Relevant bibliographies by topics / Organismal Biological Physiology

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Organismal Biological Physiology'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Organismal Biological Physiology"

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Campbell, Robert A., and Mason N. Dean. "Adaptation and Evolution of Biological Materials." Integrative and Comparative Biology 59, no. 6 (2019): 1629–35. http://dx.doi.org/10.1093/icb/icz134.

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Abstract Research into biological materials often centers on the impressive material properties produced in Nature. In the process, however, this research often neglects the ecologies of the materials, the organismal contexts relating to how a biological material is actually used. In biology, materials are vital to organismal interactions with their environment and their physiology, and also provide records of their phylogenetic relationships and the selective pressures that drive biological novelties. With the papers in this symposium, we provide a view on cutting-edge work in biological mate
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Seppänen-Laakso, Tuulikki, and Matej Orešič. "How to study lipidomes." Journal of Molecular Endocrinology 42, no. 3 (2008): 185–90. http://dx.doi.org/10.1677/jme-08-0150.

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Lipidome is loosely defined as the entire spectrum of lipids in a biological system. Given the modern lipidomics platforms for the first time empower us with the ability to obtain a snapshot of complete cellular/organismal lipidome, many surprises and discoveries are likely awaiting us in the area of lipids as related to cellular/organismal physiology. The lipidomics approaches can be applied both as the phenotyping platform and for the hypothesis-driven research aiming to elucidate, e.g., a specific pathway or gene function. Modern lipidomics methods combine the latest mass spectrometry techn
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Sureda-Vives, Macià, and Karen S. Sarkisyan. "Bioluminescence-Driven Optogenetics." Life 10, no. 12 (2020): 318. http://dx.doi.org/10.3390/life10120318.

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Bioluminescence-based technologies are among the most commonly used methods to quantify and visualise physiology at the cellular and organismal levels. However, the potential of bioluminescence beyond reporter technologies remains largely unexplored. Here, we provide an overview of the emerging approaches employing bioluminescence as a biological light source that triggers physiological events and controls cell behaviour and discuss its possible future application in synthetic biology.
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Wang, Andrew, Harding H. Luan, and Ruslan Medzhitov. "An evolutionary perspective on immunometabolism." Science 363, no. 6423 (2019): eaar3932. http://dx.doi.org/10.1126/science.aar3932.

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Metabolism is at the core of all biological functions. Anabolic metabolism uses building blocks that are either derived from nutrients or synthesized de novo to produce the biological infrastructure, whereas catabolic metabolism generates energy to fuel all biological processes. Distinct metabolic programs are required to support different biological functions. Thus, recent studies have revealed how signals regulating cell quiescence, proliferation, and differentiation also induce the appropriate metabolic programs. In particular, a wealth of new studies in the field of immunometabolism has un
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Havird, Justin C., Ryan J. Weaver, Liliana Milani, et al. "Beyond the Powerhouse: Integrating Mitonuclear Evolution, Physiology, and Theory in Comparative Biology." Integrative and Comparative Biology 59, no. 4 (2019): 856–63. http://dx.doi.org/10.1093/icb/icz132.

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Abstract Eukaryotes are the outcome of an ancient symbiosis and as such, eukaryotic cells fundamentally possess two genomes. As a consequence, gene products encoded by both nuclear and mitochondrial genomes must interact in an intimate and precise fashion to enable aerobic respiration in eukaryotes. This genomic architecture of eukaryotes is proposed to necessitate perpetual coevolution between the nuclear and mitochondrial genomes to maintain coadaptation, but the presence of two genomes also creates the opportunity for intracellular conflict. In the collection of papers that constitute this
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Huey, Raymond B., Michael R. Kearney, Andrew Krockenberger, Joseph A. M. Holtum, Mellissa Jess, and Stephen E. Williams. "Predicting organismal vulnerability to climate warming: roles of behaviour, physiology and adaptation." Philosophical Transactions of the Royal Society B: Biological Sciences 367, no. 1596 (2012): 1665–79. http://dx.doi.org/10.1098/rstb.2012.0005.

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A recently developed integrative framework proposes that the vulnerability of a species to environmental change depends on the species' exposure and sensitivity to environmental change, its resilience to perturbations and its potential to adapt to change. These vulnerability criteria require behavioural, physiological and genetic data. With this information in hand, biologists can predict organisms most at risk from environmental change. Biologists and managers can then target organisms and habitats most at risk. Unfortunately, the required data (e.g. optimal physiological temperatures) are ra
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Hanson, K. C., C. T. Hasler, M. R. Donaldson, and S. J. Cooke. "Stability of swimming performance and activity hierarchies among wild largemouth bass at multiple temporal scales: evidence for context-dependent shuffling between seasons." Canadian Journal of Zoology 88, no. 3 (2010): 324–33. http://dx.doi.org/10.1139/z10-006.

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Laboratory-based studies of locomotory performance in many taxa have noted that individuals form stable hierarchies of organismal performance. Though laboratory studies of teleost fishes have consistently demonstrated individual repeatability of swimming performance, this phenomenon has rarely been studied in the field and never across multiple years. Using a whole-lake acoustic telemetry array with submetre accuracy, we assessed the individual repeatability of two metrics of swimming performance (daily distance traveled and mean daily swimming speed) within four seasons during a year (fall, w
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Hasler, Caleb T., Lucas B. Pon, David W. Roscoe, et al. "Expanding the “toolbox” for studying the biological responses of individual fish to hydropower infrastructure and operating strategies." Environmental Reviews 17, NA (2009): 179–97. http://dx.doi.org/10.1139/a09-008.

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To date, few studies have evaluated sub-organismal responses (e.g., physiological or energetic consequences) of individual fish to hydropower infrastructure (e.g., fishways, turbines) or operations (e.g., fluctuating flows, low flows). The field of “conservation physiology” (i.e., the use of physiological information to enhance conservation) is expanding rapidly and has great promise for hydropower research. However, there is a need to both expand the “toolbox” available to practitioners and to validate these tools for use in this context. This synthetic report details the behavioural, energet
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Greenberg, Dan A., and Wendy J. Palen. "Hydrothermal physiology and climate vulnerability in amphibians." Proceedings of the Royal Society B: Biological Sciences 288, no. 1945 (2021): 20202273. http://dx.doi.org/10.1098/rspb.2020.2273.

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Concerns over the consequences of global climate change for biodiversity have spurred a renewed interest in organismal thermal physiology. However, temperature is only one of many environmental axes poised to change in the future. In particular, hydrologic regimes are also expected to shift concurrently with temperature in many regions, yet our understanding of how thermal and hydration physiology jointly affect performance and fitness is still limited for most taxonomic groups. Here, we investigated the relationship between functional performance, hydration state and temperature in three ecol
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Jentsch, Thomas J., and Michael Pusch. "CLC Chloride Channels and Transporters: Structure, Function, Physiology, and Disease." Physiological Reviews 98, no. 3 (2018): 1493–590. http://dx.doi.org/10.1152/physrev.00047.2017.

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CLC anion transporters are found in all phyla and form a gene family of eight members in mammals. Two CLC proteins, each of which completely contains an ion translocation parthway, assemble to homo- or heteromeric dimers that sometimes require accessory β-subunits for function. CLC proteins come in two flavors: anion channels and anion/proton exchangers. Structures of these two CLC protein classes are surprisingly similar. Extensive structure-function analysis identified residues involved in ion permeation, anion-proton coupling and gating and led to attractive biophysical models. In mammals,
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Dissertations / Theses on the topic "Organismal Biological Physiology"

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Nam, Seung-Hee. "Affinity Purification and Characterization of E. coli Molecular Chaperones." DigitalCommons@USU, 2002. https://digitalcommons.usu.edu/etd/5486.

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The molecular chaperones are a group of proteins that are effective in vitro and in vivo folding aids and show a well documented affinity for proteins lacking tertiary structure. Heat-induced Escherichia coli BL21 cell lysate (10 mg protein) was applied to immobilized ɑ-casein (45 mg/g beads) or β-casein (30 mg/g beads) column. After removing a majority of nonspecifically bound proteins with 1 M NaCl, the molecular chaperones were eluted with cold water, 1 mM Mg-ATP, or 6 M urea. Western analysis identified five Escherichia coli molecular chaperones including DnaK, DnaJ, GrpE, GroEL, and GroES
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Liu, Haiyan. "Synthesis and Kinetic Studies of High-Valent Metal-Oxo Species Generated by Photochemical and Chemical Methods." TopSCHOLAR®, 2018. https://digitalcommons.wku.edu/theses/2803.

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Highly reactive iron-oxo intermediates play important roles as active oxidants in enzymatic and synthetic catalytic oxidation. Many transition metal catalysts are designed for biomimetic studies of the predominant oxidation catalysts in Nature, namely cytochrome P450 enzymes. In this work, a series of iron(IV)-oxo porphyrins [FeIV(Por)O] and manganese(IV)-oxo porphyrins [MnIV(Por)O] have been successfully produced in two electron-deficient ligands by photochemical and chemical methods, and spectroscopically characterized by UV-vis, and 1H-NMR. With iodobenzene diacetate [PhI(OAc)2] as the oxyg
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Jackson, Doris Clark. "Characterization of Neuronal Nicotinic Acetylcholine Receptors and their Positive Allosteric Modulators." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6856.

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Neuronal nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that are necessary in memory and cognition. They are pentameric and consist of α and β subunits. They are most commonly heteromeric but, can sometimes be homomeric. nAChRs are activated by many ligands including nicotine (exogenous) and acetylcholine (endogenous).nAChRs are located on hippocampal interneurons. The interneurons, although sparse, control the synchronous firing of the pyramidal cells. However, the hippocampal interneuron structure and function is quite diverse and not fully characterized. Therefor
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Garcia, Gonzalez Aurian P. "Caenorhabditis elegans as a Model for Host-Microbe-Drug Interactions." eScholarship@UMMS, 2019. https://escholarship.umassmed.edu/gsbs_diss/1024.

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The microbes that inhabit the human body, our microbiota, greatly influence our physiology and propensity for disease. For instance, the gut microbiota metabolizes compounds from our diet to provide important nutrients. Similarly, the microbiota has the potential to impact drug response; directly by metabolizing drugs, or indirectly by providing metabolites to the host. The complexity of the mammalian microbiota, and the limited throughput of such models, prohibit a systematic interrogation of specific interactions between microbes and host drug response. Here, I use C. elegans and its bacteri
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Czuchra, Alexander. "The DNA Translocase of Mycobacteria Is an Essential Protein Required for Growth and Division." eScholarship@UMMS, 2021. https://escholarship.umassmed.edu/gsbs_diss/1151.

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Mycobacterium tuberculosis (Mtb) is one of the most virulent and prevalent bacterial pathogens across the world. As Mtb infects millions of people a year, it remains essential to study its physiology with the goal of developing new therapeutic interventions. A critical part of the bacteria’s ability to propagate is through successful cell division. Although the process of bacterial cell division and the key proteins therein are well understood in Escherichia coli, much remains to be understood about division in mycobacteria. Genetic and cell biological approaches have recently begun to identif
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Cello, Sally L. "Exploring the Physiological Role of Vibrio fischeri PepN." DigitalCommons@CalPoly, 2015. https://digitalcommons.calpoly.edu/theses/1443.

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The primary contributor to Vibrio fischeri aminopeptidase activity is aminopeptidase N, PepN. Colonization assays revealed the pepN mutant strain to be deficient at forming dense aggregates and populating the host’s light organ compared to wildtype within the first 12 hours of colonization; however the mutant competed normally at 24 hours. To address the role of PepN in colonization initiation and establish additional phenotypes for the pepN mutant strain, stress response and other physiological assays were employed. Marked differences were found between pepN mutant and wildtype strain in resp
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Hansen, Thorsten. "IDENTIFYING MECHANISMS OF HOST PLANT SPECIALIZATION IN APHIS CRACCIVORA AND ITS BACTERIAL SYMBIONTS." UKnowledge, 2018. https://uknowledge.uky.edu/entomology_etds/42.

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Many insects form close relationships with microbial symbionts. Insect symbionts can provide novel phenotypes to their hosts, including influencing dietary breadth. In the polyphagous cowpea aphid, Aphis craccivora, the facultative symbiont Arsenophonus improves aphid performance on one host plant (locust), but decreases performance on other plants. The goal of my thesis was to investigate the mechanism by which Arsenophonus facilitates use of locust. First, I assembled an Aphis craccivora-Arsenophonus-Buchnera reference transcriptome to conduct RNAseq analysis, comparing gene expression in ap
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Lewis, Ricky W. "TOXICITY OF ENGINEERED NANOMATERIALS TO PLANT GROWTH PROMOTING RHIZOBACTERIA." UKnowledge, 2016. http://uknowledge.uky.edu/pss_etds/77.

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Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and su
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Poe, Tyler M., and Francine Marciano-Cabral. "Illumination of the Golgi apparatus of Pathogenic and Nonpathogenic Naegleria species." VCU Scholars Compass, 2019. https://scholarscompass.vcu.edu/etd/6002.

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In this study, Naegleria fowleri, a pathogenic amoeba and the causative agent of Primary Amebic Meningoencephalitis (PAM), was utilized to determine the presence or absence of classically conserved Golgi molecules featured in the expression of a Golgi apparatus. Previous studies concluded no Golgi expression via light microscopy and transmission electron microscopy, but a recent report on Naegleria gruberi indicated the presence of dispersed Golgi tubules. Non-pathogenic species of the Naegleria genus such as Naegleria gruberi 30540 and Naegleria lovaniensis 30569 were utilized in Western immu
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Balasubramanian, Deepak. "Pseudomonas Aeruginosa AmpR Transcriptional Regulatory Network." FIU Digital Commons, 2013. http://digitalcommons.fiu.edu/etd/863.

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In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated
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Books on the topic "Organismal Biological Physiology"

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Workshop on Principles of Organization in Organisms (1990 Santa Fe, N.M.). Principles of organization in organisms: Proceedings of the Workshop on Principles of Organization in Organisms, held June, 1990 in Santa Fe, New Mexico. Edited by Mittenthal Jay E and Baskin Arthur B. Addison-Wesley, 1992.

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Dahlem Workshop on Complex Organismal Functions: Integration and Evolution in Vertebrates (1988 Berlin, Germany). Complex organismal functions: Integration and evolution in vertebrates : report of the Dahlem Workshop on Complex Organismal Functions--Integration and Evolution in Vertebrates, Berlin 1988, August 28-September 2. Edited by Wake David B and Roth, Gerhard, 1942 Aug. 15-. Wiley, 1989.

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Leon, Kreitzman, ed. Seasons of life: The biological rhythms that enable living things to thrive and survive. Yale University Press, 2009.

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service), SpringerLink (Online, ed. Biological Materials of Marine Origin: Invertebrates. Springer Science+Business Media B.V., 2010.

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X, Caddick M., ed. Microbial responses to light and time: Fifty-sixth Symposium of the Society for General Microbiology : held at the University of Nottingham, March 1998. Cambridge University Press, 1998.

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G, Williams J. Genetic engineering. BIOS Scientific Publishers, 1993.

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K, Patient R., ed. Genetic engineering. IRL Press, 1988.

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A, Ceccarelli, and Wallace A. 1963-, eds. Genetic engineering. 2nd ed. Bios, 2001.

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Gerd, Müller, and Newman Stuart, eds. Origination of organismal form: Beyond the gene in developmental and evolutionary biology. MIT Press, 2003.

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Sullivan, Mark D. Seeking the Roots of Health and Action in Biological Autonomy. Oxford University Press, 2016. http://dx.doi.org/10.1093/med/9780195386585.003.0010.

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The roots of biological autonomy and health are the same. Goals make biology distinct as a science, for without goals, we cannot understand why a biological trait exists. Organisms are autonomous biological entities because they define what is inside and what is outside themselves. This boundary between inner and outer gives the organism a self-referential purpose. Claude Bernard made experimental physiology possible with his concept of the internal environment, but he was unable to explain how the organism established the boundary between itself and its environment. Hence, homeostasis portray
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Book chapters on the topic "Organismal Biological Physiology"

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Green, T. G. Allan, and Michael C. F. Proctor. "Physiology of Photosynthetic Organisms Within Biological Soil Crusts: Their Adaptation, Flexibility, and Plasticity." In Biological Soil Crusts: An Organizing Principle in Drylands. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-30214-0_18.

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Eldredge, Niles. "The Evolutionary Hierarchies." In Unfinished Synthesis. Oxford University Press, 1986. http://dx.doi.org/10.1093/oso/9780195036336.003.0009.

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Real-world hierarchies are usually treated as patently evident manifestations of nature, a fact that has somehow rendered them trivial. Familiarity breeds contempt. Everyone knows that atoms are the building blocks of molecules, small molecules combine to form the huge molecules of living Systems, organelles and other structures composed of such molecules make up cells, cells link up to form tissues, tissues do likewise to form organs, thence organ Systems, and finally we arrive at the integrated soma of the organism. And organisms are associated to make populations, or demes, or species. The very names of the subdisciplines of biology (especially as conceived fifty years ago) reflect this organisation. Though molecular biology is a recent arrival, physiological genetics, cytology (and cytogenetics), histology, and physiology nicely recognized the components of the somatic or organismic hierarchy. Thus, the somatic hierarchy retains a heuristic value still reflected in general biology texts. The molecules-to-organism hierarchy offers a handy way of organizing biological knowledge, information about living Systems. That nature itself is organized in such a fashion seems to have slipped to secondary significance. It is, though, common to view the sequences of codons that compose functional genes, as well as other organizational features of DNA molecules, as constituting the retention of information. One major biological hierarchy, the genealogical hierarchy, is evidently a hierarchy of information. It is as if the pragmatic, heuristic, epistemological aspects of biological hierarchies, providing us with a handy way of organizing, summarizing, and communicating what we think we know about biological Systems, serve to obscure the significance of hierarchical organization to the very workings of biological nature. All of this does not deny that there is an extensive literature on hierarchies, a multidisciplinary literature that includes a long, if episodic, history within the realm of biology. The analysis I develop here surely does not arise from a vacuum. Yet the current resurgence of hierarchical outlook on evolution reflects more, I think, a return to an alternative way of looking at nature, a way dictated by a pattern of organization of nature that is there for all to see, than it does the thickening of a continuous Intellectual strand that connects us with earlier interests in hierarchy both within biology and without.
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Fabbri, Elisa, Marco Zoli, and Luigi Ferrucci. "Age-related physiologic declines." In Oxford Textbook of Geriatric Medicine. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198701590.003.0041.

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‘How and why living organisms age?’ This question has puzzled and challenged philosophers and scientists for centuries. Ageing can be defined as a progressive loss of anatomic and physiological integrity across multiple systems and organs, leading to impaired function and higher vulnerability to adverse health outcomes and death. Although the biological mechanisms that trigger and accelerate ageing are still not understood, enormous steps forward in delineating the effects of ageing has been made in recent years. Ageing induces morphological and physiological changes across multiple organs and systems, which result in progressive loss of resilience, increased vulnerability to stressors, disease susceptibility, and development of physical and cognitive frailty, disability, and adverse outcomes.
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Perlman, Robert. "An Evolutionary View of Homeostasis." In Integrating Evolutionary Biology into Medical Education. Oxford University Press, 2019. http://dx.doi.org/10.1093/oso/9780198814153.003.0007.

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Physiologists and evolutionary biologists have traditionally investigated different but complementary aspects of biological phenomena. Homeostasis, the maintenance of approximately constant conditions in bodily fluids, has been the purview of physiology. Evolutionary insights can, however, deepen our knowledge of homeostatic regulatory mechanisms. Bioenergetics has been of central concern to both physiology and evolution. Physiologists have been interested in the energetic content of foods, in the metabolic transformations of the energy derived from foods, and in the energetic costs of physiological processes, while evolutionary life history theory addresses the ways that organisms have evolved to acquire and allocate metabolic energy throughout their life course. Engineering control theory highlights the limitations as well as the benefits of different regulatory mechanisms and so helps to explain why we have evolved multiple integrated and cooperative homeostatic mechanisms. The physiological responses to pregnancy illustrate the ways in which an evolutionary perspective enriches our understanding of homeostasis.
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Weiss, Linda C., and Ralph Tollrian. "Predator-Induced Defenses in Crustacea." In Life Histories. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780190620271.003.0012.

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The capacity of an organism with a given genotype to respond to changing environmental conditions by the expression of an alternative phenotype is a fascinating biological phenomenon. Plasticity enables organisms to cope with environmental challenges by altering their morphology, behavior, physiology, and life history. Especially, predation is a major factor driving plasticity in response to seasonal fluctuations of predator populations. Therefore, many taxa have evolved strategies to adapt to this environmental challenge, including morphological defenses, life history shifts, and behavioral adaptations. The evolution of inducible defenses is dependent on 4 factors: a selective agent, a reliable cue, associated costs, and the resulting benefit. Ecologically, predator-induced defenses are of general importance because they reduce predation rates and hence dampen the dynamics of predator-prey systems to stabilize food webs. We analyze the defensive strategies in many crustacean taxa and describe how they can act in concert to reduce predation risk. Additionally, prey species may perform predation risk assessment and reduce defense expression when conspecifics are dense. With increasing numbers of conspecifics, the individual predation risk is reduced due to prey dilution, predator confusion, and increased handling times. Consequently, the need to develop a strong defense is reduced and costs for the full defenses expression can be saved.
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Lundkvist, Gabriella, and Gene D. Block. "The Suprachiasmatic Nucleus." In Handbook of Brain Microcircuits, edited by Gordon M. Shepherd and Sten Grillner. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190636111.003.0010.

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Diurnal variations in physiology and behavior are ubiquitous in higher organisms. Although some rhythms are driven directly by geophysical cycles of light or temperature, most are generated by internal timers, commonly referred to as biological clocks. In mammals, including humans, these circadian (near 24-h) properties are controlled by a central timer formed by a distinct regional network in the anterior hypothalamus close to the optic chiasm, the bilateral suprachiasmatic nuclei (SCN). Rodents, with their SCN lesioned, fail to exhibit diurnal variations in behavior. The mechanism generating rhythmicity is contained within individual neurons; however, many of the properties of the circadian timing system derive from cellular interactions within SCN. These microcircuits give rise to a functional clock capable of maintaining a circadian rhythm with a stable period and phase and driving or synchronizing circadian rhythms in other tissues.
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Saltzman, W. Mark. "Drug Permeation through Biological Barriers." In Drug Delivery. Oxford University Press, 2001. http://dx.doi.org/10.1093/oso/9780195085891.003.0010.

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In multicellular organisms, thin lipid membranes serve as semipermeable barriers between aqueous compartments. The plasma membrane of the cell separates the cytoplasm from the extracellular space; endothelial cell membranes separate the blood within the vascular space from the rest of the tissue. Properties of the lipid membrane are critically important in regulating the movement of molecules between these aqueous spaces. While certain barrier properties of membranes can be attributed to the lipid components, accessory molecules within the cell membrane—particularly transport proteins and ion channels—control the rate of permeation of many solutes. Transport proteins permit the cell to regulate the composition of its intracellular environment in response to extracellular conditions. The relationship between membrane structure, membrane function, and cell physiology is an area of active, ongoing study. Our interest here is practical: what are the basic mechanisms of drug movement through membranes and how can one best predict the rate of permeation of an agent through a membrane barrier? To answer that question, this section presents rates of permeation measured in some common experimental systems and models of membrane permeation that can be used for prediction. The external surface of the plasma membrane carries a carbohydrate-rich coat called the glycocalyx; charged groups in the glycocalyx, which are provided principally by carbohydrates containing sialic acid, cause the surface to be negatively charged. On average, the plasma membrane of human cells contains, by mass, 50% protein, 45% lipid, and 5% carbohydrate. Given the mass ratio of protein to lipid is ~ 1 : 1, and assuming reasonable values for the average molecular weight and cross-sectional area for each type of molecule (50 × Mw,lipid = Mw,protein; Alipid = 50 Å2 and Aprotein = 1,000 Å2), the area fraction of protein on a typical membrane is ~ 33%. The lipid composition varies in membranes from different cells depending on the type of cell and its function. In addition, the outermost monolayer of lipids, called the outer leaflet, has a different lipid composition from the inner leaflet.
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Raychaudhuri, Soumya. "Protein Interaction Networks." In Computational Text Analysis. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198567400.003.0017.

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Genes and proteins interact with each other in many complicated ways. For example, proteins can interact directly with each other to form complexes or to modify each other so that their function is altered. Gene expression can be repressed or induced by transcription factor proteins. In addition there are countless other types of interactions. They constitute the key physiological steps in regulating or initiating biological responses. For example the binding of transcription factors to DNA triggers the assembly of the RNA assembly machinery that transcribes the mRNA that then is used as the template for protein production. Interactions such as these have been carefully elucidated and have been described in great detail in the scientific literature. Modern assays such as yeast-2-hybrid screens offer rapid means to ascertain many of the potential protein–protein interactions in an organism in a large-scale approach. In addition, other experimental modalities such as gene-expression array assays offer indirect clues about possible genetic interactions. One area that has been greatly explored in the bioinformatics literature is the possibility of learning genetic or protein networks, both from the scientific literature and from large-scale experimental data. Indeed, as we get to know more and more genes, it will become increasingly important to appreciate their interactions with each other. An understanding of the interactions between genes and proteins in a network allows for a meaningful global view of the organism and its physiology and is necessary to better understand biology. In this chapter we will explore methods to either (1) mine the scientific literature to identify documented genetic interactions and build networks of genes or (2) to confirm protein interactions that have been proposed experimentally. Our focus here is on direct physical protein–protein interactions, though the techniques described could be extended to any type of biological interaction between genes or proteins. There are multiple steps that must be addressed in identifying genetic interaction information contained within the text. After compiling the necessary documents and text, the first step is to identify gene and protein names in the text.
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Raychaudhuri, Soumya. "Text-Based Analysis of a Single Series of Gene Expression Measurements." In Computational Text Analysis. Oxford University Press, 2006. http://dx.doi.org/10.1093/oso/9780198567400.003.0012.

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In this chapter we begin to address the issue of the analysis of gene expression data with the scientific literature. Here we describe methods for the analysis of a single experiment—one where a single expression measurement has been made for many genes within the same organism. In Chapter 7 we will address the analysis of larger data sets with multiple expression measurements for each of the genes; the questions that occur in that setting are often more complex and utilization of scientific text in that setting can be more useful. But focusing on a single series of expression measurements is an effective starting point in understanding the scientific literature and how it can be used with experimental data. The lessons here can be applied to a wide array of genomic assays besides gene arrays. These methods can be applied to any assay that assigns a single value to each gene In addition, many investigators generate single-condition expression data sets, and these methods are widely applicable. One of the great difficulties in analyzing a single expression series is that context is lacking. That is, we have a large set of isolated measurements. Each measurement corresponds to the log of the relative ratio of a single gene’s expression in an experimental condition compared to its expression in a control condition. These measurements represent a single snapshot of a cell’s physiologic status. One of the great challenges is sorting out the physiologically important expression changes compared to random experimental and physiologic aberrations and fluctuations. Gene expression measurements are subject to a great amount of noise and distinguishing true positives from genes that are not truly induced or repressed is a great challenge. Typically, investigators use their knowledge of biology to prioritize likely positives. In this chapter we argue that text-mining approaches can be used to help prioritize these genes instead. Another equally important challenge is to discern broadly what biological functions are active in a given experiment.
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Conference papers on the topic "Organismal Biological Physiology"

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Tsvankin, Vadim, Dmitry Belchenko, Devon Scott, and Wei Tan. "Anisotropic Strain Effects on Vascular Smooth Muscle Cell Physiology." In ASME 2007 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2007. http://dx.doi.org/10.1115/sbc2007-176284.

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Biological development is a complex and highly-regulated process, a significant part of which is controlled by mechanostimulus, or the strain imparted on a cell by its environment. Mechanostimulus is important for stem cell differentiation, from cytoskeletal assembly to cell-cell and cell-matrix adhesion [1]. The mechanics of cells and tissues play a critical role in organisms, under both physiological and pathological conditions; abnormal mechanotransduction — the mechanism by which cells sense and respond to strain — has been implicated in a wide range of clinical pathologies [2,3].
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