Reverse engineering and identification in systems biology: strategies, perspectives and challenges.

PubMed

Villaverde, Alejandro F; Banga, Julio R

2014-02-06

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology?

Contributions of A. Roberto Frisancho to human population biology: an introduction.

PubMed

Leonard, William R

2009-01-01

Over the span of his career, A. Roberto Frisancho has been one of the prime architects of the development and expansion of human population biology. His research and scholarly publications have helped to move the field beyond simple descriptions of human variation to address the nature and evolutionary origins of human biological diversity. Frisancho's early work in the Peruvian Andes elegantly demonstrated the importance of developmental acclimatization for promoting adaptive responses to the multiple stressors of high-altitude environments. Since mid-1970s, he has played a major role in developing and expanding the use of anthropometric techniques for assessing physical growth and nutritional status. Frisancho's influential publications have helped to make the use of anthropometric methods commonplace in the fields of nutritional science and public health. Throughout his career, Frisancho's work has examined how environmental, genetic, and developmental factors interact to influence human health and nutritional status. His research has addressed topics ranging from the determinants of low-birth weight infants in teenage mothers to the origins of obesity and associated metabolic diseases in populations of the developing world. Both the breadth and impact of Frisancho's work have been truly remarkable. The field of human population biology owes much to the tremendous contributions of A. Roberto Frisancho.

Bioorthogonal chemistry: applications in activity-based protein profiling.

PubMed

Willems, Lianne I; van der Linden, Wouter A; Li, Nan; Li, Kah-Yee; Liu, Nora; Hoogendoorn, Sascha; van der Marel, Gijs A; Florea, Bogdan I; Overkleeft, Herman S

2011-09-20

The close interaction between organic chemistry and biology goes back to the late 18th century, when the modern natural sciences began to take shape. After synthetic organic chemistry arose as a discipline, organic chemists almost immediately began to pursue the synthesis of naturally occurring compounds, thereby contributing to the understanding of their functions in biological processes. Research in those days was often remarkably interdisciplinary; in fact, it constituted chemical biology research before the phrase even existed. For example, histological dyes, both of an organic and inorganic nature, were developed and applied by independent researchers (Gram and Golgi) with the aim of visualizing cellular substructures (the bacterial cell wall and the Golgi apparatus). Over the years, as knowledge within the various fields of the natural sciences deepened, research disciplines drifted apart, becoming rather monodisciplinary. In these years, broadly ranging from the end of World War II to about the 1980s, organic chemistry continued to impact life sciences research, but contributions were of a more indirect nature. As an example, the development of the polymerase chain reaction, from which molecular biology and genetics research have greatly profited, was partly predicated on the availability of synthetic oligonucleotides. These molecules first became available in the late 1960s, the result of organic chemists pursuing the synthesis of DNA oligomers primarily because of the synthetic challenges involved. Today, academic natural sciences research is again becoming more interdisciplinary, and sometimes even multidisciplinary. What was termed "chemical biology" by Stuart Schreiber at the end of the last century can be roughly described as the use of intellectually chemical approaches to shed light on processes that are fundamentally rooted in biology. Chemical tools and techniques that are developed for biological studies in the exciting and rapidly evolving field of chemical biology research include contributions from many areas of the multifaceted discipline of chemistry, and particularly from organic chemistry. Researchers apply knowledge inherent to organic chemistry, such as reactivity and selectivity, to the manipulation of specific biomolecules in biological samples (cell extracts, living cells, and sometimes even animal models) to gain insight into the biological phenomena in which these molecules participate. In this Account, we highlight some of the recent developments in chemical biology research driven by organic chemistry, with a focus on bioorthogonal chemistry in relation to activity-based protein profiling. The rigorous demands of bioorthogonality have not yet been realized in a truly bioorthogonal reagent pair, but remarkable progress has afforded a range of tangible contributions to chemical biology research. Activity-based protein profiling, which aims to obtain information on the workings of a protein (or protein family) within the larger context of the full biological system, has in particular benefited from these advances. Both activity-based protein profiling and bioorthogonal chemistry have been around for approximately 15 years, and about 8 years ago the two fields very profitably intersected. We expect that each discipline, both separately and in concert, will continue to make important contributions to chemical biology research. © 2011 American Chemical Society

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…

Economics, human biology and inequality: A review of "puzzles" and recent contributions from a Deatonian perspective.

PubMed

Baten, Joerg

2017-05-01

The Nobel laureate Angus Deaton concentrated his work on puzzling developments and phenomena in economics. Puzzles are exciting elements in economics, because readers feel challenged by the question of how they can be solved. Among the puzzles analyzed by Deaton are: (1) Mortality increase of white, U.S. non-Hispanic men (2000 to today); (2) Why are height and income sometimes closely correlated, but not always?; (3) Height inequality among males and females; and (4) The Indian puzzle of declining consumption of calories during overall expenditure growth. This article reviews these "puzzles" and the main insights that Deaton derived from their discussion insofar as they pertain to the biological aspects of human development. I will focus on the field of this journal, Economics and Human Biology, in which Deaton has been very active over the last two decades. I will also document some of the responses by other scholars and their contributions to these puzzles, as they relate to the field of economics and human biology. Copyright © 2016 Elsevier B.V. All rights reserved.

Reverse engineering and identification in systems biology: strategies, perspectives and challenges

PubMed Central

Villaverde, Alejandro F.; Banga, Julio R.

2014-01-01

The interplay of mathematical modelling with experiments is one of the central elements in systems biology. The aim of reverse engineering is to infer, analyse and understand, through this interplay, the functional and regulatory mechanisms of biological systems. Reverse engineering is not exclusive of systems biology and has been studied in different areas, such as inverse problem theory, machine learning, nonlinear physics, (bio)chemical kinetics, control theory and optimization, among others. However, it seems that many of these areas have been relatively closed to outsiders. In this contribution, we aim to compare and highlight the different perspectives and contributions from these fields, with emphasis on two key questions: (i) why are reverse engineering problems so hard to solve, and (ii) what methods are available for the particular problems arising from systems biology? PMID:24307566

The Biological Relevance of Artificial Life: Lessons from Artificial Intelligence

NASA Technical Reports Server (NTRS)

Colombano, Silvano

2000-01-01

There is no fundamental reason why A-life couldn't simply be a branch of computer science that deals with algorithms that are inspired by, or emulate biological phenomena. However, if these are the limits we place on this field, we miss the opportunity to help advance Theoretical Biology and to contribute to a deeper understanding of the nature of life. The history of Artificial Intelligence provides a good example, in that early interest in the nature of cognition quickly was lost to the process of building tools, such as "expert systems" that, were certainly useful, but provided little insight in the nature of cognition. Based on this lesson, I will discuss criteria for increasing the biological relevance of A-life and the probability that this field may provide a theoretical foundation for Biology.

Localized structures in dissipative media: from optics to plant ecology

PubMed Central

Tlidi, M.; Staliunas, K.; Panajotov, K.; Vladimirov, A. G.; Clerc, M. G.

2014-01-01

Localized structures (LSs) in dissipative media appear in various fields of natural science such as biology, chemistry, plant ecology, optics and laser physics. The proposal for this Theme Issue was to gather specialists from various fields of nonlinear science towards a cross-fertilization among active areas of research. This is a cross-disciplinary area of research dominated by nonlinear optics due to potential applications for all-optical control of light, optical storage and information processing. This Theme Issue contains contributions from 18 active groups involved in the LS field and have all made significant contributions in recent years. PMID:25246688

Michael Akam and the rise of evolutionary developmental biology

PubMed Central

Stern, David L.; Dawes-Hoang, Rachel E.

2010-01-01

Michael Akam has been awarded the 2007 Kowalevsky medal for his many research accomplishments in the area of evolutionary developmental biology. We highlight three tributaries of Michael’s contribution to evolutionary developmental biology. First, he has made major contributions to our understanding of development of the fruit fly, Drosophila melanogaster. Second, he has maintained a consistent focus on several key problems in evolutionary developmental biology, including the evolving role of Hox genes in arthropods and, more recently, the evolution of segmentation mechanisms. Third, Michael has written a series of influential reviews that have integrated progress in developmental biology into an evolutionary perspective. Michael has also made a large impact on the field through his effective mentorship style, his selfless promotion of younger colleagues, and his leadership of the University Museum of Zoology at Cambridge and the European community of evolutionary developmental biologists. PMID:20209429

Impact of electric field from a plasma jet on biological targets

NASA Astrophysics Data System (ADS)

Douat, Claire; Darny, Thibault; Iseni, Sylvain; Damany, Xavier; Dozias, Sebastien; Pouvesle, Jean-Michel; Robert, Eric; Vijayarangan, Vinodini; Delalande, Anthony; Pichon, Chantal

2016-09-01

Atmospheric pressure plasma jets have demonstrated their ability in biomedical applications thanks to their low gas temperature and their capacity to produce radicals, ions, electrons, UV radiation and electric fields. However the understanding of the interactions between the plasma and living cells and tissues is still far from being completely understood. Recently, Robert et al characterized two components of the electric field from a plasma jet and showed that the latter can propagate deeply in tissues on several mm. In this work, we focus on the study of the electric field induced by the plasma and its influence on the cell membrane. Propidium iodide, dextran sulfate and plasmid DNA are used to measure the permeability of the membrane, while an electro-optic probe is used to measure the longitudinal and the radial components of the electric field. The two components are both spatially and temporally resolved. To investigate the contribution of the electric field on the cell membrane, a dielectric barrier is used between the plasma and the biological target. A comparison with and without the barrier will be presented for both biological and agriculture applications.

Introductory Biology Textbooks Under-Represent Scientific Process

PubMed Central

Duncan, Dara B.; Lubman, Alexandra; Hoskins, Sally G.

2011-01-01

Attrition of undergraduates from Biology majors is a long-standing problem. Introductory courses that fail to engage students or spark their curiosity by emphasizing the open-ended and creative nature of biological investigation and discovery could contribute to student detachment from the field. Our hypothesis was that introductory biology books devote relatively few figures to illustration of the design and interpretation of experiments or field studies, thereby de-emphasizing the scientific process. To investigate this possibility, we examined figures in six Introductory Biology textbooks published in 2008. On average, multistep scientific investigations were presented in fewer than 5% of the hundreds of figures in each book. Devoting such a small percentage of figures to the processes by which discoveries are made discourages an emphasis on scientific thinking. We suggest that by increasing significantly the illustration of scientific investigations, textbooks could support undergraduates’ early interest in biology, stimulate the development of design and analytical skills, and inspire some students to participate in investigations of their own. PMID:23653758

Workshop on Molecular Evolution

NASA Technical Reports Server (NTRS)

Cummings, Michael P.

2004-01-01

Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

From Extremophiles to Star Trek, The Use of Synthetic Biology in Astrobiology

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.; Fujishima, Kosuke; Lima, Ivan Paulino; Gentry, Diana; Phan, Samson; Navarette, Jesica; Palmer, Jesse; Burnier, Andre

2012-01-01

Synthetic biology – the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes – has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving biotic functions using only the most thermodynamically stable amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as bio-mining, human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

In vivo molecular and genomic imaging: new challenges for imaging physics.

PubMed

Cherry, Simon R

2004-02-07

The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.

TOPICAL REVIEW: In vivo molecular and genomic imaging: new challenges for imaging physics

NASA Astrophysics Data System (ADS)

Cherry, Simon R.

2004-02-01

The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.

Julius Wagner-Jauregg and the Legacy of Malarial Therapy for the Treatment of General Paresis of the Insane

PubMed Central

Tsay, Cynthia J.

2013-01-01

Julius Wagner-Jauregg, a preeminent Austrian psychiatrist was awarded the Nobel Prize in Medicine in 1927 for the development of malaria therapy for the treatment of neurosyphilis, or general paresis of the insane. Despite being only one of three psychiatrists to win a Nobel Prize, he has faded from public consciousness and his name recognition pales in comparison to his contemporary and fellow Austrian, Sigmund Freud. This paper explores his contributions to the field of biological psychiatry and also touches upon reasons, such as the growing bioethics movement, his controversial affiliation with the Nazi Party, and the evolution of neurosyphilis, that explain why Wagner-Jauregg is not more widely celebrated for his contributions to the field of psychiatry, even though his malarial treatment could be considered the earliest triumph of biological psychiatry over psychoanalysis. PMID:23766744

The odd couple: using biomedical and intersectional approaches to address health inequities

PubMed Central

Hankivsky, Olena; Doyal, Lesley; Einstein, Gillian; Kelly, Ursula; Shim, Janet; Weber, Lynn; Repta, Robin

2017-01-01

ABSTRACT Background: Better understanding and addressing health inequities is a growing global priority. Objective: In this paper, we contribute to the literature examining complex relationships between biological and social dimensions in the field of health inequalities. Specifically, we explore the potential of intersectionality to advance current approaches to socio-biological entwinements. Design: We provide a brief overview of current approaches to combining both biological and social factors in a single study, and then investigate the contributions of an intersectional framework to such work. Results: We offer a number of concrete examples of how intersectionality has been used empirically to bring both biological and social factors together in the areas of HIV, post-traumatic stress disorder, female genital circumcision/mutilation/cutting, and cardiovascular disease. Conclusion: We argue that an intersectional approach can further research that integrates biological and social aspects of human lives and human health and ultimately generate better and more precise evidence for effective policies and practices aimed at tackling health inequities. PMID:28641056

The odd couple: using biomedical and intersectional approaches to address health inequities.

PubMed

Hankivsky, Olena; Doyal, Lesley; Einstein, Gillian; Kelly, Ursula; Shim, Janet; Weber, Lynn; Repta, Robin

Better understanding and addressing health inequities is a growing global priority. In this paper, we contribute to the literature examining complex relationships between biological and social dimensions in the field of health inequalities. Specifically, we explore the potential of intersectionality to advance current approaches to socio-biological entwinements. We provide a brief overview of current approaches to combining both biological and social factors in a single study, and then investigate the contributions of an intersectional framework to such work. We offer a number of concrete examples of how intersectionality has been used empirically to bring both biological and social factors together in the areas of HIV, post-traumatic stress disorder, female genital circumcision/mutilation/cutting, and cardiovascular disease. We argue that an intersectional approach can further research that integrates biological and social aspects of human lives and human health and ultimately generate better and more precise evidence for effective policies and practices aimed at tackling health inequities.

Localized structures in dissipative media: from optics to plant ecology.

PubMed

Tlidi, M; Staliunas, K; Panajotov, K; Vladimirov, A G; Clerc, M G

2014-10-28

Localized structures (LSs) in dissipative media appear in various fields of natural science such as biology, chemistry, plant ecology, optics and laser physics. The proposal for this Theme Issue was to gather specialists from various fields of nonlinear science towards a cross-fertilization among active areas of research. This is a cross-disciplinary area of research dominated by nonlinear optics due to potential applications for all-optical control of light, optical storage and information processing. This Theme Issue contains contributions from 18 active groups involved in the LS field and have all made significant contributions in recent years. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Do Teachers Make All Their Students Play the Same Learning Games? A Comparative Study of Learning Games in Biology and English as a Second Language

ERIC Educational Resources Information Center

Gruson, Brigitte; Marlot, Corinne

2016-01-01

This article, based upon the field of comparative didactics, seeks to contribute to the identification of generic and specific features in the teaching and learning process. More particularly, its aim was to examine, through the study of two different school subjects: biology and English as a second language, how "passive didactic…

Apollo-Soyuz pamphlet no. 9: General science. [experimental design in Astronomy, Biology, Geophysics, Aeronomy and Materials science

NASA Technical Reports Server (NTRS)

Page, L. W.; From, T. P.

1977-01-01

The objectives and planning activities for the Apollo-Soyuz mission are summarized. Aspects of the space flight considered include the docking module and launch configurations, spacecraft orbits, and weightlessness. The 28 NASA experiments conducted onboard the spacecraft are summarized. The contributions of the mission to the fields of astronomy, geoscience, biology, and materials sciences resulting from the experiments are explored.

To What Extent Do Biology Textbooks Contribute to Scientific Literacy? Criteria for Analysing Science-Technology-Society-Environment Issues

ERIC Educational Resources Information Center

Calado, Florbela M.; Scharfenberg, Franz-Josef; Bogner, Franz X.

2015-01-01

Our article proposes a set of six criteria for analysing science-technology-society-environment (STSE) issues in regular textbooks as to how they are expected to contribute to students' scientific literacy. We chose genetics and gene technology as fields prolific in STSE issues. We derived our criteria (including 26 sub-criteria) from a literature…

Effects of lambda-cyhalothrin on mosquito larvae and predatory aquatic insects.

PubMed

Lawler, Sharon P; Dritz, Deborah A; Christiansen, Julie A; Cornel, Anthony J

2007-03-01

Agricultural insecticides can affect mosquito production in rice fields by controlling mosquitoes, disrupting biological control or contributing to selection of insecticide resistance. The duration of insecticidal activity of the pyrethroid lambda-cyhalothrin was quantified on predatory insects in rice fields and on three kinds of mosquito larva: a pyrethroid-susceptible strain of Culex tarsalis Coquillet, a pyrethroid-resistant strain of Cx pipiens L. (sensu lato) and non-resistant Cx pipiens s.l. Lambda-cyhalothrin killed most caged, susceptible mosquitoes for up to 21 days. It killed fewer resistant Cx pipiens s.l., but suppressed their survival for over a week. Lambda-cyhalothrin suppressed field populations of predatory insects through day 29. Agricultural use of lambda-cyhalothrin can provide incidental mosquito control. However, the pyrethroid persisted in sediment and gradually decreased in activity, which could contribute to selection of pyrethroid-resistant mosquitoes. Because caged mosquitoes showed good survival before predators recovered, disruption of biological control is possible. It is therefore advisable for growers and mosquito control agencies to communicate about pesticide use. Copyright 2006 Society of Chemical Industry.

Synthetic Astrobiology

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2015-01-01

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

Current Issues in Evolutionary Paleontology.

ERIC Educational Resources Information Center

Scully, Erik Paul

1987-01-01

Describes some of the contributions made by the field of paleontology to theories in geology and biology. Suggests that the two best examples of modern evolutionary paleontology relate to the theory of punctuated equilibria, and the possibility that mass extinctions may be cyclic. (TW)

Radoslav K. Andjus (1926-2003): a brief summary of his life and work.

PubMed

Stojilkovic, Stanko S; Zivadinović, Dragoslava; Hegedis, Aleksandar; Marjanović, Marina

2005-06-01

Radoslav K. Andjus was a professor of physiology and biophysics at the University of Belgrade, Serbia, from 1953 to 1992. He was an elected member of the Serbian Academy of Sciences and Arts, the International Academy of Astronautics, and the Montenegrin Academy of Sciences and Arts. He published over 190 papers in domestic and international journals and three textbooks. The main field of his research was thermophysiology. He studied hypothermia, suspended animation and resuscitation, hibernation and biological rhythms, temperature adaptation and acclimation, and cryoprotection. Professor Andjus also contributed significantly to the fields of brain metabolism, endocrinology, electroretinography, as well as biophysical modeling and theoretical biology.

Evolution of phage display technology: from discovery to application.

PubMed

Rahbarnia, Leila; Farajnia, Safar; Babaei, Hossein; Majidi, Jafar; Veisi, Kamal; Ahmadzadeh, Vahideh; Akbari, Bahman

2017-03-01

Phage display technology as a selection-based system is an attractive method for evolution of new biological drugs. Unique ability of phage libraries for displaying proteins on bacteriophage surfaces enable them to make a major contribution in diverse fields of researches related to the diagnosis and therapy of diseases. One of the great challenges facing researchers is the modification of phage display technology and the development of new applications. This article reviews the molecular basis of phage display library, and summarizes the novel and specific applications of this technique in the field of biological drugs development including therapeutic antibodies, peptides, vaccines, and catalytic antibodies.

Molecular Dynamics in Physiological Solutions: Force Fields, Alkali Metal Ions, and Ionic Strength.

PubMed

Zhang, Chao; Raugei, Simone; Eisenberg, Bob; Carloni, Paolo

2010-07-13

The monovalent ions Na(+) and K(+) and Cl(-) are present in any living organism. The fundamental thermodynamic properties of solutions containing such ions is given as the excess (electro-)chemical potential differences of single ions at finite ionic strength. This quantity is key for many biological processes, including ion permeation in membrane ion channels and DNA-protein interaction. It is given by a chemical contribution, related to the ion activity, and an electric contribution, related to the Galvani potential of the water/air interface. Here we investigate molecular dynamics based predictions of these quantities by using a variety of ion/water force fields commonly used in biological simulation, namely the AMBER (the newly developed), CHARMM, OPLS, Dang95 with TIP3P, and SPC/E water. Comparison with experiment is made with the corresponding values for salts, for which data are available. The calculations based on the newly developed AMBER force field with TIP3P water agrees well with experiment for both KCl and NaCl electrolytes in water solutions, as previously reported. The simulations based on the CHARMM-TIP3P and Dang95-SPC/E force fields agree well for the KCl and NaCl solutions, respectively. The other models are not as accurate. Single cations excess (electro-)chemical potential differences turn out to be similar for all the force fields considered here. In the case of KCl, the calculated electric contribution is consistent with higher level calculations. Instead, such agreement is not found with NaCl. Finally, we found that the calculated activities for single Cl(-) ions turn out to depend clearly on the type of counterion used, with all the force fields investigated. The implications of these findings for biomolecular systems are discussed.

Standardization in synthetic biology: an engineering discipline coming of age.

PubMed

Decoene, Thomas; De Paepe, Brecht; Maertens, Jo; Coussement, Pieter; Peters, Gert; De Maeseneire, Sofie L; De Mey, Marjan

2018-08-01

Leaping DNA read-and-write technologies, and extensive automation and miniaturization are radically transforming the field of biological experimentation by providing the tools that enable the cost-effective high-throughput required to address the enormous complexity of biological systems. However, standardization of the synthetic biology workflow has not kept abreast with dwindling technical and resource constraints, leading, for example, to the collection of multi-level and multi-omics large data sets that end up disconnected or remain under- or even unexploited. In this contribution, we critically evaluate the various efforts, and the (limited) success thereof, in order to introduce standards for defining, designing, assembling, characterizing, and sharing synthetic biology parts. The causes for this success or the lack thereof, as well as possible solutions to overcome these, are discussed. Akin to other engineering disciplines, extensive standardization will undoubtedly speed-up and reduce the cost of bioprocess development. In this respect, further implementation of synthetic biology standards will be crucial for the field in order to redeem its promise, i.e. to enable predictable forward engineering.

Where Synthetic Biology Meets ET

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2016-01-01

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

Bacteriophage-based synthetic biology for the study of infectious diseases

PubMed Central

Lu, Timothy K.

2014-01-01

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

Honors

NASA Astrophysics Data System (ADS)

2013-02-01

Sallie Chisholm received the National Medal of Science from U.S. president Barack Obama during a 1 February ceremony at the White House. Chisholm, a biological oceanographer, was cited for her "contributions to the discovery and understanding of the dominant photosynthetic organisms in the ocean, promotion of the field of microbial oceanography and influence on marine policy and management." Chisholm is the Lee and Geraldine Martin Professor of Environmental Studies and a professor of biology at the Massachusetts Institute of Technology (MIT).

Cell interactions in bone tissue engineering.

PubMed

Pirraco, R P; Marques, A P; Reis, R L

2010-01-01

Bone fractures, where the innate regenerative bone response is compromised, represent between 4 and 8 hundred thousands of the total fracture cases, just in the United States. Bone tissue engineering (TE) brought the notion that, in cases such as those, it was preferable to boost the healing process of bone tissue instead of just adding artificial parts that could never properly replace the native tissue. However, despite the hype, bone TE so far could not live up to its promises and new bottom-up approaches are needed. The study of the cellular interactions between the cells relevant for bone biology can be of essential importance to that. In living bone, cells are in a context where communication with adjacent cells is almost permanent. Many fundamental works have been addressing these communications nonetheless, in a bone TE approach, the 3D perspective, being part of the microenvironment of a bone cell, is as crucial. Works combining the study of cell-to-cell interactions in a 3D environment are not as many as expected. Therefore, the bone TE field should not only gain knowledge from the field of fundamental Biology but also contribute for further understanding the biology of bone. In this review, a summary of the main works in the field of bone TE, aiming at studying cellular interactions in a 3D environment, and how they contributed towards the development of a functional engineered bone tissue, is presented.

2017 ISCB Accomplishment by a Senior Scientist Award: Pavel Pevzner

PubMed Central

Fogg, Christiana N.; Kovats, Diane E.; Berger, Bonnie

2017-01-01

The International Society for Computational Biology ( ISCB) recognizes an established scientist each year with the Accomplishment by a Senior Scientist Award for significant contributions he or she has made to the field. This award honors scientists who have contributed to the advancement of computational biology and bioinformatics through their research, service, and education work. Pavel Pevzner, PhD, Ronald R. Taylor Professor of Computer Science and Director of the NIH Center for Computational Mass Spectrometry at University of California, San Diego, has been selected as the winner of the 2017 Accomplishment by a Senior Scientist Award. The ISCB awards committee, chaired by Dr. Bonnie Berger of the Massachusetts Institute of Technology, selected Pevzner as the 2017 winner. Pevzner will receive his award and deliver a keynote address at the 2017 Intelligent Systems for Molecular Biology-European Conference on Computational Biology joint meeting ( ISMB/ECCB 2017) held in Prague, Czech Republic from July 21-July 25, 2017. ISMB/ECCB is a biennial joint meeting that brings together leading scientists in computational biology and bioinformatics from around the globe. PMID:28713548

USSR Space Life Sciences Digest, volume 2, no. 3

NASA Technical Reports Server (NTRS)

Lewis, C. S.

1981-01-01

Soviet scientists are making significant contributions to the field of space medicine and biology through their active manned space program, frequent biosatellites, and extensive ground-based research. An overview of the developments and direction of the USSR Space Life Sciences Program is provided.

FIELD OBSERVATIONS TO RECOGNIZE THE NATURAL BIODEGRADATION OF MTBE

EPA Science Inventory

At some gasoline spill sites (perhaps a third of sites nationwide) MTBE in ground water has been biologically degraded to TBA. This natural biodegradation of MTBE contributes to the natural attenuation of MTBE, but it produces TBA as a potential contaminant. Under ordinary cond...

Parasites, nutrition, immune responses, and biology of metabolic tissues

USDA-ARS?s Scientific Manuscript database

Nutritional immunology, immunometabolism, and identification of novel immunotherapeutic targets, are all areas of active investigation in the field of parasitology. This review is focused on the factors contributing to the ability of parasitic helminths to decrease the risk of developing type 1 dia...

USSR Space Life Sciences Digest, volume 2, no. 4

NASA Technical Reports Server (NTRS)

Lewis, C. S.; Donnelly, K.

1981-01-01

Soviet scientists are making significant contributions to the field of space medicine and biology through their active manned space program, frequent biosatellites, and extensive ground-based research. An overview of the developments and direction of the USSR Space Life Sciences Program is provided.

Introduction to Focus Issue: nonlinear and stochastic physics in biology.

PubMed

Bahar, Sonya; Neiman, Alexander B; Jung, Peter; Kurths, Jürgen; Schimansky-Geier, Lutz; Showalter, Kenneth

2011-12-01

Frank Moss was a leading figure in the study of nonlinear and stochastic processes in biological systems. His work, particularly in the area of stochastic resonance, has been highly influential to the interdisciplinary scientific community. This Focus Issue pays tribute to Moss with articles that describe the most recent advances in the field he helped to create. In this Introduction, we review Moss's seminal scientific contributions and introduce the articles that make up this Focus Issue.

A Review of Current Neuromorphic Approaches for Vision, Auditory, and Olfactory Sensors.

PubMed

Vanarse, Anup; Osseiran, Adam; Rassau, Alexander

2016-01-01

Conventional vision, auditory, and olfactory sensors generate large volumes of redundant data and as a result tend to consume excessive power. To address these shortcomings, neuromorphic sensors have been developed. These sensors mimic the neuro-biological architecture of sensory organs using aVLSI (analog Very Large Scale Integration) and generate asynchronous spiking output that represents sensing information in ways that are similar to neural signals. This allows for much lower power consumption due to an ability to extract useful sensory information from sparse captured data. The foundation for research in neuromorphic sensors was laid more than two decades ago, but recent developments in understanding of biological sensing and advanced electronics, have stimulated research on sophisticated neuromorphic sensors that provide numerous advantages over conventional sensors. In this paper, we review the current state-of-the-art in neuromorphic implementation of vision, auditory, and olfactory sensors and identify key contributions across these fields. Bringing together these key contributions we suggest a future research direction for further development of the neuromorphic sensing field.

On the centennial anniversary of the birth of N.I. Bazilevich: Her contribution to the development of soil science

NASA Astrophysics Data System (ADS)

Pankova, E. I.; Tursina, T. V.; Tishkov, A. A.

2010-11-01

An analysis of the scientific heritage of N.I. Bazilevich is given, and her contribution to the development of soil science in Russia and in the world is appraised. The works of Bazilevich in the field of the genesis of soils concerned the essence of the processes of solodization, takyr formation, solonetzization, salinization, and sodification in the soils of Western Siberia. Many works of Bazilevich were devoted to the geography, cartography, and classification of salt-affected soils. She was an author and an editor of the map of the chemistry of the soil salinization in the Soviet Union. Her investigations into the fields of the biological productivity of ecosystems, biogeochemistry, the biological turnover of elements, and the evolution and dynamics of organic matter and its role in soil formation were of particular significance and brought her international fame. The scientific heritage of Bazilevich is highly acclaimed by modern science. Her students and followers continue to develop her ideas in their works.

Current status and perspectives of the development of dental research in biological anthropology of Argentina: introduction and conclusions of the symposium.

PubMed

Luna, Leandro H; Bernal, Valeria

2011-10-01

This paper describes and discusses the research in the field of dental anthropology in Argentina. It has been presented at the symposium entitled "The development of dental research in Argentine Biological Anthropology: current status and perspectives", coordinated by the authors at the IX National Meeting of Biological Anthropology of Argentina, Puerto Madryn, 20th-23rd October 2009. The aim of the symposium was to present new results and future prospects of this discipline in the country and to create a forum for discussion of current research within this field. Six contributions that focused on the study of teeth from different perspectives and analysed bioarchaeological samples from different areas of Argentina (Central Highlands, Pampa and Patagonia) were presented. After the presentations, a discussion about the state of the art of dental research in the country was generated, in which the need for the generation of methodological consensus on the criteria for the evaluation of the variables considered was stated, so that research conducted in different areas can be compared. In short, the contributions of this symposium provide insights into the diversity of dental anthropology in contemporary Argentina and the potential of these types of studies to gain important information about biological and cultural aspects of the native populations in the country. Copyright © 2011 Elsevier GmbH. All rights reserved.

How Animal Models Inform Child and Adolescent Psychiatry

PubMed Central

Stevens, Hanna E.; Vaccarino, Flora M.

2015-01-01

Objective Every available approach should be utilized to advance the field of child and adolescent psychiatry. Biological systems are important for the behavioral problems of children. Close examination of non-human animals and the biology and behavior they share with humans is an approach that must be used to advance the clinical work of child psychiatry. Method We review here how model systems are used to contribute to significant insights into childhood psychiatric disorders. Model systems have not only demonstrated causality of risk factors for psychiatric pathophysiology but have also allowed child psychiatrists to think in different ways about risks for psychiatric disorders and multiple levels that might be the basis of recovery and prevention. Results We present examples of how animal systems are utilized to benefit child psychiatry, including through environmental, genetic, and acute biological manipulations. Animal model work has been essential in our current thinking about childhood disorders, including the importance of dose and timing of risk factors, specific features of risk factors that are significant, neurochemistry involved in brain functioning, molecular components of brain development, and the importance of cellular processes previously neglected in psychiatric theories. Conclusion Animal models have clear advantages and disadvantages that must both be considered for these systems to be useful. Coupled with increasingly sophisticated methods for investigating human behavior and biology, animal model systems will continue to make essential contributions to our field. PMID:25901771

Space Biology in the 21st century

NASA Technical Reports Server (NTRS)

Halstead, Thora W.; Krauss, Robert W.

1990-01-01

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

Paving the future: finding suitable ISMB venues

PubMed Central

Rost, Burkhard; Gaasterland, Terry; Lengauer, Thomas; Linial, Michal; Morrison McKay, B.J.; Schneider, Reinhard; Horton, Paul; Kelso, Janet

2012-01-01

The International Society for Computational Biology, ISCB, organizes the largest event in the field of computational biology and bioinformatics, namely the annual international conference on Intelligent Systems for Molecular Biology, the ISMB. This year at ISMB 2012 in Long Beach, ISCB celebrated the 20th anniversary of its flagship meeting. ISCB is a young, lean and efficient society that aspires to make a significant impact with only limited resources. Many constraints make the choice of venues for ISMB a tough challenge. Here, we describe those challenges and invite the contribution of ideas for solutions. Contact: assistant@rostlab.org PMID:22796959

Evaluation of the hydraulic and biological performance of the portable floating fish collector at Cougar Reservoir and Dam, Oregon, 2014

USGS Publications Warehouse

Beeman, John W.; Evans, Scott D.; Haner, Philip V.; Hansel, Hal C.; Hansen, Amy C.; Hansen, Gabriel S.; Hatton, Tyson W.; Sprando, Jamie M.; Smith, Collin D.; Adams, Noah S.

2016-01-12

The hydraulic performance of the PFFC did not achieve the design goals of smooth acceleration of inflow culminating in a peak water velocity of 6 ft/s and, as a result, the hydraulic performance likely contributed to the low biological performance. The greatest water velocity measured in the PFFC (1.87 ft/s) was lower than designed due at least in part to the PFFC being lower in the water column than expected. Additionally, difficulties during anchor deployment prevented placement of the PFFC as near to the reservoir outlet as planned, resulting in a PFFC position outside the prevailing flow field and known areas of high fish densities. Overall, the results indicate that location, hydraulic conditions, water temperature, and shallow depth of the entrance were among the factors contributing to the low biological performance of the PFFC in 2014.

Synthetic Astrobiology

NASA Technical Reports Server (NTRS)

Rothschild, Lynn J.

2016-01-01

Synthetic biology - the design and construction of new biological parts and systems and the redesign of existing ones for useful purposes - has the potential to transform fields from pharmaceuticals to fuels. Our lab has focused on the potential of synthetic biology to revolutionize all three major parts of astrobiology: Where do we come from? Where are we going? and Are we alone? For the first and third, synthetic biology is allowing us to answer whether the evolutionary narrative that has played out on planet earth is likely to have been unique or universal. For example, in our lab we are re-evolving the biosynthetic pathways of amino acids in order to understand potential capabilities of an early organism with a limited repertoire of amino acids and developing techniques for the recovery of metals from spent electronics on other planetary bodies. And what about the limits for life? Can we create organisms that expand the envelope for life? In the future synthetic biology will play an increasing role in human activities both on earth, in fields as diverse as human health and the industrial production of novel bio-composites. Beyond earth, we will rely increasingly on biologically-provided life support, as we have throughout our evolutionary history. In order to do this, the field will build on two of the great contributions of astrobiology: studies of the origin of life and life in extreme environments.

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

PubMed

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

2012-01-01

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

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

PubMed Central

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

2011-01-01

Physics-based simulation provides a powerful framework for understanding biological form and function. Simulations can be used by biologists to study macromolecular assemblies and by clinicians to design treatments for diseases. Simulations help biomedical researchers understand the physical constraints on biological systems as they engineer novel drugs, synthetic tissues, medical devices, and surgical interventions. Although individual biomedical investigators make outstanding contributions to physics-based simulation, the field has been fragmented. Applications are typically limited to a single physical scale, and individual investigators usually must create their own software. These conditions created a major barrier to advancing simulation capabilities. In 2004, we established a National Center for Physics-Based Simulation of Biological Structures (Simbios) to help integrate the field and accelerate biomedical research. In 6 years, Simbios has become a vibrant national center, with collaborators in 16 states and eight countries. Simbios focuses on problems at both the molecular scale and the organismal level, with a long-term goal of uniting these in accurate multiscale simulations. PMID:22081222

Integration of physics and biology: synergistic undergraduate education for the 21st century.

PubMed

Woodin, Terry; Vasaly, Helen; McBride, Duncan; White, Gary

2013-06-01

This is an exciting time to be a biologist. The advances in our field and the many opportunities to expand our horizons through interaction with other disciplines are intellectually stimulating. This is as true for people tasked with helping the field move forward through support of research and education projects that serve the nation's needs as for those carrying out that research and educating the next generation of biologists. So, it is a pleasure to contribute to this edition of CBE-Life Sciences Education. This column will cover three aspects of the interactions of physics and biology as seen from the viewpoint of four members of the Division of Undergraduate Education of the National Science Foundation. The first section places the material to follow in context. The second reviews some of the many interdisciplinary physics-biology projects we support. The third highlights mechanisms available for supporting new physics-biology undergraduate education projects based on ideas that arise, focusing on those needing and warranting outside support to come to fruition.

2017 ISCB Innovator Award: Aviv Regev

PubMed Central

Fogg, Christiana N.; Kovats, Diane; Berger, Bonnie

2017-01-01

2017 marks the second year of the International Society for Computational Biology (ISCB) Innovator Award, which recognizes an ISCB scientist who is within two decades of having completed his or her graduate degree and has consistently made outstanding contributions to the field. The 2017 winner is Dr. Aviv Regev, Professor of Biology at the Massachusetts Institute of Technology (MIT), a Core Member and Chair of the Faculty of the Broad Institute of MIT and Harvard, and an HHMI Investigator. Regev will receive her award and deliver a keynote address during International Conference on Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2017 in Prague, Czech Republic (July 21 - 25, 2017). PMID:28713547

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

PubMed Central

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

2018-01-01

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

High-contrast multilayer imaging of biological organisms through dark-field digital refocusing.

PubMed

Faridian, Ahmad; Pedrini, Giancarlo; Osten, Wolfgang

2013-08-01

We have developed an imaging system to extract high contrast images from different layers of biological organisms. Utilizing a digital holographic approach, the system works without scanning through layers of the specimen. In dark-field illumination, scattered light has the main contribution in image formation, but in the case of coherent illumination, this creates a strong speckle noise that reduces the image quality. To remove this restriction, the specimen has been illuminated with various speckle-fields and a hologram has been recorded for each speckle-field. Each hologram has been analyzed separately and the corresponding intensity image has been reconstructed. The final image has been derived by averaging over the reconstructed images. A correlation approach has been utilized to determine the number of speckle-fields required to achieve a desired contrast and image quality. The reconstructed intensity images in different object layers are shown for different sea urchin larvae. Two multimedia files are attached to illustrate the process of digital focusing.

The ins and outs of lncRNA structure: How, why and what comes next?

PubMed

Blythe, Amanda J; Fox, Archa H; Bond, Charles S

2016-01-01

The field of structural biology has the unique advantage of being able to provide a comprehensive picture of biological mechanisms at the molecular and atomic level. Long noncoding RNAs (lncRNAs) represent the new frontier in the molecular biology of complex organisms yet remain the least characterised of all the classes of RNA. Thousands of new lncRNAs are being reported each year yet very little structural data exists for this rapidly expanding field. The length of lncRNAs ranges from 200 nt to over 100 kb in length and they generally exhibit low cellular abundance. Therefore, obtaining sufficient quantities of lncRNA to use for structural analysis is challenging. However, as technologies develop structures of lncRNAs are starting to emerge providing important information regarding their mechanism of action. Here we review the current methods used to determine the structure of lncRNA and lncRNA:protein complexes and describe the significant contribution structural biology has and will make to the field of lncRNA research. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy1, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa. Copyright © 2015 Elsevier B.V. All rights reserved.

The Role of Mass Spectrometry-Based Metabolomics in Medical Countermeasures Against Radiation

PubMed Central

Patterson, Andrew D.; Lanz, Christian; Gonzalez, Frank J.; Idle, Jeffrey R.

2013-01-01

Radiation metabolomics can be defined as the global profiling of biological fluids to uncover latent, endogenous small molecules whose concentrations change in a dose-response manner following exposure to ionizing radiation. In response to the potential threat of nuclear or radiological terrorism, the Center for High-Throughput Minimally Invasive Radiation Biodosimetry (CMCR) was established to develop field-deployable biodosimeters based, in principle, on rapid analysis by mass spectrometry of readily and easily obtainable biofluids. In this review, we briefly summarize radiation biology and key events related to actual and potential nuclear disasters, discuss the important contributions the field of mass spectrometry has made to the field of radiation metabolomics, and summarize current discovery efforts to use mass spectrometry-based metabolomics to identify dose-responsive urinary constituents, and ultimately to build and deploy a noninvasive high-throughput biodosimeter. PMID:19890938

3-D components of a biological neural network visualized in computer generated imagery. I - Macular receptive field organization

NASA Technical Reports Server (NTRS)

Ross, Muriel D.; Cutler, Lynn; Meyer, Glenn; Lam, Tony; Vaziri, Parshaw

1990-01-01

Computer-assisted, 3-dimensional reconstructions of macular receptive fields and of their linkages into a neural network have revealed new information about macular functional organization. Both type I and type II hair cells are included in the receptive fields. The fields are rounded, oblong, or elongated, but gradations between categories are common. Cell polarizations are divergent. Morphologically, each calyx of oblong and elongated fields appears to be an information processing site. Intrinsic modulation of information processing is extensive and varies with the kind of field. Each reconstructed field differs in detail from every other, suggesting that an element of randomness is introduced developmentally and contributes to endorgan adaptability.

Selectivity of Local Field Potentials in Macaque Inferior Temporal Cortex

DTIC Science & Technology

2004-09-01

Selectivity of Local Field Potentials in Macaque Inferior Temporal Cortex Gabriel Kreiman , Chou Hung, Tomaso Poggio and James DiCarlo AI Memo 2004...IT. Note: Gabriel Kreiman and Chou Hung contributed equally to this work This report describes research done within the Center for Biological...separate the neuronal components of the MUA by using spike sorting algorithms (Quiroga et al., 2004; Yu and Kreiman , 1999). It will be interesting to

Concise Review: Stem Cell Population Biology: Insights from Hematopoiesis.

PubMed

MacLean, Adam L; Lo Celso, Cristina; Stumpf, Michael P H

2017-01-01

Stem cells are fundamental to human life and offer great therapeutic potential, yet their biology remains incompletely-or in cases even poorly-understood. The field of stem cell biology has grown substantially in recent years due to a combination of experimental and theoretical contributions: the experimental branch of this work provides data in an ever-increasing number of dimensions, while the theoretical branch seeks to determine suitable models of the fundamental stem cell processes that these data describe. The application of population dynamics to biology is amongst the oldest applications of mathematics to biology, and the population dynamics perspective continues to offer much today. Here we describe the impact that such a perspective has made in the field of stem cell biology. Using hematopoietic stem cells as our model system, we discuss the approaches that have been used to study their key properties, such as capacity for self-renewal, differentiation, and cell fate lineage choice. We will also discuss the relevance of population dynamics in models of stem cells and cancer, where competition naturally emerges as an influential factor on the temporal evolution of cell populations. Stem Cells 2017;35:80-88. © 2016 AlphaMed Press.

Synthetic biology: programming cells for biomedical applications.

PubMed

Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

2012-01-01

The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.

The permanent relation between biology, power and war: the dual use of the biotechnological development.

PubMed

de Almeida, Maria Eneida

2015-07-01

Throughout the twentieth century, the biological advance had a closer and closer relation with the strategies of power in search of high technology. From 1970, the manipulation of genetically recombined pathogenic agents was a high technological breakthrough that radically over passed traditional biology and reinforced the war relations of science. The biotechnological revolution started along with new perspectives for the political and military field of science. From this point of the biotechnological development a new paradigm for war, as well as for the sciences of life, was then created and new challenges for International Health in the twenty first century came into scene. Through a historical account related to power, this paper is meant to present the mechanism of articulation existent between science and power and to contribute for understanding how the military field is naturally inserted in the biotechnological development which, in its essence, produces biotechnologies for civil and military uses.

Proceedings - Symposium on cheatgrass invasion, shrub die-off, and other aspects of shrub biology and management

Treesearch

E. Durant McArthur; Evan M. Romney; Stanley D. Smith; Paul T. Tueller

1990-01-01

Includes 45 papers and accounts of field trips from a symposium focused on a recent shrub die-off phenomenon and a perennial problem, cheatgrass invasion, on western rangelands. Contributions also cover shrub establishment, shrub ecosystem ecology and physiology, and plant and shrub ecosystems.

Growing Spaceships?

NASA Technical Reports Server (NTRS)

Robertson, Glen A.

2013-01-01

NASA currently has a program called the Space Synthetic Biology Project. Synthetic Biology or SynBio is the design and construction of new biological functions and systems not found in nature. Four NASA field centers, along with experts from industry and academia, have been partnering on the Space Synthetic Biology Project and are working on new breakthroughs in this increasingly useful pursuit, which is part a science discipline and part engineering. Led by researchers at NASA s Ames Research Center, the team is studying how this powerful new tool can help NASA now and in the future. The project was created to harness biology in reliable, robust, engineered systems to support the agency s exploration and science missions, to improve life on Earth and to help shape NASA's future. The program also is intended to contribute foundational tools to the synthetic biology research community.

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

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Conference Report: ESF-COST High-Level Research Conference Natural Products Chemistry, Biology and Medicine III.

PubMed

Catino, Arthur

2010-12-01

Natural Products Chemistry, Biology and Medicine III was the third conference in a series of events sponsored by the European Science Foundation (ESF) and the European Cooperation in the field of Scientific and Technical Research (COST). Scientists came together from within and outside the EU to present cutting-edge developments in chemical synthesis. Research areas included the synthesis of natural products, methods development, isolation/structural elucidation and chemical biology. As our capacity to produce new chemotherapeutic agents relies on chemical synthesis, this year's conference has never been so timely. This report highlights several of the scientific contributions presented during the meeting.

[Contributions for a statute of parts separated from the body].

PubMed

Darío Bergel, Salvador

2011-01-01

In this article the author reflects on the ethical and legal implications arising from the treatment that should be conferred on the separate parts of the human body. Thus, the status of the body is changing so rapidly, due to the new developments in biotechnology, that raises unprecedented dilemmas for the Law. Also noteworthy the relevant issues brought by the incessant progress of biomedical science, claiming regulations consistent with its implications in various fields. The following issues will be highlighted by the author: the achievements in the fields of molecular biology and genetics, the proliferation and diversification of biobanks, and the commercialization and patenting of genes, gene sequences and other biological materials, which generates a series of ethical and legal problems.

How animal models inform child and adolescent psychiatry.

PubMed

Stevens, Hanna E; Vaccarino, Flora M

2015-05-01

Every available approach should be used to advance the field of child and adolescent psychiatry. Biological systems are important for the behavioral problems of children. Close examination of nonhuman animals and the biology and behavior that they share with humans is an approach that must be used to advance the clinical work of child psychiatry. We review here how model systems are used to contribute to significant insights into childhood psychiatric disorders. Model systems have not only demonstrated causality of risk factors for psychiatric pathophysiology, but have also allowed child psychiatrists to think in different ways about risks for psychiatric disorders and multiple levels that might be the basis of recovery and prevention. We present examples of how animal systems are used to benefit child psychiatry, including through environmental, genetic, and acute biological manipulations. Animal model work has been essential in our current thinking about childhood disorders, including the importance of dose and timing of risk factors, specific features of risk factors that are significant, neurochemistry involved in brain functioning, molecular components of brain development, and the importance of cellular processes previously neglected in psychiatric theories. Animal models have clear advantages and disadvantages that must be considered for these systems to be useful. Coupled with increasingly sophisticated methods for investigating human behavior and biology, animal model systems will continue to make essential contributions to our field. Copyright © 2015 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists.

PubMed

Sanchez-Lucas, Rosa; Mehta, Angela; Valledor, Luis; Cabello-Hurtado, Francisco; Romero-Rodrıguez, M Cristina; Simova-Stoilova, Lyudmila; Demir, Sekvan; Rodriguez-de-Francisco, Luis E; Maldonado-Alconada, Ana M; Jorrin-Prieto, Ana L; Jorrín-Novo, Jesus V

2016-03-01

The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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 advancing conservation management and better predicting the consequences of disturbances on species and interactions in the fragile insular ecosystems. PMID:26722109

The Case for Biocalculus: Design, Retention, and Student Performance

ERIC Educational Resources Information Center

Eaton, Carrie Diaz; Highlander, Hannah Callender

2017-01-01

Calculus is one of the primary avenues for initial quantitative training of students in all science, technology, engineering, and mathematics fields, but life science students have been found to underperform in the traditional calculus setting. As a result, and because of perceived lack of its contribution to the understanding of biology, calculus…

The Evolution of Textbook Misconceptions about Darwin

ERIC Educational Resources Information Center

Rees, Paul A.

2007-01-01

Textbooks for GCE Advanced Level Biology have provided over-simplified and inaccurate accounts of Charles Darwin's contribution to the study of evolution over a period of many decades. They have credited him with field skills and insight that he did not possess, and repeated several historical inaccuracies. Darwin's strength was as a synthesiser…

Catalyzing sustainability: Cornell University's field practicum in conservation and sustainable development

Treesearch

John Schelhas

2000-01-01

Human society is increasingly facing a variety of complex, intertwined environmental conservation and rural development issues. For example, national park objectives have expanded from the conservation of biological diversity to also include contributing to the livelihood and development needs of local people. Human settlements in fragile uplands create conflicts...

A Review of Current Neuromorphic Approaches for Vision, Auditory, and Olfactory Sensors

PubMed Central

Vanarse, Anup; Osseiran, Adam; Rassau, Alexander

2016-01-01

Conventional vision, auditory, and olfactory sensors generate large volumes of redundant data and as a result tend to consume excessive power. To address these shortcomings, neuromorphic sensors have been developed. These sensors mimic the neuro-biological architecture of sensory organs using aVLSI (analog Very Large Scale Integration) and generate asynchronous spiking output that represents sensing information in ways that are similar to neural signals. This allows for much lower power consumption due to an ability to extract useful sensory information from sparse captured data. The foundation for research in neuromorphic sensors was laid more than two decades ago, but recent developments in understanding of biological sensing and advanced electronics, have stimulated research on sophisticated neuromorphic sensors that provide numerous advantages over conventional sensors. In this paper, we review the current state-of-the-art in neuromorphic implementation of vision, auditory, and olfactory sensors and identify key contributions across these fields. Bringing together these key contributions we suggest a future research direction for further development of the neuromorphic sensing field. PMID:27065784

Peripersonal Space and Margin of Safety around the Body: Learning Visuo-Tactile Associations in a Humanoid Robot with Artificial Skin.

PubMed

Roncone, Alessandro; Hoffmann, Matej; Pattacini, Ugo; Fadiga, Luciano; Metta, Giorgio

2016-01-01

This paper investigates a biologically motivated model of peripersonal space through its implementation on a humanoid robot. Guided by the present understanding of the neurophysiology of the fronto-parietal system, we developed a computational model inspired by the receptive fields of polymodal neurons identified, for example, in brain areas F4 and VIP. The experiments on the iCub humanoid robot show that the peripersonal space representation i) can be learned efficiently and in real-time via a simple interaction with the robot, ii) can lead to the generation of behaviors like avoidance and reaching, and iii) can contribute to the understanding the biological principle of motor equivalence. More specifically, with respect to i) the present model contributes to hypothesizing a learning mechanisms for peripersonal space. In relation to point ii) we show how a relatively simple controller can exploit the learned receptive fields to generate either avoidance or reaching of an incoming stimulus and for iii) we show how the robot can select arbitrary body parts as the controlled end-point of an avoidance or reaching movement.

Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as a Tool in Cell Biology Education.

PubMed

Augusto, Ingrid; Monteiro, Douglas; Girard-Dias, Wendell; Dos Santos, Thaisa Oliveira; Rosa Belmonte, Simone Letícia; Pinto de Oliveira, Jairo; Mauad, Helder; da Silva Pacheco, Marcos; Lenz, Dominik; Stefanon Bittencourt, Athelson; Valentim Nogueira, Breno; Lopes Dos Santos, Jorge Roberto; Miranda, Kildare; Guimarães, Marco Cesar Cunegundes

2016-01-01

The cell biology discipline constitutes a highly dynamic field whose concepts take a long time to be incorporated into the educational system, especially in developing countries. Amongst the main obstacles to the introduction of new cell biology concepts to students is their general lack of identification with most teaching methods. The introduction of elaborated figures, movies and animations to textbooks has given a tremendous contribution to the learning process and the search for novel teaching methods has been a central goal in cell biology education. Some specialized tools, however, are usually only available in advanced research centers or in institutions that are traditionally involved with the development of novel teaching/learning processes, and are far from becoming reality in the majority of life sciences schools. When combined with the known declining interest in science among young people, a critical scenario may result. This is especially important in the field of electron microscopy and associated techniques, methods that have greatly contributed to the current knowledge on the structure and function of different cell biology models but are rarely made accessible to most students. In this work, we propose a strategy to increase the engagement of students into the world of cell and structural biology by combining 3D electron microscopy techniques and 3D prototyping technology (3D printing) to generate 3D physical models that accurately and realistically reproduce a close-to-the native structure of the cell and serve as a tool for students and teachers outside the main centers. We introduce three strategies for 3D imaging, modeling and prototyping of cells and propose the establishment of a virtual platform where different digital models can be deposited by EM groups and subsequently downloaded and printed in different schools, universities, research centers and museums, thereby modernizing teaching of cell biology and increasing the accessibility to modern approaches in basic science.

Virtual Reconstruction and Three-Dimensional Printing of Blood Cells as a Tool in Cell Biology Education

PubMed Central

Girard-Dias, Wendell; dos Santos, Thaisa Oliveira; Rosa Belmonte, Simone Letícia; Pinto de Oliveira, Jairo; Mauad, Helder; da Silva Pacheco, Marcos; Lenz, Dominik; Stefanon Bittencourt, Athelson; Valentim Nogueira, Breno; Lopes dos Santos, Jorge Roberto; Miranda, Kildare; Guimarães, Marco Cesar Cunegundes

2016-01-01

The cell biology discipline constitutes a highly dynamic field whose concepts take a long time to be incorporated into the educational system, especially in developing countries. Amongst the main obstacles to the introduction of new cell biology concepts to students is their general lack of identification with most teaching methods. The introduction of elaborated figures, movies and animations to textbooks has given a tremendous contribution to the learning process and the search for novel teaching methods has been a central goal in cell biology education. Some specialized tools, however, are usually only available in advanced research centers or in institutions that are traditionally involved with the development of novel teaching/learning processes, and are far from becoming reality in the majority of life sciences schools. When combined with the known declining interest in science among young people, a critical scenario may result. This is especially important in the field of electron microscopy and associated techniques, methods that have greatly contributed to the current knowledge on the structure and function of different cell biology models but are rarely made accessible to most students. In this work, we propose a strategy to increase the engagement of students into the world of cell and structural biology by combining 3D electron microscopy techniques and 3D prototyping technology (3D printing) to generate 3D physical models that accurately and realistically reproduce a close-to-the native structure of the cell and serve as a tool for students and teachers outside the main centers. We introduce three strategies for 3D imaging, modeling and prototyping of cells and propose the establishment of a virtual platform where different digital models can be deposited by EM groups and subsequently downloaded and printed in different schools, universities, research centers and museums, thereby modernizing teaching of cell biology and increasing the accessibility to modern approaches in basic science. PMID:27526196

Directed Evolution as a Powerful Synthetic Biology Tool

PubMed Central

Cobb, Ryan E.; Sun, Ning; Zhao, Huimin

2012-01-01

At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels. PMID:22465795

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.

Christian Raetz: scientist and friend extraordinaire.

PubMed

Dowhan, William; Nikaido, Hiroshi; Stubbe, JoAnne; Kozarich, John W; Wickner, William T; Russell, David W; Garrett, Teresa A; Brozek, Kathryn; Modrich, Paul

2013-01-01

Chris Raetz passed away on August 16, 2011, still at the height of his productive years. His seminal contributions to biomedical research were in the genetics, biochemistry, and structural biology of phospholipid and lipid A biosynthesis in Escherichia coli and other gram-negative bacteria. He defined the catalytic properties and structures of many of the enzymes responsible for the "Raetz pathway for lipid A biosynthesis." His deep understanding of chemistry, coupled with knowledge of medicine, biochemistry, genetics, and structural biology, formed the underpinnings for his contributions to the lipid field. He displayed an intense passion for science and a broad interest that came from a strong commitment to curiosity-driven research, a commitment he imparted to his mentees and colleagues. What follows is a testament to both Chris's science and humanity from his friends and colleagues.

Thomas K. Jeffers: pioneer of coccidiosis research.

PubMed

Chapman, H D

2012-01-01

Thomas K. Jeffers has made many significant contributions to our understanding of the biology of the parasite Eimeria, the cause of coccidiosis in poultry. His work has had direct practical application for the control of this widespread disease. Topics discussed include Jeffers' pioneering work concerned with genetics of the host response to infection, the nature of biological and immunological intraspecific variation, drug resistance and discovery, field surveys of resistance, and his most recognized achievement-the demonstration that the lifecycle of coccidia may be altered by artificial selection. Parasites so modified are attenuated but retain their immunogenicity, a discovery that has led to the development of live vaccines that are inherently non-pathogenic. This article provides a brief biography and describes the contributions that Jeffers has made to our knowledge of coccidiosis.

Biomaterials for intervertebral disc regeneration and repair.

PubMed

Bowles, Robert D; Setton, Lori A

2017-06-01

The intervertebral disc contributes to motion, weight bearing, and flexibility of the spine, but is susceptible to damage and morphological changes that contribute to pathology with age and injury. Engineering strategies that rely upon synthetic materials or composite implants that do not interface with the biological components of the disc have not met with widespread use or desirable outcomes in the treatment of intervertebral disc pathology. Here we review bioengineering advances to treat disc disorders, using cell-supplemented materials, or acellular, biologically based materials, that provide opportunity for cell-material interactions and remodeling in the treatment of intervertebral disc disorders. While a field still in early development, bioengineering-based strategies employing novel biomaterials are emerging as promising alternatives for clinical treatment of intervertebral disc disorders. Copyright © 2017 Elsevier Ltd. All rights reserved.

PREFACE: Ultrafast biophotonics Ultrafast biophotonics

NASA Astrophysics Data System (ADS)

Gu, Min; Reid, Derryck; Ben-Yakar, Adela

2010-08-01

The use of light to explore biology can be traced to the first observations of tissue made with early microscopes in the mid-seventeenth century, and has today evolved into the discipline which we now know as biophotonics. This field encompasses a diverse range of activities, each of which shares the common theme of exploiting the interaction of light with biological material. With the rapid advancement of ultrafast optical technologies over the last few decades, ultrafast lasers have increasingly found applications in biophotonics, to the extent that the distinctive new field of ultrafast biophotonics has now emerged, where robust turnkey ultrafast laser systems are facilitating cutting-edge studies in the life sciences to take place in everyday laboratories. The broad spectral bandwidths, precision timing resolution, low coherence and high peak powers of ultrafast optical pulses provide unique opportunities for imaging and manipulating biological systems. Time-resolved studies of bio-molecular dynamics exploit the short pulse durations from such lasers, while other applications such as optical coherence tomography benefit from the broad optical bandwidths possible by using super-continuum generation and additionally allowing for high speed imaging with speeds as high as 47 000 scans per second. Continuing progress in laser-system technology is accelerating the adoption of ultrafast techniques across the life sciences, both in research laboratories and in clinical applications, such as laser-assisted in situ keratomileusis (LASIK) eye surgery. Revolutionizing the field of optical microscopy, two-photon excitation fluorescence (TPEF) microscopy has enabled higher spatial resolution with improved depth penetration into biological specimens. Advantages of this nonlinear optical process include: reduced photo-interactions, allowing for extensive imaging time periods; simultaneously exciting multiple fluorescent molecules with only one excitation wavelength; and reduced chromatic aberration effects. These extensive advantages have led to further exploration of nonlinear processes including second-harmonic generation (SHG) microscopy and third-harmonic generation (THG) microscopy. Second-harmonic generation has provided biologists with an extremely powerful tool for generating contrast in biological imaging, with the additional benefit of non-invasive three-dimensional imaging. The recent popularity of THG microscopy is largely due to the fact that three-dimensional imaging is achievable without the need for any labels, but rather relying on the intrinsic properties of the biological specimen itself. This optical nonlinear technique has attracted much attention recently from the biological community due to its non-invasive capabilities. Users of ultrafast lasers in the biological and medical fields are becoming a fast-growing community, employing pulse-shaping microscopy, resolution-enhancing microscopy techniques, linear and nonlinear micro-spectroscopy, functional deep-tissue imaging, optical coherence tomography, nonlinear fluorescence microscopy, molecular imaging and control, harmonic microscopy and femtosecond lifetime imaging, for cutting-edge research concerning the interaction of light with biological dynamics. The adaptability of ultrafast lasers to interact with a large array of materials through nonlinear excitation has enabled precise control of laser fluence allowing for highly localized material interactions, permitting micro-structured fabricated surfaces. The resultant multi-dimensional fabricated micro-structures are capable of replicating and/or manipulating microenvironments for controlled cell biology. In this special issue of Journal of Optics readers have a chance to view a collection of new contributions to the growing research field of ultrafast biophotonics. They are presented with recent advances in ultrafast technology applied to biological and medical investigations, where topics include advances in the visualization and identification of photo-reaction dynamics of biological functions under relevant physiological conditions, theoretically proposed imaging designs for obtaining super-resolved optical sectioned images in single exposures and fabricated micro-structured surfaces for biological micro-environments. We hope the collection will stimulate innovative new research in this growing field by showcasing new techniques for the visualization and manipulation of complex biological systems using linear and and nonlinear optical processes. Professor Min Gu would like to acknowledge Dr Betty Kouskousis for her contribution and support towards this editorial.

Design and integration of a problem-based biofabrication course into an undergraduate biomedical engineering curriculum.

PubMed

Raman, Ritu; Mitchell, Marlon; Perez-Pinera, Pablo; Bashir, Rashid; DeStefano, Lizanne

2016-01-01

The rapidly evolving discipline of biological and biomedical engineering requires adaptive instructional approaches that teach students to target and solve multi-pronged and ill-structured problems at the cutting edge of scientific research. Here we present a modular approach to designing a lab-based course in the emerging field of biofabrication and biological design, leading to a final capstone design project that requires students to formulate and test a hypothesis using the scientific method. Students were assessed on a range of metrics designed to evaluate the format of the course, the efficacy of the format for teaching new topics and concepts, and the depth of the contribution this course made to students training for biological engineering careers. The evaluation showed that the problem-based format of the course was well suited to teaching students how to use the scientific method to investigate and uncover the fundamental biological design rules that govern the field of biofabrication. We show that this approach is an efficient and effective method of translating emergent scientific principles from the lab bench to the classroom and training the next generation of biological and biomedical engineers for careers as researchers and industry practicians.

Integration of Physics and Biology: Synergistic Undergraduate Education for the 21st Century

PubMed Central

Woodin, Terry; Vasaly, Helen; McBride, Duncan; White, Gary

2013-01-01

This is an exciting time to be a biologist. The advances in our field and the many opportunities to expand our horizons through interaction with other disciplines are intellectually stimulating. This is as true for people tasked with helping the field move forward through support of research and education projects that serve the nation's needs as for those carrying out that research and educating the next generation of biologists. So, it is a pleasure to contribute to this edition of CBE—Life Sciences Education. This column will cover three aspects of the interactions of physics and biology as seen from the viewpoint of four members of the Division of Undergraduate Education of the National Science Foundation. The first section places the material to follow in context. The second reviews some of the many interdisciplinary physics–biology projects we support. The third highlights mechanisms available for supporting new physics–biology undergraduate education projects based on ideas that arise, focusing on those needing and warranting outside support to come to fruition. PMID:23737615

PREFACE Preface

NASA Astrophysics Data System (ADS)

Houée-Levin, Chantal; Gauduel, Yann A.

2011-01-01

The purpose of the four day COST CM0603-MELUSYN Joint Meeting 'Damages induced in Biomolecules by Low and High Energy Radiations', held in March 2010 in Paris, France, was to create a timely forum for multi-disciplinary discussions related to the recent developments on biomolecular damage triggered by low or high energy ionising radiations (photons, relativistic particles and accelerated ions). Created in September 2007, the European network COST CM0603 'Free radicals in Chemical Biology' (http://www.chembiorad.inct.pl/index.php) gathers specialists of free radical chemistry, biochemistry and biology. It aims to promote a chemical biology approach for the investigation of free radical pathways of biological interest and the improvement of communication and exchange among neighbouring scientific fields, such as chemistry with several domains of life sciences, specifically addressing the real barriers of specialist language and tools. The MELUSYN network was born in January 2006. This French think-tank and task force involves about one hundred scientists and clinicians who contribute to the emerging interdisciplinary domain of advanced spatio-temporal radiation biomedicine. One important mission of the MELUSYN network is to explore and identify new medical fields to which the specificity of 3rd generation synchrotron sources could be applied, either by themselves or in synergy with other advanced radiation sources. The network also contributes to the organization of international multidisciplinary conferences. In the framework of experimental and theoretical approaches, the conference gathered together 50 scientists from both communities and addressed a number of highly relevant aspects of bioradical chemistry and radiation biology, considering classical and more advanced radiation sources (synchrotron, ultra-short particle bunches based on high power laser technologies, microbeams) operating in the broad energy range eV-MeV, classical or semi-quantum simulations of molecular radiation processes. Considering some physical, chemical and biological aspects of radical mechanisms, including their consequences in medicine (radiotherapy for instance), the selected contributions of this Special Issue provide guidance for future interdisciplinary developments. In this way, the multi-scale aspects of radiation based bioradical chemistry and radiation biology should be considered. We would like to express our thanks to all the authors for their time and genuine efforts, and to the reviewers for their fruitful comments during the preparation of this volume. Editors Chantal Houée-LevinUniversity of Paris Sud, Orsay, France COST logo Yann A GauduelEcole Polytechnique - ENS Techniques Avancées Palaiseau, France MELUSYN logo

[Illness caused by water-based paints?].

PubMed

Birkeland, G; Zahlsen, K; Aas, K

1994-08-20

Illness caused by the indoor environment is a challenging and complicated field to investigate. Emissions from paints may contribute to the problems. Several components of water-based paints evaporate for a long time after painting, and some of them may affect human biology. We describe one patient who has experienced symptoms caused by water-based paint. Different reaction mechanisms may be involved, and these are discussed. Components which may elicit biological effects are listed and discussed. Physicians should be aware of the possibility that a few patients may suffer from illness caused by emissions from modern paints.

Multiobjective optimization in bioinformatics and computational biology.

PubMed

Handl, Julia; Kell, Douglas B; Knowles, Joshua

2007-01-01

This paper reviews the application of multiobjective optimization in the fields of bioinformatics and computational biology. A survey of existing work, organized by application area, forms the main body of the review, following an introduction to the key concepts in multiobjective optimization. An original contribution of the review is the identification of five distinct "contexts," giving rise to multiple objectives: These are used to explain the reasons behind the use of multiobjective optimization in each application area and also to point the way to potential future uses of the technique.

Decoding the Heart through Next Generation Sequencing Approaches.

PubMed

Pawlak, Michal; Niescierowicz, Katarzyna; Winata, Cecilia Lanny

2018-06-07

: Vertebrate organs develop through a complex process which involves interaction between multiple signaling pathways at the molecular, cell, and tissue levels. Heart development is an example of such complex process which, when disrupted, results in congenital heart disease (CHD). This complexity necessitates a holistic approach which allows the visualization of genome-wide interaction networks, as opposed to assessment of limited subsets of factors. Genomics offers a powerful solution to address the problem of biological complexity by enabling the observation of molecular processes at a genome-wide scale. The emergence of next generation sequencing (NGS) technology has facilitated the expansion of genomics, increasing its output capacity and applicability in various biological disciplines. The application of NGS in various aspects of heart biology has resulted in new discoveries, generating novel insights into this field of study. Here we review the contributions of NGS technology into the understanding of heart development and its disruption reflected in CHD and discuss how emerging NGS based methodologies can contribute to the further understanding of heart repair.

Chemical methods for encoding and decoding of posttranslational modifications

PubMed Central

Chuh, Kelly N.; Batt, Anna R.; Pratt, Matthew R.

2016-01-01

A large array of posttranslational modifications can dramatically change the properties of proteins and influence different aspects of their biological function such as enzymatic activity, binding interactions, and proteostasis. Despite the significant knowledge that has been gained about the function of posttranslational modifications using traditional biological techniques, the analysis of the site-specific effects of a particular modification, the identification of the full compliment of modified proteins in the proteome, and the detection of new types of modifications remains challenging. Over the years, chemical methods have contributed significantly in both of these areas of research. This review highlights several posttranslational modifications where chemistry-based approaches have made significant contributions to our ability to both prepare homogeneously modified proteins and identify and characterize particular modifications in complex biological settings. As the number and chemical diversity of documented posttranslational modifications continues to rise, we believe that chemical strategies will be essential to advance the field in years to come. PMID:26933738

Perspectives in active liquid crystals

PubMed Central

Majumdar, Apala; Cristina, Marchetti M.; Virga, Epifanio G.

2014-01-01

Active soft matter is a young, growing field, with potential applications to a wide variety of systems. This Theme Issue explores this emerging new field by highlighting active liquid crystals. The collected contributions bridge theory to experiment, mathematical theories of passive and active nematics, spontaneous flows to defect dynamics, microscopic to continuum levels of description, spontaneous activity to biological activation. While the perspectives offered here only span a small part of this rapidly evolving field, we trust that they might provide the interested reader with a taste for this new class of non-equilibrium systems and their rich behaviour. PMID:25332386

Organic chemistry and biology of the interstellar medium

NASA Technical Reports Server (NTRS)

Sagan, C.

1973-01-01

Interstellar organic chemistry is discussed as the field of study emerging from the discovery of microwave lines of formaldehyde and of hydrogen cyanide in the interstellar medium. The reliability of molecular identifications and comparisons of interstellar and cometary compounds are considered, along with the degradational origin of simple organics. It is pointed out that the contribution of interstellar organic chemistry to problems in biology is not substantive but analogical. The interstellar medium reveals the operation of chemical processes which, on earth and perhaps on vast numbers of planets throughout the universe, led to the origin of life, but the actual molecules of the interstellar medium are unlikely to play any significant biological role.

Computation as the mechanistic bridge between precision medicine and systems therapeutics.

PubMed

Hansen, J; Iyengar, R

2013-01-01

Over the past 50 years, like molecular cell biology, medicine and pharmacology have been driven by a reductionist approach. The focus on individual genes and cellular components as disease loci and drug targets has been a necessary step in understanding the basic mechanisms underlying tissue/organ physiology and drug action. Recent progress in genomics and proteomics, as well as advances in other technologies that enable large-scale data gathering and computational approaches, is providing new knowledge of both normal and disease states. Systems-biology approaches enable integration of knowledge from different types of data for precision medicine and systems therapeutics. In this review, we describe recent studies that contribute to these emerging fields and discuss how together these fields can lead to a mechanism-based therapy for individual patients.

Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials.

PubMed

Esensten, Jonathan H; Bluestone, Jeffrey A; Lim, Wendell A

2017-01-24

Engineered T cells are currently in clinical trials to treat patients with cancer, solid organ transplants, and autoimmune diseases. However, the field is still in its infancy. The design, and manufacturing, of T cell therapies is not standardized and is performed mostly in academic settings by competing groups. Reliable methods to define dose and pharmacokinetics of T cell therapies need to be developed. As of mid-2016, there are no US Food and Drug Administration (FDA)-approved T cell therapeutics on the market, and FDA regulations are only slowly adapting to the new technologies. Further development of engineered T cell therapies requires advances in immunology, synthetic biology, manufacturing processes, and government regulation. In this review, we outline some of these challenges and discuss the contributions that pathologists can make to this emerging field.

Computation as the Mechanistic Bridge Between Precision Medicine and Systems Therapeutics

PubMed Central

Hansen, J; Iyengar, R

2014-01-01

Over the past 50 years, like molecular cell biology, medicine and pharmacology have been driven by a reductionist approach. The focus on individual genes and cellular components as disease loci and drug targets has been a necessary step in understanding the basic mechanisms underlying tissue/organ physiology and drug action. Recent progress in genomics and proteomics, as well as advances in other technologies that enable large-scale data gathering and computational approaches, is providing new knowledge of both normal and disease states. Systems-biology approaches enable integration of knowledge from different types of data for precision medicine and systems therapeutics. In this review, we describe recent studies that contribute to these emerging fields and discuss how together these fields can lead to a mechanism-based therapy for individual patients. PMID:23212109

Monodispersed magnetite nanoparticles optimized for magnetic fluid hyperthermia: Implications in biological systems

NASA Astrophysics Data System (ADS)

Khandhar, Amit P.; Ferguson, R. Matthew; Krishnan, Kannan M.

2011-04-01

Magnetite (Fe3O4) nanoparticles (MNPs) are suitable materials for Magnetic Fluid Hyperthermia (MFH), provided their size is carefully tailored to the applied alternating magnetic field (AMF) frequency. Since aqueous synthesis routes produce polydisperse MNPs that are not tailored for any specific AMF frequency, we have developed a comprehensive protocol for synthesizing highly monodispersed MNPs in organic solvents, specifically tailored for our field conditions (f = 376 kHz, H0 = 13.4 kA/m) and subsequently transferred them to water using a biocompatible amphiphilic polymer. These MNPs (σavg. = 0.175) show truly size-dependent heating rates, indicated by a sharp peak in the specific loss power (SLP, W/g Fe3O4) for 16 nm (diameter) particles. For broader size distributions (σavg. = 0.266), we observe a 30% drop in overall SLP. Furthermore, heating measurements in biological medium [Dulbecco's modified Eagle medium (DMEM) + 10% fetal bovine serum] show a significant drop for SLP (˜30% reduction in 16 nm MNPs). Dynamic Light Scattering (DLS) measurements show particle hydrodynamic size increases over time once dispersed in DMEM, indicating particle agglomeration. Since the effective magnetic relaxation time of MNPs is determined by fractional contribution of the Neel (independent of hydrodynamic size) and Brownian (dependent on hydrodynamic size) components, we conclude that agglomeration in biological medium modifies the Brownian contribution and thus the net heating capacity of MNPs.

Monitoring the Spatiotemporal Activities of miRNAs in Small Animal Models Using Molecular Imaging Modalities

PubMed Central

Baril, Patrick; Ezzine, Safia; Pichon, Chantal

2015-01-01

MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy. PMID:25749473

Monitoring the spatiotemporal activities of miRNAs in small animal models using molecular imaging modalities.

PubMed

Baril, Patrick; Ezzine, Safia; Pichon, Chantal

2015-03-04

MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression by binding mRNA targets via sequence complementary inducing translational repression and/or mRNA degradation. A current challenge in the field of miRNA biology is to understand the functionality of miRNAs under physiopathological conditions. Recent evidence indicates that miRNA expression is more complex than simple regulation at the transcriptional level. MiRNAs undergo complex post-transcriptional regulations such miRNA processing, editing, accumulation and re-cycling within P-bodies. They are dynamically regulated and have a well-orchestrated spatiotemporal localization pattern. Real-time and spatio-temporal analyses of miRNA expression are difficult to evaluate and often underestimated. Therefore, important information connecting miRNA expression and function can be lost. Conventional miRNA profiling methods such as Northern blot, real-time PCR, microarray, in situ hybridization and deep sequencing continue to contribute to our knowledge of miRNA biology. However, these methods can seldom shed light on the spatiotemporal organization and function of miRNAs in real-time. Non-invasive molecular imaging methods have the potential to address these issues and are thus attracting increasing attention. This paper reviews the state-of-the-art of methods used to detect miRNAs and discusses their contribution in the emerging field of miRNA biology and therapy.

Highly cited German research contributions to the fields of radiation oncology, biology, and physics: focus on collaboration and diversity.

PubMed

Nieder, C

2012-10-01

Tight budgets and increasing competition for research funding pose challenges for highly specialized medical disciplines such as radiation oncology. Therefore, a systematic review was performed of successfully completed research that had a high impact on clinical practice. These data might be helpful when preparing new projects. Different measures of impact, visibility, and quality of published research are available, each with its own pros and cons. For this study, the article citation rate was chosen (minimum 15 citations per year on average). Highly cited German contributions to the fields of radiation oncology, biology, and physics (published between 1990 and 2010) were identified from the Scopus database. Between 1990 and 2010, 106 articles published in 44 scientific journals met the citation requirement. The median average of yearly citations was 21 (maximum 167, minimum 15). All articles with ≥ 40 citations per year were published between 2003 and 2009, consistent with the assumption that the citation rate gradually increases for up to 2 years after publication. Most citations per year were recorded for meta-analyses and randomized phase III trials, which typically were performed by collaborative groups. A large variety of clinical radiotherapy, biology, and physics topics achieved high numbers of citations. However, areas such as quality of life and side effects, palliative radiotherapy, and radiotherapy for nonmalignant disorders were underrepresented. Efforts to increase their visibility might be warranted.

Single molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

PubMed Central

Widom, Julia R.; Dhakal, Soma; Heinicke, Laurie A.; Walter, Nils G.

2015-01-01

Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution, and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy. PMID:25212907

Engineering approaches to transdermal drug delivery: a tribute to contributions of prof. Robert Langer.

PubMed

Mitragotri, S

2013-01-01

Transdermal drug delivery continues to provide an advantageous route of drug administration over injections. While the number of drugs delivered by passive transdermal patches has increased over the years, no macromolecule is currently delivered by the transdermal route. Substantial research efforts have been dedicated by a large number of researchers representing varied disciplines including biology, chemistry, pharmaceutics and engineering to understand, model and overcome the skin's barrier properties. This article focuses on engineering contributions to the field of transdermal drug delivery. The article pays tribute to Prof. Robert Langer, who pioneered the engineering approach towards transdermal drug delivery. Over a period spanning nearly 25 years since his first publication in the field of transdermal drug delivery, Bob Langer has deeply impacted the field by quantitative analysis and innovative engineering. At the same time, he has inspired several generations of engineers by collaborations and mentorship. His scientific insights, innovative technologies, translational efforts and dedicated mentorship have transformed the field. © 2013 S. Karger AG, Basel.

Ronald Breslow (1931-2017).

PubMed

Schepartz, Alanna; Bergman, Robert; Grubbs, Robert H

2018-01-02

Ronald Breslow, Samuel Latham Mitchill Professor of Chemistry at Columbia University, passed away on October 25, 2017, at the age of 86. Breslow made remarkable contributions to the fields of physical-organic and bioorganic chemistry, including biological and biomimetic transformations, and the use of molecular recognition to control reaction selectivity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Variants of Antagonist Cryptococcus flavescens OH 182.9 with Improved Efficacy in Reducing Fusarium Head Blight in Greenhouse and Field Environments

USDA-ARS?s Scientific Manuscript database

The inclusion of biological control agent Cryptococcus flavescens OH 182.9 in the integrated management of Fusarium head blight (FHB) has potential for significantly contributing to the reduction of FHB and deoxynivalenol (DON) in wheat. Experiments were conducted to determine if liquid culture gro...

The Biological and Chemical Oceanography Data Management Office

NASA Astrophysics Data System (ADS)

Allison, M. D.; Chandler, C. L.; Groman, R. C.; Wiebe, P. H.; Glover, D. M.; Gegg, S. R.

2011-12-01

Oceanography and marine ecosystem research are inherently interdisciplinary fields of study that generate and require access to a wide variety of measurements. In late 2006 the Biological and Chemical Oceanography Sections of the National Science Foundation (NSF) Geosciences Directorate Division of Ocean Sciences (OCE) funded the Biological and Chemical Oceanography Data Management Office (BCO-DMO). In late 2010 additional funding was contributed to support management of research data from the NSF Office of Polar Programs Antarctic Organisms & Ecosystems Program. The BCO-DMO is recognized in the 2011 Division of Ocean Sciences Sample and Data Policy as one of several program specific data offices that support NSF OCE funded researchers. BCO-DMO staff members offer data management support throughout the project life cycle to investigators from large national programs and medium-sized collaborative research projects, as well as researchers from single investigator awards. The office manages and serves all types of oceanographic data and information generated during the research process and contributed by the originating investigators. BCO-DMO has built a data system that includes the legacy data from several large ocean research programs (e.g. United States Joint Global Ocean Flux Study and United States GLOBal Ocean ECosystems Dynamics), to which data have been contributed from recently granted NSF OCE and OPP awards. The BCO-DMO data system can accommodate many different types of data including: in situ and experimental biological, chemical, and physical measurements; modeling results and synthesis data products. The system enables reuse of oceanographic data for new research endeavors, supports synthesis and modeling activities, provides availability of "real data" for K-12 and college level use, and provides decision-support field data for policy-relevant investigations. We will present an overview of the data management system capabilities including: map-based and text-based data discovery and access systems; recent enhancements to data search tools; data export and download utilities; and strategic use of controlled vocabularies to facilitate data integration and to improve data system interoperability.

Eduard Strasburger (1844-1912): founder of modern plant cell biology.

PubMed

Volkmann, Dieter; Baluška, František; Menzel, Diedrik

2012-10-01

Eduard Strasburger, director of the Botany Institute and the Botanical Garden at the University of Bonn from 1881 to 1912, was one of the most admirable scientists in the field of plant biology, not just as the founder of modern plant cell biology but in addition as an excellent teacher who strongly believed in "education through science." He contributed to plant cell biology by discovering the discrete stages of karyokinesis and cytokinesis in algae and higher plants, describing cytoplasmic streaming in different systems, and reporting on the growth of the pollen tube into the embryo sac and guidance of the tube by synergides. Strasburger raised many problems which are hot spots in recent plant cell biology, e.g., structure and function of the plasmodesmata in relation to phloem loading (Strasburger cells) and signaling, mechanisms of cell plate formation, vesicle trafficking as a basis for most important developmental processes, and signaling related to fertilization.

Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance

PubMed Central

Frey, Jeremy G; Bird, Colin L

2013-01-01

Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chemical, biochemical, biological, and medical information. These developments depend on a range of factors: the principles of chemical identifiers and their role in relationships between chemical and biological entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration. PMID:24432050

Lizards, ticks and contributions to Australian parasitology: C. Michael Bull (1947-2016).

PubMed

Godfrey, Stephanie S; Gardner, Michael G

2017-12-01

Professor C. Michael Bull was a great scientist and mentor, and an Associate Editor of this journal. While his research career spanned the fields of behavioural ecology, conservation biology and herpetology, in this article, we pay tribute to his major contribution to Australian parasitology. Mike authored more than eighty articles on host-parasite ecology, and revealed major insights into the biology and ecology of ticks from his long term study of the parapatric boundary of two tick species ( Amblyomma limbatum and Bothriocroton hydrosauri ) on the sleepy lizard ( Tiliqua rugosa ). In this article, we provide an overview of how this research journey developed to become one of the longest-running studies of lizards and their ticks, totalling 35 years of continuous surveys of ticks on lizards, and the insights and knowledge that he generated along that journey.

Winter losses of Canada geese at Pea Island, North Carolina

USGS Publications Warehouse

Cowan, A.B.; Herman, C.M.

1955-01-01

Report of research and findings to date. Topics discussed include: studies on life history and biology of gizzard worm; results of autopsies; experiments on survival and transmission of gizzard worm eggs and larvae in both field and laboratory; persistence of infections; and results of infections in geese of different ages. Cause of deaths has not been finally determined, but indications are that gizzard worm is an important contributing factor and that poor physical condition, brought about at least partially by malnutrition, also contributes to the losses.

Optimizing Introductory Physics for the Life Sciences: Placing Physics in Biological Context

NASA Astrophysics Data System (ADS)

Crouch, Catherine

2014-03-01

Physics is a critical foundation for today's life sciences and medicine. However, the physics content and ways of thinking identified by life scientists as most important for their fields are often not taught, or underemphasized, in traditional introductory physics courses. Furthermore, such courses rarely give students practice using physics to understand living systems in a substantial way. Consequently, students are unlikely to recognize the value of physics to their chosen fields, or to develop facility in applying physics to biological systems. At Swarthmore, as at several other institutions engaged in reforming this course, we have reorganized the introductory course for life science students around touchstone biological examples, in which fundamental physics contributes significantly to understanding biological phenomena or research techniques, in order to make explicit the value of physics to the life sciences. We have also focused on the physics topics and approaches most relevant to biology while seeking to develop rigorous qualitative reasoning and quantitative problem solving skills, using established pedagogical best practices. Each unit is motivated by and culminates with students analyzing one or more touchstone examples. For example, in the second semester we emphasize electric potential and potential difference more than electric field, and start from students' typically superficial understanding of the cell membrane potential and of electrical interactions in biochemistry to help them develop a more sophisticated understanding of electric forces, field, and potential, including in the salt water environment of life. Other second semester touchstones include optics of vision and microscopes, circuit models for neural signaling, and magnetotactic bacteria. When possible, we have adapted existing research-based curricular materials to support these examples. This talk will describe the design and development process for this course, give examples of materials, and present initial assessment data evaluating both content learning and student attitudes.

Energy deposition processes in biological tissue: nonthermal biohazards seem unlikely in the ultra-high frequency range.

PubMed

Pickard, W F; Moros, E G

2001-02-01

The prospects of ultra high frequency (UHF, 300--3000 MHz) irradiation producing a nonthermal bioeffect are considered theoretically and found to be small. First, a general formula is derived within the framework of macroscopic electrodynamics for the specific absorption rate of microwaves in a biological tissue; this involves the complex Poynting vector, the mass density of the medium, the angular frequency of the electromagnetic field, and the three complex electromagnetic constitutive parameters of the medium. In the frequency ranges used for cellular telephony and personal communication systems, this model predicts that the chief physical loss mechanism will be ionic conduction, with increasingly important contributions from dielectric relaxation as the frequency rises. However, even in a magnetite unit cell within a magnetosome the deposition rate should not exceed 1/10 k(B)T per second. This supports previous arguments for the improbability of biological effects at UHF frequencies unless a mechanism can be found for accumulating energy over time and space and focussing it. Second, three possible nonthermal accumulation mechanisms are then considered and shown to be unlikely: (i) multiphoton absorption processes; (ii) direct electric field effects on ions; (iii) cooperative effects and/or coherent excitations. Finally, it is concluded that the rate of energy deposition from a typical field and within a typical tissue is so small as to make unlikely any significant nonthermal biological effect. Copyright 2001 Wiley-Liss, Inc.

Shielding in biology and biophysics: Methodology, dosimetry, interpretation

NASA Astrophysics Data System (ADS)

Vladimirsky, B. M.; Temuryants, N. A.

2016-12-01

An interdisciplinary review of the publications on the shielding of organisms by different materials is presented. The authors show that some discrepancies between the results of different researchers might be attributed to methodological reasons, including purely biological (neglect of rhythms) and technical (specific features of the design or material of the screen) ones. In some cases, an important factor is the instability of control indices due to the variations in space weather. According to the modern concept of biological exposure to microdoses, any isolation of a biological object by any material necessarily leads to several simultaneous changes in environmental parameters, and this undermines the principle of "all other conditions being equal" in the classical differential scheme of an experiment. The shielding effects of water solution are universally recognized and their influence is to be observed for all organisms. Data on the exposure of living organisms to weak combined magnetic fields and on the influence of space weather enabled the development of theoretical models generally explaining the effect of shielding for bioorganisms. Ferromagnetic shielding results in changes of both the static magnetic field and the field of radio waves within the area protected by the screen. When screens are nonmagnetic, changes are due to the isolation from the radio waves. In both cases, some contribution to the fluctuations of measured parameters can be made by variations in the level of ionizing radiation.

Metallomics - An Interdisciplinary and Evolving Field

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

Koppenaal, David W.; Hieftje, Gary M.

2007-09-14

In an editorial earlier this year (JAAS, 22, 111, 2007), we opined that metallomics, the study of metals in biological systems, would be an increasingly important topic in elemental analysis in general and for this journal in particular . This issue of the journal, co-edited by the two of us, is a second special issue covering the subject of Metallomics (the first issue was JAAS, 19/1, 2004). The present issue is comprised of technique, application, and perspective papers that address this emerging field of study and show how atomic spectrometry is contributing to the understanding of biological systems. The subjectsmore » covered range from metal binding in plants through investigations of metal and metalloids in samples of biological fluids to the study of food supplements and drug interactions in cells. The issue includes two Critical Reviews. Yuxi Gao and colleagues discuss advanced nuclear analytical techniques for the emerging field of metalloproteomics. While Laura Liermann and her colleagues consider how micro-organisms extract metals from minerals in the environment for utilization in metabolic processes. The content of some of these papers stretches the traditional boundaries and scope of this journal, as echoed by the reviewers of some of the papers. This discussion about scope requires perhaps further debate. However, it is our view that while the Journal must remain true to its core aims, it must also strive to accommodate and motivate a wider authorship and readership. Metallomics is a field that transcends biology and microbiology, biochemistry, clinical chemistry, environmental chemistry, geochemistry, and yes, atomic spectroscopy. If JAAS aspires to be a leading force in metallomics, the Journal must expand its horizons beyond traditional analytical spectroscopy per se. Accordingly, in this special issue you will find papers that have a heavy clinical emphasis, which speak to complementary (non-atomic) spectroscopic techniques, and that provide perspectives that only touch on the use of atomic spectroscopy. The field of metallomics is still in the process of being defined and we hope to inform that definition by including the widest body of technical literature on the subject. We hope that you will find these contributions to be informative, inspiring, and enlightening and consider submitting your own research in this area to JAAS.« less

New developments in high field electron paramagnetic resonance with applications in structural biology

NASA Astrophysics Data System (ADS)

Bennati, Marina; Prisner, Thomas F.

2005-02-01

Recent developments in microwave technologies have led to a renaissance of electron paramagnetic resonance (EPR) due to the implementation of new spectrometers operating at frequencies >=90 GHz. EPR at high fields and high frequencies (HF-EPR) has been established up to THz (very high frequency (VHF) EPR) in continuous wave (cw) operation and up to about 300 GHz in pulsed operation. To date, its most prominent application field is structural biology. This review article first gives an overview of the theoretical basics and the technical aspects of HF-EPR methodologies, such as cw and pulsed HF-EPR, as well as electron nuclear double resonance at high fields (HF-ENDOR). In the second part, the article illustrates different application areas of HF-EPR in studies of protein structure and function. In particular, HF-EPR has delivered essential contributions to disentangling complex spectra of radical cofactors or reaction intermediates in photosynthetic reaction centres, radical enzymes (such as ribonucleotide reductase) and in metalloproteins. Furthermore, HF-EPR combined with site-directed spin labelling in membranes and soluble proteins provides new methods of investigating complex molecular dynamics and intermolecular distances.

Manipulation of long-term dynamics in a colloidal active matter system using speckle light fields

NASA Astrophysics Data System (ADS)

Pince, Ercag; Velu, Sabareesh K. P.; Callegari, Agnese; Elahi, Parviz; Gigan, Sylvain; Volpe, Giovanni; Volpe, Giorgio

Particles undergoing a stochastic motion within a disordered medium is a ubiquitous physical and biological phenomena. Examples can be given from organelles performing tasks in the cytoplasm to large animals moving in patchy environment. Here, we use speckle light fields to study the anomalous diffusion in an active matter system consisting of micron-sized silica particles(diameter 5 μm) and motile bacterial cells (E. coli). The speckle light fields are generated by mode mixing inside a multimode optical fiber where a small amount of incident laser power is needed to obtain an effective disordered optical landscape for the purpose of optical manipulation. We experimentally show how complex potentials contribute to the long-term dynamics of the active matter system and observed an enhanced diffusion of particles interacting with the active bacterial bath in the speckle light fields. We showed that this effect can be tuned and controlled by varying the intensity and the statistical properties of the speckle pattern. Potentially, these results could be of interest for many technological applications, such as the manipulation of microparticles inside optically disordered media of biological interest.

Teaching cell and molecular biology for gender equity.

PubMed

Sible, Jill C; Wilhelm, Dayna E; Lederman, Muriel

2006-01-01

Science, technology, engineering, and math (STEM) fields, including cell biology, are characterized by the "leaky pipeline" syndrome in which, over time, women leave the discipline. The pipeline itself and the pond into which it empties may not be neutral. Explicating invisible norms, attitudes, and practices by integrating social studies of science into science education may be the necessary first step in helping female students persist in STEM disciplines. In 2003 and 2004, a sophomore Cell and Molecular Biology course at Virginia Tech (Blacksburg, VA) was taught integrating social studies of science with standard material. The course was successfully implemented, teaching students factual content while increasing awareness of the cultures of science and their self-confidence in engaging with the subject. Course evaluation data indicated that females in particular perceived greater gains in logical thinking and problem-solving abilities than females in a traditional cell biology course. Consistent with K-12 studies, males in this class were likely to view scientists as male only, whereas females viewed scientists as male and female. This pilot project demonstrates that social studies can be integrated successfully in a cell biology course. Longitudinal studies of this cohort of students will indicate whether this approach contributes to the retention of women in the field.

Complex and biofluids: From Maxwell to nowadays

NASA Astrophysics Data System (ADS)

Misbah, Chaouqi

2009-11-01

Complex fluids are the rule in biology and in many industrial applications. Typical examples are blood, cartilage, and polymer solutions. Unlike water (as well as domestic oils, soft clear drinks, and so on), the law(s) describing the behavior of complex fluids are not yet fully established. The complexity arises from strong coupling between microscopic scales (like the motion of a red blood cell in the case of blood, or a polymer molecule for a polymer solution) and the global scale of the flow (say at the scale of a blood artery, or a channel in laboratory experiments). In this issue entitled Complex and Biofluids a large panel of experimental and theoretical problems of complex fluids is exposed. The topics range from dilute polymer solutions, food products, to biology (blood flow, cell and tissue mechanics). One of the earliest model put forward as an attempt to describe a complex fluid was suggested a long time ago by James Clerk Maxwell (in 1867). Other famous scientists, like Einstein (in 1906), and Taylor (in 1932) have made important contributions to the field, but the topic of complex fluids still continues to pose a formidable challenge to science. This field has known during the past decade an unbelievable upsurge of interest in many branches of science (physics, mechanics, chemistry, biology, medical science, mathematics, and so on). Understanding complex fluids is viewed as one of the biggest challenge of the present century. This synthesis will provide a simple introduction to the topic, summarize the main contribution of this issue, and list major open questions in this field. To cite this article: C. Misbah, C. R. Physique 10 (2009).

Opportunities for Live Cell FT-Infrared Imaging: Macromolecule Identification with 2D and 3D Localization

PubMed Central

Mattson, Eric C.; Aboualizadeh, Ebrahim; Barabas, Marie E.; Stucky, Cheryl L.; Hirschmugl, Carol J.

2013-01-01

Infrared (IR) spectromicroscopy, or chemical imaging, is an evolving technique that is poised to make significant contributions in the fields of biology and medicine. Recent developments in sources, detectors, measurement techniques and speciman holders have now made diffraction-limited Fourier transform infrared (FTIR) imaging of cellular chemistry in living cells a reality. The availability of bright, broadband IR sources and large area, pixelated detectors facilitate live cell imaging, which requires rapid measurements using non-destructive probes. In this work, we review advances in the field of FTIR spectromicroscopy that have contributed to live-cell two and three-dimensional IR imaging, and discuss several key examples that highlight the utility of this technique for studying the structure and chemistry of living cells. PMID:24256815

Microfluidic Organ/Body-on-a-Chip Devices at the Convergence of Biology and Microengineering.

PubMed

Perestrelo, Ana Rubina; Águas, Ana C P; Rainer, Alberto; Forte, Giancarlo

2015-12-10

Recent advances in biomedical technologies are mostly related to the convergence of biology with microengineering. For instance, microfluidic devices are now commonly found in most research centers, clinics and hospitals, contributing to more accurate studies and therapies as powerful tools for drug delivery, monitoring of specific analytes, and medical diagnostics. Most remarkably, integration of cellularized constructs within microengineered platforms has enabled the recapitulation of the physiological and pathological conditions of complex tissues and organs. The so-called "organ-on-a-chip" technology, which represents a new avenue in the field of advanced in vitro models, with the potential to revolutionize current approaches to drug screening and toxicology studies. This review aims to highlight recent advances of microfluidic-based devices towards a body-on-a-chip concept, exploring their technology and broad applications in the biomedical field.

Neuromarketing and consumer neuroscience: contributions to neurology.

PubMed

Javor, Andrija; Koller, Monika; Lee, Nick; Chamberlain, Laura; Ransmayr, Gerhard

2013-02-06

'Neuromarketing' is a term that has often been used in the media in recent years. These public discussions have generally centered around potential ethical aspects and the public fear of negative consequences for society in general, and consumers in particular. However, positive contributions to the scientific discourse from developing a biological model that tries to explain context-situated human behavior such as consumption have often been neglected. We argue for a differentiated terminology, naming commercial applications of neuroscientific methods 'neuromarketing' and scientific ones 'consumer neuroscience'. While marketing scholars have eagerly integrated neuroscientific evidence into their theoretical framework, neurology has only recently started to draw its attention to the results of consumer neuroscience. In this paper we address key research topics of consumer neuroscience that we think are of interest for neurologists; namely the reward system, trust and ethical issues. We argue that there are overlapping research topics in neurology and consumer neuroscience where both sides can profit from collaboration. Further, neurologists joining the public discussion of ethical issues surrounding neuromarketing and consumer neuroscience could contribute standards and experience gained in clinical research. We identify the following areas where consumer neuroscience could contribute to the field of neurology:First, studies using game paradigms could help to gain further insights into the underlying pathophysiology of pathological gambling in Parkinson's disease, frontotemporal dementia, epilepsy, and Huntington's disease.Second, we identify compulsive buying as a common interest in neurology and consumer neuroscience. Paradigms commonly used in consumer neuroscience could be applied to patients suffering from Parkinson's disease and frontotemporal dementia to advance knowledge of this important behavioral symptom.Third, trust research in the medical context lacks empirical behavioral and neuroscientific evidence. Neurologists entering this field of research could profit from the extensive knowledge of the biological foundation of trust that scientists in economically-orientated neurosciences have gained.Fourth, neurologists could contribute significantly to the ethical debate about invasive methods in neuromarketing and consumer neuroscience. Further, neurologists should investigate biological and behavioral reactions of neurological patients to marketing and advertising measures, as they could show special consumer vulnerability and be subject to target marketing.

Neuromarketing and consumer neuroscience: contributions to neurology

PubMed Central

2013-01-01

Background ‘Neuromarketing’ is a term that has often been used in the media in recent years. These public discussions have generally centered around potential ethical aspects and the public fear of negative consequences for society in general, and consumers in particular. However, positive contributions to the scientific discourse from developing a biological model that tries to explain context-situated human behavior such as consumption have often been neglected. We argue for a differentiated terminology, naming commercial applications of neuroscientific methods ‘neuromarketing’ and scientific ones ‘consumer neuroscience’. While marketing scholars have eagerly integrated neuroscientific evidence into their theoretical framework, neurology has only recently started to draw its attention to the results of consumer neuroscience. Discussion In this paper we address key research topics of consumer neuroscience that we think are of interest for neurologists; namely the reward system, trust and ethical issues. We argue that there are overlapping research topics in neurology and consumer neuroscience where both sides can profit from collaboration. Further, neurologists joining the public discussion of ethical issues surrounding neuromarketing and consumer neuroscience could contribute standards and experience gained in clinical research. Summary We identify the following areas where consumer neuroscience could contribute to the field of neurology: First, studies using game paradigms could help to gain further insights into the underlying pathophysiology of pathological gambling in Parkinson’s disease, frontotemporal dementia, epilepsy, and Huntington’s disease. Second, we identify compulsive buying as a common interest in neurology and consumer neuroscience. Paradigms commonly used in consumer neuroscience could be applied to patients suffering from Parkinson’s disease and frontotemporal dementia to advance knowledge of this important behavioral symptom. Third, trust research in the medical context lacks empirical behavioral and neuroscientific evidence. Neurologists entering this field of research could profit from the extensive knowledge of the biological foundation of trust that scientists in economically-orientated neurosciences have gained. Fourth, neurologists could contribute significantly to the ethical debate about invasive methods in neuromarketing and consumer neuroscience. Further, neurologists should investigate biological and behavioral reactions of neurological patients to marketing and advertising measures, as they could show special consumer vulnerability and be subject to target marketing. PMID:23383650

PCR-based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa

USDA-ARS?s Scientific Manuscript database

Among the Phytophthora species that cause black pod of cacao, P. megakarya is the most virulent, posing a serious threat to cacao production in Africa. Correct identification of the species causing the black pod and understanding the virulence factors involved are important for developing sustainabl...

Peripersonal Space and Margin of Safety around the Body: Learning Visuo-Tactile Associations in a Humanoid Robot with Artificial Skin

PubMed Central

Roncone, Alessandro; Fadiga, Luciano; Metta, Giorgio

2016-01-01

This paper investigates a biologically motivated model of peripersonal space through its implementation on a humanoid robot. Guided by the present understanding of the neurophysiology of the fronto-parietal system, we developed a computational model inspired by the receptive fields of polymodal neurons identified, for example, in brain areas F4 and VIP. The experiments on the iCub humanoid robot show that the peripersonal space representation i) can be learned efficiently and in real-time via a simple interaction with the robot, ii) can lead to the generation of behaviors like avoidance and reaching, and iii) can contribute to the understanding the biological principle of motor equivalence. More specifically, with respect to i) the present model contributes to hypothesizing a learning mechanisms for peripersonal space. In relation to point ii) we show how a relatively simple controller can exploit the learned receptive fields to generate either avoidance or reaching of an incoming stimulus and for iii) we show how the robot can select arbitrary body parts as the controlled end-point of an avoidance or reaching movement. PMID:27711136

Effector biology of plant-associated organisms: concepts and perspectives.

PubMed

Win, J; Chaparro-Garcia, A; Belhaj, K; Saunders, D G O; Yoshida, K; Dong, S; Schornack, S; Zipfel, C; Robatzek, S; Hogenhout, S A; Kamoun, S

2012-01-01

Every plant is closely associated with a variety of living organisms. Therefore, deciphering how plants interact with mutualistic and parasitic organisms is essential for a comprehensive understanding of the biology of plants. The field of plant-biotic interactions has recently coalesced around an integrated model. Major classes of molecular players both from plants and their associated organisms have been revealed. These include cell surface and intracellular immune receptors of plants as well as apoplastic and host-cell-translocated (cytoplasmic) effectors of the invading organism. This article focuses on effectors, molecules secreted by plant-associated organisms that alter plant processes. Effectors have emerged as a central class of molecules in our integrated view of plant-microbe interactions. Their study has significantly contributed to advancing our knowledge of plant hormones, plant development, plant receptors, and epigenetics. Many pathogen effectors are extraordinary examples of biological innovation; they include some of the most remarkable proteins known to function inside plant cells. Here, we review some of the key concepts that have emerged from the study of the effectors of plant-associated organisms. In particular, we focus on how effectors function in plant tissues and discuss future perspectives in the field of effector biology.

Protein glycosylation in gastric and colorectal cancers: Toward cancer detection and targeted therapeutics.

PubMed

Ferreira, José Alexandre; Magalhães, Ana; Gomes, Joana; Peixoto, Andreia; Gaiteiro, Cristiana; Fernandes, Elisabete; Santos, Lúcio Lara; Reis, Celso A

2017-02-28

Glycosylation is the most frequent and structurally complex posttranslational modification in cell-surface and secreted proteins. Glycans are major orchestrators of biological processes, namely, by controlling protein folding and key biological functions such as cell adhesion, migration, signaling and immune recognition. Altered glycosylation is considered a hallmark of malignant transformations that decisively contributes to disease outcome. This review comprehensively summarizes the main findings related with gastrointestinal cancers and the decisive impact of aberrant glycosylation on tumor biology toward more aggressive phenotypes. Particular emphasis is given to alterations in O-glycosylation, namely, the overexpression of immature O-glycans, and the sialylated Lewis antigens sialyl-LeA and sialyl-LeX, frequently implicated in lymphohematogenous metastasis. We further discuss how recent contributions from glycoproteomics and glycoengineering fields have broadened our understanding of the human O-glycoproteome and its implications for cancer research. Finally, we address the tremendous potential of glycans in the context of targeted therapeutics (selective inhibition of glycosylation pathways, immunotherapy) and discuss the need to include glycomics/glycoproteomics in holistic panomics models toward true precision medicine settings. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Electrodynamic eigenmodes in cellular morphology.

PubMed

Cifra, M

2012-09-01

Eigenmodes of the spherical and ellipsoidal dielectric electromagnetic resonator have been analysed. The sizes and shape of the resonators have been chosen to represent the shape of the interphase and dividing animal cell. Electromagnetic modes that have shape exactly suitable for positioning of the sufficiently large organelles in cell (centrosome, nucleus) have been identified. We analysed direction and magnitude of dielectrophoretic force exerted on large organelles by electric field of the modes. We found that the TM(1m1) mode in spherical resonator acts by centripetal force which drags the large organelles which have higher permittivity than the cytosol to the center of the cell. TM-kind of mode in the ellipsoidal resonator acts by force on large polarizable organelles in a direction that corresponds to the movement of the centrosomes (also nucleus) observed during the cell division, i.e. to the foci of the ellipsoidal cell. Minimal required force (10(-16) N), gradient of squared electric field and corresponding energy (10(-16) J) of the mode have been calculated to have biological significance within the periods on the order of time required for cell division. Minimal required energy of the mode, in order to have biological significance, can be lower in the case of resonance of organelle with the field of the cellular resonator mode. In case of sufficient energy in the biologically relevant mode, electromagnetic field of the mode will act as a positioning or steering mechanism for centrosome and nucleus in the cell, thus contribute to the spatial and dynamical self-organization in biological systems. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Managing biodiversity for a competitive ecotourism industry in tropical developing countries: New opportunities in biological fields

NASA Astrophysics Data System (ADS)

Hakim, Luchman

2017-11-01

Managing biodiversity for sustainable and competitive ecotourism destinations requires a basic understanding of the principles of biology, which are poorly understood in tropical developing countries, including Indonesia. This paper describes the current status of tourism in Indonesia, identifies environment and biodiversity vulnerability in tourism destinations, and explores the challenges of the biological field in supporting ecotourism development. This review found that tourism, especially nature-based and ecotourism, has grown significantly in Indonesia, and the contribution of Indonesian biodiversity has been identified as significant. Threats to biodiversity, however, are found in nature-based tourism destinations. Issues related to pollution, exotic plant species invasion, habitat changes and degradation, habitat loss, and wildlife disturbance are widely reported, indicating the importance of such issues in destination management. Pollution is found in both terrestrial and aquatic ecosystems. Water pollution is an important issue among lakes and rivers. To date, there are few assessments of the impact of tourism activities on aquatic ecosystems, resulting in the management of aquatic ecosystems facing numerous difficulties. These studies identify the invasive plants found, which become a crucial problem in many nature-based tourism destinations, and which significantly contribute to a reduction in the existence of many flora-fauna in a wild habitat. Habitat changes and degradation are mostly influenced by tourism infrastructure development. Massive infrastructure development often leads to habitat loss, which is a crucial step in local biodiversity extinction. Increasing and uncontrolled visitor behaviors influence animal behavior changes, which is recognized as a dangerous phenomenon affecting animal survival in the future. An agenda for future integrative biological research is needed to improve resource management, to increase sustainability and the competitiveness of the tourism industry in Indonesia.

The contribution of molecular genetics to the understanding and management of cancer: potential future applications and implications for nurses.

PubMed

Bradley, A N

1999-06-01

Cancer is an immense medical problem and as a cause of mortality it is second only to cardiovascular disease. Much of the current understanding of cancer is owed to epidemiologists who have discovered a number of causative factors implicated in its development. These causative factors can be divided into genetic, chemical, physical, viral, radiation, immune and hormonal factors. Further advances in understanding have been made over the past decade from contributions made by the field of molecular biology. From investigation and examination of the molecular processes involved in the development of cancer it is becoming increasingly clear that changes in the genetic material of the cell nuclei are the final common pathway to cancer, whatever the initial aetiology. This article will attempt to elucidate the contribution of molecular genetics to the understanding of the likely mechanisms of carcinogenesis, the management of cancer, potential future applications and directions and the implications for nurses arising from this relatively new and evolving field of knowledge.

Cholesterol - a biological compound as a building block in bionanotechnology

NASA Astrophysics Data System (ADS)

Hosta-Rigau, Leticia; Zhang, Yan; Teo, Boon M.; Postma, Almar; Städler, Brigitte

2012-12-01

Cholesterol is a molecule with many tasks in nature but also a long history in science. This feature article highlights the contribution of this small compound to bionanotechnology. We discuss relevant chemical aspects in this context followed by an overview of its self-assembly capabilities both as a free molecule and when conjugated to a polymer. Further, cholesterol in the context of liposomes is reviewed and its impact ranging from biosensing to drug delivery is outlined. Cholesterol is and will be an indispensable player in bionanotechnology, contributing to the progress of this potent field of research.

An interview with Christopher Wylie and Janet Heasman.

PubMed

Wylie, Christopher; Heasman, Janet; Grewal, Seema

2014-12-01

The 2014 Society for Developmental Biology (SDB) Lifetime Achievement Award was jointly awarded to Christopher Wylie and Janet Heasman in recognition of their outstanding and sustained contributions to the field. At the 73rd Annual SDB meeting, where they were presented with the award, we asked Chris and Janet about their careers and their advice for young researchers. © 2014. Published by The Company of Biologists Ltd.

Introductory physics in biological context: An approach to improve introductory physics for life science students

NASA Astrophysics Data System (ADS)

Crouch, Catherine H.; Heller, Kenneth

2014-05-01

We describe restructuring the introductory physics for life science students (IPLS) course to better support these students in using physics to understand their chosen fields. Our courses teach physics using biologically rich contexts. Specifically, we use examples in which fundamental physics contributes significantly to understanding a biological system to make explicit the value of physics to the life sciences. This requires selecting the course content to reflect the topics most relevant to biology while maintaining the fundamental disciplinary structure of physics. In addition to stressing the importance of the fundamental principles of physics, an important goal is developing students' quantitative and problem solving skills. Our guiding pedagogical framework is the cognitive apprenticeship model, in which learning occurs most effectively when students can articulate why what they are learning matters to them. In this article, we describe our courses, summarize initial assessment data, and identify needs for future research.

Social neuroscience and its potential contribution to psychiatry

PubMed Central

Cacioppo, John T; Cacioppo, Stephanie; Dulawa, Stephanie; Palmer, Abraham A

2014-01-01

Most mental disorders involve disruptions of normal social behavior. Social neuroscience is an interdisciplinary field devoted to understanding the biological systems underlying social processes and behavior, and the influence of the social environment on biological processes, health and well-being. Research in this field has grown dramatically in recent years. Active areas of research include brain imaging studies in normal children and adults, animal models of social behavior, studies of stroke patients, imaging studies of psychiatric patients, and research on social determinants of peripheral neural, neuroendocrine and immunological processes. Although research in these areas is proceeding along largely independent trajectories, there is increasing evidence for connections across these trajectories. We focus here on the progress and potential of social neuroscience in psychiatry, including illustrative evidence for a rapid growth of neuroimaging and genetic studies of mental disorders. We also argue that neuroimaging and genetic research focused on specific component processes underlying social living is needed. PMID:24890058

Biomechanical forces in the skeleton and their relevance to bone metastasis: biology and engineering considerations

PubMed Central

Lynch, Maureen; Fischbach, Claudia

2014-01-01

Bone metastasis represents the leading cause of breast cancer related-deaths. However, the effect of skeleton-associated biomechanical signals on the initiation, progression, and therapy response of breast cancer bone metastasis is largely unknown. This review seeks to highlight possible functional connections between skeletal mechanical signals and breast cancer bone metastasis and their contribution to clinical outcome. It provides an introduction to the physical and biological signals underlying bone functional adaptation and discusses the modulatory roles of mechanical loading and breast cancer metastasis in this process. Following a definition of biophysical design criteria, in vitro and in vivo approaches from the fields of bone biomechanics and tissue engineering will be reviewed that may be suitable to investigate breast cancer bone metastasis as a function of varied mechano-signaling. Finally, an outlook of future opportunities and challenges associated with this newly emerging field will be provided. PMID:25174311

Microfluidic Organ/Body-on-a-Chip Devices at the Convergence of Biology and Microengineering

PubMed Central

Perestrelo, Ana Rubina; Águas, Ana C. P.; Rainer, Alberto; Forte, Giancarlo

2015-01-01

Recent advances in biomedical technologies are mostly related to the convergence of biology with microengineering. For instance, microfluidic devices are now commonly found in most research centers, clinics and hospitals, contributing to more accurate studies and therapies as powerful tools for drug delivery, monitoring of specific analytes, and medical diagnostics. Most remarkably, integration of cellularized constructs within microengineered platforms has enabled the recapitulation of the physiological and pathological conditions of complex tissues and organs. The so-called “organ-on-a-chip” technology, which represents a new avenue in the field of advanced in vitro models, with the potential to revolutionize current approaches to drug screening and toxicology studies. This review aims to highlight recent advances of microfluidic-based devices towards a body-on-a-chip concept, exploring their technology and broad applications in the biomedical field. PMID:26690442

Pathobiology of germ cell tumors - applying the gossip test!

PubMed

Looijenga, Leendert H J; Oosterhuis, J Wolter

2013-01-01

Residual mature teratoma, a frequent finding in clinical pathology since the introduction of cisplatin-based chemotherapy, put Wolter Oosterhuis on the track of germ cell tumors (GCTs). These neoplasms in the borderland between developmental biology and oncology have fascinated him ever since. He tells the story on how GCTs brought him in contact with leading investigators in the field like Ivan Damjanov, Peter Andrews, and Niels Skakkebaek. His fruitful line of research was made possible through a longstanding collaboration with Bauke de Jong and, to this day, Leendert Looijenga who joined his group as a student in 1988. Probably their most important contribution to the field of GCTs is an integrated approach to GCTs, combining epidemiology, pathology, (cyto)genetics and molecular biology, that has resulted in a pathobiology-based classification of GCTs in five types. It has clinical relevance and stimulates further research on these intriguing neoplasms and their corresponding animal models.

The human biology--saturated with experience.

PubMed

Getz, Linn; Kirkengen, Anna Luise; Ulvestad, Elling

2011-04-08

The human being is a self-reflecting, relationship-oriented, goal-directed organism in search of meaning. The process of coordinating and developing knowledge about how experience associated with self-conscience, relationships and values can contribute to development of health and disease is a great challenge for the medical profession. We present a theory-guided synthesis of new scientific knowledge from fields such as epigenetics, psycho-neuro-endocrino-immunology, stress research and systems biology. The sources are articles in acknowledged journals and books, chosen to provide insight into associations between life history (biography) and the human body (biology) in a wide sense. Research shows that information about biography, i.e. experienced meaning and relationships, is literally incorporated into the human organism. Epigenetics illustrates the fundamental biological potential for context-dependent adaptation. Further, studies have shown that different types of existential strain may disturb systems for human physiological adaptation, affect structures in the brain and subsequently render the organism vulnerable for disease. However, a sense of belonging and a perception of being supported and acknowledged can contribute to strengthening or restoring health. The traditional approach to increasing biomedical knowledge has prevented insight into the medical significance of experience. The new knowledge necessitates a reorientation of theory and practice within the medical profession both with respect to individuals and society.

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

PubMed

Kawai, Fusako

2010-01-01

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

Computer modeling in developmental biology: growing today, essential tomorrow.

PubMed

Sharpe, James

2017-12-01

D'Arcy Thompson was a true pioneer, applying mathematical concepts and analyses to the question of morphogenesis over 100 years ago. The centenary of his famous book, On Growth and Form , is therefore a great occasion on which to review the types of computer modeling now being pursued to understand the development of organs and organisms. Here, I present some of the latest modeling projects in the field, covering a wide range of developmental biology concepts, from molecular patterning to tissue morphogenesis. Rather than classifying them according to scientific question, or scale of problem, I focus instead on the different ways that modeling contributes to the scientific process and discuss the likely future of modeling in developmental biology. © 2017. Published by The Company of Biologists Ltd.

Integrating physical stress, growth, and development.

PubMed

Uyttewaal, Magalie; Traas, Jan; Hamant, Olivier

2010-02-01

Linking the gene regulatory network to morphogenesis is a central question in developmental biology. Shape relies on the combined actions of biochemistry and biophysics, two parameters that are under local genetic control. The blooming of molecular biology since the 1970s has promoted a biochemical view of development, leaving behind the contribution of physical forces. Recently, the development of new techniques, such as live imaging, micromechanical approaches, and computer modeling, has revitalized the biomechanics field. In this review, we use shoot apical meristem development to illustrate how biochemistry and biomechanics cooperate to integrate the local cellular gene input into global growth patterns. Copyright 2009 Elsevier Ltd. All rights reserved.

Biophysics and systems biology.

PubMed

Noble, Denis

2010-03-13

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights.

Biophysics and systems biology

PubMed Central

Noble, Denis

2010-01-01

Biophysics at the systems level, as distinct from molecular biophysics, acquired its most famous paradigm in the work of Hodgkin and Huxley, who integrated their equations for the nerve impulse in 1952. Their approach has since been extended to other organs of the body, notably including the heart. The modern field of computational biology has expanded rapidly during the first decade of the twenty-first century and, through its contribution to what is now called systems biology, it is set to revise many of the fundamental principles of biology, including the relations between genotypes and phenotypes. Evolutionary theory, in particular, will require re-assessment. To succeed in this, computational and systems biology will need to develop the theoretical framework required to deal with multilevel interactions. While computational power is necessary, and is forthcoming, it is not sufficient. We will also require mathematical insight, perhaps of a nature we have not yet identified. This article is therefore also a challenge to mathematicians to develop such insights. PMID:20123750

Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia.

PubMed

Fogg, Christiana N; Kovats, Diane E

2015-07-01

The International Society for Computational Biology (ISCB; http://www.iscb.org) honors a senior scientist annually for his or her outstanding achievements with the ISCB Accomplishment by a Senior Scientist Award. This award recognizes a leader in the field of computational biology for his or her significant contributions to the community through research, service and education. Cyrus Chothia, an emeritus scientist at the Medical Research Council Laboratory of Molecular Biology and emeritus fellow of Wolfson College at Cambridge University, England, is the 2015 ISCB Accomplishment by a Senior Scientist Award winner.Chothia was selected by the Awards Committee, which is chaired by Dr Bonnie Berger of the Massachusetts Institute of Technology. He will receive his award and deliver a keynote presentation at 2015 Intelligent Systems for Molecular Biology/European Conference on Computational Biology in Dublin, Ireland, in July 2015. dkovats@iscb.org. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Fusion of approaches to the treatment of organ failure.

PubMed

Ogle, Brenda; Cascalho, Marilia; Platt, Jeffrey L

2004-01-01

Because organ transplantation is the preferred treatment for organ failure, the demand for human organs for transplantation is large and growing. From this demand, several fields based on new technologies for the replacement or repair of damaged tissues and organs have emerged. These fields include stem cell biology, cloning, tissue engineering and xenotransplantation. Here we evaluate the potential contribution of these to the devising of alternative approaches to organ replacement. We present our vision for the development of two structurally complex organs - the lung and the kidney - based on a 'fusion' of new and established technologies.

Are biological effects of desert shrubs more important than physical effects on soil microorganisms?

PubMed

Berg, Naama; Steinberger, Yosef

2010-01-01

Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of "fertile islands," which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a longterm research, we designed an experiment to separate the two components-the physical and biotic parts of the perennial plants-and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinity of the artificial plants, and between the shrubs (control). The contribution to microbial activity was measured by evaluation of the microbial community functions in soil. The functional aspects of the microbial community that were measured were CO2 evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community. The results of this study are presented in two ways: (1) according to the three locations/treatments; and (2) according to the phenological situation of the vegetation (annual and perennial plants) in the research field: the growing phase, the drying process, and the absence of annual plants. The only parameters that were found to affect microbial activity were the contribution of the organic matter of perennial shrubs and the growth of vegetation (annual and perennial) during the growing seasons. The physical component was found to have no effect on soil microbial functional diversity, which elucidates the important contribution of the desert shrub in enhancing biological multiplicity and activity.

Untangling the biological contributions to soil stability in semiarid shrublands

USGS Publications Warehouse

Chaudhary, V. Bala; Bowker, Matthew A.; O'Dell, Thomas E.; Grace, James B.; Redman, Andrea E.; Rillig, Matthias C.; Johnson, Nancy C.

2009-01-01

Communities of plants, biological soil crusts (BSCs), and arbuscular mycorrhizal (AM) fungi are known to influence soil stability individually, but their relative contributions, interactions, and combined effects are not well understood, particularly in arid and semiarid ecosystems. In a landscape-scale field study we quantified plant, BSC, and AM fungal communities at 216 locations along a gradient of soil stability levels in southern Utah, USA. We used multivariate modeling to examine the relative influences of plants, BSCs, and AM fungi on surface and subsurface stability in a semiarid shrubland landscape. Models were found to be congruent with the data and explained 35% of the variation in surface stability and 54% of the variation in subsurface stability. The results support several tentative conclusions. While BSCs, plants, and AM fungi all contribute to surface stability, only plants and AM fungi contribute to subsurface stability. In both surface and subsurface models, the strongest contributions to soil stability are made by biological components of the system. Biological soil crust cover was found to have the strongest direct effect on surface soil stability (0.60; controlling for other factors). Surprisingly, AM fungi appeared to influence surface soil stability (0.37), even though they are not generally considered to exist in the top few millimeters of the soil. In the subsurface model, plant cover appeared to have the strongest direct influence on soil stability (0.42); in both models, results indicate that plant cover influences soil stability both directly (controlling for other factors) and indirectly through influences on other organisms. Soil organic matter was not found to have a direct contribution to surface or subsurface stability in this system. The relative influence of AM fungi on soil stability in these semiarid shrublands was similar to that reported for a mesic tallgrass prairie. Estimates of effects that BSCs, plants, and AM fungi have on soil stability in these models are used to suggest the relative amounts of resources that erosion control practitioners should devote to promoting these communities. This study highlights the need for system approaches in combating erosion, soil degradation, and arid-land desertification.

Colonization of Wheat Heads by Fusarium Head Blight Antagonist Cryptococcus flavescens OH 182.9 when Applied Alone or in Combination with Prothioconazole and the Treatment Effect on FHB Disease Development in Field-Grown Whea

USDA-ARS?s Scientific Manuscript database

The use of yeast biological control agent Cyptococcus flavescens OH 182.9 (NRRL Y-30216) as part of an integrated management strategy against Fusarium head blight (FHB) of wheat is understudied yet has considerable potential for significantly contributing to the reduction of FHB and deoxynivalenol (...

Potential of big data analytics in the French in vitro diagnostics market.

PubMed

Dubois, Nicolas; Garnier, Nicolas; Meune, Christophe

2017-12-01

The new paradigm of the big data raises many expectations, particularly in the field of health. Curiously, even though medical biology laboratories generate a great amount of data, the opportunities offered by this new field are poorly documented. For better understanding the clinical context of chronical disease follow-up, for leveraging preventive and/or personalized medicine, the contribution of big data analytics seems very promising. It is within this framework that we have explored to use data of a Breton group of laboratories of medical biology to analyze the possible contributions of their exploitation in the improvement of the clinical practices and to anticipate the evolution of pathologies for the benefit of patients. We report here three practical applications derived from routine laboratory data from a period of 5 years (February 2010-August 2015): follow-up of patients treated with AVK according to the recommendations of the High authority of health (HAS), use of the new troponin markers HS and NT-proBNP in cardiology. While the risks and difficulties of using algorithms in the health domain should not be underestimated - quality, accessibility, and protection of personal data in particular - these first results show that use of tools and technologies of the big data repository could provide decisive support for the concept of "evidence based medicine".

Mitochondrial-epigenetic crosstalk in environmental toxicology.

PubMed

Weinhouse, Caren

2017-11-01

Crosstalk between the nuclear epigenome and mitochondria, both in normal physiological function and in responses to environmental toxicant exposures, is a developing sub-field of interest in environmental and molecular toxicology. The majority (∼99%) of mitochondrial proteins are encoded in the nuclear genome, so programmed communication among nuclear, cytoplasmic, and mitochondrial compartments is essential for maintaining cellular health. In this review, we will focus on correlative and mechanistic evidence for direct impacts of each system on the other, discuss demonstrated or potential crosstalk in the context of chemical insult, and highlight biological research questions for future study. We will first review the two main signaling systems: nuclear signaling to the mitochondria [anterograde signaling], best described in regulation of oxidative phosphorylation (OXPHOS) and mitochondrial biogenesis in response to environmental signals received by the nucleus, and mitochondrial signals to the nucleus [retrograde signaling]. Both signaling systems can communicate intracellular energy needs or a need to compensate for dysfunction to maintain homeostasis, but both can also relay inappropriate signals in the presence of dysfunction in either system and contribute to adverse health outcomes. We will first review these two signaling systems and highlight known or biologically feasible epigenetic contributions to both, then briefly discuss the emerging field of epigenetic regulation of the mitochondrial genome, and finally discuss putative "crosstalk phenotypes", including biological phenomena, such as caloric restriction, maintenance of stemness, and circadian rhythm, and states of disease or loss of function, such as cancer and aging, in which both the nuclear epigenome and mitochondria are strongly implicated. Copyright © 2017 Elsevier B.V. All rights reserved.

EDITORIAL: Nanotechnology at the interface of cell biology, materials science and medicine Nanotechnology at the interface of cell biology, materials science and medicine

NASA Astrophysics Data System (ADS)

Engel, Andreas; Miles, Mervyn

2008-09-01

The atomic force microscope (AFM) and related scanning probe microscopes have become resourceful tools to study cells, supramolecular assemblies and single biomolecules, because they allow investigations of such structures in native environments. Quantitative information has been gathered about the surface structure of membrane proteins to lateral and vertical resolutions of 0.5 nm and 0.1 nm, respectively, about the forces that keep protein-protein and protein-nucleic acid assemblies together as well as single proteins in their native conformation, and about the nanomechanical properties of cells in health and disease. Such progress has been achieved mainly because of constant development of AFM instrumentation and sample preparation methods. This special issue of Nanotechnology presents papers from leading laboratories in the field of nanobiology, covering a wide range of topics in the form of original and novel scientific contributions. It addresses achievements in instrumentation, sample preparation, automation and in biological applications. These papers document the creativity and persistence of researchers pursuing the goal to unravel the structure and dynamics of cells, supramolecuar structures and single biomolecules at work. Improved cantilever sensors, novel optical probes, and quantitative data on supports for electrochemical experiments open new avenues for characterizing biological nanomachines down to the single molecule. Comparative measurements of healthy and metastatic cells promise new methods for early detection of tumors, and possible assessments of drug efficacy. High-speed AFMs document possibilities to monitor crystal growth and to observe large structures at video rate. A wealth of information on amyloid-type fibers as well as on membrane proteins has been gathered by single molecule force spectroscopy—a technology now being automated for large-scale data collection. With the progress of basic research and a strong industry supporting instrumentation development by improving robustness and reliability and making new instruments available to the community, nanobiology has the potential to develop into a field with great impact on our understanding of the complexity of life, and to provide a major contribution to human health. This special issue of Nanotechnology on nanobiology would not have been possible without the highly professional support from Nina Couzin, Amy Harvey and the Nanotechnology team at IOP Publishing. We are thankful for their most constructive and effective help in pushing the project forward. We are also thankful to all the authors who have contributed with excellent original articles, as well as to the referees who have helped to make this special issue such an insightful document of a rapidly moving field.

Target fragmentation in radiobiology

NASA Technical Reports Server (NTRS)

Wilson, John W.; Cucinotta, Francis A.; Shinn, Judy L.; Townsend, Lawrence W.

1993-01-01

Nuclear reactions in biological systems produce low-energy fragments of the target nuclei seen as local high events of linear energy transfer (LET). A nuclear-reaction formalism is used to evaluate the nuclear-induced fields within biosystems and their effects within several biological models. On the basis of direct ionization interaction, one anticipates high-energy protons to have a quality factor and relative biological effectiveness (RBE) of unity. Target fragmentation contributions raise the effective quality factor of 10 GeV protons to 3.3 in reasonable agreement with RBE values for induced micronuclei in bean sprouts. Application of the Katz model indicates that the relative increase in RBE with decreasing exposure observed in cell survival experiments with 160 MeV protons is related solely to target fragmentation events. Target fragment contributions to lens opacity given an RBE of 1.4 for 2 GeV protons in agreement with the work of Lett and Cox. Predictions are made for the effective RBE for Harderian gland tumors induced by high-energy protons. An exposure model for lifetime cancer risk is derived from NCRP 98 risk tables, and protraction effects are examined for proton and helium ion exposures. The implications of dose rate enhancement effects on space radiation protection are considered.

The Past Achievements and Future Promises of Developmental Psychopathology: The Coming of Age of a Discipline

PubMed Central

Cicchetti, Dante; Toth, Sheree L.

2012-01-01

Over the past decades, developmental psychopathology has coalesced into a discipline that has made significant contributions toward the understanding of risk, psychopathology, and resilience in individuals across the life course. The overarching goal of the discipline has been to elucidate the interplay among biological, psychological, and social-contextual aspects of normal and abnormal development. In addition to directing efforts toward bridging fields of study and aiding in elucidating important truths about the processes underlying adaptation and maladaptation, investigators in developmental psychopathology have been equally devoted to developing and evaluating methods for preventing and ameliorating maladaptive and psychopathological outcomes. Increasingly, efforts are being made to conduct investigations at multiple levels of analysis and to translate basic research knowledge into real world contexts. In this article, the contributions, challenges, and future directions of the field are highlighted. PMID:19175810

Preface

NASA Astrophysics Data System (ADS)

Mallamace, Francesco; Quintana, Jacqueline

2002-03-01

Complex systems represent one of the richest and more fascinating fields of current scientific research. The reason behind this is the important role that the properties of complex systems and materials play in a variety of different but overlapping areas in physics, chemistry, biology, mathematics, and social sciences, like medicine and economy. Such unusually broad research field is, therefore, of primary interest nowadays in pure science and technology. The role of statistical physics in this new field of complex systems has been present since its onset and it has been accelerating recently. Methods developed for studying ordering phenomena in simple systems have been generalized for application to more complex forms of matter (polymers, biological macromolecules, glasses, etc) and complex processes (e.g. chaos, turbulence, economy, jamming, biological processes). In particular, many different phenomena (considered in the past to belong to separate research fields) have now a common description. Pillars of such a description are the concepts of scaling and universality. The International Conference on `Scaling Concepts and Complex Systems' (a satellite meeting of STATPHYS21) was devoted to give an overview on recent developments around these two concepts. The Conference took place in Merida, Yucatan, Mexico, in July 9-14 2001. The meeting was held in the Gordon Conference style and was attended by about 100 scientists, it covered a large variety of theoretical and experimental research topics of current interest in complex systems and materials. The meeting consisted of a total number of about 40 invited and contributed talks and a poster session. The topics covered included: scaling behaviour, supra-molecular systems, aggregation, aggregation kinetics, growth mechanisms, disordered systems, soft condensed matter (polymers, biological polymers, bio-colloids, gels, colloids, membranes and interfacial phenomena), granular matter, phase separation and out-of-equilibrium dynamics, non-linear dynamics, chaos, turbulence and chaotic dynamics. The present issue contains a substantial number of the invited and contributed talks presented at the meeting. We made an effort to arrange these papers with an order similar to that of presentation during the meeting. It is our pleasure to thank the scientific committee, all the speakers, the session chairs and all participants who contributed to the success of the conference. We are grateful to the Bonino-Pulejo Foundation (Messina-Italy), and to the President On. Nino Calarco, for the Patronage and the enthusiastic support. Our thanks goes also for the Messina University, the INFM (Istituto Nazionale per la Fisica della Materia, Italy), the Consejo Nacional de Ciencia y Tecnología (CONACyT, Mexico) and the Universidad Nacional Autonoma de Mexico (UNAM). The Conference was sponsored by the INFM-Sec.C, CONACyT, UNAM, the Bonino-Pulejo Foundation which contributed financial support to participants and to the publication of the present issue. We are grateful to them for the support. Last, but not the least, we express our warmest gratitude to all the members of the local organizing committee for their assistance and for the work spent in organizing this meeting and especially to Professor~Alberto Robledo for his valuable advice.

Is nanotechnology the key to unravel and engineer biological processes?

PubMed

Navarro, Melba; Planell, Josep A

2012-01-01

Regenerative medicine is an emerging field aiming to the development of new reparative strategies to treat degenerative diseases, injury, and trauma through developmental pathways in order to rebuild the architecture of the original injured organ and take over its functionality. Most of the processes and interactions involved in the regenerative process take place at subcellular scale. Nanotechnology provides the tools and technology not only to detect, to measure, or to image the interactions between the different biomolecules and biological entities, but also to control and guide the regenerative process. The relevance of nanotechnology for the development of regenerative medicine as well as an overview of the different tools that contribute to unravel and engineer biological systems are presented in this chapter. In addition, general data about the social impact and global investment in nanotechnology are provided.

Phase from defocus

NASA Astrophysics Data System (ADS)

Mandula, Ondrej; Allier, Cédric; Hervé, Lionel; Denarier, Eric; Fourest-Lieuvin, Anne; Gory-Fauré, Sylvie; Vinit, Angélique; Morales, Sophie

2018-02-01

We present a simple and compact phase imaging microscope for long-term observation of non-absorbing biological samples such as unstained cells in nutritive media. The phase image is obtained from a single defocused image taken with a standard wide-field microscope. Using a semi-coherent light source allows us to computationally re-focus image post-acquisition and recover both phase and transmission of the complex specimen. The simplicity of the system reduces both the cost and its physical size and allows a long-term observation of samples directly in a standard biological incubator. The low cost of the system can contribute to the democratization of science by allowing to perform complex long-term biological experiments to the laboratories with constrained budget. In this proceeding we present several results taken with our prototype and discuss the possibilities and limitations of our system.

Bedform development and morphodynamics in mixed cohesive sediment substrates: the importance of winnowing and flocculation

NASA Astrophysics Data System (ADS)

Ye, Leiping; Parsons, Daniel; Manning, Andrew

2016-04-01

There remains a lack of process-based knowledge of sediment dynamics within flows over bedforms generated in complex mixtures of cohesionless sand and biologically-active cohesive muds in natural estuarine flow systems. The work to be presented forms a part of the UK NERC "COHesive BEDforms (COHBED)" project which aims to fill this gap in knowledge. Herein results from a field survey in sub-tidal zone of Dee estuary (NW, England) and a set of large-scale laboratory experiments, conducted using mixtures of non-cohesive sands, cohesive muds and Xanthan gum (as a proxy for the biological stickiness of Extracellular Polymeric Substances (EPS)) will be presented. The results indicate the significance of biological-active cohesive sediments in controlling winnowing rates and flocculation dynamics, which contributes significantly to rates of bedform evolution.

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.

When physics is not "just physics": complexity science invites new measurement frames for exploring the physics of cognitive and biological development.

PubMed

Kelty-Stephen, Damian; Dixon, James A

2012-01-01

The neurobiological sciences have struggled to resolve the physical foundations for biological and cognitive phenomena with a suspicion that biological and cognitive systems, capable of exhibiting and contributing to structure within themselves and through their contexts, are fundamentally distinct or autonomous from purely physical systems. Complexity science offers new physics-based approaches to explaining biological and cognitive phenomena. In response to controversy over whether complexity science might seek to "explain away" biology and cognition as "just physics," we propose that complexity science serves as an application of recent advances in physics to phenomena in biology and cognition without reducing or undermining the integrity of the phenomena to be explained. We highlight that physics is, like the neurobiological sciences, an evolving field and that the threat of reduction is overstated. We propose that distinctions between biological and cognitive systems from physical systems are pretheoretical and thus optional. We review our own work applying insights from post-classical physics regarding turbulence and fractal fluctuations to the problems of developing cognitive structure. Far from hoping to reduce biology and cognition to "nothing but" physics, we present our view that complexity science offers new explanatory frameworks for considering physical foundations of biological and cognitive phenomena.

Active chiral fluids.

PubMed

Fürthauer, S; Strempel, M; Grill, S W; Jülicher, F

2012-09-01

Active processes in biological systems often exhibit chiral asymmetries. Examples are the chirality of cytoskeletal filaments which interact with motor proteins, the chirality of the beat of cilia and flagella as well as the helical trajectories of many biological microswimmers. Here, we derive constitutive material equations for active fluids which account for the effects of active chiral processes. We identify active contributions to the antisymmetric part of the stress as well as active angular momentum fluxes. We discuss four types of elementary chiral motors and their effects on a surrounding fluid. We show that large-scale chiral flows can result from the collective behavior of such motors even in cases where isolated motors do not create a hydrodynamic far field.

Natural selection and infectious disease in human populations

PubMed Central

Karlsson, Elinor K.; Kwiatkowski, Dominic P.; Sabeti, Pardis C.

2015-01-01

The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology. PMID:24776769

BIOINFORMATICS IN THE K-8 CLASSROOM: DESIGNING INNOVATIVE ACTIVITIES FOR TEACHER IMPLEMENTATION

PubMed Central

Shuster, Michele; Claussen, Kira; Locke, Melly; Glazewski, Krista

2016-01-01

At the intersection of biology and computer science is the growing field of bioinformatics—the analysis of complex datasets of biological relevance. Despite the increasing importance of bioinformatics and associated practical applications, these are not standard topics in elementary and middle school classrooms. We report on a pilot project and its evolution to support implementation of bioinformatics-based activities in elementary and middle school classrooms. Specifically, we ultimately designed a multi-day summer teacher professional development workshop, in which teachers design innovative classroom activities. By focusing on teachers, our design leverages enhanced teacher knowledge and confidence to integrate innovative instructional materials into K-8 classrooms and contributes to capacity building in STEM instruction. PMID:27429860

Fitness consequences of maternal and embryonic responses to environmental variation: using reptiles as models for studies of developmental plasticity.

PubMed

Warner, Daniel A

2014-11-01

Environmental factors strongly influence phenotypic variation within populations. The environment contributes to this variation in two ways: (1) by acting as a determinant of phenotypic variation (i.e., plastic responses) and (2) as an agent of selection that "chooses" among existing phenotypes. Understanding how these two environmental forces contribute to phenotypic variation is a major goal in the field of evolutionary biology and a primary objective of my research program. The objective of this article is to provide a framework to guide studies of environmental sources of phenotypic variation (specifically, developmental plasticity and maternal effects, and their adaptive significance). Two case studies from my research on reptiles are used to illustrate the general approaches I have taken to address these conceptual topics. Some key points for advancing our understanding of environmental influences on phenotypic variation include (1) merging laboratory-based research that identifies specific environmental effects with field studies to validate ecological relevance; (2) using controlled experimental approaches that mimic complex environments found in nature; (3) integrating data across biological fields (e.g., genetics, morphology, physiology, behavior, and ecology) under an evolutionary framework to provide novel insights into the underlying mechanisms that generate phenotypic variation; (4) assessing fitness consequences using measurements of survival and/or reproductive success across ontogeny (from embryos to adults) and under multiple ecologically-meaningful contexts; and (5) quantifying the strength and form of natural selection in multiple populations over multiple periods of time to understand the spatial and temporal consistency of phenotypic selection. Research programs that focus on organisms that are amenable to these approaches will provide the most promise for advancing our understanding of the environmental factors that generate the remarkable phenotypic diversity observed within populations. © The Author 2014. 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.

Secondary Ion Mass Spectrometry SIMS XI

NASA Astrophysics Data System (ADS)

Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

2003-05-01

This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

Multi-agent Simulations of Population Behavior: A Promising Tool for Systems Biology.

PubMed

Colosimo, Alfredo

2018-01-01

This contribution reports on the simulation of some dynamical events observed in the collective behavior of different kinds of populations, ranging from shape-changing cells in a Petri dish to functionally correlated brain areas in vivo. The unifying methodological approach, based upon a Multi-Agent Simulation (MAS) paradigm as incorporated in the NetLogo™ interpreter, is a direct consequence of the cornerstone that simple, individual actions within a population of interacting agents often give rise to complex, collective behavior.The discussion will mainly focus on the emergence and spreading of synchronous activities within the population, as well as on the modulation of the collective behavior exerted by environmental force-fields. A relevant section of this contribution is dedicated to the extension of the MAS paradigm to Brain Network models. In such a general framework some recent applications taken from the direct experience of the author, and exploring the activation patterns characteristic of specific brain functional states, are described, and their impact on the Systems-Biology universe underlined.

Evaluating experimental molecular physics studies of radiation damage in DNA*

NASA Astrophysics Data System (ADS)

Śmiałek, Małgorzata A.

2016-11-01

The field of Atomic and Molecular Physics (AMP) is a mature field exploring the spectroscopy, excitation, ionisation of atoms and molecules in all three phases. Understanding of the spectroscopy and collisional dynamics of AMP has been fundamental to the development and application of quantum mechanics and is applied across a broad range of disparate disciplines including atmospheric sciences, astrochemistry, combustion and environmental science, and in central to core technologies such as semiconductor fabrications, nanotechnology and plasma processing. In recent years the molecular physics also started significantly contributing to the area of the radiation damage at molecular level and thus cancer therapy improvement through both experimental and theoretical advances, developing new damage measurement and analysis techniques. It is therefore worth to summarise and highlight the most prominent findings from the AMP community that contribute towards better understanding of the fundamental processes in biologically-relevant systems as well as to comment on the experimental challenges that were met for more complex investigation targets. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic, B. Sivaraman.

Addressing the unmet need for visualizing conditional random fields in biological data

PubMed Central

2014-01-01

Background The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Model (GPM). The structure of GPMs is a uniquely good match for biological problems that range from aligning sequences to modeling the genome-to-phenome relationship. The fundamental questions that GPMs address involve making decisions based on a complex web of interacting factors. Unfortunately, while GPMs ideally fit many questions in biology, they are not an easy solution to apply. Building a GPM is not a simple task for an end user. Moreover, applying GPMs is also impeded by the insidious fact that the “complex web of interacting factors” inherent to a problem might be easy to define and also intractable to compute upon. Discussion We propose that the visualization sciences can contribute to many domains of the bio-sciences, by developing tools to address archetypal representation and user interaction issues in GPMs, and in particular a variety of GPM called a Conditional Random Field(CRF). CRFs bring additional power, and additional complexity, because the CRF dependency network can be conditioned on the query data. Conclusions In this manuscript we examine the shared features of several biological problems that are amenable to modeling with CRFs, highlight the challenges that existing visualization and visual analytics paradigms induce for these data, and document an experimental solution called StickWRLD which, while leaving room for improvement, has been successfully applied in several biological research projects. Software and tutorials are available at http://www.stickwrld.org/ PMID:25000815

Tensegrity, cellular biophysics, and the mechanics of living systems

PubMed Central

Ingber, Donald E.; Wang, Ning; Stamenović, Dimitrije

2014-01-01

The recent convergence between physics and biology has led many physicists to enter the fields of cell and developmental biology. One of the most exciting areas of interest has been the emerging field of mechanobiology that centers on how cells control their mechanical properties, and how physical forces regulate cellular biochemical responses, a process that is known as mechanotransduction. In this article, we review the central role that tensegrity (tensional integrity) architecture, which depends on tensile prestress for its mechanical stability, plays in biology. We describe how tensional prestress is a critical governor of cell mechanics and function, and how use of tensegrity by cells contributes to mechanotransduction. Theoretical tensegrity models are also described that predict both quantitative and qualitative behaviors of living cells, and these theoretical descriptions are placed in context of other physical models of the cell. In addition, we describe how tensegrity is used at multiple size scales in the hierarchy of life — from individual molecules to whole living organisms — to both stabilize three-dimensional form and to channel forces from the macroscale to the nanoscale, thereby facilitating mechanochemical conversion at the molecular level. PMID:24695087

Concise Review: Fluorescent Reporters in Human Pluripotent Stem Cells: Contributions to Cardiac Differentiation and Their Applications in Cardiac Disease and Toxicity.

PubMed

Den Hartogh, Sabine C; Passier, Robert

2016-01-01

In the last decade, since the first report of induced pluripotent stem cells, the stem cell field has made remarkable progress in the differentiation to specialized cell-types of various tissues and organs, including the heart. Cardiac lineage- and tissue-specific human pluripotent stem cell (hPSC) reporter lines have been valuable for the identification, selection, and expansion of cardiac progenitor cells and their derivatives, and for our current understanding of the underlying molecular mechanisms. In order to further advance the use of hPSCs in the fields of regenerative medicine, disease modeling, and preclinical drug development in cardiovascular research, it is crucial to identify functionally distinct cardiac subtypes and to study their biological signaling events and functional aspects in healthy and diseased conditions. In this review, we discuss the various strategies that have been followed to generate and study fluorescent reporter lines in hPSCs and provide insights how these reporter lines contribute to a better understanding and improvement of cell-based therapies and preclinical drug and toxicity screenings in the cardiac field. © AlphaMed Press.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus

PubMed Central

Karp, Peter D.; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

2015-01-01

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains as well as 3-D protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature, and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2,000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida). PMID:26097686

ISCB Ebola Award for Important Future Research on the Computational Biology of Ebola Virus.

PubMed

Karp, Peter D; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

2015-01-01

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains as well as 3-D protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature, and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2,000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology (ISMB) 2016, Orlando, Florida).

Synthetic Biology and the Translational Imperative.

PubMed

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

2017-12-18

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

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-molecular-weight protein biopharmaceuticals. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Potential effects of maternal contribution on egg and larva population dynamics of striped bass: Integrated individual-based model and directed field sampling

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

Cowan, J.H., Jr.; Rose, K.A.

1991-01-01

We have used a bioenergetically-driven, individual-based model (IBM) of striped bass as a framework for synthesizing available information on population biology and quantifying, in a relative sense, factors that potentially affect year class success. The IBM has been configured to simulate environmental conditions experienced by several striped bass populations; i.e., in the Potomac River, MD; in Hudson River, NY; in the Santee-Cooper River System, SC, and; in the San Joaquin-Sacramento River System CA. These sites represent extremes in the geographic distribution and thus, environmental variability of striped bass spawning. At each location, data describing the physio-chemical and biological characteristics ofmore » the spawning population and nursery area are being collected and synthesized by means of a prioritized, directed field sampling program that is organized by the individual-based recruitment model. Here, we employ the striped bass IBM configured for the Potomac River, MD from spawning into the larval period to evaluate the potential for maternal contribution to affect larva survival and growth. Model simulations in which the size distribution and spawning day of females are altered indicate that larva survival is enhanced (3.3-fold increase) when a high fraction of females in the spawning population are large. Larva stage duration also is less ({bar X} = 18.4 d and 22.2 d) when large and small females, respectively, are mothers in simulations. Although inconclusive, these preliminary results for Potomac River striped bass suggest that the effects of female size, timing of spawning nad maternal contribution on recruitment dynamics potentially are important and illustrate our approach to the study of recruitment in striped bass. We hope to use the model, field collections and management alternatives that vary from site to site, in an iterative manner for some time to come. 54 refs., 4 figs., 1 tab.« less

Identification of crude-oil components and microorganisms that cause souring under anaerobic conditions.

PubMed

Hasegawa, R; Toyama, K; Miyanaga, K; Tanji, Y

2014-02-01

Oil souring has important implications with respect to energy resources. Understanding the physiology of the microorganisms that play a role and the biological mechanisms are both important for the maintenance of infrastructure and mitigation of corrosion processes. The objective of this study was to identify crude-oil components and microorganisms in oil-field water that contribute to crude-oil souring. To identify the crude-oil components and microorganisms that are responsible for anaerobic souring in oil reservoirs, biological conversion of crude-oil components under anaerobic conditions was investigated. Microorganisms in oil field water in Akita, Japan degraded alkanes and aromatics to volatile fatty acids (VFAs) under anaerobic conditions, and fermenting bacteria such as Fusibacter sp. were involved in VFA production. Aromatics such as toluene and ethylbenzene were degraded by sulfate-reducing bacteria (Desulfotignum sp.) via the fumarate-addition pathway and not only degradation of VFA but also degradation of aromatics by sulfate-reducing bacteria was the cause of souring. Naphthenic acid and 2,4-xylenol were not converted.

Biomechanical forces in the skeleton and their relevance to bone metastasis: biology and engineering considerations.

PubMed

Lynch, Maureen E; Fischbach, Claudia

2014-12-15

Bone metastasis represents the leading cause of breast cancer related-deaths. However, the effect of skeleton-associated biomechanical signals on the initiation, progression, and therapy response of breast cancer bone metastasis is largely unknown. This review seeks to highlight possible functional connections between skeletal mechanical signals and breast cancer bone metastasis and their contribution to clinical outcome. It provides an introduction to the physical and biological signals underlying bone functional adaptation and discusses the modulatory roles of mechanical loading and breast cancer metastasis in this process. Following a definition of biophysical design criteria, in vitro and in vivo approaches from the fields of bone biomechanics and tissue engineering that may be suitable to investigate breast cancer bone metastasis as a function of varied mechano-signaling will be reviewed. Finally, an outlook of future opportunities and challenges associated with this newly emerging field will be provided. Copyright © 2014 Elsevier B.V. All rights reserved.

Application of bioinformatics in chronobiology research.

PubMed

Lopes, Robson da Silva; Resende, Nathalia Maria; Honorio-França, Adenilda Cristina; França, Eduardo Luzía

2013-01-01

Bioinformatics and other well-established sciences, such as molecular biology, genetics, and biochemistry, provide a scientific approach for the analysis of data generated through "omics" projects that may be used in studies of chronobiology. The results of studies that apply these techniques demonstrate how they significantly aided the understanding of chronobiology. However, bioinformatics tools alone cannot eliminate the need for an understanding of the field of research or the data to be considered, nor can such tools replace analysts and researchers. It is often necessary to conduct an evaluation of the results of a data mining effort to determine the degree of reliability. To this end, familiarity with the field of investigation is necessary. It is evident that the knowledge that has been accumulated through chronobiology and the use of tools derived from bioinformatics has contributed to the recognition and understanding of the patterns and biological rhythms found in living organisms. The current work aims to develop new and important applications in the near future through chronobiology research.

Mechanism of biological effects observed in honey bees (Apis mellifera, L. ) hived under extra-high-voltage transmission lines: implications derived from bee exposure to simulated intense electric fields and shocks

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

Bindokas, V.P.; Gauger, J.R.; Greenberg, B.

This work explores mechanisms for disturbance of honey bee colonies under a 765 kV, 60-Hz transmission line (electric (E) field = 7 kV/m) observed in previous studies. Proposed mechanisms fell into two categories: direct bee perception of enhanced in-hive E fields and perception of shock from induced currents. The adverse biological effects could be reproduced in simulations where only the worker bees were exposed to shock or to E field in elongated hive entranceways (= tunnels). We now report the results of full-scale experiments using the tunnel exposure scheme, which assesses the contribution of shock and intense E field tomore » colony disturbance. Exposure of worker bees (1400 h) to 60-Hz E fields including 100 kV/m under moisture-free conditions within a nonconductive tunnel causes no deleterious affect on colony behavior. Exposure of bees in conductive (e.g., wet) tunnels produces bee disturbance, increased mortality, abnormal propolization, and possible impairment of colony growth. We propose that this substrate dependence of bee disturbance is the result of perception of shock from coupled body currents and enhanced current densities postulated to exist in the legs and thorax of bees on conductors. Similarly, disturbance occurs when bees are exposed to step-potential-induced currents. At 275-350 nA single bees are disturbed; at 600 nA bees begin abnormal propolization behavior; and stinging occurs at 900 nA. We conclude that biological effects seen in bee colonies under a transmission line are primarily the result of electric shock from induced hive currents. This evaluation is based on the limited effects of E-field exposure in tunnels, the observed disturbance thresholds caused by shocks in tunnels, and the ability of hives exposed under a transmission line to source currents 100-1,000 times the shock thresholds.« less

Beyond patchwork precaution in the dual-use governance of synthetic biology.

PubMed

Kelle, Alexander

2013-09-01

The emergence of synthetic biology holds the potential of a major breakthrough in the life sciences by transforming biology into a predictive science. The dual-use characteristics of similar breakthroughs during the twentieth century have led to the application of benignly intended research in e.g. virology, bacteriology and aerobiology in offensive biological weapons programmes. Against this background the article raises the question whether the precautionary governance of synthetic biology can aid in preventing this techno-science witnessing the same fate? In order to address this question, this paper proceeds in four steps: it firstly introduces the emerging techno-science of synthetic biology and presents some of its potential beneficial applications. It secondly analyses contributions to the bioethical discourse on synthetic biology as well as precautionary reasoning and its application to life science research in general and synthetic biology more specifically. The paper then identifies manifestations of a moderate precautionary principle in the emerging synthetic biology dual-use governance discourse. Using a dual-use governance matrix as heuristic device to analyse some of the proposed measures, it concludes that the identified measures can best be described as "patchwork precaution" and that a more systematic approach to construct a web of dual-use precaution for synthetic biology is needed in order to guard more effectively against the field's future misuse for harmful applications.

Tissue engineering and regenerative medicine: manufacturing challenges.

PubMed

Williams, D J; Sebastine, I M

2005-12-01

Tissue engineering and regenerative medicine are interdisciplinary fields that apply principles of engineering and life sciences to develop biological substitutes, typically composed of biological and synthetic components, that restore, maintain or improve tissue function. Many tissue engineering technologies are still at a laboratory or pre-commercial scale. The short review paper describes the most significant manufacturing and bio-process challenges inherent in the commercialisation and exploitation of the exciting results emerging from the biological and clinical laboratories exploring tissue engineering and regenerative medicine. A three-generation road map of the industry has been used to structure a view of these challenges and to define where the manufacturing community can contribute to the commercial success of the products from these emerging fields. The first-generation industry is characterised by its demonstrated clinical applications and products in the marketplace, the second is characterised by emerging clinical applications, and the third generation is characterised by aspirational clinical applications. The paper focuses on the cost reduction requirement of the first generation of the industry to allow more market penetration and consequent patient impact. It indicates the technological requirements, for instance the creation of three-dimensional tissue structures, and value chain issues in the second generation of the industry. The third-generation industry challenges lie in fundamental biological and clinical science. The paper sets out a road map of these generations to identify areas for research.

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

PubMed

Wei, Min; Li, Song; Le, Weidong

2017-10-25

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

Escalating role of piezosurgery in dental therapeutics.

PubMed

Agarwal, Esha; Masamatti, Sujata Surendra; Kumar, Ashish

2014-10-01

Dentistry, an art in science and tranquilizer in medicine, has seen a lot of changing concepts over a decade and one such novel innovation is piezosurgery. Piezosurgery is a true revolution in bone surgery as it fulfils both biological and technical criteria. It has a variety of applications ranging from minor surgical procedures to complex implantology, plastic and reconstructive surgeries. Piezosurgery uses a low frequency modulated ultrasonic insert which produces microvibrations in the range of 60-200micro meter/sec and leads to safe and precise bony incision without damaging underlying vital structures like nerves, mucosa and vessels. It overcomes technical difficulties such as visibility by producing bloodless field during surgery and removes debris simultaneously through internal irrigation mechanism. The soft tissues remain safe and biological factors like release of certain cytokines promote bone healing and enhance patients recovery. This critical review outweighs piezosurgery over traditional tools and emphasizes on its clinical and biological aspects contributing to beneficial dental health.

Mass-spectrometric identification of primary biological particle markers: indication for low abundance of primary biological material in the pristine submicron aerosol of Amazonia

NASA Astrophysics Data System (ADS)

Schneider, J.; Freutel, F.; Zorn, S. R.; Chen, Q.; Farmer, D. K.; Jimenez, J. L.; Martin, S. T.; Artaxo, P.; Wiedensohler, A.; Borrmann, S.

2011-07-01

The abundance of marker compounds for primary biological particles in submicron aerosol was investigated by means of aerosol mass spectrometry. Mass spectra of amino acids, carbohydrates, small peptides, and proteins, all of which are key building blocks of biological particles, were recorded in laboratory experiments. Several characteristic marker peaks were identified. The identified marker peaks were compared with mass spectra recorded during AMAZE-08, a field campaign conducted in the pristine rainforest of the Central Amazon Basin, Brazil, during the wet season of February and March 2008. The low abundance of identified marker peaks places upper limits of 7.5 % for amino acids and 5.6 % for carbohydrates on the contribution of primary biological aerosol particles (PBAPs) to the submicron organic aerosol mass concentration during this time period. Upper limits for the absolute submicron concentrations for both compound classes range from 0.01 to 0.1 μg m-3. Carbohydrates and protein amino acids make up for about two thirds of the dry mass of a biological cell. Thus, our findings suggest an upper limit for the PBAPs mass fraction of about 20 % to the submicron organic aerosol.

Biorobotics: using robots to emulate and investigate agile locomotion.

PubMed

Ijspeert, Auke J

2014-10-10

The graceful and agile movements of animals are difficult to analyze and emulate because locomotion is the result of a complex interplay of many components: the central and peripheral nervous systems, the musculoskeletal system, and the environment. The goals of biorobotics are to take inspiration from biological principles to design robots that match the agility of animals, and to use robots as scientific tools to investigate animal adaptive behavior. Used as physical models, biorobots contribute to hypothesis testing in fields such as hydrodynamics, biomechanics, neuroscience, and prosthetics. Their use may contribute to the design of prosthetic devices that more closely take human locomotion principles into account. Copyright © 2014, American Association for the Advancement of Science.

Background ELF magnetic fields in incubators: a factor of importance in cell culture work.

PubMed

Mild, Kjell Hansson; Wilén, Jonna; Mattsson, Mats-Olof; Simko, Myrtill

2009-07-01

Extremely low frequency (ELF) magnetic fields in cell culture incubators have been measured. Values of the order of tens of muT were found which is in sharp contrast to the values found in our normal environment (0.05-0.1microT). There are numerous examples of biological effects found after exposure to MF at these levels, such as changes in gene expression, blocked cell differentiation, inhibition of the effect of tamoxifen, effects on chick embryo development, etc. We therefore recommend that people working with cell culture incubators check for the background magnetic field and take this into account in performing their experiments, since this could be an unrecognised factor of importance contributing to the variability in the results from work with cell cultures.

Editorial: The Sackler International Prize in Biophysical Sciences

NASA Astrophysics Data System (ADS)

Frydman, Lucio

2018-02-01

The Raymond and Beverly Sackler International Prize is awarded alternatively in the fields of Biophysics, Chemistry and Physics on a yearly basis, by Tel Aviv University. The price is intended to encourage dedication to science, originality and excellence, by rewarding outstanding scientists under 45 years of age, with a total purse of 100,000. The 2016 Raymond and Beverly Sackler Prize was awarded in the field of Magnetic Resonance last February in a festive symposium, to three excellent researchers: Professor John Morton (University College London), Professor Guido Pintacuda (Ecole Normale Supérieure de Lyon and CNRS), and Professor Charalampos Kalodimos (at the time at the University of Minnesota). John was recognized for his novel contributions to quantum information processing, by means of a range of highly elegant physical phenomena involving both NMR and EPR. Guido was recognized for his methodological advances in solid state NMR spectroscopy, including advances in proton detection under ultrafast MAS at ultrahigh magnetic field, and for his insightful applications to challenging biological systems. While Charalampos (Babis) was recognized for beautifully detailed characterizations of structure, function, and dynamics in challenging and important biological systems through solution NMR spectroscopy.

Electromagnetic Fields, Oxidative Stress, and Neurodegeneration

PubMed Central

Consales, Claudia; Merla, Caterina; Marino, Carmela; Benassi, Barbara

2012-01-01

Electromagnetic fields (EMFs) originating both from both natural and manmade sources permeate our environment. As people are continuously exposed to EMFs in everyday life, it is a matter of great debate whether they can be harmful to human health. On the basis of two decades of epidemiological studies, an increased risk for childhood leukemia associated with Extremely Low Frequency fields has been consistently assessed, inducing the International Agency for Research on Cancer to insert them in the 2B section of carcinogens in 2001. EMFs interaction with biological systems may cause oxidative stress under certain circumstances. Since free radicals are essential for brain physiological processes and pathological degeneration, research focusing on the possible influence of the EMFs-driven oxidative stress is still in progress, especially in the light of recent studies suggesting that EMFs may contribute to the etiology of neurodegenerative disorders. This review synthesizes the emerging evidences about this topic, highlighting the wide data uncertainty that still characterizes the EMFs effect on oxidative stress modulation, as both pro-oxidant and neuroprotective effects have been documented. Care should be taken to avoid methodological limitations and to determine the patho-physiological relevance of any alteration found in EMFs-exposed biological system. PMID:22991514

The Animal Kingdom Is Also a Bioengineering Field: Exploring the Art and Science of Vetinary Medicine [Retrospectroscope].

PubMed

Valentinuzzi, Max E

2017-01-01

Medical science developed in tandem with the evolution of biological species and their associated diseases. Because of the close interaction between humans and other animals, even those in the wild, taking care of the former also means caring for the latter. Several scientific forerunners delved into animals' anatomical and physiological secrets in their quest to better understand animal biology and functions, thereby laying the foundation for animal medicine. Here, I briefly explore the long and complex road that led to the current state of veterinary science and provide a few examples of its present standing. (Contributions from the ancient world and eastern countries are not considered, as they represent a different area of interest.).

A Journey with Elie Metchnikoff: From Innate Cell Mechanisms in Infectious Diseases to Quantum Biology

PubMed Central

Merien, Fabrice

2016-01-01

Many reviews of Elie Metchnikoff’s work have been published, all unanimously acknowledging the significant contributions of his cellular theory to the fields of immunology and infectious diseases. In 1883, he published a key paper describing phagocytic cells in frogs. His descriptions were not just about phagocytes involved in host defense, he also described how these specialized cells eliminated degenerating or dying cells of the host. This perspective focuses on key concepts developed by Metchnikoff by presenting relevant excerpts of his 1883 paper and matching these concepts with challenges of modern immunology. A new approach to macrophage polarization is included to introduce some creative thinking about the exciting emerging area of quantum biology. PMID:27379227

NETTAB 2012 on "Integrated Bio-Search"

PubMed Central

2014-01-01

The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement. PMID:24564635

FtsZ Cytoskeletal Filaments as a Template for Metallic Nanowire Fabrication.

PubMed

Ostrov, Nili; Fichman, Galit; Adler-Abramovich, Lihi; Gazit, Ehud

2015-01-01

Supramolecular protein assemblies can serve as templates for the fabrication of inorganic nanowires due to their morphological reproducibility and innate proclivity to form well-ordered structures. Amongst the variety of naturally occurring nano-scale assemblies, cytoskeletal fibers from diverse biological sources represent a unique family of scaffolds for biomimetics as they efficiently self-assemble in vitro in a controllable manner to form stable filaments. Here, we harness the bacterial FtsZ filament system as a scaffold for protein-based metal nanowires, and further demonstrate the control of wire alignment with the use of an external magnetic field. Due to the ease at which the bacterial FtsZ is overexpressed and purified, as well as the extensive studies of its ultrastructural properties and physiological significance, FtsZ filaments are an ideal substrate for large-scale production and chemical manipulation. Using a biologically compatible electroless metal deposition technique initiated by adsorption of platinum as a surface catalyst, we demonstrate the coating of assembled FtsZ filaments with iron, nickel, gold, and copper to fabricate continuous nanowires with diameters ranging from 10-50 nm. Organic-inorganic hybrid wires were analyzed using high-resolution field-emission-gun transmission and scanning electron microscopy, and confirmed by energy-dispersive elemental analysis. We also achieved alignment of ferrofluid-coated FtsZ filaments using an external magnetic field. Overall, we provide evidence for the robustness of the FtsZ filament system as a molecular scaffold, and offer an efficient, biocompatible procedure for facile bottom-up assembly of metallic wires on biological templates. We believe that bottom-up fabrication methods as reported herein significantly contribute to the expanding toolkit available for the incorporation of biological materials in nano-scale devices for electronic and electromechanical applications.

Epigenetics: A way to bridge the gap between biological fields.

PubMed

Nicoglou, Antonine; Merlin, Francesca

2017-12-01

The concept of epigenetics has evolved since Waddington defined it from the late 1930s as the study of the causal mechanisms at work in development. It has become a multi-faceted notion with different meanings, depending on the disciplinary context it is used. In this article, we first analyse the transformations of the concept of epigenetics, from Waddington to contemporary accounts, in order to identify its different meanings and traditions, and to come up with a typology of epigenetics throughout its history. Second, we show on this basis that epigenetics has progressively turned its main focus from biological problems regarding development, toward issues concerning evolution. Yet, both these different epistemological aspects of epigenetics still coexist. Third, we claim that the classical opposition between epigenesis and preformationism as ways of thinking about the developmental process is part of the history of epigenetics and has contributed to its current various meanings. With these objectives in mind, we first show how Waddington introduced the term "epigenetics" in a biological context in order to solve a developmental problem, and we then build on this by presenting Nanney's, Riggs' and Holliday's definitions, which form the basis for the current conception of "molecular epigenetics". Then, we show that the evo-devo research field is where some particular uses of epigenetics have started shifting from developmental issues to evolutionary problems. We also show that epigenetics has progressively focused on the issue of epigenetic inheritance within the Extended Evolutionary Synthesis' framework. Finally, we conclude by presenting a typology of the different conceptions of epigenetics throughout time, and analyse the connections between them. We argue that, since Waddington, epigenetics, as an integrative research area, has been used to bridge the gap between different biological fields. Copyright © 2017 Elsevier Ltd. All rights reserved.

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

NASA Astrophysics Data System (ADS)

Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.; Volkov, Sergey N.; Solov'yov, Andrey V.

2016-01-01

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Gustavo Garcia and Eugene Surdutovich.

Methodology to define biological reference values in the environmental and occupational fields: the contribution of the Italian Society for Reference Values (SIVR).

PubMed

Aprea, Maria Cristina; Scapellato, Maria Luisa; Valsania, Maria Carmen; Perico, Andrea; Perbellini, Luigi; Ricossa, Maria Cristina; Pradella, Marco; Negri, Sara; Iavicoli, Ivo; Lovreglio, Piero; Salamon, Fabiola; Bettinelli, Maurizio; Apostoli, Pietro

2017-04-21

Biological reference values (RVs) explore the relationships between humans and their environment and habits. RVs are fundamental in the environmental field for assessing illnesses possibly associated with environmental pollution, and also in the occupational field, especially in the absence of established biological or environmental limits. The Italian Society for Reference Values (SIVR) determined to test criteria and procedures for the definition of RVs to be used in the environmental and occupational fields. The paper describes the SIVR methodology for defining RVs of xenobiotics and their metabolites. Aspects regarding the choice of population sample, the quality of analytical data, statistical analysis and control of variability factors are considered. The simultaneous interlaboratory circuits involved can be expected to increasingly improve the quality of the analytical data. Examples of RVs produced by SIVR are presented. In particular, levels of chromium, mercury, ethylenethiourea, 3,5,6-trichloro-2-pyridinol, 2,5-hexanedione, 1-hydroxypyrene and t,t-muconic acid measured in urine and expressed in micrograms/g creatinine (μg/g creat) or micrograms/L (μg/L) are reported. With the proposed procedure, SIVR intends to make its activities known to the scientific community in order to increase the number of laboratories involved in the definition of RVs for the Italian population. More research is needed to obtain further RVs in different biological matrices, such as hair, nails and exhaled breath. It is also necessary to update and improve the present reference values and broaden the portfolio of chemicals for which RVs are available. In the near future, SIVR intends to expand its scientific activity by using a multivariate approach for xenobiotics that may have a common origin, and to define RVs separately for children who may be exposed more than adults and be more vulnerable.

Field Trial Assessment of Biological, Chemical, and Physical Responses of Soil to Tillage Intensity, Fertilization, and Grazing

NASA Astrophysics Data System (ADS)

Vargas Gil, Silvina; Becker, Analia; Oddino, Claudio; Zuza, Mónica; Marinelli, Adriana; March, Guillermo

2009-08-01

Soil microbial populations can fluctuate in response to environmental changes and, therefore, are often used as biological indicators of soil quality. Soil chemical and physical parameters can also be used as indicators because they can vary in response to different management strategies. A long-term field trial was conducted to study the effects of different tillage systems (NT: no tillage, DH: disc harrow, and MP: moldboard plough), P fertilization (diammonium phosphate), and cattle grazing (in terms of crop residue consumption) in maize ( Zea mays L.), sunflower ( Heliantus annuus L.), and soybean ( Glycine max L.) on soil biological, chemical, and physical parameters. The field trial was conducted for four crop years (2000/2001, 2001/2002, 2002/2003, and 2003/2004). Soil populations of Actinomycetes, Trichoderma spp., and Gliocladium spp. were 49% higher under conservation tillage systems, in soil amended with diammonium phosphate (DAP) and not previously grazed. Management practices also influenced soil chemical parameters, especially organic matter content and total N, which were 10% and 55% higher under NT than under MP. Aggregate stability was 61% higher in NT than in MP, 15% higher in P-fertilized soil, and also 9% higher in not grazed strips, bulk density being 12% lower in NT systems compared with MP. DAP application and the absence of grazing also reduced bulk density (3%). Using conservation tillage systems, fertilizing crops with DAP, and avoiding grazing contribute to soil health preservation and enhanced crop production.

Quantifying bioalbedo: a new physically based model and discussion of empirical methods for characterising biological influence on ice and snow albedo

NASA Astrophysics Data System (ADS)

Cook, Joseph M.; Hodson, Andrew J.; Gardner, Alex S.; Flanner, Mark; Tedstone, Andrew J.; Williamson, Christopher; Irvine-Fynn, Tristram D. L.; Nilsson, Johan; Bryant, Robert; Tranter, Martyn

2017-11-01

The darkening effects of biological impurities on ice and snow have been recognised as a control on the surface energy balance of terrestrial snow, sea ice, glaciers and ice sheets. With a heightened interest in understanding the impacts of a changing climate on snow and ice processes, quantifying the impact of biological impurities on ice and snow albedo (bioalbedo) and its evolution through time is a rapidly growing field of research. However, rigorous quantification of bioalbedo has remained elusive because of difficulties in isolating the biological contribution to ice albedo from that of inorganic impurities and the variable optical properties of the ice itself. For this reason, isolation of the biological signature in reflectance data obtained from aerial/orbital platforms has not been achieved, even when ground-based biological measurements have been available. This paper provides the cell-specific optical properties that are required to model the spectral signatures and broadband darkening of ice. Applying radiative transfer theory, these properties provide the physical basis needed to link biological and glaciological ground measurements with remotely sensed reflectance data. Using these new capabilities we confirm that biological impurities can influence ice albedo, then we identify 10 challenges to the measurement of bioalbedo in the field with the aim of improving future experimental designs to better quantify bioalbedo feedbacks. These challenges are (1) ambiguity in terminology, (2) characterising snow or ice optical properties, (3) characterising solar irradiance, (4) determining optical properties of cells, (5) measuring biomass, (6) characterising vertical distribution of cells, (7) characterising abiotic impurities, (8) surface anisotropy, (9) measuring indirect albedo feedbacks, and (10) measurement and instrument configurations. This paper aims to provide a broad audience of glaciologists and biologists with an overview of radiative transfer and albedo that could support future experimental design.

Contributions to Cancer Research: Finding a Niche in Communication | Office of Cancer Genomics

Cancer.gov

This past July, I started a journey into the fields of communications and cancer research when I joined the Office of Cancer Genomics (OCG) as a fellow in the National Cancer Institute (NCI) Health Communications Internship Program (HCIP). Cancer genomics and working in an office were new and uncharted territory for me: before I came to OCG, I was finishing a Ph.D. in cell biology at Vanderbilt University in Dr. Matthew Tyska’s laboratory.

Recent advances in designed coiled coils and helical bundles with inorganic prosthetic groups-from structural to functional applications.

PubMed

Peacock, Anna Fa

2016-04-01

Recent contributions to the de novo design of metalloproteins based on coiled coils and helical bundles are described herein, with examples covering mononuclear, multinuclear, and metallo-porphyrin sites, as well as membrane soluble designs. Important progress is being made in the field with a diverse range of functionalities, sometimes beyond those found in biology, being successfully engineered into these simplified scaffolds and represents an exciting prospect for the future. Copyright © 2016 Elsevier Ltd. All rights reserved.

Fundamental Studies of Electric-Field-Induced Coherent Raman Scattering

DTIC Science & Technology

2011-06-07

denote by IIR and ICARS , may be written [1,5] as   22121 EIINNCI exgIR  (1) and   22122 IINNCI exgCARS  , (2) where C1 and C2 are...biological applications [8-11], and aerodynamic controls [12]. A better understanding of the discharge mechanisms of such plasmas is expected to contribute to...the development of better plasma generation systems specific for each application. When APPs are used with low gas temperature, plasmas are

Plant developmental biologists meet on stairways in Matera.

PubMed

Beeckman, Tom; Friml, Jiri

2012-10-01

The third EMBO Conference on Plant Molecular Biology, which focused on 'Plant development and environmental interactions', was held in May 2012 in Matera, Italy. Here, we review some of the topics and themes that emerged from the various contributions; namely, steering technologies, transcriptional networks and hormonal regulation, small RNAs, cell and tissue polarity, environmental control and natural variation. We intend to provide the reader who might have missed this remarkable event with a glimpse of the recent progress made in this blossoming research field.

Metabolomic Analysis in Heart Failure.

PubMed

Ikegami, Ryutaro; Shimizu, Ippei; Yoshida, Yohko; Minamino, Tohru

2017-12-25

It is thought that at least 6,500 low-molecular-weight metabolites exist in humans, and these metabolites have various important roles in biological systems in addition to proteins and genes. Comprehensive assessment of endogenous metabolites is called metabolomics, and recent advances in this field have enabled us to understand the critical role of previously unknown metabolites or metabolic pathways in the cardiovascular system. In this review, we will focus on heart failure and how metabolomic analysis has contributed to improving our understanding of the pathogenesis of this critical condition.

Biologically inspired autonomous structural materials with controlled toughening and healing

NASA Astrophysics Data System (ADS)

Garcia, Michael E.; Sodano, Henry A.

2010-04-01

The field of structural health monitoring (SHM) has made significant contributions in the field of prognosis and damage detection in the past decade. The advantageous use of this technology has not been integrated into operational structures to prevent damage from propagating or to heal injured regions under real time loading conditions. Rather, current systems relay this information to a central processor or human operator, who then determines a course of action such as altering the mission or scheduling repair maintenance. Biological systems exhibit advanced sensory and healing traits that can be applied to the design of material systems. For instance, bone is the major structural component in vertebrates; however, unlike modern structural materials, bone has many properties that make it effective for arresting the propagation of cracks and subsequent healing of the fractured area. The foremost goal for the development of future adaptive structures is to mimic biological systems, similar to bone, such that the material system can detect damage and deploy defensive traits to impede damage from propagating, thus preventing catastrophic failure while in operation. After sensing and stalling the propagation of damage, the structure must then be repaired autonomously using self healing mechanisms motivated by biological systems. Here a novel autonomous system is developed using shape memory polymers (SMPs), that employs an optical fiber network as both a damage detection sensor and a network to deliver stimulus to the damage site initiating adaptation and healing. In the presence of damage the fiber optic fractures allowing a high power laser diode to deposit a controlled level of thermal energy at the fractured sight locally reducing the modulus and blunting the crack tip, which significantly slows the crack growth rate. By applying a pre-induced strain field and utilizing the shape memory recovery effect, thermal energy can be deployed to close the crack and return the system to its original operating state. The entire system will effectively detect, self toughen, and subsequently heal damage as biological materials such as bone does.

Information Complexity and Biology

NASA Astrophysics Data System (ADS)

Bagnoli, Franco; Bignone, Franco A.; Cecconi, Fabio; Politi, Antonio

Kolmogorov contributed directly to Biology in essentially three problems: the analysis of population dynamics (Lotka-Volterra equations), the reaction-diffusion formulation of gene spreading (FKPP equation), and some discussions about Mendel's laws. However, the widely recognized importance of his contribution arises from his work on algorithmic complexity. In fact, the limited direct intervention in Biology reflects the generally slow growth of interest of mathematicians towards biological issues. From the early work of Vito Volterra on species competition, to the slow growth of dynamical systems theory, contributions to the study of matter and the physiology of the nervous system, the first 50-60 years have witnessed important contributions, but as scattered pieces apparently uncorrelated, and in branches often far away from Biology. Up to the 40' it is hard to see the initial loose build up of a convergence, for those theories that will become mainstream research by the end of the century, and connected by the study of biological systems per-se.

Activins in reproductive biology and beyond.

PubMed

Wijayarathna, R; de Kretser, D M

2016-04-01

Activins are members of the pleiotrophic family of the transforming growth factor-beta (TGF-β) superfamily of cytokines, initially isolated for their capacity to induce the release of FSH from pituitary extracts. Subsequent research has demonstrated that activins are involved in multiple biological functions including the control of inflammation, fibrosis, developmental biology and tumourigenesis. This review summarizes the current knowledge on the roles of activin in reproductive and developmental biology. It also discusses interesting advances in the field of modulating the bioactivity of activins as a therapeutic target, which would undoubtedly be beneficial for patients with reproductive pathology. A comprehensive literature search was carried out using PUBMED and Google Scholar databases to identify studies in the English language which have contributed to the advancement of the field of activin biology, since its initial isolation in 1987 until July 2015. 'Activin', 'testis', 'ovary', 'embryonic development' and 'therapeutic targets' were used as the keywords in combination with other search phrases relevant to the topic of activin biology. Activins, which are dimers of inhibin β subunits, act via a classical TGF-β signalling pathway. The bioactivity of activin is regulated by two endogenous inhibitors, inhibin and follistatin. Activin is a major regulator of testicular and ovarian development. In the ovary, activin A promotes oocyte maturation and regulates granulosa cell steroidogenesis. It is also essential in endometrial repair following menstruation, decidualization and maintaining pregnancy. Dysregulation of the activin-follistatin-inhibin system leads to disorders of female reproduction and pregnancy, including polycystic ovary syndrome, ectopic pregnancy, miscarriage, fetal growth restriction, gestational diabetes, pre-eclampsia and pre-term birth. Moreover, a rise in serum activin A, accompanied by elevated FSH, is characteristic of female reproductive aging. In the male, activin A is an autocrine and paracrine modulator of germ cell development and Sertoli cell proliferation. Disruption of normal activin signalling is characteristic of many tumours affecting reproductive organs, including endometrial carcinoma, cervical cancer, testicular and ovarian cancer as well as prostate cancer. While activin A and B aid the progression of many tumours of the reproductive organs, activin C acts as a tumour suppressor. Activins are important in embryonic induction, morphogenesis of branched glandular organs, development of limbs and nervous system, craniofacial and dental development and morphogenesis of the Wolffian duct. The field of activin biology has advanced considerably since its initial discovery as an FSH stimulating agent. Now, activin is well known as a growth factor and cytokine that regulates many aspects of reproductive biology, developmental biology and also inflammation and immunological mechanisms. Current research provides evidence for novel roles of activins in maintaining the structure and function of reproductive and other organ systems. The fact that activin A is elevated both locally as well as systemically in major disorders of the reproductive system makes it an important biomarker. Given the established role of activin A as a pro-inflammatory and pro-fibrotic agent, studies of its involvement in disorders of reproduction resulting from these processes should be examined. Follistatin, as a key regulator of the biological actions of activin, should be evaluated as a therapeutic agent in conditions where activin A overexpression is established as a contributing factor. © The Author 2016. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Mapping the Emergence of Synthetic Biology

PubMed Central

2016-01-01

In this paper, we apply an original scientometric analyses to a corpus comprising synthetic biology (SynBio) publications in Thomson Reuters Web of Science to characterize the emergence of this new scientific field. Three results were drawn from this empirical investigation. First, despite the exponential growth of publications, the study of population level statistics (newcomers proportion, collaboration network structure) shows that SynBio has entered a stabilization process since 2010. Second, the mapping of textual and citational networks shows that SynBio is characterized by high heterogeneity and four different approaches: the central approach, where biobrick engineering is the most widespread; genome engineering; protocell creation; and metabolic engineering. We suggest that synthetic biology acts as an umbrella term allowing for the mobilization of resources, and also serves to relate scientific content and promises of applications. Third, we observed a strong intertwinement between epistemic and socio-economic dynamics. Measuring scientific production and impact and using structural analysis data, we identified a core set of mostly American scientists. Biographical analysis shows that these central and influential scientists act as “boundary spanners,” meaning that their importance to the field lies not only in their academic contributions, but also in their capacity to interact with other social spaces that are outside the academic sphere. PMID:27611324

[Construction of individual-based ecological model for Scomber japonicas at its early growth stages in East China Sea].

PubMed

Li, Yue-Song; Chen, Xin-Jun; Yang, Hong

2012-06-01

By adopting FVCOM-simulated 3-D physical field and based on the biological processes of chub mackerel (Scomber japonicas) in its early life history from the individual-based biological model, the individual-based ecological model for S. japonicas at its early growth stages in the East China Sea was constructed through coupling the physical field in March-July with the biological model by the method of Lagrange particle tracking. The model constructed could well simulate the transport process and abundance distribution of S. japonicas eggs and larvae. The Taiwan Warm Current, Kuroshio, and Tsushima Strait Warm Current directly affected the transport process and distribution of the eggs and larvae, and indirectly affected the growth and survive of the eggs and larvae through the transport to the nursery grounds with different water temperature and foods. The spawning grounds in southern East China Sea made more contributions to the recruitment to the fishing grounds in northeast East China Sea, but less to the Yangtze estuary and Zhoushan Island. The northwestern and southwestern parts of spawning grounds had strong connectivity with the nursery grounds of Cheju and Tsushima Straits, whereas the northeastern and southeastern parts of the spawning ground had strong connectivity with the nursery grounds of Kyushu and Pacific Ocean.

In memoriam : Miriam Dorothy (Posner) Finkel (1916-1999).

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

Reilly, C. A.; Environmental Research

Miriam P. Finkel, pioneer radiobiologist, passed away on August 20, 1999, at her home in Tucson, AZ. She was born on January 22, 1916, in Chicago to Russian immigrants. She spent much of her youth in Davenport, IA. She returned to Chicago for her college education, and received a B.S. in zoology in 1938 from the University of Chicago. While continuing her formal education in zoology, Miriam served as a laboratory instructor at Wilson Junior College. She received her Ph.D. in 1944 from the University of Chicago. She began her scientific career at the dawning of the nuclear age andmore » seized upon the scientific opportunity present in the new field of radiobiology to be a life-long contributor to the understanding of the biological effects of radiation. Her technical insights and discoveries helped form the foundation for many of the health standards (i.e. permissible levels of internal radionuclide exposure) in use today. She also made a significant contribution to the field of molecular biology. Her isolation of a murine osteogenic sarcoma virus, the Finkel-Biskis-Jenkins or FBJ virus, led to fundamental discoveries in viral-induced tumors and ultimately provided the now universally used molecular biological tool, the FOS gene.« less

Applications of next-generation sequencing to blood and marrow transplantation.

PubMed

Chapman, Michael; Warren, Edus H; Wu, Catherine J

2012-01-01

Since the advent of next-generation sequencing (NGS) in 2005, there has been an explosion of published studies employing the technology to tackle previously intractable questions in many disparate biological fields. This has been coupled with technology development that has occurred at a remarkable pace. This review discusses the potential impact of this new technology on the field of blood and marrow stem cell transplantation. Hematologic malignancies have been among the forefront of those cancers whose genomes have been the subject of NGS. Hence, these studies have opened novel areas of biology that can be exploited for prognostic, diagnostic, and therapeutic means. Because of the unprecedented depth, resolution and accuracy achievable by NGS, this technology is well-suited for providing detailed information on the diversity of receptors that govern antigen recognition; this approach has the potential to contribute important insights into understanding the biologic effects of transplantation. Finally, the ability to perform comprehensive tumor sequencing provides a systematic approach to the discovery of genetic alterations that can encode peptides with restricted tumor expression, and hence serve as potential target antigens of graft-versus-leukemia responses. Altogether, this increasingly affordable technology will undoubtedly impact the future practice and care of patients with hematologic malignancies. Copyright © 2012 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.

A field reciprocal transplant experiment reveals asymmetric costs of migration between lake and river ecotypes of three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

Kaufmann, J; Lenz, T L; Kalbe, M; Milinski, M; Eizaguirre, C

2017-05-01

Theory of local adaptation predicts that nonadapted migrants will suffer increased costs compared to local residents. Ultimately this process can result in the reduction of gene flow and culminate in speciation. Here, we experimentally investigated the relative fitness of migrants in foreign habitats, focusing on diverging lake and river ecotypes of three-spined sticklebacks. A reciprocal transplant experiment performed in the field revealed asymmetric costs of migration: whereas mortality of river fish was increased under lake conditions, lake migrants suffered from reduced growth relative to river residents. Selection against migrants thus involved different traits in each habitat but generally contributed to bidirectional reduction in gene flow. Focusing particularly on the parasitic environments, migrant fish differed from resident fish in the parasite community they harboured. This pattern correlated with both cellular phenotypes of innate immunity as well as with allelic variation at the genes of the major histocompatibility complex. In addition to showing the costs of migration in three-spined sticklebacks, this study highlights the role of asymmetric selection particularly from parasitism in genotype sorting and in the emergence of local adaptation. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Chasing Ghosts in Space Radiobiology Research: The Lost Focus on Non-Targeted Effects

NASA Astrophysics Data System (ADS)

Cucinotta, Francis; Saganti, Premkumar; Cacao, Eliedonna

2016-07-01

The doses and dose-rates of astronaut exposures to galactic cosmic rays (GCR) are accurately known, and lead to particle hits per cell nucleus from high charge and energy (HZE) particles of much less than one hit per cell per week. A large number of experiments have shown that additivity of biological effects is a valid assumption for space radiation exposures, while experiments at higher doses and dose-rates than occur in space continue to be a focus of the majority of space radiobiology research. Furthermore HZE particle exposures with mono-energetic particles manifest themselves as a mixed-radiation field due to the contributions of delta-rays and the random impact parameter of a particles track core to DNA and non-DNA targets in cells and tissues. The mixed-field manifestation of mono-energetic HZE particle exposures is well known from theoretical studies of microdosimetry and track structure. Additional mixed-field effects occur for single species experiments due to nuclear fragmentation in particle accelerator beam-lines and biological samples along with energy straggling. In contrast to these well known aspects of space radiobiology there are many open questions on the contribution of non-targeted effects to low dose and dose-rate exposures. Non-targeted effects (NTEs) include bystander effects and genomic instability, and have been shown to be the most important outstanding question for reducing uncertainties in space radiation cancer risk assessment. The dose-rate and radiation quality dependence of NTE's has not been established, while there is an over-arching need to develop 21st century experimental models of human cancer risk. We review possible mechanisms of NTE's and how new experiments to address these issues could be designed.

Carbon budgets of biological soil crusts at micro-, meso-, and global scales

USGS Publications Warehouse

Sancho, Leopoldo G; Belnap, Jayne; Colesie, Claudia; Raggio, Jose; Weber, Bettina

2016-01-01

The importance of biocrusts in the ecology of arid lands across all continents is widely recognized. In spite of this broad distribution, contributions of biocrusts to the global biogeochemical cycles have only recently been considered. While these studies opened a new view on the global role of biocrusts, they also clearly revealed the lack of data for many habitats and of overall standards for measurements and analysis. In order to understand carbon cycling in biocrusts and the progress which has been made during the last 15 years, we offer a multi-scale approach covering different climatic regions. We also include a discussion on available measurement techniques at each scale: A micro-scale section focuses on the individual organism level, including modeling based on the combination of field and lab data. The meso-scale section addresses the CO2 exchange of a complete ecosystem or at the community level. Finally, we consider the contribution of biocrusts at a global scale, giving a general perspective of the most relevant findings regarding the role of biological soil crusts in the global terrestrial carbon cycle.

On the biological basis of musicality.

PubMed

Honing, Henkjan

2018-03-15

In recent years, music and musicality have been the focus of an increasing amount of research effort. This has led to a growing role and visibility of the contribution of (bio)musicology to the field of neuroscience and cognitive sciences at large. While it has been widely acknowledged that there are commonalities between speech, language, and musicality, several researchers explain this by considering musicality as an epiphenomenon of language. However, an alternative hypothesis is that musicality is an innate and widely shared capacity for music that can be seen as a natural, spontaneously developing set of traits based on and constrained by our cognitive abilities and their underlying biology. A comparative study of musicality in humans and well-known animal models (monkeys, birds, pinnipeds) will further our insights on which features of musicality are exclusive to humans and which are shared between humans and nonhuman animals, contribute to an understanding of the musical phenotype, and further constrain existing evolutionary theories of music and musicality. © 2018 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

Identifying gene networks underlying the neurobiology of ethanol and alcoholism.

PubMed

Wolen, Aaron R; Miles, Michael F

2012-01-01

For complex disorders such as alcoholism, identifying the genes linked to these diseases and their specific roles is difficult. Traditional genetic approaches, such as genetic association studies (including genome-wide association studies) and analyses of quantitative trait loci (QTLs) in both humans and laboratory animals already have helped identify some candidate genes. However, because of technical obstacles, such as the small impact of any individual gene, these approaches only have limited effectiveness in identifying specific genes that contribute to complex diseases. The emerging field of systems biology, which allows for analyses of entire gene networks, may help researchers better elucidate the genetic basis of alcoholism, both in humans and in animal models. Such networks can be identified using approaches such as high-throughput molecular profiling (e.g., through microarray-based gene expression analyses) or strategies referred to as genetical genomics, such as the mapping of expression QTLs (eQTLs). Characterization of gene networks can shed light on the biological pathways underlying complex traits and provide the functional context for identifying those genes that contribute to disease development.

2017 Outstanding Contributions to ISCB Award: Fran Lewitter.

PubMed

Fogg, Christiana N; Kovats, Diane E; Berger, Bonnie

2017-01-01

The Outstanding Contributions to the International Society for Computational Biology (ISCB) Award was launched in 2015 to recognize individuals who have made lasting and valuable contributions to the Society through their leadership, service, and educational work, or a combination of these areas. Fran Lewitter is the 2017 winner of the Outstanding Contributions to ISCB Award and will be recognized at the 2017 Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology, meeting in Prague, Czech Republic being held from July 21-25, 2017.

2017 Outstanding Contributions to ISCB Award: Fran Lewitter

PubMed Central

Fogg, Christiana N.; Kovats, Diane E.; Berger, Bonnie

2017-01-01

The Outstanding Contributions to the International Society for Computational Biology (ISCB) Award was launched in 2015 to recognize individuals who have made lasting and valuable contributions to the Society through their leadership, service, and educational work, or a combination of these areas. Fran Lewitter is the 2017 winner of the Outstanding Contributions to ISCB Award and will be recognized at the 2017 Intelligent Systems for Molecular Biology (ISMB)/European Conference on Computational Biology, meeting in Prague, Czech Republic being held from July 21-25, 2017. PMID:28713545

[Biogeography: geography or biology?].

PubMed

Kafanov, A I

2009-01-01

General biogeography is an interdisciplinary science, which combines geographic and biological aspects constituting two distinct research fields: biological geography and geographic biology. These fields differ in the nature of their objects of study, employ different methods and represent Earth sciences and biological sciences, respectively. It is suggested therefore that the classification codes for research fields and the state professional education standard should be revised.

Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology.

PubMed

Zhou, Jie; Du, Xuewen; Xu, Bing

2015-01-01

Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine.

Prion-like nanofibrils of small molecules (PriSM): A new frontier at the intersection of supramolecular chemistry and cell biology

PubMed Central

Zhou, Jie; Du, Xuewen; Xu, Bing

2015-01-01

Abstract Formed by non-covalent interactions and not defined at genetic level, the assemblies of small molecules in biology are complicated and less explored. A common morphology of the supramolecular assemblies of small molecules is nanofibrils, which coincidentally resembles the nanofibrils formed by proteins such as prions. So these supramolecular assemblies are termed as prion-like nanofibrils of small molecules (PriSM). Emerging evidence from several unrelated fields over the past decade implies the significance of PriSM in biology and medicine. This perspective aims to highlight some recent advances of the research on PriSM. This paper starts with description of the intriguing similarities between PriSM and prions, discusses the paradoxical features of PriSM, introduces the methods for elucidating the biological functions of PriSM, illustrates several examples of beneficial aspects of PriSM, and finishes with the promises and current challenges in the research of PriSM. We anticipate that the research of PriSM will contribute to the fundamental understanding at the intersection of supramolecular chemistry and cell biology and ultimately lead to a new paradigm of molecular (or supramolecular) therapeutics for biomedicine. PMID:25738892

The Promise of Systems Biology Approaches for Revealing Host Pathogen Interactions in Malaria

PubMed Central

Zuck, Meghan; Austin, Laura S.; Danziger, Samuel A.; Aitchison, John D.; Kaushansky, Alexis

2017-01-01

Despite global eradication efforts over the past century, malaria remains a devastating public health burden, causing almost half a million deaths annually (WHO, 2016). A detailed understanding of the mechanisms that control malaria infection has been hindered by technical challenges of studying a complex parasite life cycle in multiple hosts. While many interventions targeting the parasite have been implemented, the complex biology of Plasmodium poses a major challenge, and must be addressed to enable eradication. New approaches for elucidating key host-parasite interactions, and predicting how the parasite will respond in a variety of biological settings, could dramatically enhance the efficacy and longevity of intervention strategies. The field of systems biology has developed methodologies and principles that are well poised to meet these challenges. In this review, we focus our attention on the Liver Stage of the Plasmodium lifecycle and issue a “call to arms” for using systems biology approaches to forge a new era in malaria research. These approaches will reveal insights into the complex interplay between host and pathogen, and could ultimately lead to novel intervention strategies that contribute to malaria eradication. PMID:29201016

Transmission x-ray microscopy at Diamond-Manchester I13 Imaging Branchline

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

Vila-Comamala, Joan, E-mail: joan.vila.comamala@gmail.com; Wagner, Ulrich; Bodey, Andrew J.

2016-01-28

Full-field Transmission X-ray Microscopy (TXM) has been shown to be a powerful method for obtaining quantitative internal structural and chemical information from materials at the nanoscale. The installation of a Full-field TXM station will extend the current microtomographic capabilities of the Diamond-Manchester I13 Imaging Branchline at Diamond Light Source (UK) into the sub-100 nm spatial resolution range using photon energies from 8 to 14 keV. The dedicated Full-field TXM station will be built in-house with contributions of Diamond Light Source support divisions and via collaboration with the X-ray Optics Group of Paul Scherrer Institut (Switzerland) which will develop state-of-the-art diffractive X-raymore » optical elements. Preliminary results of the I13 Full-field TXM station are shown. The Full-field TXM will become an important Diamond Light Source direct imaging asset for material science, energy science and biology at the nanoscale.« less

Retrospective estimation of the electric and magnetic field exposure conditions in in vitro experimental reports reveal considerable potential for uncertainty.

PubMed

Portelli, Lucas A; Falldorf, Karsten; Thuróczy, György; Cuppen, Jan

2018-04-01

Experiments on cell cultures exposed to extremely low frequency (ELF, 3-300 Hz) magnetic fields are often subject to multiple sources of uncertainty associated with specific electric and magnetic field exposure conditions. Here we systemically quantify these uncertainties based on exposure conditions described in a group of bioelectromagnetic experimental reports for a representative sampling of the existing literature. The resulting uncertainties, stemming from insufficient, ambiguous, or erroneous description, design, implementation, or validation of the experimental methods and systems, were often substantial enough to potentially make any successful reproduction of the original experimental conditions difficult or impossible. Without making any assumption about the true biological relevance of ELF electric and magnetic fields, these findings suggest another contributing factor which may add to the overall variability and irreproducibility traditionally associated with experimental results of in vitro exposures to low-level ELF magnetic fields. Bioelectromagnetics. 39:231-243, 2018. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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

PubMed

Rojas-Chapana, Jose A; Giersig, Michael

2006-02-01

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

The Genetics of Sex Differences in Brain and Behavior

PubMed Central

Ngun, Tuck C; Ghahramani, Negar; Sánchez, Francisco J.; Bocklandt, Sven; Vilain, Eric

2010-01-01

Biological differences between men and women contribute to many sex-specific illnesses and disorders. Historically, it was argued that such differences were largely, if not exclusively, due to gonadal hormone secretions. However, emerging research has shown that some differences are mediated by mechanisms other than the action of these hormone secretions and in particular by products of genes located on the X and Y chromosomes, which we refer to as direct genetic effects. This paper reviews the evidence for direct genetic effects in behavioral and brain sex differences. We highlight the `four core genotypes' model and sex differences in the midbrain dopaminergic system, specifically focusing on the role of Sry. We also discuss novel research being done on unique populations including people attracted to the same sex and people with a cross-gender identity. As science continues to advance our understanding of biological sex differences, a new field is emerging that is aimed at better addressing the needs of both sexes: gender-based biology and medicine. Ultimately, the study of the biological basis for sex differences will improve healthcare for both men and women. PMID:20951723

Molecular Imaging in the Era of Personalized Medicine

PubMed Central

Jung, Kyung-Ho; Lee, Kyung-Han

2015-01-01

Clinical imaging creates visual representations of the body interior for disease assessment. The role of clinical imaging significantly overlaps with that of pathology, and diagnostic workflows largely depend on both fields. The field of clinical imaging is presently undergoing a radical change through the emergence of a new field called molecular imaging. This new technology, which lies at the intersection between imaging and molecular biology, enables noninvasive visualization of biochemical processes at the molecular level within living bodies. Molecular imaging differs from traditional anatomical imaging in that biomarkers known as imaging probes are used to visualize target molecules-of-interest. This ability opens up exciting new possibilities for applications in oncologic, neurological and cardiovascular diseases. Molecular imaging is expected to make major contributions to personalized medicine by allowing earlier diagnosis and predicting treatment response. The technique is also making a huge impact on pharmaceutical development by optimizing preclinical and clinical tests for new drug candidates. This review will describe the basic principles of molecular imaging and will briefly touch on three examples (from an immense list of new techniques) that may contribute to personalized medicine: receptor imaging, angiogenesis imaging, and apoptosis imaging. PMID:25812652

Molecular imaging in the era of personalized medicine.

PubMed

Jung, Kyung-Ho; Lee, Kyung-Han

2015-01-01

Clinical imaging creates visual representations of the body interior for disease assessment. The role of clinical imaging significantly overlaps with that of pathology, and diagnostic workflows largely depend on both fields. The field of clinical imaging is presently undergoing a radical change through the emergence of a new field called molecular imaging. This new technology, which lies at the intersection between imaging and molecular biology, enables noninvasive visualization of biochemical processes at the molecular level within living bodies. Molecular imaging differs from traditional anatomical imaging in that biomarkers known as imaging probes are used to visualize target molecules-of-interest. This ability opens up exciting new possibilities for applications in oncologic, neurological and cardiovascular diseases. Molecular imaging is expected to make major contributions to personalized medicine by allowing earlier diagnosis and predicting treatment response. The technique is also making a huge impact on pharmaceutical development by optimizing preclinical and clinical tests for new drug candidates. This review will describe the basic principles of molecular imaging and will briefly touch on three examples (from an immense list of new techniques) that may contribute to personalized medicine: receptor imaging, angiogenesis imaging, and apoptosis imaging.

Methodology for the passive detection and discrimination of chemical and biological aerosols

NASA Astrophysics Data System (ADS)

Marinelli, William J.; Shokhirev, Kirill N.; Konno, Daisei; Rossi, David C.; Richardson, Martin

2013-05-01

The standoff detection and discrimination of aerosolized biological and chemical agents has traditionally been addressed through LIDAR approaches, but sensor systems using these methods have yet to be deployed. We discuss the development and testing of an approach to detect these aerosols using the deployed base of passive infrared hyperspectral sensors used for chemical vapor detection. The detection of aerosols requires the inclusion of down welling sky and up welling ground radiation in the description of the radiative transfer process. The wavelength and size dependent ratio of absorption to scattering provides much of the discrimination capability. The approach to the detection of aerosols utilizes much of the same phenomenology employed in vapor detection; however, the sensor system must acquire information on non-line-of-sight sources of radiation contributing to the scattering process. We describe the general methodology developed to detect chemical or biological aerosols, including justifications for the simplifying assumptions that enable the development of a real-time sensor system. Mie scattering calculations, aerosol size distribution dependence, and the angular dependence of the scattering on the aerosol signature will be discussed. This methodology will then be applied to two test cases: the ground level release of a biological aerosol (BG) and a nonbiological confuser (kaolin clay) as well as the debris field resulting from the intercept of a cruise missile carrying a thickened VX warhead. A field measurement, conducted at the Utah Test and Training Range will be used to illustrate the issues associated with the use of the method.

Etiologic Field Effect: Reappraisal of the Field Effect Concept in Cancer Predisposition and Progression

PubMed Central

Lochhead, Paul; Chan, Andrew T; Nishihara, Reiko; Fuchs, Charles S; Beck, Andrew H; Giovannucci, Edward; Ogino, Shuji

2014-01-01

The term “field effect” (also known as field defect, field cancerization, or field carcinogenesis) has been used to describe a field of cellular and molecular alteration, which predisposes to the development of neoplasms within that territory. We explore an expanded, integrative concept, “etiologic field effect”, which asserts that various etiologic factors (the exposome including dietary, lifestyle, environmental, microbial, hormonal, and genetic factors) and their interactions (the interactome) contribute to a tissue microenvironmental milieu that constitutes a “field of susceptibility” to neoplasia initiation, evolution, and progression. Importantly, etiological fields predate the acquisition of molecular aberrations commonly considered to indicate presence of filed effect. Inspired by molecular pathological epidemiology (MPE) research, which examines the influence of etiologic factors on cellular and molecular alterations during disease course, an etiologically-focused approach to field effect can: 1) broaden the horizons of our inquiry into cancer susceptibility and progression at molecular, cellular, and environmental levels, during all stages of tumor evolution; 2) embrace host-environment-tumor interactions (including gene-environment interactions) occurring in the tumor microenvironment; and, 3) help explain intriguing observations, such as shared molecular features between bilateral primary breast carcinomas, and between synchronous colorectal cancers, where similar molecular changes are absent from intervening normal colon. MPE research has identified a number of endogenous and environmental exposures which can influence not only molecular signatures in the genome, epigenome, transcriptome, proteome, metabolome and interactome, but also host immunity and tumor behavior. We anticipate that future technological advances will allow the development of in vivo biosensors capable of detecting and quantifying “etiologic field effect” as abnormal network pathology patterns of cellular and microenvironmental responses to endogenous and exogenous exposures. Through an “etiologic field effect” paradigm, and holistic systems pathology (systems biology) approaches to cancer biology, we can improve personalized prevention and treatment strategies for precision medicine. PMID:24925058

Diamond-Based Magnetic Imaging with Fourier Optical Processing

NASA Astrophysics Data System (ADS)

Backlund, Mikael P.; Kehayias, Pauli; Walsworth, Ronald L.

2017-11-01

Diamond-based magnetic field sensors have attracted great interest in recent years. In particular, wide-field magnetic imaging using nitrogen-vacancy (NV) centers in diamond has been previously demonstrated in condensed matter, biological, and paleomagnetic applications. Vector magnetic imaging with NV ensembles typically requires a significant applied field (>10 G ) to resolve the contributions from four crystallographic orientations, hindering studies of magnetic samples that require measurement in low or independently specified bias fields. Here we model and measure the complex amplitude distribution of NV emission at the microscope's Fourier plane and show that by modulating this collected light at the Fourier plane, one can decompose the NV ensemble magnetic resonance spectrum into its constituent orientations by purely optical means. This decomposition effectively extends the dynamic range at a given bias field and enables wide-field vector magnetic imaging at arbitrarily low bias fields, thus broadening potential applications of NV imaging and sensing. Our results demonstrate that NV-based microscopy stands to benefit greatly from Fourier optical approaches, which have already found widespread utility in other branches of microscopy.

Lucien J. Rubinstein: enduring contributions to neuro-oncology.

PubMed

Mut, Melike; Lopes, M Beatriz S; Shaffrey, Mark

2005-04-15

Dr. Lucien Rubinstein is best remembered for his significant contributions to the field of neuropathology, particularly in the classification of nervous system tumors. His accomplishments in basic neuro-oncology and in the formulation of diagnostic principles reflected a unique talent for synthesizing fundamental clinicopathological concepts based on skillful diagnostic investigation and a thorough understanding of neurobiology. Dr. Rubinstein was the leader in the establishment of cell cultures from central nervous system (CNS) tumors. He meticulously analyzed both light and electron microscopic features of CNS tumors, recorded his findings, and patiently drew sketches to be shared generously with his colleagues and students. As a pioneer in neuropathology, in his work Dr. Rubinstein set the foundation for many enduring concepts in neurosurgery, neuro-oncology, neurology, and basic tumor biology.

Concise review: modeling central nervous system diseases using induced pluripotent stem cells.

PubMed

Zeng, Xianmin; Hunsberger, Joshua G; Simeonov, Anton; Malik, Nasir; Pei, Ying; Rao, Mahendra

2014-12-01

Induced pluripotent stem cells (iPSCs) offer an opportunity to delve into the mechanisms underlying development while also affording the potential to take advantage of a number of naturally occurring mutations that contribute to either disease susceptibility or resistance. Just as with any new field, several models of screening are being explored, and innovators are working on the most efficient methods to overcome the inherent limitations of primary cell screens using iPSCs. In the present review, we provide a background regarding why iPSCs represent a paradigm shift for central nervous system (CNS) disease modeling. We describe the efforts in the field to develop more biologically relevant CNS disease models, which should provide screening assays useful for the pharmaceutical industry. We also provide some examples of successful uses for iPSC-based screens and suggest that additional development could revolutionize the field of drug discovery. The development and implementation of these advanced iPSC-based screens will create a more efficient disease-specific process underpinned by the biological mechanism in a patient- and disease-specific manner rather than by trial-and-error. Moreover, with careful and strategic planning, shared resources can be developed that will enable exponential advances in the field. This will undoubtedly lead to more sensitive and accurate screens for early diagnosis and allow the identification of patient-specific therapies, thus, paving the way to personalized medicine. ©AlphaMed Press.

Ionizing radiation induced cataracts: Recent biological and mechanistic developments and perspectives for future research.

PubMed

Ainsbury, Elizabeth A; Barnard, Stephen; Bright, Scott; Dalke, Claudia; Jarrin, Miguel; Kunze, Sarah; Tanner, Rick; Dynlacht, Joseph R; Quinlan, Roy A; Graw, Jochen; Kadhim, Munira; Hamada, Nobuyuki

The lens of the eye has long been considered as a radiosensitive tissue, but recent research has suggested that the radiosensitivity is even greater than previously thought. The 2012 recommendation of the International Commission on Radiological Protection (ICRP) to substantially reduce the annual occupational equivalent dose limit for the ocular lens has now been adopted in the European Union and is under consideration around the rest of the world. However, ICRP clearly states that the recommendations are chiefly based on epidemiological evidence because there are a very small number of studies that provide explicit biological, mechanistic evidence at doses <2Gy. This paper aims to present a review of recently published information on the biological and mechanistic aspects of cataracts induced by exposure to ionizing radiation (IR). The data were compiled by assessing the pertinent literature in several distinct areas which contribute to the understanding of IR induced cataracts, information regarding lens biology and general processes of cataractogenesis. Results from cellular and tissue level studies and animal models, and relevant human studies, were examined. The main focus was the biological effects of low linear energy transfer IR, but dosimetry issues and a number of other confounding factors were also considered. The results of this review clearly highlight a number of gaps in current knowledge. Overall, while there have been a number of recent advances in understanding, it remains unknown exactly how IR exposure contributes to opacification. A fuller understanding of how exposure to relatively low doses of IR promotes induction and/or progression of IR-induced cataracts will have important implications for prevention and treatment of this disease, as well as for the field of radiation protection. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

PubMed

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Evolutionary Biology in Research and Control of Liver Flukes in Southeast Asia

PubMed Central

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F.; Wilcox, Bruce A.

2016-01-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. PMID:27197053

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

PubMed

de Lorenzo, Víctor; Schmidt, Markus

2018-01-25

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

More than the genes, the tumor microenvironment in neuroblastoma

PubMed Central

Borriello, Lucia; Seeger, Robert C.; Asgharzadeh, Shahab; DeClerck, Yves A.

2017-01-01

Neuroblastoma is the second most common solid tumor in children. Since the seminal discovery of the role of amplification of the MYCN oncogene in the pathogenesis of neuroblastoma in the 1980s, much focus has been on the contribution of genetic alterations in the progression of this cancer. However it is now clear that not only genetic events play a role but that the tumor microenvironment (TME) substantially contributes to the biology of neuroblastoma. In this article, we present a comprehensive review of the literature on the contribution of the TME to the ten hallmarks of cancer in neuroblastoma and discuss the mechanisms of communication between neuroblastoma cells and the TME that underlie the influence of the TME on neuroblastoma progression. We end our review by discussing how the knowledge acquired over the last two decades in this field is now leading to new clinical trials targeting the TME. PMID:26597947

More than the genes, the tumor microenvironment in neuroblastoma.

PubMed

Borriello, Lucia; Seeger, Robert C; Asgharzadeh, Shahab; DeClerck, Yves A

2016-09-28

Neuroblastoma is the second most common solid tumor in children. Since the seminal discovery of the role of amplification of the MYCN oncogene in the pathogenesis of neuroblastoma in the 1980s, much focus has been on the contribution of genetic alterations in the progression of this cancer. However it is now clear that not only genetic events play a role but that the tumor microenvironment (TME) substantially contributes to the biology of neuroblastoma. In this article, we present a comprehensive review of the literature on the contribution of the TME to the ten hallmarks of cancer in neuroblastoma and discuss the mechanisms of communication between neuroblastoma cells and the TME that underlie the influence of the TME on neuroblastoma progression. We end our review by discussing how the knowledge acquired over the last two decades in this field is now leading to new clinical trials targeting the TME. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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

David Kisailus; Lara Estroff; Himadri S. Gupta

The technical presentations and discussions at this symposium disseminated and assessed current research and defined future directions in biomaterials research, with a focus on structure-function relationships in biological and biomimetic composites. The invited and contributed talks covered a diverse range of topics from fundamental biology, physics, chemistry, and materials science to potential applications in developing areas such as light-weight composites, multifunctional and smart materials, biomedical engineering, and nanoscaled sensors. The invited speakers were chosen to create a stimulating program with a mixture of established and junior faculty, industrial and academic researchers, and American and international experts in the field. Thismore » symposium served as an excellent introduction to the area for younger scientists (graduate students and post-doctoral researchers). Direct interactions between participants also helped to promote potential future collaborations involving multiple disciplines and institutions.« less

Reading and Language Disorders: The Importance of Both Quantity and Quality

PubMed Central

Newbury, Dianne F.; Monaco, Anthony P.; Paracchini, Silvia

2014-01-01

Reading and language disorders are common childhood conditions that often co-occur with each other and with other neurodevelopmental impairments. There is strong evidence that disorders, such as dyslexia and Specific Language Impairment (SLI), have a genetic basis, but we expect the contributing genetic factors to be complex in nature. To date, only a few genes have been implicated in these traits. Their functional characterization has provided novel insight into the biology of neurodevelopmental disorders. However, the lack of biological markers and clear diagnostic criteria have prevented the collection of the large sample sizes required for well-powered genome-wide screens. One of the main challenges of the field will be to combine careful clinical assessment with high throughput genetic technologies within multidisciplinary collaborations. PMID:24705331

A quick guide for building a successful bioinformatics community.

PubMed

Budd, Aidan; Corpas, Manuel; Brazas, Michelle D; Fuller, Jonathan C; Goecks, Jeremy; Mulder, Nicola J; Michaut, Magali; Ouellette, B F Francis; Pawlik, Aleksandra; Blomberg, Niklas

2015-02-01

"Scientific community" refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop "The 'How To Guide' for Establishing a Successful Bioinformatics Network" at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB).

Physics and Its Interfaces with Medicinal Chemistry and Drug Design

NASA Astrophysics Data System (ADS)

Santos, Ricardo N.; Andricopulo, Adriano D.

2013-08-01

Medicinal chemistry is a multidisciplinary subject that integrates knowledge from a variety of fields of science, including, but not limited to, chemistry, biology, and physics. The area of drug design involves the cooperative work of scientists with a diverse range of backgrounds and technical skills, trying to tackle complex problems using an integration of approaches and methods. One important contribution to this field comes from physics through studies that attempt to identify and quantify the molecular interactions between small molecules (drugs) and biological targets (receptors), such as the forces that govern the interactions, the thermodynamics of the drug-receptor interactions, and so on. In this context, the interfaces of physics, medicinal chemistry, and drug design are of vital importance for the development of drugs that not only have the right chemistry but also the right intermolecular properties to interact at the macromolecular level, providing useful information about the principles and molecular mechanisms underlying the therapeutic action of drugs. This article highlights some of the most important connections between physics and medicinal chemistry in the design of new drugs.

Plant Genome Size Research: A Field In Focus

PubMed Central

BENNETT, M. D.; LEITCH, I. J.

2005-01-01

This Special Issue contains 18 papers arising from presentations at the Second Plant Genome Size Workshop and Discussion Meeting (hosted by the Royal Botanic Gardens, Kew, 8–12 September, 2003). This preface provides an overview of these papers, setting their key contents in the broad framework of this highly active field. It also highlights a few overarching issues with wide biological impact or interest, including (1) the need to unify terminology relating to C-value and genome size, (2) the ongoing quest for accurate gold standards for accurate plant genome size estimation, (3) how knowledge of species' DNA amounts has increased in recent years, (4) the existence, causes and significance of intraspecific variation, (5) recent progress in understanding the mechanisms and evolutionary patterns of genome size change, and (6) the impact of genome size knowledge on related biological activities such as genetic fingerprinting and quantitative genetics. The paper offers a vision of how increased knowledge and understanding of genome size will contribute to holisitic genomic studies in both plants and animals in the next decade. PMID:15596455

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders

PubMed Central

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J.

2014-01-01

Abstract. Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed. PMID:26157976

Establishment of the Vertebrate Germ Layers.

PubMed

Tseng, Wei-Chia; Munisha, Mumingjiang; Gutierrez, Juan B; Dougan, Scott T

2017-01-01

The process of germ layer formation is a universal feature of animal development. The germ layers separate the cells that produce the internal organs and tissues from those that produce the nervous system and outer tissues. Their discovery in the early nineteenth century transformed embryology from a purely descriptive field into a rigorous scientific discipline, in which hypotheses could be tested by observation and experimentation. By systematically addressing the questions of how the germ layers are formed and how they generate overall body plan, scientists have made fundamental contributions to the fields of evolution, cell signaling, morphogenesis, and stem cell biology. At each step, this work was advanced by the development of innovative methods of observing cell behavior in vivo and in culture. Here, we take an historical approach to describe our current understanding of vertebrate germ layer formation as it relates to the long-standing questions of developmental biology. By comparing how germ layers form in distantly related vertebrate species, we find that highly conserved molecular pathways can be adapted to perform the same function in dramatically different embryonic environments.

Review of quantitative phase-digital holographic microscopy: promising novel imaging technique to resolve neuronal network activity and identify cellular biomarkers of psychiatric disorders.

PubMed

Marquet, Pierre; Depeursinge, Christian; Magistretti, Pierre J

2014-10-01

Quantitative phase microscopy (QPM) has recently emerged as a new powerful quantitative imaging technique well suited to noninvasively explore a transparent specimen with a nanometric axial sensitivity. In this review, we expose the recent developments of quantitative phase-digital holographic microscopy (QP-DHM). Quantitative phase-digital holographic microscopy (QP-DHM) represents an important and efficient quantitative phase method to explore cell structure and dynamics. In a second part, the most relevant QPM applications in the field of cell biology are summarized. A particular emphasis is placed on the original biological information, which can be derived from the quantitative phase signal. In a third part, recent applications obtained, with QP-DHM in the field of cellular neuroscience, namely the possibility to optically resolve neuronal network activity and spine dynamics, are presented. Furthermore, potential applications of QPM related to psychiatry through the identification of new and original cell biomarkers that, when combined with a range of other biomarkers, could significantly contribute to the determination of high risk developmental trajectories for psychiatric disorders, are discussed.

Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks.

PubMed

Havugimana, Pierre C; Hu, Pingzhao; Emili, Andrew

2017-10-01

Elucidation of the networks of physical (functional) interactions present in cells and tissues is fundamental for understanding the molecular organization of biological systems, the mechanistic basis of essential and disease-related processes, and for functional annotation of previously uncharacterized proteins (via guilt-by-association or -correlation). After a decade in the field, we felt it timely to document our own experiences in the systematic analysis of protein interaction networks. Areas covered: Researchers worldwide have contributed innovative experimental and computational approaches that have driven the rapidly evolving field of 'functional proteomics'. These include mass spectrometry-based methods to characterize macromolecular complexes on a global-scale and sophisticated data analysis tools - most notably machine learning - that allow for the generation of high-quality protein association maps. Expert commentary: Here, we recount some key lessons learned, with an emphasis on successful workflows, and challenges, arising from our own and other groups' ongoing efforts to generate, interpret and report proteome-scale interaction networks in increasingly diverse biological contexts.

Emerging aspects of nanotoxicology in health and disease: From agriculture and food sector to cancer therapeutics.

PubMed

Piperigkou, Zoi; Karamanou, Konstantina; Engin, Ayse Basak; Gialeli, Chrysostomi; Docea, Anca Oana; Vynios, Demitrios H; Pavão, Mauro S G; Golokhvast, Kirill S; Shtilman, Mikhail I; Argiris, Athanassios; Shishatskaya, Ekaterina; Tsatsakis, Aristidis M

2016-05-01

Nanotechnology is an evolving scientific field that has allowed the manufacturing of materials with novel physicochemical and biological properties, offering a wide spectrum of potential applications. Properties of nanoparticles that contribute to their usefulness include their markedly increased surface area in relation to mass, surface reactivity and insolubility, ability to agglomerate or change size in different media and enhanced endurance over conventional-scale substance. Here, we review nanoparticle classification and their emerging applications in several fields; from active food packaging to drug delivery and cancer research. Nanotechnology has exciting therapeutic applications, including novel drug delivery for the treatment of cancer. Additionally, we discuss that exposure to nanostructures incorporated to polymer composites, may result in potential human health risks. Therefore, the knowledge of processes, including absorption, distribution, metabolism and excretion, as well as careful toxicological assessment is critical in order to determine the effects of nanomaterials in humans and other biological systems. Expanding the knowledge of nanoparticle toxicity will facilitate designing of safer nanocomposites and their application in a beneficial manner. Copyright © 2016 Elsevier Ltd. All rights reserved.

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology.

PubMed

Bonham, Kevin S; Stefan, Melanie I

2017-10-01

While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance.

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

PubMed

Medina, Miguel Ángel

2013-03-01

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

Interactive learning and action: realizing the promise of synthetic biology for global health.

PubMed

Betten, A Wieke; Roelofsen, Anneloes; Broerse, Jacqueline E W

2013-09-01

The emerging field of synthetic biology has the potential to improve global health. For example, synthetic biology could contribute to efforts at vaccine development in a context in which vaccines and immunization have been identified by the international community as being crucial to international development efforts and, in particular, the millennium development goals. However, past experience with innovations shows that realizing a technology's potential can be difficult and complex. To achieve better societal embedding of synthetic biology and to make sure it reaches its potential, science and technology development should be made more inclusive and interactive. Responsible research and innovation is based on the premise that a broad range of stakeholders with different views, needs and ideas should have a voice in the technological development and deployment process. The interactive learning and action (ILA) approach has been developed as a methodology to bring societal stakeholders into a science and technology development process. This paper proposes an ILA in five phases for an international effort, with national case studies, to develop socially robust applications of synthetic biology for global health, based on the example of vaccine development. The design is based on results of a recently initiated ILA project on synthetic biology; results from other interactive initiatives described in the literature; and examples of possible applications of synthetic biology for global health that are currently being developed.

High-throughput Crystallography for Structural Genomics

PubMed Central

Joachimiak, Andrzej

2009-01-01

Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

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

PubMed

Gausemeier, Bernd

2010-01-01

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

[Industry regulation and its relationship to the rapid marketing of medical devices].

PubMed

Matsuoka, Atsuko

2012-01-01

In the market of medical devices, non-Japanese products hold a large part even in Japan. To overcome this situation, the Japanese government has been announcing policies to encourage the medical devices industry, such as the 5-year strategy for medical innovation (June 6, 2012). The Division of Medical Devices has been contributing to rapid marketing of medical devices by working out the standards for approval review and accreditation of medical devices, guidances on evaluation of medical devices with emerging technology, and test methods for biological safety evaluation of medical devices, as a part of practice in the field of regulatory science. The recent outcomes are 822 standards of accreditation for Class II medical devices, 14 guidances on safety evaluation of medical devices with emerging technology, and the revised test methods for biological safety evaluation (MHLW Notification by Director, OMDE, Yakushokuki-hatsu 0301 No. 20 "Basic Principles of Biological Safety Evaluation Required for Application for Approval to Market Medical Devices").

[Problems of world outlook and methodology of science integration in biological studies].

PubMed

Khododova, Iu D

1981-01-01

Problems of worldoutlook and methodology of the natural-science knowledge are considered basing on the analysis of tendencies in the development of the membrane theory of cell processes and the use of principles of biological membrane functioning when solving some scientific and applied problems pertaining to different branches of chemistry and biology. The notion scientific knowledge integration is defined as interpenetration of approaches, methods and ideas of different branches of knowledge and enrichment on this basis of their content resulting in knowledge augmentation in each field taken separately. These processes are accompanied by appearance of new branches of knowledge - sciences "on junction" and their subsequent differentiations. The analysis of some gnoseological situations shows that integration of sciences contributes to coordination and some agreement of thinking styles of different specialists, puts forward keen personality of a scientist demanding, in particular, his high professional mobility. Problems of scientific activity organization are considered, which involve social sciences into the integration processes. The role of philosophy in the integration processes is emphasized.

Chemistry and biology of natural and designed enediynes.

PubMed Central

Nicolaou, K C; Smith, A L; Yue, E W

1993-01-01

Ever since the initial reports of the enediyne anticancer antibiotics in the late 1980s, researchers from a number of disciplines have been devoting increasing attention to their chemistry, biology, and potential medical applications. Synthetic chemists and molecular designers have been engaged in attempts to synthesize these molecules and to model their unique architecture. Considerable efforts have been directed at understanding and mimicking the various processes involved in the targeting, activation, and DNA cleavage associated with these natural products. This review summarizes the main contributions to the field, with particular emphasis on work from our laboratories. Highlights include studies of the Bergman reaction, which is central to the mechanism of action of enediynes, the design and chemical synthesis of a number of these systems, and biological studies with selected molecules. Finally, the total synthesis of calicheamicin gamma 1I, the most prominent member of this class of naturally occurring compounds, is discussed. Images Fig. 2 Fig. 5 Fig. 6 PMID:8327459

Coffee berry borer Hypothenemus hampei (Coleoptera: Curculionidae): searching for sustainable control strategies.

PubMed

Jaramillo, J; Borgemeister, C; Baker, P

2006-06-01

The coffee berry borer Hypothenemus hampei (Ferrari) is the most serious pest of the world's most valuable tropical export crop. Since the last review on this insect was published six years ago, many new studies have contributed to an improved insight into the biology and ecology of the beetle, and have indicated new avenues for integrated and biological control. The latest developments in research, both laboratory and field, on the pest, its natural enemies and their implications for integrated control of H. hampei are summarized, with a particular focus on the situation in The Americas. Lately, the global coffee industry has changed radically; it has suffered a long cycle of lowest-ever world market prices caused by overproduction and technological change. At the same time, the advent of sustainable certification schemes has had a major impact on the industry. The role of integrated pest management and biological control of H. hampei in an era of changes in the coffee industry is discussed.

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

PubMed Central

Jedlicka, Peter

2017-01-01

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system’s behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics. PMID:29163041

Geogenic lead isotope signatures from meat products in Great Britain: Potential for use in food authentication and supply chain traceability.

PubMed

Evans, Jane A; Pashley, Vanessa; Richards, Gemma J; Brereton, Nicola; Knowles, Toby G

2015-12-15

This paper presents lead (Pb) isotope data from samples of farm livestock raised in three areas of Britain that have elevated natural Pb levels: Central Wales, the Mendips and the Derbyshire Peak District. This study highlights three important observations; that the Pb found in modern British meat from these three areas is geogenic and shows no clear evidence of modern tetraethyl anthropogenic Pb contribution; that the generally excellent match between the biological samples and the ore field data, particularly for the Mendip and Welsh data, suggests that this technique might be used to provenance biological products to specific ore sites, under favourable conditions; and that modern systems reflect the same process of biosphere averaging that is analogous to cultural focusing in human archaeological studies that is the process of biological averaging leading to an homogenised isotope signature with increasing Pb concentration. Copyright © 2015. Published by Elsevier B.V.

``Recycling'' Geophysics: Monitoring and Isotopic Analysis of Engineered Biological Systems

NASA Astrophysics Data System (ADS)

Doherty, R.; Singh, K. P.; Ogle, N.; Ntarlagiannis, D.

2010-12-01

The emerging sub discipline of biogeophysics has provoked debate on the mechanisms of microbial processes that may contribute to geophysical signatures. At field scales geophysical signatures are often non unique due to the many parameters (physical, chemical, and biological) that are involved. It may be easier to apply geophysical techniques such as electrodic potential (EP), self potential (SP) and induced polarization (IP) to engineered biological systems where there is a degree of control over the design of the physical and chemical domain. Here we present results of a column experiment that was designed to anaerobically biodegrade dissolved organic matter in landfill leachate. The column utilises a recycled porous media (concrete) to help sequester organic carbon. Electrodic potential, self potential and induced polarisation are used in conjunction with chemical and isotopic techniques to monitor the effectiveness of this approach. Preliminary carbon and oxygen isotopic analysis on concrete from the column in contact with leachate show isotopic enrichment suggesting abiotic precipitation of carbonates.

Revisiting the Quantum Brain Hypothesis: Toward Quantum (Neuro)biology?

PubMed

Jedlicka, Peter

2017-01-01

The nervous system is a non-linear dynamical complex system with many feedback loops. A conventional wisdom is that in the brain the quantum fluctuations are self-averaging and thus functionally negligible. However, this intuition might be misleading in the case of non-linear complex systems. Because of an extreme sensitivity to initial conditions, in complex systems the microscopic fluctuations may be amplified and thereby affect the system's behavior. In this way quantum dynamics might influence neuronal computations. Accumulating evidence in non-neuronal systems indicates that biological evolution is able to exploit quantum stochasticity. The recent rise of quantum biology as an emerging field at the border between quantum physics and the life sciences suggests that quantum events could play a non-trivial role also in neuronal cells. Direct experimental evidence for this is still missing but future research should address the possibility that quantum events contribute to an extremely high complexity, variability and computational power of neuronal dynamics.

Development and Mining of a Volatile Organic Compound Database

PubMed Central

Abdullah, Azian Azamimi; Ono, Naoaki; Sugiura, Tadao; Morita, Aki Hirai; Katsuragi, Tetsuo; Muto, Ai; Nishioka, Takaaki; Kanaya, Shigehiko

2015-01-01

Volatile organic compounds (VOCs) are small molecules that exhibit high vapor pressure under ambient conditions and have low boiling points. Although VOCs contribute only a small proportion of the total metabolites produced by living organisms, they play an important role in chemical ecology specifically in the biological interactions between organisms and ecosystems. VOCs are also important in the health care field as they are presently used as a biomarker to detect various human diseases. Information on VOCs is scattered in the literature until now; however, there is still no available database describing VOCs and their biological activities. To attain this purpose, we have developed KNApSAcK Metabolite Ecology Database, which contains the information on the relationships between VOCs and their emitting organisms. The KNApSAcK Metabolite Ecology is also linked with the KNApSAcK Core and KNApSAcK Metabolite Activity Database to provide further information on the metabolites and their biological activities. The VOC database can be accessed online. PMID:26495281

Cancer metabolism: strategic diversion from targeting cancer drivers to targeting cancer suppliers.

PubMed

Kim, Soo-Youl

2015-03-01

Drug development groups are close to discovering another pot of gold-a therapeutic target-similar to the success of imatinib (Gleevec) in the field of cancer biology. Modern molecular biology has improved cancer therapy through the identification of more pharmaceutically viable targets, and yet major problems and risks associated with late-phase cancer therapy remain. Presently, a growing number of reports have initiated a discussion about the benefits of metabolic regulation in cancers. The Warburg effect, a great discovery approximately 70 years ago, addresses the "universality" of cancer characteristics. For instance, most cancer cells prefer aerobic glycolysis instead of mitochondrial respiration. Recently, cancer metabolism has been explained not only by metabolites but also through modern molecular and chemical biological techniques. Scientists are seeking context-dependent universality among cancer types according to metabolic and enzymatic pathway signatures. This review presents current cancer metabolism studies and discusses future directions in cancer therapy targeting bio-energetics, bio-anabolism, and autophagy, emphasizing the important contribution of cancer metabolism in cancer therapy.

Biological nitrogen fixation and biomass accumulation within poplar clones as a result of inoculations with diazotrophic endophyte consortia.

PubMed

Knoth, Jenny L; Kim, Soo-Hyung; Ettl, Gregory J; Doty, Sharon L

2014-01-01

Sustainable production of biomass for bioenergy relies on low-input crop production. Inoculation of bioenergy crops with plant growth-promoting endophytes has the potential to reduce fertilizer inputs through the enhancement of biological nitrogen fixation (BNF). Endophytes isolated from native poplar growing in nutrient-poor conditions were selected for a series of glasshouse and field trials designed to test the overall hypothesis that naturally occurring diazotrophic endophytes impart growth promotion of the host plants. Endophyte inoculations contributed to increased biomass over uninoculated control plants. This growth promotion was more pronounced with multi-strain consortia than with single-strain inocula. Biological nitrogen fixation was estimated through (15)N isotope dilution to be 65% nitrogen derived from air (Ndfa). Phenotypic plasticity in biomass allocation and branch production observed as a result of endophyte inoculations may be useful in bioenergy crop breeding and engineering programs. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Escalating Role of Piezosurgery in Dental Therapeutics

PubMed Central

Masamatti, Sujata Surendra; Kumar, Ashish

2014-01-01

Dentistry, an art in science and tranquilizer in medicine, has seen a lot of changing concepts over a decade and one such novel innovation is piezosurgery. Piezosurgery is a true revolution in bone surgery as it fulfils both biological and technical criteria. It has a variety of applications ranging from minor surgical procedures to complex implantology, plastic and reconstructive surgeries. Piezosurgery uses a low frequency modulated ultrasonic insert which produces microvibrations in the range of 60-200micro meter/sec and leads to safe and precise bony incision without damaging underlying vital structures like nerves, mucosa and vessels. It overcomes technical difficulties such as visibility by producing bloodless field during surgery and removes debris simultaneously through internal irrigation mechanism. The soft tissues remain safe and biological factors like release of certain cytokines promote bone healing and enhance patients recovery. This critical review outweighs piezosurgery over traditional tools and emphasizes on its clinical and biological aspects contributing to beneficial dental health. PMID:25478473

Paleoclimates: Understanding climate change past and present

USGS Publications Warehouse

Cronin, Thomas M.

2010-01-01

The field of paleoclimatology relies on physical, chemical, and biological proxies of past climate changes that have been preserved in natural archives such as glacial ice, tree rings, sediments, corals, and speleothems. Paleoclimate archives obtained through field investigations, ocean sediment coring expeditions, ice sheet coring programs, and other projects allow scientists to reconstruct climate change over much of earth's history. When combined with computer model simulations, paleoclimatic reconstructions are used to test hypotheses about the causes of climatic change, such as greenhouse gases, solar variability, earth's orbital variations, and hydrological, oceanic, and tectonic processes. This book is a comprehensive, state-of-the art synthesis of paleoclimate research covering all geological timescales, emphasizing topics that shed light on modern trends in the earth's climate. Thomas M. Cronin discusses recent discoveries about past periods of global warmth, changes in atmospheric greenhouse gas concentrations, abrupt climate and sea-level change, natural temperature variability, and other topics directly relevant to controversies over the causes and impacts of climate change. This text is geared toward advanced undergraduate and graduate students and researchers in geology, geography, biology, glaciology, oceanography, atmospheric sciences, and climate modeling, fields that contribute to paleoclimatology. This volume can also serve as a reference for those requiring a general background on natural climate variability.

Opportunities in Biological Sciences; [VGM Career Horizons Series].

ERIC Educational Resources Information Center

Winter, Charles A.

This book provides job descriptions and discusses career opportunities in various fields of the biological sciences. These fields include: (1) biotechnology, genetics, biomedical engineering, microbiology, mycology, systematic biology, marine and aquatic biology, botany, plant physiology, plant pathology, ecology, and wildlife biology; (2) the…

Study of vortex beam and orbital angular momentum by metasurface

NASA Astrophysics Data System (ADS)

Mei, Shengtao

Recent explosive growth of research on metasurfaces has created a myriad of attractive applications within the field of flat optics, paving an avenue for extending current research results to other fields such as biology and physics. This thesis mainly focused on the research topics of manipulation of vortex beams via metasurfaces, including generation/reception, hologram and tuning mechanism. To be specific, the main contributions can be summarized as: 1) semi-ring slits for OAM detection and discrimination; 2) nano-void photon sieves array to realize complex OAM multiplexing strategy; 3) titanium dioxide (TiO2) metasurfaces for the demonstration of vortex holograms; and 4) reconfigurable chalcogenide compound Ge2Sb2Te5 (GST) metasurfaces to demonstrate the intriguing tunable scheme.

Cognition and Culture in Evolutionary Context.

PubMed

Colmenares, Fernando; Hernández-Lloreda, María Victoria

2017-01-09

In humans and other animals, the individuals' ability to adapt efficiently and effectively to the niches they have actively contributed to construct relies heavily on an evolved psychology which has been shaped by biological, social, and cultural processes over evolutionary time. As expected, although many of the behavioral and cognitive components of this evolved psychology are widely shared across species, many others are species-unique. Although many animal species are known to acquire group-specific traditions (or cultures) via social learning, human culture is unique in terms of its contents and characteristics (observable and unobservable products, cumulative effects, norm conformity, and norm enforcement) and of its cognitive underpinnings (imitation, instructed teaching, and language). Here we provide a brief overview of some of the issues that are currently tackled in the field. We also highlight some of the strengths of a biological, comparative, non-anthropocentric and evolutionarily grounded approach to the study of culture. The main contributions of this approach to the science of culture are its emphasis (a) on the integration of information on mechanisms, function, and evolution, and on mechanistic factors located at different levels of the biological hierarchy, and (b) on the search for general principles that account for commonalities and differences between species, both in the cultural products and in the processes of innovation, dissemination, and accumulation involved that operate during developmental and evolutionary timespans.

Optical fiber tips for biological applications: From light confinement, biosensing to bioparticles manipulation.

PubMed

Paiva, Joana S; Jorge, Pedro A S; Rosa, Carla C; Cunha, João P S

2018-05-01

The tip of an optical fiber has been considered an attractive platform in Biology. The simple cleaved end of an optical fiber can be machined, patterned and/or functionalized, acquiring unique properties enabling the exploitation of novel optical phenomena. Prompted by the constant need to measure and manipulate nanoparticles, the invention of the Scanning Near-field Optical Microscopy (SNOM) triggered the optimization and development of novel fiber tip microfabrication methods. In fact, the fiber tip was soon considered a key element in SNOM by confining light to sufficiently small extensions, challenging the diffraction limit. As result and in consequence of the newly proposed "Lab On Tip" concept, several geometries of fiber tips were applied in three main fields: imaging (in Microscopy/Spectroscopy), biosensors and micromanipulation (Optical Fiber Tweezers, OFTs). These are able to exert forces on microparticles, trap and manipulate them for relevant applications, as biomolecules mechanical study or protein aggregates unfolding. This review presents an overview of the main achievements, most impactful studies and limitations of fiber tip-based configurations within the above three fields, along the past 10 years. OFTs could be in future a valuable tool for studying several cellular phenomena such as neurodegeneration caused by abnormal protein fibrils or manipulating organelles within cells. This could contribute to understand the mechanisms of some diseases or biophenomena, as the axonal growth in neurons. To the best of our knowledge, no other review article has so far provided such a broad view. Despite of the limitations, fiber tips have key roles in Biology/Medicine. Copyright © 2018 Elsevier B.V. All rights reserved.

Integrating interactive computational modeling in biology curricula.

PubMed

Helikar, Tomáš; Cutucache, Christine E; Dahlquist, Lauren M; Herek, Tyler A; Larson, Joshua J; Rogers, Jim A

2015-03-01

While the use of computer tools to simulate complex processes such as computer circuits is normal practice in fields like engineering, the majority of life sciences/biological sciences courses continue to rely on the traditional textbook and memorization approach. To address this issue, we explored the use of the Cell Collective platform as a novel, interactive, and evolving pedagogical tool to foster student engagement, creativity, and higher-level thinking. Cell Collective is a Web-based platform used to create and simulate dynamical models of various biological processes. Students can create models of cells, diseases, or pathways themselves or explore existing models. This technology was implemented in both undergraduate and graduate courses as a pilot study to determine the feasibility of such software at the university level. First, a new (In Silico Biology) class was developed to enable students to learn biology by "building and breaking it" via computer models and their simulations. This class and technology also provide a non-intimidating way to incorporate mathematical and computational concepts into a class with students who have a limited mathematical background. Second, we used the technology to mediate the use of simulations and modeling modules as a learning tool for traditional biological concepts, such as T cell differentiation or cell cycle regulation, in existing biology courses. Results of this pilot application suggest that there is promise in the use of computational modeling and software tools such as Cell Collective to provide new teaching methods in biology and contribute to the implementation of the "Vision and Change" call to action in undergraduate biology education by providing a hands-on approach to biology.

Unconscious bias when experts are invited - and the results of conscious action

NASA Astrophysics Data System (ADS)

Stadmark, Johanna; Conley, Daniel J.

2016-04-01

Visibility of different kinds is important in academic work. We publish papers, present results at conferences and are invited to give seminars and write contributions and reviews about other scientists' work. A few years back we reacted on the invitation-only sections in two of the leading scientific journals. We asked: "Who are invited to write about other researchers' newly published results?" The short answer could be: Experts in the field. However, we found that it was mainly male experts in the field when we reviewed/categorized the authors of the invitation-only sections News & Views and Perspective in Nature and Science, respectively, during the years 2010 and 2011 (in total 1663 authors). The proportion of female authors was compared to the proportion of female scientists within their respective fields within academia. We found that female scientists were invited less often than their male colleagues. We notified the two journals about the mismatch (Nature 2012: 488) and their encouraging reply was that they needed to improve how they reflect women's contributions to science (Nature 2012: 491). In 2013 and 2014 the invitation-only sections (with in total 1845 authors) had reached parity (compared to the pool of available scientists) for contributions regarding Earth and Environmental Science, and made steps forward for Medical/Biological/Chemical sciences and Physical sciences. By raising awareness about the unconscious biases we all have, e.g. both men and women, we can act to make progress towards parity in science.

Space life sciences strategic plan, 1991

NASA Technical Reports Server (NTRS)

1992-01-01

Over the last three decades the life sciences program has significantly contributed to NASA's manned and unmanned exploration of space, while acquiring new knowledge in the fields of space biology and medicine. The national and international events which have led to the development and revision of NASA strategy will significantly affect the future of life sciences programs both in scope and pace. This document serves as the basis for synthesizing the option to be pursued during the next decade, based on the decisions, evolution, and guiding principles of the National Space Policy.

Genetically Engineered Mouse Models of Pituitary Tumors

PubMed Central

Cano, David A.; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso

2014-01-01

Animal models constitute valuable tools for investigating the pathogenesis of cancer as well as for preclinical testing of novel therapeutics approaches. However, the pathogenic mechanisms of pituitary-tumor formation remain poorly understood, particularly in sporadic adenomas, thus, making it a challenge to model pituitary tumors in mice. Nevertheless, genetically engineered mouse models (GEMMs) of pituitary tumors have provided important insight into pituitary tumor biology. In this paper, we review various GEMMs of pituitary tumors, highlighting their contributions and limitations, and discuss opportunities for research in the field. PMID:25136513

Synthetic Plasma Liquid Based Electronic Circuits Realization-A Novel Concept.

PubMed

Pandya, Killol V; Kosta, ShivPrasad

2016-09-01

Biomedical research is contributing significant role in the field of biomedical engineering and applied science. It brings research and innovations to a different level. This study investigated artificial human blood -synthetic plasma liquid as conductive medium. Keeping in mind the conductivity of synthetic plasma, astable multivibrator as well as differential amplifier circuit were demonstrated. The circuits were given normal input voltages at regular temperature and ideal conditions. The result shows desired response which supports the novel concept. For both the circuits, phase shift of 180° achieved by analysing biological electronic circuits.

Women are underrepresented in computational biology: An analysis of the scholarly literature in biology, computer science and computational biology

PubMed Central

2017-01-01

While women are generally underrepresented in STEM fields, there are noticeable differences between fields. For instance, the gender ratio in biology is more balanced than in computer science. We were interested in how this difference is reflected in the interdisciplinary field of computational/quantitative biology. To this end, we examined the proportion of female authors in publications from the PubMed and arXiv databases. There are fewer female authors on research papers in computational biology, as compared to biology in general. This is true across authorship position, year, and journal impact factor. A comparison with arXiv shows that quantitative biology papers have a higher ratio of female authors than computer science papers, placing computational biology in between its two parent fields in terms of gender representation. Both in biology and in computational biology, a female last author increases the probability of other authors on the paper being female, pointing to a potential role of female PIs in influencing the gender balance. PMID:29023441

Modelling the influence of thermal effects induced by radio frequency electric field on the dynamics of the ATPase nano-biomolecular motors.

PubMed

Lohrasebi, A; Mohamadi, S; Fadaie, S; Rafii-Tabar, H

2012-07-01

We model the dynamics of the F(0) component of the F(0)F(1)-ATPase mitochondrion-based nano-motor operating in a stochastically-fluctuating medium that represents the intracellular environment. The stochastic dynamics are modeled via Langevin equation of motion wherein fluctuations are treated as white noise. We have investigated the influence of an applied alternating electric field on the rotary motion of the F(0) rotor in such an environment. The exposure to the field induces a temperature rise in the mitochondrion's membrane, within which the F(0) is embedded. The external field also induces an electric potential that promotes a change in the mitochondrion's transmembrane potential (TMP). Both the induced temperature and the change in TMP contribute to a change in the dynamics of the F(0). We have found that for external fields in the radio frequency (RF) range, normally present in the environment and encountered by biological systems, the contribution of the induced thermal effects, relative to that of the induced TMP, to the dynamics of the F(0) is more significant. The changes in the dynamics of the F(0) part affect the frequency of the rotary motion of the F(0)F(1)-ATPase protein motor which, in turn, affects the production rate of the ATP molecules. Copyright © 2011 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Evolutionary and ecological approaches to the study of personality

PubMed Central

Réale, Denis; Dingemanse, Niels J.; Kazem, Anahita J. N.; Wright, Jonathan

2010-01-01

This introduction to the themed issue on Evolutionary and ecological approaches to the study of personality provides an overview of conceptual, theoretical and methodological progress in research on animal personalities over the last decade, and places the contributions to this volume in context. The issue has three main goals. First, we aimed to bring together theoreticians to contribute to the development of models providing adaptive explanations for animal personality that could guide empiricists, and stimulate exchange of ideas between the two groups of researchers. Second, we aimed to stimulate cross-fertilization between different scientific fields that study personality, namely behavioural ecology, psychology, genomics, quantitative genetics, neuroendocrinology and developmental biology. Third, we aimed to foster the application of an evolutionary framework to the study of personality. PMID:21078646

An Untold Story in Biology: The Historical Continuity of Evolutionary Ideas of Muslim Scholars from the 8th Century to Darwin's Time

ERIC Educational Resources Information Center

Malik, Aamina H.; Ziermann, Janine M.; Diogo, Rui

2018-01-01

Textbooks on the history of biology and evolutionary thought do not mention the evolutionary ideas of Muslim scholars before Darwin's time. This is part of a trend in the West to minimise the contributions of non-Western scientists to biology, human anatomy and evolutionary biology. Therefore, this paper focuses on the contributions of…

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.

"A mission-driven discipline": the growth of conservation biology.

PubMed

Meine, Curt; Soulé, Michael; Noss, Reed E

2006-06-01

Conservation biology emerged in the mid-1980s, drawing on established disciplines and integrating them in pursuit of a coherent goal: the protection and perpetuation of the Earth's biological diversity. Opportunistic in its borrowing and application of knowledge, conservation biology had its roots within the established biological sciences and resource management disciplines but has continually incorporated insights from the empirical experience of resource managers, from the social sciences and humanities, and from diverse cultural sources. The Society for Conservation Biology (SCB) has represented the field's core constituency, while expanding that constituency in keeping with the field's integrative spirit. Conservation Biology has served as SCB's flagship publication, promoting research, dialog, debate, and application of the field's essential concepts. Over the last 20 years the field, SCB, and the journal have evolved to meet changing conservation needs, to explore gaps in our knowledge base, to incorporate new information from related fields, to build professional capacity, and to provide expanded opportunities for international participation. In turn, the field, SCB, and journal have prompted change in related fields, organizations, and publications. In its dedication to advancing the scientific foundations of biodiversity conservation and placing that science at the service of society in a world whose variety, wildness, and beauty we care for conservation biology represents both a continuation and radical reconfiguration of the traditional relationship between science and conservation.

Functions of MicroRNAs in Cardiovascular Biology and Disease

PubMed Central

Hata, Akiko

2015-01-01

In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

Epigenomics and the concept of degeneracy in biological systems

PubMed Central

Mason, Paul H.; Barron, Andrew B.

2014-01-01

Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability. PMID:24335757

Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology

PubMed Central

Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal

2015-01-01

Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein–protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies. PMID:25970732

Meat science: From proteomics to integrated omics towards system biology.

PubMed

D'Alessandro, Angelo; Zolla, Lello

2013-01-14

Since the main ultimate goal of farm animal raising is the production of proteins for human consumption, research tools to investigate proteins play a major role in farm animal and meat science. Indeed, proteomics has been applied to the field of farm animal science to monitor in vivo performances of livestock animals (growth performances, fertility, milk quality etc.), but also to further our understanding of the molecular processes at the basis of meat quality, which are largely dependent on the post mortem biochemistry of the muscle, often in a species-specific way. Post mortem alterations to the muscle proteome reflect the biological complexity of the process of "muscle to meat conversion," a process that, despite decades of advancements, is all but fully understood. This is mainly due to the enormous amounts of variables affecting meat tenderness per se, including biological factors, such as animal species, breed specific-characteristic, muscle under investigation. However, it is rapidly emerging that the tender meat phenotype is not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as the rearing environment, feeding conditions, physical activity, administration of hormonal growth promotants, pre-slaughter handling and stress, post mortem handling. From this intricate scenario, biochemical approaches and systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion. The growing integration of omics disciplines in the field of systems biology will soon contribute to take further steps forward. Copyright © 2012 Elsevier B.V. All rights reserved.

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

PubMed

Horii, Ikuo

2016-01-01

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

Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms

USGS Publications Warehouse

Goldberg, Caren S.; Strickler, Katherine M.; Pilliod, David S.

2015-01-01

The discovery that macroorganisms can be detected from their environmental DNA (eDNA) in aquatic systems has immense potential for the conservation of biological diversity. This special issue contains 11 papers that review and advance the field of eDNA detection of vertebrates and other macroorganisms, including studies of eDNA production, transport, and degradation; sample collection and processing to maximize detection rates; and applications of eDNA for conservation using citizen scientists. This body of work is an important contribution to the ongoing efforts to take eDNA detection of macroorganisms from technical breakthrough to established, reliable method that can be used in survey, monitoring, and research applications worldwide. While the rapid advances in this field are remarkable, important challenges remain, including consensus on best practices for collection and analysis, understanding of eDNA diffusion and transport, and avoidance of inhibition in sample collection and processing. Nonetheless, as demonstrated in this special issue, eDNA techniques for research and monitoring are beginning to realize their potential for contributing to the conservation of biodiversity globally.

Biological effects of high ultraviolet radiation on early earth--a theoretical evaluation.

PubMed

Cockell, C S

1998-08-21

The surface of early Earth was exposed to both UVC radiation (< 280 nm) and higher doses of UVB (280-315 nm) compared with the surface of present day Earth. The degree to which this radiation environment acted as a selection pressure on organisms and biological systems has rarely been theoretically examined with respect to the biologically effective irradiances that ancient organisms would receive. Here action spectra for DNA inactivation and isolated chloroplast inhibition are used to estimate biologically effective irradiances on archean Earth. Comparisons are made with present day Earth. The theoretical estimations on the UV radiation screening required to protect DNA on archean Earth compare well with field and laboratory observations on protection strategies found in present day microbial communities. They suggest that many physical and biological methods may have been effective and would have allowed for the radiation of life even under the high UV radiation regimes of archean Earth. Such strategies would also have provided effective reduction of photoinhibition by UV radiation. The data also suggest that the UV regime on the surface of Mars is not a life limiting factor per se, although other environmental factors such as desiccation and low temperatures may contribute towards the apparent lack of a surface biota.

Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus.

PubMed

Karp, Peter D; Berger, Bonnie; Kovats, Diane; Lengauer, Thomas; Linial, Michal; Sabeti, Pardis; Hide, Winston; Rost, Burkhard

2015-02-15

Speed is of the essence in combating Ebola; thus, computational approaches should form a significant component of Ebola research. As for the development of any modern drug, computational biology is uniquely positioned to contribute through comparative analysis of the genome sequences of Ebola strains and three-dimensional protein modeling. Other computational approaches to Ebola may include large-scale docking studies of Ebola proteins with human proteins and with small-molecule libraries, computational modeling of the spread of the virus, computational mining of the Ebola literature and creation of a curated Ebola database. Taken together, such computational efforts could significantly accelerate traditional scientific approaches. In recognition of the need for important and immediate solutions from the field of computational biology against Ebola, the International Society for Computational Biology (ISCB) announces a prize for an important computational advance in fighting the Ebola virus. ISCB will confer the ISCB Fight against Ebola Award, along with a prize of US$2000, at its July 2016 annual meeting (ISCB Intelligent Systems for Molecular Biology 2016, Orlando, FL). dkovats@iscb.org or rost@in.tum.de. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Multidisciplinary Russian biomedical research in space

NASA Astrophysics Data System (ADS)

Orlov, O. I.; Sychev, V. N.; Samarin, G. I.; Ilyin, E. A.; Belakovskiy, M. S.; Kussmaul, A. R.

2014-08-01

Research activities on a comprehensive multidisciplinary program are vital for enhancement of the system of crew's medical care, environmental health and hygiene in space missions. The primary goal of the program must be identification of patterns, intensity and dynamics of structural and functional shifts in organism induced by an aggregate of spaceflight factors including microgravity, isolation, artificial environment, space radiation, etc. Also, the program must pursue differential assessment of emerging deviations from the standpoint of adequacy to the spaceflight conditions and prospects of returning to Earth and guide the development of principles, methods and techniques necessary to maintain health and working capacity of humans during short- and long-duration missions and on return to Earth. Over 50 years, since 1963, the IBMP researchers apply systemic and innovational approaches to fundamental and exploratory studies in the fields of medical sciences, radiation biology, engineering science, biotechnology, etc. with participation of various biological specimens and human volunteers. Investigations aboard manned spacecrafts and biological satellites as well as in ground-based laboratories further enhancement of the medical care system for crews on orbital and remote space missions; they give insight into the fundamental problems of gravitational physiology and biology, psychophysiology, radiation biology, and contribute thereby to the development of knowledge, methods and technologies, as well as medical and scientific equipment.

The contribution of molecular epidemiology to the identification of human carcinogens: current status and future perspectives.

PubMed

Boffetta, P; Islami, F

2013-04-01

The use of biological-based markers of exposure, intermediate effect, outcome, and susceptibility has become standard practice in cancer epidemiology, which has contributed to identification of several carcinogenic agents. Nevertheless, with the exception of biological agents, this contribution, in terms of providing sufficiently strong evidence as required by the International Agency for Research on Cancer (IARC) monographs, has been modest. We discuss the overall contribution of molecular epidemiology to identification of carcinogens, with focus on IARC monographs. For many carcinogens, valid biological markers of exposure and mechanisms of actions are not available. Molecular markers are usually assessed in single biological samples, which may not represent the actual exposure or biological events related to carcinogens. The contribution of molecular epidemiology to identification of carcinogens has mainly been limited to the carcinogens acting through a genotoxic mechanism, i.e. when carcinogens induce DNA damage. A number of factors, including certain hormones and overweight/obesity, may show carcinogenic effects through nongenotoxic pathways, for which mechanisms of carcinogenicity are not well identified and their biomarkers are sparse. Longitudinal assessment of biomarkers may provide more informative data in molecular epidemiology studies. For many carcinogens and mechanistic pathways, in particular nongenotoxic carcinogenicity, valid biological markers still need to be identified.

Materiomics: biological protein materials, from nano to macro.

PubMed

Cranford, Steven; Buehler, Markus J

2010-11-12

Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics - discovering Nature's complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature's materials have been hindered by our lack of fundamental understanding of these materials' intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties. Recent advances in analytical tools and experimental methods allow a holistic view of such a hierarchical biological material system. The integration of these approaches and amalgamation of material properties at all scale levels to develop a complete description of a material system falls within the emerging field of materiomics. Materiomics is the result of the convergence of engineering and materials science with experimental and computational biology in the context of natural and synthetic materials. Through materiomics, fundamental advances in our understanding of structure-property-process relations of biological systems contribute to the mechanistic understanding of certain diseases and facilitate the development of novel biological, biologically inspired, and completely synthetic materials for applications in medicine (biomaterials), nanotechnology, and engineering.

Materiomics: biological protein materials, from nano to macro

PubMed Central

Cranford, Steven; Buehler, Markus J

2010-01-01

Materiomics is an emerging field of science that provides a basis for multiscale material system characterization, inspired in part by natural, for example, protein-based materials. Here we outline the scope and explain the motivation of the field of materiomics, as well as demonstrate the benefits of a materiomic approach in the understanding of biological and natural materials as well as in the design of de novo materials. We discuss recent studies that exemplify the impact of materiomics – discovering Nature’s complexity through a materials science approach that merges concepts of material and structure throughout all scales and incorporates feedback loops that facilitate sensing and resulting structural changes at multiple scales. The development and application of materiomics is illustrated for the specific case of protein-based materials, which constitute the building blocks of a variety of biological systems such as tendon, bone, skin, spider silk, cells, and tissue, as well as natural composite material systems (a combination of protein-based and inorganic constituents) such as nacre and mollusk shells, and other natural multiscale systems such as cellulose-based plant and wood materials. An important trait of these materials is that they display distinctive hierarchical structures across multiple scales, where molecular details are exhibited in macroscale mechanical responses. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function despite severe limitations in the quality and quantity of material building blocks. However, up until now, our attempts to analyze and replicate Nature’s materials have been hindered by our lack of fundamental understanding of these materials’ intricate hierarchical structures, scale-bridging mechanisms, and complex material components that bestow protein-based materials their unique properties. Recent advances in analytical tools and experimental methods allow a holistic view of such a hierarchical biological material system. The integration of these approaches and amalgamation of material properties at all scale levels to develop a complete description of a material system falls within the emerging field of materiomics. Materiomics is the result of the convergence of engineering and materials science with experimental and computational biology in the context of natural and synthetic materials. Through materiomics, fundamental advances in our understanding of structure–property–process relations of biological systems contribute to the mechanistic understanding of certain diseases and facilitate the development of novel biological, biologically inspired, and completely synthetic materials for applications in medicine (biomaterials), nanotechnology, and engineering. PMID:24198478

Joint actions of environmental nonionizing electromagnetic fields and chemical pollution in cancer promotion.

PubMed Central

Adey, W R

1990-01-01

Studies of environmental electromagnetic (EM) field interactions in tissues have contributed to a new understanding of both normal growth and the biology of cancer in cell growth. From cancer research comes a floodtide of new knowledge about the disruption of communication by cancer-promoting chemicals with an onset of unregulated growth. Bioelectromagnetic research reveals clear evidence of joint actions at cell membranes of chemical cancer promoters and environmental electromagnetic fields. The union of these two disciplines has resulted in the first major new approach to tumor formation in 75 years, directing attention to dysfunctions in inward and outward streams of signals at cell membranes, rather than to damage DNA in cell nuclei, and to synergic actions of chemical pollutants and environmental electromagnetic fields. We are witnesses and, in great measure, participants in one of the great revolutions in the history of biology. In little more than a century, we have moved from organs, to tissues, to cells, and finally to the molecules that are the elegant fabric of living tissues. Today, we stand at a new frontier. It may be more difficult to comprehend, but it is far more significant; for it is at the atomic level, rather than the molecular, that physical, rather than chemical, processes appear to shape the flow of signals that are at the essence of living matter. To pursue these problems in the environment and in the laboratory, our needs for further research with appropriate budgets are great.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2205491

Photoionization of water molecules by a train of attosecond pulses assisted by a near-infrared laser: delay and polarization control

NASA Astrophysics Data System (ADS)

Martini, Lara; Boll, Diego I. R.; Fojón, Omar A.

2017-08-01

Basic reactions involving water molecules are essential to understand the interaction between radiation and the biological tissue because living cells are composed mostly by water. Therefore, the knowledge of ionization of the latter is crucial in many domains of Biology and Physics. So, we study theoretically the photoionization of water molecules by extreme ultraviolet attopulse trains assisted by lasers in the near-infrared range. We use a separable Coulomb-Volkov model in which the temporal evolution of the system can be divided into three stages allowing spatial and temporal separation for the Coulomb and Volkov final state wavefunctions. First, we analyze photoelectron angular distributions for different delays between the attopulse train and the assistant laser field. We compare our results for water and Ne atoms as they belong to the same isoelectronic series. Moreover, we contrast our calculations with previous theoretical and experimental work for Ar atoms due to the similarities of the orbitals involved in the reaction. Second, we study the effect of varying the relative orientations of the attopulse and laser field polarizations and we compare our predictions with other theories and experiments. We expect these studies contribute to the improvement of polarization experiments and the development of the attopulse trains and assistant laser fields technologies. Finally, we hope our work promote progress on the control of the chemical reactivity of water molecules since this could be useful in different fields such as radiobiology and medical physics.

Mass-spectrometric identification of primary biological particle markers and application to pristine submicron aerosol measurements in Amazonia

NASA Astrophysics Data System (ADS)

Schneider, J.; Freutel, F.; Zorn, S. R.; Chen, Q.; Farmer, D. K.; Jimenez, J. L.; Martin, S. T.; Artaxo, P.; Wiedensohler, A.; Borrmann, S.

2011-11-01

The detection of primary biological material in submicron aerosol by means of thermal desorption/electron impact ionization aerosol mass spectrometry was investigated. Mass spectra of amino acids, carbohydrates, small peptides, and proteins, all of which are key building blocks of biological particles, were recorded in laboratory experiments. Several characteristic marker fragments were identified. The intensity of the marker signals relative to the total organic mass spectrum allows for an estimation of the content of primary biological material in ambient organic aerosol. The developed method was applied to mass spectra recorded during AMAZE-08, a field campaign conducted in the pristine rainforest of the central Amazon Basin, Brazil, during the wet season of February and March 2008. The low abundance of identified marker fragments places upper limits of 7.5% for amino acids and 5.6% for carbohydrates on the contribution of primary biological aerosol particles (PBAP) to the submicron organic aerosol mass concentration during this time period. Upper limits for the absolute submicron concentrations for both compound classes range from 0.01 to 0.1 μg m-3. Carbohydrates and proteins (composed of amino acids) make up for about two thirds of the dry mass of a biological cell. Thus, our findings suggest an upper limit for the PBAP mass fraction of about 20% to the submicron organic aerosol measured in Amazonia during AMAZE-08.

History of the molecular biology of cytomegaloviruses.

PubMed

Stinski, Mark F

2014-01-01

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

Landscape Context Affects Aphid Parasitism by Lysiphlebus testaceipes (Hymenoptera: Aphidiinae) in Wheat Fields.

PubMed

Elliott, Norman C; Brewer, Michael J; Giles, Kristopher L

2018-04-12

Winter wheat is Oklahoma's most widely grown crop, and is planted during September and October, grows from fall through spring, and is harvested in June. Winter wheat fields are typically interspersed in a mosaic of habitats in other uses, and we hypothesized that the spatial and temporal composition and configuration of landscape elements, which contribute to agroecosystem diversity also influence biological control of common aphid pests. The parasitoid Lysiphlebus testaceipes (Cresson; Hymenoptera: Aphidiinae) is highly effective at reducing aphid populations in wheat in Oklahoma, and though a great deal is known about the biology and ecology of L. testaceipes, there are gaps in knowledge that limit predicting when and where it will be effective at controlling aphid infestations in wheat. Our objective was to determine the influence of landscape structure on parasitism of cereal aphids by L. testaceipes in wheat fields early in the growing season when aphid and parasitoid colonization occurs and later in the growing season when aphid and parasitoid populations are established in wheat fields. Seventy fields were studied during the three growing seasons. Significant correlations between parasitism by L. testaceipes and landscape variables existed for patch density, fractal dimension, Shannon's patch diversity index, percent wheat, percent summer crops, and percent wooded land. Correlations between parasitism and landscape variables were generally greatest at a 3.2 km radius surrounding the wheat field. Correlations between parasitism and landscape variables that would be expected to increase with increasing landscape diversity were usually positive. Subsequent regression models for L. testaceipes parasitism in wheat fields in autumn and spring showed that landscape variables influenced parasitism and indicated that parasitism increased with increasing landscape diversity. Overall, results indicate that L. testaceipes utilizes multiple habitats throughout the year depending on their availability and acceptability, and frequently disperses among habitats. Colonization of wheat fields by L. testaceipes in autumn appears to be enhanced by proximity to fields of summer crops and semi-natural habitats other than grasslands.

Global research priorities for sea turtles: Informing management and conservation in the 21st century

USGS Publications Warehouse

Hamann, M.; Godfrey, M.H.; Seminoff, J.A.; Barata, P.C.R.; Bjorndal, K.A.; Bolten, A.B.; Broderick, A.C.; Campbell, L.M.; Carreras, C.; Casale, P.; Chaloupka, M.; Chan, S.-K.; Coyne, M.; Crowder, L.B.; Diez, C.E.; Dutton, P.H.; Epperly, S.P.; FitzSimmons, N.N.; Formia, A.; Girondot, M.; Hays, G.C.; Cheng, I.J.; Kaska, Y.; Lewison, R.; Mortimer, J.A.; Nichols, W.J.; Reina, R.D.; Shanker, K.; Spotila, J.R.; Tomás, J.; Wallace, B.P.; Work, Thierry M.; Zbinden, N.; Godley, B.J.

2010-01-01

Over the past 3 decades, the status of sea turtles and the need for their protection to aid population recovery have increasingly captured the interest of government agencies, non-governmental organisations (NGOs) and the general public worldwide. This interest has been matched by increased research attention, focusing on a wide variety of topics relating to sea turtle biology and ecology, together with the interrelations of sea turtles with the physical and natural environments. Although sea turtles have been better studied than most other marine fauna, management actions and their evaluation are often hindered by the lack of data on turtle biology, human–turtle interactions, turtle population status and threats. In an effort to inform effective sea turtle conservation a list of priority research questions was assembled based on the opinions of 35 sea turtle researchers from 13 nations working in fields related to turtle biology and/or conservation. The combined experience of the contributing researchers spanned the globe as well as many relevant disciplines involved in conservation research. An initial list of more than 200 questions gathered from respondents was condensed into 20 metaquestions and classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies.

Eugenics from the New Deal to the Great Society: genetics, demography and population quality.

PubMed

Ramsden, Edmund

2008-12-01

The relationship between biological and social scientists as regards the study of human traits and behavior has often been perceived in terms of mutual distrust, even antipathy. In the interwar period, population study seemed an area that might allow for closer relations between them-united as they were by a concern to improve the eugenic quality of populations. Yet these relations were in tension: by the early post-war era, social demographers were denigrating the contributions of biologists to the study of population problems as embodying the elitist ideology of eugenics. In response to this loss of credibility, the eugenics movement pursued a simultaneous program of withdrawal and expansion: its leaders helped focus concern with biological quality onto the developing field of medical genetics, while at the same moment, extended their scope to improving the social quality of populations through birth control policies, guided by demography. While this approach maintained boundaries between the social and the biological, in the 1960s, a revitalized American Eugenics Society helped reunite leading demographers and geneticists. This paper will assess the reasons for this period of influence for eugenics, and explore its implications for the social and biological study of human populations.

Cytokinin signalling inhibitory fields provide robustness to phyllotaxis

NASA Astrophysics Data System (ADS)

Besnard, Fabrice; Refahi, Yassin; Morin, Valérie; Marteaux, Benjamin; Brunoud, Géraldine; Chambrier, Pierre; Rozier, Frédérique; Mirabet, Vincent; Legrand, Jonathan; Lainé, Stéphanie; Thévenon, Emmanuel; Farcot, Etienne; Cellier, Coralie; Das, Pradeep; Bishopp, Anthony; Dumas, Renaud; Parcy, François; Helariutta, Ykä; Boudaoud, Arezki; Godin, Christophe; Traas, Jan; Guédon, Yann; Vernoux, Teva

2014-01-01

How biological systems generate reproducible patterns with high precision is a central question in science. The shoot apical meristem (SAM), a specialized tissue producing plant aerial organs, is a developmental system of choice to address this question. Organs are periodically initiated at the SAM at specific spatial positions and this spatiotemporal pattern defines phyllotaxis. Accumulation of the plant hormone auxin triggers organ initiation, whereas auxin depletion around organs generates inhibitory fields that are thought to be sufficient to maintain these patterns and their dynamics. Here we show that another type of hormone-based inhibitory fields, generated directly downstream of auxin by intercellular movement of the cytokinin signalling inhibitor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6 (AHP6), is involved in regulating phyllotactic patterns. We demonstrate that AHP6-based fields establish patterns of cytokinin signalling in the meristem that contribute to the robustness of phyllotaxis by imposing a temporal sequence on organ initiation. Our findings indicate that not one but two distinct hormone-based fields may be required for achieving temporal precision during formation of reiterative structures at the SAM, thus indicating an original mechanism for providing robustness to a dynamic developmental system.

Colloquium and Report on Systems Microbiology: Beyond Microbial Genomics

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

Merry R. Buckley

The American Academy of Microbiology convened a colloquium June 4-6, 2004 to confer about the scientific promise of systems microbiology. Participants discussed the power of applying a systems approach to the study of biology and to microbiology in particular, specifics about current research efforts, technical bottlenecks, requirements for data acquisition and maintenance, educational needs, and communication issues surrounding the field. A number of recommendations were made for removing barriers to progress in systems microbiology and for improving opportunities in education and collaboration. Systems biology, as a concept, is not new, but the recent explosion of genomic sequences and related datamore » has revived interest in the field. Systems microbiology, a subset of systems biology, represents a different approach to investigating biological systems. It attempts to examine the emergent properties of microorganisms that arise from the interplay of genes, proteins, other macromolecules, small molecules, organelles, and the environment. It is these interactions, often nonlinear, that lead to the emergent properties of biological systems that are generally not tractable by traditional approaches. As a complement to the long-standing trend toward reductionism, systems microbiology seeks to treat the organism or community as a whole, integrating fundamental biological knowledge with genomics, metabolomics, and other data to create an integrated picture of how a microbial cell or community operates. Systems microbiology promises not only to shed light on the activities of microbes, but will also provide biology the tools and approaches necessary for achieving a better understanding of life and ecosystems. Microorganisms are ideal candidates for systems biology research because they are relatively easy to manipulate and because they play critical roles in health, environment, agriculture, and energy production. Potential applications of systems microbiology research range from improvements in the management of bacterial infections to the development of commercial-scale microbial hydrogen generation. A number of technical challenges must be met to realize the potential of systems microbiology. Development of a new, comprehensive systems microbiology database that would be available to the entire research community was identified as the single most critical need. Other challenges include difficulties in measuring single-cell parameters, limitations in identifying and measuring metabolites and other products, the inability to cultivate diverse microbes, limits on data accessibility, computational limitations associated with data integration, the lack of sufficient functional gene annotations, needs for quantitative proteomics, and the inapplicability of current high throughput methods to all areas of systems microbiology. Difficulties have also been encountered in acquiring the necessary data, assuring the quality of that data, and in making data available to the community in a useful format. Problems with data quality assurance and data availability could be partially offset by launching a dedicated systems microbiology database. To be of greatest value to the field, a database should include systems data from all levels of analysis, including sequences, microarray data, proteomics data, metabolite measurements, data on protein-protein or protein-nucleic interactions, carbohydrate and small RNA profiles, information on cell surface markers, and appropriate supporting data. Regular updates of these databases and adherence to agreed upon data format standards are critical to the success of these resources. It was recommended that educational requirements for undergraduate and graduate students in microbiology be amended to better prepare the next generation of researchers for the quantitative requirements of applying systems microbiology methods in their work. Systems microbiology research is too complex to be the sole property of any single academic discipline. The contributions of microbiologists, computer scientists, control theorists, biostatisticians, and others are all required to move the field forward. Since research in systems microbiology demands the contributions of a diverse array of professionals, collaboration across disciplines and national borders should be strongly encouraged by research bodies and funding agencies. Although the details of systems microbiology research are probably not of interest to the average individual, the potential applications and benefits of these types of investigations should be conveyed to the lay public.« less

Effects of Diffusion in Magnetically Inhomogeneous Media on Rotating Frame Spin-Lattice Relaxation

PubMed Central

Spear, John T.; Gore, John C.

2014-01-01

In an aqueous medium containing magnetic inhomogeneities, diffusion amongst the intrinsic susceptibility gradients contributes to the relaxation rate R1ρ of water protons to a degree that depends on the magnitude of the local field variations ΔBz, the geometry of the perturbers inducing these fields, and the rate of diffusion of water, D. This contribution can be reduced by using stronger locking fields, leading to a dispersion in R1ρ that can be analyzed to derive quantitative characteristics of the material. A theoretical expression was recently derived to describe these effects for the case of sinusoidal local field variations of a well-defined spatial frequency q. To evaluate the degree to which this dispersion may be extended to more realistic field patterns, finite difference Bloch-McConnell simulations were performed with a variety of three-dimensional structures to reveal how simple geometries affect the dispersion of spin-locking measurements. Dispersions were fit to the recently derived expression to obtain an estimate of the correlation time of the field variations experienced by the spins, and from this the mean squared gradient and an effective spatial frequency were obtained to describe the fields. This effective spatial frequency was shown to vary directly with the second moment of the spatial frequency power spectrum of the ΔBz field, which is a measure of the average spatial dimension of the field variations. These results suggest the theory may be more generally applied to more complex media to derive useful descriptors of the nature of field inhomogeneities. The simulation results also confirm that such diffusion effects disperse over a range of locking fields of lower amplitude than typical chemical exchange effects, and should be detectable in a variety of magnetically inhomogeneous media including regions of dense microvasculature within biological tissues. PMID:25462950

Assessing the Biological Safety Profession's Evaluation and Control of Risks Associated with the Field Collection of Potentially Infectious Specimens.

PubMed

Patlovich, Scott J; Emery, Robert J; Whitehead, Lawrence W; Brown, Eric L; Flores, Rene

2015-03-01

Because the origins of the biological safety profession are rooted in the control and prevention of laboratory-associated infections, the vocation focuses primarily on the safe handling of specimens within the laboratory. But in many cases, the specimens and samples handled in the lab are originally collected in the field where a broader set of possible exposure considerations may be present, each with varying degrees of controllability. The failure to adequately control the risks associated with collecting biological specimens in the field may result in illness or injury, and could have a direct impact on laboratory safety, if infectious specimens were packaged or transported inappropriately, for example. This study developed a web-based survey distributed to practicing biological safety professionals to determine the prevalence of and extent to which biological safety programs consider and evaluate field collection activities. In cases where such issues were considered, the data collected characterize the types of controls and methods of oversight at the institutional level that are employed. Sixty-one percent (61%) of the survey respondents indicated that research involving the field collection of biological specimens is conducted at their institutions. A majority (79%) of these field collection activities occur at academic institutions. Twenty-seven percent (27%) of respondents indicated that their safety committees do not consider issues related to biological specimens collected in the field, and only 25% with an oversight committee charged to review field collection protocols have generated a field research-specific risk assessment form to facilitate the assembly of pertinent information for a project risk assessment review. The results also indicated that most biosafety professionals (73% overall; 71% from institutions conducting field collection activities) have not been formally trained on the topic, but many (64% overall; 87% from institutions conducting field collection activities) indicated that training on field research safety issues would be helpful, and even more (71% overall; 93% from institutions conducting field collection activities) would consider participation in such a training course. Results obtained from this study can be used to develop a field research safety toolkit and associated training curricula specifically targeted to biological safety professionals.

Nitrosative Stress in the Nervous System: Guidelines for Designing Experimental Strategies to Study Protein S-Nitrosylation.

PubMed

Nakamura, Tomohiro; Lipton, Stuart A

2016-03-01

Reactive nitrogen species, such as nitric oxide (NO), exert their biological activity in large part through post-translational modification of cysteine residues, forming S-nitrosothiols. This chemical reaction proceeds via a process that we and our colleagues have termed protein S-nitrosylation. Under conditions of normal NO production, S-nitrosylation regulates the activity of many normal proteins. However, in degenerative conditions characterized by nitrosative stress, increased levels of NO lead to aberrant S-nitrosylation that contributes to the pathology of the disease. Thus, S-nitrosylation has been implicated in a wide range of cellular mechanisms, including mitochondrial function, proteostasis, transcriptional regulation, synaptic activity, and cell survival. In recent years, the research area of protein S-nitrosylation has become prominent due to improvements in the detection systems as well as the demonstration that protein S-nitrosylation plays a critical role in the pathogenesis of neurodegenerative and other neurological disorders. To further promote our understanding of how protein S-nitrosylation affects cellular systems, guidelines for the design and conduct of research on S-nitrosylated (or SNO-)proteins would be highly desirable, especially for those newly entering the field. In this review article, we provide a strategic overview of designing experimental approaches to study protein S-nitrosylation. We specifically focus on methods that can provide critical data to demonstrate that an S-nitrosylated protein plays a (patho-)physiologically-relevant role in a biological process. Hence, the implementation of the approaches described herein will contribute to further advancement of the study of S-nitrosylated proteins, not only in neuroscience but also in other research fields.

A Quick Guide for Building a Successful Bioinformatics Community

PubMed Central

Budd, Aidan; Corpas, Manuel; Brazas, Michelle D.; Fuller, Jonathan C.; Goecks, Jeremy; Mulder, Nicola J.; Michaut, Magali; Ouellette, B. F. Francis; Pawlik, Aleksandra; Blomberg, Niklas

2015-01-01

“Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and the scientific field as a whole. It is thus beneficial at many different levels to understand the general features of successful, high-impact bioinformatics communities; how individual participants can contribute to the success of these communities; and the role of education and training within these communities. We present here a quick guide to building and maintaining a successful, high-impact bioinformatics community, along with an overview of the general benefits of participating in such communities. This article grew out of contributions made by organizers, presenters, panelists, and other participants of the ISMB/ECCB 2013 workshop “The ‘How To Guide’ for Establishing a Successful Bioinformatics Network” at the 21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 12th European Conference on Computational Biology (ECCB). PMID:25654371

Expanding the chemical information science gateway.

PubMed

Bajorath, Jürgen

2017-01-01

Broadly defined, chemical information science (CIS) covers chemical structure and data analysis including biological activity data as well as processing, organization, and retrieval of any form of chemical information. The CIS Gateway (CISG) of F1000Research was created to communicate research involving the entire spectrum of chemical information, including chem(o)informatics. CISG provides a forum for high-quality publications and a meaningful alternative to conventional journals. This gateway is supported by leading experts in the field recognizing the need for open science and a flexible publication platform enabling off-the-beaten path contributions. This editorial aims to further rationalize the scope of CISG, position it within its scientific environment, and open it up to a wider audience. Chemical information science is an interdisciplinary field with high potential to interface with experimental work.

Tip-enhanced Raman scattering (TERS) and high-resolution bio nano-analysis--a comparison.

PubMed

Deckert-Gaudig, Tanja; Deckert, Volker

2010-10-14

This perspective presents and assesses the development and capabilities of tip-enhanced Raman scattering (TERS) since its discovery in 2000. So far, this technique has proven to be valuable for studies of a variety of inorganic, organic and biochemical specimens. Due to its ability to provide chemical and topographic characterization in a single experiment at a sub-100 nm resolution, TERS has gained importance in super-resolution structural analysis. In this contribution the focus is set on applications with relevance in the biology and medical fields. The potential and challenges of this near-field technique are discussed with respect to state-of-the-art microscopic and spectroscopic imaging methods. Furthermore, possible ways to surpass current boundaries and an outlook to future projects are presented.

Expanding the chemical information science gateway

PubMed Central

Bajorath, Jürgen

2017-01-01

Broadly defined, chemical information science (CIS) covers chemical structure and data analysis including biological activity data as well as processing, organization, and retrieval of any form of chemical information. The CIS Gateway (CISG) of F1000Research was created to communicate research involving the entire spectrum of chemical information, including chem(o)informatics. CISG provides a forum for high-quality publications and a meaningful alternative to conventional journals. This gateway is supported by leading experts in the field recognizing the need for open science and a flexible publication platform enabling off-the-beaten path contributions. This editorial aims to further rationalize the scope of CISG, position it within its scientific environment, and open it up to a wider audience. Chemical information science is an interdisciplinary field with high potential to interface with experimental work. PMID:29043072

Meeting Report: Synthetic Biology Jamboree for Undergraduates

ERIC Educational Resources Information Center

Campbell, A. Malcolm

2005-01-01

The field of synthetic biology (the name is derived from an analogy to synthetic chemistry) has recognized itself as a "field" only since about 2002. Synthetic biology has gotten some high-profile attention recently, but most people are not aware the field even exists. Synthetic biologists apply engineering principles to genomic circuits to…

CO2 Flux From Antarctic Dry Valley Soils: Determining the Source and Environmental Controls

NASA Astrophysics Data System (ADS)

Risk, D. A.; Macintyre, C. M.; Shanhun, F.; Almond, P. C.; Lee, C.; Cary, C.

2014-12-01

Soils within the McMurdo Dry Valleys are known to respire carbon dioxide (CO2), but considerable debate surrounds the contributing sources and mechanisms that drive temporal variability. While some of the CO2 is of biological origin, other known contributors to variability include geochemical sources within, or beneath, the soil column. The relative contribution from each of these sources will depend on seasonal and environmental drivers such as temperature and wind that exert influence on temporal dynamics. To supplement a long term CO2­ surface flux monitoring station that has now recorded fluxes over three full annual cycles, in January 2014 an automated flux and depth concentration monitoring system was installed in the Spaulding Pond area of Taylor Valley, along with standard meteorological sensors, to assist in defining source contributions through time. During two weeks of data we observed marked diel variability in CO2 concentrations within the profile (~100 ppm CO2 above or below atmospheric), and of CO2 moving across the soil surface. The pattern at many depths suggested an alternating diel-scale transition from source to sink that seemed clearly correlated with temperature-driven changes in the solubility of CO2 in water films. This CO2 solution storage flux was very highly coupled to soil temperature. A small depth source of unknown origin also appeared to be present. A controlled laboratory soil experiment was conducted to confirm the magnitude of fluxes into and out of soil water films, and confirmed the field results and temperature dependence. Ultimately, this solution storage flux needs to be well understood if the small biological fluxes from these soils are to be properly quantified and monitored for change. Here, we present results from the 2013/2014 field season and these supplementary experiments, placed in the context of 3 year long term continuous measurement of soil CO2 flux within the Dry Valleys.

Early life stages contribute strongly to local adaptation in Arabidopsis thaliana.

PubMed

Postma, Froukje M; Ågren, Jon

2016-07-05

The magnitude and genetic basis of local adaptation is of fundamental interest in evolutionary biology. However, field experiments usually do not consider early life stages, and therefore may underestimate local adaptation and miss genetically based tradeoffs. We examined the contribution of differences in seedling establishment to adaptive differentiation and the genetic architecture of local adaptation using recombinant inbred lines (RIL) derived from a cross between two locally adapted populations (Italy and Sweden) of the annual plant Arabidopsis thaliana We planted freshly matured, dormant seeds (>180 000) representing >200 RILs at the native field sites of the parental genotypes, estimated the strength of selection during different life stages, mapped quantitative trait loci (QTL) for fitness and its components, and quantified selection on seed dormancy. We found that selection during the seedling establishment phase contributed strongly to the fitness advantage of the local genotype at both sites. With one exception, local alleles of the eight distinct establishment QTL were favored. The major QTL for establishment and total fitness showed evidence of a fitness tradeoff and was located in the same region as the major seed dormancy QTL and the dormancy gene DELAY OF GERMINATION 1 (DOG1). RIL seed dormancy could explain variation in seedling establishment and fitness across the life cycle. Our results demonstrate that genetically based differences in traits affecting performance during early life stages can contribute strongly to adaptive differentiation and genetic tradeoffs, and should be considered for a full understanding of the ecology and genetics of local adaptation.

Static magnetic fields: A summary of biological interactions, potential health effects, and exposure guidelines

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

Tenforde, T.S.

1992-05-01

Interest in the mechanisms of interaction and the biological effects of static magnetic fields has increased significantly during the past two decades as a result of the growing number of applications of these fields in research, industry and medicine. A major stimulus for research on the bioeffects of static magnetic fields has been the effort to develop new technologies for energy production and storage that utilize intense magnetic fields (e.g., thermonuclear fusion reactors and superconducting magnet energy storage devices). Interest in the possible biological interactions and health effects of static magnetic fields has also been increased as a result ofmore » recent developments in magnetic levitation as a mode of public transportation. In addition, the rapid emergence of magnetic resonance imaging as a new clinical diagnostic procedure has, in recent years, provided a strong rationale for defining the possible biological effects of magnetic fields with high flux densities. In this review, the principal interaction mechanisms of static magnetic fields will be described, and a summary will be given of the present state of knowledge of the biological, environmental, and human health effects of these fields.« less

A multidisciplinary approach to understand interactions of red wood ants (Formica rufa-group) and geotectonic processes

NASA Astrophysics Data System (ADS)

Berberich, G. M.; Berberich, M. B.; Grumpe, A.; Becker, A.; Tejeda, A.; Simpson, H.; Obamwonyi, S.; Schumann, M.; Hartmann, J.; Wöhler, C.; Ellison, A. M.

2016-12-01

Red wood ants (RWA; Formica rufa-group) are biological indicators of seismically active, gas-permeable faults and nest most successfully atop of them. Exploratory testing of gases in and around RWA nests revealed that geochemical anomalies were absent from nearby, tectonically inactive, areas. Changes in activity patterns of RWA were correlated with regularly changing gas concentrations and tectonic events. Field work was done from March to September 2016 in the seismically active East Eifel Volcanic Field (western Germany) to investigate relationships at time scales of two weeks and, during one month, eight hours, respectively, between activity patterns of F. polyctena recorded and analyzed with an image-based monitoring system (AntCam); gas concentrations (CO2, He, Rn, H2S, CH4) in nests, soil, and nearby mineral springs; CH4 concentrations in nest gas to determine the origin (biogenic, geogenic) of d13CCH4; geophysical processes (seismic events, earth-tides); influences from space weather on Earth's magnetic field (e.g., Kp-index, hourly mean values of the magnetic variations); local weather and climatic conditions. We analyzed geochemical, geophysical, and biological data with spatiotemporal Bayesian statistics and principal component analysis to identify possible causes of associations among RWA activity, degassing, and earthquakes. We observed significantly increased He and Rn concentrations in mineral gas and moderate increases in nest gas after two low-magnitude earthquakes. We expect more unknown geo-bio-correlations following additional analysis on the acquired data. The combination of seismically active fault zones and biological activity in RWA nests may contribute significantly to greenhouse gas emissions and ongoing climatic change. Funded by VW Foundation-Initiative "Experiment!" (Az 91 140).

Spontaneous ultraweak photon emission from biological systems and the endogenous light field.

PubMed

Schwabl, Herbert; Klima, Herbert

2005-04-01

Still one of the most astonishing biological electromagnetic phenomena is the ultraweak photon emission (UPE) from living systems. Organisms and tissues spontaneously emit measurable intensities of light, i.e. photons in the visible part of the electromagnetic spectrum (380-780 nm), in the range from 1 to 1,000 photons x s-1 x cm-2, depending on their condition and vitality. It is important not to confuse UPE from living systems with other biogenic light emitting processes such as bioluminescence or chemiluminescence. This article examines with basic considerations from physics on the quantum nature of photons the empirical phenomenon of UPE. This leads to the description of the non-thermal origin of this radiation. This is in good correspondence with the modern understanding of life phenomena as dissipative processes far from thermodynamic equilibrium. UPE also supports the understanding of life sustaining processes as basically driven by electromagnetic fields. The basic features of UPE, like intensity and spectral distribution, are known in principle for many experimental situations. The UPE of human leukocytes contributes to an endogenous light field of about 1011 photons x s-1 which can be influenced by certain factors. Further research is needed to reveal the statistical properties of UPE and in consequence to answer questions about the underlying mechanics of the biological system. In principle, statistical properties of UPE allow to reconstruct phase-space dynamics of the light emitting structures. Many open questions remain until a proper understanding of the electromagnetic interaction of the human organism can be achieved: which structures act as receptors and emitters for electromagnetic radiation? How is electromagnetic information received and processed within cells?

J D Bernal and the genesis of structural biology

NASA Astrophysics Data System (ADS)

Caffrey, Martin

2007-02-01

I was invited to participate in this Symposium a month or so before the event. At that time however, I knew little about J D Bernal. I vaguely remembered a brief conversation on the topic over a decade ago with Professor Vittorio Luzzati as we ambled around the gardens at the Palace of Varsailles. Vittorio likely knew Bernal through his friend Rosalind Franklin who worked with Bernal at Birbeck College. But beyond that I knew nothing about the man or his science. And so it was most fortunate that Andrew Brown's book J D Bernal: The Sage of Science appeared in 2005 and I was able to call on it. Indeed, much of the material included in this chapter is based on that source and on Dorothy Hodgkin's biographic memoir of J D Bernal, her postgraduate supervisor. Given that this chapter is to be published in a Physics journal I thought it appropriate to provide some background to the theme of my presentation, structural biology. Accordingly, I will begin with an introduction to proteins, one of structural biology's central characters, and to which Bernal devoted much energy and attention. How the molecular structure of a protein determines its activity and function will then be described. Bernal's major contribution in this area was to X-ray crystallography, the primary method by which a protein's structure is determined. The method, and aspects of its development, will be described. I will also make reference to some of Bernal's additional contributions in related fields. Finally, Vincent Casey, the symposium organizer, asked that I comment on how structural biology might impact on society. I will attempt to address that at the close of my presentation.

Teaching Biology Field Courses in the Wake of Environmental Disasters.

ERIC Educational Resources Information Center

Baca, Bart J.

1982-01-01

A biology field course organized to study the effects of the June 1979 Mexican oil spill on the marine biology of the shores of south Texas and Mexico is described, demonstrating how to effectively couple a biology classroom course with a natural or human caused environmental disaster. (Author/DC)

The impact of exotic parasitoids on populations of a native Hawaiian moth assessed using life table studies.

PubMed

Kaufman, Leyla V; Wright, Mark G

2009-03-01

The impact of alien species on native organisms is a cause for concern worldwide, with biological invasions commonplace today. Suppression efforts targeting many invasive species have included introductions of biological control agents. The numerous releases of biological control agents in the Hawaiian archipelago have resulted in considerable concern for non-target impacts, due to high levels of non-target parasitism observed to occur in some cases. This study investigated the impact of introduced Hymenoptera parasitoids on a Hawaiian moth. The endemic Hawaiian moth Udea stellata (Butler) has seven alien parasitoids associated with it, two purposely introduced, three adventive, and two of uncertain origin. The objective of this study was to determine the relative contribution of the seven parasitoid species to the population dynamics of U. stellata by constructing partial life tables. Marginal attack rates and associated k-values were calculated to allow comparison of mortality factors between experimental sites. Sentinel larvae were deployed on potted host plants and left in the field for 3-day intervals in open and exclusion treatments. The factors that contributed to total mortality in the open treatment were: disappearance (42.1%), death due to unknown reasons during rearing (16.5%) and parasitism (4.9%). The open treatment incurred significantly higher larval disappearance compared to the exclusion treatment (7.8%), which suggests that in large part disappearance is the result of predation. Adventive parasitoids inflicted greater total larval mortality attributable to parasitism (97.0%) than purposely introduced species (3.0%).

SIMBIOS Project

NASA Technical Reports Server (NTRS)

Fargion, Giulietta S.; McClain, Charles R.

2002-01-01

The purpose of this technical report is to provide current documentation of the Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project activities, NASA Research Announcement (NRA) research status, satellite data processing, data product validation, and field calibration. This documentation is necessary to ensure that critical information is related to the scientific community and NASA management. This critical information includes the technical difficulties and challenges of validating and combining ocean color data from an array of independent satellite systems to form consistent and accurate global bio-optical time series products. This technical report is not meant as a substitute for scientific literature. Instead, it will provide a ready and responsive vehicle for the multitude of technical reports issued by an operational project. The SIMBIOS Science Team Principal Investigators' (PIs) original contributions to this report are in chapters four and above. The purpose of these contributions is to describe the current research status of the SIMBIOS-NRA-96 funded research. The contributions are published as submitted, with the exception of minor edits to correct obvious grammatical or clerical errors.

Super-resolution photoacoustic microscopy using a localized near-field of a plasmonic nanoaperture: a three-dimensional simulation study

NASA Astrophysics Data System (ADS)

Park, Byullee; Lee, Hongki; Upputuri, Paul Kumar; Pramanik, Manojit; Kim, Donghyun; Kim, Chulhong

2018-02-01

Super-resolution microscopy has been increasingly important to delineate nanoscale biological structures or nanoparticles. With these increasing demands, several imaging modalities, including super-resolution fluorescence microscope (SRFM) and electron microscope (EM), have been developed and commercialized. These modalities achieve nanoscale resolution, however, SRFM cannot image without fluorescence, and sample preparation of EM is not suitable for biological specimens. To overcome those disadvantages, we have numerically studied the possibility of superresolution photoacoustic microscopy (SR-PAM) based on near-field localization of light. Photoacoustic (PA) signal is generally acquired based on optical absorption contrast; thus it requires no agents or pre-processing for the samples. The lateral resolution of the conventional photoacoustic microscopy is limited to 200 nm by diffraction limit, therefore reducing the lateral resolution is a major research impetus. Our approach to breaking resolution limit is to use laser pulses of extremely small spot size as a light source. In this research, we simulated the PA signal by constructing the three dimensional SR-PAM system environment using the k-Wave toolbox. As the light source, we simulated ultrashort light pulses using geometrical nanoaperture with near-field localization of surface plasmons. Through the PA simulation, we have successfully distinguish cuboids spaced 3 nm apart. In the near future, we will develop the SR-PAM and it will contribute to biomedical and material sciences.

Relative Contributions of Selected Teachers' Variables and Students' Attitudes toward Academic Achievement in Biology among Senior Secondary School Students in Ondo State, Nigeria

ERIC Educational Resources Information Center

Gbore, L. O.; Daramola, C. A.

2013-01-01

This study investigated the relative contributions of selected teachers' variables and students' attitude towards academic achievement in biology among senior secondary schools in Ondo State, Nigeria. It involved descriptive survey research and ex-post facto research designs. The sample, 360 respondents which consists of 180 biology teachers and…

Complementarity among natural enemies enhances pest suppression.

PubMed

Dainese, Matteo; Schneider, Gudrun; Krauss, Jochen; Steffan-Dewenter, Ingolf

2017-08-15

Natural enemies have been shown to be effective agents for controlling insect pests in crops. However, it remains unclear how different natural enemy guilds contribute to the regulation of pests and how this might be modulated by landscape context. In a field exclusion experiment in oilseed rape (OSR), we found that parasitoids and ground-dwelling predators acted in a complementary way to suppress pollen beetles, suggesting that pest control by multiple enemies attacking a pest during different periods of its occurrence in the field improves biological control efficacy. The density of pollen beetle significantly decreased with an increased proportion of non-crop habitats in the landscape. Parasitism had a strong effect on pollen beetle numbers in landscapes with a low or intermediate proportion of non-crop habitats, but not in complex landscapes. Our results underline the importance of different natural enemy guilds to pest regulation in crops, and demonstrate how biological control can be strengthened by complementarity among natural enemies. The optimization of natural pest control by adoption of specific management practices at local and landscape scales, such as establishing non-crop areas, low-impact tillage, and temporal crop rotation, could significantly reduce dependence on pesticides and foster yield stability through ecological intensification in agriculture.

Genome-environment interactions and prospective technology assessment: evolution from pharmacogenomics to nutrigenomics and ecogenomics.

PubMed

Ozdemir, Vural; Motulsky, Arno G; Kolker, Eugene; Godard, Béatrice

2009-02-01

The relationships between food, nutrition science, and health outcomes have been mapped over the past century. Genomic variation among individuals and populations is a new factor that enriches and challenges our understanding of these complex relationships. Hence, the confluence of nutritional science and genomics-nutrigenomics--was the focus of the OMICS: A Journal of Integrative Biology in December 2008 (Part 1). The 2009 Special Issue (Part 2) concludes the analysis of nutrigenomics research and innovations. Together, these two issues expand the scope and depth of critical scholarship in nutrigenomics, in keeping with an integrated multidisciplinary analysis across the bioscience, omics technology, social, ethical, intellectual property and policy dimensions. Historically, the field of pharmacogenetics provided the first examples of specifically identifiable gene variants predisposing to unexpected responses to drugs since the 1950s. Brewer coined the term ecogenetics in 1971 to broaden the concept of gene-environment interactions from drugs and nutrition to include environmental agents in general. In the mid-1990s, introduction of high-throughput technologies led to the terms pharmacogenomics, nutrigenomics and ecogenomics to describe, respectively, the contribution of genomic variability to differential responses to drugs, food, and environment defined in the broadest sense. The distinctions, if any, between these newer fields (e.g., nutrigenomics) and their predecessors (e.g., nutrigenetics) remain to be delineated. For nutrigenomics, its reliance on genome-wide analyses may lead to detection of new biological mechanisms governing host response to food. Recognizing "genome-environment interactions" as the conceptual thread that connects and runs through pharmacogenomics, nutrigenomics, and ecogenomics may contribute toward anticipatory governance and prospective real-time analysis of these omics fields. Such real-time analysis of omics technologies and innovations is crucial, because it can influence and positively shape them as these approaches develop, and help avoid predictable pitfalls, and thus ensure their effective and ethical application in the laboratory, clinic, and society.

HONO fluxes from soil surfaces: an overview

NASA Astrophysics Data System (ADS)

Wu, Dianming; Sörgel, Matthias; Tamm, Alexandra; Ruckteschler, Nina; Rodriguez-Caballero, Emilio; Cheng, Yafang; Pöschl, Ulrich; Weber, Bettina

2016-04-01

Gaseous nitrous acid (HONO) contributes up to 80% of atmospheric hydroxyl (OH) radicals and is also linked to health risks through reactions with tobacco smoke forming carcinogens. Field and modeling results suggested a large unknown HONO source in the troposphere during daytime. By measuring near ground HONO mixing ratio, up to 30% of HONO can be released from forest, rural and urban ground as well as snow surfaces. This source has been proposed to heterogeneous reactions of nitrogen dioxide (NO2) on humic acid surfaces or nitric acid photolysis. Laboratory studies showed that HONO emissions from bulk soil samples can reach 258 ng m-2 s-1 (in term of nitrogen), which corresponding to 1.1 × 1012 molecules cm-2 s-1and ˜ 100 times higher than most of the field studies, as measured by a dynamic chamber system. The potential mechanisms for soil HONO emissions include chemical equilibrium of acid-base reaction and gas-liquid partitioning between soil nitrite and HONO, but the positive correlation of HONO fluxes with pH (largest at neutral and slightly alkaline) points to the dominance of the formation process by ammonia-oxidizing bacteria (AOB). In general soil surface acidity, nitrite concentration and abundance of ammonia-oxidizing bacteria mainly regulate the HONO release from soil. A recent study showed that biological soil crusts in drylands can also emit large quantities of HONO and NO, corresponding to ˜20% of global nitrogen oxide emissions from soils under natural vegetation. Due to large concentrations of microorganisms in biological soil crusts, particularly high HONO and NO emissions were measured after wetting events. Considering large areas of arid and arable lands as well as peatlands, up to 70% of global soils are able to emitting HONO. However, the discrepancy between large soil HONO emissions measured in lab and low contributions of HONO flux from ground surfaces in field as well as the role of microorganisms should be further investigated.

[Contributions to a feminist anthropology of health: the study of the menstrual cycle].

PubMed

Rodríguez, Maribel Blázquez; Gallardo, Eva Bolaños

2017-01-01

Medical or Health Anthropology focused on the study of women continues to be a main area of anthropological study in Spain. The contributions of two referential figures in feminist health anthropology, Marcia Inhorn and Mari Luz Esteban, are applied to review the findings of a qualitative research study on the menstrual cycle carried out through 20 interviews with women between the ages of 16 and 44 years, between 2013 and 2014, in the municipality of Madrid. The analysis shows that menstruation is a clear example of the reproductive essentialization of women, of biological reductionism, of the medicalization of women's bodies and, above all, of the standardization of bodies. The visibilization and questioning of these assumptions through the voices of the women interviewed highlight the importance of this field within medical anthropology.

Pharmacogenomics in pediatric rheumatology.

PubMed

Becker, Mara L

2012-09-01

Despite major advancements in therapeutics, variability in drug response remains a challenge in both adults and children diagnosed with rheumatic disease. The genetic contribution to interindividual variability has emerged as a promising avenue of exploration; however, challenges remain in making this knowledge relevant in the clinical realm. New genetic associations in patients with rheumatic disease have been reported for disease modifying antirheumatic drugs, antimetabolites and biologic drugs. However, many of these findings are in need of replication, and few have taken into account the concept of ontogeny, specific to pediatrics. In the current era in which we practice, genetic variation will undoubtedly contribute to variability in therapeutic response and may be a factor that will ultimately impact individualized care. However, preliminary studies have shown that there are many hurdles that need to be overcome as we explore pharmacogenomic associations specifically in the field of pediatric rheumatology.

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.

Glucose Oxidase Biosensor Modeling and Predictors Optimization by Machine Learning Methods.

PubMed

Gonzalez-Navarro, Felix F; Stilianova-Stoytcheva, Margarita; Renteria-Gutierrez, Livier; Belanche-Muñoz, Lluís A; Flores-Rios, Brenda L; Ibarra-Esquer, Jorge E

2016-10-26

Biosensors are small analytical devices incorporating a biological recognition element and a physico-chemical transducer to convert a biological signal into an electrical reading. Nowadays, their technological appeal resides in their fast performance, high sensitivity and continuous measuring capabilities; however, a full understanding is still under research. This paper aims to contribute to this growing field of biotechnology, with a focus on Glucose-Oxidase Biosensor (GOB) modeling through statistical learning methods from a regression perspective. We model the amperometric response of a GOB with dependent variables under different conditions, such as temperature, benzoquinone, pH and glucose concentrations, by means of several machine learning algorithms. Since the sensitivity of a GOB response is strongly related to these dependent variables, their interactions should be optimized to maximize the output signal, for which a genetic algorithm and simulated annealing are used. We report a model that shows a good generalization error and is consistent with the optimization.

Planting molecular functions in an ecological context with Arabidopsis thaliana.

PubMed

Krämer, Ute

2015-03-25

The vascular plant Arabidopsis thaliana is a central genetic model and universal reference organism in plant and crop science. The successful integration of different fields of research in the study of A. thaliana has made a large contribution to our molecular understanding of key concepts in biology. The availability and active development of experimental tools and resources, in combination with the accessibility of a wealth of cumulatively acquired knowledge about this plant, support the most advanced systems biology approaches among all land plants. Research in molecular ecology and evolution has also brought the natural history of A. thaliana into the limelight. This article showcases our current knowledge of the natural history of A. thaliana from the perspective of the most closely related plant species, providing an evolutionary framework for interpreting novel findings and for developing new hypotheses based on our knowledge of this plant.

Adoption: biological and social processes linked to adaptation.

PubMed

Grotevant, Harold D; McDermott, Jennifer M

2014-01-01

Children join adoptive families through domestic adoption from the public child welfare system, infant adoption through private agencies, and international adoption. Each pathway presents distinctive developmental opportunities and challenges. Adopted children are at higher risk than the general population for problems with adaptation, especially externalizing, internalizing, and attention problems. This review moves beyond the field's emphasis on adoptee-nonadoptee differences to highlight biological and social processes that affect adaptation of adoptees across time. The experience of stress, whether prenatal, postnatal/preadoption, or during the adoption transition, can have significant impacts on the developing neuroendocrine system. These effects can contribute to problems with physical growth, brain development, and sleep, activating cascading effects on social, emotional, and cognitive development. Family processes involving contact between adoptive and birth family members, co-parenting in gay and lesbian adoptive families, and racial socialization in transracially adoptive families affect social development of adopted children into adulthood.

Comparative 3D QSAR study on β1-, β2-, and β3-adrenoceptor agonists

PubMed Central

Senthil Kumar, P.

2009-01-01

A quantitative structure–activity relationship study of tryptamine-based derivatives of β1-, β2-, and β3-adrenoceptor agonists was conducted using comparative molecular field analysis (CoMFA). Correlation coefficients (cross-validated r2) of 0.578, 0.595, and 0.558 were obtained for the three subtypes, respectively, in three different CoMFA models. All three CoMFA models have different steric and electrostatic contributions, implying different requirements inside the binding cavity. The CoMFA coefficient contour plots of the three models and comparisons among these plots provide clues regarding the main chemical features responsible for the biological activity variations and also result in predictions which correlate very well with the observed biological activity. Based on the analysis, a summary regeospecific description of the requirements for improving β-adrenoceptor subtype selectivity is given. PMID:21170122

Nitrogen transformations in modern agriculture and the role of biological nitrification inhibition.

PubMed

Coskun, Devrim; Britto, Dev T; Shi, Weiming; Kronzucker, Herbert J

2017-06-06

The nitrogen (N)-use efficiency of agricultural plants is notoriously poor. Globally, about 50% of the N fertilizer applied to cropping systems is not absorbed by plants, but lost to the environment as ammonia (NH 3 ), nitrate (NO 3 - ), and nitrous oxide (N 2 O, a greenhouse gas with 300 times the heat-trapping capacity of carbon dioxide), raising agricultural production costs and contributing to pollution and climate change. These losses are driven by volatilization of NH 3 and by a matrix of nitrification and denitrification reactions catalysed by soil microorganisms (chiefly bacteria and archaea). Here, we discuss mitigation of the harmful and wasteful process of agricultural N loss via biological nitrification inhibitors (BNIs) exuded by plant roots. We examine key recent discoveries in the emerging field of BNI research, focusing on BNI compounds and their specificity and transport, and discuss prospects for their role in improving agriculture while reducing its environmental impact.

Small group gender ratios impact biology class performance and peer evaluations.

PubMed

Sullivan, Lauren L; Ballen, Cissy J; Cotner, Sehoya

2018-01-01

Women are underrepresented in science, technology, engineering, and mathematics (STEM) disciplines. Evidence suggests the microclimate of the classroom is an important factor influencing female course grades and interest, which encourages retention of women in STEM fields. Here, we test whether the gender composition of small (8-9 person) learning groups impacts course performance, sense of social belonging, and intragroup peer evaluations of intellectual contributions. Across two undergraduate active learning courses in introductory biology, we manipulated the classroom microclimate by varying the gender ratios of learning groups, ranging from 0% female to 100% female. We found that as the percent of women in groups increased, so did overall course performance for all students, regardless of gender. Additionally, women assigned higher peer- evaluations in groups with more women than groups with less women. Our work demonstrates an added benefit of the retention of women in STEM: increased performance for all, and positive peer perceptions for women.

[The assimilation of the books on animals of Aristotle in the medicine of Arnau de Vilanova (c. 1240-1311)].

PubMed

2015-01-01

The Latin translation of Aristotle's books on animals, which was carried out during the middle ages, lead to the dissemination of new theories in the field of biology and zoology in the western culture. From the second half of the 13th century, this group of books contributed to the development of a new medical practice based on the recovery of classical authorities and natural philosophy. On different occasions, Arnau de Vilanova (c. 1240-1311)--one of the most preeminent physicians of the Latin middle ages--used the books on animals to describe biological and physiological processes, and also to formulate a new medical discipline within the framework of discussions between natural philosophy and medicine in Montpellier; this took place at the end of the 13th century and early 14h century.

Soil Physicochemical and Biological Properties of Paddy-Upland Rotation: A Review

PubMed Central

Lv, Teng-Fei; Chen, Yong; Westby, Anthony P.; Ren, Wan-Jun

2014-01-01

Paddy-upland rotation is an unavoidable cropping system for Asia to meet the increasing demand for food. The reduction in grain yields has increased the research interest on the soil properties of rice-based cropping systems. Paddy-upland rotation fields are unique from other wetland or upland soils, because they are associated with frequent cycling between wetting and drying under anaerobic and aerobic conditions; such rotations affect the soil C and N cycles, make the chemical speciation and biological effectiveness of soil nutrient elements varied with seasons, increase the diversity of soil organisms, and make the soil physical properties more difficult to analyze. Consequently, maintaining or improving soil quality at a desirable level has become a complicated issue. Therefore, fully understanding the soil characteristics of paddy-upland rotation is necessary for the sustainable development of the system. In this paper, we offer helpful insight into the effect of rice-upland combinations on the soil chemical, physical, and biological properties, which could provide guidance for reasonable cultivation management measures and contribute to the improvement of soil quality and crop yield. PMID:24995366

A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes.

PubMed

Mueller, A J; Tew, S R; Vasieva, O; Clegg, P D; Canty-Laird, E G

2016-09-27

Phenotypic plasticity of adult somatic cells has provided emerging avenues for the development of regenerative therapeutics. In musculoskeletal biology the mechanistic regulatory networks of genes governing the phenotypic plasticity of cartilage and tendon cells has not been considered systematically. Additionally, a lack of strategies to effectively reproduce in vitro functional models of cartilage and tendon is retarding progress in this field. De- and redifferentiation represent phenotypic transitions that may contribute to loss of function in ageing musculoskeletal tissues. Applying a systems biology network analysis approach to global gene expression profiles derived from common in vitro culture systems (monolayer and three-dimensional cultures) this study demonstrates common regulatory mechanisms governing de- and redifferentiation transitions in cartilage and tendon cells. Furthermore, evidence of convergence of gene expression profiles during monolayer expansion of cartilage and tendon cells, and the expression of key developmental markers, challenges the physiological relevance of this culture system. The study also suggests that oxidative stress and PI3K signalling pathways are key modulators of in vitro phenotypes for cells of musculoskeletal origin.

Development of an Item Bank for the Assessment of Knowledge on Biology in Argentine University Students.

PubMed

Cupani, Marcos; Zamparella, Tatiana Castro; Piumatti, Gisella; Vinculado, Grupo

The calibration of item banks provides the basis for computerized adaptive testing that ensures high diagnostic precision and minimizes participants' test burden. This study aims to develop a bank of items to measure the level of Knowledge on Biology using the Rasch model. The sample consisted of 1219 participants that studied in different faculties of the National University of Cordoba (mean age = 21.85 years, SD = 4.66; 66.9% are women). The items were organized in different forms and into separate subtests, with some common items across subtests. The students were told they had to answer 60 questions of knowledge on biology. Evaluation of Rasch model fit (Zstd >|2.0|), differential item functioning, dimensionality, local independence, item and person separation (>2.0), and reliability (>.80) resulted in a bank of 180 items with good psychometric properties. The bank provides items with a wide range of content coverage and may serve as a sound basis for computerized adaptive testing applications. The contribution of this work is significant in the field of educational assessment in Argentina.

The Enigma of Tripeptidyl-Peptidase II: Dual Roles in Housekeeping and Stress

PubMed Central

Preta, Giulio; de Klark, Rainier; Gavioli, Riccardo; Glas, Rickard

2010-01-01

The tripeptidyl-peptidase II complex consists of repeated 138 kDa subunits, assembled into two twisted strands that form a high molecular weight complex (>5 MDa). TPPII, like many other cytosolic peptidases, plays a role in the ubiquitin-proteasome pathway downstream of the proteasome as well as in the production and destruction of MHC class I antigens and degradation of neuropeptides. Tripeptidyl-peptidase II activity is increased in cells with an increased demand for protein degradation, but whether degradation of cytosolic peptides is the only cell biological role for TPPII has remained unclear. Recent data indicated that TPPII translocates into the nucleus to control DNA damage responses in malignant cells, supporting that cytosolic “housekeeping peptidases” may have additional roles in cell biology, besides their contribution to protein turnover. Overall, TPPII has an emerging importance in several cancer-related fields, such as metabolism, cell death control, and control of genome integrity; roles that are not understood in detail. The present paper reviews the cell biology of TPPII and discusses distinct roles for TPPII in the nucleus and cytosol. PMID:20847939

An octopus-bioinspired solution to movement and manipulation for soft robots.

PubMed

Calisti, M; Giorelli, M; Levy, G; Mazzolai, B; Hochner, B; Laschi, C; Dario, P

2011-09-01

Soft robotics is a challenging and promising branch of robotics. It can drive significant improvements across various fields of traditional robotics, and contribute solutions to basic problems such as locomotion and manipulation in unstructured environments. A challenging task for soft robotics is to build and control soft robots able to exert effective forces. In recent years, biology has inspired several solutions to such complex problems. This study aims at investigating the smart solution that the Octopus vulgaris adopts to perform a crawling movement, with the same limbs used for grasping and manipulation. An ad hoc robot was designed and built taking as a reference a biological hypothesis on crawling. A silicone arm with cables embedded to replicate the functionality of the arm muscles of the octopus was built. This novel arm is capable of pushing-based locomotion and object grasping, mimicking the movements that octopuses adopt when crawling. The results support the biological observations and clearly show a suitable way to build a more complex soft robot that, with minimum control, can perform diverse tasks.

Virtual Round Table on ten leading questions for network research

NASA Astrophysics Data System (ADS)

2004-03-01

The following discussion is an edited summary of the public debate started during the conference “Growing Networks and Graphs in Statistical Physics, Finance, Biology and Social Systems” held in Rome in September 2003. Drafts documents were circulated electronically among experts in the field and additions and follow-up to the original discussion have been included. Among the scientists participating to the discussion L.A.N. Amaral, A. Barrat, A.L. Barabasi, G. Caldarelli, P. De Los Rios, A. Erzan, B. Kahng, R. Mantegna, J.F.F. Mendes, R. Pastor-Satorras, A. Vespignani are acknowledged for their contributions and editing.

Partial automation of database processing of simulation outputs from L-systems models of plant morphogenesis.

PubMed

Chen, Yi- Ping Phoebe; Hanan, Jim

2002-01-01

Models of plant architecture allow us to explore how genotype environment interactions effect the development of plant phenotypes. Such models generate masses of data organised in complex hierarchies. This paper presents a generic system for creating and automatically populating a relational database from data generated by the widely used L-system approach to modelling plant morphogenesis. Techniques from compiler technology are applied to generate attributes (new fields) in the database, to simplify query development for the recursively-structured branching relationship. Use of biological terminology in an interactive query builder contributes towards making the system biologist-friendly.

Integrating evolutionary game theory into epigenetic study of embryonic development. Comment on ;Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition; by Qian Wang et al.

NASA Astrophysics Data System (ADS)

Wang, Zuoheng

2017-03-01

DNA methylation is an essential component in the epigenetic regulation of embryonic development, and plays a crucial role in various biological processes, including repression of gene transcription, parent-of-origin genomic imprinting, and X-chromosome inactivation [1-5]. Understanding the epigenetic processes in different stages of embryo development has become an important research topic in the field. It has potential to offer new insight into reproductive medicine and contribute to the improvement of long-term health outcomes.

The Gut Microbiome as Therapeutic Target in Central Nervous System Diseases: Implications for Stroke.

PubMed

Winek, Katarzyna; Dirnagl, Ulrich; Meisel, Andreas

2016-10-01

Research on commensal microbiota and its contribution to health and disease is a new and very dynamically developing field of biology and medicine. Recent experimental and clinical investigations underscore the importance of gut microbiota in the pathogenesis and course of stroke. Importantly, microbiota may influence the outcome of cerebral ischemia by modulating central nervous system antigen-specific immune responses. In this review we summarize studies linking gut microbiota with physiological function and disorders of the central nervous system. Based on these insights we speculate about targeting the gut microbiome in order to treat stroke.

Handbook of ecotoxicology, second edition

USGS Publications Warehouse

Hoffman, David J.; Rattner, Barnett A.; Burton, G. Allen; Cairns, John

2003-01-01

Handbook of Ecotoxicology, Second Edition focuses on toxic substances and how they affect ecosystems worldwide. It presents methods for quantifying and measuring ecotoxicological effects in the field and in the lab, as well as methods for estimating, predicting, and modeling in ecotoxicology studies. Completely revised and updated with 18 new chapters, this second edition includes contributions from over 75 international experts. Also, a Technical Review Board reviewed all manuscripts for accuracy and currency. This authoritative work is the definitive reference for students, researchers, consultants, and other professionals in the environmental sciences, toxicology, chemistry, biology, and ecology - in academia, industry, and government.

Pervasive transcription: detecting functional RNAs in bacteria.

PubMed

Lybecker, Meghan; Bilusic, Ivana; Raghavan, Rahul

2014-01-01

Pervasive, or genome-wide, transcription has been reported in all domains of life. In bacteria, most pervasive transcription occurs antisense to protein-coding transcripts, although recently a new class of pervasive RNAs was identified that originates from within annotated genes. Initially considered to be non-functional transcriptional noise, pervasive transcription is increasingly being recognized as important in regulating gene expression. The function of pervasive transcription is an extensively debated question in the field of transcriptomics and regulatory RNA biology. Here, we highlight the most recent contributions addressing the purpose of pervasive transcription in bacteria and discuss their implications.

Magnetic field effects in proteins

NASA Astrophysics Data System (ADS)

Jones, Alex R.

2016-06-01

Many animals can sense the geomagnetic field, which appears to aid in behaviours such as migration. The influence of man-made magnetic fields on biology, however, is potentially more sinister, with adverse health effects being claimed from exposure to fields from mobile phones or high voltage power lines. Do these phenomena have a common, biophysical origin, and is it even plausible that such weak fields can profoundly impact noisy biological systems? Radical pair intermediates are widespread in protein reaction mechanisms, and the radical pair mechanism has risen to prominence as perhaps the most plausible means by which even very weak fields might impact biology. In this New Views article, I will discuss the literature over the past 40 years that has investigated the topic of magnetic field effects in proteins. The lack of reproducible results has cast a shadow over the area. However, magnetic field and spin effects have proven to be useful mechanistic tools for radical mechanism in biology. Moreover, if a magnetic effect on a radical pair mechanism in a protein were to influence a biological system, the conditions necessary for it to do so appear increasing unlikely to have come about by chance.

Computational analyses in cognitive neuroscience: in defense of biological implausibility.

PubMed

Dror, I E; Gallogly, D P

1999-06-01

Because cognitive neuroscience researchers attempt to understand the human mind by bridging behavior and brain, they expect computational analyses to be biologically plausible. In this paper, biologically implausible computational analyses are shown to have critical and essential roles in the various stages and domains of cognitive neuroscience research. Specifically, biologically implausible computational analyses can contribute to (1) understanding and characterizing the problem that is being studied, (2) examining the availability of information and its representation, and (3) evaluating and understanding the neuronal solution. In the context of the distinct types of contributions made by certain computational analyses, the biological plausibility of those analyses is altogether irrelevant. These biologically implausible models are nevertheless relevant and important for biologically driven research.

FOREWORD: Focus on nanobiomaterials and technologies for breakthrough in future medicine Focus on nanobiomaterials and technologies for breakthrough in future medicine

NASA Astrophysics Data System (ADS)

Miyahara, Yuji; Kobayashi, Hisatoshi; Chen, Guoping; Kikuchi, Masanori

2010-02-01

In biomedical fields, various materials are used for different purposes such as therapy, diagnostics and drugs. Some of them come into direct contact with blood and tissues in the human body, while many others are used in advanced medical equipment. Without these materials, current advances in medicine would never be achieved. Even in the 21st century, we still face the challenge of incurable or intractable diseases such as cancer, as well as the emergence of new infectious diseases. Global action is necessary to deal with these issues. Recent developments in nanoscience and nanotechnology have provided new strategies for material design that are based on the structural control of atoms and molecules. These strategies have revolutionized the field of advanced functional materials. Their combination with the enormous amount of knowledge in molecular and cellular biology accumulated over the last few decades has lead to the conception of new medical technologies. These technologies are represented in cell therapy, drug targeting and regenerative medicine, and are being widely and intensively investigated for realization at an industrial scale. In order to find solutions to remaining issues in life science, it is necessary to accelerate the fusion between nano- and biotechnologies and to promote research and development in these interdisciplinary fields. In this context, National Institute for Materials Science (NIMS)—one of the leading research institutes in the field of materials science—held a series of symposia in the week of 21-24 July 2009, 'NIMS Week 2009' and 'Nanobio-materials and technologies: breakthrough for future medicine', that aimed to present advances in medical fields from the perspective of materials science and technologies. During NIMS Week, various activities were carried out, including perspective reviews and invited lectures by international leading researchers in the 'nanobio' field, in addition to four organized sessions and related satellite symposia. Professor Kazunori Kataoka of the University of Tokyo received the NIMS Award 2009 for his outstanding research achievements and contributions to developing functional nanodevices for drug and gene delivery. This focus issue includes his review article 'Multifunctional nanoassemblies of block copolymers for future cancer therapy'. Eleven other plenary and invited speakers from NIMS Week 2009 have contributed review articles that may have great impact on research and development in nanobiomaterials and technologies Research in the nanobio field requires multi-disciplinary collaboration between specialists in biology, medicine, chemistry, physics, electronics, material engineering and other areas. We believe that this focus issue contains useful information for these researchers and provides an outline of breakthroughs for future medicine.

Field Markup Language: biological field representation in XML.

PubMed

Chang, David; Lovell, Nigel H; Dokos, Socrates

2007-01-01

With an ever increasing number of biological models available on the internet, a standardized modeling framework is required to allow information to be accessed or visualized. Based on the Physiome Modeling Framework, the Field Markup Language (FML) is being developed to describe and exchange field information for biological models. In this paper, we describe the basic features of FML, its supporting application framework and its ability to incorporate CellML models to construct tissue-scale biological models. As a typical application example, we present a spatially-heterogeneous cardiac pacemaker model which utilizes both FML and CellML to describe and solve the underlying equations of electrical activation and propagation.

Varieties of noise: analogical reasoning in synthetic biology.

PubMed

Knuuttila, Tarja; Loettgers, Andrea

2014-12-01

The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue that the actual situation is more nuanced and complex. Synthetic biology is a highly interdisciplinary field of research located at the interface of physics, chemistry, biology, and computational science. All of these fields provide concepts, metaphors, mathematical tools, and models, which are typically utilized by synthetic biologists by drawing analogies between the different fields of inquiry. We will study analogical reasoning in synthetic biology through the emergence of the functional meaning of noise, which marks an important shift in how engineering concepts are employed in this field. The notion of noise serves also to highlight the differences between the two branches of synthetic biology: the basic science-oriented branch and the engineering-oriented branch, which differ from each other in the way they draw analogies to various other fields of study. Moreover, we show that fixing the mapping between a source domain and the target domain seems not to be the goal of analogical reasoning in actual scientific practice.

High spatial resolution microdosimetry with monolithic ΔE-E detector on 12C beam: Monte Carlo simulations and experiment

NASA Astrophysics Data System (ADS)

Tran, Linh T.; Bolst, David; Guatelli, Susanna; Biasi, Giordano; Fazzi, Alberto; Sagia, Eleni; Prokopovich, Dale A.; Reinhard, Mark I.; Keat, Ying C.; Petasecca, Marco; Lerch, Michael L. F.; Pola, Andrea; Agosteo, Stefano; Matsufuji, Naruhiro; Jackson, Michael; Rosenfeld, Anatoly B.

2018-04-01

Nuclear fragmentation produced in 12C ion therapeutic beams contributes significantly to the Relative Biological Effectiveness (RBE)-weighted dose in the distal edge of the Spread out Bragg Peak (SOBP) and surrounding tissues in out-of-field. Complex mixed radiation field originated by the therapeutic 12C ion beam in a phantom is difficult to measure. This study presents a new method to characterise the radiation field produced in a 12C ion beam using a monolithic ΔE-E telescope which provides the capability to identify the particle components of the mixed radiation field as well as the microdosimetric spectra that allows derivation of the RBE based on a radiobiological model. The response of the monolithic ΔE-E telescope to a 290 MeV/u 12C ion beam at defined positions along the pristine Bragg Peak was studied using the Geant4 Monte Carlo toolkit. The microdosimetric spectra derived from the ΔE stage and the two-dimensional scatter plots of energy deposition in ΔE and E stages of the device in coincidence are presented, as calculated in-field and out-of-field. Partial dose weighted contribution to the microdosimetric spectra from nuclear fragments and recoils, such as 1H, 4He, 3He, 7Li, 9Be and 11B, have been analysed for each position. Comparison of simulation and experimental results are presented and demonstrates that the microdosimetric spectra changes dramatically within 0.5 mm depth increments close to and at the distal edge of the Bragg Peak which is impossible to identify using conventional Tissue Equivalent Proportional Counter (TEPC).

What makes the desert bloom? Contribution of dust and crusts to soil fertility on the Colorado Plateau

Treesearch

Jayne Belnap; Richard Reynolds; Marith Reheis; Susan L. Phillips

2001-01-01

Eolian dust (windblown silt and clay) and biological soil crusts are both important to ecosystem functioning of arid lands. Dust furnishes essential nutrients, influences hydrology, contributes to soil formation, and renders surfaces vulnerable to erosion. Biological soil crusts contribute directly to soil fertility by fixing carbon and nitrogen, and indirectly by...

Environmental Variability, Bowhead Whale Distributions, and Inupiat Subsistence Whaling in the Coastal Arctic Ocean

NASA Astrophysics Data System (ADS)

Ashjian, C. J.; Campbell, R. G.; George, J. C.; Moore, S. E.; Okkonen, S. R.; Sherr, B. F.; Sherr, E. B.

2006-12-01

The annual migration of bowhead whales (Balaena mysticetus) past Barrow, Alaska has provided subsistence hunting opportunities to Native whalers for centuries. Bowheads regularly feed along the Arctic coast near Barrow in autumn, presumably to utilize recurrent aggregations of their zooplankton prey (e.g., copepods, euphausiids). Oceanographic field-sampling on the narrow continental shelf near Barrow and in Elson Lagoon was conducted during mid-August to mid-September of 2005 and 2006 to describe the different water mass types and plankton communities, to identify exchange of water and material between the shelf and lagoon and offshore, and to identify biological and physical mechanisms of plankton aggregation. High spatial resolution profiles of temperature, salinity, fluorescence, optical backscatter, and C-DOM were collected using an Acrobat undulating towed vehicle in the lagoon and across the shelf from near-shore to the ~150 m isobath. Discrete sampling for nutrients, chlorophyll a, and phytoplankton, and microzooplankton and mesozooplankton abundance and composition was conducted in distinct water types and across frontal boundaries identified from the high-resolution data. The distributions of bowhead whales were documented using aerial surveys. Inter-annual and shorter-term (days to weeks) variability in the distribution of water masses and intrinsic biological properties was observed. Distinct hydrographic and biological-chemical regions were located across the shelf that may contribute to the formation of bowhead whale prey aggregations. The lagoon system is an important interface between the ocean and land and may be critical to the formation of nearshore bowhead whale prey aggregations. Results from the field sampling will be coupled to biological-physical modeling and retrospective analyses to understand the response of this complex environment-whale-human system to climate variability.

Creating biological nanomaterials using synthetic biology.

PubMed

Rice, MaryJoe K; Ruder, Warren C

2014-02-01

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

77 FR 46373 - Field Release of Aphelinus glycinis for the Biological Control of the Soybean Aphid in the...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-03

... Inspection Service [Docket No APHIS-2012-0061] Field Release of Aphelinus glycinis for the Biological Control... for the biological control of the soybean aphid, Aphis glycines, in the continental United States. We... glycinis for the Biological Control of the Soybean Aphid in the Continental United States'' (March 2012...

An investigation of the practice of scientific inquiry in secondary science and agriculture courses

NASA Astrophysics Data System (ADS)

Grady, Julie R.

The purpose of this exploratory qualitative study was to investigate the practice of scientific inquiry in two secondary biology classes and one agriculture class from different schools in different communities. The focus was on teachers' interests and intentions for the students' participation in inquiry, the voices contributing to the inquiry, and students' opportunities to confront their conceptions of the nature of science (NOS). The Partnership for Research and Education in Plants (PREP) served as the context by providing students with opportunities to design and conduct original experiments to help elucidate the function(s) of a disabled gene in Arabidopsis thaliana . Transcripts of teacher and student semi-structured interviews, field notes of classroom observations and classroom conversations, and documents (e.g., student work, teacher handouts, school websites, PREP materials) were analyzed for evidence of the practice of scientific inquiry. Teachers were interested in implementing inquiry because of potential student learning about scientific research and because PREP supports course content and is connected to a larger scientific project outside of the school. Teachers' intentions regarding the implementation of inquiry reflected the complexity of their courses and the students' previous experiences. All inquiries were student-directed. The biology students' participation more closely mirrored the practice of scientists, while the agriculture students were more involved with the procedural display of scientific inquiry. All experiences could have been enhanced from additional knowledge-centered activities regarding scientific reasoning. No activities brought explicit attention to NOS. Biology activities tended to implicitly support NOS while the agriculture class activities tended to implicitly contradict NOS. Scientists' interactions contributed to implied support of the NOS. There were missed opportunities for explicit attention to NOS in all classes. The major voices contributing to the inquiry in all classrooms included those of teachers, students, technology, scientists, textbooks, and mandated standards; however, they were more prevalent in the biology classrooms than the agriculture classroom. The powers influencing the voice frequency may be related to the teachers' own teaching and research experiences, as well as the alignment of the expectations and values of students' participation in scientific inquiry and those associated with the school-classroom communities and the students' identities.

The Midwest Stream Quality Assessment—Influences of human activities on streams

USGS Publications Warehouse

Van Metre, Peter C.; Mahler, Barbara J.; Carlisle, Daren M.; Coles, James F.

2018-04-16

Healthy streams and the fish and other organisms that live in them contribute to our quality of life. Extensive modification of the landscape in the Midwestern United States, however, has profoundly affected the condition of streams. Row crops and pavement have replaced grasslands and woodlands, streams have been straightened, and wetlands and fields have been drained. Runoff from agricultural and urban land brings sediment and chemicals to streams. What is the chemical, physical, and biological condition of Midwestern streams? Which physical and chemical stressors are adversely affecting biological communities, what are their origins, and how might we lessen or avoid their adverse effects?In 2013, the U.S. Geological Survey (USGS) conducted the Midwest Stream Quality Assessment to evaluate how human activities affect the biological condition of Midwestern streams. In collaboration with the U.S. Environmental Protection Agency National Rivers and Streams Assessment, the USGS sampled 100 streams, chosen to be representative of the different types of watersheds in the region. Biological condition was evaluated based on the number and diversity of fish, algae, and invertebrates in the streams. Changes to the physical habitat and chemical characteristics of the streams—“stressors”—were assessed, and their relation to landscape factors and biological condition was explored by using mathematical models. The data and models help us to better understand how the human activities on the landscape are affecting streams in the region.

Into the field: naturalistic education and the future of conservation.

PubMed

Hayes, Mark A

2009-10-01

Some educational psychologists and researchers have argued that there are multiple ways of being intelligent. In the early 1980s, Howard Gardner presented a theory of multiple intelligences by proposing that humans can be described not by a single kind of intelligence, or intelligence quotient score, but rather by a variety of kinds of intelligence. This idea of considering multiple views of intelligence has helped educators look at intelligence from a less rigid, more expansive perspective. I considered how the relatively new concept of naturalistic intelligence, which is the cognitive potential to process information that is exhibited by expert naturalists, might influence the design of undergraduate biology curricula. Naturalistic intelligence can be fostered in undergraduate biology students by emphasizing the need for well-rounded scientific naturalists; developing curricula that involves students in outdoor inquiry-based projects; and helping students learn how to observe both the natural world and their own learning, skills that are essential to developing expert naturalistic knowledge. Professors, graduate students, and administrators can improve the naturalistic intelligence of undergraduate biology students by giving these students opportunities to be involved in outdoor research. Time spent outdoors alone and among people with expertise in natural history, ecology, and conservation biology will have important influences on the knowledge and skills biology undergraduates learn, the careers they pursue, and the contributions they make to conserving Earth's biodiversity.

Harmonising phenomics information for a better interoperability in the rare disease field.

PubMed

Maiella, Sylvie; Olry, Annie; Hanauer, Marc; Lanneau, Valérie; Lourghi, Halima; Donadille, Bruno; Rodwell, Charlotte; Köhler, Sebastian; Seelow, Dominik; Jupp, Simon; Parkinson, Helen; Groza, Tudor; Brudno, Michael; Robinson, Peter N; Rath, Ana

2018-02-07

HIPBI-RD (Harmonising phenomics information for a better interoperability in the rare disease field) is a three-year project which started in 2016 funded via the E-Rare 3 ERA-NET program. This project builds on three resources largely adopted by the rare disease (RD) community: Orphanet, its ontology ORDO (the Orphanet Rare Disease Ontology), HPO (the Human Phenotype Ontology) as well as PhenoTips software for the capture and sharing of structured phenotypic data for RD patients. Our project is further supported by resources developed by the European Bioinformatics Institute and the Garvan Institute. HIPBI-RD aims to provide the community with an integrated, RD-specific bioinformatics ecosystem that will harmonise the way phenomics information is stored in databases and patient files worldwide, and thereby contribute to interoperability. This ecosystem will consist of a suite of tools and ontologies, optimized to work together, and made available through commonly used software repositories. The project workplan follows three main objectives: The HIPBI-RD ecosystem will contribute to the interpretation of variants identified through exome and full genome sequencing by harmonising the way phenotypic information is collected, thus improving diagnostics and delineation of RD. The ultimate goal of HIPBI-RD is to provide a resource that will contribute to bridging genome-scale biology and a disease-centered view on human pathobiology. Achievements in Year 1. Copyright © 2018. Published by Elsevier Masson SAS.

Personalised medicine in 2012: editorial to the special issue of New Biotechnology on "molecular diagnostics & personalised medicine".

PubMed

Desiere, Frank; Romano Spica, Vincenzo

2012-09-15

This special issue of New Biotechnology is focused on molecular diagnostics and personalised medicine and appears at an epochal moment in the development of the field. The practice of medicine is taking a significant and irrevocable turn towards personalisation, due to the great progress in areas such as genomics, pharmacogenomics and molecular diagnosis. It becomes increasingly apparent that to deliver the promise of personalised treatments, more and more novel medicines discovered today will be presented together with innovative companion diagnostics. The contributions to this volume touch on many disciplines, ranging from cell biology to genetics, immunology, molecular diagnostics, pharmaceutics and economic issues. The contributions of clinicians and basic scientists are synergistically presented to underline better the wide spectrum of studies that can contribute to the new field of personalised medicine. The promising perspectives of individualised treatments are related not only to higher effectiveness, but also to increased efficiency. This is relevant not only for the individual patient, but even more so for the general public, within a wider economical perspective where resources are limited and it becomes more and more mandatory to close the gap between social costs and benefits. This approach follows the steps of a stratified and individualised medicine and finds its final goal in an individualised healthcare. Copyright © 2012 Elsevier B.V. All rights reserved.

Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions.

PubMed

Olsson, Lennart; Levit, Georgy S; Hossfeld, Uwe

2010-11-01

Evolutionary theory has been likened to a "universal acid" (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research--evolutionary developmental biology--has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin's Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the "Jena school" of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about "biometabolic modi" are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research--heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of evolution in Russia and is only partly known outside of the Russian-reading world because only one of his many books was translated into English early on. He made many important contributions to evolutionary theory and we point out the important parallels between Schmalhausen's ideas (stabilizing selection, autonomization) and C. H. Waddington's (canalization, genetic assimilation). This is one of the many parallels that have contributed to an increased appreciation of the internationality of progress in evolutionary thinking in the first half of the twentieth century. A direct link between German and Russian evolutionary biology is provided by N. V. Timoféeff-Ressovsky, whose work on, e.g., fly genetics in Berlin is a crucial part of the history of evo-devo. To emphasize the international nature of heterochrony research as predecessor to the modern era of EvoDevo, we include Sir G. R. de Beer's work in the UK. This historical part is followed by a short review of the discovery and importance of homeobox genes and of some of the major concepts that form the core of modern EvoDevo, such as modularity, constraints, and evolutionary novelties. Major trends in contemporary EvoDevo are then outlined, such as increased use of genomics and molecular genetics, computational and bioinformatics approaches, ecological developmental biology (eco-devo), and phylogenetically informed comparative embryology. Based on our survey, we end the review with an outlook on future trends and important issues in EvoDevo.

A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination

PubMed Central

González-Ramírez, Laura R.; Ahmed, Omar J.; Cash, Sydney S.; Wayne, C. Eugene; Kramer, Mark A.

2015-01-01

Epilepsy—the condition of recurrent, unprovoked seizures—manifests in brain voltage activity with characteristic spatiotemporal patterns. These patterns include stereotyped semi-rhythmic activity produced by aggregate neuronal populations, and organized spatiotemporal phenomena, including waves. To assess these spatiotemporal patterns, we develop a mathematical model consistent with the observed neuronal population activity and determine analytically the parameter configurations that support traveling wave solutions. We then utilize high-density local field potential data recorded in vivo from human cortex preceding seizure termination from three patients to constrain the model parameters, and propose basic mechanisms that contribute to the observed traveling waves. We conclude that a relatively simple and abstract mathematical model consisting of localized interactions between excitatory cells with slow adaptation captures the quantitative features of wave propagation observed in the human local field potential preceding seizure termination. PMID:25689136

Conservation endocrinology

USGS Publications Warehouse

McCormick, Stephen; Romero, L. Michael

2017-01-01

Endocrinologists can make significant contributions to conservation biology by helping to understand the mechanisms by which organisms cope with changing environments. Field endocrine techniques have advanced rapidly in recent years and can provide substantial information on the growth, stress, and reproductive status of individual animals, thereby providing insight into current and future responses of populations to changes in the environment. Environmental stressors and reproductive status can be detected nonlethally by measuring a number of endocrine-related endpoints, including steroids in plasma, living and nonliving tissue, urine, and feces. Information on the environmental or endocrine requirements of individual species for normal growth, development, and reproduction will provide critical information for species and ecosystem conservation. For many taxa, basic information on endocrinology is lacking, and advances in conservation endocrinology will require approaches that are both “basic” and “applied” and include integration of laboratory and field approaches.

"They Sweat for Science": The Harvard Fatigue Laboratory and Self-Experimentation in American Exercise Physiology.

PubMed

Johnson, Andi

2015-08-01

In many scientific fields, the practice of self-experimentation waned over the course of the twentieth century. For exercise physiologists working today, however, the practice of self-experimentation is alive and well. This paper considers the role of the Harvard Fatigue Laboratory and its scientific director, D. Bruce Dill, in legitimizing the practice of self-experimentation in exercise physiology. Descriptions of self-experimentation are drawn from papers published by members of the Harvard Fatigue Lab. Attention is paid to the ethical and practical justifications for self-experimentation in both the lab and the field. Born out of the practical, immediate demands of fatigue protocols, self-experimentation performed the long-term, epistemological function of uniting physiological data across time and space, enabling researchers to contribute to a general human biology program.

PHYSICAL AND BIOLOGICAL CONTROLS ON DISSOLVED OXYGEN DYNAMICS IN PENSACOLA BAY, FL

EPA Science Inventory

Nutrient enrichment of estuaries and coastal waters can contribute to hypoxia (low dissolved oxygen) by increasing primary production and biological oxygen demand. Other factors, however, contribute to hypoxia and affect the susceptibility of coastal waters to hypoxia. Hypoxia fo...

Photonic surface waves on metamaterial interfaces

NASA Astrophysics Data System (ADS)

Takayama, O.; Bogdanov, A. A.; Lavrinenko, A. V.

2017-11-01

A surface wave (SW) in optics is a light wave, which is supported at an interface of two dissimilar media and propagates along the interface with its field amplitude exponentially decaying away from the boundary. Research on surface waves has been flourishing in the last few decades due to their unique properties of surface sensitivity and field localization. These features have resulted in applications in nano-guiding, sensing, light-trapping and imaging based on near-field techniques, contributing to the establishment of nanophotonics as a field of research. Up to now, a wide variety of surface waves has been investigated in numerous material and structure settings. This article reviews the recent progress and development in the physics of SWs localized at metamaterial interfaces, as well as bulk media in order to provide broader perspectives on optical surface waves in general. For each type of surface wave, we discuss the material and structural platforms. We mainly focus on experimental realizations in the visible and near-infrared wavelength ranges. We also address existing and potential application of SWs in chemical and biological sensing, and experimental excitation and characterization methods.

ALS Biomarkers for Therapy Development: State of the Field & Future Directions

PubMed Central

Benatar, Michael; Boylan, Kevin; Jeromin, Andreas; Rutkove, Seward B.; Berry, James; Atassi, Nazem; Bruijn, Lucie

2015-01-01

Biomarkers have become the focus of intense research in the field of amyotrophic lateral sclerosis (ALS), with the hope that they might aid therapy development efforts. Notwithstanding the discovery of many candidate biomarkers, none have yet emerged as validated tools for drug development. In this review we present a nuanced view of biomarkers based on the perspective of the FDA; highlight the distinction between discovery and validation; describe existing and emerging resources; review leading biological fluid-based, electrophysiological and neuroimaging candidates relevant to therapy development efforts; discuss lessons learned from biomarker initiatives in related neurodegenerative diseases; and outline specific steps that we, as a field, might take in order to hasten the development and validation of biomarkers that will prove useful in enhancing efforts to develop effective treatments for ALS patients. Most important among these perhaps is the proposal to establish a federated ALS Biomarker Consortium (ABC) in which all interested and willing stakeholders may participate with equal opportunity to contribute to the broader mission of biomarker development and validation. PMID:26574709

Habitat affinity of resident natural enemies of the invasive Aphis glycines (Hemiptera: Aphididae), on soybean, with comments on biological control.

PubMed

Brewer, Michael J; Noma, Takuji

2010-06-01

We integrated a natural enemy survey of the broader landscape into a more traditional survey for Aphis glycines Matsumura (Hemiptera: Aphididae), parasitoids and predatory flies on soybean using A. glycines-infested soybean, Glycine max (L.) Merr., placed in cropped and noncropped plant systems to complement visual field observations. Across three sites and 5 yr, 18 parasitoids and predatory flies in total (Hymenoptera: Aphelinidae [two species] and Bracondae [seven species], Diptera: Cecidomyiidae [one species], Syrphidae [seven species], Chamaemyiidae [one species]) were detected, with significant variability in recoveries detected across plant system treatments and strong contrasts in habitat affinity detected among species. Lysiphlebus testaceipes Cresson was the most frequently detected parasitoid, and no differences in abundance were detected in cropped (soybean, wheat [Triticum aestivum L.], corn [Zea mays L.], and alfalfa [Medicago sativa L.]) and noncropped (poplar [Populus euramericana (Dode) Guinier] and early successional vegetation) areas. In contrast, Binodoxys kelloggensis Pike, Starý & Brewer had strong habitat affinity for poplar and early successional vegetation. The low recoveries seasonally and across habitats of Aphelinus asychis Walker, Aphelinus sp., and Aphidius colemoni Viereck make their suitability to A. glycines on soybean highly suspect. The widespread occurrence of many of the flies reflects their broad habitat affinity and host aphid ranges. The consistent low field observations of parasitism and predation suggest that resident parasitoids and predatory flies are unlikely to contribute substantially to A. glycines suppression, at least during the conventional time period early in the pest invasion when classical biological control activities are considered. For selected species that were relatively well represented across plant systems (i.e., L. testaceipes and Aphidoletes aphidimyza Rondani), conservation biological control efforts may be fruitful. The additional information gained from expanding the natural enemy survey into the broader landscape was essential in making these distinctions relevant to conservation biological control, while adding agroecosystem-specific information valuable to classical biological control.

Preservation of the soft protein corona in distinct flow allows identification of weakly bound proteins.

PubMed

Weber, C; Simon, J; Mailänder, V; Morsbach, S; Landfester, K

2018-06-08

Nanocarriers that are used for targeted drug delivery come in contact with biological liquids and subsequently proteins will adsorb to the nanocarriers' surface to form the so called 'protein corona'. The protein corona defines the biological identity and determines the biological response towards the nanocarriers in the body. To make nanomedicine safe and reliable it is required to get a better insight into this protein corona and, therefore, the adsorbed proteins have to be characterized. Currently, centrifugation is the common method to isolate the protein corona for further investigations. However, with this method it is only possible to investigate the strongly bound proteins, also referred to as 'hard protein corona'. Therefore, we want to introduce a new separation technique to separate nanoparticles including the soft protein corona containing also loosely bound proteins for further characterization. The used separation technique is the asymmetric flow field-flow fractionation (AF4). We were able to separate the nanoparticles with proteins forming the soft protein corona and were able to show that in our system only the hard protein corona directly influenced the cell uptake behavior. Currently, there is an ongoing debate whether only strongly bound proteins (hard corona) or also loosely bound proteins (soft corona) contribute to the biological identity of nanocarriers, because up to now isolation of the soft corona was not possible. Here, asymmetric flow field-flow fractionation was used to isolate nanoparticles with a preserved soft corona from the biological medium. This enabled the characterization of the soft corona composition and to evaluate its influence on cellular uptake. For our system we found that only the strongly bound proteins (hard corona) determined cell internalization. This method can now be used to evaluate the impact of the soft corona further and to characterize nanomaterials that cannot be separated from blood plasma by other means. Copyright © 2018 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Spatial Patterns of Plant Litter and Sedimentation in a Tidal Freshwater Marsh and Implications for Marsh Persistence

NASA Astrophysics Data System (ADS)

Elmore, A. J.; Cadol, D. D.; Palinkas, C. M.; Engelhardt, K. A.

2014-12-01

The maintenance of marsh platform elevation under sea level rise is dependent on sedimentation and biomass conversion to soil organic material. These physical and biological processes interact within the tidal zone, resulting in elevation-dependent processes contributing to marsh accretion. Here we explore spatial pattern in plant litter, a variable related to productivity, to understand its role in physical and biological interactions in a freshwater marsh. Plant litter that persists through the dormant season has an extended period of influence on ecosystem processes. We conducted a field and remote sensing analysis of plant litter height, biomass, vertical cover, and stem density (collectively termed plant litter structure) at a tidal freshwater marsh located along the Potomac River estuary. We completed two years of repeat RTK GPS surveys with corresponding measurements of litter height (over 2000 observations) to train a non-parametric random forest decision tree to predict litter height. LiDAR and field observations show that plant litter height increases with increasing elevation, although important deviations from this relationship are apparent. These spatial patterns exhibit stability from year to year and lead to corresponding patterns in soil organic matter content, revealed by loss on ignition of surface sediments. The amount of mineral material embedded within plant litter decreases with increasing elevation, representing an important trade-off with litter structure. Therefore, at low elevations where litter structure is short and sparse, the role of plant litter is to capture sediment; at high elevations where litter structure is tall and dense, litter contributes organic matter to soil development. Despite these tradeoffs, changes in elevation over time are consistent across elevation, with only small positive differences in elevation gain over time at elevations where the most sediment is deposited or where litter exhibits the most biomass.

Spatio-Temporal Distribution of Particulate and Dissolved Organic Matter in the Mississippi River Bight From Optical Measurements

NASA Technical Reports Server (NTRS)

DSa, E. J.; Miller, R. L.; DelCastillo, C.

2003-01-01

The Mississippi River Bight is a highly dynamic region influenced by the seasonally variable outflow from the Mississippi River. In an effort to characterize the distribution of particulate and dissolved organic matter in the region, we conducted a two-year field program in the spring and fall (high and low flow river discharge) of 2000 and 2002. We collected a comprehensive set of bio-optical measurements consisting of vertical profiles (absorption, scattering, chlorophyll fluorescence and radiometry) and discrete measurements (pigment concentrations, particulate and CDOM absorption) that enabled us to obtain better insight into the seasonal and spatial variability of some important biogeochemical parameters. Our field measurements generally showed higher phytoplankton clorophyll concentrations in the plume waters (associated with lower surface salinities) and confirmed the high biological activity abserved in other studies. The seasonal flow of river discharge and advective currents due to wind forcing exerted a strong influence on the biological and optical properties of the region. An examination of absorption at 440 nm by the algal and non-algal fraction of the particulate pool and of CDOM revealed that at nearshore stations, contributions by the non-algal particles were high (about 40%) and decresed with increasing salinities. While CDOM absorption exhibited conservative mixing, its relative contribution to the total absorption was variable. Surface waters at most stations had lower salinities that generalliy increased with dept. Particulate matter and CDOM also decreased with depth as evidenced by absorption and scattering measurements. Good correlations in surface waters between concentrations of particulate and dissolved matter, the inherent optical properties of absorption and ackscattering and remote sensing reflectance values has allowed the development of robust empirical algorithms for phytoplankton chlorophyll and CDOM absorption.

Timeseries Signal Processing for Enhancing Mobile Surveys: Learning from Field Studies

NASA Astrophysics Data System (ADS)

Risk, D. A.; Lavoie, M.; Marshall, A. D.; Baillie, J.; Atherton, E. E.; Laybolt, W. D.

2015-12-01

Vehicle-based surveys using laser and other analyzers are now commonplace in research and industry. In many cases when these studies target biologically-relevant gases like methane and carbon dioxide, the minimum detection limits are often coarse (ppm) relative to the analyzer's capabilities (ppb), because of the inherent variability in the ambient background concentrations across the landscape that creates noise and uncertainty. This variation arises from localized biological sinks and sources, but also atmospheric turbulence, air pooling, and other factors. Computational processing routines are widely used in many fields to increase resolution of a target signal in temporally dense data, and offer promise for enhancing mobile surveying techniques. Signal processing routines can both help identify anomalies at very low levels, or can be used inversely to remove localized industrially-emitted anomalies from ecological data. This presentation integrates learnings from various studies in which simple signal processing routines were used successfully to isolate different temporally-varying components of 1 Hz timeseries measured with laser- and UV fluorescence-based analyzers. As illustrative datasets, we present results from industrial fugitive emission studies from across Canada's western provinces and other locations, and also an ecological study that aimed to model near-surface concentration variability across different biomes within eastern Canada. In these cases, signal processing algorithms contributed significantly to the clarity of both industrial, and ecological processes. In some instances, signal processing was too computationally intensive for real-time in-vehicle processing, but we identified workarounds for analyzer-embedded software that contributed to an improvement in real-time resolution of small anomalies. Signal processing is a natural accompaniment to these datasets, and many avenues are open to researchers who wish to enhance existing, and future datasets.

Resolution enhancement techniques in microscopy

NASA Astrophysics Data System (ADS)

Cremer, Christoph; Masters, Barry R.

2013-05-01

We survey the history of resolution enhancement techniques in microscopy and their impact on current research in biomedicine. Often these techniques are labeled superresolution, or enhanced resolution microscopy, or light-optical nanoscopy. First, we introduce the development of diffraction theory in its relation to enhanced resolution; then we explore the foundations of resolution as expounded by the astronomers and the physicists and describe the conditions for which they apply. Then we elucidate Ernst Abbe's theory of optical formation in the microscope, and its experimental verification and dissemination to the world wide microscope communities. Second, we describe and compare the early techniques that can enhance the resolution of the microscope. Third, we present the historical development of various techniques that substantially enhance the optical resolution of the light microscope. These enhanced resolution techniques in their modern form constitute an active area of research with seminal applications in biology and medicine. Our historical survey of the field of resolution enhancement uncovers many examples of reinvention, rediscovery, and independent invention and development of similar proposals, concepts, techniques, and instruments. Attribution of credit is therefore confounded by the fact that for understandable reasons authors stress the achievements from their own research groups and sometimes obfuscate their contributions and the prior art of others. In some cases, attribution of credit is also made more complex by the fact that long term developments are difficult to allocate to a specific individual because of the many mutual connections often existing between sometimes fiercely competing, sometimes strongly collaborating groups. Since applications in biology and medicine have been a major driving force in the development of resolution enhancing approaches, we focus on the contribution of enhanced resolution to these fields.

Biological and Health Effects of Electromagnetic Fields Related to the Operation of MRI/TMS

NASA Astrophysics Data System (ADS)

Shigemitsu, Tsukasa; Ueno, Shoogo

This paper reviews issues of biological effects and safety aspects of the electromagnetic fields related to both Magnetic Resonance Imaging (MRI) and Transcranial Magnetic Stimulation (TMS) as a diagnostic technique. The noninvasive character of these diagnostic techniques is based on the utilization of the electromagnetic fields such as the static magnetic field, time-varying magnetic field, and radiofrequency electromagnetic field. Following the short view of the history and the principle of these noninvasive techniques, we review the biological effects of the electromagnetic fields, the health effects and safety issues related to MRI/TMS environments. Through a discussion of biological and health effects, it shows briefly guidelines which provide a consideration in human risk for both patients and medical staff. Finally, safety issues related to MRI/TMS are discussed with the highlighting of the guideline such as the International Commission on NonIonizing Radiation Protection (ICNIRP) and EMF Directive (Directve2013/35/EU) of European Union.

Biological effects of exposure to magnetic resonance imaging: an overview

PubMed Central

Formica, Domenico; Silvestri, Sergio

2004-01-01

The literature on biological effects of magnetic and electromagnetic fields commonly utilized in magnetic resonance imaging systems is surveyed here. After an introduction on the basic principles of magnetic resonance imaging and the electric and magnetic properties of biological tissues, the basic phenomena to understand the bio-effects are described in classical terms. Values of field strengths and frequencies commonly utilized in these diagnostic systems are reported in order to allow the integration of the specific literature on the bio-effects produced by magnetic resonance systems with the vast literature concerning the bio-effects produced by electromagnetic fields. This work gives an overview of the findings about the safety concerns of exposure to static magnetic fields, radio-frequency fields, and time varying magnetic field gradients, focusing primarily on the physics of the interactions between these electromagnetic fields and biological matter. The scientific literature is summarized, integrated, and critically analyzed with the help of authoritative reviews by recognized experts, international safety guidelines are also cited. PMID:15104797

Classifying Life, Reconstructing History and Teaching Diversity: Philosophical Issues in the Teaching of Biological Systematics and Biodiversity

ERIC Educational Resources Information Center

Reydon, Thomas A. C.

2013-01-01

Classification is a central endeavor in every scientific field of work. Classification in biology, however, is distinct from classification in other fields of science in a number of ways. Thus, understanding how biological classification works is an important element in understanding the nature of biological science. In the present paper, I…

Environmental metabolomics: a SWOT analysis (strengths, weaknesses, opportunities, and threats).

PubMed

Miller, Marion G

2007-02-01

Metabolomic approaches have the potential to make an exceptional contribution to understanding how chemicals and other environmental stressors can affect both human and environmental health. However, the application of metabolomics to environmental exposures, although getting underway, has not yet been extensively explored. This review will use a SWOT analysis model to discuss some of the strengths, weaknesses, opportunities, and threats that are apparent to an investigator venturing into this relatively new field. SWOT has been used extensively in business settings to uncover new outlooks and identify problems that would impede progress. The field of environmental metabolomics provides great opportunities for discovery, and this is recognized by a high level of interest in potential applications. However, understanding the biological consequence of environmental exposures can be confounded by inter- and intra-individual differences. Metabolomic profiles can yield a plethora of data, the interpretation of which is complex and still being evaluated and researched. The development of the field will depend on the availability of technologies for data handling and that permit ready access metabolomic databases. Understanding the relevance of metabolomic endpoints to organism health vs adaptation vs variation is an important step in understanding what constitutes a substantive environmental threat. Metabolomic applications in reproductive research are discussed. Overall, the development of a comprehensive mechanistic-based interpretation of metabolomic changes offers the possibility of providing information that will significantly contribute to the protection of human health and the environment.

Engineering ultrasmall water-soluble gold and silver nanoclusters for biomedical applications.

PubMed

Luo, Zhentao; Zheng, Kaiyuan; Xie, Jianping

2014-05-25

Gold and silver nanoclusters or Au/Ag NCs with core sizes smaller than 2 nm have been an attractive frontier of nanoparticle research because of their unique physicochemical properties such as well-defined molecular structure, discrete electronic transitions, quantized charging, and strong luminescence. As a result of these unique properties, ultrasmall size, and good biocompatibility, Au/Ag NCs have great potential for a variety of biomedical applications, such as bioimaging, biosensing, antimicrobial agents, and cancer therapy. In this feature article, we will first discuss some critical biological considerations, such as biocompatibility and renal clearance, of Au/Ag NCs that are applied for biomedical applications, leading to some design criteria for functional Au/Ag NCs in the biological settings. According to these biological considerations, we will then survey some efficient synthetic strategies for the preparation of protein- and peptide-protected Au/Ag NCs with an emphasis on our recent contributions in this fast-growing field. In the last part, we will highlight some potential biomedical applications of these protein- and peptide-protected Au/Ag NCs. It is believed that with continued efforts to understand the interactions of biomolecule-protected Au/Ag NCs with the biological systems, scientists can largely realize the great potential of Au/Ag NCs for biomedical applications, which could finally pave their way towards clinical use.

Experimental strategies to assess the biological ramifications of multiple drivers of global ocean change-A review.

PubMed

Boyd, Philip W; Collins, Sinead; Dupont, Sam; Fabricius, Katharina; Gattuso, Jean-Pierre; Havenhand, Jonathan; Hutchins, David A; Riebesell, Ulf; Rintoul, Max S; Vichi, Marcello; Biswas, Haimanti; Ciotti, Aurea; Gao, Kunshan; Gehlen, Marion; Hurd, Catriona L; Kurihara, Haruko; McGraw, Christina M; Navarro, Jorge M; Nilsson, Göran E; Passow, Uta; Pörtner, Hans-Otto

2018-06-01

Marine life is controlled by multiple physical and chemical drivers and by diverse ecological processes. Many of these oceanic properties are being altered by climate change and other anthropogenic pressures. Hence, identifying the influences of multifaceted ocean change, from local to global scales, is a complex task. To guide policy-making and make projections of the future of the marine biosphere, it is essential to understand biological responses at physiological, evolutionary and ecological levels. Here, we contrast and compare different approaches to multiple driver experiments that aim to elucidate biological responses to a complex matrix of ocean global change. We present the benefits and the challenges of each approach with a focus on marine research, and guidelines to navigate through these different categories to help identify strategies that might best address research questions in fundamental physiology, experimental evolutionary biology and community ecology. Our review reveals that the field of multiple driver research is being pulled in complementary directions: the need for reductionist approaches to obtain process-oriented, mechanistic understanding and a requirement to quantify responses to projected future scenarios of ocean change. We conclude the review with recommendations on how best to align different experimental approaches to contribute fundamental information needed for science-based policy formulation. © 2018 John Wiley & Sons Ltd.

The Promises and Pitfalls of Genoeconomics*

PubMed Central

Benjamin, Daniel J.; Cesarini, David; Chabris, Christopher F.; Glaeser, Edward L.; Laibson, David I.; Guðnason, Vilmundur; Harris, Tamara B.; Launer, Lenore J.; Purcell, Shaun; Smith, Albert Vernon; Johannesson, Magnus; Magnusson, Patrik K.E.; Beauchamp, Jonathan P.; Christakis, Nicholas A.; Atwood, Craig S.; Hebert, Benjamin; Freese, Jeremy; Hauser, Robert M.; Hauser, Taissa S.; Grankvist, Alexander; Hultman, Christina M.; Lichtenstein, Paul

2012-01-01

This article reviews existing research at the intersection of genetics and economics, presents some new findings that illustrate the state of genoeconomics research, and surveys the prospects of this emerging field. Twin studies suggest that economic outcomes and preferences, once corrected for measurement error, appear to be about as heritable as many medical conditions and personality traits. Consistent with this pattern, we present new evidence on the heritability of permanent income and wealth. Turning to genetic association studies, we survey the main ways that the direct measurement of genetic variation across individuals is likely to contribute to economics, and we outline the challenges that have slowed progress in making these contributions. The most urgent problem facing researchers in this field is that most existing efforts to find associations between genetic variation and economic behavior are based on samples that are too small to ensure adequate statistical power. This has led to many false positives in the literature. We suggest a number of possible strategies to improve and remedy this problem: (a) pooling data sets, (b) using statistical techniques that exploit the greater information content of many genes considered jointly, and (c) focusing on economically relevant traits that are most proximate to known biological mechanisms. PMID:23482589

Biological and Agricultural Studies on Application of Discharge Plasma and Electromagnetic Fields 5. Effects of High Electric Fields on Animals

NASA Astrophysics Data System (ADS)

Isaka, Katsuo

The biological effects of extremely low frequency electric fields on animals are reviewed with emphasis on studies of the nervous system, behavior, endocrinology, and blood chemistry. First, this paper provides a histrical overview of studies on the electric field effects initiated in Russia and the United States mainly regarding electric utility workers in high voltage substations and transmission lines. Then, the possible mechanisms of electric field effects are explained using the functions of surface electric fields and induced currents in biological objects. The real mechanisms have not yet been identified. The thresholds of electric field perception levels for rats, baboons, and humans are introduced and compared. The experimental results concerning the depression of melatonin secretion in rats exposed to electric fields are described.

Activated by Combined Magnrtic Field Gravitropic Reaction Reply on Nanodose of Biologicaly Active Compounds

NASA Astrophysics Data System (ADS)

Sheykina, Nadezhda; Bogatina, Nina

The new science direction nanotechnologies initiated a big jump in the pharmacology and medicine. This leads to the big development of homeopathy. The most interest appeared while investigating of the reaction of biological object on the nano dose of iologically substances. The changing of concentration (in nmol/l) of biologically active material is also possible during weak energy action. For instance, weak combined magnetic field may change a little the concentration of ions that are oriented parallel to the external magnetic field and, by the analogy with said above, lead to the similar effects. Simple estimations give the value for the threshold to the magnetic field by two orders smaller than the geomagnetic field. By this investigation we wanted to understand whether the analogy in the action of nano dose of biologically active substances and weak combined magnetic field presents and whether the action of one of these factors may be replaced by other one. The effect of one of biologically active substances NPA (Naphtyl-Phtalame Acid) solution with the concentration 0.01 mol/l on the gravitropic reaction of cress roots was investigated. It was shown that its effect was the inhibition of cress roots gravitropic reaction. The same inhibition was achieved by the combined magnetic field action on the cress roots, germinated in water. The alternative component of the combined magnetic field coincided formally with the cyclotron frequency of NPA ions. So the analogy in the action of nano dose of biologically active substances and weak combined magnetic field was shown. The combined magnetic field using allows to decrease sufficiently the dose of biologically active substances. This fact can be of great importance in pharmacy and medicine.

Induction and transmission of tolerance to the synthetic pesticide emamectin benzoate in field and laboratory populations of diamondback moth.

PubMed

Rahman, M M; Baker, G; Powis, K J; Roush, R T; Schmidt, O

2010-08-01

Field surveys of pest insect pest populations in agroecosystems reveal low but significant levels of tolerance to synthetic and biological pesticides but fail to uncover resistance alleles in test crosses. To study the potential of inducible mechanisms to generate tolerance to synthetic pesticides, we performed baseline susceptibility studies in field and laboratory populations of diamondback moth, Plutella xylostella (L.), to commercial formulations of emamectin benzoate. Pesticide exposure in the field caused elevated levels of tolerance, which decreased in field-collected populations after maintaining insects with pesticide-free diet in the laboratory. Because no significant resistance alleles were identified in back-crossed individuals, the observed increase in tolerance was probably not based on preexisting recessive resistance mechanisms in the population. Instead, the genetic analysis after five and 12 generations is compatible with a transient up-regulation of an immune and metabolic status in tolerant insects that can be transmitted to offspring by a maternal effect. Although the epigenetic effects contributed to incremental increases in tolerance in the first five generations, other resistance mechanisms that are transmitted genetically predominate after 12 generations of increased exposure to the pesticide.

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.

[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.

Putting Biology Students Out to Grass: the Nettlecombe Experiment After Thirteen Years.

ERIC Educational Resources Information Center

Crothers, J. H.; Lucas, A. M.

1982-01-01

The importance of examining both the natural history of organisms being investigated and numerical data from long-term field experiments is illustrated by describing a long-running field experiment at an English Field Study Council Centre. Sample results are discussed and alternative methods of using field studies in biology instruction are…

Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view.

PubMed

Smith, Rob; Mathis, Andrew D; Ventura, Dan; Prince, John T

2014-01-01

For decades, mass spectrometry data has been analyzed to investigate a wide array of research interests, including disease diagnostics, biological and chemical theory, genomics, and drug development. Progress towards solving any of these disparate problems depends upon overcoming the common challenge of interpreting the large data sets generated. Despite interim successes, many data interpretation problems in mass spectrometry are still challenging. Further, though these challenges are inherently interdisciplinary in nature, the significant domain-specific knowledge gap between disciplines makes interdisciplinary contributions difficult. This paper provides an introduction to the burgeoning field of computational mass spectrometry. We illustrate key concepts, vocabulary, and open problems in MS-omics, as well as provide invaluable resources such as open data sets and key search terms and references. This paper will facilitate contributions from mathematicians, computer scientists, and statisticians to MS-omics that will fundamentally improve results over existing approaches and inform novel algorithmic solutions to open problems.

Cells, Scaffolds and Their Interactions in Myocardial Tissue Regeneration.

PubMed

Gorabi, Armita Mahdavi; Tafti, Seyed Hossein Ahmadi; Soleimani, Masoud; Panahi, Yunes; Sahebkar, Amirhossein

2017-08-01

Cardiac regenerative therapy includes several techniques to repair and replace damaged tissues and organs using cells, biomaterials, molecules, or a combination of these factors. Generation of heart muscle is the most important challenge in this field, although it is well known that new advances in stem cell isolation and culture techniques in bioreactors and synthesis of bioactive materials contribute to the creation of cardiac tissue regeneration in vitro. Some investigations in stem cell biology shows that stem cells are an important source for regeneration of heart muscle cells and blood vessels and can thus clinically contribute to the regeneration of damaged heart tissue. The aim of this review was to explain the principles and challenges of myocardial tissue regeneration with an emphasis on stem cells and scaffolds. J. Cell. Biochem. 118: 2454-2462, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Parasites as drivers of key processes in aquatic ecosystems: Facts and future directions.

PubMed

Sures, B; Nachev, M; Pahl, M; Grabner, D; Selbach, C

2017-09-01

Despite the advances in our understanding of the ecological importance of parasites that we have made in recent years, we are still far away from having a complete picture of the ecological implications connected to parasitism. In the present paper we highlight key issues that illustrate (1) important contributions of parasites to biodiversity, (2) their integral role in ecosystems, (3) as well as their ecological effects as keystone species (4) and in biological invasion processes. By using selected examples from aquatic ecosystems we want to provide an insight and generate interest into the topic, and want to show directions for future research in the field of ecological parasitology. This may help to convince more parasitologists and ecologists contributing and advancing our understanding of the complex and fascinating interplay of parasites, hosts and ecosystems. Copyright © 2017 Elsevier Inc. All rights reserved.

Infusing Outdoor Field Experiences into the Secondary Biology Curriculum.

ERIC Educational Resources Information Center

Owens, Ginny

1984-01-01

To offer students biological field experiences, teachers should use their own basic skills, be enthusiastic motivators, participate in community programs/courses/workshops to acquire additional skills/knowledge for outdoor biological education, plan outdoor excursions with safety considerations in mind, and use available resources for classroom…

Improving communication for interdisciplinary teams working on storage of digital information in DNA.

PubMed

Hesketh, Emily E; Sayir, Jossy; Goldman, Nick

2018-01-01

Close collaboration between specialists from diverse backgrounds and working in different scientific domains is an effective strategy to overcome challenges in areas that interface between biology, chemistry, physics and engineering. Communication in such collaborations can itself be challenging.  Even when projects are successfully concluded, resulting publications - necessarily multi-authored - have the potential to be disjointed. Few, both in the field and outside, may be able to fully understand the work as a whole. This needs to be addressed to facilitate efficient working, peer review, accessibility and impact to larger audiences. We are an interdisciplinary team working in a nascent scientific area, the repurposing of DNA as a storage medium for digital information. In this note, we highlight some of the difficulties that arise from such collaborations and outline our efforts to improve communication through a glossary and a controlled vocabulary and accessibility via short plain-language summaries. We hope to stimulate early discussion within this emerging field of how our community might improve the description and presentation of our work to facilitate clear communication within and between research groups and increase accessibility to those not familiar with our respective fields - be it molecular biology, computer science, information theory or others that might become relevant in future. To enable an open and inclusive discussion we have created a glossary and controlled vocabulary as a cloud-based shared document and we invite other scientists to critique our suggestions and contribute their own ideas.

Proposed imaging of the ultrafast electronic motion in samples using x-ray phase contrast.

PubMed

Dixit, Gopal; Slowik, Jan Malte; Santra, Robin

2013-03-29

Tracing the motion of electrons has enormous relevance to understanding ubiquitous phenomena in ultrafast science, such as the dynamical evolution of the electron density during complex chemical and biological processes. Scattering of ultrashort x-ray pulses from an electronic wave packet would appear to be the most obvious approach to image the electronic motion in real time and real space with the notion that such scattering patterns, in the far-field regime, encode the instantaneous electron density of the wave packet. However, recent results by Dixit et al. [Proc. Natl. Acad. Sci. U.S.A. 109, 11636 (2012)] have put this notion into question and have shown that the scattering in the far-field regime probes spatiotemporal density-density correlations. Here, we propose a possible way to image the instantaneous electron density of the wave packet via ultrafast x-ray phase contrast imaging. Moreover, we show that inelastic scattering processes, which plague ultrafast scattering in the far-field regime, do not contribute in ultrafast x-ray phase contrast imaging as a consequence of an interference effect. We illustrate our general findings by means of a wave packet that lies in the time and energy range of the dynamics of valence electrons in complex molecular and biological systems. This present work offers a potential to image not only instantaneous snapshots of nonstationary electron dynamics, but also the laplacian of these snapshots which provide information about the complex bonding and topology of the charge distributions in the systems.

Proposed Imaging of the Ultrafast Electronic Motion in Samples using X-Ray Phase Contrast

NASA Astrophysics Data System (ADS)

Dixit, Gopal; Slowik, Jan Malte; Santra, Robin

2013-03-01

Tracing the motion of electrons has enormous relevance to understanding ubiquitous phenomena in ultrafast science, such as the dynamical evolution of the electron density during complex chemical and biological processes. Scattering of ultrashort x-ray pulses from an electronic wave packet would appear to be the most obvious approach to image the electronic motion in real time and real space with the notion that such scattering patterns, in the far-field regime, encode the instantaneous electron density of the wave packet. However, recent results by Dixit et al. [Proc. Natl. Acad. Sci. U.S.A. 109, 11 636 (2012)] have put this notion into question and have shown that the scattering in the far-field regime probes spatiotemporal density-density correlations. Here, we propose a possible way to image the instantaneous electron density of the wave packet via ultrafast x-ray phase contrast imaging. Moreover, we show that inelastic scattering processes, which plague ultrafast scattering in the far-field regime, do not contribute in ultrafast x-ray phase contrast imaging as a consequence of an interference effect. We illustrate our general findings by means of a wave packet that lies in the time and energy range of the dynamics of valence electrons in complex molecular and biological systems. This present work offers a potential to image not only instantaneous snapshots of nonstationary electron dynamics, but also the Laplacian of these snapshots which provide information about the complex bonding and topology of the charge distributions in the systems.

Understanding Mechanobiology: Physical Therapists as a Force in Mechanotherapy and Musculoskeletal Regenerative Rehabilitation

PubMed Central

Thompson, William R.; Scott, Alexander; Loghmani, M. Terry; Ward, Samuel R.

2016-01-01

Achieving functional restoration of diseased or injured tissues is the ultimate goal of both regenerative medicine approaches and physical therapy interventions. Proper integration and healing of the surrogate cells, tissues, or organs introduced using regenerative medicine techniques are often dependent on the co-introduction of therapeutic physical stimuli. Thus, regenerative rehabilitation represents a collaborative approach whereby rehabilitation specialists, basic scientists, physicians, and surgeons work closely to enhance tissue restoration by creating tailored rehabilitation treatments. One of the primary treatment regimens that physical therapists use to promote tissue healing is the introduction of mechanical forces, or mechanotherapies. These mechanotherapies in regenerative rehabilitation activate specific biological responses in musculoskeletal tissues to enhance the integration, healing, and restorative capacity of implanted cells, tissues, or synthetic scaffolds. To become future leaders in the field of regenerative rehabilitation, physical therapists must understand the principles of mechanobiology and how mechanotherapies augment tissue responses. This perspective article provides an overview of mechanotherapy and discusses how mechanical signals are transmitted at the tissue, cellular, and molecular levels. The synergistic effects of physical interventions and pharmacological agents also are discussed. The goals are to highlight the critical importance of mechanical signals on biological tissue healing and to emphasize the need for collaboration within the field of regenerative rehabilitation. As this field continues to emerge, physical therapists are poised to provide a critical contribution by integrating mechanotherapies with regenerative medicine to restore musculoskeletal function. PMID:26637643

Identification of molecular descriptors for design of novel Isoalloxazine derivatives as potential Acetylcholinesterase inhibitors against Alzheimer's disease.

PubMed

Gurung, Arun Bahadur; Aguan, Kripamoy; Mitra, Sivaprasad; Bhattacharjee, Atanu

2017-06-01

In Alzheimer's disease (AD), the level of Acetylcholine (ACh) neurotransmitter is reduced. Since Acetylcholinesterase (AChE) cleaves ACh, inhibitors of AChE are very much sought after for AD treatment. The side effects of current inhibitors necessitate development of newer AChE inhibitors. Isoalloxazine derivatives have proved to be promising (AChE) inhibitors. However, their structure-activity relationship studies have not been reported till date. In the present work, various quantitative structure-activity relationship (QSAR) building methods such as multiple linear regression (MLR), partial least squares ,and principal component regression were employed to derive 3D-QSAR models using steric and electrostatic field descriptors. Statistically significant model was obtained using MLR coupled with stepwise selection method having r 2  = .9405, cross validated r 2 (q 2 ) = .6683, and a high predictability (pred_r 2  = .6206 and standard error, pred_r 2 se = .2491). Steric and electrostatic contribution plot revealed three electrostatic fields E_496, E_386 and E_577 and one steric field S_60 contributing towards biological activity. A ligand-based 3D-pharmacophore model was generated consisting of eight pharmacophore features. Isoalloxazine derivatives were docked against human AChE, which revealed critical residues implicated in hydrogen bonds as well as hydrophobic interactions. The binding modes of docked complexes (AChE_IA1 and AChE_IA14) were validated by molecular dynamics simulation which showed their stable trajectories in terms of root mean square deviation and molecular mechanics/Poisson-Boltzmann surface area binding free energy analysis revealed key residues contributing significantly to overall binding energy. The present study may be useful in the design of more potent Isoalloxazine derivatives as AChE inhibitors.

Greenhouse Gas Emissions from Septic Systems in New York State.

PubMed

Truhlar, Allison M; Rahm, Brian G; Brooks, Rachael A; Nadeau, Sarah A; Makarsky, Erin T; Walter, M Todd

2016-07-01

Onsite septic systems use microbial processes to eliminate organic wastes and nutrients such as nitrogen; these processes can contribute to air pollution through the release of greenhouse gases (GHGs). Current USEPA estimates for septic system GHG emissions are based on one study conducted in north-central California and are limited to methane; therefore, the contribution of these systems to the overall GHG emission budget is unclear. This study quantified and compared septic system GHG emissions from the soil over leach fields and the roof vent, which are the most likely locations for gas emissions during normal septic system operation. At each of eight septic systems, we measured fluxes of CH, CO, and NO using a static chamber method. The roof vent released the majority of septic system gas emissions. In addition, the leach field was a significant source of NO fluxes. Comparisons between leach field and vent emissions suggest that biological processes in the leach field soil may influence the type and quantity of gas released. Overall, our results suggest that (i) revisions are needed in USEPA guidance (e.g., septic systems are not currently listed as a source of NO emissions) and (ii) similar studies representing a wider range of climatic and geographic settings are needed. The total vent, sand filter, and leach field GHG emissions were 0.17, 0.045, and 0.050 t CO-equivalents capita yr, respectively. In total, this represents about 1.5% of the annual carbon footprint of an individual living in the United States. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

CALL FOR PAPERS: Special issue on the random search problem: trends and perspectives

NASA Astrophysics Data System (ADS)

da Luz, Marcos G. E.; Grosberg, Alexander Y.; Raposo, Ernesto P.; Viswanathan, Gandhi M.

2008-11-01

This is a call for contributions to a special issue of Journal of Physics A: Mathematical and Theoretical dedicated to the subject of the random search problem. The motivation behind this special issue is to summarize in a single comprehensive publication, the main aspects (past and present), latest developments, different viewpoints and the directions being followed in this multidisciplinary field. We hope that such a special issue could become a particularly valuable reference for the broad scientific community working with the general random search problem. The Editorial Board has invited Marcos G E da Luz, Alexander Y Grosberg, Ernesto P Raposo and Gandhi M Viswanathan to serve as Guest Editors for the special issue. The general question of how to optimize the search for specific target objects in either continuous or discrete environments when the information available is limited is of significant importance in a broad range of fields. Representative examples include ecology (animal foraging, dispersion of populations), geology (oil recovery from mature reservoirs), information theory (automated researchers of registers in high-capacity database), molecular biology (proteins searching for their sites, e.g., on DNA ), etc. One reason underlying the richness of the random search problem relates to the `ignorance' of the locations of the randomly located `targets'. A statistical approach to the search problem can deal adequately with incomplete information and so stochastic strategies become advantageous. The general problem of how to search efficiently for randomly located target sites can thus be quantitatively described using the concepts and methods of statistical physics and stochastic processes. Scope Thus far, to the best of our knowledge, no recent textbook or review article in a physics journal has appeared on this topic. This makes a special issue with review and research articles attractive to those interested in acquiring a general introduction to the field. The subject can be approached from the perspective of different fields: ecology, networks, transport problems, molecular biology, etc. The study of the problem is particularly suited to the concepts and methods of statistical physics and stochastic processes; for example, fractals, random walks, anomalous diffusion. Discrete landscapes can be approached via graph theory, random lattices and complex networks. Such topics are regularly discussed in Journal of Physics A: Mathematical and Theoretical. All such aspects of the problem fall within the scope and focus of this special issue on the random search problem: trends and perspectives. Editorial policy All contributions to the special issue will be refereed in accordance with the refereeing policy of the journal. In particular, all research papers will be expected to be original work reporting substantial new results. The issue will also contain a number of review articles by invitation only. The Guest Editors reserve the right to judge whether a contribution fits the scope of the special issue. Guidelines for preparation of contributions We aim to publish the special issue in August 2009. To realize this, the DEADLINE for contributed papers is 15 January 2009. There is a page limit of 15 printed pages (approximately 9000 words) per contribution. For papers exceeding this limit, the Guest Editors reserve the right to request a reduction in length. Further advice on document preparation can be found at www.iop.org/Journals/jphysa. Contributions to the special issue should if possible be submitted electronically by web upload at www.iop.org/Journals/jphysa, or by email to jphysa@iop.org, quoting 'J. Phys. A Special Issue— Random Search Problem'. Please state whether the paper has been invited or is contributed. Submissions should ideally be in standard LaTeX form. Please see the website for further information on electronic submissions. Authors unable to submit electronically may send hard-copy contributions to: Publishing Administrators, Journal of Physics A, Institute of Physics Publishing, Dirac House, Temple Back, Bristol BS1 6BE, UK, enclosing electronic code on CD if available and quoting 'J. Phys. A Special Issue—Random Search Problem'. All contributions should be accompanied by a read-me file or covering letter giving the postal and e-mail addresses for correspondence. The Publishing Office should be notified of any subsequent change of address. This special issue will be published in the paper and online version of the journal. The corresponding author of each contribution will receive a complimentary copy of the issue.

Nanomaterials and nanofabrication for biomedical applications

NASA Astrophysics Data System (ADS)

Cheng, Chao-Min; Chia-Wen Wu, Kevin

2013-08-01

Traditional boundaries between materials science and engineering and life sciences are rapidly disintegrating as interdisciplinary research teams develop new materials-science-based tools for exploring fundamental issues in both medicine and biology. With recent technological advances in multiple research fields such as materials science, cell and molecular biology and micro-/nano-technology, much attention is shifting toward evaluating the functional advantages of nanomaterials and nanofabrication, at the cellular and molecular levels, for specific, biomedically relevant applications. The pursuit of this direction enhances the understanding of the mechanisms of, and therapeutic potentials for, some of the most lethal diseases, including cardiovascular diseases, organ fibrosis and cancers. This interdisciplinary approach has generated great interest among researchers working in a wide variety of communities including industry, universities and research laboratories. The purpose of this focus issue in Science and Technology of Advanced Materials is to bridge nanotechnology and biology with medicine, focusing more on the applications of nanomaterials and nanofabrication in biomedically relevant issues. This focus issue, we believe, will provide a more comprehensive understanding of (i) the preparation of nanomaterials and the underlying mechanisms of nanofabrication, and (ii) the linkage of nanomaterials and nanofabrication with biomedical applications. The multidisciplinary focus issue that we have attempted to organize is of interest to various research fields including biomaterials and tissue engineering, bioengineering, nanotechnology and nanomaterials, i.e. chemistry, physics and engineering. Nanomaterials and nanofabrication topics addressed in this focus issue include sensing and diagnosis (e.g. immunosensing and diagnostic devices for diseases), cellular and molecular biology (e.g. probing cellular behaviors and stem cell differentiation) and drug delivery carriers (e.g. polymers, gold nanoparticles, Prussian blue nanoparticles, mesoporous silica nanoparticles and carbon-based nanomaterials). Here, we would like to show our deep appreciation to all authors and reviewers. Without their great help and contributions, this focus issue, including the review and original papers, would not have been published on schedule. This focus issue may not cover all issues in this emerging scientific field; however, we believe that our efforts have great potential 'to hurl a boulder to draw a jade' and ignite innovation and challenging discussion in the relevant scientific communities.

Molecular and chemical engineering of bacteriophages for potential medical applications.

PubMed

Hodyra, Katarzyna; Dąbrowska, Krystyna

2015-04-01

Recent progress in molecular engineering has contributed to the great progress of medicine. However, there are still difficult problems constituting a challenge for molecular biology and biotechnology, e.g. new generation of anticancer agents, alternative biosensors or vaccines. As a biotechnological tool, bacteriophages (phages) offer a promising alternative to traditional approaches. They can be applied as anticancer agents, novel platforms in vaccine design, or as target carriers in drug discovery. Phages also offer solutions for modern cell imaging, biosensor construction or food pathogen detection. Here we present a review of bacteriophage research as a dynamically developing field with promising prospects for further development of medicine and biotechnology.

Tissue Engineering and Regenerative Medicine 2017: A Year in Review.

PubMed

Park, Kyung Min; Shin, Young Min; Kim, Kyobum; Shin, Heungsoo

2018-04-26

In 2017, a new paradigm change caused by artificial intelligence and big data analysis resulted in innovation in each field of science and technology, and also significantly influenced progress in tissue engineering and regenerative medicine (TERM). TERM has continued to make technological advances based on interdisciplinary approaches and has contributed to the overall field of biomedical technology, including cancer biology, personalized medicine, development biology, and cell-based therapeutics. While researchers are aware that there is still a long way to go until TERM reaches the ultimate goal of patient treatment through clinical translation, the rapid progress in convergence studies led by technological improvements in TERM has been encouraging. In this review, we highlighted the significant advances made in TERM in 2017 (with an overlap of 5 months in 2016). We identified major progress in TERM in a manner similar to previous reviews published in the last few years. In addition, we carefully considered all four previous reviews during the selection process and chose main themes that minimize the duplication of the topics. Therefore, we have identified three areas that have been the focus of most journal publications in the TERM community in 2017: (i) advanced biomaterials and three-dimensional (3D) cell printing, (ii) exosomes as bioactive agents for regenerative medicine, and (iii) 3D culture in regenerative medicine.

Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis.

PubMed

Lee, Jessica J Y; Gottlieb, Michael M; Lever, Jake; Jones, Steven J M; Blau, Nenad; van Karnebeek, Clara D M; Wasserman, Wyeth W

2018-05-01

Phenomics is the comprehensive study of phenotypes at every level of biology: from metabolites to organisms. With high throughput technologies increasing the scope of biological discoveries, the field of phenomics has been developing rapid and precise methods to collect, catalog, and analyze phenotypes. Such methods have allowed phenotypic data to be widely used in medical applications, from assisting clinical diagnoses to prioritizing genomic diagnoses. To channel the benefits of phenomics into the field of inborn errors of metabolism (IEM), we have recently launched IEMbase, an expert-curated knowledgebase of IEM and their disease-characterizing phenotypes. While our efforts with IEMbase have realized benefits, taking full advantage of phenomics requires a comprehensive curation of IEM phenotypes in core phenomics projects, which is dependent upon contributions from the IEM clinical and research community. Here, we assess the inclusion of IEM biochemical phenotypes in a core phenomics project, the Human Phenotype Ontology. We then demonstrate the utility of biochemical phenotypes using a text-based phenomics method to predict gene-disease relationships, showing that the prediction of IEM genes is significantly better using biochemical rather than clinical profiles. The findings herein provide a motivating goal for the IEM community to expand the computationally accessible descriptions of biochemical phenotypes associated with IEM in phenomics resources.

Increasing College Students' Interest and Engagement in STEM: A Comparison of Strategies for Challenging STEM Stereotypes

NASA Astrophysics Data System (ADS)

Shin, Jiyun Elizabeth L.

Increasing science, technology, engineering, and mathematics (STEM) graduates has become an important part of the education agenda in the U.S. in recent years. Stereotypes about STEM (i.e., belief that STEM abilities are innate, and that European American men are best suited for STEM) have been identified as one of the critical factors that may contribute to low recruitment and retention of STEM students. Drawing from the literatures on biological essentialism and role models, this study compared different strategies for challenging STEM stereotypes among undergraduate students in STEM and non-STEM fields. STEM stereotypes were challenged directly with research articles that provided non-biological explanations for STEM success and interest (a strategy used in the essentialism research) and indirectly with biographies of successful STEM role models who are underrepresented in their field and who succeeded through hard work (a strategy used in the role model research). Contrary to the predictions, exposure to the role model biographies, research articles, or combination of both did not have statistically significant effects on participants' reported STEM interest and academic intentions. Possible explanations for the lack of significant findings as well as suggestions for developing effective interventions to promote STEM engagement among students are discussed.

Redox Biology in Neurological Function, Dysfunction, and Aging.

PubMed

Franco, Rodrigo; Vargas, Marcelo R

2018-04-23

Reduction oxidation (redox) reactions are central to life and when altered, they can promote disease progression. In the brain, redox homeostasis is recognized to be involved in all aspects of central nervous system (CNS) development, function, aging, and disease. Recent studies have uncovered the diverse nature by which redox reactions and homeostasis contribute to brain physiology, and when dysregulated to pathological consequences. Redox reactions go beyond what is commonly described as oxidative stress and involve redox mechanisms linked to signaling and metabolism. In contrast to the nonspecific nature of oxidative damage, redox signaling involves specific oxidation/reduction reactions that regulate a myriad of neurological processes such as neurotransmission, homeostasis, and degeneration. This Forum is focused on the role of redox metabolism and signaling in the brain. Six review articles from leading scientists in the field that appraise the role of redox metabolism and signaling in different aspects of brain biology including neurodevelopment, neurotransmission, aging, neuroinflammation, neurodegeneration, and neurotoxicity are included. An original research article exemplifying these concepts uncovers a novel link between oxidative modifications, redox signaling, and neurodegeneration. This Forum highlights the recent advances in the field and we hope it encourages future research aimed to understand the mechanisms by which redox metabolism and signaling regulate CNS physiology and pathophysiology. Antioxid. Redox Signal. 00, 000-000.

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

PubMed

Paton, Robert S; Goodman, Jonathan M

2009-04-01

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

The equally wonderful field: Ernst Mayr and organismic biology.

PubMed

Milam, Erika Lorraine

2010-01-01

Biologists in the 1960s witnessed a period of intense intra-disciplinary negotiations, especially the positioning of organismic biologists relative to molecular biologists. The perceived valorization of the physical sciences by "molecular" biologists became a catalyst creating a unified front of "organismic" biology that incorporated not just evolutionary biologists, but also students of animal behavior, ecology, systematics, botany - in short, almost any biological community that predominantly conducted their research in the field or museum and whose practitioners felt the pinch of the prestige and funding accruing to molecular biologists and biochemists. Ernst Mayr, Theodosius Dobzhansky, and George Gaylord Simpson took leading roles in defending alternatives to what they categorized as the mechanistic approach of chemistry and physics applied to living systems - the "equally wonderful field of organismic biology." Thus, it was through increasingly tense relations with molecular biology that organismic biologists cohered into a distinct community, with their own philosophical grounding, institutional security, and historical identity. Because this identity was based in large part on a fundamental rejection of the physical sciences as a desirable model within biology, organismic biologists succeeded in protecting the future of their field by emphasizing deep divisions that ran through the biological sciences as a whole.

SIMBIOS Project; 2003 Annual Report

NASA Technical Reports Server (NTRS)

McClain, Charles R.; Fargion, Giulietta S.

2003-01-01

The purpose of this technical report is to provide current documentation of the the Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project activities, NASA Research Announcement (NRA) research status, satellite data processing, data product validation, and field calibration. This documentation is necessary to ensure that critical information is related to the scientific community and NASA management. This critical information includes the technical difficulties and challenges of validating and combining ocean color data from an array of independent satellite systems to form consistent and accurate global bio-optical time series products. This technical report is not meant as a substitute for scientific literature. Instead, it will provide a ready and responsive vehicle for the multitude of technical reports issued by an operational project. The SIMBIOS Science Team Principal Investigators (PIs) original contributions to this report are in chapters four and above. The purpose of these contributions is to describe the current research status of the SIMBIOS-NRA-99 funded research. The contributions are published as submitted, with the exception of minor edits to correct obvious grammatical or clerical errors.

Searching for the Perfect Wave: The Effect of Radiofrequency Electromagnetic Fields on Cells

PubMed Central

Gherardini, Lisa; Ciuti, Gastone; Tognarelli, Selene; Cinti, Caterina

2014-01-01

There is a growing concern in the population about the effects that environmental exposure to any source of “uncontrolled” radiation may have on public health. Anxiety arises from the controversial knowledge about the effect of electromagnetic field (EMF) exposure to cells and organisms but most of all concerning the possible causal relation to human diseases. Here we reviewed those in vitro and in vivo and epidemiological works that gave a new insight about the effect of radio frequency (RF) exposure, relating to intracellular molecular pathways that lead to biological and functional outcomes. It appears that a thorough application of standardized protocols is the key to reliable data acquisition and interpretation that could contribute a clearer picture for scientists and lay public. Moreover, specific tuning of experimental and clinical RF exposure might lead to beneficial health effects. PMID:24681584

Combining field work and laboratory work in the study of financial risk-taking.

PubMed

Coates, John; Gurnell, Mark

2017-06-01

A contribution to a special issue on Hormones and Human Competition. Financial markets are periodically destabilized by bubbles and crashes during which investors display respectively what has been called "irrational exuberance" and "irrational pessimism". How can we best study these pathologies in competitive and risk-taking behaviours? In this article, we argue that a science of risk-taking and of the financial markets needs to draw heavily on physiology and especially endocrinology, due to their central roles in moderating human behaviour. Importantly, this science of competition and risk requires the same spectrum of research protocols as is found in mature biological and medical sciences, a spectrum running from field work conducted within financial institutions themselves to more controlled laboratory studies, which permit cause to be distinguished from effect. Such a spectrum of studies is especially important for translational behavioural science. Copyright © 2017 Elsevier Inc. All rights reserved.

Tails and Ties. Editorial

NASA Astrophysics Data System (ADS)

Carbone, A.; Kaniadakis, G.; Scarfone, A. M.

2007-05-01

The study of behavioural and social phenomena has experienced a surge of interest over the last decade. One reason for this great attention is the huge amount of high quality data made available by the internet technologies. The many studies spanning concepts and problems belonging to economics, biology, ecology, physics and computer science, clearly indicates increasing interdisciplinary cross-fertilization, commonalities in the different approaches and communication across these disciplines. This issue of The European Physical Journal B is devoted to the interdisciplinary field of Sociophysics. The papers have been selected from the contributions presented at the 5th International Conference on “Applications of Physics in Financial Analysis" (APFA5) held in Torino from June 29th to July 1st 2006 ( http://www.polito.it/apfa5). The synergy and richness of results obtained from the investigation of problems belonging to the area of complexity science from different perspectives clearly indicates future directions and research methodologies in this field.

Stem-like plasticity and heterogeneity of circulating tumor cells: current status and prospect challenges in liver cancer

PubMed Central

Correnti, Margherita; Raggi, Chiara

2017-01-01

Poor prognosis and high recurrence remain leading causes of primary liver cancerassociated mortality. The spread of circulating tumor cells (CTCs) in the blood plays a major role in the initiation of metastasis and tumor recurrence after surgery. Nevertheless, only a subset of CTCs can survive, migrate to distant sites and establish secondary tumors. Consistent with cancer stem cell (CSC) hypothesis, stem-like CTCs might represent a potential source for cancer relapse and distant metastasis. Thus, identification of stem-like metastasis-initiating CTC-subset may provide useful clinically prognostic information. This review will emphasize the most relevant findings of CTCs in the context of stem-like biology associated to liver carcinogenesis. In this view, the emerging field of stem-like CTCs may deliver substantial contribution in liver cancer field in order to move to personalized approaches for diagnosis, prognosis and therapy. PMID:27738343

Caenorhabditis elegans: nature and nurture gift to nematode parasitologists.

PubMed

Salinas, Gustavo; Risi, Gastón

2017-12-06

The free-living nematode Caenorhabditis elegans is the simplest animal model organism to work with. Substantial knowledge and tools have accumulated over 50 years of C. elegans research. The use of C. elegans relating to parasitic nematodes from a basic biology standpoint or an applied perspective has increased in recent years. The wealth of information gained on the model organism, the use of the powerful approaches and technologies that have advanced C. elegans research to parasitic nematodes and the enormous success of the omics fields have contributed to bridge the divide between C. elegans and parasite nematode researchers. We review key fields, such as genomics, drug discovery and genetics, where C. elegans and nematode parasite research have convened. We advocate the use of C. elegans as a model to study helminth metabolism, a neglected area ready to advance. How emerging technologies being used in C. elegans can pave the way for parasitic nematode research is discussed.

Polyphenols: Physicochemical and Biological Properties and Perspectives of Their Use in a Zero-Waste Society.

PubMed

Cheynier, Véronique; Halbwirth, Heidi

2017-08-09

The 28th International Conference on Polyphenols, held in Vienna (Austria) in July 2016, offered a venue for global exchanges on the active research on polyphenols and for the presentation and discussion of the latest advances. The multidisciplinary event attracted 280 scientists from four continents working in different fields, from analytical and biosynthetic chemistry through genetic and metabolic engineering, plant physiology, and ecology to food nutrition and health sciences as well as industrial applications. This special issue presents a selection of papers from oral presentations and poster contributions shown within the framework of sessions focusing on research in the fields of (1) chemistry and physicochemistry, (2) food, nutrition, and health, and (3) applied polyphenolics. This introductory paper also briefly summarizes general properties of this versatile and largest group of secondary metabolites and their use in bioeconomical approaches.

Unraveling Gender Bias from Student Evaluations of their High School Physics Teachers

NASA Astrophysics Data System (ADS)

Hazari, Zahra; Potvin, Geoff; Tai, Robert; Sadler, Philip

2009-05-01

In this talk, the evaluation of high school physics, chemistry, and biology teachers by their students is examined according to the gender of the student and the gender of the teacher. Female teachers are rated significantly lower than male teachers by male students in all three disciplines, while female students under-rate female teachers only in physics. Interestingly, physics is also the field that suffers the greatest lack of females and has been criticized most for its androcentric culture. The gender bias in teacher ratings persists even after accounting for academic performance, classroom experiences, and family support. Further, male and female teachers in each discipline appear equally effective at preparing their students for future science study in college, suggesting that students have a discipline-specific gender bias. Such a bias may negatively impact female students and contribute to the loss of females in STEM fields.

Toward a New Outlook on Primate Learning and Behavior: Complex Learning and Emergent Processes in Comparative Perspective

NASA Technical Reports Server (NTRS)

Rumbaugh, Duane M.; Savage-Rumbaugh, E. Sue; Washburn, David A.

1996-01-01

Primate research of the 20th century has established the validity of Darwin's postulation of psychological as well as biological continuity between humans and other primates, notably the great apes. Its data make clear that Descartes' view of animals as unfeeling 'beast-machines' is invalid and should be discarded. Traditional behavioristic frameworks, that emphasize the concepts of stimulus, response, and reinforcement and an 'empty-organism' psychology, are in need of major revisions. Revised frameworks should incorporate the fact that, in contrast to the lifeless databases of the 'hard' sciences, the database of psychology entails properties novel to life and its attendant phenomena. The contributions of research this century, achieved by field and laboratory researchers from around the world, have been substantial, indeed revolutionary. It is time to celebrate the progress of our field, to anticipate its significance, and to emphasize conservation of primates in their natural habitats.

Insecticidal activity of plant lectins and potential application in crop protection.

PubMed

Macedo, Maria Lígia R; Oliveira, Caio F R; Oliveira, Carolina T

2015-01-27

Lectins constitute a complex group of proteins found in different organisms. These proteins constitute an important field for research, as their structural diversity and affinity for several carbohydrates makes them suitable for numerous biological applications. This review addresses the classification and insecticidal activities of plant lectins, providing an overview of the applicability of these proteins in crop protection. The likely target sites in insect tissues, the mode of action of these proteins, as well as the use of lectins as biotechnological tools for pest control are also described. The use of initial bioassays employing artificial diets has led to the most recent advances in this field, such as plant breeding and the construction of fusion proteins, using lectins for targeting the delivery of toxins and to potentiate expected insecticide effects. Based on the data presented, we emphasize the contribution that plant lectins may make as tools for the development of integrated insect pest control strategies.

The invisibility of informal interpreting in mental health care in South Africa: notes towards a contextual understanding.

PubMed

Swartz, Leslie; Kilian, Sanja

2014-12-01

Despite South Africa's constitutional commitment to equality, represented by 11 official languages and the promotion of South African Sign Language, many users of the public health system receive treatment from people who cannot speak their language, and there are no formal interpreting services. This is a legacy of service provision from the apartheid era, and interpreting is currently undertaken by nurses, cleaners, security guards, and family members of patients, amongst others. We provide a preliminary outline of proximal and distal issues which may bear upon this situation. Changing understandings of the nature of careers in the health field, international trends in mental health theory and practice toward crude biologism, and ongoing patterns of social exclusion and stigma all contribute not only to a continuing state of compromised linguistic access to mental health care, but also to processes of rendering invisible the actual work of care in the mental health field.

Enzymatic mechanisms of biological magnetic sensitivity.

PubMed

Letuta, Ulyana G; Berdinskiy, Vitaly L; Udagawa, Chikako; Tanimoto, Yoshifumi

2017-10-01

Primary biological magnetoreceptors in living organisms is one of the main research problems in magnetobiology. Intracellular enzymatic reactions accompanied by electron transfer have been shown to be receptors of magnetic fields, and spin-dependent ion-radical processes can be a universal mechanism of biological magnetosensitivity. Magnetic interactions in intermediate ion-radical pairs, such as Zeeman and hyperfine (HFI) interactions, in accordance with proposed strict quantum mechanical theory, can determine magnetic-field dependencies of reactions that produce biologically important molecules needed for cell growth. Hyperfine interactions of electrons with nuclear magnetic moments of magnetic isotopes can explain the most important part of biomagnetic sensitivities in a weak magnetic field comparable to the Earth's magnetic field. The theoretical results mean that magnetic-field dependencies of enzymatic reaction rates in a weak magnetic field that can be independent of HFI constant a, if H < a, and are determined by the rate constant of chemical transformations in the enzyme active site. Both Zeeman and HFI interactions predict strong magnetic-field dependence in weak magnetic fields and magnetic-field independence of enzymatic reaction rate constants in strong magnetic fields. The theoretical results can explain the magnetic sensitivity of E. coli cell and demonstrate that intracellular enzymatic reactions are primary magnetoreceptors in living organisms. Bioelectromagnetics. 38:511-521, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

FIELD INVESTIGATION OF BIOLOGICAL TOILET SYSTEMS AND GREY WATER TREATMENT

EPA Science Inventory

The objective of the field program was to determine the operational characteristics and overall acceptability of popular models of biological toilets and a few select grey water systems. A field observation scheme was devised to take advantage of in-use sites throughout the State...

INLAND BIOLOGICAL FIELD STATIONS OF THE UNITED STATES.

ERIC Educational Resources Information Center

ARVEY, M. DALE; RIEMER, WILLIAM J.

INFORMATION ABOUT 42 INLAND BIOLOGY FIELD STATIONS IN THE UNITED STATES IS PRESENTED. DATA WERE OBTAINED THROUGH VISITS BY REPRESENTATIVES OF THE NATIONAL SCIENCE FOUNDATION. IN AN INTRODUCTORY SECTION THE CHARACTERISTICS, FUNCTIONS, AND PROBLEMS GENERALLY ASSOCIATED WITH FIELD STATIONS ARE REVIEWED. INDIVIDUAL STATIONS ARE LISTED ALPHABETICALLY,…

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)

Finding Clarity by Fostering Confusion: Reflections on Teaching an Undergraduate Integrated Biological Systems Course

ERIC Educational Resources Information Center

Martin, Kirsten H.

2015-01-01

Undergraduate biology programs in smaller liberal arts colleges are increasingly becoming focused on health science fields. This narrowing of focus potentially decreases opportunities for these students to explore other sub-fields of biology. This perspectives article highlights how one small university in Connecticut decided to institute a…

Outdoor Education, Junior Biology Field Studies.

ERIC Educational Resources Information Center

Aikman, John H.; And Others

Field studies for grade nine and ten biology students are developed in this teacher and student guide for outdoor education. A small section is devoted to teacher pre-planning and final sections are concerned with equipment, audio-visual resources, and a large booklist. Twenty-three investigations related to earth science and biology topics are…

The mammary gland in domestic ruminants: a systems biology perspective.

PubMed

Ferreira, Ana M; Bislev, Stine L; Bendixen, Emøke; Almeida, André M

2013-12-06

Milk and dairy products are central elements in the human diet. It is estimated that 108kg of milk per year are consumed per person worldwide. Therefore, dairy production represents a relevant fraction of the economies of many countries, being cattle, sheep, goat, water buffalo, and other ruminants the main species used worldwide. An adequate management of dairy farming cannot be achieved without the knowledge on the biological mechanisms behind lactation in ruminants. Thus, understanding the morphology, development and regulation of the mammary gland in health, disease and production is crucial. Presently, innovative and high-throughput technologies such as genomics, transcriptomics, proteomics and metabolomics allow a much broader and detailed knowledge on such issues. Additionally, the application of a systems biology approach to animal science is vastly growing, as new advances in one field of specialization or animal species lead to new lines of research in other areas or/and are expanded to other species. This article addresses how modern research approaches may help us understand long-known issues in mammary development, lactation biology and dairy production. Dairy production depends upon the knowledge of the morphology and regulation of the mammary gland and lactation. High-throughput technologies allow a much broader and detailed knowledge on the biology of the mammary gland. This paper reviews the major contributions that genomics, transcriptomics, metabolomics and proteomics approaches have provided to understand the regulation of the mammary gland in health, disease and production. In the context of mammary gland "omics"-based research, the integration of results using a Systems Biology Approach is of key importance. © 2013.

THE RETICULATING PHYLOGENY OF ISLAND BIOGEOGRAPHY THEORY

PubMed Central

Lomolino, Mark V.; Brown, James H.

2010-01-01

Biogeographers study all patterns in the geographic variation of life, from the spatial variation in genetic and physiological characteristics of cells and individuals, to the diversity and dynamics of biological communities among continental biotas or across oceanic archipelagoes. The field of island biogeography, in particular, has provided some genuinely transformative insights for the biological sciences, especially ecology and evolutionary biology. Our purpose here is to review the historical development of island biogeography theory during the 20th century by identifying the common threads that run through four sets of contributions made during this period, including those by Eugene Gordon Munroe (1948, 1953), Edward O. Wilson (1959, 1961), Frank W. Preston (1962a,b), and the seminal collaborations between Wilson and Robert H. MacArthur (1963, 1967), which revolutionized the field and served as its paradigm for nearly four decades. This epistemological account not only reviews the intriguing history of island theory, but it also includes fundamental lessons for advancing science through transformative integrations. Indeed, as is likely the case with many disciplines, island theory advanced not as a simple accumulation of facts and an orderly succession of theories and paradigms, but rather in fits and starts through a reticulating phylogeny of ideas and alternating periods of specialization and reintegration. We conclude this review with a summary of the salient features of this scientific revolution in the context of Kuhn’s structure, which strongly influenced theoretical advances during this period, and we then describe some of the fundamental assumptions and tenets of an emerging reintegration of island biogeography theory. PMID:20039528

Vignettes from the field of mathematical biology: the application of mathematics to biology and medicine.

PubMed

Murray, J D

2012-08-06

The application of mathematical models in biology and medicine has a long history. From the sparse number of papers in the first half of the twentieth century with a few scientists working in the field it has become vast with thousands of active researchers. We give a brief, and far from definitive history, of how some parts of the field have developed and how the type of research has changed. We describe in more detail just two examples of specific models which are directly related to real biological problems, namely animal coat patterns and the growth and image enhancement of glioblastoma brain tumours.

Saccharomyces cerevisiae: A novel and efficient biological control agent for Colletotrichum acutatum during pre-harvest.

PubMed

Lopes, Marcos Roberto; Klein, Mariana Nadjara; Ferraz, Luriany Pompeo; da Silva, Aline Caroline; Kupper, Katia Cristina

2015-06-01

In this study, we evaluated the efficiency of six isolates of Saccharomyces cerevisiae in controlling Colletotrichum acutatum, the causal agent of postbloom fruit drop that occur in pre-harvest citrus. We analyzed the mechanisms of action involved in biological control such as: production of antifungal compounds, nutrient competition, detection of killer activity, and production of hydrolytic enzymes of the isolates of S. cerevisiae on C. acutatum and their efficiency in controlling postbloom fruit drop on detached citrus flowers. Our results showed that all six S. cerevisiae isolates produced antifungal compounds, competed for nutrients, inhibited pathogen germination, and produced killer activity and hydrolytic enzymes when in contact with the fungus wall. The isolates were able to control the disease when detached flowers were artificially inoculated, both preventively and curatively. In this work we identified a novel potential biological control agent for C. acutatum during pre-harvest. This is the first report of yeast efficiency for the biocontrol of postbloom fruit drop, which represents an important contribution to the field of biocontrol of diseases affecting citrus populations worldwide. Copyright © 2015 Elsevier GmbH. All rights reserved.

Assessment of biological half life using in silico QSPkR approach: a self organizing molecular field analysis (SOMFA) on a series of antimicrobial quinolone drugs.

PubMed

Goel, Honey; Sinha, V R; Thareja, Suresh; Aggarwal, Saurabh; Kumar, Manoj

2011-08-30

The quinolones belong to a family of synthetic potent broad-spectrum antibiotics and particularly active against gram-negative organisms, especially Pseudomonas aeruginosa. A 3D-QSPkR approach has been used to obtain the quantitative structure pharmacokinetic relationship for a series of quinolone drugs using SOMFA. The series consisting of 28 molecules have been investigated for their pharmacokinetic performance using biological half life (t(1/2)). A statistically validated robust model for a diverse group of quinolone drugs having flexibility in structure and pharmacokinetic profile (t(1/2)) obtained using SOMFA having good cross-validated correlation coefficient r(cv)(2) (0.6847), non cross-validated correlation coefficient r(2) values (0.7310) and high F-test value (33.9663). Analysis of 3D-QSPkR models through electrostatic and shape grids provide useful information about the shape and electrostatic potential contributions on t(1/2). The analysis of SOMFA results provide an insight for the generation of novel molecular architecture of quinolones with optimal half life and improved biological profile. Copyright © 2011 Elsevier B.V. All rights reserved.

The Role of Biomarkers in the Assessment of Aquatic Ecosystem Health

PubMed Central

Hook, Sharon E; Gallagher, Evan P; Batley, Graeme E

2016-01-01

Ensuring the health of aquatic ecosystems and identifying species at risk from the detrimental effects of environmental contaminants can be facilitated by integrating analytical chemical analysis with carefully selected biological endpoints measured in tissues of species of concern. These biological endpoints include molecular, biochemical and physiological markers (i.e. biomarkers) that when integrated, can clarify issues of contaminant bioavailability, bioaccumulation and ecological effects while enabling a better understanding of the effects of non-chemical stressors. In the case of contaminant stressors, an understanding of chemical modes of toxicity can be incorporated with diagnostic markers of aquatic animal physiology to help understand the health status of aquatic organisms in the field. Furthermore, new approaches in functional genomics and bioinformatics can help discriminate individual chemicals, or groups of chemicals among complex mixtures that may contribute to adverse biological effects. While the use of biomarkers is not a new paradigm, such approaches have been underutilized in the context of ecological risk assessment and natural resource damage assessment. From a regulatory standpoint, these approaches can help better assess the complex effects from coastal development activities to assessing ecosystem integrity pre- and post-development or site remediation. PMID:24574147

Chemical Variability and Biological Activities of Eucalyptus spp. Essential Oils.

PubMed

Barbosa, Luiz Claudio Almeida; Filomeno, Claudinei Andrade; Teixeira, Robson Ricardo

2016-12-07

Many plant species produce mixtures of odorous and volatile compounds known as essential oils (EOs). These mixtures play important roles in Nature and have been utilized by mankind for different purposes, such as pharmaceuticals, agrochemicals, aromatherapy, and food flavorants. There are more than 3000 EOs reported in the literature, with approximately 300 in commercial use, including the EOs from Eucalyptus species. Most EOs from Eucalyptus species are rich in monoterpenes and many have found applications in pharmaceuticals, agrochemicals, food flavorants, and perfumes. Such applications are related to their diverse biological and organoleptic properties. In this study, we review the latest information concerning the chemical composition and biological activities of EOs from different species of Eucalyptus . Among the 900 species and subspecies of the Eucalyptus genus, we examined 68 species. The studies associated with these species were conducted in 27 countries. We have focused on the antimicrobial, acaricidal, insecticidal and herbicidal activities, hoping that such information will contribute to the development of research in this field. It is also intended that the information described in this study can be useful in the rationalization of the use of Eucalyptus EOs as components for pharmaceutical and agrochemical applications as well as food preservatives and flavorants.

The Effectiveness of a Virtual Field Trip (VFT) Module in Learning Biology

ERIC Educational Resources Information Center

Haris, Norbaizura; Osman, Kamisah

2015-01-01

Virtual Field Trip is a computer aided module of science developed to study the Colonisation and Succession in Mangrove Swamps, as an alternative to the real field trip in Form for Biology. This study is to identify the effectiveness of the Virtual Field Trip (VFT) module towards the level of achievement in the formative test for this topic. This…

Will Systems Biology Deliver Its Promise and Contribute to the Development of New or Improved Vaccines? What Really Constitutes the Study of "Systems Biology" and How Might Such an Approach Facilitate Vaccine Design.

PubMed

Germain, Ronald N

2017-10-16

A dichotomy exists in the field of vaccinology about the promise versus the hype associated with application of "systems biology" approaches to rational vaccine design. Some feel it is the only way to efficiently uncover currently unknown parameters controlling desired immune responses or discover what elements actually mediate these responses. Others feel that traditional experimental, often reductionist, methods for incrementally unraveling complex biology provide a more solid way forward, and that "systems" approaches are costly ways to collect data without gaining true insight. Here I argue that both views are inaccurate. This is largely because of confusion about what can be gained from classical experimentation versus statistical analysis of large data sets (bioinformatics) versus methods that quantitatively explain emergent properties of complex assemblies of biological components, with the latter reflecting what was previously called "physiology." Reductionist studies will remain essential for generating detailed insight into the functional attributes of specific elements of biological systems, but such analyses lack the power to provide a quantitative and predictive understanding of global system behavior. But by employing (1) large-scale screening methods for discovery of unknown components and connections in the immune system ( omics ), (2) statistical analysis of large data sets ( bioinformatics ), and (3) the capacity of quantitative computational methods to translate these individual components and connections into models of emergent behavior ( systems biology ), we will be able to better understand how the overall immune system functions and to determine with greater precision how to manipulate it to produce desired protective responses. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

[Fundamental aspects of extreme aging].

PubMed

Tréton, J

2002-07-01

Major developments in molecular biology in invertebrates have recently shown the determining effect of genetics on aging. The first finding was that artificial selection can highlight the genetic aspect of the aging process, demonstrating the polygenetic property of longevity. Another finding showed that certain gene transfers can modulate the lifespan of an organism. Recent progress has been made in three fields: genetic markers of aging, biological basis of cell maintenance, and hereditary factors contributing to late onset genetic disease. These new developments open new avenues of research in clinical biology. In regard to genetic markers of aging, it has been demonstrated that the ends of the chromosomes, telomeres, play a role in cell senescence. Telomeres can be viewed as markers of aging. Shortened telomeres are associated with replicative senescence and antitumor action. DNA anomalies are also more frequent: simple or double breaks, additions and base substitutions. Data on the biological basis of cell maintenance obtained in invertebrates show the polygenetic property of aging involving four significant mechanisms, control of metabolism, resistance to stress, chromatin-dependent gene regulation of genetic homeostasis. Finally, recent studies have shown that late onset hereditary diseases would be linked with particular genes, some of which have been identified. Two non-exclusive mechanisms could be involved: an adaptive mechanism involving gene selection during the evolutionary process, for example in obesity; and non-adaptive accumulation of gene expression during the post-reproductive phase, for example in Alzheimer's disease. These findings open a new era for the biology of aging.

Maps, books and other metaphors for systems biology.

PubMed

Ouzounis, Christos; Mazière, Pierre

2006-07-01

We briefly review the use of metaphors in science and progressively focus on fields from biology and molecular biology to genomics and bioinformatics. We discuss how metaphors are both a tool for scientific exploration and a medium for public communication of complex subjects, by various short examples. Finally, we propose a metaphor for systems biology that provides an illuminating perspective for the ambitious goals of this field and delimits its current agenda.

Biological field stations: research legacies and sites for serendipity

Treesearch

William K. Michener; Keith L. Bildstein; Arthur McKee; Robert R. Parmenter; William W. Hargrove; Deedra McClearn; Mark Stromberg

2009-01-01

Biological field stations are distributed throughout North America, capturing much of the ecological variability present at the continental scale and encompassing many unique habitats. In addition to their role in supporting research and education, field stations offer legacies of data, specimens, and accumulated knowledge. Such legacies often provide the only...

Teaching Field Biology with Photography

ERIC Educational Resources Information Center

Jenkins, Ronald L.; Howell, W. Mike; Davenport, L. J.; Wood, Linda F.

2003-01-01

Photography makes an easy and excellent tool for teaching field biology courses, allowing students to study nature without harming it. This photographic technique is used in capturing images of vertebrates, invertebrates, and plants during class field trips, then making these images available for students to identify and study from a departmental…

Tracking the emergence of synthetic biology.

PubMed

Shapira, Philip; Kwon, Seokbeom; Youtie, Jan

2017-01-01

Synthetic biology is an emerging domain that combines biological and engineering concepts and which has seen rapid growth in research, innovation, and policy interest in recent years. This paper contributes to efforts to delineate this emerging domain by presenting a newly constructed bibliometric definition of synthetic biology. Our approach is dimensioned from a core set of papers in synthetic biology, using procedures to obtain benchmark synthetic biology publication records, extract keywords from these benchmark records, and refine the keywords, supplemented with articles published in dedicated synthetic biology journals. We compare our search strategy with other recent bibliometric approaches to define synthetic biology, using a common source of publication data for the period from 2000 to 2015. The paper details the rapid growth and international spread of research in synthetic biology in recent years, demonstrates that diverse research disciplines are contributing to the multidisciplinary development of synthetic biology research, and visualizes this by profiling synthetic biology research on the map of science. We further show the roles of a relatively concentrated set of research sponsors in funding the growth and trajectories of synthetic biology. In addition to discussing these analyses, the paper notes limitations and suggests lines for further work.

The Wolffian roots of Kant's teleology.

PubMed

van den Berg, Hein

2013-12-01

Kant's teleology as presented in the Critique of Judgment is commonly interpreted in relation to the late eighteenth-century biological research of Johann Friedrich Blumenbach. In the present paper, I show that this interpretative perspective is incomplete. Understanding Kant's views on teleology and biology requires a consideration of the teleological and biological views of Christian Wolff and his rationalist successors. By reconstructing the Wolffian roots of Kant's teleology, I identify several little known sources of Kant's views on biology. I argue that one of Kant's main contributions to eighteenth-century debates on biology consisted in demarcating biology from metaphysics. Kant rejected Wolffian views on the hierarchy of sciences, according to which propositions specifying the functions of organisms are derived from theological truths. In addition, Kant argued that organic self-organization necessitates a teleological description in order to show that self-organization does not support materialism. By demarcating biology and metaphysics, Kant made a small yet important contribution to establishing biology as a science. Copyright © 2013 Elsevier Ltd. All rights reserved.

Artificial intelligence and synthetic biology: A tri-temporal contribution.

PubMed

Bianchini, Francesco

2016-10-01

Artificial intelligence can make numerous contributions to synthetic biology. I would like to suggest three that are related to the past, present and future of artificial intelligence. From the past, works in biology and artificial systems by Turing and von Neumann prove highly interesting to explore within the new framework of synthetic biology, especially with regard to the notions of self-modification and self-replication and their links to emergence and the bottom-up approach. The current epistemological inquiry into emergence and research on swarm intelligence, superorganisms and biologically inspired cognitive architecture may lead to new achievements on the possibilities of synthetic biology in explaining cognitive processes. Finally, the present-day discussion on the future of artificial intelligence and the rise of superintelligence may point to some research trends for the future of synthetic biology and help to better define the boundary of notions such as "life", "cognition", "artificial" and "natural", as well as their interconnections in theoretical synthetic biology. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Evolutionary developmental biology: its concepts and history with a focus on Russian and German contributions

NASA Astrophysics Data System (ADS)

Olsson, Lennart; Levit, Georgy S.; Hoßfeld, Uwe

2010-11-01

Evolutionary theory has been likened to a “universal acid” (Dennett 1995) that eats its way into more and more areas of science. Recently, developmental biology has been infused by evolutionary concepts and perspectives, and a new field of research—evolutionary developmental biology—has been created and is often called EvoDevo for short. However, this is not the first attempt to make a synthesis between these two areas of biology. In contrast, beginning right after the publication of Darwin’s Origin in 1859, Ernst Haeckel formulated his biogenetic law in 1872, famously stating that ontogeny recapitulates phylogeny. Haeckel was in his turn influenced by pre-Darwinian thinkers such as Karl Ernst von Baer, who had noted that earlier developmental stages show similarities not seen in the adults. In this review, written for an audience of non-specialists, we first give an overview of the history of EvoDevo, especially the tradition emanating from Haeckel and other comparative embryologists and morphologists, which has often been neglected in discussions about the history of EvoDevo and evolutionary biology. Here we emphasize contributions from Russian and German scientists to compensate for the Anglo-American bias in the literature. In Germany, the direct influence of Ernst Haeckel was felt particularly in Jena, where he spent his entire career as a professor, and we give an overview of the “Jena school” of evolutionary morphology, with protagonists such as Oscar Hertwig, Ludwig Plate, and Victor Franz, who all developed ideas that we would nowadays think of as belonging to EvoDevo. Franz ideas about “biometabolic modi” are similar to those of a Russian comparative morphologist that visited Jena repeatedly, A. N. Sewertzoff, who made important contributions to what we now call heterochrony research—heterochrony meaning changes in the relative timing of developmental events. His student I. I. Schmalhausen became an important contributor to the synthetic theory of evolution in Russia and is only partly known outside of the Russian-reading world because only one of his many books was translated into English early on. He made many important contributions to evolutionary theory and we point out the important parallels between Schmalhausen’s ideas (stabilizing selection, autonomization) and C. H. Waddington’s (canalization, genetic assimilation). This is one of the many parallels that have contributed to an increased appreciation of the internationality of progress in evolutionary thinking in the first half of the twentieth century. A direct link between German and Russian evolutionary biology is provided by N. V. Timoféeff-Ressovsky, whose work on, e.g., fly genetics in Berlin is a crucial part of the history of evo-devo. To emphasize the international nature of heterochrony research as predecessor to the modern era of EvoDevo, we include Sir G. R. de Beer’s work in the UK. This historical part is followed by a short review of the discovery and importance of homeobox genes and of some of the major concepts that form the core of modern EvoDevo, such as modularity, constraints, and evolutionary novelties. Major trends in contemporary EvoDevo are then outlined, such as increased use of genomics and molecular genetics, computational and bioinformatics approaches, ecological developmental biology (eco-devo), and phylogenetically informed comparative embryology. Based on our survey, we end the review with an outlook on future trends and important issues in EvoDevo.

Imaging of the interaction of low frequency electric fields with biological tissues by optical coherence tomography

NASA Astrophysics Data System (ADS)

Peña, Adrian F.; Devine, Jack; Doronin, Alexander; Meglinski, Igor

2014-03-01

We report the use of conventional Optical Coherence Tomography (OCT) for visualization of propagation of low frequency electric field in soft biological tissues ex vivo. To increase the overall quality of the experimental images an adaptive Wiener filtering technique has been employed. Fourier domain correlation has been subsequently applied to enhance spatial resolution of images of biological tissues influenced by low frequency electric field. Image processing has been performed on Graphics Processing Units (GPUs) utilizing Compute Unified Device Architecture (CUDA) framework in the frequencydomain. The results show that variation in voltage and frequency of the applied electric field relates exponentially to the magnitude of its influence on biological tissue. The magnitude of influence is about twice more for fresh tissue samples in comparison to non-fresh ones. The obtained results suggest that OCT can be used for observation and quantitative evaluation of the electro-kinetic changes in biological tissues under different physiological conditions, functional electrical stimulation, and potentially can be used non-invasively for food quality control.

Preface

NASA Astrophysics Data System (ADS)

Lindgård, Per-Anker

2003-05-01

This special issue presents a series of papers on biological physics. It emphasizes the fact that Journal of Physics: Condensed Matter welcomes papers in this area and foresees a fruitful cross-fertilization between this and other more conventional condensed matter fields. The work was presented at the conference ÂNanophysics in Life SciencesÂ' held in Copenhagen on 21-22 June 2002. The meeting was arranged by, and marked the start of, the new Division of Physics in Life Sciences (DPL) within the European Physical Society (EPS). It also celebrated the opening of a new Danish research centre on quantum protein physics (QUP), which was co-organizer and co-sponsor. The meeting was organized at short notice and yet attracted some 80 participants from a number of countries (despite the fact that the chosen weekend included the `midsummer night', a feast nobody in the Northern Scandinavian countries would wish to miss - even when offered an event in the beautiful venue of the Carlsberg estate). The audience included many young people and students, demonstrating the great interest in the field of biological physics and in the topics chosen within that field. The selection represented, furthermore, the present scope of the new DPL division. All but one of the board members of DPL were able to attend and present their work, among others. They have subsequently delivered valuable contributions to this special issue. The subjects cover a large area (the full programme can be found on the division's web-page: DPL.risoe.dk). To mention a few: the dynamical and optical properties of biomolecules (proteins), experimental studies of single biomolecules, various theoretical approaches to the protein folding problem and DNA motion, biomolecular motor and transport functions, quantum chemical calculations. Many of these problems are closely related to those studied in conventional condensed matter. To emphasize one topic we have written the Viewpoint article (pages V5-V9) which ties together the concepts of solitons, self-trapping, polarons and pump-probe experiments used in both realms. The scope of biological physics is of course still wider. All biological processes occur in water, hence an important topic is how proteins and biomolecules behave and interact in liquids. There is in this case a strong overlap between subjects generally published in the Liquids, Soft Matter and Biophysics section of Journal of Physics: Condensed Matter, but not covered in this issue. Another branch not covered is the more mathematical, generally non-linear models of physiological processes. It is hoped that this issue will serve as a valuable current state-of-the-art overview of interesting and important problems in biological physics, which will stimulate the interest of the general readership of Journal of Physics: Condensed Matter and inspire the application of the knowledge and expertise accumulated in condensed matter physics. I wish to thank the participants for their contributions to the meeting and to this special issue, Institute of Physics Publishing editorial staff for the efficient and smooth handling of the refereeing of the articles, and finally the QUP Center, The Danish Graduate School of Biophysics, EPS and The Carlsberg Academy for financial and other support.

Interaction of Inorganic Nanoparticles With Cell Membranes

DTIC Science & Technology

2008-10-20

the field of colloidal and biological behaviour of nanoparticles. Questions regarding the colloidal behavior of particles in biological liquids...better the behaviour of nanoparticles in living systems. 2. Research work During the preparation phase of this project we have defined following...unique knowledge of the participating researgroups in the field of colloidal and biological behaviour of nanoparticles. Questions regarding the

Information Use by PhD Students in Agriculture and Biology: A Dissertation Citation Analysis

ERIC Educational Resources Information Center

Kuruppu, Pali U.; Moore, Debra C.

2008-01-01

This article reports the findings of a study conducted to examine the types of information used by graduate students in the fields of biological and agricultural sciences at Iowa State University (ISU). The citations of doctoral dissertations submitted in nine agriculture and biological science subject fields (crop production and physiology;…

Field Trip to Kazdagi National Park: Views of Prospective Biology Teachers

ERIC Educational Resources Information Center

Çetin, Gülcan

2014-01-01

The purpose of the study was to investigate the views of the prospective biology teachers about the field trip to Kazdagi National Park. Participants were 12 prospective Biology teachers studying in Necatibey Faculty of Education in Balikesir University, Turkey. A semi-structured interview form was used as a data collection instrument. Data were…

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

PubMed Central

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

2007-01-01

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

Glucose Oxidase Biosensor Modeling and Predictors Optimization by Machine Learning Methods †

PubMed Central

Gonzalez-Navarro, Felix F.; Stilianova-Stoytcheva, Margarita; Renteria-Gutierrez, Livier; Belanche-Muñoz, Lluís A.; Flores-Rios, Brenda L.; Ibarra-Esquer, Jorge E.

2016-01-01

Biosensors are small analytical devices incorporating a biological recognition element and a physico-chemical transducer to convert a biological signal into an electrical reading. Nowadays, their technological appeal resides in their fast performance, high sensitivity and continuous measuring capabilities; however, a full understanding is still under research. This paper aims to contribute to this growing field of biotechnology, with a focus on Glucose-Oxidase Biosensor (GOB) modeling through statistical learning methods from a regression perspective. We model the amperometric response of a GOB with dependent variables under different conditions, such as temperature, benzoquinone, pH and glucose concentrations, by means of several machine learning algorithms. Since the sensitivity of a GOB response is strongly related to these dependent variables, their interactions should be optimized to maximize the output signal, for which a genetic algorithm and simulated annealing are used. We report a model that shows a good generalization error and is consistent with the optimization. PMID:27792165

Integrating Epigenomics into the Understanding of Biomedical Insight.

PubMed

Han, Yixing; He, Ximiao

2016-01-01

Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics.

Integrating Epigenomics into the Understanding of Biomedical Insight

PubMed Central

Han, Yixing; He, Ximiao

2016-01-01

Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics. PMID:27980397

Small group gender ratios impact biology class performance and peer evaluations

PubMed Central

Cotner, Sehoya

2018-01-01

Women are underrepresented in science, technology, engineering, and mathematics (STEM) disciplines. Evidence suggests the microclimate of the classroom is an important factor influencing female course grades and interest, which encourages retention of women in STEM fields. Here, we test whether the gender composition of small (8–9 person) learning groups impacts course performance, sense of social belonging, and intragroup peer evaluations of intellectual contributions. Across two undergraduate active learning courses in introductory biology, we manipulated the classroom microclimate by varying the gender ratios of learning groups, ranging from 0% female to 100% female. We found that as the percent of women in groups increased, so did overall course performance for all students, regardless of gender. Additionally, women assigned higher peer- evaluations in groups with more women than groups with less women. Our work demonstrates an added benefit of the retention of women in STEM: increased performance for all, and positive peer perceptions for women. PMID:29614091

Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives

DOE PAGES

Jagiello, Karolina; Grzonkowska, Monika; Swirog, Marta; ...

2016-08-29

In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure–Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure–Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide themore » recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.« less

How Genetically Engineered Mouse Tumor Models Provide Insights Into Human Cancers

PubMed Central

Politi, Katerina; Pao, William

2011-01-01

Genetically engineered mouse models (GEMMs) of human cancer were first created nearly 30 years ago. These early transgenic models demonstrated that mouse cells could be transformed in vivo by expression of an oncogene. A new field emerged, dedicated to generating and using mouse models of human cancer to address a wide variety of questions in cancer biology. The aim of this review is to highlight the contributions of mouse models to the diagnosis and treatment of human cancers. Because of the breadth of the topic, we have selected representative examples of how GEMMs are clinically relevant rather than provided an exhaustive list of experiments. Today, as detailed here, sophisticated mouse models are being created to study many aspects of cancer biology, including but not limited to mechanisms of sensitivity and resistance to drug treatment, oncogene cooperation, early detection, and metastasis. Alternatives to GEMMs, such as chemically induced or spontaneous tumor models, are not discussed in this review. PMID:21263096

Non-Simian Foamy Viruses: Molecular Virology, Tropism and Prevalence and Zoonotic/Interspecies Transmission

PubMed Central

Kehl, Timo; Tan, Juan; Materniak, Magdalena

2013-01-01

Within the field of retrovirus, our knowledge of foamy viruses (FV) is still limited. Their unique replication strategy and mechanism of viral persistency needs further research to gain understanding of the virus-host interactions, especially in the light of the recent findings suggesting their ancient origin and long co-evolution with their nonhuman hosts. Unquestionably, the most studied member is the primate/prototype foamy virus (PFV) which was originally isolated from a human (designated as human foamy virus, HFV), but later identified as chimpanzee origin; phylogenetic analysis clearly places it among other Old World primates. Additionally, the study of non-simian animal FVs can contribute to a deeper understanding of FV-host interactions and development of other animal models. The review aims at highlighting areas of special interest regarding the structure, biology, virus-host interactions and interspecies transmission potential of primate as well as non-primate foamy viruses for gaining new insights into FV biology. PMID:24064793

Advantages and limitations of classic and 3D QSAR approaches in nano-QSAR studies based on biological activity of fullerene derivatives

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

Jagiello, Karolina; Grzonkowska, Monika; Swirog, Marta

In this contribution, the advantages and limitations of two computational techniques that can be used for the investigation of nanoparticles activity and toxicity: classic nano-QSAR (Quantitative Structure–Activity Relationships employed for nanomaterials) and 3D nano-QSAR (three-dimensional Quantitative Structure–Activity Relationships, such us Comparative Molecular Field Analysis, CoMFA/Comparative Molecular Similarity Indices Analysis, CoMSIA analysis employed for nanomaterials) have been briefly summarized. Both approaches were compared according to the selected criteria, including: efficiency, type of experimental data, class of nanomaterials, time required for calculations and computational cost, difficulties in the interpretation. Taking into account the advantages and limitations of each method, we provide themore » recommendations for nano-QSAR modellers and QSAR model users to be able to determine a proper and efficient methodology to investigate biological activity of nanoparticles in order to describe the underlying interactions in the most reliable and useful manner.« less

Neurobiology of Adolescent Substance Use and Addictive Behaviors: Prevention and Treatment Implications

PubMed Central

Hammond, Christopher J.; Mayes, Linda C.; Potenza, Marc N.

2015-01-01

Psychoactive substance and nonsubstance/behavioral addictions are major public health concerns associated with significant societal cost. Adolescence is a period of dynamic biologic, psychological, and behavioral changes. Adolescence is also associated with an increased risk for substance use and addictive disorders. During adolescence, developmental changes in neural circuitry of reward processing, motivation, cognitive control, and stress may contribute to vulnerability for increased levels of engagement in substance use and nonsubstance addictive behaviors. Current biologic models of adolescent vulnerability for addictions incorporate existing data on allostatic changes in function and structure of the midbrain dopaminergic system, stress-associated neuroplasticity, and maturational imbalances between cognitive control and reward reactivity. When characterizing adolescent vulnerability, identifying subgroups of adolescents at high risk for addictive behaviors is a major goal of the addiction field. Genetics, epigenetics, and intermediate phenotypes/endophenotypes may assist in characterizing children and adolescents at risk. Improved understanding of the neurobiology of adolescence and addiction vulnerability has the potential to refine screening, enhance prevention and intervention strategies, and inform public policy. PMID:25022184

Advances in ultrasensitive mass spectrometry of organic molecules.

PubMed

Kandiah, Mathivathani; Urban, Pawel L

2013-06-21

Ultrasensitive mass spectrometric analysis of organic molecules is important for various branches of chemistry, and other fields including physics, earth and environmental sciences, archaeology, biomedicine, and materials science. It finds applications--as an enabling tool--in systems biology, biological imaging, clinical analysis, and forensics. Although there are a number of technical obstacles associated with the analysis of samples by mass spectrometry at ultratrace level (for example analyte losses during sample preparation, insufficient sensitivity, ion suppression), several noteworthy developments have been made over the years. They include: sensitive ion sources, loss-free interfaces, ion optics components, efficient mass analyzers and detectors, as well as "smart" sample preparation strategies. Some of the mass spectrometric methods published to date can achieve sensitivity which is by several orders of magnitude higher than that of alternative approaches. Femto- and attomole level limits of detection are nowadays common, while zepto- and yoctomole level limits of detection have also been reported. We envision that the ultrasensitive mass spectrometric assays will soon contribute to new discoveries in bioscience and other areas.

Ushering in the study and treatment of preclinical Alzheimer disease.

PubMed

Langbaum, Jessica B; Fleisher, Adam S; Chen, Kewei; Ayutyanont, Napatkamon; Lopera, Francisco; Quiroz, Yakeel T; Caselli, Richard J; Tariot, Pierre N; Reiman, Eric M

2013-07-01

Researchers have begun to characterize the subtle biological and cognitive processes that precede the clinical onset of Alzheimer disease (AD), and to set the stage for accelerated evaluation of experimental treatments to delay the onset, reduce the risk of, or completely prevent clinical decline. In this Review, we provide an overview of the experimental strategies, and brain imaging and cerebrospinal fluid biomarker measures that are used in early detection and tracking of AD, highlighting at-risk individuals who could be suitable for preclinical monitoring. We discuss how advances in the field have contributed to reconceptualization of AD as a sequence of biological changes that occur during progression from preclinical AD, to mild cognitive impairment and finally dementia, and we review recently proposed research criteria for preclinical AD. Advances in the study of preclinical AD have driven the recognition that efficacy of at least some AD therapies may depend on initiation of treatment before clinical manifestation of disease, leading to a new era of AD prevention research.

X-ray mosaic nanotomography of large microorganisms.

PubMed

Mokso, R; Quaroni, L; Marone, F; Irvine, S; Vila-Comamala, J; Blanke, A; Stampanoni, M

2012-02-01

Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state. Copyright © 2012 Elsevier Inc. All rights reserved.

Disposal of Industrial and Domestic Wastes: Land and Sea Alternatives.

DTIC Science & Technology

1984-01-01

square kilometers. The rough classification of physical, chemical , and biological processes into near field versus far field and short term versus...contaminants by sedimentation is slowed. Chemical Precipitation and Dissolution During the few minutes of the initial dilution of a buoyant plume ...model. Time and space scales of physical, chemical , and biological processes often provide natural divisions in such modeling. Near -field and far-field

Review of russian literature on biological action of DC and low-frequency AC magnetic fields.

PubMed

Zhadin, M N

2001-01-01

This review considers the Russian scientific literature on the influence of weak static and of low-frequency alternating magnetic fields on biological systems. The review covers the most interesting works and the main lines of investigation during the period 1900 to the present. Shown here are the historical roots, beginning with the ideas of V. Vernadsky and A. Chizhevsky, which led in the field of Russian biology to an increasing interest in magnetic fields, based on an intimate connection between solar activity and life on the Earth, and which determined the peculiar development of Russian magnetobiology. The variety of studies on the effects of magnetic storms and extremely low-frequency, periodic variations of the geomagnetic field on human beings and animals as well as on social phenomena are described. The diverse experiments involving artificial laboratory magnetic fields acting on different biological entities under different conditions are also considered. A series of theoretical advances are reviewed that have paved the way for a step-by-step understanding of the mechanisms of magnetic field effects on biological systems. The predominantly unfavorable influence of magnetic fields on living beings is shown, but the cases of favorable influence of magnetic fields on human beings and lower animals are demonstrated as well. The majority of Russian investigations in this area of science has been unknown among the non-Russian speaking audience for many reasons, primarily because of a language barrier. Therefore, it is hoped that this review may be of interest to the international scientific community. Copyright 2001 Wiley-Liss, Inc.

From a word to a world: the current situation in the interdisciplinary field of synthetic biology

PubMed Central

Hu, Xiaojun

2015-01-01

Using a carefully designed search query, we describe the field of synthetic biology in terms of leading countries, organizations and funding sources. Besides articles we also paid some attention to patents. The USA is the leading country in this field, followed by China. There is a clear exponential growth in the field of synthetic biology over the latest 14 years. Keywords were analyzed using the notion of year-based h-indices, core gap and relative core gap. We conclude that the term “synthetic biology” hides a large world ready to be explored by interdisciplinary research. PMID:25650074

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

NASA Astrophysics Data System (ADS)

Suwono, Hadi; Wibowo, Agung

2018-01-01

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

Synthetic biology through biomolecular design and engineering.

PubMed

Channon, Kevin; Bromley, Elizabeth H C; Woolfson, Derek N

2008-08-01

Synthetic biology is a rapidly growing field that has emerged in a global, multidisciplinary effort among biologists, chemists, engineers, physicists, and mathematicians. Broadly, the field has two complementary goals: To improve understanding of biological systems through mimicry and to produce bio-orthogonal systems with new functions. Here we review the area specifically with reference to the concept of synthetic biology space, that is, a hierarchy of components for, and approaches to generating new synthetic and functional systems to test, advance, and apply our understanding of biological systems. In keeping with this issue of Current Opinion in Structural Biology, we focus largely on the design and engineering of biomolecule-based components and systems.

The Biology of Cancer Health Disparities

Cancer.gov

These examples show how biology contributes to health disparities (differences in disease incidence and outcomes among distinct racial and ethnic groups, ), and how biological factors interact with other relevant factors, such as diet and the environment.

Method for high resolution magnetic resonance analysis using magic angle technique

DOEpatents

Wind, Robert A.; Hu, Jian Zhi

2003-11-25

A method of performing a magnetic resonance analysis of a biological object that includes placing the biological object in a main magnetic field and in a radio frequency field, the main magnetic field having a static field direction; rotating the biological object at a rotational frequency of less than about 100 Hz around an axis positioned at an angle of about 54.degree.44' relative to the main magnetic static field direction; pulsing the radio frequency to provide a sequence that includes a magic angle turning pulse segment; and collecting data generated by the pulsed radio frequency. According to another embodiment, the radio frequency is pulsed to provide a sequence capable of producing a spectrum that is substantially free of spinning sideband peaks.

Biology-inspired AMO physics

NASA Astrophysics Data System (ADS)

Mathur, Deepak

2015-01-01

This Topical Review presents an overview of increasingly robust interconnects that are being established between atomic, molecular and optical (AMO) physics and the life sciences. AMO physics, outgrowing its historical role as a facilitator—a provider of optical methodologies, for instance—now seeks to partner biology in its quest to link systems-level descriptions of biological entities to insights based on molecular processes. Of course, perspectives differ when AMO physicists and biologists consider various processes. For instance, while AMO physicists link molecular properties and dynamics to potential energy surfaces, these have to give way to energy landscapes in considerations of protein dynamics. But there are similarities also: tunnelling and non-adiabatic transitions occur both in protein dynamics and in molecular dynamics. We bring to the fore some such differences and similarities; we consider imaging techniques based on AMO concepts, like 4D fluorescence microscopy which allows access to the dynamics of cellular processes, multiphoton microscopy which offers a built-in confocality, and microscopy with femtosecond laser beams to saturate the suppression of fluorescence in spatially controlled fashion so as to circumvent the diffraction limit. Beyond imaging, AMO physics contributes with optical traps that probe the mechanical and dynamical properties of single ‘live’ cells, highlighting differences between healthy and diseased cells. Trap methodologies have also begun to probe the dynamics governing of neural stem cells adhering to each other to form neurospheres and, with squeezed light to probe sub-diffusive motion of yeast cells. Strong field science contributes not only by providing a source of energetic electrons and γ-rays via laser-plasma accelerations schemes, but also via filamentation and supercontinuum generation, enabling mainstream collision physics into play in diverse processes like DNA damage induced by low-energy collisions to invoking dissociative attachment in quantification of stress levels in humans. The prognosis is extremely good for more intense interaction of AMO physics and biology; by way of future predictions attention is drawn to only two of very many opportunities for such interactions: application of attosecond techniques and tunnelling experiments to biological problems.

Engineering Concepts in Stem Cell Research.

PubMed

Narayanan, Karthikeyan; Mishra, Sachin; Singh, Satnam; Pei, Ming; Gulyas, Balazs; Padmanabhan, Parasuraman

2017-12-01

The field of regenerative medicine integrates advancements made in stem cells, molecular biology, engineering, and clinical methodologies. Stem cells serve as a fundamental ingredient for therapeutic application in regenerative medicine. Apart from stem cells, engineering concepts have equally contributed to the success of stem cell based applications in improving human health. The purpose of various engineering methodologies is to develop regenerative and preventive medicine to combat various diseases and deformities. Explosion of stem cell discoveries and their implementation in clinical setting warrants new engineering concepts and new biomaterials. Biomaterials, microfluidics, and nanotechnology are the major engineering concepts used for the implementation of stem cells in regenerative medicine. Many of these engineering technologies target the specific niche of the cell for better functional capability. Controlling the niche is the key for various developmental activities leading to organogenesis and tissue homeostasis. Biomimetic understanding not only helped to improve the design of the matrices or scaffolds by incorporating suitable biological and physical components, but also ultimately aided adoption of designs that helped these materials/devices have better function. Adoption of engineering concepts in stem cell research improved overall achievement, however, several important issues such as long-term effects with respect to systems biology needs to be addressed. Here, in this review the authors will highlight some interesting breakthroughs in stem cell biology that use engineering methodologies. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Models to study gravitational biology of Mammalian reproduction

NASA Technical Reports Server (NTRS)

Tou, Janet; Ronca, April; Grindeland, Richard; Wade, Charles

2002-01-01

Mammalian reproduction evolved within Earth's 1-g gravitational field. As we move closer to the reality of space habitation, there is growing scientific interest in how different gravitational states influence reproduction in mammals. Habitation of space and extended spaceflight missions require prolonged exposure to decreased gravity (hypogravity, i.e., weightlessness). Lift-off and re-entry of the spacecraft are associated with exposure to increased gravity (hypergravity). Existing data suggest that spaceflight is associated with a constellation of changes in reproductive physiology and function. However, limited spaceflight opportunities and confounding effects of various nongravitational factors associated with spaceflight (i.e., radiation, stress) have led to the development of ground-based models for studying the effects of altered gravity on biological systems. Human bed rest and rodent hindlimb unloading paradigms are used to study exposure to hypogravity. Centrifugation is used to study hypergravity. Here, we review the results of spaceflight and ground-based models of altered gravity on reproductive physiology. Studies utilizing ground-based models that simulate hyper- and hypogravity have produced reproductive results similar to those obtained from spaceflight and are contributing new information on biological responses across the gravity continuum, thereby confirming the appropriateness of these models for studying reproductive responses to altered gravity and the underlying mechanisms of these responses. Together, these unique tools are yielding new insights into the gravitational biology of reproduction in mammals.

Stressing Escherichia coli to educate students about research: A CURE to investigate multiple levels of gene regulation.

PubMed

McDonough, Janet; Goudsouzian, Lara K; Papaj, Agllai; Maceli, Ashley R; Klepac-Ceraj, Vanja; Peterson, Celeste N

2017-09-01

Course-based undergraduate research experiences (CUREs) have been shown to increase student retention and learning in the biological sciences. Most CURES cover only one aspect of gene regulation, such as transcriptional control. Here we present a new inquiry-based lab that engages understanding of gene expression from multiple perspectives. Students carry out a forward genetic screen to identify regulators of the stationary phase master regulator RpoS in the model organism Escherichia coli and then use a series of reporter fusions to determine if the regulation is at the level of transcription or the post-transcription level. This easy-to-implement course has been run both as a 9-week long project and a condensed 5-6 week version in three different schools and types of courses. A majority of the genes found in the screen are novel, thus giving students the opportunity to contribute to original findings to the field. Assessments of this CURE show student gains in learning in many knowledge areas. In addition, attitudinal surveys suggest the students are enthusiastic about the screen and their learning about gene regulation. In summary, this lab would be an appropriate addition to an intermediate or advanced level Molecular Biology, Genetics, or Microbiology curriculum. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):449-458, 2017. © 2017 The International Union of Biochemistry and Molecular Biology.

From biological neural networks to thinking machines: Transitioning biological organizational principles to computer technology

NASA Technical Reports Server (NTRS)

Ross, Muriel D.

1991-01-01

The three-dimensional organization of the vestibular macula is under study by computer assisted reconstruction and simulation methods as a model for more complex neural systems. One goal of this research is to transition knowledge of biological neural network architecture and functioning to computer technology, to contribute to the development of thinking computers. Maculas are organized as weighted neural networks for parallel distributed processing of information. The network is characterized by non-linearity of its terminal/receptive fields. Wiring appears to develop through constrained randomness. A further property is the presence of two main circuits, highly channeled and distributed modifying, that are connected through feedforward-feedback collaterals and biasing subcircuit. Computer simulations demonstrate that differences in geometry of the feedback (afferent) collaterals affects the timing and the magnitude of voltage changes delivered to the spike initiation zone. Feedforward (efferent) collaterals act as voltage followers and likely inhibit neurons of the distributed modifying circuit. These results illustrate the importance of feedforward-feedback loops, of timing, and of inhibition in refining neural network output. They also suggest that it is the distributed modifying network that is most involved in adaptation, memory, and learning. Tests of macular adaptation, through hyper- and microgravitational studies, support this hypothesis since synapses in the distributed modifying circuit, but not the channeled circuit, are altered. Transitioning knowledge of biological systems to computer technology, however, remains problematical.

Space Magnets Attracting Interest on Earth: Applications of Physical and Biological Techniques In the Study of Gravisensing and Response System of Plants

NASA Technical Reports Server (NTRS)

Hasenstein, Karl H.; Boody, April; Cox, David (Technical Monitor)

2002-01-01

The BioTube/Magnetic Field Apparatus (MFA) research is designed to provide insight into the organization and operation of the gravity sensing systems of plants and other small organisms. This experiment on STS-107 uses magnetic fields to manipulate sensory cells in plant roots, thus using magnetic fields as a tool to study gravity-related phenomena. The experiment will be located in the SPACEHAB module and is about the size of a household microwave oven. The goal of the experiment is to improve our understanding of the basic phenomenon of how plants respond to gravity. The BioTube/MFA experiment specifically examines how gravitational forces serve as a directional signal for growth in the low-gravity environment of space. As with all basic research, this study will contribute to an improved understanding of how plants grow and will have important implications for improving plant growth and productivity on Earth. In BioTube/MFA, magnetic fields will be used to determine whether the distribution of subcellular starch grains, called amyloplasts, within plant cells predicts the direction in which roots will grow and curve in microgravity.

Application of Asymmetric Flow Field-Flow Fractionation hyphenations for liposome-antimicrobial peptide interaction.

PubMed

Iavicoli, Patrizia; Urbán, Patricia; Bella, Angelo; Ryadnov, Maxim G; Rossi, François; Calzolai, Luigi

2015-11-27

Asymmetric Flow Field-Flow Fractionation (AF4) combined with multidetector analysis form a promising technique in the field of nanoparticle characterization. This system is able to measure the dimensions and physicochemical properties of nanoparticles with unprecedented accuracy and precision. Here, for the first time, this technique is optimized to characterize the interaction between an archetypal antimicrobial peptide and synthetic membranes. By using charged and neutral liposomes it is possible to mimic some of the charge characteristics of biological membranes. The use of AF4 system allows determining, in a single analysis, information regarding the selectivity of the peptides, the quantity of peptides bound to each liposome, the induced change in the size distribution and morphology of the liposomes. The results obtained provide relevant information for the study of structure-activity relationships in the context of membrane-induced antimicrobial action. This information will contribute to the rational design of potent antimicrobial agents in the future. Moreover, the application of this method to other liposome systems is straightforward and would be extremely useful for a comprehensive characterization with regard to size distribution and protein interaction in the nanomedicine field. Copyright © 2015. Published by Elsevier B.V.

Photonics surface waves on metamaterials interfaces.

PubMed

Takayama, Osamu; Bogdanov, Andrey; Lavrinenko, Andrei V

2017-09-12

A surface wave (SW) in optics is a light wave, which is supported at an interface of two dissimilar media and propagates along the interface with its field amplitude exponentially decaying away from the boundary. The research on surface waves has been flourishing in last few decades thanks to their unique properties of surface sensitivity and field localization. These features have resulted in applications in nano-guiding, sensing, light-trapping and imaging based on the near-field techniques, contributing to the establishment of the nanophotonics as a field of research. Up to present, a wide variety of surface waves has been investigated in numerous material and structure settings. This paper reviews the recent progress and development in the physics of SWs localized at metamaterial interfaces, as well as bulk media in order to provide broader perspectives on optical surface waves in general. For each type of the surface waves, we discuss material and structural platforms. We mainly focus on experimental realizations in the visible and near-infrared wavelength ranges. We also address existing and potential application of SWs in chemical and biological sensing, and experimental excitation and characterization methods. © 2017 IOP Publishing Ltd.

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

PubMed Central

Bhat, Nisar A.; Riar, Amritbir; Ramesh, Aketi; Iqbal, Sanjeeda; Sharma, Mahaveer P.; Sharma, Sanjay K.; Bhullar, Gurbir S.

2017-01-01

Mobilization of unavailable phosphorus (P) to plant available P is a prerequisite to sustain crop productivity. Although most of the agricultural soils have sufficient amounts of phosphorus, low availability of native soil P remains a key limiting factor to increasing crop productivity. Solubilization and mineralization of applied and native P to plant available form is mediated through a number of biological and biochemical processes that are strongly influenced by soil carbon/organic matter, besides other biotic and abiotic factors. Soils rich in organic matter are expected to have higher P availability potentially due to higher biological activity. In conventional agricultural systems mineral fertilizers are used to supply P for plant growth, whereas organic systems largely rely on inputs of organic origin. The soils under organic management are supposed to be biologically more active and thus possess a higher capability to mobilize native or applied P. In this study we compared biological activity in soil of a long-term farming systems comparison field trial in vertisols under a subtropical (semi-arid) environment. Soil samples were collected from plots under 7 years of organic and conventional management at five different time points in soybean (Glycine max) -wheat (Triticum aestivum) crop sequence including the crop growth stages of reproductive significance. Upon analysis of various soil biological properties such as dehydrogenase, β-glucosidase, acid and alkaline phosphatase activities, microbial respiration, substrate induced respiration, soil microbial biomass carbon, organically managed soils were found to be biologically more active particularly at R2 stage in soybean and panicle initiation stage in wheat. We also determined the synergies between these biological parameters by using the methodology of principle component analysis. At all sampling points, P availability in organic and conventional systems was comparable. Our findings clearly indicate that owing to higher biological activity, organic systems possess equal capabilities of supplying P for crop growth as are conventional systems with inputs of mineral P fertilizers. PMID:28928758

Vignettes from the field of mathematical biology: the application of mathematics to biology and medicine

PubMed Central

Murray, J. D.

2012-01-01

The application of mathematical models in biology and medicine has a long history. From the sparse number of papers in the first half of the twentieth century with a few scientists working in the field it has become vast with thousands of active researchers. We give a brief, and far from definitive history, of how some parts of the field have developed and how the type of research has changed. We describe in more detail just two examples of specific models which are directly related to real biological problems, namely animal coat patterns and the growth and image enhancement of glioblastoma brain tumours. PMID:23919124

Guidelines for Setting Up an Extended Field Trip to Florida and the Florida Keys: An Interactive Experiential Training Field Biology Program Consisting of Pretrip Instruction, Search Image Training, Field Exercises, and Observations of Tropical Habitats and Coral Reefs.

ERIC Educational Resources Information Center

Baker, Claude D.; And Others

The importance of experiential aspects of biological study is addressed using multi-dimensional classroom and field classroom approaches to student learning. This document includes a guide to setting up this style of field experience. Several teaching innovations are employed to introduce undergraduate students to the literature, techniques, and…

A systematic review of synthetic and biologic materials for abdominal wall reinforcement in contaminated fields.

PubMed

Lee, Lawrence; Mata, Juan; Landry, Tara; Khwaja, Kosar A; Vassiliou, Melina C; Fried, Gerald M; Feldman, Liane S

2014-09-01

Guidelines recommend the use of bioprosthetics for abdominal wall reinforcement in contaminated fields, but the evidence supporting the use of biologic over synthetic non-absorbable prosthetics for this indication is poor. Therefore, the objective was to perform a systematic review of outcomes after synthetic non-absorbable and biologic prosthetics for ventral hernia repair or prophylaxis in contaminated fields. The systematic literature search identified all articles published up to 2013 that reported outcomes after abdominal wall reinforcement using synthetic non-absorbable or biologic prosthetics in contaminated fields. Studies were included if they included at least 10 cases (excluding inguinal and parastomal hernias). Quality assessment was performed using the MINORS instrument. The main outcomes measures were the incidence of wound infection and hernia at follow-up. Weighted pooled proportions were calculated using a random effects model. A total of 32 studies met the inclusion criteria and were included for synthesis. Mean sample size was 41.4 (range 10-190), and duration of follow-up was >1 year in 72 % of studies. Overall quality was low (mean 6.2, range 1-12). Pooled wound infection rates were 31.6 % (95 % CI 14.5-48.7) with biologic and 6.4 % (95 % CI 3.4-9.4) with synthetic non-absorbable prosthetics in clean-contaminated cases, with similar hernia rates. In contaminated and/or dirty fields, wound infection rates were similar, but pooled hernia rates were 27.2 % (95 % CI 9.5-44.9) with biologic and 3.2 % (95 % CI 0.0-11.0) with synthetic non-absorbable. Other outcomes were comparable. The available evidence is limited, but does not support the superiority of biologic over synthetic non-absorbable prosthetics in contaminated fields.

History and conceptual developments in vascular biology and angiogenesis research: a personal view.

PubMed

Bikfalvi, Andreas

2017-11-01

Vascular biology is an important scientific domain that has gradually penetrated many medical and scientific fields. Scientists are most often focused on present problems in their daily scientific work and lack awareness regarding the evolution of their domain throughout history and of how philosophical issues are related to their research field. In this article, I provide a personal view with an attempt to conceptualize vascular development research that articulates lessons taken from history, philosophy, biology and medicine. I discuss selected aspects related to the history and the philosophy of sciences that can be extracted from the study of vascular development and how conceptual progress in this research field has been made. I will analyze paradigm shifts, cross-fertilization of different fields, technological advances and its impact on angiogenesis and discuss issues related to evolutionary biology, proximity of different molecular systems and scientific methodologies. Finally, I discuss briefly my views where the field is heading in the future.

Evolutionary cell biology: two origins, one objective.

PubMed

Lynch, Michael; Field, Mark C; Goodson, Holly V; Malik, Harmit S; Pereira-Leal, José B; Roos, David S; Turkewitz, Aaron P; Sazer, Shelley

2014-12-02

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.

Evolutionary cell biology: Two origins, one objective

PubMed Central

Lynch, Michael; Field, Mark C.; Goodson, Holly V.; Malik, Harmit S.; Pereira-Leal, José B.; Roos, David S.; Turkewitz, Aaron P.; Sazer, Shelley

2014-01-01

All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology. PMID:25404324

Improving chemical shift encoding‐based water–fat separation based on a detailed consideration of magnetic field contributions

PubMed Central

Ruschke, Stefan; Eggers, Holger; Meineke, Jakob; Rummeny, Ernst J.; Karampinos, Dimitrios C.

2018-01-01

Purpose To improve the robustness of existing chemical shift encoding‐based water–fat separation methods by incorporating a priori information of the magnetic field distortions in complex‐based water–fat separation. Methods Four major field contributions are considered: inhomogeneities of the scanner magnet, the shim field, an object‐based field map estimate, and a residual field. The former two are completely determined by spherical harmonic expansion coefficients directly available from the magnetic resonance (MR) scanner. The object‐based field map is forward simulated from air–tissue interfaces inside the field of view (FOV). The missing residual field originates from the object outside the FOV and is investigated by magnetic field simulations on a numerical whole body phantom. In vivo the spatially linear first‐order component of the residual field is estimated by measuring echo misalignments after demodulation of other field contributions resulting in a linear residual field. Gradient echo datasets of the cervical and the ankle region without and with shimming were acquired, where all four contributions were incorporated in the water–fat separation with two algorithms from the ISMRM water–fat toolbox and compared to water–fat separation with less incorporated field contributions. Results Incorporating all four field contributions as demodulation steps resulted in reduced temporal and spatial phase wraps leading to almost swap‐free water–fat separation results in all datasets. Conclusion Demodulating estimates of major field contributions reduces the phase evolution to be driven by only small differences in local tissue susceptibility, which supports the field smoothness assumption of existing water–fat separation techniques. PMID:29424458

Cell biology: at the center of modern biomedicine.

PubMed

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

2012-10-01

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

Contributions of poroelastic-wave potentials to seismoelectromagnetic wavefields and validity of the quasi-static calculation: a view from a borehole model

NASA Astrophysics Data System (ADS)

Guan, Wei; Shi, Peng; Hu, Hengshan

2018-01-01

In this study, we theoretically analyse the contributions of the four poroelastic-wave potentials to seismoelectromagnetic (SEM) wavefields, verify the validity of the quasi-static calculation of the electric field and provide a method to calculate the magnetic field by using the curl-free electric field. Calculations show that both the fast and slow P waves and the SH and SV waves have non-negligible contributions to the SEM fields. The S waves have indirect contribution to the electric field through the EM conversion from the magnetic field, although the direct contribution due to streaming current is negligible if EM wavenumbers are much smaller than those of the S waves. The P waves have indirect contribution to the magnetic field through EM conversion from the electric field, although the direct contribution is absent. The quasi-static calculation of the electric field is practicable since it is normally satisfied in reality that the EM wavenumbers are much smaller than those of poroelastic waves. While the direct contribution of the S waves and the higher-order EM conversions are ignored, the first-order EM conversion from the S-wave-induced magnetic field is reserved through the continuity of the electric-current density. To calculate the magnetic field on this basis, we separate the quasi-static electric field into a rotational and an irrotational part. The magnetic-field solutions are derived through Hertz vectors in which the coefficients of the magnetic Hertz vector are determined from the magnetic-field continuities and those of the electric Hertz vector originate from the irrotational part of the quasi-static electric field.

The Taguchi methodology as a statistical tool for biotechnological applications: a critical appraisal.

PubMed

Rao, Ravella Sreenivas; Kumar, C Ganesh; Prakasham, R Shetty; Hobbs, Phil J

2008-04-01

Success in experiments and/or technology mainly depends on a properly designed process or product. The traditional method of process optimization involves the study of one variable at a time, which requires a number of combinations of experiments that are time, cost and labor intensive. The Taguchi method of design of experiments is a simple statistical tool involving a system of tabulated designs (arrays) that allows a maximum number of main effects to be estimated in an unbiased (orthogonal) fashion with a minimum number of experimental runs. It has been applied to predict the significant contribution of the design variable(s) and the optimum combination of each variable by conducting experiments on a real-time basis. The modeling that is performed essentially relates signal-to-noise ratio to the control variables in a 'main effect only' approach. This approach enables both multiple response and dynamic problems to be studied by handling noise factors. Taguchi principles and concepts have made extensive contributions to industry by bringing focused awareness to robustness, noise and quality. This methodology has been widely applied in many industrial sectors; however, its application in biological sciences has been limited. In the present review, the application and comparison of the Taguchi methodology has been emphasized with specific case studies in the field of biotechnology, particularly in diverse areas like fermentation, food processing, molecular biology, wastewater treatment and bioremediation.

Dimensions of integration in interdisciplinary explanations of the origin of evolutionary novelty.

PubMed

Love, Alan C; Lugar, Gary L

2013-12-01

Many philosophers of biology have embraced a version of pluralism in response to the failure of theory reduction but overlook how concepts, methods, and explanatory resources are in fact coordinated, such as in interdisciplinary research where the aim is to integrate different strands into an articulated whole. This is observable for the origin of evolutionary novelty-a complex problem that requires a synthesis of intellectual resources from different fields to arrive at robust answers to multiple allied questions. It is an apt locus for exploring new dimensions of explanatory integration because it necessitates coordination among historical and experimental disciplines (e.g., geology and molecular biology). These coordination issues are widespread for the origin of novel morphologies observed in the Cambrian Explosion. Despite an explicit commitment to an integrated, interdisciplinary explanation, some potential disciplinary contributors are excluded. Notable among these exclusions is the physics of ontogeny. We argue that two different dimensions of integration-data and standards-have been insufficiently distinguished. This distinction accounts for why physics-based explanatory contributions to the origin of novelty have been resisted: they do not integrate certain types of data and differ in how they conceptualize the standard of uniformitarianism in historical, causal explanations. Our analysis of these different dimensions of integration contributes to the development of more adequate and integrated explanatory frameworks. Copyright © 2013 Elsevier Ltd. All rights reserved.

Regeneration of the lung: Lung stem cells and the development of lung mimicking devices.

PubMed

Schilders, Kim A A; Eenjes, Evelien; van Riet, Sander; Poot, André A; Stamatialis, Dimitrios; Truckenmüller, Roman; Hiemstra, Pieter S; Rottier, Robbert J

2016-04-23

Inspired by the increasing burden of lung associated diseases in society and an growing demand to accommodate patients, great efforts by the scientific community produce an increasing stream of data that are focused on delineating the basic principles of lung development and growth, as well as understanding the biomechanical properties to build artificial lung devices. In addition, the continuing efforts to better define the disease origin, progression and pathology by basic scientists and clinicians contributes to insights in the basic principles of lung biology. However, the use of different model systems, experimental approaches and readout systems may generate somewhat conflicting or contradictory results. In an effort to summarize the latest developments in the lung epithelial stem cell biology, we provide an overview of the current status of the field. We first describe the different stem cells, or progenitor cells, residing in the homeostatic lung. Next, we focus on the plasticity of the different cell types upon several injury-induced activation or repair models, and highlight the regenerative capacity of lung cells. Lastly, we summarize the generation of lung mimics, such as air-liquid interface cultures, organoids and lung on a chip, that are required to test emerging hypotheses. Moreover, the increasing collaboration between distinct specializations will contribute to the eventual development of an artificial lung device capable of assisting reduced lung function and capacity in human patients.

A Contribution Toward Understanding the Biospherical Significance of Antarctic Ozone Depletion

NASA Astrophysics Data System (ADS)

Lubin, Dan; Mitchell, B. Greg; Frederick, John E.; Alberts, Amy D.; Booth, C. R.; Lucas, Timothy; Neuschuler, David

1992-05-01

Measurements of biologically active UV radiation made by the National Science Foundation (NSF) scanning spectroradiometer (UV-monitor) at Palmer Station, Antarctica, during the Austral springs of 1988, 1989, and 1990 are presented and compared. Column ozone abundance above Palmer Station is computed from these measurements using a multiple wavelength algorithm. Two contrasting action spectra (biological weighting functions) are used to estimate the biologically relevant dose from the spectral measurements: a standard weighting function for damage to DNA, and a new action spectrum representing the potential for photosynthesis inhibition in Antarctic phytoplankton. The former weights only UV-B wavelengths (280-320 nm) and gives the most weight to wavelengths shorter than 300 nm, while the latter includes large contributions out to 355 nm. The latter is the result of recent Antarctic field work and is relevant in that phytoplankton constitute the base of the Antarctic food web. The modest ozone hole of 1988, in which the ozone abundance above Palmer Station never fell below 200 Dobson units (DU), brought about summerlike doses of DNA-effective UV radiation 2 months early, but UV doses which could inhibit photosynthesis in phytoplankton did not exceed a clear-sky "maximum normal" dose for that time of year. The severe ozone holes of 1989 and 1990, in which the ozone abundance regularly fell below 200 DU, brought about increases in UV surface irradiance weighted by either action spectrum. Ozone abundances and dose-weighted irradiances provided by the NSF UV-monitor are used to derive the radiation amplification factors (RAFs) for both DNA-effective irradiance and phytoplankton-effective irradiance. The RAF for DNA-effective irradiance is nonlinear in ozone abundance and is in excess of the popular "two for one" rule, while the RAF for phytoplankton-effective irradiance approximately follows a "one for one" rule.