professor in Molecular Cell Biology at the Northwestern University Feinberg School of Medicine (IL, USA). He is also the Director of the Center for Advanced Microscopy (CAM) and Nikon Imaging Center (NIC), a large core facility consisting of eight members of staff that support around 200 different laboratories.

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

PubMed

Wagner, James M; Alper, Hal S

2016-04-01

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

Recent Advances in the Chemistry and Biology of Naturally Occurring Antibiotics

PubMed Central

Chen, Jason S.; Edmonds, David J.; Estrada, Anthony A.

2009-01-01

Lead-in Ever since the world-shaping discovery of penicillin, nature’s molecular diversity has been extensively screened for new medications and lead compounds in drug discovery. The search for anti-infective agents intended to combat infectious diseases has been of particular interest and has enjoyed a high degree of success. Indeed, the history of antibiotics is marked with impressive discoveries and drug development stories, the overwhelming majority of which have their origins in nature. Chemistry, and in particular chemical synthesis, has played a major role in bringing naturally occurring antibiotics and their derivatives to the clinic, and no doubt these disciplines will continue to be key enabling technologies for future developments in the field. In this review article, we highlight a number of recent discoveries and advances in the chemistry, biology, and medicine of naturally occurring antibiotics, with particular emphasis on the total synthesis, analog design, and biological evaluation of molecules with novel mechanisms of action. PMID:19130444

Entry to medical schools with 'A' level in mathematics rather than biology.

PubMed

Spurgin, C B

1975-09-01

The majority of British medical schools now accept for their shortest courses students who have mathematics at A level in place of the former requirement of biology A level. Only a small fraction of the entry, less than one-fifth, enters this way, in spite of statements by most medical schools that they make no distinction between those with mathematics and those with biology when making conditional offers of places. There is no evidence that those without biology are at a disadvantage in the courses. If the prospects of entry without A level biology were better publicized medical schools would have a wider field of possibly abler entrants, and pupils entering sixth forms could defer for a year a choice between a medical (or dental) career and one involving physical science, engineering, or other mathematics-based university education.

[Biology and immunotherapy advance of interleukin 2 and interleukin 15-review].

PubMed

Chen, Guang-Hua; Wu, De-Pei

2009-08-01

IL-2 and IL-15 play an important roles in regulating the lymphocyte function and homeostasis. Advances in understanding of the cellular and molecular biology of IL-2 and IL-15 and their receptor complex have provided rationale to better utilize them to expand and activate immune effectors in patients with cancer. These two cytokines stimulate similar responses from lymphocytes in vitro, but play markedly distinct roles in lymphoid biology in vivo. Their distinct physiological functions can be ascribed to distinct signaling pathways initiated by distinct cytokine receptor subunits, differential expression patterns of their receptors. Recently, the discovery of a novel mechanism of IL-15 cytokine signaling, trans-presentation, has provided insights into the divergent ways of these cytokine function. Although their heterotrimeric receptors have two receptor subunits in common, these two cytokines have contrasting roles in adaptive immune responses. The unique role of interleukin 2 is in the elimination of self-reactive T cells to prevent autoimmunity. By contrast, interleukin 15 is dedicated to the prolonged maintenance of memory T-cell responses to pathogens. As discussed in this article, the biology of IL-2 and IL-15 two cytokines will affect the development of novel treatment for malignancies and autoimmune diseases.

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

PubMed

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

2007-01-01

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

Quantum biology at the cellular level--elements of the research program.

PubMed

Bordonaro, Michael; Ogryzko, Vasily

2013-04-01

Quantum biology is emerging as a new field at the intersection between fundamental physics and biology, promising novel insights into the nature and origin of biological order. We discuss several elements of QBCL (quantum biology at cellular level) - a research program designed to extend the reach of quantum concepts to higher than molecular levels of biological organization. We propose a new general way to address the issue of environmentally induced decoherence and macroscopic superpositions in biological systems, emphasizing the 'basis-dependent' nature of these concepts. We introduce the notion of 'formal superposition' and distinguish it from that of Schroedinger's cat (i.e., a superposition of macroscopically distinct states). Whereas the latter notion presents a genuine foundational problem, the former one contradicts neither common sense nor observation, and may be used to describe cellular 'decision-making' and adaptation. We stress that the interpretation of the notion of 'formal superposition' should involve non-classical correlations between molecular events in a cell. Further, we describe how better understanding of the physics of Life can shed new light on the mechanism driving evolutionary adaptation (viz., 'Basis-Dependent Selection', BDS). Experimental tests of BDS and the potential role of synthetic biology in closing the 'evolvability mechanism' loophole are also discussed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

``Physical Concepts in Cell Biology,'' an upper level interdisciplinary course in cell biophysics/mathematical biology

NASA Astrophysics Data System (ADS)

Vavylonis, Dimitrios

2009-03-01

I will describe my experience in developing an interdisciplinary biophysics course addressed to students at the upper undergraduate and graduate level, in collaboration with colleagues in physics and biology. The students had a background in physics, biology and engineering, and for many the course was their first exposure to interdisciplinary topics. The course did not depend on a formal knowledge of equilibrium statistical mechanics. Instead, the approach was based on dynamics. I used diffusion as a universal ``long time'' law to illustrate scaling concepts. The importance of statistics and proper counting of states/paths was introduced by calculating the maximum accuracy with which bacteria can measure the concentration of diffuse chemicals. The use of quantitative concepts and methods was introduced through specific biological examples, focusing on model organisms and extremes at the cell level. Examples included microtubule dynamic instability, the search and capture model, molecular motor cooperativity in muscle cells, mitotic spindle oscillations in C. elegans, polymerization forces and propulsion of pathogenic bacteria, Brownian ratchets, bacterial cell division and MinD oscillations.

Specification for Qualification and Certification for Level II - Advanced Welders.

ERIC Educational Resources Information Center

American Welding Society, Miami, FL.

This document defines the requirements and program for the American Welding Society (AWS) to certify advanced-level welders through an evaluation process entailing performance qualification and practical knowledge tests requiring the use of advanced reading, computational, and manual skills. The following items are included: statement of the…

Biological Oceanography

NASA Astrophysics Data System (ADS)

Dyhrman, Sonya

2004-10-01

The ocean is arguably the largest habitat on the planet, and it houses an astounding array of life, from microbes to whales. As a testament to this diversity and its importance, the discipline of biological oceanography spans studies of all levels of biological organization, from that of single genes, to organisms, to their population dynamics. Biological oceanography also includes studies on how organisms interact with, and contribute to, essential global processes. Students of biological oceanography are often as comfortable looking at satellite images as they are electron micrographs. This diversity of perspective begins the textbook Biological Oceanography, with cover graphics including a Coastal Zone Color Scanner image representing chlorophyll concentration, an electron micrograph of a dinoflagellate, and a photograph of a copepod. These images instantly capture the reader's attention and illustrate some of the different scales on which budding oceanographers are required to think. Having taught a core graduate course in biological oceanography for many years, Charlie Miller has used his lecture notes as the genesis for this book. The text covers the subject of biological oceanography in a manner that is targeted to introductory graduate students, but it would also be appropriate for advanced undergraduates.

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

EPA Science Inventory

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

Cell Biology and Microbiology: A Continuous Cross-Feeding.

PubMed

Pizarro-Cerdá, Javier; Cossart, Pascale

2016-07-01

Microbiology and cell biology both involve the study of cells, albeit at different levels of complexity and scale. Interactions between both fields during the past 25 years have led to major conceptual and technological advances that have reshaped the whole biology landscape and its biomedical applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Teaching information literacy skills to sophomore-level biology majors.

PubMed

Thompson, Leigh; Blankinship, Lisa Ann

2015-05-01

Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university's databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner.

Teaching Information Literacy Skills to Sophomore-Level Biology Majors

PubMed Central

Thompson, Leigh; Blankinship, Lisa Ann

2015-01-01

Many undergraduate students lack a sound understanding of information literacy. The skills that comprise information literacy are particularly important when combined with scientific writing for biology majors as they are the foundation skills necessary to complete upper-division biology course assignments, better train students for research projects, and prepare students for graduate and professional education. To help undergraduate biology students develop and practice information literacy and scientific writing skills, a series of three one-hour hands-on library sessions, discussions, and homework assignments were developed for Biological Literature, a one-credit, one-hour-per-week, required sophomore-level course. The embedded course librarian developed a learning exercise that reviewed how to conduct database and web searches, the difference between primary and secondary sources, source credibility, and how to access articles through the university’s databases. Students used the skills gained in the library training sessions for later writing assignments including a formal lab report and annotated bibliography. By focusing on improving information literacy skills as well as providing practice in scientific writing, Biological Literature students are better able to meet the rigors of upper-division biology courses and communicate research findings in a more professional manner. PMID:25949754

Clinical and Biological Predictors of Plasma Levels of Soluble RAGE in Critically Ill Patients: Secondary Analysis of a Prospective Multicenter Observational Study

PubMed Central

Pranal, Thibaut; Pereira, Bruno; Berthelin, Pauline; Roszyk, Laurence; Chabanne, Russell; Eisenmann, Nathanael; Lautrette, Alexandre; Belville, Corinne; Blondonnet, Raiko; Gillart, Thierry; Skrzypczak, Yvan; Souweine, Bertrand; Bouvier, Damien; Constantin, Jean-Michel

2018-01-01

Rationale Although soluble forms of the receptor for advanced glycation end products (RAGE) have been recently proposed as biomarkers in multiple acute or chronic diseases, few studies evaluated the influence of usual clinical and biological parameters, or of patient characteristics and comorbidities, on circulating levels of soluble RAGE in the intensive care unit (ICU) setting. Objectives To determine, among clinical and biological parameters that are usually recorded upon ICU admission, which variables, if any, could be associated with plasma levels of soluble RAGE. Methods Data for this ancillary study were prospectively obtained from adult patients with at least one ARDS risk factor upon ICU admission enrolled in a large multicenter observational study. At ICU admission, plasma levels of total soluble RAGE (sRAGE) and endogenous secretory (es)RAGE were measured by duplicate ELISA and baseline patient characteristics, comorbidities, and usual clinical and biological indices were recorded. After univariate analyses, significant variables were used in multivariate, multidimensional analyses. Measurements and Main Results 294 patients were included in this ancillary study, among whom 62% were admitted for medical reasons, including septic shock (11%), coma (11%), and pneumonia (6%). Although some variables were associated with plasma levels of RAGE soluble forms in univariate analysis, multidimensional analyses showed no significant association between admission parameters and baseline plasma sRAGE or esRAGE. Conclusions We found no obvious association between circulating levels of soluble RAGE and clinical and biological indices that are usually recorded upon ICU admission. This trial is registered with NCT02070536. PMID:29861796

Biological Features of the Soil: Advanced Crop and Soil Science. A Course of Study.

ERIC Educational Resources Information Center

Miller, Larry E.

The course of study represents the third of six modules in advanced crop and soil science and introduces the agriculture student to biological features of soil. Upon completing the two day lesson, the student will: (1) realize the vast amount of life present in the soil, (2) be able to list representative animal and plant life in the soil by size,…

Biological Terrorism: US Policies to Reduce Global Biothreats

DTIC Science & Technology

2008-09-01

program for pro- jects that advance BEP objectives. Global Cooperation to develop bio- safety and pathogen security stan- dards that are consistent with...security. The Organization for Economic Cooperation and Development ( OECD ) has recently developed voluntary biosecurity guidelines for implementation...Abbreviations AG Australia Group BEP Biosecurity Engagement Program BSL Biosafety level BWC Biological Weapons Convention BWC-ISU Biological Weapons

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

PubMed Central

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

2014-01-01

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

Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of heterogeneous Fenton oxidation and biological process.

PubMed

Xu, Peng; Han, Hongjun; Zhuang, Haifeng; Hou, Baolin; Jia, Shengyong; Xu, Chunyan; Wang, Dexin

2015-04-01

Laboratorial scale experiments were conducted in order to investigate a novel system integrating heterogeneous Fenton oxidation (HFO) with anoxic moving bed biofilm reactor (ANMBBR) and biological aerated filter (BAF) process on advanced treatment of biologically pretreated coal gasification wastewater (CGW). The results indicated that HFO with the prepared catalyst (FeOx/SBAC, sewage sludge based activated carbon (SBAC) which loaded Fe oxides) played a key role in eliminating COD and COLOR as well as in improving the biodegradability of raw wastewater. The surface reaction and hydroxyl radicals (OH) oxidation were the mechanisms for FeOx/SBAC catalytic reaction. Compared with ANMBBR-BAF process, the integrated system was more effective in abating COD, BOD5, total phenols (TPs), total nitrogen (TN) and COLOR and could shorten the retention time. Therefore, the integrated system was a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Oral Histories of Six African American Males in Their Ecology of Advanced Placement Biology

ERIC Educational Resources Information Center

Halasa, Katrina Bassam

2012-01-01

The major purpose of this qualitative study was to examine the past in order to understand the complex phenomenon of students engaging in science (Newman, Ridenour, Newman, & DeMarco, 2003) specifically through the oral histories of six self-identified African American males enrolled in a high school Advanced Placement Biology class and the…

Recent advances in medical device triage technologies for chemical, biological, radiological, and nuclear events.

PubMed

Lansdowne, Krystal; Scully, Christopher G; Galeotti, Loriano; Schwartz, Suzanne; Marcozzi, David; Strauss, David G

2015-06-01

In 2010, the US Food and Drug Administration (Silver Spring, Maryland USA) created the Medical Countermeasures Initiative with the mission of development and promoting medical countermeasures that would be needed to protect the nation from identified, high-priority chemical, biological, radiological, or nuclear (CBRN) threats and emerging infectious diseases. The aim of this review was to promote regulatory science research of medical devices and to analyze how the devices can be employed in different CBRN scenarios. Triage in CBRN scenarios presents unique challenges for first responders because the effects of CBRN agents and the clinical presentations of casualties at each triage stage can vary. The uniqueness of a CBRN event can render standard patient monitoring medical device and conventional triage algorithms ineffective. Despite the challenges, there have been recent advances in CBRN triage technology that include: novel technologies; mobile medical applications ("medical apps") for CBRN disasters; electronic triage tags, such as eTriage; diagnostic field devices, such as the Joint Biological Agent Identification System; and decision support systems, such as the Chemical Hazards Emergency Medical Management Intelligent Syndromes Tool (CHEMM-IST). Further research and medical device validation can help to advance prehospital triage technology for CBRN events.

Just the facts? Introductory undergraduate biology courses focus on low-level cognitive skills.

PubMed

Momsen, Jennifer L; Long, Tammy M; Wyse, Sara A; Ebert-May, Diane

2010-01-01

Introductory biology courses are widely criticized for overemphasizing details and rote memorization of facts. Data to support such claims, however, are surprisingly scarce. We sought to determine whether this claim was evidence-based. To do so we quantified the cognitive level of learning targeted by faculty in introductory-level biology courses. We used Bloom's Taxonomy of Educational Objectives to assign cognitive learning levels to course goals as articulated on syllabi and individual items on high-stakes assessments (i.e., exams and quizzes). Our investigation revealed the following: 1) assessment items overwhelmingly targeted lower cognitive levels, 2) the cognitive level of articulated course goals was not predictive of the cognitive level of assessment items, and 3) there was no influence of course size or institution type on the cognitive levels of assessments. These results support the claim that introductory biology courses emphasize facts more than higher-order thinking.

Recent advances in chromaffin cell biology: summing up the last International Symposium on Chromaffin Cell Biology.

PubMed

Cárdenas, Ana M

2004-01-01

The International Symposium on Chromaffin Cell Biology (ISCCB) brings together a group of approximately 150 scientists from around the world who meet every 2 years to discuss recent advances in our understanding of biogenesis and motion of secretory vesicles, synthesis, storage and release of secreted products (catecholamines, chromogranins, ATP), and mechanisms involving the excitation-secretion coupling, membrane ion channels, intracellular calcium homeostasis and exocytosis. The development of new technologies that allow an accurate measurement of catecholamines, vesicle motion, exocytosis, etc. are also analyzed. The 12th ISCCB, organized by Ricardo Borges, took place on September 20-26, 2003, in La Palma, Canary Islands, Spain. In this article we describe the most recent and significant contributions to the 12th ISCCB.

[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

PubMed

Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.

Low-level radiation: biological interactions, risks, and benefits. A bibliography

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

None

1978-09-01

The bibliography contains 3294 references that were selected from the Department of Energy's data base (EDB). The subjects covered are lower-level radiation effects on man, environmental radiation, and other biological interactions of radiation that appear to be applicable to the low-level radiation problem.

Quantum biology of the retina.

PubMed

Sia, Paul Ikgan; Luiten, André N; Stace, Thomas M; Wood, John Pm; Casson, Robert J

2014-08-01

The emerging field of quantum biology has led to a greater understanding of biological processes at the microscopic level. There is recent evidence to suggest that non-trivial quantum features such as entanglement, tunnelling and coherence have evolved in living systems. These quantum features are particularly evident in supersensitive light-harvesting systems such as in photosynthesis and photoreceptors. A biomimetic strategy utilizing biological quantum phenomena might allow new advances in the field of quantum engineering, particularly in quantum information systems. In addition, a better understanding of quantum biological features may lead to novel medical diagnostic and therapeutic developments. In the present review, we discuss the role of quantum physics in biological systems with an emphasis on the retina. © 2014 Royal Australian and New Zealand College of Ophthalmologists.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

PubMed

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

ERIC Educational Resources Information Center

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest…

Cyanobacterial Metabolite Calothrixins: Recent Advances in Synthesis and Biological Evaluation

PubMed Central

Xu, Su; Nijampatnam, Bhavitavya; Dutta, Shilpa; Velu, Sadanandan E.

2016-01-01

The marine environment is host to unparalleled biological and chemical diversity, making it an attractive resource for the discovery of new therapeutics for a plethora of diseases. Compounds that are extracted from cyanobacteria are of special interest due to their unique structural scaffolds and capacity to produce potent pharmaceutical and biotechnological traits. Calothrixins A and B are two cyanobacterial metabolites with a structural assembly of quinoline, quinone, and indole pharmacophores. This review surveys recent advances in the synthesis and evaluation of the biological activities of calothrixins. Due to the low isolation yields from the marine source and the promise this scaffold holds for anticancer and antimicrobial drugs, organic and medicinal chemists around the world have embarked on developing efficient synthetic routes to produce calothrixins. Since the first review appeared in 2009, 11 novel syntheses of calothrixins have been published in the efforts to develop methods that contain fewer steps and higher-yielding reactions. Calothrixins have shown their potential as topoisomerase I poisons for their cytotoxicity in cancer. They have also been observed to target various aspects of RNA synthesis in bacteria. Further investigation into the exact mechanism for their bioactivity is still required for many of its analogs. PMID:26771620

Issue-Oriented Science: Using Socioscientific Issues to Engage Biology Students

ERIC Educational Resources Information Center

Lenz, Laura; Willcox, Maia K.

2012-01-01

In today's global society, with science and technology advancing at a rapid pace, issues about biological topics are common. A typical standards-based high school or general college-level biology classroom naturally lends itself to teaching issue-oriented science. In an issue-oriented classroom, students analyze and discuss personal, societal, and…

Just the Facts? Introductory Undergraduate Biology Courses Focus on Low-Level Cognitive Skills

ERIC Educational Resources Information Center

Momsen, Jennifer L.; Long, Tammy M.; Wyse, Sara A.; Ebert-May, Diane

2010-01-01

Introductory biology courses are widely criticized for overemphasizing details and rote memorization of facts. Data to support such claims, however, are surprisingly scarce. We sought to determine whether this claim was evidence-based. To do so we quantified the cognitive level of learning targeted by faculty in introductory-level biology courses.…

Biological materials by design.

PubMed

Qin, Zhao; Dimas, Leon; Adler, David; Bratzel, Graham; Buehler, Markus J

2014-02-19

In this topical review we discuss recent advances in the use of physical insight into the way biological materials function, to design novel engineered materials 'from scratch', or from the level of fundamental building blocks upwards and by using computational multiscale methods that link chemistry to material function. We present studies that connect advances in multiscale hierarchical material structuring with material synthesis and testing, review case studies of wood and other biological materials, and illustrate how engineered fiber composites and bulk materials are designed, modeled, and then synthesized and tested experimentally. The integration of experiment and simulation in multiscale design opens new avenues to explore the physics of materials from a fundamental perspective, and using complementary strengths from models and empirical techniques. Recent developments in this field illustrate a new paradigm by which complex material functionality is achieved through hierarchical structuring in spite of simple material constituents.

Growing trend of CE at the omics level: the frontier of systems biology--an update.

PubMed

Ban, Eunmi; Park, Soo Hyun; Kang, Min-Jung; Lee, Hyun-Jung; Song, Eun Joo; Yoo, Young Sook

2012-01-01

Omics is the study of proteins, peptides, genes, and metabolites in living organisms. Systems biology aims to understand the system through the study of the relationship between elements such as genes and proteins in biological system. Recently, systems biology emerged as the result of the advanced development of high-throughput analysis technologies such as DNA sequencers, DNA arrays, and mass spectrometry for omics studies. Among a number of analytical tools and technologies, CE and CE coupled to MS are promising and relatively rapidly developing tools with the potential to provide qualitative and quantitative analyses of biological molecules. With an emphasis on CE for systems biology, this review summarizes the method developments and applications of CE for the genomic, transcriptomic, proteomic, and metabolomic studies focusing on the drug discovery and disease diagnosis and therapies since 2009. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advancing Small Satellite Electronics Heritage for Microfluidic Biological Experiments

NASA Technical Reports Server (NTRS)

White, Bruce; Mazmanian, Edward; Tapio, Eric

2016-01-01

DLR's Eu:CROPIS (Euglena and Combined Regenerative Organic-Food Production in Space) mission, launching in 2017, will carry multiple biological payloads into a sun-synchronous orbit, including NASA Ames' PowerCell experiment. PowerCell will attempt to characterize the viability of synthetic biology at micro-g, Lunar, and Martian gravity levels. PowerCell experiment requirements demand an electronic system similar to previous microfluidic biology payloads, but with an expanded feature set. As such, the system was based on PharmaSat (Diaz-Aguado et al. 2009), a previous successful biology payload from NASA Ames, and improved upon. Newer, more miniaturized electronics allow for greater capability with a lower part count and smaller size. Two identical PowerCell enclosures will fly. Each enclosure contains two separate and identical experiments with a 48-segment optical density measurement system, grow light system, microfluidic system for nutrient delivery and waste flushing, plus thermal control and environmental sensing/housekeeping including temperature, pressure, humidity, and acceleration. Electronics consist of a single Master PCB that interfaces to the spacecraft bus and regulates power and communication, plus LED, Detector, and Valve Manifold PCBs for each experiment. To facilitate ease of reuse on future missions, experiment electronics were designed to be compatible with a standard 3U small sat form factor and power bus, or to interface with a Master power/comm PCB for use in a larger satellite as in the case of PowerCell's flight on Eu:CROPIS.

A three-level advanced static VAr compensator

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

Ekanayake, J.B.; Jenkins, N.

1996-01-01

An Advanced Static VAr Compensator (ASVC) employing a three level inverter has been investigated for three phase applications. The paper describes the operating principles of the ASVC using an elementary single phase ASVC circuit. The construction of a hardware model of the three phase, three level ASVC is then presented. The performance of the ASVC is obtained from an experimental study carried out on this laboratory model. The use of the selective harmonic elimination modulation (SHEM) technique to minimize harmonics is explored. Experimental studies have been carried out to determine the speed of response of the scheme by controlling itmore » in a closed loop.« less

Mechanisms Underpinning Increased Plasma Creatinine Levels in Patients Receiving Vemurafenib for Advanced Melanoma

PubMed Central

Hurabielle, Charlotte; Pillebout, Evangéline; Stehlé, Thomas; Pagès, Cécile; Roux, Jennifer; Schneider, Pierre; Chevret, Sylvie; Chaffaut, Cendrine; Boutten, Anne; Mourah, Samia; Basset-Seguin, Nicole; Vidal-Petiot, Emmanuelle; Lebbé, Céleste; Flamant, Martin

2016-01-01

Context Serum creatinine has been reported to increase in patients receiving Vemurafenib, yet neither the prevalence nor the mechanism of this adverse event are known. Objective We aimed to evaluate the frequency and the mechanisms of increases in plasma creatinine level in patients receiving Vemurafenib for advanced melanoma. Methods We performed a retrospective monocentric study including consecutive patients treated with Vemurafenib for an advanced melanoma. We collected clinical and biological data concerning renal function before introduction of Vemurafenib and in the course of monthly follow-up visits from March 2013 to December 2014. Cystatin C-derived glomerular filtration rate was evaluated before and after Vemurafenib initiation, as increase in serum cystatin C is specific to a decrease in the glomerular filtration rate. We also performed thorough renal explorations in 3 patients, with measurement of tubular secretion of creatinine before and after Vemurafenib initiation and a renal biopsy in 2 patients. Results 70 patients were included: 97% of them displayed an immediate, and thereafter stable, increase in creatinine (+22.8%) after Vemurafenib initiation. In 44/52 patients in whom Vemurafenib was discontinued, creatinine levels returned to baseline. Serum cystatin C increased, although proportionally less than serum creatinine, showing that creatinine increase under vemurafenib was indeed partly due to a renal function impairment. In addition, renal explorations demonstrated that Vemurafenib induced an inhibition of creatinine tubular secretion. Conclusion Thus, Vemurafenib induces a dual mechanism of increase in plasma creatinine with both an inhibition of creatinine tubular secretion and slight renal function impairment. However, this side effect is mostly reversible when Vemurafenib is discontinued, and should not lead physicians to discontinue the treatment if it is effective. PMID:26930506

Mechanisms Underpinning Increased Plasma Creatinine Levels in Patients Receiving Vemurafenib for Advanced Melanoma.

PubMed

Hurabielle, Charlotte; Pillebout, Evangéline; Stehlé, Thomas; Pagès, Cécile; Roux, Jennifer; Schneider, Pierre; Chevret, Sylvie; Chaffaut, Cendrine; Boutten, Anne; Mourah, Samia; Basset-Seguin, Nicole; Vidal-Petiot, Emmanuelle; Lebbé, Céleste; Flamant, Martin

2016-01-01

Serum creatinine has been reported to increase in patients receiving Vemurafenib, yet neither the prevalence nor the mechanism of this adverse event are known. We aimed to evaluate the frequency and the mechanisms of increases in plasma creatinine level in patients receiving Vemurafenib for advanced melanoma. We performed a retrospective monocentric study including consecutive patients treated with Vemurafenib for an advanced melanoma. We collected clinical and biological data concerning renal function before introduction of Vemurafenib and in the course of monthly follow-up visits from March 2013 to December 2014. Cystatin C-derived glomerular filtration rate was evaluated before and after Vemurafenib initiation, as increase in serum cystatin C is specific to a decrease in the glomerular filtration rate. We also performed thorough renal explorations in 3 patients, with measurement of tubular secretion of creatinine before and after Vemurafenib initiation and a renal biopsy in 2 patients. 70 patients were included: 97% of them displayed an immediate, and thereafter stable, increase in creatinine (+22.8%) after Vemurafenib initiation. In 44/52 patients in whom Vemurafenib was discontinued, creatinine levels returned to baseline. Serum cystatin C increased, although proportionally less than serum creatinine, showing that creatinine increase under vemurafenib was indeed partly due to a renal function impairment. In addition, renal explorations demonstrated that Vemurafenib induced an inhibition of creatinine tubular secretion. Thus, Vemurafenib induces a dual mechanism of increase in plasma creatinine with both an inhibition of creatinine tubular secretion and slight renal function impairment. However, this side effect is mostly reversible when Vemurafenib is discontinued, and should not lead physicians to discontinue the treatment if it is effective.

Understanding Biological Regulation Through Synthetic Biology.

PubMed

Bashor, Caleb J; Collins, James J

2018-05-20

Engineering synthetic gene regulatory circuits proceeds through iterative cycles of design, building, and testing. Initial circuit designs must rely on often-incomplete models of regulation established by fields of reductive inquiry-biochemistry and molecular and systems biology. As differences in designed and experimentally observed circuit behavior are inevitably encountered, investigated, and resolved, each turn of the engineering cycle can force a resynthesis in understanding of natural network function. Here, we outline research that uses the process of gene circuit engineering to advance biological discovery. Synthetic gene circuit engineering research has not only refined our understanding of cellular regulation but furnished biologists with a toolkit that can be directed at natural systems to exact precision manipulation of network structure. As we discuss, using circuit engineering to predictively reorganize, rewire, and reconstruct cellular regulation serves as the ultimate means of testing and understanding how cellular phenotype emerges from systems-level network function.

Advancing the Science of Community-Level Interventions

PubMed Central

Beehler, Sarah; Deutsch, Charles; Green, Lawrence W.; Hawe, Penelope; McLeroy, Kenneth; Miller, Robin Lin; Rapkin, Bruce D.; Schensul, Jean J.; Schulz, Amy J.; Trimble, Joseph E.

2011-01-01

Community interventions are complex social processes that need to move beyond single interventions and outcomes at individual levels of short-term change. A scientific paradigm is emerging that supports collaborative, multilevel, culturally situated community interventions aimed at creating sustainable community-level impact. This paradigm is rooted in a deep history of ecological and collaborative thinking across public health, psychology, anthropology, and other fields of social science. The new paradigm makes a number of primary assertions that affect conceptualization of health issues, intervention design, and intervention evaluation. To elaborate the paradigm and advance the science of community intervention, we offer suggestions for promoting a scientific agenda, developing collaborations among professionals and communities, and examining the culture of science. PMID:21680923

Biological/Genetic Regulation of Physical Activity Level: Consensus from GenBioPAC.

PubMed

Lightfoot, J Timothy; DE Geus, Eco J C; Booth, Frank W; Bray, Molly S; DEN Hoed, Marcel; Kaprio, Jaakko; Kelly, Scott A; Pomp, Daniel; Saul, Michael C; Thomis, Martine A; Garland, Theodore; Bouchard, Claude

2018-04-01

Physical activity unquestionably maintains and improves health; however, physical activity levels globally are low and not rising despite all the resources devoted to this goal. Attention in both the research literature and the public policy domain has focused on social-behavioral factors; however, a growing body of literature suggests that biological determinants play a significant role in regulating physical activity levels. For instance, physical activity level, measured in various manners, has a genetic component in both humans and nonhuman animal models. This consensus article, developed as a result of an American College of Sports Medicine-sponsored round table, provides a brief review of the theoretical concepts and existing literature that supports a significant role of genetic and other biological factors in the regulation of physical activity. Future research on physical activity regulation should incorporate genetics and other biological determinants of physical activity instead of a sole reliance on social and other environmental determinants.

Energy utilization in fluctuating biological energy converters

PubMed Central

Szőke, Abraham; Hajdu, Janos

2016-01-01

We have argued previously [Szoke et al., FEBS Lett. 553, 18–20 (2003); Curr. Chem. Biol. 1, 53–57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systems fluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems. PMID:27191009

Some ozone advanced oxidation processes to improve the biological removal of selected pharmaceutical contaminants from urban wastewater.

PubMed

Espejo, Azahara; Aguinaco, Almudena; Amat, Ana M; Beltrán, Fernando J

2014-01-01

Removal of nine pharmaceutical compounds--acetaminophen (AAF), antipyrine (ANT), caffeine (CAF), carbamazepine (CRB), diclofenac (DCF), hydrochlorothiazide (HCT), ketorolac (KET), metoprolol (MET) and sulfamethoxazole (SMX)-spiked in a primary sedimentation effluent of a municipal wastewater has been studied with sequential aerobic biological and ozone advanced oxidation systems. Combinations of ozone, UVA black light and Fe(III) or Fe3O4 constituted the chemical systems. During the biological treatment (hydraulic residence time, HRT = 24 h), only AAF and CAF were completely eliminated, MET, SMX and HCT reached partial removal rates and the rest of compounds were completely refractory. With any ozone advanced oxidation process applied, the remaining pharmaceuticals disappear in less than 10 min. Fe3O4 or Fe(III) photocatalytic ozonation leads to 35% mineralization compared to 13% reached during ozonation alone after about 30-min reaction. Also, biodegradability of the treated wastewater increased 50% in the biological process plus another 150% after the ozonation processes. Both untreated and treated wastewater was non-toxic for Daphnia magna (D. magna) except when Fe(III) was used in photocatalytic ozonation. In this case, toxicity was likely due to the ferryoxalate formed in the process. Kinetic information on ozone processes reveals that pharmaceuticals at concentrations they have in urban wastewater are mainly removed through free radical oxidation.

Retention of Preservative Levels of Formaldehyde in Desiccated Biological Products

PubMed Central

Pemberton, John R.

1975-01-01

Concentrations ranging from 8 to 100% of the preservative level of formalin (37% formaldehyde solution) were retained by desiccated biologics, with most products retaining about 50% regardless of the amount originally present. PMID:972183

Who Studies Religion at Advanced Level: Why and to What Effect?

ERIC Educational Resources Information Center

Francis, Leslie J.; Astley, Jeff; Parker, Stephen G.

2016-01-01

This study was established to profile students currently studying religion at Advanced level (A level) in terms of their demography, motivation, experience and attitudes. Eight specific areas were identified for examination: their personal motivation to study religion at A level, the personal challenges posed by the subject, their personal…

Proteomic insights into floral biology.

PubMed

Li, Xiaobai; Jackson, Aaron; Xie, Ming; Wu, Dianxing; Tsai, Wen-Chieh; Zhang, Sheng

2016-08-01

The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. Copyright © 2016 Elsevier B.V. All rights reserved.

Systems Biology Analysis of Heterocellular Signaling.

PubMed

Tape, Christopher J

2016-08-01

Tissues comprise multiple heterotypic cell types (e.g., epithelial, mesenchymal, and immune cells). Communication between heterotypic cell types is essential for biological cohesion and is frequently dysregulated in disease. Despite the importance of heterocellular communication, most systems biology techniques do not report cell-specific signaling data from mixtures of cells. As a result, our existing perspective of cellular behavior under-represents the influence of heterocellular signaling. Recent technical advances now permit the resolution of systems-level cell-specific signaling data. This review discusses how new physical, spatial, and isotopic resolving methods are facilitating unique systems biology studies of heterocellular communication. Copyright © 2016 Elsevier Ltd. All rights reserved.

Advances in enhanced biological phosphorus removal: from micro to macro scale.

PubMed

Oehmen, Adrian; Lemos, Paulo C; Carvalho, Gilda; Yuan, Zhiguo; Keller, Jürg; Blackall, Linda L; Reis, Maria A M

2007-06-01

The enhanced biological phosphorus removal (EBPR) process has been implemented in many wastewater treatment plants worldwide. While the EBPR process is indeed capable of efficient phosphorus (P) removal performance, disturbances and prolonged periods of insufficient P removal have been observed at full-scale plants on numerous occasions under conditions that are seemingly favourable for EBPR. Recent studies in this field have utilised a wide range of approaches to address this problem, from studying the microorganisms that are primarily responsible for or detrimental to this process, to determining their biochemical pathways and developing mathematical models that facilitate better prediction of process performance. The overall goal of each of these studies is to obtain a more detailed insight into how the EBPR process works, where the best way of achieving this objective is through linking together the information obtained using these different approaches. This review paper critically assesses the recent advances that have been achieved in this field, particularly relating to the areas of EBPR microbiology, biochemistry, process operation and process modelling. Potential areas for future research are also proposed. Although previous research in this field has undoubtedly improved our level of understanding, it is clear that much remains to be learned about the process, as many unanswered questions still remain. One of the challenges appears to be the integration of the existing and growing scientific knowledge base with the observations and applications in practice, which this paper hopes to partially achieve.

Advances in Wilms Tumor Treatment and Biology: Progress Through International Collaboration.

PubMed

Dome, Jeffrey S; Graf, Norbert; Geller, James I; Fernandez, Conrad V; Mullen, Elizabeth A; Spreafico, Filippo; Van den Heuvel-Eibrink, Marry; Pritchard-Jones, Kathy

2015-09-20

Clinical trials in Wilms tumor (WT) have resulted in overall survival rates of greater than 90%. This achievement is especially remarkable because improvements in disease-specific survival have occurred concurrently with a reduction of therapy for large patient subgroups. However, the outcomes for certain patient subgroups, including those with unfavorable histologic and molecular features, bilateral disease, and recurrent disease, remain well below the benchmark survival rate of 90%. Therapy for WT has been advanced in part by an increasingly complex risk-stratification system based on patient age; tumor stage, histology, and volume; response to chemotherapy; and loss of heterozygosity at chromosomes 1p and 16q. A consequence of this system has been the apportionment of patients into such small subgroups that only collaboration between large international WT study groups will support clinical trials that are sufficiently powered to answer challenging questions that move the field forward. This article gives an overview of the Children's Oncology Group and International Society of Pediatric Oncology approaches to WT and focuses on four subgroups (stage IV, initially inoperable, bilateral, and relapsed WT) for which international collaboration is pressing. In addition, biologic insights resulting from collaborative laboratory research are discussed. A coordinated expansion of international collaboration in both clinical trials and laboratory science will provide real opportunity to improve the treatment and outcomes for children with renal tumors on a global level. © 2015 by American Society of Clinical Oncology.

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

PubMed

Rüdt, Matthias; Briskot, Till; Hubbuch, Jürgen

2017-03-24

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

Recent advances and industrial viewpoint for biological treatment of wastewaters by oleaginous microorganisms.

PubMed

Huang, Chao; Luo, Mu-Tan; Chen, Xue-Fang; Xiong, Lian; Li, Xiao-Mei; Chen, Xin-De

2017-05-01

Recently, technology of using oleaginous microorganisms for biological treatment of wastewaters has become one hot topic in biochemical and environmental engineering for its advantages such as easy for operation in basic bioreactor, having potential to produce valuable bio-products, efficient wastewaters treatment in short period, etc. To promote its industrialization, this article provides some comprehensive analysis of this technology such as its advances, issues, and outlook especially from industrial viewpoint. In detail, the types of wastewaters can be treated and the kinds of oleaginous microorganisms used for biological treatment are introduced, the potential of industrial application and issues (relatively low COD removal, low lipid yield, cost of operation, and lack of scale up application) of this technology are presented, and some critical outlook mainly on co-culture method, combination with other treatments, process controlling and adjusting are discussed systematically. By this article, some important information to develop this technology can be obtained. Copyright © 2017 Elsevier Ltd. All rights reserved.

Controversial Issues and the Teaching of A-Level Biology: Possibilities and Problems.

ERIC Educational Resources Information Center

Van Rooy, Wilhelmina

This thesis focuses on the espoused beliefs, values, and attitudes of experienced A-Level Biology teachers in relation to the teaching of controversial biological issues. Of major interest is the thinking behind what the teachers in this study regard as the possibilities and problems for the teaching of controversial issues given the teaching…

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

PubMed Central

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

2016-01-01

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

Apoptosis: a four-week laboratory investigation for advanced molecular and cellular biology students.

PubMed

DiBartolomeis, Susan M; Moné, James P

2003-01-01

Over the past decade, apoptosis has emerged as an important field of study central to ongoing research in many diverse fields, from developmental biology to cancer research. Apoptosis proceeds by a highly coordinated series of events that includes enzyme activation, DNA fragmentation, and alterations in plasma membrane permeability. The detection of each of these phenotypic changes is accessible to advanced undergraduate cell and molecular biology students. We describe a 4-week laboratory sequence that integrates cell culture, fluorescence microscopy, DNA isolation and analysis, and western blotting (immunoblotting) to follow apoptosis in cultured human cells. Students working in teams chemically induce apoptosis, and harvest, process, and analyze cells, using their data to determine the order of events during apoptosis. We, as instructors, expose the students to an environment closely simulating what they would encounter in an active cell or molecular biology research laboratory by having students coordinate and perform multiple tasks simultaneously and by having them experience experimental design using current literature, data interpretation, and analysis to answer a single question. Students are assessed by examination of laboratory notebooks for completeness of experimental protocols and analysis of results and for completion of an assignment that includes questions pertaining to data interpretation and apoptosis.

Synthetic biology: insights into biological computation.

PubMed

Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

2016-04-18

Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

Biological Networks for Cancer Candidate Biomarkers Discovery

PubMed Central

Yan, Wenying; Xue, Wenjin; Chen, Jiajia; Hu, Guang

2016-01-01

Due to its extraordinary heterogeneity and complexity, cancer is often proposed as a model case of a systems biology disease or network disease. There is a critical need of effective biomarkers for cancer diagnosis and/or outcome prediction from system level analyses. Methods based on integrating omics data into networks have the potential to revolutionize the identification of cancer biomarkers. Deciphering the biological networks underlying cancer is undoubtedly important for understanding the molecular mechanisms of the disease and identifying effective biomarkers. In this review, the networks constructed for cancer biomarker discovery based on different omics level data are described and illustrated from recent advances in the field. PMID:27625573

Recent advances and future directions in the management of knee osteoarthritis: Can biological joint reconstruction replace joint arthroplasty and when?

PubMed Central

Paschos, Nikolaos K

2015-01-01

In this article, a concise description of the recent advances in the field of osteoarthritis management is presented. The main focus is to highlight the most promising techniques that emerge in both biological joint replacement and artificial joint arthroplasty. A critical view of high quality evidence regarding outcome and safety profile of these techniques is presented. The potential role of kinematically aligned total knee replacement, navigation, and robotic-assisted surgery is outlined. A critical description of both primary and stem cell-based therapies, the cell homing theory, the use of biologic factors and recent advancements in tissue engineering and regenerative medicine is provided. Based on the current evidence, some thoughts on a realistic approach towards answering these questions are attempted. PMID:26495242

Sequential ozone advanced oxidation and biological oxidation processes to remove selected pharmaceutical contaminants from an urban wastewater.

PubMed

Espejo, Azahara; Aguinaco, Almudena; García-Araya, J F; Beltrán, Fernando J

2014-01-01

Sequential treatments consisting in a chemical process followed by a conventional biological treatment, have been applied to remove mixtures of nine contaminants of pharmaceutical type spiked in a primary sedimentation effluent of a municipal wastewater. Combinations of ozone, UVA black light (BL) and Fe(III) or Fe₃O₄ catalysts constituted the chemical systems. Regardless of the Advanced Oxidation Process (AOP), the removal of pharmaceutical compounds was achieved in 1 h of reaction, while total organic carbon (TOC) only diminished between 3.4 and 6%. Among selected ozonation systems to be implemented before the biological treatment, the application of ozone alone in the pre-treatment stage is recommended due to the increase of the biodegradability observed. The application of ozone followed by the conventional biological treatment leads high TOC and COD removal rates, 60 and 61%, respectively, and allows the subsequent biological treatment works with shorter hydraulic residence time (HRT). Moreover, the influence of the application of AOPs before and after a conventional biological process was compared, concluding that the decision to take depends on the characterization of the initial wastewater with pharmaceutical compounds.

Recent advances in understanding the biology of marginal zone lymphoma

PubMed Central

Zucca, Emanuele

2018-01-01

There are three different marginal zone lymphomas (MZLs): the extranodal MZL of mucosa-associated lymphoid tissue (MALT) type (MALT lymphoma), the splenic MZL, and the nodal MZL. The three MZLs share common lesions and deregulated pathways but also present specific alterations that can be used for their differential diagnosis. Although trisomies of chromosomes 3 and 18, deletions at 6q23, deregulation of nuclear factor kappa B, and chromatin remodeling genes are frequent events in all of them, the three MZLs differ in the presence of recurrent translocations, mutations affecting the NOTCH pathway, and the transcription factor Kruppel like factor 2 ( KLF2) or the receptor-type protein tyrosine phosphatase delta ( PTPRD). Since a better understanding of the molecular events underlying each subtype may have practical relevance, this review summarizes the most recent and main advances in our understanding of the genetics and biology of MZLs. PMID:29657712

Advanced Rotating Biological Surface Operation. Training Module 2.122.4.77.

ERIC Educational Resources Information Center

Paulson, W. L.

This document is an instructional module package prepared in objective form for use by an instructor familiar with operation and maintenance of a rotating biological surface (RBS) wastewater treatment system. Included are objectives, instructor guides, student handouts, and transparency masters. This is the third level of a three module series and…

Report of the matrix of biological knowledge workshop

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

Morowitz, H.J.; Smith, T.

1987-10-30

Current understanding of biology involves complex relationships rooted in enormous amounts of data. These data include entries from biochemistry, ecology, genetics, human and veterinary medicine, molecular structure studies, agriculture, embryology, systematics, and many other disciplines. The present wealth of biological data goes beyond past accumulations now include new understandings from molecular biology. Several important biological databases are currently being supported, and more are planned; however, major problems of interdatabase communication and management efficiency abound. Few scientists are currently capable of keeping up with this ever-increasing wealth of knowledge, let alone searching it efficiently for new or unsuspected links and importantmore » analogies. Yet this is what is required if the continued rapid generation of such data is to lead most effectively to the major conceptual, medical, and agricultural advances anticipated over the coming decades in the United States. The opportunity exists to combine the potential of modern computer science, database management, and artificial intelligence in a major effort to organize the vast wealth of biological and clinical data. The time is right because the amount of data is still manageable even in its current highly-fragmented form; important hardware and computer science tools have been greatly improved; and there have been recent fundamental advances in our comprehension of biology. This latter is particularly true at the molecular level where the information for nearly all higher structure and function is encoded. The organization of all biological experimental data coordinately within a structure incorporating our current understanding - the Matrix of Biological Knowledge - will provide the data and structure for the major advances foreseen in the years ahead.« less

Hologenomics: Systems-Level Host Biology.

PubMed

Theis, Kevin R

2018-01-01

The hologenome concept of evolution is a hypothesis explaining host evolution in the context of the host microbiomes. As a hypothesis, it needs to be evaluated, especially with respect to the extent of fidelity of transgenerational coassociation of host and microbial lineages and the relative fitness consequences of repeated associations within natural holobiont populations. Behavioral ecologists are in a prime position to test these predictions because they typically focus on animal phenotypes that are quantifiable, conduct studies over multiple generations within natural animal populations, and collect metadata on genetic relatedness and relative reproductive success within these populations. Regardless of the conclusion on the hologenome concept as an evolutionary hypothesis, a hologenomic perspective has applied value as a systems-level framework for host biology, including in medicine. Specifically, it emphasizes investigating the multivarious and dynamic interactions between patient genomes and the genomes of their diverse microbiota when attempting to elucidate etiologies of complex, noninfectious diseases.

ESL for Hotel/Hospitality Industry. Level: Advanced Beginner/Intermediate.

ERIC Educational Resources Information Center

Western Suffolk County Board of Cooperative Educational Services, Northport, NY.

This document contains 16 lesson plans for an advanced beginning and intermediate course in work-related English for non-English- or limited-English-speaking entry-level employees in the hotel and hospitality industry. Course objectives are as follows: helping participants understand and use job-specific vocabulary; receive and understand…

Insights into Monascus biology at the genetic level.

PubMed

Shao, Yanchun; Lei, Ming; Mao, Zejing; Zhou, Youxiang; Chen, Fusheng

2014-05-01

The genus of Monascus was nominated by van Tieghem in 1884, but its fermented product-red mold rice (RMR), namely red yeast rice, has been used as folk medicines, food colorants, and fermentation starters for more than thousands of years in oriental countries. Nowadays, RMR is widely developed as food supplements around the world due to its functional compounds such as monacolin K (MK, also called lovastatin) and γ-aminobutyric acid. But the usage of RMR also incurs controversy resulting from contamination of citrinin (a kind of mycotoxin) produced by some Monascus strains. In the past decade, it has made great progress to Monascus spp. at the genetic level with the application of molecular biology techniques to restrain the citrinin production and increase the yields of MK and pigment in RMR, as well as aid Monascus classification and phylogenesis. Up to now, hundreds of papers about Monascus molecular biology (MMB) have been published in the international primary journals. However, to our knowledge, there is no MMB review issued until now. In this review, current understanding of Monascus spp. from the view of molecular biology will be covered and insights into research areas that need to be further investigated will also be discussed.

Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications.

PubMed

Kang, Zhen; Huang, Hao; Zhang, Yunfeng; Du, Guocheng; Chen, Jian

2017-01-01

Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

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

PubMed

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

2015-09-04

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

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

PubMed

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

2016-08-01

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

Trichoderma-plant-pathogen interactions: advances in genetics of biological control.

PubMed

Mukherjee, Mala; Mukherjee, Prasun K; Horwitz, Benjamin A; Zachow, Christin; Berg, Gabriele; Zeilinger, Susanne

2012-12-01

Trichoderma spp. are widely used in agriculture as biofungicides. Induction of plant defense and mycoparasitism (killing of one fungus by another) are considered to be the most important mechanisms of Trichoderma-mediated biological control. Understanding these mechanisms at the molecular level would help in developing strains with superior biocontrol properties. In this article, we review our current understanding of the genetics of interactions of Trichoderma with plants and plant pathogens.

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

PubMed

Gilad, Assaf A; Shapiro, Mikhail G

2017-06-01

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

Job Satisfaction Levels of Secondary School Physics, Chemistry and Biology Teachers

ERIC Educational Resources Information Center

Maskan, A. Kadir

2014-01-01

The purpose of this study is to determine the job satisfaction levels of the teachers participating in the study and to investigate whether their job satisfaction levels differ with respect to certain variables. The participants of the study were 297 science teachers (physics: 104, chemistry: 105, biology: 87 and 1 N/A) from secondary schools in…

Learning and remembering strategies of novice and advanced jazz dancers for skill level appropriate dance routines.

PubMed

Poon, P P; Rodgers, W M

2000-06-01

This study examined the influence of the challenge level of to-be-learned stimulus on learning strategies in novice and advanced dancers. In Study 1, skill-level appropriate dance routines were developed for novice and advanced jazz dancers. In Study 2, 8 novice and 9 advanced female jazz dancers attempted to learn and remember the two routines in mixed model factorial design, with one between-participants factor: skill level (novice or advanced) and two within-participants factors: routine (easy or difficult) and performance (immediate or delayed). Participants were interviewed regarding the strategies used to learn and remember the routines. Results indicated that advanced performers used atypical learning strategies for insufficiently challenging stimuli, which may reflect characteristics of the stimuli rather than the performer. The qualitative data indicate a clear preference of novice and advanced performers for spatial compatibility of stimuli and response.

A review of soft-tissue sarcomas: translation of biological advances into treatment measures

PubMed Central

Mann, Michael J; Tolani, Bhairavi

2018-01-01

Soft-tissue sarcomas are rare malignant tumors arising from connective tissues and have an overall incidence of about five per 100,000 per year. While this diverse family of malignancies comprises over 100 histological subtypes and many molecular aberrations are prevalent within specific sarcomas, very few are therapeutically targeted. Instead of utilizing molecular signatures, first-line sarcoma treatment options are still limited to traditional surgery and chemotherapy, and many of the latter remain largely ineffective and are plagued by disease resistance. Currently, the mechanism of sarcoma oncogenesis remains largely unknown, thus necessitating a better understanding of pathogenesis. Although substantial progress has not occurred with molecularly targeted therapies over the past 30 years, increased knowledge about sarcoma biology could lead to new and more effective treatment strategies to move the field forward. Here, we discuss biological advances in the core molecular determinants in some of the most common soft-tissue sarcomas – liposarcoma, angiosarcoma, leiomyosarcoma, rhabdomyosarcoma, Ewing’s sarcoma, and synovial sarcoma – with an emphasis on emerging genomic and molecular pathway targets and immunotherapeutic treatment strategies to combat this confounding disease. PMID:29785138

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications

PubMed Central

Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner. PMID:28531174

Genome Partitioner: A web tool for multi-level partitioning of large-scale DNA constructs for synthetic biology applications.

PubMed

Christen, Matthias; Del Medico, Luca; Christen, Heinz; Christen, Beat

2017-01-01

Recent advances in lower-cost DNA synthesis techniques have enabled new innovations in the field of synthetic biology. Still, efficient design and higher-order assembly of genome-scale DNA constructs remains a labor-intensive process. Given the complexity, computer assisted design tools that fragment large DNA sequences into fabricable DNA blocks are needed to pave the way towards streamlined assembly of biological systems. Here, we present the Genome Partitioner software implemented as a web-based interface that permits multi-level partitioning of genome-scale DNA designs. Without the need for specialized computing skills, biologists can submit their DNA designs to a fully automated pipeline that generates the optimal retrosynthetic route for higher-order DNA assembly. To test the algorithm, we partitioned a 783 kb Caulobacter crescentus genome design. We validated the partitioning strategy by assembling a 20 kb test segment encompassing a difficult to synthesize DNA sequence. Successful assembly from 1 kb subblocks into the 20 kb segment highlights the effectiveness of the Genome Partitioner for reducing synthesis costs and timelines for higher-order DNA assembly. The Genome Partitioner is broadly applicable to translate DNA designs into ready to order sequences that can be assembled with standardized protocols, thus offering new opportunities to harness the diversity of microbial genomes for synthetic biology applications. The Genome Partitioner web tool can be accessed at https://christenlab.ethz.ch/GenomePartitioner.

The impact of an introductory college-level biology class on biology self-efficacy and attitude towards science

NASA Astrophysics Data System (ADS)

Thomas, Megan Elizabeth

Self-efficacy theory was first introduced in a seminal article by Albert Bandura in 1977 entitled "Self-efficacy: Toward a unifying theory of behavioral change". Since its original introduction, self-efficacy has been a major focus of academic performance, anxiety, career development, and teacher retention research. Self-efficacy can be defined as the belief an individual possesses about their ability to perform a given task. Bandura proposed that self-efficacy should be measured at the highest level of specificity due to the fact that different people are efficacious in different areas. Interested in students' efficacy toward biology, Ebert-May, Baldwin, & Allred (1997) created and validated a survey to measure students' biology self-efficacy. Their survey was modeled after the guidelines for science literacy, and loaded to three sub-factors; methods of biology, generalization to other science courses, and application of the concepts. As self-efficacy theory has been related to effort expenditure and persistence (Bandura, 1977; 1997), one might think it would have some effect on students' attitudes toward the topic at hand. The current research investigated what changes in biology self-efficacy occurred after an introductory biology course with an inquiry based laboratory learning environment. In addition, changes in students' attitudes towards science were explored and how self-efficacy might affect them.

Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock.

PubMed

Tyagi, Rahul; Joachim, Anja; Ruttkowski, Bärbel; Rosa, Bruce A; Martin, John C; Hallsworth-Pepin, Kymberlie; Zhang, Xu; Ozersky, Philip; Wilson, Richard K; Ranganathan, Shoba; Sternberg, Paul W; Gasser, Robin B; Mitreva, Makedonka

2015-11-01

Many infectious diseases caused by eukaryotic pathogens have a devastating, long-term impact on animal health and welfare. Hundreds of millions of animals are affected by parasitic nematodes of the order Strongylida. Unlocking the molecular biology of representatives of this order, and understanding nematode-host interactions, drug resistance and disease using advanced technologies could lead to entirely new ways of controlling the diseases that they cause. Oesophagostomum dentatum (nodule worm; superfamily Strongyloidea) is an economically important strongylid nematode parasite of swine worldwide. The present article reports recent advances made in biology and animal biotechnology through the draft genome and developmental transcriptome of O. dentatum, in order to support biological research of this and related parasitic nematodes as well as the search for new and improved interventions. This first genome of any member of the Strongyloidea is 443 Mb in size and predicted to encode 25,291 protein-coding genes. Here, we review the dynamics of transcription throughout the life cycle of O. dentatum, describe double-stranded RNA interference (RNAi) machinery and infer molecules involved in development and reproduction, and in inducing or modulating immune responses or disease. The secretome predicted for O. dentatum is particularly rich in peptidases linked to interactions with host tissues and/or feeding activity, and a diverse array of molecules likely involved in immune responses. This research progress provides an important resource for future comparative genomic and molecular biological investigations as well as for biotechnological research toward new anthelmintics, vaccines and diagnostic tests. Copyright © 2015 Elsevier Inc. All rights reserved.

Has Modern Biology Entered the Mouth? The Clinical Impact of Biological Research.

ERIC Educational Resources Information Center

Baum, Bruce J.

1991-01-01

Three areas of biological research that are beginning to have an impact on clinical medicine are examined, including molecular biology, cell biology, and biotechnology. It is concluded that oral biologists and educators must work cooperatively to bring rapid biological and biomedical advances into dental training in a meaningful way. (MSE)

Advances in systems biology: computational algorithms and applications.

PubMed

Huang, Yufei; Zhao, Zhongming; Xu, Hua; Shyr, Yu; Zhang, Bing

2012-01-01

The 2012 International Conference on Intelligent Biology and Medicine (ICIBM 2012) was held on April 22-24, 2012 in Nashville, Tennessee, USA. The conference featured six technical sessions, one tutorial session, one workshop, and 3 keynote presentations that covered state-of-the-art research activities in genomics, systems biology, and intelligent computing. In addition to a major emphasis on the next generation sequencing (NGS)-driven informatics, ICIBM 2012 aligned significant interests in systems biology and its applications in medicine. We highlight in this editorial the selected papers from the meeting that address the developments of novel algorithms and applications in systems biology.

Building biological foundries for next-generation synthetic biology.

PubMed

Chao, Ran; Yuan, YongBo; Zhao, HuiMin

2015-07-01

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

How Do Pharmacists Develop into Advanced Level Practitioners? Learning from the Experiences of Critical Care Pharmacists.

PubMed

Seneviratne, Ruth E; Bradbury, Helen; Bourne, Richard S

2017-07-07

The national UK standards for critical care highlight the need for clinical pharmacists to practise at an advanced level (equivalent to Royal Pharmaceutical Society, Great Britain, Faculty Advanced Stage II (MFRPSII)) and above. Currently the UK is unable to meet the workforce capacity requirements set out in the national standards in terms of numbers of pharmacist working at advanced level and above. The aim of this study was to identify the strategies, barriers and challenges to achieving Advanced Level Practice (ALP) by learning from the experiences of advanced level critical care pharmacists within the UK. Eight participants were recruited to complete semi-structured interviews on their views and experiences of ALP. The interviews were analysed thematically and three overarching themes were identified; support, work-based learning and reflective practice. The results of this study highlight that to increase the number of MFRPSII level practitioners within critical care support for their ALP development is required. This support involves developing face-to-face access to expert critical care pharmacists within a national training programme. Additionally, chief pharmacists need to implement drivers including in house mentorship and peer review programmes and the need to align job descriptions and appraisals to the Royal Pharmaceutical Society, Great Britain, Advanced Practice Framework (APF).

How Do Pharmacists Develop into Advanced Level Practitioners? Learning from the Experiences of Critical Care Pharmacists

PubMed Central

Seneviratne, Ruth E.; Bradbury, Helen

2017-01-01

The national UK standards for critical care highlight the need for clinical pharmacists to practise at an advanced level (equivalent to Royal Pharmaceutical Society, Great Britain, Faculty Advanced Stage II (MFRPSII)) and above. Currently the UK is unable to meet the workforce capacity requirements set out in the national standards in terms of numbers of pharmacist working at advanced level and above. The aim of this study was to identify the strategies, barriers and challenges to achieving Advanced Level Practice (ALP) by learning from the experiences of advanced level critical care pharmacists within the UK. Eight participants were recruited to complete semi-structured interviews on their views and experiences of ALP. The interviews were analysed thematically and three overarching themes were identified; support, work-based learning and reflective practice. The results of this study highlight that to increase the number of MFRPSII level practitioners within critical care support for their ALP development is required. This support involves developing face-to-face access to expert critical care pharmacists within a national training programme. Additionally, chief pharmacists need to implement drivers including in house mentorship and peer review programmes and the need to align job descriptions and appraisals to the Royal Pharmaceutical Society, Great Britain, Advanced Practice Framework (APF). PMID:28970450

Quantitative biological surface science: challenges and recent advances.

PubMed

Höök, Fredrik; Kasemo, Bengt; Grunze, Michael; Zauscher, Stefan

2008-12-23

Biological surface science is a broad, interdisciplinary subfield of surface science, where properties and processes at biological and synthetic surfaces and interfaces are investigated, and where biofunctional surfaces are fabricated. The need to study and to understand biological surfaces and interfaces in liquid environments provides sizable challenges as well as fascinating opportunities. Here, we report on recent progress in biological surface science that was described within the program assembled by the Biomaterial Interface Division of the Science and Technology of Materials, Interfaces and Processes (www.avs.org) during their 55th International Symposium and Exhibition held in Boston, October 19-24, 2008. The selected examples show that the rapid progress in nanoscience and nanotechnology, hand-in-hand with theory and simulation, provides increasingly sophisticated methods and tools to unravel the mechanisms and details of complex processes at biological surfaces and in-depth understanding of biomolecular surface interactions.

An analysis of the impact of three high school schedules on student achievement in advanced placement biology classes

NASA Astrophysics Data System (ADS)

Arons-Polan, Bonnie

This study examined the effect of three schedule types on student achievement in Advanced Placement Biology classes. AP Biology test scores from students on three types of full-year schedules were analyzed to assess the impact schedule type had on student achievement. The three schedules included the block and traditional schedules, and the rotating/hybrid, a blend of the former two schedules. The results indicated the variable most closely associated with success on the AP Biology exam was the length of experience the teachers had teaching the course, regardless of schedule type. Although significant differences were seen in mean AP Biology test scores among the three schedule types, this could be explained by the relationship between instructors' experience and schedule type. Regression analysis determined the two strongest predictors of successful performance on the AP Biology exam were instructors' experience and perceived teaching style, regardless of schedule type. It appears that the economically developed suburbs, had teachers with the largest amount of experience teaching AP Biology, and these teachers reported using a direct approach to teaching, using lecture greater than 50% of the time. The results of this study also suggest when restructuring to improve student achievement, educators should examine other variables in addition to the high school schedule. Restructuring the day to allow for longer classes must be accompanied by professional staff development to allow teachers to develop new teaching methods. Most of the teachers in the survey reported using lecture a great deal of the time, regardless of schedule type. Comments from the teachers from the various schedules revealed that the ability to add student centered, inquiry based activities and labs were dependent on adequate class time. No information on whether or not the teachers were given professional development to expand their repertoire of teaching methods when the school adopted a block

[Organization of anesthesia management and advanced life support at military medical evacuation levels].

PubMed

Shchegolev, A V; Petrakov, V A; Savchenko, I F

2014-07-01

Anesthesia management and advanced life support for the severely wounded personnel at military medical evacuation levels in armed conflict (local war) is time-consuming and resource-requiring task. One of the mathematical modeling methods was used to evaluate capabilities of anesthesia and intensive care units at tactical level. Obtained result allows us to tell that there is a need to make several system changes of the existing system of anesthesia management and advanced life support for the severely wounded personnel at military medical evacuation levels. In addition to increasing number of staff of anesthesiology-critical care during the given period of time another solution should be the creation of an early evacuation to a specialized medical care level by special means while conducting intensive monitoring and treatment.

Molecular insights into the novel aspects of diatom biology.

PubMed

Scala, S; Bowler, C

2001-10-01

Diatoms are unicellular photosynthetic eukaryotes that are thought to contribute as much as 25% of global primary productivity. In spite of their ecological importance in the worlds oceans, very little information is available at the molecular level about the novel aspects of their biology. Recent advances, such as the development of gene transfer protocols, are now allowing the genetic dissection of diatom biology. Notable examples are advances in understanding the genetic basis for the silica-based bioinorganic pattern formation of their cell walls and for elucidating key aspects of diatom ecophysiology. The potentiation of current research will allow an evaluation of the use of diatoms to construct submicrometre-scale silicon structures for the nanotechnology industry and will reveal the molecular secrets underlying their ecological success.

Measurement Frontiers in Molecular Biology

NASA Astrophysics Data System (ADS)

Laderman, Stephen

2009-03-01

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

Advanced biological activated carbon filter for removing pharmaceutically active compounds from treated wastewater.

PubMed

Sbardella, Luca; Comas, Joaquim; Fenu, Alessio; Rodriguez-Roda, Ignasi; Weemaes, Marjoleine

2018-04-28

Through their release of effluents, conventional wastewater treatment plants (WWTPs) represent a major pollution point sources for pharmaceutically active compounds (PhACs) in water bodies. The combination of a biological activated carbon (BAC) filter coupled with an ultrafiltration (UF) unit was evaluated as an advanced treatment for PhACs removal at pilot scale. The BAC-UF pilot plant was monitored for one year. The biological activity of the biofilm that developed on the granular activated carbon (GAC) particles and the contribution of this biofilm to the overall removal of PhACs were evaluated. Two different phases were observed during the long-term monitoring of PhACs removal. During the first 9200 bed volumes (BV; i.e., before GAC saturation), 89, 78, 83 and 79% of beta-blockers, psychiatric drugs, antibiotics and a mix of other therapeutic groups were removed, respectively. The second phase was characterized by deterioration of the overall performances during the period between 9200 and 13,800 BV. To quantify the respective contribution of adsorption and biodegradation, a lab-scale setup was operated for four months and highlighted the essential role played by GAC in biofiltration units. Physical adsorption was indeed the main removal mechanism. Nevertheless, a significant contribution due to biological activity was detected for some PhACs. The biofilm contributed to the removal of 22, 25, 30, 32 and 35% of ciprofloxacin, bezafibrate, ofloxacin, azithromycin and sulfamethoxazole, respectively. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

PubMed

Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Industrialization of Biology. A Roadmap to Accelerate the Advanced Manufacturing of Chemicals

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

Friedman, Douglas C.

The report stresses the need for efforts to inform the public of the nature of industrial biotechnology and of its societal benefits, and to make sure that concerns are communicated effectively between the public and other stakeholders. In addition to scientific advances, a number of governance and societal factors will influence the industrialization of biology. Industry norms and standards need to be established in areas such as read/write accuracy for DNA, data and machine technology specifications, and organism performance in terms of production rates and yields. An updated regulatory regime is also needed to accelerate the safe commercialization of newmore » host organisms, metabolic pathways, and chemical products, and regulations should be coordinated across nations to enable rapid, safe, and global access to new technologies and products.« less

Advances in three-dimensional rapid prototyping of microfluidic devices for biological applications

PubMed Central

O'Neill, P. F.; Ben Azouz, A.; Vázquez, M.; Liu, J.; Marczak, S.; Slouka, Z.; Chang, H. C.; Diamond, D.; Brabazon, D.

2014-01-01

The capability of 3D printing technologies for direct production of complex 3D structures in a single step has recently attracted an ever increasing interest within the field of microfluidics. Recently, ultrafast lasers have also allowed developing new methods for production of internal microfluidic channels within the bulk of glass and polymer materials by direct internal 3D laser writing. This review critically summarizes the latest advances in the production of microfluidic 3D structures by using 3D printing technologies and direct internal 3D laser writing fabrication methods. Current applications of these rapid prototyped microfluidic platforms in biology will be also discussed. These include imaging of cells and living organisms, electrochemical detection of viruses and neurotransmitters, and studies in drug transport and induced-release of adenosine triphosphate from erythrocytes. PMID:25538804

Technology readiness levels for advanced nuclear fuels and materials development

DOE PAGES

Carmack, W. J.; Braase, L. A.; Wigeland, R. A.; ...

2016-12-23

The Technology Readiness Level (TRL) process is used to quantitatively assess the maturity of a given technology. It was pioneered by the National Aeronautics and Space Administration (NASA) in the 1980s to develop and deploy new systems for space applications. The process was subsequently adopted by the Department of Defense (DoD) to develop and deploy new technology and systems for defense applications as well as the Department of Energy (DOE) to evaluate the maturity of new technologies in major construction projects. Advanced nuclear fuels and materials development is a critical technology needed for improving the performance and safety of currentmore » and advanced reactors, and ultimately closing the nuclear fuel cycle. Because deployment of new nuclear fuel forms requires a lengthy and expensive research, development, and demonstration program, applying the TRL concept to the advanced fuel development program is very useful as a management, communication and tracking tool. Furthermore, this article provides examples regarding the methods by which TRLs are currently used to assess the maturity of nuclear fuels and materials under development in the DOE Fuel Cycle Research and Development (FCRD) Program within the Advanced Fuels Campaign (AFC).« less

Technology readiness levels for advanced nuclear fuels and materials development

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

Carmack, W. J.; Braase, L. A.; Wigeland, R. A.

The Technology Readiness Level (TRL) process is used to quantitatively assess the maturity of a given technology. It was pioneered by the National Aeronautics and Space Administration (NASA) in the 1980s to develop and deploy new systems for space applications. The process was subsequently adopted by the Department of Defense (DoD) to develop and deploy new technology and systems for defense applications as well as the Department of Energy (DOE) to evaluate the maturity of new technologies in major construction projects. Advanced nuclear fuels and materials development is a critical technology needed for improving the performance and safety of currentmore » and advanced reactors, and ultimately closing the nuclear fuel cycle. Because deployment of new nuclear fuel forms requires a lengthy and expensive research, development, and demonstration program, applying the TRL concept to the advanced fuel development program is very useful as a management, communication and tracking tool. Furthermore, this article provides examples regarding the methods by which TRLs are currently used to assess the maturity of nuclear fuels and materials under development in the DOE Fuel Cycle Research and Development (FCRD) Program within the Advanced Fuels Campaign (AFC).« less

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

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

Davidson, George S.; Brown, William Michael

2007-09-01

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

Investigating the Group-Level Impact of Advanced Dual-Echo fMRI Combinations

PubMed Central

Kettinger, Ádám; Hill, Christopher; Vidnyánszky, Zoltán; Windischberger, Christian; Nagy, Zoltán

2016-01-01

Multi-echo fMRI data acquisition has been widely investigated and suggested to optimize sensitivity for detecting the BOLD signal. Several methods have also been proposed for the combination of data with different echo times. The aim of the present study was to investigate whether these advanced echo combination methods provide advantages over the simple averaging of echoes when state-of-the-art group-level random-effect analyses are performed. Both resting-state and task-based dual-echo fMRI data were collected from 27 healthy adult individuals (14 male, mean age = 25.75 years) using standard echo-planar acquisition methods at 3T. Both resting-state and task-based data were subjected to a standard image pre-processing pipeline. Subsequently the two echoes were combined as a weighted average, using four different strategies for calculating the weights: (1) simple arithmetic averaging, (2) BOLD sensitivity weighting, (3) temporal-signal-to-noise ratio weighting and (4) temporal BOLD sensitivity weighting. Our results clearly show that the simple averaging of data with the different echoes is sufficient. Advanced echo combination methods may provide advantages on a single-subject level but when considering random-effects group level statistics they provide no benefit regarding sensitivity (i.e., group-level t-values) compared to the simple echo-averaging approach. One possible reason for the lack of clear advantages may be that apart from increasing the average BOLD sensitivity at the single-subject level, the advanced weighted averaging methods also inflate the inter-subject variance. As the echo combination methods provide very similar results, the recommendation is to choose between them depending on the availability of time for collecting additional resting-state data or whether subject-level or group-level analyses are planned. PMID:28018165

Recent advances in systems metabolic engineering tools and strategies.

PubMed

Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

2017-10-01

Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Comparison of the Effects of an Advanced Organizer and/or Behavioral Objectives on the Achievement of Disadvantaged Biology Students.

ERIC Educational Resources Information Center

Kahle, Jane Butler

The use of an advanced organizer (a generalizable, encompassing concept) prior to an individualized instructional sequence in a self-paced, audiotutorial learning format was accompanied by gains in individual unit achievement and in retention by disadvantaged biology students. Although behavioral objectives generally were shown to make no…

Merkel cell carcinoma - recent advances in the biology, diagnostics and treatment.

PubMed

Czapiewski, Piotr; Biernat, Wojciech

2014-08-01

Merkel cell carcinoma (MCC) is an uncommon primary cutaneous carcinoma with neuroendocrine differentiation. Since recent discovery of MCCs strong association with Merkel cell polyomavirus (MCPyV), there has been a rapid increase in the understanding of the carcinomas genetics, molecular biology and pathogenesis. In our study, we reviewed recent advances and controversies concerning MCC histogenesis, epidemiology, diagnostic and prognostic markers. We analyzed the association of MCPyV with MCC and the possible new targets for therapy. We also examined English-based literature regarding MCC pathogenesis published between 2008 and 2013, which lead to a deeper understanding of the topic. Our study showed that the association of MCPyV strongly influences the course of MCC. Additionally, it has been shown that a immunological response to MCPyV may in the future give hope to identify new therapeutic strategies in treatment of this fatal malignancy. This article is part of a Directed Issue entitled: Rare Cancers. Copyright © 2014 Elsevier Ltd. All rights reserved.

Biological Activation of Inert Ceramics: Recent Advances Using Tailored Self-Assembled Monolayers on Implant Ceramic Surfaces

PubMed Central

Böke, Frederik; Schickle, Karolina; Fischer, Horst

2014-01-01

High-strength ceramics as materials for medical implants have a long, research-intensive history. Yet, especially on applications where the ceramic components are in direct contact with the surrounding tissue, an unresolved issue is its inherent property of biological inertness. To combat this, several strategies have been investigated over the last couple of years. One promising approach investigates the technique of Self-Assembled Monolayers (SAM) and subsequent chemical functionalization to create a biologically active tissue-facing surface layer. Implementation of this would have a beneficial impact on several fields in modern implant medicine such as hip and knee arthroplasty, dental applications and related fields. This review aims to give a summarizing overview of the latest advances in this recently emerging field, along with thorough introductions of the underlying mechanism of SAMs and surface cell attachment mechanics on the cell side. PMID:28788687

Student selection: are the school-leaving A-level grades in biology and chemistry important?

PubMed

Green, A; Peters, T J; Webster, D J

1993-01-01

This study determined the relationships of grades in A-level biology and chemistry with examination success or failure during the medical course. By inspection of medical student records, A-level grades at entry to medical school and examination performance were obtained for 128 (91%) of the students who sat their final MBBCh examination at the University of Wales College of Medicine in June 1988. The majority, 92 (72%), completed their medical school careers with no professional examination failures; 15 failed examinations just in the period up to 2nd MB; 11 failed examinations in the clinical period only and 10 failed examinations in both periods. Whereas grade achieved in A-level chemistry was not associated with undergraduate examination performance, students with a grade A or B in A-level biology were less likely to have problems than the others (21% compared with 47%; the difference of 26% has a 95% confidence interval of 7% to 44%). Specifically, there appears to be a strong relationship between a low grade in biology and difficulties in the preclinical examinations. Moreover, for those who have difficulties at this stage, this association continues later in the course.

Recent advances in synthetic biology of cyanobacteria.

PubMed

Sengupta, Annesha; Pakrasi, Himadri B; Wangikar, Pramod P

2018-05-09

Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO 2 . Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO 2 , diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this "green" chassis.

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

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

Unkefer, Clifford J.; Sayre, Richard T.; Magnuson, Jon K.

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortiumbegan, littlewas known about themolecular basis of algal biomass or oil production. Very fewalgal genome sequenceswere available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played bymetabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oil yields were in their infancy. Genomemore » sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. This review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.« less

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

DOE PAGES

Unkefer, Clifford Jay; Sayre, Richard Thomas; Magnuson, Jon K.; ...

2016-06-21

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oilmore » yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. Our review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.« less

Review of the algal biology program within the National Alliance for Advanced Biofuels and Bioproducts

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

Unkefer, Clifford Jay; Sayre, Richard Thomas; Magnuson, Jon K.

In 2010,when the National Alliance for Advanced Biofuels and Bioproducts (NAABB) consortium began, little was known about the molecular basis of algal biomass or oil production. Very few algal genome sequences were available and efforts to identify the best-producing wild species through bioprospecting approaches had largely stalled after the U.S. Department of Energy's Aquatic Species Program. This lack of knowledge included how reduced carbon was partitioned into storage products like triglycerides or starch and the role played by metabolite remodeling in the accumulation of energy-dense storage products. Furthermore, genetic transformation and metabolic engineering approaches to improve algal biomass and oilmore » yields were in their infancy. Genome sequencing and transcriptional profiling were becoming less expensive, however; and the tools to annotate gene expression profiles under various growth and engineered conditions were just starting to be developed for algae. It was in this context that an integrated algal biology program was introduced in the NAABB to address the greatest constraints limiting algal biomass yield. Our review describes the NAABB algal biology program, including hypotheses, research objectives, and strategies to move algal biology research into the twenty-first century and to realize the greatest potential of algae biomass systems to produce biofuels.« less

Incorporating Allee effects into the potential biological removal level

USGS Publications Warehouse

Hadier, Humza; Oldfield, Sarah; Tu, Tiffany; Moreno, Rosa; Diffendorfer, Jay E.; Eager, Eric A.; Erickson, Richard A.

2017-01-01

Potential biological removal (PBR) is an approach used to calculate sustainable harvest and “take” limits for populations. PBR was originally derived assuming logistic growth while ignoring the effects of small population size (i.e., an Allee effect). We derived a version of PBR that includes an Allee effect (i.e., small population size or densities limiting population growth rates). We found that PBR becomes less conservative when it fails to consider an Allee effect. Specifically, sustainable harvest and take levels based upon PBR with an Allee effect were between approximately 51% and 66% of levels based upon PBR without an Allee effect. Managers and biologists using PBR may need to consider the limitations if an Allee effect may be present in the species being modeled.

Synthetic biology: tools to design microbes for the production of chemicals and fuels.

PubMed

Seo, Sang Woo; Yang, Jina; Min, Byung Eun; Jang, Sungho; Lim, Jae Hyung; Lim, Hyun Gyu; Kim, Seong Cheol; Kim, Se Yeon; Jeong, Jun Hong; Jung, Gyoo Yeol

2013-11-01

The engineering of biological systems to achieve specific purposes requires design tools that function in a predictable and quantitative manner. Recent advances in the field of synthetic biology, particularly in the programmable control of gene expression at multiple levels of regulation, have increased our ability to efficiently design and optimize biological systems to perform designed tasks. Furthermore, implementation of these designs in biological systems highlights the potential of using these tools to build microbial cell factories for the production of chemicals and fuels. In this paper, we review current developments in the design of tools for controlling gene expression at transcriptional, post-transcriptional and post-translational levels, and consider potential applications of these tools. Copyright © 2013 Elsevier Inc. All rights reserved.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course.

PubMed

Ziegler, Brittany; Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students' perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students' perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. © 2014 B. Ziegler and L. Montplaisir. CBE—Life Sciences Education © 2014 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

A Biochemical Magic Frequency Based on the Reduction Level of Biological Carbon

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1995-01-01

We have calculated the average number of electron pairs required for the chemical reduction of carbon dioxide to biological carbon using (a) estimates of the reducing equivalents (electron pairs) needed to synthesize biomolecules from carbon dioxide, and (b) measurements of the molecular composition of different organisms. These calculations showed that the carbon of the Earth's biosphere is at the reduction level of formaldehyde that requires two electron pairs per carbon atom to be synthesized from carbon dioxide. This was also the reduction level of cellular carbon when fuel stored as lipid was not used in the estimate. Since this chemical characteristic of life is probably universal, it could be the one thing we know about other carbon-based life in the universe, and the one thing that other intelligent life knows about us. We believe that this common knowledge that biological carbon throughout the universe is at the reduction level of formaldehyde could lead to the selection of the 72.83814 GHz line of the 0, 0, 0 yields 1, 1, 1 rotational transition of formaldehyde as a frequency for interstellar communication.

Multiweek Cell Culture Project for Use in Upper-Level Biology Laboratories

ERIC Educational Resources Information Center

Marion, Rebecca E.; Gardner, Grant E.; Parks, Lisa D.

2012-01-01

This article describes a laboratory protocol for a multiweek project piloted in a new upper-level biology laboratory (BIO 426) using cell culture techniques. Human embryonic kidney-293 cells were used, and several culture media and supplements were identified for students to design their own experiments. Treatments included amino acids, EGF,…

Advanced High-Level Waste Glass Research and Development Plan

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

Peeler, David K.; Vienna, John D.; Schweiger, Michael J.

2015-07-01

The U.S. Department of Energy Office of River Protection (ORP) has implemented an integrated program to increase the loading of Hanford tank wastes in glass while meeting melter lifetime expectancies and process, regulatory, and product quality requirements. The integrated ORP program is focused on providing a technical, science-based foundation from which key decisions can be made regarding the successful operation of the Hanford Tank Waste Treatment and Immobilization Plant (WTP) facilities. The fundamental data stemming from this program will support development of advanced glass formulations, key process control models, and tactical processing strategies to ensure safe and successful operations formore » both the low-activity waste (LAW) and high-level waste (HLW) vitrification facilities with an appreciation toward reducing overall mission life. The purpose of this advanced HLW glass research and development plan is to identify the near-, mid-, and longer-term research and development activities required to develop and validate advanced HLW glasses and their associated models to support facility operations at WTP, including both direct feed and full pretreatment flowsheets. This plan also integrates technical support of facility operations and waste qualification activities to show the interdependence of these activities with the advanced waste glass (AWG) program to support the full WTP mission. Figure ES-1 shows these key ORP programmatic activities and their interfaces with both WTP facility operations and qualification needs. The plan is a living document that will be updated to reflect key advancements and mission strategy changes. The research outlined here is motivated by the potential for substantial economic benefits (e.g., significant increases in waste throughput and reductions in glass volumes) that will be realized when advancements in glass formulation continue and models supporting facility operations are implemented. Developing and applying

The Main Biological Hazards in Animal Biosafety Level 2 Facilities and Strategies for Control.

PubMed

Li, Xiao Yan; Xue, Kang Ning; Jiang, Jin Sheng; Lu, Xuan Cheng

2016-04-01

Concern about the biological hazards involved in microbiological research, especially research involving laboratory animals, has increased in recent years. Working in an animal biosafety level 2 facility (ABSL-2), commonly used for research on infectious diseases, poses various biological hazards. Here, the regulations and standards related to laboratory biosafety in China are introduced, the potential biological hazards present in ABSL-2 facilities are analyzed, and a series of strategies to control the hazards are presented. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Advanced carbon manufacturing for energy and biological applications

NASA Astrophysics Data System (ADS)

Turon Teixidor, Genis

The science of miniaturization has experienced revolutionary advances during the last decades, witnessing the development of the Integrated Circuit and the emergence of MEMS and Nanotechnology. Particularly, MEMS technology has pioneered the use of non-traditional materials in microfabrication by including polymers, ceramics and composites to the well known list of metals and semiconductors. One of the latest additions to this set of materials is carbon, which represents a very important inclusion given its significance in electrochemical energy conversion systems and in applications where it is used as sensor probe material. For these applications, carbon is optimal in several counts: It has a wide electrochemical stability window, good electrical and thermal conductivity, high corrosion resistance and mechanical stability, and is available in high purity at a low cost. Furthermore carbon is biocompatible. This thesis presents several microfabricated devices that take advantage of these properties. The thesis has two clearly differentiated parts. In the first one, applications of micromachined carbon in the field of energy conversion and energy storage are presented. These applications include lithium ion micro batteries and the development of new carbon electrodes with fractal geometries. In the second part, the focus shifts to biological applications. First, the study of the interaction of living cells with micromachined carbon is presented, followed by the description of a sensor based on interdigitated nano-electrode arrays, and finally the development of the new instrumentation needed to address arrays of carbon electrodes, a multiplexed potentiostat. The underlying theme that connects all these seemingly different topics is the use of carbon microfabrication techniques in electrochemical systems.

A Systems Biology Approach to Iron Metabolism

PubMed Central

Chifman, J.; Laubenbacher, R.; Torti, S.V.

2015-01-01

Iron is critical to the survival of almost all living organisms. However, inappropriately low or high levels of iron are detrimental and contribute to a wide range of diseases. Recent advances in the study of iron metabolism have revealed multiple intricate pathways that are essential to the maintenance of iron homeostasis. Further, iron regulation involves processes at several scales, ranging from the subcellular to the organismal. This complexity makes a systems biology approach crucial, with its enabling technology of computational models based on a mathematical description of regulatory systems. Systems biology may represent a new strategy for understanding imbalances in iron metabolism and their underlying causes. PMID:25480643

Biological applications of nanobiotechnology.

PubMed

de Morais, Michele Greque; Martins, Vilásia Guimarães; Steffens, Daniela; Pranke, Patricia; da Costa, Jorge Alberto Vieira

2014-01-01

Nanotechnology is a multidisciplinary field that covers a vast and diverse array of devices derived from engineering, physics, chemistry, and biology. Nanotechnology has opened up by rapid advances in science and technology, creating new opportunities for advances in the fields of medicine, electronics, foods, and the environment. Nanoscale structures and materials (nanoparticles, nanowires, nanofibers, nanotubes) have been explored in many biological applications (biosensing, biological separation, molecular imaging, anticancer therapy) because their novel properties and functions differ drastically from their bulk counterparts. Their high volume/surface ratio, improved solubility, and multifunctionality open many new possibilities. The objective of this review is to describe the potential benefits and impacts of the nanobiotechnology in different areas.

The relationship of certified flight instructors' emotional intelligence levels on flight student advancement

NASA Astrophysics Data System (ADS)

Hokeness, Mark Merrill

Aviation researchers estimate airline companies will require nearly 500,000 pilots in the next 20 years. The role of a Certified Flight Instructor (CFI) is to move student pilots to professional pilots with training typically conducted in one-on-one student and instructor sessions. The knowledge of aviation, professionalism as a teacher, and the CFI’s interpersonal skills can directly affect the successes and advancement of a student pilot. A new and emerging assessment of people skills is known as emotional intelligence (EI). The EI of the CFI can and will affect a flight students’ learning experiences. With knowledge of emotional intelligence and its effect on flight training, student pilot dropouts from aviation may be reduced, thus helping to ensure an adequate supply of pilots. Without pilots, the growth of the commercial aviation industry will be restricted. This mixed method research study established the correlation between a CFI’s measured EI levels and the advancement of flight students. The elements contributing to a CFI’s EI level were not found to be teaching or flight-related experiences, suggesting other life factors are drawn upon by the CFI and are reflected in their emotional intelligence levels presented to flight students. Students respond positively to CFIs with higher levels of emotional intelligence. Awareness of EI skills by both the CFI and flight student contribute to flight student successes and advancement.

Advancing Systems Biology in the International Conference on Intelligent Biology and Medicine (ICIBM) 2015.

PubMed

Zhao, Zhongming; Liu, Yunlong; Huang, Yufei; Huang, Kun; Ruan, Jianhua

2016-08-26

The 2015 International Conference on Intelligent Biology and Medicine (ICIBM 2015) was held on November 13-15, 2015 in Indianapolis, Indiana, USA. ICIBM 2015 included eight scientific sessions, three tutorial sessions, one poster session, and four keynote presentations that covered the frontier research in broad areas related to bioinformatics, systems biology, big data science, biomedical informatics, pharmacogenomics, and intelligent computing. Here, we present a summary of the 10 research articles that were selected from ICIBM 2015 and included in the supplement to BMC Systems Biology.

Advances in the cellular and molecular biology of angiogenesis.

PubMed

Egginton, Stuart; Bicknell, Roy

2011-12-01

Capillaries have been recognized for over a century as one of the most important components in regulating tissue oxygen transport, and their formation or angiogenesis a pivotal element of tissue remodelling during development and adaptation. Clinical interest stems from observations that both excessive and inadequate vascular growth plays a major role in human diseases, and novel developments in treatments for cancer and eye disease increasingly rely on anti-angiogenic therapies. Although the discovery of VEGF (vascular endothelial growth factor) provided the first clue for specificity of signalling in endothelial cell activation, understanding the integrative response that drives angiogenesis requires a much broader perspective. The Advances in the Cellular and Molecular Biology of Angiogenesis meeting brought together researchers at the forefront of this rapidly moving field to provide an update on current understanding, and the most recent insights into molecular and cellular mechanisms of vascular growth. The plenary lecture highlighted the integrative nature of the angiogenic process, whereas invited contributions from basic and clinician scientists described fundamental mechanisms and disease-associated issues of blood vessel formation, grouped under a number of themes to aid discussion. These articles will appeal to academic, clinical and pharmaceutical scientists interested in the molecular and cellular basis of angiogenesis, their modulation or dysfunction in human diseases, and application of these findings towards translational medicine.

Advances in Campylobacter biology and implications for biotechnological applications.

PubMed

Jeon, Byeonghwa; Muraoka, Wayne T; Zhang, Qijing

2010-05-01

Campylobacter jejuni is a major foodborne pathogen of animal origin and a leading cause of bacterial gastroenteritis in humans. During the past decade, especially since the publication of the first C. jejuni genome sequence, major advances have been made in understanding the pathobiology and physiology of this organism. It is apparent that C. jejuni utilizes sophisticated mechanisms for effective colonization of the intestinal tracts in various animal species. Although Campylobacter is fragile in the environment and requires fastidious growth conditions, it exhibits great flexibility in the adaptation to various habitats including the gastrointestinal tract. This high adaptability is attributable to its genetically, metabolically and phenotypically diverse population structure and its ability to change in response to various challenges. Unlike other enteric pathogens, such as Escherichia coli and Salmonella, Campylobacter is unable to utilize exogenous glucose and mainly depends on the catabolism of amino acids as a carbon source. Campylobacter proves highly mutable in response to antibiotic treatments and possesses eukaryote-like dual protein glycosylation systems, which modify flagella and other surface proteins with specific sugar structures. In this review we will summarize the distinct biological traits of Campylobacter and discuss the potential biotechnological approaches that can be developed to control this enteric pathogen. © 2009 The Authors. Journal compilation © 2009 Society for Applied Microbiology and Blackwell Publishing Ltd.

Applications of systems biology towards microbial fuel production.

PubMed

Gowen, Christopher M; Fong, Stephen S

2011-10-01

Harnessing the immense natural diversity of biological functions for economical production of fuel has enormous potential benefits. Inevitably, however, the native capabilities for any given organism must be modified to increase the productivity or efficiency of a biofuel bioprocess. From a broad perspective, the challenge is to sufficiently understand the details of cellular functionality to be able to prospectively predict and modify the cellular function of a microorganism. Recent advances in experimental and computational systems biology approaches can be used to better understand cellular level function and guide future experiments. With pressure to quickly develop viable, renewable biofuel processes a balance must be maintained between obtaining depth of biological knowledge and applying that knowledge. Copyright © 2011 Elsevier Ltd. All rights reserved.

Advanced unresectable hepatocellular carcinoma: new biologics as fresh ammunition or clues to disease understanding?

PubMed

Dekervel, Jeroen; van Pelt, Jos; Verslype, Chris

2013-07-01

Hepatocellular carcinoma (HCC) is a prevalent malignancy associated with a guarded prognosis. At present, sorafenib is the only approved systemic therapy for patients with advanced disease. The effect of sorafenib on overall survival is modest and limited in time by the occurrence of drug resistance. Together with the increasing knowledge of molecular pathways involved in HCC, targeted molecules have been developed and tested in first and second line following sorafenib. These include antiangiogenic drugs, as well as biologicals inhibiting cell proliferation and survival. Recent phase III trials investigated sunitinib, linifanib, brivanib and erlotinib, but none of them were found superior to sorafenib. New findings in mechanisms of drug resistance create opportunities in the treatment of sorafenib-refractory disease, with cMET inhibition as the most promising approach. This article reviews the pathways involved in HCC and their targets as well as potential strategies for drug development in the future. Advanced HCC has been the subject of intensive clinical research following the success of sorafenib. Despite many failures, some agents show promising results in phase II trials. Targeting new pathways, using multidrug regimens and tailoring treatment guided by predictive markers should allow new successes.

Methods for biological data integration: perspectives and challenges

PubMed Central

Gligorijević, Vladimir; Pržulj, Nataša

2015-01-01

Rapid technological advances have led to the production of different types of biological data and enabled construction of complex networks with various types of interactions between diverse biological entities. Standard network data analysis methods were shown to be limited in dealing with such heterogeneous networked data and consequently, new methods for integrative data analyses have been proposed. The integrative methods can collectively mine multiple types of biological data and produce more holistic, systems-level biological insights. We survey recent methods for collective mining (integration) of various types of networked biological data. We compare different state-of-the-art methods for data integration and highlight their advantages and disadvantages in addressing important biological problems. We identify the important computational challenges of these methods and provide a general guideline for which methods are suited for specific biological problems, or specific data types. Moreover, we propose that recent non-negative matrix factorization-based approaches may become the integration methodology of choice, as they are well suited and accurate in dealing with heterogeneous data and have many opportunities for further development. PMID:26490630

Towards Engineering Biological Systems in a Broader Context.

PubMed

Venturelli, Ophelia S; Egbert, Robert G; Arkin, Adam P

2016-02-27

Significant advances have been made in synthetic biology to program information processing capabilities in cells. While these designs can function predictably in controlled laboratory environments, the reliability of these devices in complex, temporally changing environments has not yet been characterized. As human society faces global challenges in agriculture, human health and energy, synthetic biology should develop predictive design principles for biological systems operating in complex environments. Natural biological systems have evolved mechanisms to overcome innumerable and diverse environmental challenges. Evolutionary design rules should be extracted and adapted to engineer stable and predictable ecological function. We highlight examples of natural biological responses spanning the cellular, population and microbial community levels that show promise in synthetic biology contexts. We argue that synthetic circuits embedded in host organisms or designed ecologies informed by suitable measurement of biotic and abiotic environmental parameters could be used as engineering substrates to achieve target functions in complex environments. Successful implementation of these methods will broaden the context in which synthetic biological systems can be applied to solve important problems. Copyright © 2015 Elsevier Ltd. All rights reserved.

Recent advances in mass spectrometry-based approaches for proteomics and biologics: Great contribution for developing therapeutic antibodies.

PubMed

Iwamoto, Noriko; Shimada, Takashi

2018-05-01

Since the turn of the century, mass spectrometry (MS) technologies have continued to improve dramatically, and advanced strategies that were impossible a decade ago are increasingly becoming available. The basic characteristics behind these advancements are MS resolution, quantitative accuracy, and information science for appropriate data processing. The spectral data from MS contain various types of information. The benefits of improving the resolution of MS data include accurate molecular structural-derived information, and as a result, we can obtain a refined biomolecular structure determination in a sequential and large-scale manner. Moreover, in MS data, not only accurate structural information but also the generated ion amount plays an important rule. This progress has greatly contributed a research field that captures biological events as a system by comprehensively tracing the various changes in biomolecular dynamics. The sequential changes of proteome expression in biological pathways are very essential, and the amounts of the changes often directly become the targets of drug discovery or indicators of clinical efficacy. To take this proteomic approach, it is necessary to separate the individual MS spectra derived from each biomolecule in the complexed biological samples. MS itself is not so infinite to perform the all peak separation, and we should consider improving the methods for sample processing and purification to make them suitable for injection into MS. The above-described characteristics can only be achieved using MS with any analytical instrument. Moreover, MS is expected to be applied and expand into many fields, not only basic life sciences but also forensic medicine, plant sciences, materials, and natural products. In this review, we focus on the technical fundamentals and future aspects of the strategies for accurate structural identification, structure-indicated quantitation, and on the challenges for pharmacokinetics of high

Biology of advanced uveal melanoma and next steps for clinical therapeutics.

PubMed

Luke, Jason J; Triozzi, Pierre L; McKenna, Kyle C; Van Meir, Erwin G; Gershenwald, Jeffrey E; Bastian, Boris C; Gutkind, J Silvio; Bowcock, Anne M; Streicher, Howard Z; Patel, Poulam M; Sato, Takami; Sossman, Jeffery A; Sznol, Mario; Welch, Jack; Thurin, Magdalena; Selig, Sara; Flaherty, Keith T; Carvajal, Richard D

2015-03-01

Uveal melanoma is the most common intraocular malignancy although it is a rare subset of all melanomas. Uveal melanoma has distinct biology relative to cutaneous melanoma, with widely divergent patient outcomes. Patients diagnosed with a primary uveal melanoma can be stratified for risk of metastasis by cytogenetics or gene expression profiling, with approximately half of patients developing metastatic disease, predominately hepatic in location, over a 15-yr period. Historically, no systemic therapy has been associated with a clear clinical benefit for patients with advanced disease, and median survival remains poor. Here, as a joint effort between the Melanoma Research Foundation's ocular melanoma initiative, CURE OM and the National Cancer Institute, the current understanding of the molecular and immunobiology of uveal melanoma is reviewed, and on-going laboratory research into the disease is highlighted. Finally, recent investigations relevant to clinical management via targeted and immunotherapies are reviewed, and next steps in the development of clinical therapeutics are discussed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

FROM ORGANISMS TO POPULATIONS: MODELING AQUATIC TOXICITY DATA ACROSS TWO LEVELS OF BIOLOGICAL ORGANIZATION.

EPA Science Inventory

A critical step in estimating the ecological effects of a toxicant is extrapolating organism-level response data across higher levels of biological organization. In the present study, the organism-to-population link is made for the mysid, Americamysis bahia, exposed to a range of...

Advancing Ecological Models to Compare Scale in Multi-Level Educational Change

ERIC Educational Resources Information Center

Woo, David James

2016-01-01

Education systems as units of analysis have been metaphorically likened to ecologies to model change. However, ecological models to date have been ineffective in modelling educational change that is multi-scale and occurs across multiple levels of an education system. Thus, this paper advances two innovative, ecological frameworks that improve on…

Theranostic Profiling for Actionable Aberrations in Advanced High Risk Osteosarcoma with Aggressive Biology Reveals High Molecular Diversity: The Human Fingerprint Hypothesis.

PubMed

Egas-Bejar, Daniela; Anderson, Pete M; Agarwal, Rishi; Corrales-Medina, Fernando; Devarajan, Eswaran; Huh, Winston W; Brown, Robert E; Subbiah, Vivek

2014-03-12

The survival of patients with advanced osteosarcoma is poor with limited therapeutic options. There is an urgent need for new targeted therapies based on biomarkers. Recently, theranostic molecular profiling services for cancer patients by CLIA-certified commercial companies as well as in-house profiling in academic medical centers have expanded exponentially. We evaluated molecular profiles of patients with advanced osteosarcoma whose tumor tissue had been analyzed by one of the following methods: 1. 182-gene next-generation exome sequencing (Foundation Medicine, Boston, MA), 2. Immunohistochemistry (IHC)/PCR-based panel (CARIS Target Now, Irving, Tx), 3.Comparative genome hybridization (Oncopath, San Antonio, TX). 4. Single-gene PCR assays, PTEN IHC (MDACC CLIA), 5. UT Houston morphoproteomics (Houston, TX). The most common actionable aberrations occur in the PI3K/PTEN/mTOR pathway. No patterns in genomic alterations beyond the above are readily identifiable, and suggest both high molecular diversity in osteosarcoma and the need for more analyses to define distinct subgroups of osteosarcoma defined by genomic alterations. Based on our preliminary observations we hypothesize that the biology of aggressive and the metastatic phenotype osteosarcoma at the molecular level is similar to human fingerprints, in that no two tumors are identical. Further large scale analyses of osteosarcoma samples are warranted to test this hypothesis.

Synthetic Nanoelectronic Probes for Biological Cells and Tissue

PubMed Central

2013-01-01

Research at the interface between nanoscience and biology has the potential to produce breakthroughs in fundamental science and lead to revolutionary technologies. In this review, we focus on nanoelectronic/biological interfaces. First, we discuss nanoscale field effect transistors (nanoFETs) as probes to study cellular systems, including the realization of nanoFET comparable in size to biological nanostructures involved in communication using synthesized nanowires. Second, we overview current progress in multiplexed extracellular sensing using planar nanoFET arrays. Third, we describe the design and implementation of three distinct nanoFETs used to realize the first intracellular electrical recording from single cells. Fourth, we present recent progress in merging electronic and biological systems at the 3D tissue level by using macroporous nanoelectronic scaffolds. Finally, we discuss future development in this research area, the unique challenges and opportunities, and the tremendous impact these nanoFET based technologies might have in advancing biology and medical sciences. PMID:23451719

[Advance in flavonoids biosynthetic pathway and synthetic biology].

PubMed

Zou, Li-Qiu; Wang, Cai-Xia; Kuang, Xue-Jun; Li, Ying; Sun, Chao

2016-11-01

Flavonoids are the valuable components in medicinal plants, which possess a variety of pharmacological activities, including anti-tumor, antioxidant and anti-inflammatory activities. There is an unambiguous understanding about flavonoids biosynthetic pathway, that is,2S-flavanones including naringenin and pinocembrin are the skeleton of other flavonoids and they can transform to other flavonoids through branched metabolic pathway. Elucidation of the flavonoids biosynthetic pathway lays a solid foundation for their synthetic biology. A few flavonoids have been produced in Escherichia coli or yeast with synthetic biological technologies, such as naringenin, pinocembrin and fisetin. Synthetic biology will provide a new way to get valuable flavonoids and promote the research and development of flavonoid drugs and health products, making flavonoids play more important roles in human diet and health. Copyright© by the Chinese Pharmaceutical Association.

Attempts to develop a new nuclear measurement technique of β-glucuronidase levels in biological samples

NASA Astrophysics Data System (ADS)

Ünak, T.; Avcibasi, U.; Yildirim, Y.; Çetinkaya, B.

2003-01-01

β-Glucuronidase is one of the most important hydrolytic enzymes in living systems and plays an essential role in the detoxification pathway of toxic materials incorporated into the metabolism. Some organs, especially liver and some tumour tissues, have high level of β-glucuronidase activity. As a result the enzymatic activity of some kind of tumour cells, the radiolabelled glucuronide conjugates of cytotoxic, as well as radiotoxic compounds have potentially very valuable diagnostic and therapeutic applications in cancer research. For this reason, a sensitive measurement of β-glucuronidase levels in normal and tumour tissues is a very important step for these kinds of applications. According to the classical measurement method of β-glucuronidase activity, in general, the quantity of phenolphthalein liberated from its glucuronide conjugate, i.e. phenolphthalein-glucuronide, by β-glucuronidase has been measured by use of the spectrophotometric technique. The lower detection limit of phenolphthalein by the spectrophotometric technique is about 1-3 μg. This means that the β-glucuronidase levels could not be detected in biological samples having lower levels of β-glucuronidase activity and therefore the applications of the spectrophotometric technique in cancer research are very seriously limited. Starting from this consideration, we recently attempted to develop a new nuclear technique to measure much lower concentrations of β-glucuronidase in biological samples. To improve the detection limit, phenolphthalein-glucuronide and also phenyl-N-glucuronide were radioiodinated with 131I and their radioactivity was measured by use of the counting technique. Therefore, the quantity of phenolphthalein or aniline radioiodinated with 131I and liberated by the deglucuronidation reactivity of β-glucuronidase was used in an attempt to measure levels lower than the spectrophotometric measurement technique. The results obtained clearly verified that 0.01 pg level of

FROM INDIVIDUALS TO POPULATIONS: MODELING TOXICITY DATA ACROSS LEVELS OF BIOLOGICAL ORGANIZATION

EPA Science Inventory

Raimondo, Sandy and Charles L. McKenney, Jr. In press. From Individuals to Populations: Modeling Toxicity Data Across Levels of Biological Organization (Abstract). To be presented at the SETAC Fourth World Congress, 14-18 November 2004, Portland, OR. 1 p. (ERL,GB R1012).

...

Computational biology and bioinformatics in Nigeria.

PubMed

Fatumo, Segun A; Adoga, Moses P; Ojo, Opeolu O; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

2014-04-01

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries.

Computational Biology and Bioinformatics in Nigeria

PubMed Central

Fatumo, Segun A.; Adoga, Moses P.; Ojo, Opeolu O.; Oluwagbemi, Olugbenga; Adeoye, Tolulope; Ewejobi, Itunuoluwa; Adebiyi, Marion; Adebiyi, Ezekiel; Bewaji, Clement; Nashiru, Oyekanmi

2014-01-01

Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological data generated by the scientific community. The critical need to process and analyze such a deluge of data and turn it into useful knowledge has caused bioinformatics to gain prominence and importance. Bioinformatics is an interdisciplinary research area that applies techniques, methodologies, and tools in computer and information science to solve biological problems. In Nigeria, bioinformatics has recently played a vital role in the advancement of biological sciences. As a developing country, the importance of bioinformatics is rapidly gaining acceptance, and bioinformatics groups comprised of biologists, computer scientists, and computer engineers are being constituted at Nigerian universities and research institutes. In this article, we present an overview of bioinformatics education and research in Nigeria. We also discuss professional societies and academic and research institutions that play central roles in advancing the discipline in Nigeria. Finally, we propose strategies that can bolster bioinformatics education and support from policy makers in Nigeria, with potential positive implications for other developing countries. PMID:24763310

The HMI Report on Advanced Level Work in Business Education and Economics 1991.

ERIC Educational Resources Information Center

Butler, John

1992-01-01

Evaluates 1991 report of Her Majesty's Inspectorate (HMI) on advanced level work in business education and economics for levels 16-19 in United Kingdom. Discusses areas of improvement and specific examples of good practice identified by HMI. Reports HMI's desire for better, more formalized departmental organization and the need for more in-service…

Auto-induction for high level production of biologically active reteplase in Escherichia coli.

PubMed

Fathi-Roudsari, Mehrnoosh; Maghsoudi, Nader; Maghsoudi, Amirhossein; Niazi, Sepideh; Soleiman, Morvarid

2018-06-07

Reteplase is a third generation tissue plasminogen activator (tPA) with a modified structure and prolonged half-life in comparison to native tPA. As a non-glycosylated protein, reteplase is expressed in Escherichia coli. Due to presence of several disulfide bonds, high level production of reteplase is complicated and needs extra steps for conversion to biologically active form. Auto-induction represents a method for high-yield growth of bacterial cells and higher expression of recombinant proteins. Here we have tried to optimize the auto-induction procedure for soluble and active expression of reteplase in E. coli. Results showed that using auto-induction strategy at 37 °C, Rosetta-gami (DE3) had the highest level of active and soluble reteplase production in comparison to E. coli strains BL21 (DE3), and Shuffel T7. Temperature dominantly affected the level of active reteplase production. Decreasing the temperature to 25 and 18 °C increased the level of active reteplase by 20 and 60%, respectively. The composition of auto-induction medium also dramatically changed the active production of reteplase in cytoplasm. Using higher enriched auto-induction medium, super broth base including trace elements, significantly increased biologically active reteplase by 30%. It is demonstrated here that auto-induction is a powerful method for expression of biologically active reteplase in oxidative cytoplasm of Rosetta-gami. Optimizing expression condition by decreasing temperature and using an enriched auto-induction medium resulted in at least three times higher level of active reteplase production. Production of correctly folded and active reteplase in spite of its complex structure helps for removal of inefficient and cumbersome step of refolding. Copyright © 2018. Published by Elsevier Inc.

Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals.

PubMed

Darvishi, Farshad; Ariana, Mehdi; Marella, Eko Roy; Borodina, Irina

2018-07-01

Oleaginous yeast Yarrowia lipolytica is an important industrial host for the production of enzymes, oils, fragrances, surfactants, cosmetics, and pharmaceuticals. More recently, improved synthetic biology tools have allowed more extensive engineering of this yeast species, which lead to the production of non-native metabolites. In this review, we summarize the recent advances of genome editing tools for Y. lipolytica, including the application of CRISPR/Cas9 system and discuss case studies, where Y. lipolytica was engineered to produce various non-native chemicals: short-chain fatty alcohols and alkanes as biofuels, polyunsaturated fatty acids for nutritional and pharmaceutical applications, polyhydroxyalkanoates and dicarboxylic acids as precursors for biodegradable plastics, carotenoid-type pigments for food and feed, and campesterol as a precursor for steroid drugs.

Synthetic Biology for Specialty Chemicals.

PubMed

Markham, Kelly A; Alper, Hal S

2015-01-01

In this review, we address recent advances in the field of synthetic biology and describe how those tools have been applied to produce a wide variety of chemicals in microorganisms. Here we classify the expansion of the synthetic biology toolbox into three different categories based on their primary function in strain engineering-for design, for construction, and for optimization. Next, focusing on recent years, we look at how chemicals have been produced using these new synthetic biology tools. Advances in producing fuels are briefly described, followed by a more thorough treatment of commodity chemicals, specialty chemicals, pharmaceuticals, and nutraceuticals. Throughout this review, an emphasis is placed on how synthetic biology tools are applied to strain engineering. Finally, we discuss organism and host strain diversity and provide a future outlook in the field.

The Contribution of CALL to Advanced-Level Foreign/Second Language Instruction

ERIC Educational Resources Information Center

Burston, Jack; Arispe, Kelly

2016-01-01

This paper evaluates the contribution of instructional technology to advanced-level foreign/second language learning (AL2) over the past thirty years. It is shown that the most salient feature of AL2 practice and associated Computer-Assisted Language Learning (CALL) research are their rarity and restricted nature. Based on an analysis of four…

Recent advances in the molecular and cellular biology of bunyaviruses.

PubMed

Walter, Cheryl T; Barr, John N

2011-11-01

The family Bunyaviridae of segmented, negative-stranded RNA viruses includes over 350 members that infect a bewildering variety of animals and plants. Many of these bunyaviruses are the causative agents of serious disease in their respective hosts, and are classified as emerging viruses because of their increased incidence in new populations and geographical locations throughout the world. Emerging bunyaviruses, such as Crimean-Congo hemorrhagic fever virus, tomato spotted wilt virus and Rift Valley fever virus, are currently attracting great interest due to migration of their arthropod vectors, a situation possibly linked to climate change. These and other examples of continued emergence suggest that bunyaviruses will probably continue to pose a sustained global threat to agricultural productivity, animal welfare and human health. The threat of emergence is particularly acute in light of the lack of effective preventative or therapeutic treatments for any of these viruses, making their study an important priority. This review presents recent advances in the understanding of the bunyavirus life cycle, including aspects of their molecular, cellular and structural biology. Whilst special emphasis is placed upon the emerging bunyaviruses, we also describe the extensive body of work involving model bunyaviruses, which have been the subject of major contributions to our overall understanding of this important group of viruses.

Increasing advance personal planning: the need for action at the community level.

PubMed

Waller, Amy; Sanson-Fisher, Rob; Ries, Nola; Bryant, Jamie

2018-05-09

Advance personal planning is the process by which people consider, document and communicate their preferences for personal, financial and health matters in case they lose the ability to make decisions or express their wishes in the future. Advance personal planning is most often undertaken by individuals who are seriously ill, often in the context of a medical crisis and/or at the time of admission to hospital. However, the clinical utility and legal validity of the planning process may be compromised in these circumstances. Patients may lack sufficient capacity to meaningfully engage in advance personal planning; there may be insufficient time to adequately reflect on and discuss wishes with key others; and there may also be limited opportunity for inter-professional input and collaboration in the process. Here, we propose an agenda for research to advance the science of advance personal planning by promoting a 'whole community' approach. Adoption of advance personal planning at a community level may be achieved using a variety of strategies including public media campaigns, intervening with professionals across a range of health care and legal settings, and mobilising support from influential groups and local government. One potentially promising method for encouraging earlier adoption of advance personal planning among a broader population involves a community action approach, whereby multiple evidence-based strategies are integrated across multiple access points. Community action involves calling on community members, professionals, community and/or government organisations to work collaboratively to design and systematically implement intervention strategies with the aim of bringing about desired behaviour change. An example of a community action trial to improving uptake and quality of advance personal planning is described. While promising, there is a need for rigorous evidence to demonstrate whether a community action approach is effective in

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

PubMed

Beach, Dale L; Alvarez, Consuelo J

2015-12-01

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

Gastric cancer: a primer on the epidemiology and biology of the disease and an overview of the medical management of advanced disease.

PubMed

Shah, Manish A; Kelsen, David P

2010-04-01

Gastric cancer is a cause of significant morbidity and cancer-related mortality worldwide. Despite recent advances in targeted therapy and understanding of the biology and development of the malignancy, progress in the treatment of gastric cancer has been limited. Most newly diagnosed patients will present with incurable disease, and have a median survival of less than 1 year. Although the disease has widespread ethnic and epidemiologic differences, medical management of gastric cancer does not distinguish among the various disease subtypes. The recent report of the ToGA phase III study has validated Her2 as a molecular target in this disease, supporting the concept that a greater understanding of the biology of gastric cancer subsets may improve treatment selection and overall outcome of individual patients. This article summarizes the epidemiology and ethnic variation of this disease to crystalize subtypes of gastric cancer in the context of current and future medical management of advanced disease.

Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals.

PubMed

Susaki, Etsuo A; Ueda, Hiroki R

2016-01-21

Organism-level systems biology aims to identify, analyze, control and design cellular circuits in organisms. Many experimental and computational approaches have been developed over the years to allow us to conduct these studies. Some of the most powerful methods are based on using optical imaging in combination with fluorescent labeling, and for those one of the long-standing stumbling blocks has been tissue opacity. Recently, the solutions to this problem have started to emerge based on whole-body and whole-organ clearing techniques that employ innovative tissue-clearing chemistry. Here, we review these advancements and discuss how combining new clearing techniques with high-performing fluorescent proteins or small molecule tags, rapid volume imaging and efficient image informatics is resulting in comprehensive and quantitative organ-wide, single-cell resolution experimental data. These technologies are starting to yield information on connectivity and dynamics in cellular circuits at unprecedented resolution, and bring us closer to system-level understanding of physiology and diseases of complex mammalian systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Growing trend of CE at the omics level: the frontier of systems biology.

PubMed

Oh, Eulsik; Hasan, Md Nabiul; Jamshed, Muhammad; Park, Soo Hyun; Hong, Hye-Min; Song, Eun Joo; Yoo, Young Sook

2010-01-01

In a novel attempt to comprehend the complexity of life, systems biology has recently emerged as a state-of-the-art approach for biological research in contrast to the reductionist approaches that have been used in molecular cell biology since the 1950s. Because a massive amount of information is required in many systems biology studies of life processes, we have increasingly come to depend on techniques that provide high-throughput omics data. CE and CE coupled to MS have served as powerful analytical tools for providing qualitative and quantitative omics data. Recent systems biology studies have focused strongly on the diagnosis and treatment of diseases. The increasing number of clinical research papers on drug discovery and disease therapies reflects this growing interest among scientists. Since such clinical research reflects one of the ultimate purposes of bioscience, these trends will be sustained for a long time. Thus, this review mainly focuses on the application of CE and CE-MS in diagnosis as well as on the latest CE methods developed. Furthermore, we outline the new challenges that arose in 2008 and later in elucidating the system-level functions of the bioconstituents of living organisms.

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

PubMed

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

2010-01-01

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

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

PubMed Central

Davies, Robin; Hodge, Terrell; Enyedi, Alexander

2010-01-01

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

Advanced imaging techniques for the study of plant growth and development.

PubMed

Sozzani, Rosangela; Busch, Wolfgang; Spalding, Edgar P; Benfey, Philip N

2014-05-01

A variety of imaging methodologies are being used to collect data for quantitative studies of plant growth and development from living plants. Multi-level data, from macroscopic to molecular, and from weeks to seconds, can be acquired. Furthermore, advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions. Image-processing capabilities allow for 3D or 4D reconstruction of image data and automated quantification of biological features. These advances facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mediating between Discourse Worlds: Developing the Symbolic Competence of Advanced-Level Bilingual Learners of Japanese through Translation

ERIC Educational Resources Information Center

Koshiba, Kenta

2017-01-01

This paper explores the role that translation may play in developing the symbolic competence of advanced-level bilingual learners. To this end, it examines how a group of bilingual learners engaged with a translation task that was assigned to them as part of their study in an advanced-level Japanese language class at an Australian university.…

Desegregating undergraduate mathematics and biology--interdisciplinary instruction with emphasis on ongoing biomedical research.

PubMed

Robeva, Raina

2009-01-01

The remarkable advances in the field of biology in the last decade, specifically in the areas of biochemistry, genetics, genomics, proteomics, and systems biology, have demonstrated how critically important mathematical models and methods are in addressing questions of vital importance for these disciplines. There is little doubt that the need for utilizing and developing mathematical methods for biology research will only grow in the future. The rapidly increasing demand for scientists with appropriate interdisciplinary skills and knowledge, however, is not being reflected in the way undergraduate mathematics and biology courses are structured and taught in most colleges and universities nationwide. While a number of institutions have stepped forward and addressed this need by creating and offering interdisciplinary courses at the juncture of mathematics and biology, there are still many others at which there is little, if any, interdisciplinary interaction between the curricula. This chapter describes an interdisciplinary course and a textbook in mathematical biology developed collaboratively by faculty from Sweet Briar College and the University of Virginia School of Medicine. The course and textbook are designed to provide a bridge between the mathematical and biological sciences at the lower undergraduate level. The course is developed for and is being taught in a liberal arts setting at Sweet Briar College, Virginia, but some of the advanced modules are used in a course at the University of Virginia for advanced undergraduate and beginning graduate students. The individual modules are relatively independent and can be used as stand-alone projects in conventional mathematics and biology courses. Except for the introductory material, the course and textbook topics are based on current biomedical research.

Synthetic Biology: Putting Synthesis into Biology

PubMed Central

Liang, Jing; Luo, Yunzi; Zhao, Huimin

2010-01-01

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

The superconducting high-resolution soft X-ray spectrometer at the advanced biological and environmental X-ray facility

NASA Astrophysics Data System (ADS)

Friedrich, S.; Drury, O. B.; George, S. J.; Cramer, S. P.

2007-11-01

We have built a 36-pixel superconducting tunnel junction X-ray spectrometer for chemical analysis of dilute samples in the soft X-ray band. It offers an energy resolution of ˜10-20 eV FWHM below 1 keV, a solid angle coverage of ˜10 -3, and can be operated at total rates of up to ˜10 6 counts/s. Here, we describe the spectrometer performance in speciation measurements by fluorescence-detected X-ray absorption spectroscopy at the Advanced Biological and Environmental X-ray facility at the ALS synchrotron.

Interdisciplinary education - a predator-prey model for developing a skill set in mathematics, biology and technology

NASA Astrophysics Data System (ADS)

van der Hoff, Quay

2017-08-01

The science of biology has been transforming dramatically and so the need for a stronger mathematical background for biology students has increased. Biological students reaching the senior or post-graduate level often come to realize that their mathematical background is insufficient. Similarly, students in a mathematics programme, interested in biological phenomena, find it difficult to master the complex systems encountered in biology. In short, the biologists do not have enough mathematics and the mathematicians are not being taught enough biology. The need for interdisciplinary curricula that includes disciplines such as biology, physical science, and mathematics is widely recognized, but has not been widely implemented. In this paper, it is suggested that students develop a skill set of ecology, mathematics and technology to encourage working across disciplinary boundaries. To illustrate such a skill set, a predator-prey model that contains self-limiting factors for both predator and prey is suggested. The general idea of dynamics, is introduced and students are encouraged to discover the applicability of this approach to more complex biological systems. The level of mathematics and technology required is not advanced; therefore, it is ideal for inclusion in a senior-level or introductory graduate-level course for students interested in mathematical biology.

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.

Process for measuring low cadmium levels in blood and other biological specimens

DOEpatents

Peterson, David P.; Huff, Edmund A.; Bhattacharyya, Maryka H.

1994-01-01

A process for measuring low levels of cadmium in blood and other biological specimens is provided without interference from high levels of alkali metal contaminants by forming an aqueous solution and without contamination by environmental cadmium absent the proteins from the specimen, selectively removing cadmium from the aqueous solution on an anion exchange resin, thereby removing the alkali metal contaminants, resolubilizing cadmium from the resin to form a second solution and analyzing the second solution for cadmium, the process being carried out in a cadmium-free environment.

Process for measuring low cadmium levels in blood and other biological specimens

DOEpatents

Peterson, David P.; Huff, Edmund A.; Bhattacharyya, Maryka H.

1994-05-03

A process for measuring low levels of cadmium in blood and other biological specimens is provided without interference from high levels of alkali metal contaminants by forming an aqueous solution and without contamination by environmental cadmium absent the proteins from the specimen, selectively removing cadmium from the aqueous solution on an anion exchange resin, thereby removing the alkali metal contaminants, resolubilizing cadmium from the resin to form a second solution and analyzing the second solution for cadmium, the process being carried out in a cadmium-free environment.

Biologic Treatments for Sports Injuries II Think Tank—Current Concepts, Future Research, and Barriers to Advancement, Part 2

PubMed Central

Murray, Iain R.; LaPrade, Robert F.; Musahl, Volker; Geeslin, Andrew G.; Zlotnicki, Jason P.; Mann, Barton J.; Petrigliano, Frank A.

2016-01-01

Rotator cuff tears are common and result in considerable morbidity. Tears within the tendon substance or at its insertion into the humeral head represent a considerable clinical challenge because of the hostile local environment that precludes healing. Tears often progress without intervention, and current surgical treatments are inadequate. Although surgical implants, instrumentation, and techniques have improved, healing rates have not improved, and a high failure rate remains for large and massive rotator cuff tears. The use of biologic adjuvants that contribute to a regenerative microenvironment have great potential for improving healing rates and function after surgery. This article presents a review of current and emerging biologic approaches to augment rotator cuff tendon and muscle regeneration focusing on the scientific rationale, preclinical, and clinical evidence for efficacy, areas for future research, and current barriers to advancement and implementation. PMID:27099865

Metabolic systems biology: a brief primer.

PubMed

Edwards, Lindsay M

2017-05-01

In the early to mid-20th century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome. The complexity and scale of these data require computational models for their interpretation. The combination of these - systems thinking, high-dimensional data and computation - defines systems biology, typically accompanied by some notion of iterative model refinement. Only sequencing-based technologies, however, offer full coverage. Other 'omics' platforms trade coverage for sensitivity, although the densely connected nature of biological networks suggests that full coverage may not be necessary. Systems biology models are often characterised as either 'bottom-up' (mechanistic) or 'top-down' (statistical). This distinction can mislead, as all models rely on data and all are, to some degree, 'middle-out'. Systems biology has matured as a discipline, and its methods are commonplace in many laboratories. However, many challenges remain, especially those related to large-scale data integration. © 2016 The Authors. The Journal of Physiology © 2016 The Physiological Society.

Applications of Microfluidics in Quantitative Biology.

PubMed

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

2018-05-01

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

Fostering synergy between cell biology and systems biology.

PubMed

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

2015-08-01

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

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.

Team-Teaching a Current Events-Based Biology Course for Nonmajors

ERIC Educational Resources Information Center

Bondos, Sarah E.; Phillips, Dereth

2008-01-01

Rice University has created a team-taught interactive biology course for nonmajors with a focus on cutting edge biology in the news--advances in biotechnology, medicine, and science policy, along with the biological principles and methodology upon which these advances are based. The challenges inherent to teaching current topics were minimized by…

Antibiotic resistance shaping multi-level population biology of bacteria

PubMed Central

Baquero, Fernando; Tedim, Ana P.; Coque, Teresa M.

2013-01-01

Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent “population biologies.” Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of “clinical” antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level

Antibiotic resistance shaping multi-level population biology of bacteria.

PubMed

Baquero, Fernando; Tedim, Ana P; Coque, Teresa M

2013-01-01

Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level

Using the Biology Card Sorting Task to Measure Changes in Conceptual Expertise during Postsecondary Biology Education

PubMed Central

Bissonnette, Sarah A.; Combs, Elijah D.; Nagami, Paul H.; Byers, Victor; Fernandez, Juliana; Le, Dinh; Realin, Jared; Woodham, Selina; Smith, Julia I.; Tanner, Kimberly D.

2017-01-01

While there have been concerted efforts to reform undergraduate biology toward teaching students to organize their conceptual knowledge like experts, there are few tools that attempt to measure this. We previously developed the Biology Card Sorting Task (BCST), designed to probe how individuals organize their conceptual biological knowledge. Previous results showed the BCST could differentiate between different populations, namely non–biology majors (NBM) and biology faculty (BF). In this study, we administered the BCST to three additional populations, using a cross-sectional design: entering biology majors (EBM), advanced biology majors (ABM), and biology graduate students (BGS). Intriguingly, ABM did not initially sort like experts any more frequently than EBM. However, once the deep-feature framework was revealed, ABM were able to sort like experts more readily than did EBM. These results are consistent with the conclusion that biology education enables advanced biology students to use an expert-like conceptual framework. However, these results are also consistent with a process of “selection,” wherein students who persist in the major may have already had an expert-like conceptual framework to begin with. These results demonstrate the utility of the BCST in measuring differences between groups of students over the course of their undergraduate education. PMID:28213584

Biological efficacy and toxic effect of emergency water disinfection process based on advanced oxidation technology.

PubMed

Tian, Yiping; Yuan, Xiaoli; Xu, Shujing; Li, Rihong; Zhou, Xinying; Zhang, Zhitao

2015-12-01

An innovative and removable water treatment system consisted of strong electric field discharge and hydrodynamic cavitation based on advanced oxidation technologies was developed for reactive free radicals producing and waterborne pathogens eliminating in the present study. The biological efficacy and toxic effects of this advanced oxidation system were evaluated during water disinfection treatments. Bench tests were carried out with synthetic microbial-contaminated water, as well as source water in rainy season from a reservoir of Dalian city (Liaoning Province, China). Results showed that high inactivation efficiency of Escherichia coli (>5 log) could be obtained for synthetic contaminated water at a low concentration (0.5-0.7 mg L(-1)) of total oxidants in 3-10 s. The numbers of wild total bacteria (108 × 10(3) CFU mL(-1)) and total coliforms (260 × 10(2) MPN 100 mL(-1)) in source water greatly reduced to 50 and 0 CFU mL(-1) respectively after treated by the advanced oxidation system, which meet the microbiological standards of drinking water, and especially that the inactivation efficiency of total coliforms could reach 100%. Meanwhile, source water qualities were greatly improved during the disinfection processes. The values of UV254 in particular were significantly reduced (60-80%) by reactive free radicals. Moreover, the concentrations of possible disinfection by-products (formaldehyde and bromide) in treated water were lower than detection limits, indicating that there was no harmful effect on water after the treatments. These investigations are helpful for the ecotoxicological studies of advanced oxidation system in the treatments of chemical polluted water or waste water. The findings of this work suggest that the developed water treatment system is ideal in the acute phases of emergencies, which also could offer additional advantages over a wide range of applications in water pollution control.

Ensuring Biologics Advanced Development and Manufacturing Capability for the United States Government: A Summary of Key Findings and Conclusions

DTIC Science & Technology

2009-10-06

Government: A Summary of Key Findings and Conclusions. This report has passed the Department of Defense’s security review process and is approved for...manufacturing and combine advance development and production of biologics in a multi-product facility focused on satisfying USG needs. Finally, the study...MCM needs of both DoD and HHS, an extensive survey was conducted. This included a review of all published requirements, the biodefense R&D portfolio

Advances and unresolved challenges in the structural characterization of isomeric lipids.

PubMed

Hancock, Sarah E; Poad, Berwyck L J; Batarseh, Amani; Abbott, Sarah K; Mitchell, Todd W

2017-05-01

As the field of lipidomics grows and its application becomes wide and varied it is important that we don't forget its foundation, i.e. the identification and measurement of molecular lipids. Advances in liquid chromatography and the emergence of ion mobility as a useful tool in lipid analysis are allowing greater separation of lipid isomers than ever before. At the same time, novel ion activation techniques, such as ozone-induced dissociation, are pushing lipid structural characterization by mass spectrometry to new levels. Nevertheless, the quantitative capacity of these techniques is yet to be proven and further refinements are required to unravel the high level of lipid complexity found in biological samples. At present there is no one technique capable of providing full structural characterization of lipids from a biological sample. There are however, numerous techniques now available (as discussed in this review) that could be deployed in a targeted approach. Moving forward, the combination of advanced separation and ion activation techniques is likely to provide mass spectrometry-based lipidomics with its best opportunity to achieve complete molecular-level lipid characterization and measurement from complex mixtures. Crown Copyright © 2016. Published by Elsevier Inc. All rights reserved.

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

PubMed Central

Beach, Dale L.; Alvarez, Consuelo J.

2015-01-01

Synthetic biology offers an ideal opportunity to promote undergraduate laboratory courses with research-style projects, immersing students in an inquiry-based program that enhances the experience of the scientific process. We designed a semester-long, project-based laboratory curriculum using synthetic biology principles to develop a novel sensory device. Students develop subject matter knowledge of molecular genetics and practical skills relevant to molecular biology, recombinant DNA techniques, and information literacy. During the spring semesters of 2014 and 2015, the Synthetic Biology Laboratory Project was delivered to sophomore genetics courses. Using a cloning strategy based on standardized BioBrick genetic “parts,” students construct a “reporter plasmid” expressing a reporter gene (GFP) controlled by a hybrid promoter regulated by the lac-repressor protein (lacI). In combination with a “sensor plasmid,” the production of the reporter phenotype is inhibited in the presence of a target environmental agent, arabinose. When arabinose is absent, constitutive GFP expression makes cells glow green. But the presence of arabinose activates a second promoter (pBAD) to produce a lac-repressor protein that will inhibit GFP production. Student learning was assessed relative to five learning objectives, using a student survey administered at the beginning (pre-survey) and end (post-survey) of the course, and an additional 15 open-ended questions from five graded Progress Report assignments collected throughout the course. Students demonstrated significant learning gains (p < 0.05) for all learning outcomes. Ninety percent of students indicated that the Synthetic Biology Laboratory Project enhanced their understanding of molecular genetics. The laboratory project is highly adaptable for both introductory and advanced courses. PMID:26753032

The Singapore-Cambridge General Certificate of Education Advanced-Level General Paper Examination

ERIC Educational Resources Information Center

Hassan, Nurul Huda; Shih, Chih-Min

2013-01-01

This article describes and reviews the Singapore-Cambridge General Certificate of Education Advanced Level General Paper (GP) examination. As a written test that is administered to preuniversity students, the GP examination is internationally recognised and accepted by universities and employers as proof of English competence. In this article, the…

Institute for Genomics and Systems Biology

Science.gov Websites

Institute for Genomics and Systems Biology Discover. Predict. Improve. Advancing Human and , 2015 See all Research Papers Featured Video Introduction to Systems Biology Video: Introduction to Systems Biology News Jack Gilbert Heading UChicago Startup that Aims to Predict Behavior of Trillions of

Deep Neural Networks: A New Framework for Modeling Biological Vision and Brain Information Processing.

PubMed

Kriegeskorte, Nikolaus

2015-11-24

Recent advances in neural network modeling have enabled major strides in computer vision and other artificial intelligence applications. Human-level visual recognition abilities are coming within reach of artificial systems. Artificial neural networks are inspired by the brain, and their computations could be implemented in biological neurons. Convolutional feedforward networks, which now dominate computer vision, take further inspiration from the architecture of the primate visual hierarchy. However, the current models are designed with engineering goals, not to model brain computations. Nevertheless, initial studies comparing internal representations between these models and primate brains find surprisingly similar representational spaces. With human-level performance no longer out of reach, we are entering an exciting new era, in which we will be able to build biologically faithful feedforward and recurrent computational models of how biological brains perform high-level feats of intelligence, including vision.

The Generalizability of Students' Interests in Biology Across Gender, Country and Religion

NASA Astrophysics Data System (ADS)

Hagay, G.; Baram-Tsabari, A.; Ametller, J.; Cakmakci, G.; Lopes, B.; Moreira, A.; Pedrosa-de-Jesus, H.

2013-06-01

In order to bridge the existing gap between biology curricula and students' interests in biology, a strategy for identifying students' interest based on their questions and integrating them into the curriculum was developed. To characterize the level of generalizability of students' science interests over 600 high school students from Portugal, Turkey, England and Israel, who chose biology as an advanced subject, their interest level was ranked in 36 questions that were originally raised by Israeli students. Results indicate that students from four different countries show interest in similar science questions. The most intriguing questions were the ones that dealt with human health and new developments in reproduction and genetics. Religious affiliation had the strongest effect on students' interest level, followed by national affiliation and gender. The findings suggest that students' interest in one context is relevant to the development of interest-based learning materials in a different context. However, despite these similarities, cultural and sociological differences need to be taken into account.

Are food advanced glycation end products toxic in biological systems?

PubMed

Chuyen, N V; Arai, H; Nakanishi, T; Utsunomiya, N

2005-06-01

Model food advanced glycation end products (AGEs) were prepared as glycated casein (GC) and glycated soy protein (GS) by the reaction of casein or soy protein with glucose at 50 degrees C, relative humidity 75% for seven days in a powder state. These browned proteins were used as materials for animal experiments. A mixture of 20% glycated proteins (GC:GS = 1:1) diet was fed to streptozotocin (STZ)-diabetic rats for 11 weeks. The results showed that: (1) fructoselysine was observed in the hepatic portal veins, arteries, and femoral veins of rats fed with glycated proteins after 2 h of feeding; (2) blood sugar of glycated protein-fed rats was lower than that of diabetic rats fed with intact protein, while HbA1C in blood and glucose in urine of both groups were similar; (3) lipid peroxidation status in serum, liver, and kidney of both groups was similar; (4) superoxide dismutase (SOD) and glutathione-S-transferase (GST) enzymatic activity in serum and liver of both groups were also similar; (5) there were no differences in degree of cataract formation and concentration of glucose, fructose, sorbitol, and lipid peroxide in the lenses of both groups. From the above results, it can be estimated that food AGEs are not toxic in biological systems, and reactive oxygen species increase in diabetic rats is not caused by glycated proteins but by other pathways.

Advancing Biological Understanding and Therapeutics Discovery with Small Molecule Probes

PubMed Central

Schreiber, Stuart L.; Kotz, Joanne D.; Li, Min; Aubé, Jeffrey; Austin, Christopher P.; Reed, John C.; Rosen, Hugh; White, E. Lucile; Sklar, Larry A.; Lindsley, Craig W.; Alexander, Benjamin R.; Bittker, Joshua A.; Clemons, Paul A.; de Souza, Andrea; Foley, Michael A.; Palmer, Michelle; Shamji, Alykhan F.; Wawer, Mathias J.; McManus, Owen; Wu, Meng; Zou, Beiyan; Yu, Haibo; Golden, Jennifer E.; Schoenen, Frank J.; Simeonov, Anton; Jadhav, Ajit; Jackson, Michael R.; Pinkerton, Anthony B.; Chung, Thomas D.Y.; Griffin, Patrick R.; Cravatt, Benjamin F.; Hodder, Peter S.; Roush, William R.; Roberts, Edward; Chung, Dong-Hoon; Jonsson, Colleen B.; Noah, James W.; Severson, William E.; Ananthan, Subramaniam; Edwards, Bruce; Oprea, Tudor I.; Conn, P. Jeffrey; Hopkins, Corey R.; Wood, Michael R.; Stauffer, Shaun R.; Emmitte, Kyle A.

2015-01-01

Small-molecule probes can illuminate biological processes and aid in the assessment of emerging therapeutic targets by perturbing biological systems in a manner distinct from other experimental approaches. Despite the tremendous promise of chemical tools for investigating biology and disease, small-molecule probes were unavailable for most targets and pathways as recently as a decade ago. In 2005, the U.S. National Institutes of Health launched the decade-long Molecular Libraries Program with the intent of innovating in and broadening access to small-molecule science. This Perspective describes how novel small-molecule probes identified through the program are enabling the exploration of biological pathways and therapeutic hypotheses not otherwise testable. These experiences illustrate how small-molecule probes can help bridge the chasm between biological research and the development of medicines, but also highlight the need to innovate the science of therapeutic discovery. PMID:26046436

[THE INCONSISTENCIES OF REGULATION OF METABOLISM IN PHYLOGENESIS AT THREE LEVELS OF "RELATIVE BIOLOGICAL PERFECTION": ETIOLOGY OF METABOLIC PANDEMICS].

PubMed

Titov, V N

2015-11-01

The regulation of metabolism in vivo can be comprehended by considering stages of becoming inphylogenesis of humoral, hormonal, vegetative regulators separately: at the level of cells; in paracrin-regulated cenosises of cells; organs and systems under open blood circulation and closed system of blood flow. The levels of regulations formed at different stages of phylogenesis. Their completion occurred at achievement of "relative biological perfection". Only this way need of cells in functional, structural interaction and forming of multicellular developed. The development of organs and systems of organs also completed at the level of "relative biological perfection". From the same level the third stage of becoming of regulation of metabolism at the level of organism started. When three conditions of "relative biological perfection" achieved consequently at level in vivo are considered in species Homo sapiens using system approach it is detected that "relative biological perfection" in vivo is accompanied by different inconsistencies of regulation of metabolism. They are etiologic factors of "metabolic pandemics ". The inconsistencies (etiological factors) are consider as exemplified by local (at the level of paracrin-regulated cenosises of cells) and system (at the level of organism) regulation of biological reaction metabolism-microcirculation that results in dysfunction of target organs and development of pathogenesis of essential metabolic arterial hypertension. The article describes phylogenetic difference between visceral fatty cells and adpocytes, regulation of metabolism by phylogenetically late insulin, reaction of albumin at increasing of content of unesterified fatty acids in blood plasma, difference of function of resident macrophage and monocytes-macrophages in pathogenesis of atherosclerosis, metabolic syndrome, insulin resistance, obesity, under diabetes mellitus and essential metabolic arterial hypertension.

Incentivizing Advanced Mathematics Study at Upper Secondary Level: The Case of Bonus Points in Ireland

ERIC Educational Resources Information Center

Treacy, Páraic Thomas

2018-01-01

Secondary level mathematics education in Ireland has recently experienced a period of significant change with the introduction of new curricula and the addition of an incentive to study upper secondary mathematics at the most advanced level (Higher Level). This incentive, typically referred to as 'bonus points', appears to have aided a significant…

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

PubMed

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

2016-01-01

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

Impact of mandibular advancement devices on C-reactive protein levels in patients with obstructive sleep apnea.

PubMed

Yalamanchali, Sreeya; Salapatas, Anna M; Hwang, Michelle S; Pott, Thomas R; Lundgren, Mary E; Joseph, Ninos J; Friedman, Michael

2015-07-01

To determine the effect of treatment of obstructive sleep apnea (OSA) with custom-made mandibular advancement devices (MADs) on C-reactive protein (CRP) levels in patients with obstructive sleep apnea/hypopnea syndrome (OSAHS). Case series with chart review. Charts of consecutive patients fitted with custom-made mandibular advancement devices for treatment of OSAHS between December 2011 and November 2012 were reviewed. Demographics such as age, sex, and body mass index (BMI) were collected. Prefitting and postfitting polysomnograms were reviewed. Pre- and posttreatment apnea-hypopnea index (AHI) and average O2 saturation were compared. Only patients with documented CRP levels determined prior to mandibular advancement device fitting and again after improvement of OSAHS symptoms were included. Forty-nine patients (77.6% male, age 47.4 ± 11.7 years, BMI 29.6 ± 5.0 kg/m(2)) were included in this study. Patients initially had elevated CRP levels (2.5 ± 1.8 mg/dl), which decreased significantly following use of their custom-made mandibular advancement device (1.9 ± 1.3 mg/dl, P = 0.006) by approximately 24%. AHI decreased significantly from 33.3 ± 21.7 pretreatment to 12.1 ± 22.3 posttreatment (P < 0.001). Treatment with MADs reduced AHI by approximately 69.3%. Minimum oxygen saturation significantly improved from 85.1% ± 5.9 pretreatment to 90.7% ± 3.6 posttreatment (P < 0.001). Treatment with custom-made mandibular advancement devices significantly reduced elevated CRP levels in patients with mild to severe OSAHS. Therapy achieves reasonable response and cure rates in the observed patients with a significant reduction in AHI. © 2014 The American Laryngological, Rhinological and Otological Society, Inc.

Biology-inspired Architecture for Situation Management

NASA Technical Reports Server (NTRS)

Jones, Kennie H.; Lodding, Kenneth N.; Olariu, Stephan; Wilson, Larry; Xin, Chunsheng

2006-01-01

Situation Management is a rapidly developing science combining new techniques for data collection with advanced methods of data fusion to facilitate the process leading to correct decisions prescribing action. Current research focuses on reducing increasing amounts of diverse data to knowledge used by decision makers and on reducing time between observations, decisions and actions. No new technology is more promising for increasing the diversity and fidelity of observations than sensor networks. However, current research on sensor networks concentrates on a centralized network architecture. We believe this trend will not realize the full potential of situation management. We propose a new architecture modeled after biological ecosystems where motes are autonomous and intelligent, yet cooperate with local neighborhoods. Providing a layered approach, they sense and act independently when possible, and cooperate with neighborhoods when necessary. The combination of their local actions results in global effects. While situation management research is currently dominated by military applications, advances envisioned for industrial and business applications have similar requirements. NASA has requirements for intelligent and autonomous systems in future missions that can benefit from advances in situation management. We describe requirements for the Integrated Vehicle Health Management program where our biology-inspired architecture provides a layered approach and decisions can be made at the proper level to improve safety, reduce costs, and improve efficiency in making diagnostic and prognostic assessments of the structural integrity, aerodynamic characteristics, and operation of aircraft.

AICD -- Advanced Industrial Concepts Division Biological and Chemical Technologies Research Program. 1993 Annual summary report

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

Petersen, G.; Bair, K.; Ross, J.

1994-03-01

The annual summary report presents the fiscal year (FY) 1993 research activities and accomplishments for the United States Department of Energy (DOE) Biological and Chemical Technologies Research (BCTR) Program of the Advanced Industrial Concepts Division (AICD). This AICD program resides within the Office of Industrial Technologies (OIT) of the Office of Energy Efficiency and Renewable Energy (EE). The annual summary report for 1993 (ASR 93) contains the following: A program description (including BCTR program mission statement, historical background, relevance, goals and objectives), program structure and organization, selected technical and programmatic highlights for 1993, detailed descriptions of individual projects, a listingmore » of program output, including a bibliography of published work, patents, and awards arising from work supported by BCTR.« less

Advancements in mass spectrometry for biological samples: Protein chemical cross-linking and metabolite analysis of plant tissues

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

Klein, Adam

2015-01-01

This thesis presents work on advancements and applications of methodology for the analysis of biological samples using mass spectrometry. Included in this work are improvements to chemical cross-linking mass spectrometry (CXMS) for the study of protein structures and mass spectrometry imaging and quantitative analysis to study plant metabolites. Applications include using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to further explore metabolic heterogeneity in plant tissues and chemical interactions at the interface between plants and pests. Additional work was focused on developing liquid chromatography-mass spectrometry (LC-MS) methods to investigate metabolites associated with plant-pest interactions.

Advancements in Transmitters and Sensors for Biological Tissue Imaging in Magnetic Induction Tomography

PubMed Central

Zakaria, Zulkarnay; Rahim, Ruzairi Abdul; Mansor, Muhammad Saiful Badri; Yaacob, Sazali; Ayub, Nor Muzakkir Nor; Muji, Siti Zarina Mohd.; Rahiman, Mohd Hafiz Fazalul; Aman, Syed Mustafa Kamal Syed

2012-01-01

Magnetic Induction Tomography (MIT), which is also known as Electromagnetic Tomography (EMT) or Mutual Inductance Tomography, is among the imaging modalities of interest to many researchers around the world. This noninvasive modality applies an electromagnetic field and is sensitive to all three passive electromagnetic properties of a material that are conductivity, permittivity and permeability. MIT is categorized under the passive imaging family with an electrodeless technique through the use of excitation coils to induce an electromagnetic field in the material, which is then measured at the receiving side by sensors. The aim of this review is to discuss the challenges of the MIT technique and summarize the recent advancements in the transmitters and sensors, with a focus on applications in biological tissue imaging. It is hoped that this review will provide some valuable information on the MIT for those who have interest in this modality. The need of this knowledge may speed up the process of adopted of MIT as a medical imaging technology. PMID:22969341

Symptom Levels in Care-Seeking Bangladeshi and Nepalese Adults With Advanced Cancer

PubMed Central

Ferdousy, Tahmina; Paudel, Bishnu D.; Nahar, Shamsun; Dowla, Rumana; Adibuzzaman, Mohammad; Ahsan, Golam Mushih Tanimul; Uddin, Miftah; Salim, Reza; Ahamed, Sheikh Iqbal

2017-01-01

Purpose Three-fourths of patients with advanced cancer are reported to suffer from pain. A primary barrier to provision of adequate symptom treatment is failure to appreciate the intensity of the symptoms patients are experiencing. Because data on Bangladeshi and Nepalese patients’ perceptions of their symptomatic status are limited, we sought such information using a cell phone questionnaire. Methods At tertiary care centers in Dhaka and Kathmandu, we recruited 640 and 383 adult patients, respectively, with incurable malignancy presenting for outpatient visits and instructed them for that single visit on one-time completion of a cell phone platform 15-item survey of questions about common cancer-associated symptoms and their magnitudes using Likert scales of 0 to 10. The questions were taken from the Edmonton Symptom Assessment System and the Brief Pain Inventory instruments. Results All but two Bangladeshi patients recruited agreed to study participation. Two-thirds of Bangladeshi patients reported usual pain levels ≥ 5, and 50% of Nepalese patients reported usual pain levels ≥ 4 (population differences significant at P < .001). Conclusion Bangladeshi and Nepalese adults with advanced cancer are comfortable with cell phone questionnaires about their symptoms and report high levels of pain. Greater attention to the suffering of these patients is warranted. PMID:28717768

French on the Advanced Level.

ERIC Educational Resources Information Center

Pawlik, Teresa Wilkinson

1969-01-01

Presented in this article is an outline of some of the special interest course work included in the curriculum guidelines being developed in the Atlanta Public Schools System for advanced secondary school French classes. Titles of the audiolingually-oriented courses described are--(1) "Teenagers and Teenage Life in France Today," (2)…

The role of differentiation and standards-based grading in the science learning of struggling and advanced learners in a detracked high school honors biology classroom

NASA Astrophysics Data System (ADS)

MacDonald, Michelina Ruth Carter

The accountability movement in education resulting from the passage of The No Child Left Behind Act of 2001 has brought to light the disparities that exist in student achievement in the United States which play out along racial and socioeconomic lines. Three educational practices hold promise for reducing this achievement gap: differentiated instruction, standards-based assessment, and elimination of academic tracking. The purpose of this practitioner research study was to examine the ways that differentiation and standards-based assessment can support struggling learners and challenge advanced learners in a detracked, honors biology classroom. To gain insight into the role that differentiation and standards-based assessment played in supporting struggling and advanced learners, I used practitioner research to examine the development and implementation of a differentiated, standards-based instructional unit around the conceptual topic of protein synthesis. I collected multiple data pieces for 10 students in the study: two advanced learners, four struggling learners, and four strong learners who struggled in biology. Data analyzed included formative, self-, and summative assessment results; student artifacts; informal and formal student interviews; and, a practitioner reflection journal chronicling critical incidents and actions taken during the development and implementation of this unit and notes from peer debriefing during and following the unit's implementation. As I analyzed the data collected, my four findings fell into two overarching categories related to student grouping. My first three findings reflect what I learned about homogeneous grouping: (1) Pre-assessment based on unit outcomes is not useful for determining groups for tiered instruction; (2) Decisions about differentiation and grouping for differentiation must be made in the act of teaching using formative assessment results; and, (3) Flexible grouping structures are effective for both struggling

Chemical Biology Probes from Advanced DNA-encoded Libraries.

PubMed

Salamon, Hazem; Klika Škopić, Mateja; Jung, Kathrin; Bugain, Olivia; Brunschweiger, Andreas

2016-02-19

The identification of bioactive compounds is a crucial step toward development of probes for chemical biology studies. Screening of DNA-encoded small molecule libraries (DELs) has emerged as a validated technology to interrogate vast chemical space. DELs consist of chimeric molecules composed of a low-molecular weight compound that is conjugated to a DNA identifier tag. They are screened as pooled libraries using selection to identify "hits." Screening of DELs has identified numerous bioactive compounds. Some of these molecules were instrumental in gaining a deeper understanding of biological systems. One of the main challenges in the field is the development of synthesis methodology for DELs.

Predicting in vivo effect levels for repeat-dose systemic toxicity using chemical, biological, kinetic and study covariates.

PubMed

Truong, Lisa; Ouedraogo, Gladys; Pham, LyLy; Clouzeau, Jacques; Loisel-Joubert, Sophie; Blanchet, Delphine; Noçairi, Hicham; Setzer, Woodrow; Judson, Richard; Grulke, Chris; Mansouri, Kamel; Martin, Matthew

2018-02-01

In an effort to address a major challenge in chemical safety assessment, alternative approaches for characterizing systemic effect levels, a predictive model was developed. Systemic effect levels were curated from ToxRefDB, HESS-DB and COSMOS-DB from numerous study types totaling 4379 in vivo studies for 1247 chemicals. Observed systemic effects in mammalian models are a complex function of chemical dynamics, kinetics, and inter- and intra-individual variability. To address this complex problem, systemic effect levels were modeled at the study-level by leveraging study covariates (e.g., study type, strain, administration route) in addition to multiple descriptor sets, including chemical (ToxPrint, PaDEL, and Physchem), biological (ToxCast), and kinetic descriptors. Using random forest modeling with cross-validation and external validation procedures, study-level covariates alone accounted for approximately 15% of the variance reducing the root mean squared error (RMSE) from 0.96 log 10 to 0.85 log 10  mg/kg/day, providing a baseline performance metric (lower expectation of model performance). A consensus model developed using a combination of study-level covariates, chemical, biological, and kinetic descriptors explained a total of 43% of the variance with an RMSE of 0.69 log 10  mg/kg/day. A benchmark model (upper expectation of model performance) was also developed with an RMSE of 0.5 log 10  mg/kg/day by incorporating study-level covariates and the mean effect level per chemical. To achieve a representative chemical-level prediction, the minimum study-level predicted and observed effect level per chemical were compared reducing the RMSE from 1.0 to 0.73 log 10  mg/kg/day, equivalent to 87% of predictions falling within an order-of-magnitude of the observed value. Although biological descriptors did not improve model performance, the final model was enriched for biological descriptors that indicated xenobiotic metabolism gene expression, oxidative stress, and

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

PubMed

Watanabe, Shin-Ya; Numata, Shusuke; Iga, Jun-Ichi; Kinoshita, Makoto; Umehara, Hidehiro; Ishii, Kazuo; Ohmori, Tetsuro

2017-01-01

Recently, we could distinguished patients with major depressive disorder (MDD) from nonpsychiatric controls with high accuracy using a panel of five gene expression markers ( ARHGAP24, HDAC5, PDGFC, PRNP , and SLC6A4 ) in leukocyte. In the present study, we examined whether this biological test is able to discriminate patients with MDD from those without MDD, including those with schizophrenia and bipolar disorder. We measured messenger ribonucleic acid expression levels of the aforementioned five genes in peripheral leukocytes in 17 patients with schizophrenia and 36 patients with bipolar disorder using quantitative real-time polymerase chain reaction (PCR), and we combined these expression data with our previous expression data of 25 patients with MDD and 25 controls. Subsequently, a linear discriminant function was developed for use in discriminating between patients with MDD and without MDD. This expression panel was able to segregate patients with MDD from those without MDD with a sensitivity and specificity of 64% and 67.9%, respectively. Further research to identify MDD-specific markers is needed to improve the performance of this biological test.

Recent advances in superhydrophobic surfaces and their relevance to biology and medicine.

PubMed

Ciasca, G; Papi, M; Businaro, L; Campi, G; Ortolani, M; Palmieri, V; Cedola, A; De Ninno, A; Gerardino, A; Maulucci, G; De Spirito, M

2016-02-04

By mimicking naturally occurring superhydrophobic surfaces, scientists can now realize artificial surfaces on which droplets of a few microliters of water are forced to assume an almost spherical shape and an extremely high contact angle. In recent decades, these surfaces have attracted much attention due to their technological applications for anti-wetting and self-cleaning materials. Very recently, researchers have shifted their interest to investigate whether superhydrophobic surfaces can be exploited to study biological systems. This research effort has stimulated the design and realization of new devices that allow us to actively organize, visualize and manipulate matter at both the microscale and nanoscale levels. Such precise control opens up wide applications in biomedicine, as it allows us to directly manipulate objects at the typical length scale of cells and macromolecules. This progress report focuses on recent biological and medical applications of superhydrophobicity. Particular regard is paid to those applications that involve the detection, manipulation and study of extremely small quantities of molecules, and to those that allow high throughput cell and biomaterial screening.

The emerging genomics and systems biology research lead to systems genomics studies.

PubMed

Yang, Mary Qu; Yoshigoe, Kenji; Yang, William; Tong, Weida; Qin, Xiang; Dunker, A; Chen, Zhongxue; Arbania, Hamid R; Liu, Jun S; Niemierko, Andrzej; Yang, Jack Y

2014-01-01

Synergistically integrating multi-layer genomic data at systems level not only can lead to deeper insights into the molecular mechanisms related to disease initiation and progression, but also can guide pathway-based biomarker and drug target identification. With the advent of high-throughput next-generation sequencing technologies, sequencing both DNA and RNA has generated multi-layer genomic data that can provide DNA polymorphism, non-coding RNA, messenger RNA, gene expression, isoform and alternative splicing information. Systems biology on the other hand studies complex biological systems, particularly systematic study of complex molecular interactions within specific cells or organisms. Genomics and molecular systems biology can be merged into the study of genomic profiles and implicated biological functions at cellular or organism level. The prospectively emerging field can be referred to as systems genomics or genomic systems biology. The Mid-South Bioinformatics Centre (MBC) and Joint Bioinformatics Ph.D. Program of University of Arkansas at Little Rock and University of Arkansas for Medical Sciences are particularly interested in promoting education and research advancement in this prospectively emerging field. Based on past investigations and research outcomes, MBC is further utilizing differential gene and isoform/exon expression from RNA-seq and co-regulation from the ChiP-seq specific for different phenotypes in combination with protein-protein interactions, and protein-DNA interactions to construct high-level gene networks for an integrative genome-phoneme investigation at systems biology level.

A novel integration of three-dimensional electro-Fenton and biological activated carbon and its application in the advanced treatment of biologically pretreated Lurgi coal gasification wastewater.

PubMed

Hou, Baolin; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Jia, Shengyong; Li, Kun

2015-11-01

A novel integrated process with three-dimensional electro-Fenton (3D EF) and biological activated carbon (BAC) was employed in advanced treatment of biologically pretreated Lurgi coal gasification wastewater. SAC-Fe (sludge deserved activated carbon from sewage and iron sludge) and SAC (sludge deserved activated carbon) were used in 3D EF as catalytic particle electrodes (CPEs) and in BAC as carriers respectively. Results indicated that 3D EF with SAC-Fe as CPEs represented excellent pollutants and COLOR removals as well as biodegradability improvement. The efficiency enhancement attributed to generating more H2O2 and OH. The integrated process exhibited efficient performance of COD, BOD5, total phenols, TOC, TN and COLOR removals at a much shorter retention time, with the corresponding concentrations in effluent of 31.18, 6.69, 4.29, 17.82, 13.88mg/L and <20 times, allowing discharge criteria to be met. The integrated system was efficient, cost-effective and ecological sustainable and could be a promising technology for engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

Low-level luminescence as a method of detecting the UV influence on biological systems

NASA Astrophysics Data System (ADS)

Mei, Wei-Ping; Popp, Fritz A.

1995-02-01

It is well known that low-level luminescence is correlated to many physiological and biological parameters, e.g. cell cycle, temperature, oxidation- and UV-stress. We report some new approaches on low-level luminescence measurements and UV influence on different biological systems. One example concerns yeast cultures, which show an increasing intensity of luminescence after UV-treatment with a maximum after 1.5 h. Investigations on normal human fibroblasts and keratinocytes display different longtime kinetics: The former show no changes of the luminescence in time, the latter an increase that reaches the maximum after 9 h. The time-dependent spectral measurement on xeroderma pigmentosum after UV-treatment displays a time-shift of the action-spectra shifting the maximum from 400 nm to 420 nm in 12 h. Some results on neutrophils reveals spectral UV influence on respiratory burst and the cellular repair system. The results on human skin display spectral changes of low-level luminescence after UV-treatment. These results provide a useful tool of analyzing UV influence on human skin.

Advanced Applications of Next-Generation Sequencing Technologies to Orchid Biology.

PubMed

Yeh, Chuan-Ming; Liu, Zhong-Jian; Tsai, Wen-Chieh

2018-01-01

Next-generation sequencing technologies are revolutionizing biology by permitting, transcriptome sequencing, whole-genome sequencing and resequencing, and genome-wide single nucleotide polymorphism profiling. Orchid research has benefited from this breakthrough, and a few orchid genomes are now available; new biological questions can be approached and new breeding strategies can be designed. The first part of this review describes the unique features of orchid biology. The second part provides an overview of the current next-generation sequencing platforms, many of which are already used in plant laboratories. The third part summarizes the state of orchid transcriptome and genome sequencing and illustrates current achievements. The genetic sequences currently obtained will not only provide a broad scope for the study of orchid biology, but also serves as a starting point for uncovering the mystery of orchid evolution.

Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of catalytic ultrasound oxidation and membrane bioreactor.

PubMed

Jia, Shengyong; Han, Hongjun; Zhuang, Haifeng; Xu, Peng; Hou, Baolin

2015-01-01

Laboratorial scale experiments were conducted to investigate a novel system integrating catalytic ultrasound oxidation (CUO) with membrane bioreactor (CUO-MBR) on advanced treatment of biologically pretreated coal gasification wastewater. Results indicated that CUO with catalyst of FeOx/SBAC (sewage sludge based activated carbon (SBAC) which loaded Fe oxides) represented high efficiencies in eliminating TOC as well as improving the biodegradability. The integrated CUO-MBR system with low energy intensity and high frequency was more effective in eliminating COD, BOD5, TOC and reducing transmembrane pressure than either conventional MBR or ultrasound oxidation integrated MBR. The enhanced hydroxyl radical oxidation, facilitation of substrate diffusion and improvement of cell enzyme secretion were the mechanisms for CUO-MBR performance. Therefore, the integrated CUO-MBR was the promising technology for advanced treatment in engineering applications. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed

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

2018-03-01

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

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

PubMed Central

2018-01-01

Emerging infectious diseases (EIDs) pose a major threat to public health and security. Given the dynamic nature and significant impact of EIDs, the most effective way to prevent and protect against them is to develop vaccines in advance. Systems biology approaches provide an integrative way to understand the complex immune response to pathogens. They can lead to a greater understanding of EID pathogenesis and facilitate the evaluation of newly developed vaccine-induced immunity in a timely manner. In recent years, advances in high throughput technologies have enabled researchers to successfully apply systems biology methods to analyze immune responses to a variety of pathogens and vaccines. Despite recent advances, computational and biological challenges impede wider application of systems biology approaches. This review highlights recent advances in the fields of systems immunology and vaccinology, and presents ways that systems biology-based platforms can be applied to accelerate a deeper understanding of the molecular mechanisms of immunity against EIDs. PMID:29436184

The Math–Biology Values Instrument: Development of a Tool to Measure Life Science Majors’ Task Values of Using Math in the Context of Biology

PubMed Central

Andrews, Sarah E.; Runyon, Christopher; Aikens, Melissa L.

2017-01-01

In response to calls to improve the quantitative training of undergraduate biology students, there have been increased efforts to better integrate math into biology curricula. One challenge of such efforts is negative student attitudes toward math, which are thought to be particularly prevalent among biology students. According to theory, students’ personal values toward using math in a biological context will influence their achievement and behavioral outcomes, but a validated instrument is needed to determine this empirically. We developed the Math–Biology Values Instrument (MBVI), an 11-item college-level self-­report instrument grounded in expectancy-value theory, to measure life science students’ interest in using math to understand biology, the perceived usefulness of math to their life science career, and the cost of using math in biology courses. We used a process that integrates multiple forms of validity evidence to show that scores from the MBVI can be used as a valid measure of a student’s value of math in the context of biology. The MBVI can be used by instructors and researchers to help identify instructional strategies that influence math–biology values and understand how math–biology values are related to students’ achievement and decisions to pursue more advanced quantitative-based courses. PMID:28747355

Developing information fluency in introductory biology students in the context of an investigative laboratory.

PubMed

Lindquester, Gary J; Burks, Romi L; Jaslow, Carolyn R

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100 students suggest that increases occurred, some statistically significant, in the number of students using various library-related resources, in the numbers and confidence level of students using various technologies, and in the numbers and confidence levels of students involved in various activities related to the scientific method. Following this course, students should be better prepared for more advanced and independent study.

Developing Information Fluency in Introductory Biology Students in the Context of an Investigative Laboratory

PubMed Central

2005-01-01

Students of biology must learn the scientific method for generating information in the field. Concurrently, they should learn how information is reported and accessed. We developed a progressive set of exercises for the undergraduate introductory biology laboratory that combine these objectives. Pre- and postassessments of approximately 100 students suggest that increases occurred, some statistically significant, in the number of students using various library-related resources, in the numbers and confidence level of students using various technologies, and in the numbers and confidence levels of students involved in various activities related to the scientific method. Following this course, students should be better prepared for more advanced and independent study. PMID:15746979

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

PubMed

van Boxtel, Jeroen J A; Lu, Hongjing

2013-01-01

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

Impaired Global, and Compensatory Local, Biological Motion Processing in People with High Levels of Autistic Traits

PubMed Central

van Boxtel, Jeroen J. A.; Lu, Hongjing

2013-01-01

People with Autism Spectrum Disorder (ASD) are hypothesized to have poor high-level processing but superior low-level processing, causing impaired social recognition, and a focus on non-social stimulus contingencies. Biological motion perception provides an ideal domain to investigate exactly how ASD modulates the interaction between low and high-level processing, because it involves multiple processing stages, and carries many important social cues. We investigated individual differences among typically developing observers in biological motion processing, and whether such individual differences associate with the number of autistic traits. In Experiment 1, we found that individuals with fewer autistic traits were automatically and involuntarily attracted to global biological motion information, whereas individuals with more autistic traits did not show this pre-attentional distraction. We employed an action adaptation paradigm in the second study to show that individuals with more autistic traits were able to compensate for deficits in global processing with an increased involvement in local processing. Our findings can be interpreted within a predictive coding framework, which characterizes the functional relationship between local and global processing stages, and explains how these stages contribute to the perceptual difficulties associated with ASD. PMID:23630514

Providing Vertical Coherence in Explanations and Promoting Reasoning across Levels of Biological Organization When Teaching Evolution

ERIC Educational Resources Information Center

Jördens, Janina; Asshoff, Roman; Kullmann, Harald; Hammann, Marcus

2016-01-01

Students' explanations of biological phenomena are frequently characterized by disconnects between levels and confusion of levels. The purpose of this research is to investigate the effects of a hands-on lab activity that aims at fostering the ability to reason across levels. A total of 197 students (18 years of age) participated in a randomized,…

Guide for the Training and Qualification of Welding Personnel. Level II - Advanced Welders.

ERIC Educational Resources Information Center

American Welding Society, Miami, FL.

This guide is designed to help education and training facilities develop and administer competency-based training programs to qualify and certify trainees in accordance with the American Welding Society (AWS) requirements for level II (advanced) welders. Presented first are the scope, objectives, and requirements of the AWS…

Marine molecular biology: an emerging field of biological sciences.

PubMed

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

2008-01-01

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

High School and College Biology: A Multi-Level Model of the Effects of High School Courses on Introductory Course Performance

ERIC Educational Resources Information Center

Loehr, John F.; Almarode, John T.; Tai, Robert H.; Sadler, Philip M.

2012-01-01

In a climate where increasing numbers of students are encouraged to pursue post-secondary education, the level of preparedness students have for college-level coursework is not far from the minds of all educators, especially high school teachers. Specifically within the biological sciences, introductory biology classes often serve as the…

Relatives’ level of satisfaction with advanced cancer care in Greenland – a mixed methods study

PubMed Central

Augustussen, Mikaela; Hounsgaard, Lise; Pedersen, Michael Lynge; Sjøgren, Per; Timm, Helle

2017-01-01

ABSTRACT Palliative cancer care in Greenland is provided by health professionals at local level, the national Queen Ingrid’s Hospital and at Rigshospitalet in Denmark. To improve and develop care for relatives of patients with advanced cancer, we conducted a mixed method study examining relatives’ level of satisfaction with care and treatment and their current main concerns. The aim was to investigate relatives’ level of satisfaction with advanced cancer care and bring to light their current main concerns. The FAMCARE-20 questionnaire was translated to Greenlandic and pilot tested. The questionnaire was supplemented by open-ended questions about relative’s current main concerns and analyzed with a phenomenological hermeneutical approach. Greenlandic patients with advanced cancer who were previously participating in a prospective study were asked if their closest adult relative would participate in the study. Telephone interviews were conducted and relatives responded to the questionnaire. A total of thirty-two relatives were contacted by telephone and 30 (94%) completed the FAMCARE-20 questionnaire and answered open-ended questions. The highest rate of satisfaction was with the availability of a hospital bed (66%) and relatives were the most dissatisfied with the lack of inclusion in decision making related to treatment and care (71%) and the length of time required to diagnose cancer (70%). Responses to the open-ended questions revealed that relatives faced challenges in gaining access to information from health professionals. They experienced a lack of security, worries about the future and a lack of support at home. The study showed a substantial level of dissatisfaction among relatives of patients with advanced cancer. We strongly recommend a focus on psychosocial care, more access to information and to include relatives in decision making and in the future planning of palliative care services. An assessment of relatives’ needs is essential to develop

Visualizing time-related data in biology, a review

PubMed Central

Secrier, Maria; Schneider, Reinhard

2014-01-01

Time is of the essence in biology as in so much else. For example, monitoring disease progression or the timing of developmental defects is important for the processes of drug discovery and therapy trials. Furthermore, an understanding of the basic dynamics of biological phenomena that are often strictly time regulated (e.g. circadian rhythms) is needed to make accurate inferences about the evolution of biological processes. Recent advances in technologies have enabled us to measure timing effects more accurately and in more detail. This has driven related advances in visualization and analysis tools that try to effectively exploit this data. Beyond timeline plots, notable attempts at more involved temporal interpretation have been made in recent years, but awareness of the available resources is still limited within the scientific community. Here, we review some advances in biological visualization of time-driven processes and consider how they aid data analysis and interpretation. PMID:23585583

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

A Suggested Syllabus for the Advanced Level English Course at Gendarmerie Schools Command in Accordance with NATO STANAG 6001 Level 3 Perspective

ERIC Educational Resources Information Center

Solak, Ekrem

2010-01-01

The aim of this study is to prepare a suggested syllabus in accordance with NATO Stanag 6001 Level 3 perspective for the Advanced Level English Course at Gendarmerie Schools Command which is subordinate to Gendarmerie General Command. It is believed that this study will contribute to other studies in the context of NATO Stanag 6001 language…

Advanced Initiation Systems Manufacturing Level 2 Milestone Completion Summary

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

Chow, R; Schmidt, M

2009-10-01

Milestone Description - Advanced Initiation Systems Detonator Design and Prototype. Milestone Grading Criteria - Design new generation chip slapper detonator and manufacture a prototype using advanced manufacturing processes, such as all-dry chip metallization and solvent-less flyer coatings. The advanced processes have been developed for manufacturing detonators with high material compatibility and reliability to support future LEPs, e.g. the B61, and new weapons systems. Perform velocimetry measurements to determine slapper velocity as a function of flight distance. A prototype detonator assembly and stripline was designed for low-energy chip slappers. Pictures of the prototype detonator and stripline are shown. All-dry manufacturing processesmore » were used to address compatibility issues. KCP metallized the chips in a physical vapor deposition system through precision-aligned shadow masks. LLNL deposited a solvent-less polyimide flyer with a processes called SLIP, which stands for solvent-less vapor deposition followed by in-situ polymerization. LANL manufactured the high-surface-area (HSA) high explosive (HE) pellets. Test fires of two chip slapper designs, radius and bowtie, were performed at LLNL in the High Explosives Application Facility (HEAF). Test fires with HE were conducted to establish the threshold firing voltages. pictures of the chip slappers before and after test fires are shown. Velocimetry tests were then performed to obtain slapper velocities at or above the threshold firing voltages. Figure 5 shows the slapper velocity as a function of distance and time at the threshold voltage, for both radius and bowtie bridge designs. Both designs were successful at initiating the HE at low energy levels. Summary of Accomplishments are: (1) All-dry process for chip manufacture developed; (2) Solventless process for slapper materials developed; (3) High-surface area explosive pellets developed; (4) High performance chip slappers developed; (5) Low

Altered serum glyceraldehyde-derived advanced glycation end product (AGE) and soluble AGE receptor levels indicate carbonyl stress in patients with schizophrenia.

PubMed

Takeda, Mayu; Ohnuma, Tohru; Takeuchi, Masayoshi; Katsuta, Narimasa; Maeshima, Hitoshi; Takebayashi, Yuto; Higa, Motoyuki; Nakamura, Toru; Nishimon, Shohei; Sannohe, Takahiro; Hotta, Yuri; Hanzawa, Ryo; Higashiyama, Ryoko; Shibata, Nobuto; Gohda, Tomohito; Suzuki, Yusuke; Yamagishi, Sho-ichi; Tomino, Yasuhiko; Arai, Heii

2015-04-23

Recent cross-sectional and longitudinal studies indicate that measurements of peripheral blood carbonyl stress markers such as the advanced glycation end product (AGE) pentosidine and the reactive carbonyl-detoxifying B6 vitamin pyridoxal could be used as therapeutic biological markers in subpopulations of schizophrenia patients. Glyceraldehyde-derived AGEs (Glycer-AGE) have strong neurotoxicity, and soluble receptors for AGEs (sRAGE) may ameliorate the effects of AGEs. In the present study, we measured Glycer-AGEs and sRAGE levels to determine their potential as diagnostic, therapeutic, or clinical biological markers in patients with schizophrenia. After enrollment of 61 admitted Japanese patients with acute schizophrenia and 39 healthy volunteers, 54 patients were followed up from the acute stage to remission. Serum biomarkers were measured in blood samples taken before breakfast using competitive enzyme-linked immunosorbent assays, and Glycer-AGEs were significantly higher and sRAGE levels were significantly lower in patients with acute schizophrenia than in healthy controls. Glycer-AGEs/sRAGE ratios were also higher in schizophrenia patients and were stable during the clinical course. Furthermore, discriminant analyses confirmed that Glycer-AGEs and Glycer-AGEs/sRAGE ratios are significant diagnostic markers for schizophrenia, and distinguished between patients and healthy controls in 70.0% of cases. However, these markers of carbonyl stress were not correlated with clinical features, including disease severity, or with daily chlorpromazine doses. These data indicate the potential of Glycer-AGEs, RAGEs, and their relative ratios as diagnostic markers for patients with schizophrenia. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Advancing Cell Biology Through Proteomics in Space and Time (PROSPECTS)*

PubMed Central

Lamond, Angus I.; Uhlen, Mathias; Horning, Stevan; Makarov, Alexander; Robinson, Carol V.; Serrano, Luis; Hartl, F. Ulrich; Baumeister, Wolfgang; Werenskiold, Anne Katrin; Andersen, Jens S.; Vorm, Ole; Linial, Michal; Aebersold, Ruedi; Mann, Matthias

2012-01-01

The term “proteomics” encompasses the large-scale detection and analysis of proteins and their post-translational modifications. Driven by major improvements in mass spectrometric instrumentation, methodology, and data analysis, the proteomics field has burgeoned in recent years. It now provides a range of sensitive and quantitative approaches for measuring protein structures and dynamics that promise to revolutionize our understanding of cell biology and molecular mechanisms in both human cells and model organisms. The Proteomics Specification in Time and Space (PROSPECTS) Network is a unique EU-funded project that brings together leading European research groups, spanning from instrumentation to biomedicine, in a collaborative five year initiative to develop new methods and applications for the functional analysis of cellular proteins. This special issue of Molecular and Cellular Proteomics presents 16 research papers reporting major recent progress by the PROSPECTS groups, including improvements to the resolution and sensitivity of the Orbitrap family of mass spectrometers, systematic detection of proteins using highly characterized antibody collections, and new methods for absolute as well as relative quantification of protein levels. Manuscripts in this issue exemplify approaches for performing quantitative measurements of cell proteomes and for studying their dynamic responses to perturbation, both during normal cellular responses and in disease mechanisms. Here we present a perspective on how the proteomics field is moving beyond simply identifying proteins with high sensitivity toward providing a powerful and versatile set of assay systems for characterizing proteome dynamics and thereby creating a new “third generation” proteomics strategy that offers an indispensible tool for cell biology and molecular medicine. PMID:22311636

Technological advances in precision medicine and drug development.

PubMed

Maggi, Elaine; Patterson, Nicole E; Montagna, Cristina

New technologies are rapidly becoming available to expand the arsenal of tools accessible for precision medicine and to support the development of new therapeutics. Advances in liquid biopsies, which analyze cells, DNA, RNA, proteins, or vesicles isolated from the blood, have gained particular interest for their uses in acquiring information reflecting the biology of tumors and metastatic tissues. Through advancements in DNA sequencing that have merged unprecedented accuracy with affordable cost, personalized treatments based on genetic variations are becoming a real possibility. Extraordinary progress has been achieved in the development of biological therapies aimed to even further advance personalized treatments. We provide a summary of current and future applications of blood based liquid biopsies and how new technologies are utilized for the development of biological therapeutic treatments. We discuss current and future sequencing methods with an emphasis on how technological advances will support the progress in the field of precision medicine.

Joining Forces: The Chemical Biology-Medicinal Chemistry Continuum.

PubMed

Plowright, Alleyn T; Ottmann, Christian; Arkin, Michelle; Auberson, Yves P; Timmerman, Henk; Waldmann, Herbert

2017-09-21

The scientific advances being made across all disciplines are creating ever-increasing opportunities to enhance our knowledge of biological systems and how they relate to human disease. One of the central driving forces in discovering new medicines is medicinal chemistry, where the design and synthesis of novel compounds has led to multiple drugs. Chemical biology, sitting at the interface of many disciplines, has now emerged as a major contributor to the understanding of biological systems and is becoming an integral part of drug discovery. Bringing chemistry and biology much closer and blurring the boundaries between disciplines is creating new opportunities to probe and understand biology; both disciplines play key roles and need to join forces and work together effectively to synergize their impact. The power of chemical biology will then reach its full potential and drive innovation, leading to the discovery of transformative medicines to treat patients. Advances in cancer biology and drug discovery highlight this potential. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural biology computing: Lessons for the biomedical research sciences.

PubMed

Morin, Andrew; Sliz, Piotr

2013-11-01

The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields. Copyright © 2013 Wiley Periodicals, Inc.

Engineering scalable biological systems

PubMed Central

2010-01-01

Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic and performing output functions. In the last decade, significant progress has been made in developing basic designs for a wide range of biological circuits in bacteria, yeast and mammalian systems. However, significant challenges in the construction, probing, modulation and debugging of synthetic biological systems must be addressed in order to achieve scalable higher-complexity biological circuits. Furthermore, concomitant efforts to evaluate the safety and biocontainment of engineered organisms and address public and regulatory concerns will be necessary to ensure that technological advances are translated into real-world solutions. PMID:21468204

Ordinary differential equations with applications in molecular biology.

PubMed

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

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

Examining the Impact of State Level Merit-Aid Policies on Advanced Placement Participation

ERIC Educational Resources Information Center

Kramer, Dennis A., II

2016-01-01

This study examines the impact of merit-aid programs on secondary course taking patterns. Specifically, this study uses difference-in-differences to analyze state-level Advanced Placement (AP) participation and examination data pre and post merit-aid adoption. Results indicate increases in AP participation and number of total examinations after…

Metabolomics and malaria biology

PubMed Central

Lakshmanan, Viswanathan; Rhee, Kyu Y.; Daily, Johanna P.

2010-01-01

Metabolomics has ushered in a novel and multi-disciplinary realm in biological research. It has provided researchers with a platform to combine powerful biochemical, statistical, computational, and bioinformatics techniques to delve into the mysteries of biology and disease. The application of metabolomics to study malaria parasites represents a major advance in our approach towards gaining a more comprehensive perspective on parasite biology and disease etiology. This review attempts to highlight some of the important aspects of the field of metabolomics, and its ongoing and potential future applications to malaria research. PMID:20970461

Action Biology. Advanced Placement for the Second Year. First Edition.

ERIC Educational Resources Information Center

Davis, Mary Pitt

This document provides biology experiments designed for students who have completed a first year biology course. This self contained laboratory booklet contains four sections. In section 1, "Instrumentation in the Study of Cells," discussion sections and suggestions for teacher demonstrations are provided. It also includes some basic materials…

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 .

Advanced Satellite-Based Frequency Transfer at the 10-16 Level.

PubMed

Fujieda, Miho; Yang, Sung-Hoon; Gotoh, Tadahiro; Hwang, Sang-Wook; Hachisu, Hidekazu; Kim, Huidong; Lee, Young Kyu; Tabuchi, Ryo; Ido, Tetsuya; Lee, Won-Kyu; Heo, Myoung-Sun; Park, Chang Yong; Yu, Dai-Hyuk; Petit, Gerard

2018-06-01

Advanced satellite-based frequency transfers by two-way carrier-phase (TWCP) and integer precise point positioning have been performed between the National Institute of Information and Communications Technology and Korea Research Institute of Standards and Science. We confirm that the disagreement between them is less than at an averaging time of several days. In addition, an overseas frequency ratio measurement of Sr and Yb optical lattice clocks was directly performed by TWCP. We achieved an uncertainty at the mid-10 -16 level after a total measurement time of 12 h. The frequency ratio was consistent with the recently reported values within the uncertainty.

Barriers and Facilitators to Career Advancement by Top-Level, Entry-Level and Non-Administrative Women in Public School Districts: A Mixed Methods Study

ERIC Educational Resources Information Center

Ahmed, Eman Ibrahim El-Desouki

2011-01-01

The purpose of this study was to investigate the barriers and facilitators to career advancement among women administrators occupying top-level positions, those occupying entry-level positions and those in non-administrative positions in both rural and urban public school districts in central Pennsylvania. The need to increase the awareness of the…

Technological advances for interrogating the human kinome.

PubMed

Baharani, Akanksha; Trost, Brett; Kusalik, Anthony; Napper, Scott

2017-02-08

There is increasing appreciation among researchers and clinicians of the value of investigating biology and pathobiology at the level of cellular kinase (kinome) activity. Kinome analysis provides valuable opportunity to gain insights into complex biology (including disease pathology), identify biomarkers of critical phenotypes (including disease prognosis and evaluation of therapeutic efficacy), and identify targets for therapeutic intervention through kinase inhibitors. The growing interest in kinome analysis has fueled efforts to develop and optimize technologies that enable characterization of phosphorylation-mediated signaling events in a cost-effective, high-throughput manner. In this review, we highlight recent advances to the central technologies currently available for kinome profiling and offer our perspectives on the key challenges remaining to be addressed. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Single-cell metabolomics: analytical and biological perspectives.

PubMed

Zenobi, R

2013-12-06

There is currently much interest in broad molecular profiling of single cells; a cell's metabolome-its full complement of small-molecule metabolites-is a direct indicator of phenotypic diversity of single cells and a nearly immediate readout of how cells react to environmental influences. However, the metabolome is very difficult to measure at the single-cell level because of rapid metabolic dynamics, the structural diversity of the molecules, and the inability to amplify or tag small-molecule metabolites. Measurement techniques including mass spectrometry, capillary electrophoresis, and, to a lesser extent, optical spectroscopy and fluorescence detection have led to impressive advances in single-cell metabolomics. Even though none of these methodologies can currently measure the metabolome of a single cell completely, rapidly, and nondestructively, progress has been sufficient such that the field is witnessing a shift from feasibility studies to investigations that yield new biological insight. Particularly interesting fields of application are cancer biology, stem cell research, and monitoring of xenobiotics and drugs in tissue sections at the single-cell level.

Structural Biology of Supramolecular Assemblies by Magic Angle Spinning NMR Spectroscopy

PubMed Central

Quinn, Caitlin M.; Polenova, Tatyana

2017-01-01

In recent years, exciting developments in instrument technology and experimental methodology have advanced the field of magic angle spinning (MAS) NMR to new heights. Contemporary MAS NMR yields atomic-level insights into structure and dynamics of an astounding range of biological systems, many of which cannot be studied by other methods. With the advent of fast magic angle spinning, proton detection, and novel pulse sequences, large supramolecular assemblies, such as cytoskeletal proteins and intact viruses, are now accessible for detailed analysis. In this review, we will discuss the current MAS NMR methodologies that enable characterization of complex biomolecular systems and will present examples of applications to several classes of assemblies comprising bacterial and mammalian cytoskeleton as well as HIV-1 and bacteriophage viruses. The body of work reviewed herein is representative of the recent advancements in the field, with respect to the complexity of the systems studied, the quality of the data, and the significance to the biology. PMID:28093096

Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks.

PubMed

D'Souza, Mark; Sulakhe, Dinanath; Wang, Sheng; Xie, Bing; Hashemifar, Somaye; Taylor, Andrew; Dubchak, Inna; Conrad Gilliam, T; Maltsev, Natalia

2017-01-01

Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.

Recent advances in the biology and treatment of brain metastases of non-small cell lung cancer: summary of a multidisciplinary roundtable discussion

PubMed Central

Preusser, Matthias; Winkler, Frank; Valiente, Manuel; Manegold, Christian; Moyal, Elizabeth; Widhalm, Georg; Tonn, Jörg-Christian; Zielinski, Christoph

2018-01-01

This article is the result of a round table discussion held at the European Lung Cancer Conference (ELCC) in Geneva in May 2017. Its purpose is to explore and discuss the advances in the knowledge about the biology and treatment of brain metastases originating from non-small cell lung cancer. The authors propose a series of recommendations for research and treatment within the discussed context. PMID:29387475

Using the Biology Card Sorting Task to Measure Changes in Conceptual Expertise during Postsecondary Biology Education.

PubMed

Bissonnette, Sarah A; Combs, Elijah D; Nagami, Paul H; Byers, Victor; Fernandez, Juliana; Le, Dinh; Realin, Jared; Woodham, Selina; Smith, Julia I; Tanner, Kimberly D

2017-01-01

While there have been concerted efforts to reform undergraduate biology toward teaching students to organize their conceptual knowledge like experts, there are few tools that attempt to measure this. We previously developed the Biology Card Sorting Task (BCST), designed to probe how individuals organize their conceptual biological knowledge. Previous results showed the BCST could differentiate between different populations, namely non-biology majors (NBM) and biology faculty (BF). In this study, we administered the BCST to three additional populations, using a cross-sectional design: entering biology majors (EBM), advanced biology majors (ABM), and biology graduate students (BGS). Intriguingly, ABM did not initially sort like experts any more frequently than EBM. However, once the deep-feature framework was revealed, ABM were able to sort like experts more readily than did EBM. These results are consistent with the conclusion that biology education enables advanced biology students to use an expert-like conceptual framework. However, these results are also consistent with a process of "selection," wherein students who persist in the major may have already had an expert-like conceptual framework to begin with. These results demonstrate the utility of the BCST in measuring differences between groups of students over the course of their undergraduate education. © 2017 S. A. Bissonnette et al. CBE—Life Sciences Education © 2017 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Systems cell biology

PubMed Central

Mast, Fred D.; Ratushny, Alexander V.

2014-01-01

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. PMID:25225336

[CYFRA 21.1 cytosol levels in lung adenocarcinomas. Correlation with other clinico-biological parameters].

PubMed

Ruibal, A; Núñez, M I; Del Río, M C; Lapeña, G; Rodríguez, J

2002-01-01

Cyfra 21.1 are soluble cytokeratin 19 fragments present in several biological fluids. The aim of this work was to study cyfra 21.1 cytosolic levels in lung adenocarcinomas and their possible correlation with other clinical-biological parameters. Cyfra 21.1 was determined, using an immunoradiometric assay (CIS BioInternational. France), in 58 tissue samples of lung adenocarcinomas patients. Other parameters included in the study were the following: clinical stage, histological grade, ploidy, S-phase cellular fraction, as well as cathepsin D, CA 125 and hyaluronic acid levels in cytosols. Likewise, AH, erbB2 oncoprotein, CD44s, CD44v5 and CD44v6 levels in cell surfaces were assayed. Cyfra 21.1 cytosolic levels oscillated between 24.8 and 6,774 ng/mg prot. (median 1,147.5) and were higher (p:0.00074) than those observed in 16 normal lung samples of the same patients. We did not observe any statistically significant differences in cyfra 21.1 values when clinical stage, ploidy, S-phase and histological grade were considered. When lung adenocarcinomas were classified according to cyfra 21.1 positivity, using 1,499 ng/mg prot. as cut-off, which represents the 75th percentile of the whole group, we noted that positive cases had higher levels of cathepsin D (p:0.00218), cytosolic hyaluronic acid (p:0.02947), erbB2 protein (p:0.06272) and CA 125 (p:0.07243) than negative carcinomas. These results suggest the possibility that high cytosolic cyfra 21.1 levels could be associated with a poor outcome in lung adenocarcinomas.

Sporotrichosis: From KOH to Molecular Biology.

PubMed

Arenas, Roberto; Sánchez-Cardenas, Carlos D; Ramirez-Hobak, Lourdes; Ruíz Arriaga, Leon Felipe; Vega Memije, Ma Elisa

2018-05-23

Sporotrichosis is a cosmopolitan, chronic granulomatous mycosis, acquired by traumatic inoculation and caused by Sporothrix schenckii complex . Several methods of diagnostic are available, from KOH to molecular biology. In this review, we describe from the simplest (clinical diagnosis) to the most advanced diagnostic techniques (molecular biology).

Robotics-inspired biology.

PubMed

Gravish, Nick; Lauder, George V

2018-03-29

For centuries, designers and engineers have looked to biology for inspiration. Biologically inspired robots are just one example of the application of knowledge of the natural world to engineering problems. However, recent work by biologists and interdisciplinary teams have flipped this approach, using robots and physical models to set the course for experiments on biological systems and to generate new hypotheses for biological research. We call this approach robotics-inspired biology; it involves performing experiments on robotic systems aimed at the discovery of new biological phenomena or generation of new hypotheses about how organisms function that can then be tested on living organisms. This new and exciting direction has emerged from the extensive use of physical models by biologists and is already making significant advances in the areas of biomechanics, locomotion, neuromechanics and sensorimotor control. Here, we provide an introduction and overview of robotics-inspired biology, describe two case studies and suggest several directions for the future of this exciting new research area. © 2018. Published by The Company of Biologists Ltd.

Advancing haematopoietic stem and progenitor cell biology through single-cell profiling.

PubMed

Hamey, Fiona K; Nestorowa, Sonia; Wilson, Nicola K; Göttgens, Berthold

2016-11-01

Haematopoietic stem and progenitor cells (HSPCs) sit at the top of the haematopoietic hierarchy, and their fate choices need to be carefully controlled to ensure balanced production of all mature blood cell types. As cell fate decisions are made at the level of the individual cells, recent technological advances in measuring gene and protein expression in increasingly large numbers of single cells have been rapidly adopted to study both normal and pathological HSPC function. In this review we emphasise the importance of combining the correct computational models with single-cell experimental techniques, and illustrate how such integrated approaches have been used to resolve heterogeneities in populations, reconstruct lineage differentiation, identify regulatory relationships and link molecular profiling to cellular function. © 2016 Federation of European Biochemical Societies.

New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

PubMed Central

Hamon, Morgan; Hong, Jong Wook

2013-01-01

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

The Histochemistry and Cell Biology compendium: a review of 2012.

PubMed

Taatjes, Douglas J; Roth, Jürgen

2013-06-01

The year 2012 was another exciting year for Histochemistry and Cell Biology. Innovations in immunohistochemical techniques and microscopy-based imaging have provided the means for advances in the field of cell biology. Over 130 manuscripts were published in the journal during 2012, representing methodological advancements, pathobiology of disease, and cell and tissue biology. This annual review of the manuscripts published in the previous year in Histochemistry and Cell Biology serves as an abbreviated reference for the readership to quickly peruse and discern trends in the field over the past year. The review has been broadly divided into multiple sections encompassing topics such as method advancements, subcellular components, extracellular matrix, and organ systems. We hope that the creation of this subdivision will serve to guide the reader to a specific topic of interest, while simultaneously providing a concise and easily accessible encapsulation of other topics in the broad area of Histochemistry and Cell Biology.

Using Active Learning to Teach Concepts and Methods in Quantitative Biology.

PubMed

Waldrop, Lindsay D; Adolph, Stephen C; Diniz Behn, Cecilia G; Braley, Emily; Drew, Joshua A; Full, Robert J; Gross, Louis J; Jungck, John A; Kohler, Brynja; Prairie, Jennifer C; Shtylla, Blerta; Miller, Laura A

2015-11-01

This article provides a summary of the ideas discussed at the 2015 Annual Meeting of the Society for Integrative and Comparative Biology society-wide symposium on Leading Students and Faculty to Quantitative Biology through Active Learning. It also includes a brief review of the recent advancements in incorporating active learning approaches into quantitative biology classrooms. We begin with an overview of recent literature that shows that active learning can improve students' outcomes in Science, Technology, Engineering and Math Education disciplines. We then discuss how this approach can be particularly useful when teaching topics in quantitative biology. Next, we describe some of the recent initiatives to develop hands-on activities in quantitative biology at both the graduate and the undergraduate levels. Throughout the article we provide resources for educators who wish to integrate active learning and technology into their classrooms. © The Author 2015. 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.

The Application of Advanced Cultivation Techniques in the Long Term Maintenance of Space Flight Plant Biological Systems

NASA Technical Reports Server (NTRS)

Heyenga, A. G.

2003-01-01

The development of the International Space Station (ISS) presents extensive opportunities for the implementation of long duration space life sciences studies. Continued attention has been placed in the development of plant growth chamber facilities capable of supporting the cultivation of plants in space flight microgravity conditions. The success of these facilities is largely dependent on their capacity to support the various growth requirements of test plant species. The cultivation requirements for higher plant species are generally complex, requiring specific levels of illumination, temperature, humidity, water, nutrients, and gas composition in order to achieve normal physiological growth and development. The supply of water, nutrients, and oxygen to the plant root system is a factor, which has proven to be particularly challenging in a microgravity space flight environment. The resolution of this issue is particularly important for the more intensive crop cultivation of plants envisaged in Nasa's advanced life support initiative. BioServe Space Technologies is a NASA, Research Partnership Center (RPC) at the University of Colorado, Boulder. BioServe has designed and operated various space flight plant habitat systems, and placed specific emphasis on the development and enhanced performance of subsystem components such as water and nutrient delivery, illumination, gas exchange and atmosphere control, temperature and humidity control. The further development and application of these subsystems to next generation habitats is of significant benefit and contribution towards the development of both the Space Plant biology and the Advanced Life Support Programs. The cooperative agreement between NASA Ames Research center and BioServe was established to support the further implementation of advanced cultivation techniques and protocols to plant habitat systems being coordinated at NASA Ames Research Center. Emphasis was placed on the implementation of passive

Unexpected Levels of Biological Activity during the Polar Night Offer New Perspectives on a Warming Arctic.

PubMed

Berge, Jørgen; Daase, Malin; Renaud, Paul E; Ambrose, William G; Darnis, Gerald; Last, Kim S; Leu, Eva; Cohen, Jonathan H; Johnsen, Geir; Moline, Mark A; Cottier, Finlo; Varpe, Øystein; Shunatova, Natalia; Bałazy, Piotr; Morata, Nathalie; Massabuau, Jean-Charles; Falk-Petersen, Stig; Kosobokova, Ksenia; Hoppe, Clara J M; Węsławski, Jan Marcin; Kukliński, Piotr; Legeżyńska, Joanna; Nikishina, Daria; Cusa, Marine; Kędra, Monika; Włodarska-Kowalczuk, Maria; Vogedes, Daniel; Camus, Lionel; Tran, Damien; Michaud, Emma; Gabrielsen, Tove M; Granovitch, Andrei; Gonchar, Anya; Krapp, Rupert; Callesen, Trine A

2015-10-05

The current understanding of Arctic ecosystems is deeply rooted in the classical view of a bottom-up controlled system with strong physical forcing and seasonality in primary-production regimes. Consequently, the Arctic polar night is commonly disregarded as a time of year when biological activities are reduced to a minimum due to a reduced food supply. Here, based upon a multidisciplinary ecosystem-scale study from the polar night at 79°N, we present an entirely different view. Instead of an ecosystem that has entered a resting state, we document a system with high activity levels and biological interactions across most trophic levels. In some habitats, biological diversity and presence of juvenile stages were elevated in winter months compared to the more productive and sunlit periods. Ultimately, our results suggest a different perspective regarding ecosystem function that will be of importance for future environmental management and decision making, especially at a time when Arctic regions are experiencing accelerated environmental change [1]. Copyright © 2015 Elsevier Ltd. All rights reserved.

Advancing the science of Forest Hydrology

Treesearch

Devendra M. Amatya; R. Wayne Skaggs; Carl C. Trettin

2009-01-01

For more than a century, agricultural and biological engineers have provided major advances in science, engineering, and technology to increase food and fiber production to meet the demands of a rapidly growing global population. The land base for these technological advances has...

A SYSTEMS BIOLOGY APPROACH TO DEVELOPMENTAL TOXICOLOGY

EPA Science Inventory

Abstract
Recent advances in developmental biology have yielded detailed models of gene regulatory networks (GRNs) involved in cell specification and other processes in embryonic differentiation. Such networks form the bedrock on which a systems biology approach to developme...

Integrative assessment of Evolutionary theory acceptance and knowledge levels of Biology undergraduate students from a Brazilian university

NASA Astrophysics Data System (ADS)

Tavares, Gustavo Medina; Bobrowski, Vera Lucia

2018-03-01

The integrative role that Evolutionary theory plays within Biology is recognised by most scientific authors, as well as in governmental education policies, including Brazilian policies. However, teaching and learning evolution seems problematic in many countries, and Brazil is among those. Many factors may affect teachers' and students' perceptions towards evolution, and studies can help to reveal those factors. We used a conceptual questionnaire, the Measure of Acceptance of the Theory of Evolution (MATE) instrument, and a Knowledge test to assess (1) the level of acceptance and understanding of 23 undergraduate Biology students nearing the end of their course, (2) other factors that could affect these levels, including course structure, and (3) the most difficult topics regarding evolutionary biology. The results of this study showed that the students, on average, had a 'Very High Acceptance' (89.91) and a 'Very Low Knowledge' (59.42%) of Evolutionary theory, and also indicated a moderate positive correlation between the two (r = 0.66, p = .001). The most difficult topics were related to the definition of evolution and dating techniques. We believe that the present study provides evidence for policymakers to reformulate current school and university curricula in order to improve the teachers' acceptance and understanding of evolution and other biological concepts, consequently, helping students reduce their misconceptions related to evolutionary biology.

Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis.

PubMed

Yi, Ming; Mudunuri, Uma; Che, Anney; Stephens, Robert M

2009-06-29

One of the challenges in the analysis of microarray data is to integrate and compare the selected (e.g., differential) gene lists from multiple experiments for common or unique underlying biological themes. A common way to approach this problem is to extract common genes from these gene lists and then subject these genes to enrichment analysis to reveal the underlying biology. However, the capacity of this approach is largely restricted by the limited number of common genes shared by datasets from multiple experiments, which could be caused by the complexity of the biological system itself. We now introduce a new Pathway Pattern Extraction Pipeline (PPEP), which extends the existing WPS application by providing a new pathway-level comparative analysis scheme. To facilitate comparing and correlating results from different studies and sources, PPEP contains new interfaces that allow evaluation of the pathway-level enrichment patterns across multiple gene lists. As an exploratory tool, this analysis pipeline may help reveal the underlying biological themes at both the pathway and gene levels. The analysis scheme provided by PPEP begins with multiple gene lists, which may be derived from different studies in terms of the biological contexts, applied technologies, or methodologies. These lists are then subjected to pathway-level comparative analysis for extraction of pathway-level patterns. This analysis pipeline helps to explore the commonality or uniqueness of these lists at the level of pathways or biological processes from different but relevant biological systems using a combination of statistical enrichment measurements, pathway-level pattern extraction, and graphical display of the relationships of genes and their associated pathways as Gene-Term Association Networks (GTANs) within the WPS platform. As a proof of concept, we have used the new method to analyze many datasets from our collaborators as well as some public microarray datasets. This tool provides a

Biology II Curriculum Guide. Bulletin 1820.

ERIC Educational Resources Information Center

Louisiana State Dept. of Education, Baton Rouge. Div. of Academic Programs.

In 1986, the Louisiana State Board of Elementary and Secondary Education requested that an advanced course in Biology II be developed. The resulting curriculum guide contains grade appropriate goals, skills, and competencies; suggested activities; suggested materials of instruction; and minimum time allotments for instruction. Biology II is a…

Population Biology, Conservation Biology, and the Future of Humanity.

ERIC Educational Resources Information Center

Ehrlich, Paul R.

1987-01-01

Recounts some of the progress that has been made in the field of population biology. Presents some of the important advances made in the field, along with some of their applications to societal problems. Calls for more cooperation between population scientists and social scientists, and more environmental education for the public. (TW)

Biological treatment of winery wastewater: an overview.

PubMed

Andreottola, G; Foladori, P; Ziglio, G

2009-01-01

The treatment of winery wastewater can realised using several biological processes based both on aerobic or anaerobic systems using suspended biomass or biofilms. Several systems are currently offered by technology providers and current research envisages the availability of new promising technologies for winery wastewater treatment. The present paper intends to present a brief state of the art of the existing status and advances in biological treatment of winery wastewater in the last decade, considering both lab, pilot and full-scale studies. Advantages, drawbacks, applied organic loads, removal efficiency and emerging aspects of the main biological treatments were considered and compared. Nevertheless in most treatments the COD removal efficiency was around 90-95% (remaining COD is due to the un-biodegradable soluble fraction), the applied organic loads are very different depending on the applied technology, varying for an order of magnitude. Applied organic loads are higher in biofilm systems than in suspended biomass while anaerobic biofilm processes have the smaller footprint but in general a higher level of complexity.

Cellular burdens and biological effects on tissue level caused by inhaled radon progenies.

PubMed

Madas, B G; Balásházy, I; Farkas, Á; Szoke, I

2011-02-01

In the case of radon exposure, the spatial distribution of deposited radioactive particles is highly inhomogeneous in the central airways. The object of this research is to investigate the consequences of this heterogeneity regarding cellular burdens in the bronchial epithelium and to study the possible biological effects at tissue level. Applying computational fluid and particle dynamics techniques, the deposition distribution of inhaled radon daughters has been determined in a bronchial airway model for 23 min of work in the New Mexico uranium mine corresponding to 0.0129 WLM exposure. A numerical epithelium model based on experimental data has been utilised in order to quantify cellular hits and doses. Finally, a carcinogenesis model considering cell death-induced cell-cycle shortening has been applied to assess the biological responses. Present computations reveal that cellular dose may reach 1.5 Gy, which is several orders of magnitude higher than tissue dose. The results are in agreement with the histological finding that the uneven deposition distribution of radon progenies may lead to inhomogeneous spatial distribution of tumours in the bronchial airways. In addition, at the macroscopic level, the relationship between cancer risk and radiation burden seems to be non-linear.

Intuitive biological thought: Developmental changes and effects of biology education in late adolescence.

PubMed

Coley, John D; Arenson, Melanie; Xu, Yian; Tanner, Kimberly D

2017-02-01

A large body of cognitive research has shown that people intuitively and effortlessly reason about the biological world in complex and systematic ways. We addressed two questions about the nature of intuitive biological reasoning: How does intuitive biological thinking change during adolescence and early adulthood? How does increasing biology education influence intuitive biological thinking? To do so, we developed a battery of measures to systematically test three components of intuitive biological thought: anthropocentric thinking, teleological thinking and essentialist thinking, and tested 8th graders and university students (both biology majors, and non-biology majors). Results reveal clear evidence of persistent intuitive reasoning among all populations studied, consistent but surprisingly small differences between 8th graders and college students on measures of intuitive biological thought, and consistent but again surprisingly small influence of increasing biology education on intuitive biological reasoning. Results speak to the persistence of intuitive reasoning, the importance of taking intuitive knowledge into account in science classrooms, and the necessity of interdisciplinary research to advance biology education. Further studies are necessary to investigate how cultural context and continued acquisition of expertise impact intuitive biology thinking. Copyright © 2016 Elsevier Inc. All rights reserved.

The interactions of peripheral membrane proteins with biological membranes

DOE PAGES

Johs, Alexander; Whited, A. M.

2015-07-29

The interactions of peripheral proteins with membrane surfaces are critical to many biological processes, including signaling, recognition, membrane trafficking, cell division and cell structure. On a molecular level, peripheral membrane proteins can modulate lipid composition, membrane dynamics and protein-protein interactions. Biochemical and biophysical studies have shown that these interactions are in fact highly complex, dominated by several different types of interactions, and have an interdependent effect on both the protein and membrane. Here we examine three major mechanisms underlying the interactions between peripheral membrane proteins and membranes: electrostatic interactions, hydrophobic interactions, and fatty acid modification of proteins. While experimental approachesmore » continue to provide critical insights into specific interaction mechanisms, emerging bioinformatics resources and tools contribute to a systems-level picture of protein-lipid interactions. Through these recent advances, we begin to understand the pivotal role of protein-lipid interactions underlying complex biological functions at membrane interfaces.« less

Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks.

PubMed

Agapakis, Christina M; Silver, Pamela A

2009-07-01

Synthetic biology has been used to describe many biological endeavors over the past thirty years--from designing enzymes and in vitro systems, to manipulating existing metabolisms and gene expression, to creating entirely synthetic replicating life forms. What separates the current incarnation of synthetic biology from the recombinant DNA technology or metabolic engineering of the past is an emphasis on principles from engineering such as modularity, standardization, and rigorously predictive models. As such, synthetic biology represents a new paradigm for learning about and using biological molecules and data, with applications in basic science, biotechnology, and medicine. This review covers the canonical examples as well as some recent advances in synthetic biology in terms of what we know and what we can learn about the networks underlying biology, and how this endeavor may shape our understanding of living systems.

Systems cell biology.

PubMed

Mast, Fred D; Ratushny, Alexander V; Aitchison, John D

2014-09-15

Systems cell biology melds high-throughput experimentation with quantitative analysis and modeling to understand many critical processes that contribute to cellular organization and dynamics. Recently, there have been several advances in technology and in the application of modeling approaches that enable the exploration of the dynamic properties of cells. Merging technology and computation offers an opportunity to objectively address unsolved cellular mechanisms, and has revealed emergent properties and helped to gain a more comprehensive and fundamental understanding of cell biology. © 2014 Mast et al.

Towards a heterarchical approach to biology and cognition.

PubMed

Bruni, Luis Emilio; Giorgi, Franco

2015-12-01

In this article we challenge the pervasive notion of hierarchy in biological and cognitive systems and delineate the basis for a complementary heterarchical approach starting from the seminal ideas of Warren McCullock and Gregory Bateson. We intend these considerations as a contribution to the different scientific disciplines working towards a multilevel integrative perspective of biological and cognitive processes, such as systems and integrative biology and neuroscience, social and cultural neuroscience, social signal transduction and psychoneuroimmunology, for instance. We argue that structures and substrates are by necessity organized hierarchically, while communication processes - and their embeddedness - are rather organized heterarchically. Before getting into the implications of the heterarchical approach and its congeniality with the semiotic perspective to biology and cognition, we introduce a set of notions and concepts in order to advance a framework that considers the heterarchical embeddedness of different layers of physiological, behavioral, affective, cognitive, technological and socio-cultural levels implicit in networks of interacting minds, considering the dynamic complementarity of bottom-up and top-down causal links. This should contribute to account for the integration, interpretation and response to complex aggregates of information at different levels of organization in a developmental context. We illustrate the dialectical nature of embedded heterarchical processes by addressing the simultaneity and circularity of cognition and volition, and how such dialectics can be present in primitive instances of proto-cognition and proto-volition, giving rise to our claim that subjectivity and semiotic freedom are scalar properties. We collate the framework with recent empirical systemic approaches to biology and integrative neuroscience, and conclude with a reflection on its implications to the understanding of the emergence of pathological

AOX removal from industrial wastewaters using advanced oxidation processes: assessment of a combined chemical-biological oxidation.

PubMed

Luyten, J; Sniegowski, K; Van Eyck, K; Maertens, D; Timmermans, S; Liers, Sven; Braeken, L

2013-01-01

In this paper, the abatement of adsorbable halogenated organic compounds (AOX) from an industrial wastewater containing relatively high chloride concentrations by a combined chemical and biological oxidation is assessed. For chemical oxidation, the O(3)/UV, H(2)O(2)/UV and photo-Fenton processes are evaluated on pilot scale. Biological oxidation is simulated in a 4 h respirometry experiment with periodic aeration. The results show that a selective degradation of AOX with respect to the matrix compounds (expressed as chemical oxygen demand) could be achieved. For O(3)/UV, lowering the ratio of O(3) dosage to UV intensity leads to a better selectivity for AOX. During O(3)-based experiments, the AOX removal is generally less than during the H(2)O(2)-based experiments. However, after biological oxidation, the AOX levels are comparable. For H(2)O(2)/UV, optimal operating parameters for UV and H(2)O(2) dosage are next determined in a second run with another wastewater sample.

Recent advances in stable isotope labeling based techniques for proteome relative quantification.

PubMed

Zhou, Yuan; Shan, Yichu; Zhang, Lihua; Zhang, Yukui

2014-10-24

The large scale relative quantification of all proteins expressed in biological samples under different states is of great importance for discovering proteins with important biological functions, as well as screening disease related biomarkers and drug targets. Therefore, the accurate quantification of proteins at proteome level has become one of the key issues in protein science. Herein, the recent advances in stable isotope labeling based techniques for proteome relative quantification were reviewed, from the aspects of metabolic labeling, chemical labeling and enzyme-catalyzed labeling. Furthermore, the future research direction in this field was prospected. Copyright © 2014 Elsevier B.V. All rights reserved.

Project Work in Social Biology at GCE Advanced Level

ERIC Educational Resources Information Center

Gadd, P.; Smith, S. Tyrell

1977-01-01

The system by which projects are submitted, modified, and approved is outlined and an indication is given of the standards and quantity of work expected. Criteria on which assessment is based are explained, the range of individual studies is summarized, and cases for and against project work are given. (Author/AJ)

Biologically inspired technologies using artificial muscles

NASA Astrophysics Data System (ADS)

Bar-Cohen, Yoseph

2005-01-01

After billions of years of evolution, nature developed inventions that work, which are appropriate for the intended tasks and that last. The evolution of nature led to the introduction of highly effective and power efficient biological mechanisms that are scalable from micron to many meters in size. Imitating these mechanisms offers enormous potentials for the improvement of our life and the tools we use. Humans have always made efforts to imitate nature and we are increasingly reaching levels of advancement where it becomes significantly easier to imitate, copy, and adapt biological methods, processes and systems. Some of the biomimetic technologies that have emerged include artificial muscles, artificial intelligence, and artificial vision to which significant advances in materials science, mechanics, electronics, and computer science have contributed greatly. One of the newest fields of biomimetics is the electroactive polymers (EAP) that are also known as artificial muscles. To take advantage of these materials, efforts are made worldwide to establish a strong infrastructure addressing the need for comprehensive analytical modeling of their operation mechanism and develop effective processing and characterization techniques. The field is still in its emerging state and robust materials are not readily available however in recent years significant progress has been made and commercial products have already started to appear. This paper covers the state-of-the-art and challenges to making artificial muscles and their potential biomimetic applications.

Yeast synthetic biology toolbox and applications for biofuel production.

PubMed

Tsai, Ching-Sung; Kwak, Suryang; Turner, Timothy L; Jin, Yong-Su

2015-02-01

Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Biological Control Strategies for Mosquito Vectors of Arboviruses.

PubMed

Huang, Yan-Jang S; Higgs, Stephen; Vanlandingham, Dana L

2017-02-10

Historically, biological control utilizes predatory species and pathogenic microorganisms to reduce the population of mosquitoes as disease vectors. This is particularly important for the control of mosquito-borne arboviruses, which normally do not have specific antiviral therapies available. Although development of resistance is likely, the advantages of biological control are that the resources used are typically biodegradable and ecologically friendly. Over the past decade, the advancement of molecular biology has enabled optimization by the manipulation of genetic materials associated with biological control agents. Two significant advancements are the discovery of cytoplasmic incompatibility induced by Wolbachia bacteria, which has enhanced replacement programs, and the introduction of dominant lethal genes into local mosquito populations through the release of genetically modified mosquitoes. As various arboviruses continue to be significant public health threats, biological control strategies have evolved to be more diverse and become critical tools to reduce the disease burden of arboviruses.

Biological Control Strategies for Mosquito Vectors of Arboviruses

PubMed Central

Huang, Yan-Jang S.; Higgs, Stephen; Vanlandingham, Dana L.

2017-01-01

Historically, biological control utilizes predatory species and pathogenic microorganisms to reduce the population of mosquitoes as disease vectors. This is particularly important for the control of mosquito-borne arboviruses, which normally do not have specific antiviral therapies available. Although development of resistance is likely, the advantages of biological control are that the resources used are typically biodegradable and ecologically friendly. Over the past decade, the advancement of molecular biology has enabled optimization by the manipulation of genetic materials associated with biological control agents. Two significant advancements are the discovery of cytoplasmic incompatibility induced by Wolbachia bacteria, which has enhanced replacement programs, and the introduction of dominant lethal genes into local mosquito populations through the release of genetically modified mosquitoes. As various arboviruses continue to be significant public health threats, biological control strategies have evolved to be more diverse and become critical tools to reduce the disease burden of arboviruses. PMID:28208639

The oral histories of six African American males in their ecology of Advanced Placement Biology

NASA Astrophysics Data System (ADS)

Halasa, Katrina Bassam

The major purpose of this qualitative study was to examine the past in order to understand the complex phenomenon of students engaging in science (Newman, Ridenour, Newman, & DeMarco, 2003) specifically through the oral histories of six self-identified African American males enrolled in a high school Advanced Placement Biology class and the oral histories about events that followed during their post high school experiences. To elucidate an understanding of this phenomenon, this research explored the ecology of African American males' descriptions of their school science, their peer school science community, their lived experiences during and after graduation, and their meso-community (Bronfenbrenner, 1979). Many minority and low-income students are less likely to enroll in rigorous courses during high school (Education Trust, 2006). This study is of utmost importance because capturing the informants' oral histories may improve rigorous science education. Many African American male students are attending urban schools with an ever growing achievement gap among their White counterparts (Norman, Ault, Bentz, & Meskimen, 2001); therefore, they are disengaging in science. As a result, African American males are underrepresented in both science careers and achievements in science (Atwater, 2000; National Science Foundation, 1994). The six oral histories highlighted the ecological factors that affected African American males regarding (1) the impact of their relationship with their mothers, (2) the understanding of personal responsibility, (3) the notion of a scientist, (4) the issue of gender being more of an obstacle than race, (5) the understanding that education is valuable, (6) the interactions and influence of relationships with others on their decisions, (7) the development of integrity through the participation in sports, (8) the ecological neighborhood environment influences an image, (9) the enrollment of Advanced Placement Biology course helped the transition

Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine.

PubMed

Weston, Andrea D; Hood, Leroy

2004-01-01

The emergence of systems biology is bringing forth a new set of challenges for advancing science and technology. Defining ways of studying biological systems on a global level, integrating large and disparate data types, and dealing with the infrastructural changes necessary to carry out systems biology, are just a few of the extraordinary tasks of this growing discipline. Despite these challenges, the impact of systems biology will be far-reaching, and significant progress has already been made. Moving forward, the issue of how to use systems biology to improve the health of individuals must be a priority. It is becoming increasingly apparent that the field of systems biology and one of its important disciplines, proteomics, will have a major role in creating a predictive, preventative, and personalized approach to medicine. In this review, we define systems biology, discuss the current capabilities of proteomics and highlight some of the necessary milestones for moving systems biology and proteomics into mainstream health care.

Information Literacy in Biology Education: An Example from an Advanced Cell Biology Course

ERIC Educational Resources Information Center

Porter, John R.

2005-01-01

Information literacy skills are critically important for the undergraduate biology student. The ability to find, understand, evaluate, and use information, whether from the scientific literature or from Web resources, is essential for a good understanding of a topic and for the conduct of research. A project in which students receive information…

News: Synthetic biology leading to specialty chemicals

EPA Science Inventory

Synthetic biology can combine the disciplines of biology, engineering, and chemistry productively to form molecules of great scientific and commercial value. Recent advances in the new field are explored for their connection to new tools that have been used to elucidate productio...

78 FR 68058 - Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-13

... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology..., computational, and systems biology data can better inform risk assessment. This draft document is available for...

Office of Biological Informatics and Outreach geospatial technology activities

USGS Publications Warehouse

,

1998-01-01

The U.S. Geological Survey (USGS) Office of Biological Informatics and Outreach (OBIO) in Reston, Virginia, and its Center for Biological Informatics (CBI) in Denver, Colorado, provide leadership in the development and use of geospatial technologies to advance the Nation's biological science activities.

A New Biology for the 21st Century; Ensuring the United States Leads the Coming Biology Revolution. Final committee report

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

None None

2012-05-10

In July, 2008, the National Institutes of Health (NIH), National Science Foundation (NSF), and Department of Energy (DOE) asked the National Research Council’s Board on Life Sciences to convene a committee to examine the current state of biological research in the United States and recommend how best to capitalize on recent technological and scientific advances that have allowed biologists to integrate biological research findings, collect and interpret vastly increased amounts of data, and predict the behavior of complex biological systems. From September 2008 through July of 2009, a committee of 16 experts from the fields of biology, engineering and computationalmore » science undertook to delineate those scientific and technological advances and come to a consensus on how the U.S. might best capitalize on them. This report, authored by the Committee on a New Biology for the 21st Century, describes the committee’s work and conclusions.« less

Recent advances in the development of extraction chromatographic materials for the isolation of radionuclides from biological and environmental samples.

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

Dietz, M. L.

1998-11-30

The determination of low levels of radionuclides in environmental and biological samples is often hampered by the complex and variable nature of the samples. One approach to circumventing this problem is to incorporate into the analytical scheme a separation and preconcentration step by which the species of interest can be isolated from the major constituents of the sample. Extraction chromatography (EXC), a form of liquid chromatography in which the stationary phase comprises an extractant or a solution of an extractant in an appropriate diluent coated onto an inert support, provides a simple and efficient means of performing a wide varietymore » of metal ion separations. Recent advances in extractant design, in particular the development of extractants capable of metal ion recognition or of strong complex formation even in acidic media, have substantially improved the utility of the method. For the preconcentration of actinides, for example, an EXC resin consisting of a liquid diphosphonic acid supported on a polymeric substrate has been shown to exhibit extraordinarily strong retention of these elements from acidic chloride media. This resin, together with other related materials, can provide the basis of a number of efficient and flexible schemes for the separation and preconcentration of radionuclides form a variety of samples for subsequent determination.« less

Exploring the Alignment of the Intended and Implemented Curriculum through Teachers' Interpretation: A Case Study of A-Level Biology Practical Work

ERIC Educational Resources Information Center

Phaeton, Mukaro Joe; Stears, Michèle

2017-01-01

The research reported on here is part of a larger study exploring the alignment of the intended, implemented and attained curriculum with regard to practical work in the Zimbabwean A-level Biology curriculum. In this paper we focus on the alignment between the intended and implemented A-Level Biology curriculum through the lens of teachers'…

Studying cell biology in the skin.

PubMed

Morrow, Angel; Lechler, Terry

2015-11-15

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

From biological and social network metaphors to coupled bio-social wireless networks

PubMed Central

Barrett, Christopher L.; Eubank, Stephen; Anil Kumar, V.S.; Marathe, Madhav V.

2010-01-01

Biological and social analogies have been long applied to complex systems. Inspiration has been drawn from biological solutions to solve problems in engineering products and systems, ranging from Velcro to camouflage to robotics to adaptive and learning computing methods. In this paper, we present an overview of recent advances in understanding biological systems as networks and use this understanding to design and analyse wireless communication networks. We expand on two applications, namely cognitive sensing and control and wireless epidemiology. We discuss how our work in these two applications is motivated by biological metaphors. We believe that recent advances in computing and communications coupled with advances in health and social sciences raise the possibility of studying coupled bio-social communication networks. We argue that we can better utilise the advances in our understanding of one class of networks to better our understanding of the other. PMID:21643462

Exploring Zimbabwean Advanced Level Chemistry Students' Approaches to Investigations from a Learning Perspective

ERIC Educational Resources Information Center

Chirikure, Tamirirofa; Hobden, Paul; Hobden, Sally

2018-01-01

In this paper we report on the findings of a study on Advanced Level Chemistry students' approaches to investigations from a learning perspective in the Zimbabwean educational context. Students' approaches to investigations are inextricably linked to the quality of learning and performances in these practical activities. An explanatory…

The Correlation Between Metacognition Level with Self-Efficacy of Biology Education College Students

NASA Astrophysics Data System (ADS)

Ridlo, S.; Lutfiya, F.

2017-04-01

Self-efficacy is a strong predictor of academic achievement. Self-efficacy refers to the ability of college students to achieve the desired results. The metacognition level can influence college student’s self-efficacy. This study aims to identify college student’s metacognition level and self-efficacy, as well as determine the relationship between self-efficacy and metacognition level for college students of Biology Education 2013, Semarang State University. The ex-post facto quantitative research was conducted on 99 students Academic Year 2015/2016. Saturation sampling technique determined samples. E-D scale collected data for self-efficacy identification. Data for assess the metacognition level collected by Metacognitive Awareness Inventory. Data were analysed quantitatively by Pearson correlation and linear regression. Most college students have the high level of metacognition and average self-efficacy. Pearson correlation coefficient result was 0.367. This result showed that metacognition level and self-efficacy has a weak relationship. Based on linear regression test, self-efficacy influenced by metacognition level up to 13.5%. The results of the study showed that positive and significant relationships exist between metacognition level and self-efficacy. Therefore, if the metacognition level is high, then self-efficacy will also be high (appropriate).

78 FR 59927 - Next Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-30

... Generation Risk Assessment: Incorporation of Recent Advances in Molecular, Computational, and Systems Biology..., Computational, and Systems Biology [External Review Draft]'' (EPA/600/R-13/214A). EPA is also announcing that... Advances in Molecular, Computational, and Systems Biology [External Review Draft]'' is available primarily...

'The Relation of Biology to Astronomy' and Theology: Panspermia and Panentheism; Revolutionary Convergences Advanced by Fred Hoyle and Chandra Wickramasinghe

NASA Astrophysics Data System (ADS)

Walker, Theodore, Jr.

2012-06-01

In contrast to the Copernican revolution in astro-geometry, the Hoyle-Wickramasinghe contribution to the recent and continuing revolution in astrobiology - "cometary panspermia" - features astronomy and biology converging toward theology. They employed astro-biotic reasoning (often labeled "anthropic" reasoning) to demonstrate that life is made possible by the deliberate controlling influence of the living all-embracing "intelligent universe." This is consistent with panentheism [pan-en-theos-ism, not pantheism]. As advanced by Hoyle and Wickramasinghe, cometary panspermia is panentheistic. Also, neoclassical panentheism requires generic panspermia, and favors cometary panspermia.

Advances in distributed watershed modeling: a review and application of the AgroEcoSystem-Watershed (AgES-W) model

USDA-ARS?s Scientific Manuscript database

Progress in the understanding of physical, chemical, and biological processes influencing water quality, coupled with advancements in the collection and analysis of hydrologic data, provide opportunities for significant innovations in the manner and level with which watershed-scale processes may be ...

Advances and Computational Tools towards Predictable Design in Biological Engineering

PubMed Central

2014-01-01

The design process of complex systems in all the fields of engineering requires a set of quantitatively characterized components and a method to predict the output of systems composed by such elements. This strategy relies on the modularity of the used components or the prediction of their context-dependent behaviour, when parts functioning depends on the specific context. Mathematical models usually support the whole process by guiding the selection of parts and by predicting the output of interconnected systems. Such bottom-up design process cannot be trivially adopted for biological systems engineering, since parts function is hard to predict when components are reused in different contexts. This issue and the intrinsic complexity of living systems limit the capability of synthetic biologists to predict the quantitative behaviour of biological systems. The high potential of synthetic biology strongly depends on the capability of mastering this issue. This review discusses the predictability issues of basic biological parts (promoters, ribosome binding sites, coding sequences, transcriptional terminators, and plasmids) when used to engineer simple and complex gene expression systems in Escherichia coli. A comparison between bottom-up and trial-and-error approaches is performed for all the discussed elements and mathematical models supporting the prediction of parts behaviour are illustrated. PMID:25161694

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Multilevel functional genomics data integration as a tool for understanding physiology: a network biology perspective.

PubMed

Davidsen, Peter K; Turan, Nil; Egginton, Stuart; Falciani, Francesco

2016-02-01

The overall aim of physiological research is to understand how living systems function in an integrative manner. Consequently, the discipline of physiology has since its infancy attempted to link multiple levels of biological organization. Increasingly this has involved mathematical and computational approaches, typically to model a small number of components spanning several levels of biological organization. With the advent of "omics" technologies, which can characterize the molecular state of a cell or tissue (intended as the level of expression and/or activity of its molecular components), the number of molecular components we can quantify has increased exponentially. Paradoxically, the unprecedented amount of experimental data has made it more difficult to derive conceptual models underlying essential mechanisms regulating mammalian physiology. We present an overview of state-of-the-art methods currently used to identifying biological networks underlying genomewide responses. These are based on a data-driven approach that relies on advanced computational methods designed to "learn" biology from observational data. In this review, we illustrate an application of these computational methodologies using a case study integrating an in vivo model representing the transcriptional state of hypoxic skeletal muscle with a clinical study representing muscle wasting in chronic obstructive pulmonary disease patients. The broader application of these approaches to modeling multiple levels of biological data in the context of modern physiology is discussed. Copyright © 2016 the American Physiological Society.

Parasites as biological tags to assess host population structure: Guidelines, recent genetic advances and comments on a holistic approach☆

PubMed Central

Catalano, Sarah R.; Whittington, Ian D.; Donnellan, Stephen C.; Gillanders, Bronwyn M.

2013-01-01

We review the use of parasites as biological tags of marine fishes and cephalopods in host population structure studies. The majority of the work published has focused on marine fish and either single parasite species or more recently, whole parasite assemblages, as biological tags. There is representation of host organisms and parasites from a diverse range of taxonomic groups, although focus has primarily been on host species of commercial importance. In contrast, few studies have used parasites as tags to assess cephalopod population structure, even though records of parasites infecting cephalopods are well-documented. Squid species are the only cephalopod hosts for which parasites as biological tags have been applied, with anisakid nematode larvae and metacestodes being the parasite taxa most frequently used. Following a brief insight into the importance of accurate parasite identification, the population studies that have used parasites as biological tags for marine fishes and cephalopods are reviewed, including comments on the dicyemid mesozoans. The advancement of molecular genetic techniques is discussed in regards to the new ways parasite genetic data can be incorporated into population structure studies, alongside host population genetic analyses, followed by an update on the guidelines for selecting a parasite species as a reliable tag candidate. As multiple techniques and methods can be used to assess the population structure of marine organisms (e.g. artificial tags, phenotypic characters, biometrics, life history, genetics, otolith microchemistry and parasitological data), we conclude by commenting on a holistic approach to allow for a deeper insight into population structuring. PMID:25197624

Professional equity as reported by biology teachers

NASA Astrophysics Data System (ADS)

Douglas, Claudia B.; Lakes Matyas, Marsha; Butler Kahle, Jane

In 1982, the National Association of Biology Teachers surveyed its membership in order to assess the role and status of women in biology education. Items describing roles, salaries, assignments, professional activities, and sexual bias were included in the survey. This paper compares the responses of male and female biology educators, draws conclusions from the data, and suggests implications for the science education profession. Inequality in several professional areas was revealed. More women than men were single and reported no dependent children. Women exceeded men in both the lower and upper ends of the distribution of years of experience. However, the percentage of men exceeded that of women in most salary brackets beyond $20,000 and more men reported paid consulting opportunities. Men tended to teach at larger institutions and, at all academic levels, more men taught advanced classes. More men than women were involved with research activities. However, neither sex felt that the other one received preferential treatment in regard to salary and promotion. The majority of education administrators as well as science and biology faculties were male. However, the recent influx of women into science education positions may produce important changes. It is recommended that a comparative study be conducted in five years.

The efficacy of self-directed modules for clinical learning: advanced competencies in entry-level physical therapy education.

PubMed

Peck, Kirk; Paschal, Karen; Black, Lisa; Nelson, Kelly

2014-01-01

Prior to graduation, students often express an interest to advance clinical and professional skills in teaching, research, administration, and various niche practice areas. The acquisition of advanced education in selected areas of practice is believed to improve employment opportunities, accelerate career advancement including eligibility for professional certifications, and contribute to personal satisfaction in the profession. The purpose of this paper is to (1) describe an innovative model of education, the Directed Practice Experience (DPE) elective, that incorporates a student-initiated learning process designed to achieve student-identified professional goals, and (2) report the outcomes for graduates who have completed the DPE in an entry-level program in physical therapy education. Students who met select criteria were eligible to complete a DPE. Applicants designed a 4- to 6-week clinical education experience consisting of stated rationale for personal and professional growth, examples of leadership and service, and self-directed objectives that are beyond entry-level expectations as measured by the revised Physical Therapist Clinical Performance Instrument, version 2006. Twenty-six students have completed DPEs since 2005. Fifty percent resulted in new academic partnerships. At least 25% of graduates now serve as clinical instructors for the entry-level program. Those who participated in DPEs have also completed post-graduate residencies, attained ABPTS Board certifications, authored peer-reviewed publications, and taught in both PT and residency programs. The DPE model allows qualified students to acquire advanced personal skills and knowledge prior to graduation in areas of professional practice that exceed entry-level expectations. The model is applicable to all CAPTE accredited physical therapy education programs and is especially beneficial for academic programs desiring to form new community partnerships for student clinical education.

Advanced treatment of biologically pretreated coal gasification wastewater by a novel integration of three-dimensional catalytic electro-Fenton and membrane bioreactor.

PubMed

Jia, Shengyong; Han, Hongjun; Hou, Baolin; Zhuang, Haifeng

2015-12-01

Laboratorial scale experiments were conducted to investigate a novel system three-dimensional catalytic electro-Fenton (3DCEF, catalyst of sewage sludge based activated carbon which loaded Fe3O4) integrating with membrane bioreactor (3DCEF-MBR) on advanced treatment of biologically pretreated coal gasification wastewater. The results indicated that 3DCEF-MBR represented high efficiencies in eliminating COD and total organic carbon, giving the maximum removal efficiencies of 80% and 75%, respectively. The integrated 3DCEF-MBR system significantly reduced the transmembrane pressure, giving 35% lower than conventional MBR after 30 days operation. The enhanced hydroxyl radical oxidation and bacteria self repair function were the mechanisms for 3DCEF-MBR performance. Therefore, the integrated 3DCEF-MBR was expected to be the promising technology for advanced treatment in engineering applications. Copyright © 2015. Published by Elsevier Ltd.

A Checklist for Successful Quantitative Live Cell Imaging in Systems Biology

PubMed Central

Sung, Myong-Hee

2013-01-01

Mathematical modeling of signaling and gene regulatory networks has provided unique insights about systems behaviors for many cell biological problems of medical importance. Quantitative single cell monitoring has a crucial role in advancing systems modeling of molecular networks. However, due to the multidisciplinary techniques that are necessary for adaptation of such systems biology approaches, dissemination to a wide research community has been relatively slow. In this essay, I focus on some technical aspects that are often under-appreciated, yet critical in harnessing live cell imaging methods to achieve single-cell-level understanding and quantitative modeling of molecular networks. The importance of these technical considerations will be elaborated with examples of successes and shortcomings. Future efforts will benefit by avoiding some pitfalls and by utilizing the lessons collectively learned from recent applications of imaging in systems biology. PMID:24709701

Robust Design of Biological Circuits: Evolutionary Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

2011-01-01

Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise. PMID:22187523

Robust design of biological circuits: evolutionary systems biology approach.

PubMed

Chen, Bor-Sen; Hsu, Chih-Yuan; Liou, Jing-Jia

2011-01-01

Artificial gene circuits have been proposed to be embedded into microbial cells that function as switches, timers, oscillators, and the Boolean logic gates. Building more complex systems from these basic gene circuit components is one key advance for biologic circuit design and synthetic biology. However, the behavior of bioengineered gene circuits remains unstable and uncertain. In this study, a nonlinear stochastic system is proposed to model the biological systems with intrinsic parameter fluctuations and environmental molecular noise from the cellular context in the host cell. Based on evolutionary systems biology algorithm, the design parameters of target gene circuits can evolve to specific values in order to robustly track a desired biologic function in spite of intrinsic and environmental noise. The fitness function is selected to be inversely proportional to the tracking error so that the evolutionary biological circuit can achieve the optimal tracking mimicking the evolutionary process of a gene circuit. Finally, several design examples are given in silico with the Monte Carlo simulation to illustrate the design procedure and to confirm the robust performance of the proposed design method. The result shows that the designed gene circuits can robustly track desired behaviors with minimal errors even with nontrivial intrinsic and external noise.

Recent advances in plant centromere biology.

PubMed

Feng, Chao; Liu, YaLin; Su, HanDong; Wang, HeFei; Birchler, James; Han, FangPu

2015-03-01

The centromere, which is one of the essential parts of a chromosome, controls kinetochore formation and chromosome segregation during mitosis and meiosis. While centromere function is conserved in eukaryotes, the centromeric DNA sequences evolve rapidly and have few similarities among species. The histone H3 variant CENH3 (CENP-A in human), which mostly exists in centromeric nucleosomes, is a universal active centromere mark in eukaryotes and plays an essential role in centromere identity determination. The relationship between centromeric DNA sequences and centromere identity determination is one of the intriguing questions in studying centromere formation. Due to the discoveries in the past decades, including "neocentromeres" and "centromere inactivation", it is now believed that the centromere identity is determined by epigenetic mechanisms. This review will present recent progress in plant centromere biology.

Bioinformatics approaches to single-cell analysis in developmental biology.

PubMed

Yalcin, Dicle; Hakguder, Zeynep M; Otu, Hasan H

2016-03-01

Individual cells within the same population show various degrees of heterogeneity, which may be better handled with single-cell analysis to address biological and clinical questions. Single-cell analysis is especially important in developmental biology as subtle spatial and temporal differences in cells have significant associations with cell fate decisions during differentiation and with the description of a particular state of a cell exhibiting an aberrant phenotype. Biotechnological advances, especially in the area of microfluidics, have led to a robust, massively parallel and multi-dimensional capturing, sorting, and lysis of single-cells and amplification of related macromolecules, which have enabled the use of imaging and omics techniques on single cells. There have been improvements in computational single-cell image analysis in developmental biology regarding feature extraction, segmentation, image enhancement and machine learning, handling limitations of optical resolution to gain new perspectives from the raw microscopy images. Omics approaches, such as transcriptomics, genomics and epigenomics, targeting gene and small RNA expression, single nucleotide and structural variations and methylation and histone modifications, rely heavily on high-throughput sequencing technologies. Although there are well-established bioinformatics methods for analysis of sequence data, there are limited bioinformatics approaches which address experimental design, sample size considerations, amplification bias, normalization, differential expression, coverage, clustering and classification issues, specifically applied at the single-cell level. In this review, we summarize biological and technological advancements, discuss challenges faced in the aforementioned data acquisition and analysis issues and present future prospects for application of single-cell analyses to developmental biology. © The Author 2015. Published by Oxford University Press on behalf of the European

Team-teaching a current events-based biology course for nonmajors.

PubMed

Bondos, Sarah E; Phillips, Dereth

2008-01-01

Rice University has created a team-taught interactive biology course for nonmajors with a focus on cutting edge biology in the news-advances in biotechnology, medicine, and science policy, along with the biological principles and methodology upon which these advances are based. The challenges inherent to teaching current topics were minimized by team-teaching the course, providing knowledgeable and enthusiastic lecturers for every topic while distributing the effort required to update material. Postdoctoral associates and advanced graduate students served as lecturers, providing an opportunity for them to develop their teaching skills and learn to communicate effectively with nonscientists on newsworthy topics related to their research. Laboratory tours, in-class demonstrations, and mock-ups helped lecturers convey surprisingly advanced ideas with students who lacked a strong theoretical or practical science background. A faculty member and co-coordinator administer the class, organize class activities, and mentor the speakers on teaching techniques and lecture design. Course design, lecture topics, hands-on activities, and approaches to successfully solve the difficulties inherent to team teaching are discussed. Course evaluations reflect student involvement in, and enjoyment of, the class. Copyright © 2008 International Union of Biochemistry and Molecular Biology, Inc.

Synthetic Biology Guides Biofuel Production

PubMed Central

Connor, Michael R.; Atsumi, Shota

2010-01-01

The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges. PMID:20827393

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Hoops, Stefan; Keating, Sarah M.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528564

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

BIOLOGY I, NEW APPROACHES AND OBJECTIVES.

ERIC Educational Resources Information Center

COKER, ROBERT; AND OTHERS

THE PRINCIPLES OF MODERN BIOLOGY SHOULD BE PRESENTED IN A DYNAMIC AND CHALLENGING WAY TO CAPABLE STUDENTS TO DEVELOP LASTING INTEREST IN THE SUBJECT AND TO PLACE EMPHASIS UPON THE ROLE OF THE PHYSICAL SCIENCES IN BIOLOGY IN ACCORD WITH NATIONWIDE TENDENCY. THE COURSE IS COMPLETE IN ITSELF BUT PROVIDES A BASIS FOR STUDENTS WHO ELECT ADVANCED WORK.…

Systems Biology-an interdisciplinary approach.

PubMed

Friboulet, Alain; Thomas, Daniel

2005-06-15

System-level approaches in biology are not new but foundations of "Systems Biology" are achieved only now at the beginning of the 21st century [Kitano, H., 2001. Foundations of Systems Biology. MIT Press, Cambridge, MA]. The renewed interest for a system-level approach is linked to the progress in collecting experimental data and to the limits of the "reductionist" approach. System-level understanding of native biological and pathological systems is needed to provide potential therapeutic targets. Examples of interdisciplinary approach in Systems Biology are described in U.S., Japan and Europe. Robustness in biology, metabolic engineering and idiotypic networks are discussed in the framework of Systems Biology.

How to integrate biological research into society and exclude errors in biomedical publications? Progress in theoretical and systems biology releases pressure on experimental research.

PubMed

Volkov, Vadim

2014-01-01

This brief opinion proposes measures to increase efficiency and exclude errors in biomedical research under the existing dynamic situation. Rapid changes in biology began with the description of the three dimensional structure of DNA 60 years ago; today biology has progressed by interacting with computer science and nanoscience together with the introduction of robotic stations for the acquisition of large-scale arrays of data. These changes have had an increasing influence on the entire research and scientific community. Future advance demands short-term measures to ensure error-proof and efficient development. They can include the fast publishing of negative results, publishing detailed methodical papers and excluding a strict connection between career progression and publication activity, especially for younger researchers. Further development of theoretical and systems biology together with the use of multiple experimental methods for biological experiments could also be helpful in the context of years and decades. With regards to the links between science and society, it is reasonable to compare both these systems, to find and describe specific features for biology and to integrate it into the existing stream of social life and financial fluxes. It will increase the level of scientific research and have mutual positive effects for both biology and society. Several examples are given for further discussion.

Advances in the biological effects of terahertz wave radiation.

PubMed

Zhao, Li; Hao, Yan-Hui; Peng, Rui-Yun

2014-01-01

The terahertz (THz) band lies between microwave and infrared rays in wavelength and consists of non-ionizing radiation. Both domestic and foreign research institutions, including the army, have attached considerable importance to the research and development of THz technology because this radiation exhibits both photon-like and electron-like properties, which grant it considerable application value and potential. With the rapid development of THz technology and related applications, studies of the biological effects of THz radiation have become a major focus in the field of life sciences. Research in this field has only just begun, both at home and abroad. In this paper, research progress with respect to THz radiation, including its biological effects, mechanisms and methods of protection, will be reviewed.

Engineering for the 21st century: synthetic biology.

PubMed

Munnelly, Kevin

2013-05-17

For years, scientists have hoped that biology would find its engineering counterpart--a series of principles that could be used as reliably as chemical engineering is for chemistry. Thanks to major advances in synthetic biology, those hopes may soon be realized.

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

PubMed

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

2015-05-15

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

Elevated circulating level of osteopontin is associated with advanced disease state of non-small cell lung cancer.

PubMed

Chang, Yoon Soo; Kim, Hyung Jung; Chang, Joon; Ahn, Chul Min; Kim, Sung Kyu; Kim, Se Kyu

2007-09-01

Osteopontin (OPN) plays important roles in tumor progression and metastasis through binding to OPN receptors such as alpha(v)beta(beta) integrin and CD44, and its overexpression in tumor is associated poor clinical outcome of NSCLC patients. Circulating OPN levels, measured by ELISA in 130 NSCLC cases that had not been treated for cancer at the time of sampling, were analyzed according to clinical, pathologic parameters and single nucleotide polymorphisms (SNPs) in the OPN gene promoter. Advanced disease states had higher circulating levels of OPN (T4 versus T1-3, N3 versus N0-2, and M1 versus M0, P=.029, .001, and .001, respectively, Kruskal-Wallis H-test), reflected by higher level of OPN in stage IV than stage I-III (P=.029, Kruskal-Wallis H-test). Among the clinical and pathological parameters including age, gender, smoking status, histologic subtypes and grade of differentiation, smoking status influences circulating OPN level showing higher level of OPN in ex-smokers than current and non-smokers (P=.038, Kruskal-Wallis H-test). Variation at nucleotide (nt) -443 of the OPN gene promoter had no influence on circulating OPN levels, however, patients with G/G at nt -156 showed higher concentrations of OPN than those with G/GG or GG/GG (P=.003, Kruskal-Wallis H-test). A patient with G/G at nt -156 was more frequently diagnosed with advanced stage (IIIB-IV) than with early stage (I-IIIA) NSCLC (P=.048, Mantel-Haenszel-test). In multivariate analysis, stage is the only independent factor influencing circulating level of OPN. Although circulating level of OPN in the patients with bone metastasis was higher than in those without bone metastasis (P=.028, Mann-Whitney U-test), there was no difference in the OPN levels between bone metastasis group and non-bone metastasis group. Given that the elevated levels of OPN is associated with advanced stages of NSCLC, elucidating OPN regulatory mechanisms may contribute to the development of a new therapeutic modality for NSCLC.

Advances in point-of-care technologies for molecular diagnostics.

PubMed

Zarei, Mohammad

2017-12-15

Advances in miniaturization, nanotechnology, and microfluidics, along with developments in cloud-connected point-of-care (POC) diagnostics technologies are pushing the frontiers of POC devices toward low-cost, user-friendly, and enhanced sensitivity molecular-level diagnostics. The combination of various bio-sensing platforms within smartphone-integrated electronic readers provides accurate on-site and on-time diagnostics based on various types of chemical and biological targets. Further, 3D printing technology shows a huge potential toward fabrication and improving the performance of POC devices. Integration of skin-like flexible sensors with wireless communication technology creates a unique opportunity for continuous, real-time monitoring of patients for both preventative healthcare and during disease outbreaks. Here, we review recent developments and advances in POC technologies and describe how these advances enhance the performance of POC platforms. Also, this review describes challenges, directions, and future trends on application of emerging technologies in POC diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

Grand challenges in space synthetic biology

PubMed Central

Montague, Michael G.; Cumbers, John; Hogan, John A.

2015-01-01

Space synthetic biology is a branch of biotechnology dedicated to engineering biological systems for space exploration, industry and science. There is significant public and private interest in designing robust and reliable organisms that can assist on long-duration astronaut missions. Recent work has also demonstrated that such synthetic biology is a feasible payload minimization and life support approach as well. This article identifies the challenges and opportunities that lie ahead in the field of space synthetic biology, while highlighting relevant progress. It also outlines anticipated broader benefits from this field, because space engineering advances will drive technological innovation on Earth. PMID:26631337

Determining the satisfaction levels of the family members of patients with advanced-stage cancer.

PubMed

Ozcelik, Hanife; Cakmak, Deniz Ezgi; Fadiloglu, Cicek; Yildirim, Yasemin; Uslu, Ruchan

2015-06-01

The objective of our study was to determine the satisfaction levels of family members of patients with advanced-stage cancer. This descriptive study was conducted in the palliative care and medical oncology clinics of a university hospital in the province of Izmir between April of 2011 and January of 2012. The study sample consisted of a total of 145 family members, who were selected from among the family members of patients with advanced-stage cancer receiving palliative treatment. The study data were obtained using the Patient Description Form and Family Satisfaction Scale during face-to-face interviews with patients. Some 67% of patients were female and 33% male, 70% were married, 35% were high school graduates, and 34.5% were housewives. The average total family satisfaction score was 76.87 ± 1.14, and the average scores for the component variables were as follows: information giving 74.37 ± 1.28, availability of care 78.40 ± 1.17, physical care 78.99 ± 1.09, and psychosocial care 74.52 ± 1.30. We found a relationship between the level of satisfaction of family members and (1) gender, (2) occupation, (3) presence of someone supporting the care, and (4) possession of sufficient information about the patient (p < 0.05). Satisfaction levels of participants were determined to be high. We found that family member satisfaction levels were affected by gender and occupation, the existence of someone supporting the care, and possession of sufficient information about the patient.

CINRG: Systems Biology of Glucocorticoids in Muscle Disease

DTIC Science & Technology

2012-10-01

Duchenne Muscular dystrophy , Glucocorticoids, Systems biology, Drug mechanism CINRG: Systems Biology of Glucocorticoids in Muscle Disease Zuyi Wang, Ph.D...2011-2012) for Contract W81XWH-09-1-0726 SYSTEMS BIOLOGY OF GLUCOCORTICOIDS IN MUSCLE DISEASE Introduction Duchenne muscular dystrophy ...DMD) is the most common and incurable muscular dystrophy of childhood. Muscle regeneration fails with advancing age, leading to considerable fibrosis

Specialty Tier-Level Cost Sharing and Biologic Agent Use in the Medicare Part D Initial Coverage Period Among Beneficiaries With Rheumatoid Arthritis.

PubMed

Doshi, Jalpa A; Hu, Tianyan; Li, Pengxiang; Pettit, Amy R; Yu, Xinyan; Blum, Marissa

2016-11-01

To examine associations between specialty tier-level cost sharing and use of biologic agents for rheumatoid arthritis (RA) during Medicare Part D's initial coverage period (ICP). This was a retrospective study using 2007-2010 5% sample Medicare files to examine RA patients with use of a Part D RA biologic agent in the prior year. Patients without low-income subsidies (non-LIS group), who faced specialty tier-level cost sharing, were compared to a control group of low-income subsidy patients (LIS group), who faced nominal out-of-pocket costs in the ICP. Outcomes included use of a Part D or Part B RA biologic agent during the ICP and presence of a ≥30-day continuous gap in treatment among Part D biologic agent users in the ICP. Risk-adjusted outcomes were estimated using logistic regressions, controlling for patient demographic, clinical, and Part D plan characteristics. On average, a 30-day Part D biologic agent supply cost the non-LIS group $484 out of pocket (29.9% cost sharing) versus $5 (0.3% cost sharing) for the LIS group. The non-LIS group was less likely to fill Part D biologic agents (61.2% versus 72.7%, odds ratio [OR] 0.58 [95% confidence interval (95% CI) 0.46-0.72]; P < 0.001), more than twice as likely to receive Part B biologic agents (9.9% versus 4.4%, OR 2.41 [95% CI 1.61-3.60]; P < 0.001), and less likely to use any biologic agent (70.1% versus 76.9%, OR 0.69 [95% CI 0.55-0.88]; P = 0.002). The non-LIS subgroup filling Part D biologic agents had approximately twice the odds of a gap in both Part D biologic agent and any biologic agent availability. Specialty tier-level cost sharing was associated with interruptions in RA biologic agent treatment among Medicare patients. © 2016, American College of Rheumatology.

Plant systems biology: network matters.

PubMed

Lucas, Mikaël; Laplaze, Laurent; Bennett, Malcolm J

2011-04-01

Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology. © 2011 Blackwell Publishing Ltd.

The relative role of "A" level chemistry, physics and biology in the medical course.

PubMed

Tomilson, R W; Clack, G B; Pettingale, K W; Anderson, J; Ryan, K C

1977-03-01

The performance of 209 students in the 2nd MBBS, first clinical year and final MBBS examinations has been compared retrospectively with their grades in chemistry, physics and biology at "A" level. The mean grade has also been determined for students from different social classes and secondary education. Significant differences in marks for biology were found between successful and not so successful students, especially in the pre-clinical part of the course. Significnat differences in marks and significant correlations were also found for physics but not to any great extent for chemistry. The relative role of these three basic sciences in the medical course is discussed. The suggestion is made that there is a need for a re-appraisal of the privleged position of chemistry and an unquestioned science requirement for entry to medical school.

Telomere biology in aging and cancer: early history and perspectives.

PubMed

Hayashi, Makoto T

2018-01-20

The ends of eukaryotic linear chromosomes are protected from undesired enzymatic activities by a nucleoprotein complex called the telomere. Expanding evidence indicates that telomeres have central functions in human aging and tumorigenesis. While it is undoubtedly important to follow current advances in telomere biology, it is also fruitful to be well informed in seminal historical studies for a comprehensive understanding of telomere biology, and for the anticipation of future directions. With this in mind, I here summarize the early history of telomere biology and current advances in the field, mostly focusing on mammalian studies relevant to aging and cancer.

Coupling biology and oceanography in models.

PubMed

Fennel, W; Neumann, T

2001-08-01

The dynamics of marine ecosystems, i.e. the changes of observable chemical-biological quantities in space and time, are driven by biological and physical processes. Predictions of future developments of marine systems need a theoretical framework, i.e. models, solidly based on research and understanding of the different processes involved. The natural way to describe marine systems theoretically seems to be the embedding of chemical-biological models into circulation models. However, while circulation models are relatively advanced the quantitative theoretical description of chemical-biological processes lags behind. This paper discusses some of the approaches and problems in the development of consistent theories and indicates the beneficial potential of the coupling of marine biology and oceanography in models.

Perspectives on Performance Indicators: GCE Advanced Level and Differences Between Institution Types in Cost Effectiveness.

ERIC Educational Resources Information Center

Fielding, A.

1998-01-01

Applies multilevel models of cost-effectiveness to numerous types of (British) institutions providing courses of instruction in the General Certificate of Education at Advanced Level. Different impressions may be gained about an institution's relative effectiveness when cost considerations are combined with outcome measures. Data evaluation needs…

Yeast synthetic biology for high-value metabolites.

PubMed

Dai, Zhubo; Liu, Yi; Guo, Juan; Huang, Luqi; Zhang, Xueli

2015-02-01

Traditionally, high-value metabolites have been produced through direct extraction from natural biological sources which are inefficient, given the low abundance of these compounds. On the other hand, these high-value metabolites are usually difficult to be synthesized chemically, due to their complex structures. In the last few years, the discovery of genes involved in the synthetic pathways of these metabolites, combined with advances in synthetic biology tools, has allowed the construction of increasing numbers of yeast cell factories for production of these metabolites from renewable biomass. This review summarizes recent advances in synthetic biology in terms of the use of yeasts as microbial hosts for the identification of the pathways involved in the synthesis, as well as for the production of high-value metabolites. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Biological and Environmental Research Exascale Requirements Review. An Office of Science review sponsored jointly by Advanced Scientific Computing Research and Biological and Environmental Research, March 28-31, 2016, Rockville, Maryland

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

Arkin, Adam; Bader, David C.; Coffey, Richard

Understanding the fundamentals of genomic systems or the processes governing impactful weather patterns are examples of the types of simulation and modeling performed on the most advanced computing resources in America. High-performance computing and computational science together provide a necessary platform for the mission science conducted by the Biological and Environmental Research (BER) office at the U.S. Department of Energy (DOE). This report reviews BER’s computing needs and their importance for solving some of the toughest problems in BER’s portfolio. BER’s impact on science has been transformative. Mapping the human genome, including the U.S.-supported international Human Genome Project that DOEmore » began in 1987, initiated the era of modern biotechnology and genomics-based systems biology. And since the 1950s, BER has been a core contributor to atmospheric, environmental, and climate science research, beginning with atmospheric circulation studies that were the forerunners of modern Earth system models (ESMs) and by pioneering the implementation of climate codes onto high-performance computers. See http://exascaleage.org/ber/ for more information.« less

[Future directions of molecular bone cell biology].

PubMed

Yoneda, T

2001-01-01

Introduction of genetic approaches using knockout and/or transgenic mice has produced many pieces of information that can't be obtained by conventional cell biological studies and profoundly advanced our understanding of bone biology and metabolism. Here, the author will first briefly summarize the current findings in the recent bone research and subsequently attempt to predict future directions to which bone research is going to proceed with a special emphasis of osteoclast and osteoblast biology.

Advances in synthetic peptides reagent discovery

NASA Astrophysics Data System (ADS)

Adams, Bryn L.; Sarkes, Deborah A.; Finch, Amethist S.; Stratis-Cullum, Dimitra N.

2013-05-01

Bacterial display technology offers a number of advantages over competing display technologies (e.g, phage) for the rapid discovery and development of peptides with interaction targeted to materials ranging from biological hazards through inorganic metals. We have previously shown that discovery of synthetic peptide reagents utilizing bacterial display technology is relatively simple and rapid to make laboratory automation possible. This included extensive study of the protective antigen system of Bacillus anthracis, including development of discovery, characterization, and computational biology capabilities for in-silico optimization. Although the benefits towards CBD goals are evident, the impact is far-reaching due to our ability to understand and harness peptide interactions that are ultimately extendable to the hybrid biomaterials of the future. In this paper, we describe advances in peptide discovery including, new target systems (e.g. non-biological materials), advanced library development and clone analysis including integrated reporting.

The Relationship between Biology Classes and Biological Reasoning and Common Heath Misconceptions

ERIC Educational Resources Information Center

Keselman, Alla; Hundal, Savreen; Chentsova-Dutton, Yulia; Bibi, Raquel; Edelman, Jay A.

2015-01-01

This study investigates the relationship among (1) college major, (2) knowledge used in reasoning about common health beliefs, and (3) judgment about the accuracy of those beliefs. Seventy-four college students, advanced biology and non-science majors, indicated their agreement or disagreement with commonly believed, but often inaccurate,…

The Role of Synthetic Biology in NASA's Missions

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2016-01-01

The time has come to for NASA to exploit synthetic biology in pursuit of its missions, including aeronautics, earth science, astrobiology and most notably, human exploration. Conversely, NASA advances the fundamental technology of synthetic biology as no one else can because of its unique expertise in the origin of life and life in extreme environments, including the potential for alternate life forms. This enables unique, creative "game changing" advances. NASA's requirement for minimizing upmass in flight will also drive the field toward miniaturization and automation. These drivers will greatly increase the utility of synthetic biology solutions for military, health in remote areas and commercial purposes. To this end, we have begun a program at NASA to explore the use of synthetic biology in NASA's missions, particular space exploration. As part of this program, we began hosting an iGEM team of undergraduates drawn from Brown and Stanford Universities to conduct synthetic biology research at NASA Ames Research Center. The 2011 team (http://2011.igem.org/Team:Brown-Stanford) produced an award-winning project on using synthetic biology as a basis for a human Mars settlement.

Recent Advances in Fiber Lasers for Nonlinear Microscopy

PubMed Central

Xu, C.; Wise, F. W.

2013-01-01

Nonlinear microscopy techniques developed over the past two decades have provided dramatic new capabilities for biological imaging. The initial demonstrations of nonlinear microscopies coincided with the development of solid-state femtosecond lasers, which continue to dominate applications of nonlinear microscopy. Fiber lasers offer attractive features for biological and biomedical imaging, and recent advances are leading to high-performance sources with the potential for robust, inexpensive, integrated instruments. This article discusses recent advances, and identifies challenges and opportunities for fiber lasers in nonlinear bioimaging. PMID:24416074

Advances on plant-pathogen interactions from molecular toward systems biology perspectives.

PubMed

Peyraud, Rémi; Dubiella, Ullrich; Barbacci, Adelin; Genin, Stéphane; Raffaele, Sylvain; Roby, Dominique

2017-05-01

In the past 2 decades, progress in molecular analyses of the plant immune system has revealed key elements of a complex response network. Current paradigms depict the interaction of pathogen-secreted molecules with host target molecules leading to the activation of multiple plant response pathways. Further research will be required to fully understand how these responses are integrated in space and time, and exploit this knowledge in agriculture. In this review, we highlight systems biology as a promising approach to reveal properties of molecular plant-pathogen interactions and predict the outcome of such interactions. We first illustrate a few key concepts in plant immunity with a network and systems biology perspective. Next, we present some basic principles of systems biology and show how they allow integrating multiomics data and predict cell phenotypes. We identify challenges for systems biology of plant-pathogen interactions, including the reconstruction of multiscale mechanistic models and the connection of host and pathogen models. Finally, we outline studies on resistance durability through the robustness of immune system networks, the identification of trade-offs between immunity and growth and in silico plant-pathogen co-evolution as exciting perspectives in the field. We conclude that the development of sophisticated models of plant diseases incorporating plant, pathogen and climate properties represent a major challenge for agriculture in the future. © 2016 The Authors. The Plant Journal published by John Wiley & Sons Ltd and Society for Experimental Biology.

[Comparison study between biological vision and computer vision].

PubMed

Liu, W; Yuan, X G; Yang, C X; Liu, Z Q; Wang, R

2001-08-01

The development and bearing of biology vision in structure and mechanism were discussed, especially on the aspects including anatomical structure of biological vision, tentative classification of reception field, parallel processing of visual information, feedback and conformity effect of visual cortical, and so on. The new advance in the field was introduced through the study of the morphology of biological vision. Besides, comparison between biological vision and computer vision was made, and their similarities and differences were pointed out.

Personal protection during resuscitation of casualties contaminated with chemical or biological warfare agents--a survey of medical first responders.

PubMed

Brinker, Andrea; Prior, Kate; Schumacher, Jan

2009-01-01

The threat of mass casualties caused by an unconventional terrorist attack is a challenge for the public health system, with special implications for emergency medicine, anesthesia, and intensive care. Advanced life support of patients injured by chemical or biological warfare agents requires an adequate level of personal protection. The aim of this study was to evaluate the personal protection knowledge of emergency physicians and anesthetists who would be at the frontline of the initial health response to a chemical/biological warfare agent incident. After institutional review board approval, knowledge of personal protection measures among emergency medicine (n = 28) and anesthetics (n = 47) specialty registrars in the South Thames Region of the United Kingdom was surveyed using a standardized questionnaire. Participants were asked for the recommended level of personal protection if a chemical/biological warfare agent(s) casualty required advanced life support in the designated hospital resuscitation area. The best awareness within both groups was regarding severe acute respiratory syndrome, and fair knowledge was found regarding anthrax, plague, Ebola, and smallpox. In both groups, knowledge about personal protection requirements against chemical warfare agents was limited. Knowledge about personal protection measures for biological agents was acceptable, but was limited for chemical warfare agents. The results highlight the need to improve training and education regarding personal protection measures for medical first receivers.

Last Deglacial Sea Level: A Curated Database of Indicators of Past Sea Levels from Biological and Geomorphological Archives

NASA Astrophysics Data System (ADS)

Hibbert, F. D.; Williams, F. H.; Fallon, S.; Rohling, E. J.

2017-12-01

The last deglacial was an interval of rapid climate and sea-level change, including the collapse of large continental ice sheets. This database collates carefully assessed sea-level data from peer-reviewed sources for the interval 0 to 25 thousand years ago (ka), from the last glacial maximum to the present interglacial conditions. In addition to facilitating site-specific reconstructions of past sea levels, the database provides a suite of data beyond the range of modern/instrumental variability that may help hone future sea-level projections. The database is global in scope, internally consistent, and contains U-series and radiocarbon dated indicators from both biological and geomorpohological archives. We focus on far-field data (i.e., away from the sites of the former continental ice sheets), but some key intermediate (i.e., from the Caribbean) data are also included. All primary fields (i.e., sample location, elevation, age and context) possess quantified uncertainties, which - in conjunction with available metadata - allows the reconstructed sea levels to be interpreted within both their uncertainties and geological context. Consistent treatment of each of the individual records in the database, and incorporation of fully expressed uncertainties, allows datasets to be easily compared. The compilation contains 145 studies from 40 locations (>2,000 data points) and includes all raw information and metadata.

Space biology research development

NASA Technical Reports Server (NTRS)

Bonting, Sjoerd L.

1993-01-01

The purpose of the Search for Extraterrestrial Intelligence (SETI) Institute is to conduct and promote research related activities regarding the search for extraterrestrial life, particularly intelligent life. Such research encompasses the broad discipline of 'Life in the Universe', including all scientific and technological aspects of astronomy and the planetary sciences, chemical evolution, the origin of life, biological evolution, and cultural evolution. The primary purpose was to provide funding for the Principal Investigator to collaborate with the personnel of the SETI Institute and the NASA-Ames Research center in order to plan and develop space biology research on and in connection with Space Station Freedom; to promote cooperation with the international partners in the space station; to conduct a study on the use of biosensors in space biology research and life support system operation; and to promote space biology research through the initiation of an annual publication 'Advances in Space Biology and Medicine'.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2018-03-09

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Synergism of Nanomaterials with Physical Stimuli for Biology and Medicine.

PubMed

Shin, Tae-Hyun; Cheon, Jinwoo

2017-03-21

Developing innovative tools that facilitate the understanding of sophisticated biological systems has been one of the Holy Grails in the physical and biological sciences. In this Commentary, we discuss recent advances, opportunities, and challenges in the use of nanomaterials as a precision tool for biology and medicine.

Student Perceived and Determined Knowledge of Biology Concepts in an Upper-Level Biology Course

PubMed Central

Montplaisir, Lisa

2014-01-01

Students who lack metacognitive skills can struggle with the learning process. To be effective learners, students should recognize what they know and what they do not know. This study examines the relationship between students’ perception of their knowledge and determined knowledge in an upper-level biology course utilizing a pre/posttest approach. Significant differences in students’ perception of their knowledge and their determined knowledge exist at the beginning (pretest) and end (posttest) of the course. Alignment between student perception and determined knowledge was significantly more accurate on the posttest compared with the pretest. Students whose determined knowledge was in the upper quartile had significantly better alignment between their perception and determined knowledge on the pre- and posttest than students in the lower quartile. No difference exists between how students perceived their knowledge between upper- and lower-quartile students. There was a significant difference in alignment of perception and determined knowledge between males and females on the posttest, with females being more accurate in their perception of knowledge. This study provides evidence of discrepancies that exist between what students perceive they know and what they actually know. PMID:26086662

An end-to-end workflow for engineering of biological networks from high-level specifications.

PubMed

Beal, Jacob; Weiss, Ron; Densmore, Douglas; Adler, Aaron; Appleton, Evan; Babb, Jonathan; Bhatia, Swapnil; Davidsohn, Noah; Haddock, Traci; Loyall, Joseph; Schantz, Richard; Vasilev, Viktor; Yaman, Fusun

2012-08-17

We present a workflow for the design and production of biological networks from high-level program specifications. The workflow is based on a sequence of intermediate models that incrementally translate high-level specifications into DNA samples that implement them. We identify algorithms for translating between adjacent models and implement them as a set of software tools, organized into a four-stage toolchain: Specification, Compilation, Part Assignment, and Assembly. The specification stage begins with a Boolean logic computation specified in the Proto programming language. The compilation stage uses a library of network motifs and cellular platforms, also specified in Proto, to transform the program into an optimized Abstract Genetic Regulatory Network (AGRN) that implements the programmed behavior. The part assignment stage assigns DNA parts to the AGRN, drawing the parts from a database for the target cellular platform, to create a DNA sequence implementing the AGRN. Finally, the assembly stage computes an optimized assembly plan to create the DNA sequence from available part samples, yielding a protocol for producing a sample of engineered plasmids with robotics assistance. Our workflow is the first to automate the production of biological networks from a high-level program specification. Furthermore, the workflow's modular design allows the same program to be realized on different cellular platforms simply by swapping workflow configurations. We validated our workflow by specifying a small-molecule sensor-reporter program and verifying the resulting plasmids in both HEK 293 mammalian cells and in E. coli bacterial cells.

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

PubMed

Dreuw, Andreas

2006-11-13

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

You can exercise your way out of HIV and other stories: The role of biological knowledge in adolescents' evaluation of myths

NASA Astrophysics Data System (ADS)

Keselman, Alla; Kaufman, David R.; Patel, Vimla L.

2004-07-01

A primary objective for science education is to impart robust knowledge that has applicability to real-world problems. This article presents research investigating the relationship between adolescents' conceptual understanding of the biological basis of HIV and critical reasoning. Middle and high school students were interviewed about their understanding of HIV and were subsequently asked to evaluate scenarios that contained myths about HIV. On the basis of their responses to the interview questions, students' understanding of HIV was categorized into three models, naïve, intermediate, and advanced. The results indicate that knowledge mediated students' responses in specific ways. Students at different levels of HIV knowledge reasoned in qualitatively different ways about the myths. A significant relationship was found between students' understanding of HIV biology and the level of biological reasoning. We found that students who employed cellular-level biological reasoning were more likely to reject the myths than students who employed just system-level reasoning or nonspecific biological reasoning. The findings emphasize the importance of conceptual understanding in the critical evaluation of information that may serve as a basis for making decisions about HIV. We conclude with discussing the implications of the findings for science and health education.