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Journal articles on the topic 'Organism in biology'

Author: Grafiati

Published: 24 April 2022

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1

Peterson, Anne Siebels. "Matter in Biology." American Catholic Philosophical Quarterly 92, no. 2 (2018): 353–71. http://dx.doi.org/10.5840/acpq2018315150.

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Aristotle insists that the organic matter composing an organism depends for its being and becoming upon the living organism whose organic matter it is. An evolutionary context may at first seem to secure autonomy for an organism’s organic matter: after all, in such a context not only can organisms in divergent taxa have the same trait, but a trait can remain the same through thoroughgoing changes in its form, function, composition, and organismic context over evolutionary time. The biological homology concept attempts to capture this mysterious relationship of trait sameness. However, accounts of biological homology that have dominated the contemporary scene face compelling problems—these problems, I will argue, arise from their exclusion of the organism as an explanatory locus for the being and becoming of biological traits. An evolutionary framework in fact supports an account of homology that retains these two aspects of Aristotle’s views on organic matter.

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2

Leonelli, Sabina, and Rachel A. Ankeny. "Re-thinking organisms: The impact of databases on model organism biology." Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43, no. 1 (March 2012): 29–36. http://dx.doi.org/10.1016/j.shpsc.2011.10.003.

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3

Ueda, Hiroki R. "Towards Organism-level Systems Biology." Proceedings for Annual Meeting of The Japanese Pharmacological Society WCP2018 (2018): JPS—FS—1. http://dx.doi.org/10.1254/jpssuppl.wcp2018.0_jps-fs-1.

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4

Schjelderup, Vilhelm. "Eciwo Biology and Bio-Holographic Acupuncture." Acupuncture in Medicine 10, no. 1 (May 1992): 29–31. http://dx.doi.org/10.1136/aim.10.1.29.

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ECIWO stands for “Embryo Containing information of the Whole Organism”. ECIWO biology is a new biological discipline that has been developed in China. It is based on the hypothesis that living organisms have a mosaic structure, being composed of parts that have embryonic properties and contain information relating to the whole organism. ECIWO biology is being applied to different fields of the life sciences, including medicine. It explains the acupuncture microsystems and gives a new scientific basis for the study of acupuncture. A new micro-system of acupuncture based on the second metacarpal is described.

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5

Bandi, Gergely. "Emulating biology: the virtual living organism." Journal of Biological Physics and Chemistry 11, no. 3 (September 30, 2011): 97–106. http://dx.doi.org/10.4024/20ba11a.jbpc.11.03.

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6

Fields, S. "CELL BIOLOGY: Whither Model Organism Research?" Science 307, no. 5717 (March 25, 2005): 1885–86. http://dx.doi.org/10.1126/science.1108872.

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7

Pepper, John W., and Matthew D. Herron. "Does Biology Need an Organism Concept?" Biological Reviews 83, no. 4 (October 20, 2008): 621–27. http://dx.doi.org/10.1111/j.1469-185x.2008.00057.x.

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8

Hull, David L., Rodney E. Langman, and Sigrid S. Glenn. "A general account of selection: Biology, immunology, and behavior." Behavioral and Brain Sciences 24, no. 3 (June 2001): 511–28. http://dx.doi.org/10.1017/s0140525x01004162.

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Authors frequently refer to gene-based selection in biological evolution, the reaction of the immune system to antigens, and operant learning as exemplifying selection processes in the same sense of this term. However, as obvious as this claim may seem on the surface, setting out an account of “selection” that is general enough to incorporate all three of these processes without becoming so general as to be vacuous is far from easy. In this target article, we set out such a general account of selection to see how well it accommodates these very different sorts of selection. The three fundamental elements of this account are replication, variation, and environmental interaction. For selection to occur, these three processes must be related in a very specific way. In particular, replication must alternate with environmental interaction so that any changes that occur in replication are passed on differentially because of environmental interaction.One of the main differences among the three sorts of selection that we investigate concerns the role of organisms. In traditional biological evolution, organisms play a central role with respect to environmental interaction. Although environmental interaction can occur at other levels of the organizational hierarchy, organisms are the primary focus of environmental interaction. In the functioning of the immune system, organisms function as containers. The interactions that result in selection of antibodies during a lifetime are between entities (antibodies and antigens) contained within the organism. Resulting changes in the immune system of one organism are not passed on to later organisms. Nor are changes in operant behavior resulting from behavioral selection passed on to later organisms. But operant behavior is not contained in the organism because most of the interactions that lead to differential replication include parts of the world outside the organism. Changes in the organism's nervous system are the effects of those interactions. The role of genes also varies in these three systems. Biological evolution is gene-based (i.e., genes are the primary replicators). Genes play very different roles in operant behavior and the immune system. However, in all three systems, iteration is central. All three selection processes are also incredibly wasteful and inefficient. They can generate complexity and novelty primarily because they are so wasteful and inefficient.

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9

Nyhart, Lynn K. "The Political Organism." Historical Studies in the Natural Sciences 47, no. 5 (November 1, 2017): 602–28. http://dx.doi.org/10.1525/hsns.2017.47.5.602.

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How do the discourses of biology and politics interact? This article uses the case of Carl Vogt (1817–1895), the notorious German “radical materialist” zoologist and political revolutionary, to analyze the traffic across these discourses before, during, and after the revolutions of 1848. Arguing that metaphors of the organism and the state did different work in the discourse communities of German political theorists and biologists through the 1840s, it then traces Vogt’s life and work to show how politics and biology came together in his biography. It draws on Vogt’s political rhetoric, his satirical post-1849 writings, and his scientific studies to examine the parallels he drew between animal organization and human social and political organization in the 1840s and ’50s. Broadening back out, I suggest that the discourses of organismal and state organization, both somewhat transformed, would align more closely over the 1850s and thereafter—yet asymmetrically. Although the state metaphor became more attractive for biologists, the organism as state did not harden into a dominant concept in biology. On the political side, a new wave of political theorizing increasingly viewed the state as resembling a biological organism. These shifts, I speculate, brought the discourses closer together in the post-revolutionary era, and may be seen as contributing to a new configuration of mutual legitimation between science and the state. This essay is part of a special issue entitled REVOLUTIONARY POLITICS AND BIOLOGICAL ORGANIZATION IN NINETEENTH-CENTURY FRANCE AND GERMANY edited by Lynn K. Nyhart and Florence Vienne.

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10

Sturdy, Steve. "Biology as Social Theory: John Scott Haldane and Physiological Regulation." British Journal for the History of Science 21, no. 3 (September 1988): 315–40. http://dx.doi.org/10.1017/s0007087400025012.

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During the first forty years of this century, the concept of a living organism was discussed widely and publicly by biologists and philosophers. Two questions in particular excited discussion. In what ways should organisms be considered different from or the same as dead matter? And what can we learn about the nature of human society by regarding it as analogous to a living organism? Inevitably, these questions were closely related; the conclusions to be drawn about the social organism would depend upon the particular properties attributed to the biological organism. In more recent years, discussion of these issues has largely been in abeyance, as biologists have with-drawn from debate over social policy into a more remote academia. A few biologists who still see their work as relevant to a wider social agenda have continued to treat the nature of life as a contentious issue. But the focus of interest has shifted away from the organismic analogy, which concerns the organization of society as a whole, to issues like sociobiology and evolutionary theory, which emphasize social differentiation and the treatment of out-groups and minorities.

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Bechtel, William, and Leonardo Bich. "Grounding cognition: heterarchical control mechanisms in biology." Philosophical Transactions of the Royal Society B: Biological Sciences 376, no. 1820 (January 25, 2021): 20190751. http://dx.doi.org/10.1098/rstb.2019.0751.

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We advance an account that grounds cognition, specifically decision-making, in an activity all organisms as autonomous systems must perform to keep themselves viable—controlling their production mechanisms. Production mechanisms, as we characterize them, perform activities such as procuring resources from their environment, putting these resources to use to construct and repair the organism's body and moving through the environment. Given the variable nature of the environment and the continual degradation of the organism, these production mechanisms must be regulated by control mechanisms that select when a production is required and how it should be carried out. To operate on production mechanisms, control mechanisms need to procure information through measurement processes and evaluate possible actions. They are making decisions. In all organisms, these decisions are made by multiple different control mechanisms that are organized not hierarchically but heterarchically. In many cases, they employ internal models of features of the environment with which the organism must deal. Cognition, in the form of decision-making, is thus fundamental to living systems which must control their production mechanisms. This article is part of the theme issue ‘Basal cognition: conceptual tools and the view from the single cell’.

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Van Norman, Jaimie M., and Philip N. Benfey. "Arabidopsisthalianaas a model organism in systems biology." Wiley Interdisciplinary Reviews: Systems Biology and Medicine 1, no. 3 (November 2009): 372–79. http://dx.doi.org/10.1002/wsbm.25.

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13

Marcum, James A. "Whitehead’s Philosophy of Organism and Systems Biology." chromatikon 4 (2008): 143–52. http://dx.doi.org/10.5840/chromatikon2008413.

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14

Botstein, D., and G. Fink. "Yeast: an experimental organism for modern biology." Science 240, no. 4858 (June 10, 1988): 1439–43. http://dx.doi.org/10.1126/science.3287619.

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15

Baitubayеv, D. G. "Biology of increased tolerance and validation of the psychoactive substance dependence." Addiction Research and Adolescent Behaviour 5, no. 1 (January 6, 2022): 01–05. http://dx.doi.org/10.31579/2688-7517/029.

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The article shows that the current level of physiology does not disclose the biological mechanisms of the organism transition from one range to adapt to a higher with an increase in the regular forces of the stimulus above sub-extreme. A new trend in the physiology of adaptation - proqredient adaptation, explains the mechanism of increasing the tolerance of the organism, with dependence on psychoactive substances (PAS ). It is scientifically proved, that dependences of the organism on PAS are the states of progredient adaptation.

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16

Baedke, Jan. "O Organism, Where Art Thou? Old and New Challenges for Organism-Centered Biology." Journal of the History of Biology 52, no. 2 (November 21, 2018): 293–324. http://dx.doi.org/10.1007/s10739-018-9549-4.

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17

Pearce, Xavier G., Sarah J. Annesley, and Paul R. Fisher. "The Dictyostelium model for mitochondrial biology and disease." International Journal of Developmental Biology 63, no. 8-9-10 (2019): 497–508. http://dx.doi.org/10.1387/ijdb.190233pf.

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The unicellular slime mould Dictyostelium discoideum is a valuable eukaryotic model organism in the study of mitochondrial biology and disease. As a member of the Amoebozoa, a sister clade to the animals and fungi, Dictyostelium mitochondrial biology shares commonalities with these organisms, but also exhibits some features of plants. As such it has made significant contributions to the study of eukaryotic mitochondrial biology. This review provides an overview of the advances in mitochondrial biology made by the study of Dictyostelium and examines several examples where Dictyostelium has and will contribute to the understanding of mitochondrial disease. The study of Dictyostelium’s mitochondrial biology has contributed to the understanding of mitochondrial genetics, transcription, protein import, respiration, morphology and trafficking, and the role of mitochondria in cellular differentiation. Dictyostelium is also proving to be a versatile model organism in the study both of classical mitochondrial disease e.g. Leigh syndrome, and in mitochondria-associated neurodegenerative diseases like Parkinson’s disease. The study of mitochondrial diseases presents a unique challenge due to the cryptic nature of their genotype-phenotype relationship. The use of Dictyostelium can contribute to resolving this problem by providing a genetically tractable, haploid eukaryotic organism with a suite of readily characterised phenotype readouts of cellular signalling pathways. Dictyostelium has provided insight into the signalling pathways involved in multiple neurodegenerative diseases and will continue to provide a significant contribution to the understanding of mitochondrial biology and disease.

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18

Paley, Suzanne, Richard Billington, James Herson, Markus Krummenacker, and Peter D. Karp. "Pathway Tools Visualization of Organism-Scale Metabolic Networks." Metabolites 11, no. 2 (January 22, 2021): 64. http://dx.doi.org/10.3390/metabo11020064.

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Metabolomics, synthetic biology, and microbiome research demand information about organism-scale metabolic networks. The convergence of genome sequencing and computational inference of metabolic networks has enabled great progress toward satisfying that demand by generating metabolic reconstructions from the genomes of thousands of sequenced organisms. Visualization of whole metabolic networks is critical for aiding researchers in understanding, analyzing, and exploiting those reconstructions. We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network. The software generates metabolic-network diagrams for unicellular organisms, for multi-cellular organisms, and for pan-genomes and organism communities. Search tools enable users to find genes, metabolites, enzymes, reactions, and pathways within a diagram. The diagrams are zoomable to enable researchers to study local neighborhoods in detail and to see the big picture. The diagrams also serve as tools for comparison of metabolic networks and for interpreting high-throughput datasets, including transcriptomics, metabolomics, and reaction fluxes computed by metabolic models. These data can be overlaid on the metabolic charts to produce animated zoomable displays of metabolic flux and metabolite abundance. The BioCyc.org website contains whole-network diagrams for more than 18,000 sequenced organisms. The ready availability of organism-specific metabolic network diagrams and associated tools for almost any sequenced organism are useful for researchers working to better understand the metabolism of their organism and to interpret high-throughput datasets in a metabolic context.

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19

Alim, Karen. "Fluid flows shaping organism morphology." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1747 (April 9, 2018): 20170112. http://dx.doi.org/10.1098/rstb.2017.0112.

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A dynamic self-organized morphology is the hallmark of network-shaped organisms like slime moulds and fungi. Organisms continuously reorganize their flexible, undifferentiated body plans to forage for food. Among these organisms the slime mould Physarum polycephalum has emerged as a model to investigate how an organism can self-organize their extensive networks and act as a coordinated whole. Cytoplasmic fluid flows flowing through the tubular networks have been identified as the key driver of morphological dynamics. Inquiring how fluid flows can shape living matter from small to large scales opens up many new avenues for research. This article is part of the theme issue ‘Self-organization in cell biology’.

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20

Drubin, David G., and Anthony A. Hyman. "Stem cells: the new “model organism”." Molecular Biology of the Cell 28, no. 11 (June 2017): 1409–11. http://dx.doi.org/10.1091/mbc.e17-03-0183.

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Human tissue culture cells have long been a staple of molecular and cell biology research. However, although these cells are derived from humans, they have often lost considerable aspects of natural physiological function. Here we argue that combined advances in genome editing, stem cell production, and organoid derivation from stem cells represent a revolution in cell biology. These advances have important ramifications for the study of basic cell biology mechanisms, as well as for the ways in which discoveries in mechanisms are translated into understanding of disease.

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21

Drusano, G. L., O. O. Okusanya, A. O. Okusanya, B. van Scoy, D. L. Brown, C. Fregeau, R. Kulawy, et al. "Impact of Spore Biology on the Rate of Kill and Suppression of Resistance in Bacillus anthracis." Antimicrobial Agents and Chemotherapy 53, no. 11 (August 17, 2009): 4718–25. http://dx.doi.org/10.1128/aac.00802-09.

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ABSTRACT Bacillus anthracis is complex because of its spore form. The spore is invulnerable to antibiotic action. It also has an impact on the emergence of resistance. We employed the hollow-fiber infection model to study the impacts of different doses and schedules of moxifloxacin on the total-organism population, the spore population, and the subpopulations of vegetative- and spore-phase organisms that were resistant to moxifloxacin. We then generated a mathematical model of the impact of moxifloxacin, administered by continuous infusion or once daily, on vegetative- and spore-phase organisms. The ratio of the rate constant for vegetative-phase cells going to spore phase (K vs) to the rate constant for spore-phase cells going to vegetative phase (K sv) determines the rate of organism clearance. The continuous-infusion drug profile is more easily sensed as a threat; the K vs/K sv ratio increases at lower drug exposures (possibly related to quorum sensing). This movement to spore phase protects the organism but makes the emergence of resistance less likely. Suppression of resistance requires a higher level of drug exposure with once-daily administration than with a continuous infusion, a difference that is related to vegetative-to-spore (and back) transitioning. Spore biology has a major impact on drug therapy and resistance suppression. These findings explain why all drugs of different classes have approximately the same rate of organism clearance for Bacillus anthracis.

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22

Prem Swaroop Adhikarla, Pavithra Bhavanasi, and Raj Sekhar Bollapragada. "Understanding Cell Biology." International Journal of Research In Phytochemical And Pharmacological Sciences 1, no. 1 (July 2, 2019): 39–45. http://dx.doi.org/10.33974/ijrpps.v1i1.108.

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The cell is the structural and functional unit of all living organisms and is sometimes called the "building block of life.” All living things are made from one or more cells. A cell is the simplest unit of life and they are responsible for keeping an organism alive and functioning. Almost every different type of cell contains genetic material, a membrane and cytoplasm. The most basic categorization of Earth’s organisms is determined by different types of cells. All cells can be divided into one of two classifications: prokaryotic cells and eukaryotic cells. Prokaryotic cells are found in bacteria and archaea. Eukaryotic cells are found in organisms from the domain Eukaryota which includes animals, plants, fungi and protists. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules and perform other biological functions. Cells were discovered by Robert Hooke in 1665, who named them for their resemblance to cells inhabited by Christian monks in a monastery. Cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that cells are the fundamental unit of structure and function in all living organisms, and that all cells come from pre-existing cells. Cells emerged on Earth at least 3.5 billion years ago. The study of cells is called cell biology or cellular biology.

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23

Botstein, David, and Gerald R. Fink. "Yeast: An Experimental Organism for 21st Century Biology." Genetics 189, no. 3 (November 2011): 695–704. http://dx.doi.org/10.1534/genetics.111.130765.

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24

D??Souza, Deepak Cyril, and John H. Krystal. "Perturbing the Organism: The Biology of Stressful Experience." Journal of Nervous and Mental Disease 182, no. 2 (February 1994): 126. http://dx.doi.org/10.1097/00005053-199402000-00023.

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25

Nielsen, Jens. "Yeast Systems Biology: Model Organism and Cell Factory." Biotechnology Journal 14, no. 9 (May 20, 2019): 1800421. http://dx.doi.org/10.1002/biot.201800421.

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26

McEwen, Bruce S. "Perturbing the Organism: The Biology of Stressful Experience." JAMA: The Journal of the American Medical Association 269, no. 10 (March 10, 1993): 1315. http://dx.doi.org/10.1001/jama.1993.03500100115046.

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27

Keseler, Ingrid M., Amanda Mackie, Martin Peralta-Gil, Alberto Santos-Zavaleta, Socorro Gama-Castro, César Bonavides-Martínez, Carol Fulcher, et al. "EcoCyc: fusing model organism databases with systems biology." Nucleic Acids Research 41, no. D1 (November 7, 2012): D605—D612. http://dx.doi.org/10.1093/nar/gks1027.

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28

Huxtable, Ryan J. "Perturbing the organism: The biology of stressful experience." Trends in Pharmacological Sciences 13 (January 1992): 335–36. http://dx.doi.org/10.1016/0165-6147(92)90103-d.

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29

Wilson, Andrew. "Perturbing the organism. The biology of stressful experience." Journal of Psychosomatic Research 37, no. 4 (May 1993): 435–36. http://dx.doi.org/10.1016/0022-3999(93)90150-e.

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30

Samudra Guha, Joyeeta Talukdar, Abhibrato Karmakar, Sandeep Goswami, Arun Kumar, Ruby Dhar, and Subhradip Karmakar. "Synthetic Biology: The New Era." Asian Journal of Medical Sciences 13, no. 4 (April 1, 2022): 200–203. http://dx.doi.org/10.3126/ajms.v13i4.43880.

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Synthetic biology is an emerging discipline of science, at the intersection of biology, engineering, and chemistry that involves redesigning organisms to have new phenotypes and customized abilities. While synthetic biology seems to have originated from genetic engineering, over the years, it has matured as well as diverged from it. It involves not just the transfer of genes from one or cell to another creating some variants, it also involves the assembly of an altogether novel organism or cell created part by part by the assembly of individual components of the desired function in a logical fashion. In this minireview, we will explore this new discipline and its possible applications and future promises to serve the humanity

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31

Lehmann, Ruth, Connie M. Lee, Erika C. Shugart, Marta Benedetti, R. Alta Charo, Zev Gartner, Brigid Hogan, Jürgen Knoblich, Celeste M. Nelson, and Kevin M. Wilson. "Human organoids: a new dimension in cell biology." Molecular Biology of the Cell 30, no. 10 (May 2019): 1129–37. http://dx.doi.org/10.1091/mbc.e19-03-0135.

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Organoids derived from stem cells or tissues in culture can develop into structures that resemble the in vivo anatomy and physiology of intact organs. Human organoid cultures provide the potential to study human development and model disease processes with the same scrutiny and depth of analysis customary for research with nonhuman model organisms. Resembling the complexity of the actual tissue or organ, patient-derived human organoid studies may accelerate medical research, creating new opportunities for tissue engineering and regenerative medicine, generating knowledge and tools for preclinical studies, including drug development and testing. Biologists are drawn to this system as a new “model organism” to study complex disease phenotypes and genetic variability among individuals using patient-derived tissues. The American Society for Cell Biology convened a task force to report on the potential, challenges, and limitations for human organoid research. The task force suggests ways to ease the entry for new researchers into the field and how to facilitate broader use of this new model organism within the research community. This includes guidelines for reproducibility, culturing, sharing of patient materials, patient consent, training, and communication with the public.

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Rosslenbroich, Bernd. "The Significance of an Enhanced Concept of the Organism for Medicine." Evidence-Based Complementary and Alternative Medicine 2016 (2016): 1–15. http://dx.doi.org/10.1155/2016/1587652.

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Recent developments in evolutionary biology, comparative embryology, and systems biology suggest the necessity of a conceptual shift in the way we think about organisms. It is becoming increasingly evident that molecular and genetic processes are subject to extremely refined regulation and control by the cell and the organism, so that it becomes hard to define single molecular functions or certain genes as primary causes of specific processes. Rather, the molecular level is integrated into highly regulated networks within the respective systems. This has consequences for medical research in general, especially for the basic concept of personalized medicine or precision medicine. Here an integrative systems concept is proposed that describes the organism as a multilevel, highly flexible, adaptable, and, in this sense, autonomous basis for a human individual. The hypothesis is developed that these properties of the organism, gained from scientific observation, will gradually make it necessary to rethink the conceptual framework of physiology and pathophysiology in medicine.

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de Souza, Natalie. "Networking an organism." Nature Methods 5, no. 3 (March 2008): 217. http://dx.doi.org/10.1038/nmeth0308-217.

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Ohtani, Naoto, Masaru Tomita, and Mitsuhiro Itaya. "An Extreme Thermophile, Thermus thermophilus, Is a Polyploid Bacterium." Journal of Bacteriology 192, no. 20 (August 20, 2010): 5499–505. http://dx.doi.org/10.1128/jb.00662-10.

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ABSTRACT An extremely thermophilic bacterium, Thermus thermophilus HB8, is one of the model organisms for systems biology. Its genome consists of a chromosome (1.85 Mb), a megaplasmid (0.26 Mb) designated pTT27, and a plasmid (9.3 kb) designated pTT8, and the complete sequence is available. We show here that T. thermophilus is a polyploid organism, harboring multiple genomic copies in a cell. In the case of the HB8 strain, the copy number of the chromosome was estimated to be four or five, and the copy number of the pTT27 megaplasmid seemed to be equal to that of the chromosome. It has never been discussed whether T. thermophilus is haploid or polyploid. However, the finding that it is polyploid is not surprising, as Deinococcus radiodurans, an extremely radioresistant bacterium closely related to Thermus, is well known to be a polyploid organism. As is the case for D. radiodurans in the radiation environment, the polyploidy of T. thermophilus might allow for genomic DNA protection, maintenance, and repair at elevated growth temperatures. Polyploidy often complicates the recognition of an essential gene in T. thermophilus as a model organism for systems biology.

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35

Gasch, Audrey P., Bret A. Payseur, and John E. Pool. "The Power of Natural Variation for Model Organism Biology." Trends in Genetics 32, no. 3 (March 2016): 147–54. http://dx.doi.org/10.1016/j.tig.2015.12.003.

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36

Jungblut, Benno, André Pires-Da Silva, Andreas Eizinger, Kwang-Zin Lee, Jagan Srinivasan, Kaj Grandien, Ralf Sommer, et al. "Pristionchus pacificus: a satellite organism in evolutionary developmental biology." Nematology 2, no. 1 (2000): 81–88. http://dx.doi.org/10.1163/156854100508791.

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AbstractPristionchus pacificus has been described as a satellite organism, for functional comparative studies with Caenorhabditis elegans. Like C. elegans, P. pacificus is also easily cultured in the laboratory on a lawn of E. coli bacteria. P. pacificus is a hermaphroditic species with a 4-day life cycle, but unlike most nematodes which pass through four juvenile stages during their development, P. pacificus has only three juvenile stages. The combination of genetic, molecular and cell-biological studies have made P. pacificus a model system in the new field of evolutionary developmental biology. One process that has been studied in detail is the development of the vulva. Genetic and molecular studies revealed that the function of several genes involved in vulva development differs between P. pacificus and C. elegans. Here, we review our genetic and molecular studies of P. pacificus. We show that P. pacificus is well-suited as a satellite organism not only for understanding the cellular and genetic aspects of evolutionary change, but also for addressing questions of molecular evolution at the genomic level. Pristionchus pacificus wurde vor mehrerern Jahren als “Satelitten-Organism” für funktionelle-vergleichende Studien mit dem Modellorganismus C. elegans beschrieben. P. pacificus ist eine hermaphroditische Art mit einer Generationszeit von 4 Tagen und kann auf E. coli gezüchtet werden. Die Analyse des Lebenszyklus hat gezeigt dass diese Art im Gegensatz zu den meisten Nematoden nur drei Juvenilstadien durchläuft. Da in P. pacificus genetische, molekular-biologische und zelluläre Methoden in ähnlicher Weise zum Einsatz kommen können wie in C. elegans, ist diese Art ein ideales Modellsystem für evolutionäre entwicklungsbiologische Fragestellungen. Ein besonders detailliert analysierter Entwicklungsprozess ist die Bildung der Vulva. Genetische und molekulare Arbeiten haben gezeigt dass einige in beiden Arten an der Vulva-Bildung beteiligte homologen Gene, sich in ihrer detaillierten Funktion deutlich voneinander unterscheiden. Die vorliegende Arbeit gibt einen Überblick über die genetischen und molekularen Aspekte der Vulva-Entwicklung in P. pacificus und zeigt die Potenzen der Art auch für zukünftige molekulare und genomische Untersuchungen.

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Ukai, Hideki, Kenta Sumiyama, and Hiroki R. Ueda. "Next-generation human genetics for organism-level systems biology." Current Opinion in Biotechnology 58 (August 2019): 137–45. http://dx.doi.org/10.1016/j.copbio.2019.03.003.

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Sivasubramaniam, Sudhakar. "The Earthworm Eudrilus Eugeniae: a Model Organism for Regenerative Biology." Genetics & Genomic Sciences 6, no. 1 (February 25, 2021): 1–4. http://dx.doi.org/10.24966/ggs-2485/100023.

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The earthworm, Eudrilus eugeniae is an economical model system for cell and molecular biological experiments to study regeneration and stem cell biology. The purpose of this brief review is to summarize those published studies on the regeneration biology using E. eugenia and to provide the advantages of the model system.

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Baedke, Jan. "Publisher Correction to: O Organism, Where Art Thou? Old and New Challenges for Organism-Centered Biology." Journal of the History of Biology 52, no. 4 (August 12, 2019): 747. http://dx.doi.org/10.1007/s10739-019-09581-6.

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Kukharchyshyn, Mariia. "Іnterdisciplinary Terminological Correlation in the Process of Transterminologization (on the Material of the Biological Terminology)." Terminological Bulletin, no. 5 (2019): 246–53. http://dx.doi.org/10.37919/2221-8807-2019-5-34.

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The article describes the transterminologization as a result of the interaction between terminology systems of scientific fields on the conceptual level. Transterminology is not limited to migration of only certain terms, but also entire groups of terms and scientific theories. Biology as a science is rich in heuristic ideas and fundamental discoveries. It is a donor for many scientific disciplines. The influence of biological terminology on the terminology of humanities is shown on the example of Ch. Darwin’s theory of the evolution. Biological laws of the organic world evolution, the struggle for existence, natural selection are used in the linguistics, sociology, management. The biological direction appeared in linguistics under the influence of Darwin’s theory. Its founder was A. Schleicher. The biologists interpret language as a biological phenomenon, as a living organism. In such a way the associative field “language – an organism” was formed. For the language analysis, the following terms: birth, growth, development, aging, death are used. The biologic direction also appeared in sociology. Its main feature is the application of concepts and laws of biology for the analysis of social life. The biologic direction in sociology is represented by several schools: Social Darwinism, Organic School, Genetic Sociology. Sociologists use such biological terms as organism, social tissues, organs, mimicry, pathology, reproduction of society. So the associative field “society – an organism” was formed. In management, under the influence of biology, were formed such concepts as Organizational Darwinism and Population Ecology of Organizations. According to these concepts, to survive the organization must adapt to changes in the environment. This way the associative field “organization – an organism” was formed. Biological terms life cycle, maturity, population are used in management. So, due to transterminologization, the generation of scientific theories takes place.

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Tikhonovich, Igor A. "Meaning of symbiogenetics for biological education." Ecological genetics 5, no. 1 (March 15, 2007): 8–17. http://dx.doi.org/10.17816/ecogen518-17.

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The annotation of lecture course "Symbiogenetics" is suggested which represents the novel brunch of modern biology. It addresses the super-organism genetic systems which are formed due to interactions of non-related organisms (including pro- and eukaryotes) and ensure formation of the novel properties which extend the partners' ecological capacities. Elucidation of the universal mechanisms for establishment of inter-organisms communications enables us to develop the technologies for improving the extant symbiotic complexes and to construct the novel ones for being used in different areas of applied biology.

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Noble, Denis. "Models and reality: The role of computational biology." Biochemist 27, no. 2 (April 1, 2005): 7–10. http://dx.doi.org/10.1042/bio02702007.

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The last half of the 20th century saw the phenomenal success of the reductionist approach to biology. The structures of numerous macromolecules were unravelled, the chemical nature of DNA was discovered, and the genome sequences of a number of organisms were largely or completely determined. Readers of The Biochemist need no reminding -- the Biochemical Society played a major role in these monumental achievements. But this very success has created a difficult challenge for the 21st century: what does all this data mean? Could we imagine that with this information and limitless computing power we could simulate the complete functioning of an organism in an exhaustive bottom-up fashion?

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Bronner-Fraser, M. "From egg to organism." Development 130, no. 23 (December 1, 2003): 5555. http://dx.doi.org/10.1242/dev.00787.

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Insall, Robert H. "The Whole Organism, and nothing but the Organism." Cell 107, no. 3 (November 2001): 279–81. http://dx.doi.org/10.1016/s0092-8674(01)00558-x.

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Vivoda, Maja, Ivana Cirkovic, Djordje Aleksic, Lazar Ranin, and Slobodanka Djukic. "Biology and intracellular life of chlamydia." Medical review 64, no. 11-12 (2011): 561–64. http://dx.doi.org/10.2298/mpns1112561v.

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Introduction. Chlamydiae are Gram-negative obligate intracellular bacteria. The developmental cycle of Chlamydiae is specific and different from other bacteria. The elementary body is the infectious form of the organism, responsible for attaching to the target host cell and promoting its entry. The reticulate body is the larger, metabolically active form of the organism, synthesizing deoxyribonucleic acid, ribonucleic acid and proteins. The elementary body and reticulate body represent evolutionary adaptations to extracellular and intracellular environments. Intracellular persistence of Chlamydia. Predisposition of Chlamydia to persist within the host cell has been recognized as a major factor in the pathogenesis of chlamydial disease. The persistence implies a long-term association between chlamydiae and their host cell that may not manifest as clinically recognizable disease. The ability of chlamydia to remain within one morphological state for a long time in response to exogenous factors suggests an innate ability of these organisms to persist intracellulary in a unique developmental form. Chlamydiae induce interferon ? and exhibit growth inhibition in their presence. While the high levels of interferon ? completely restrict the development of chlamydia, its low levels induce the development of morphologically aberrant intracellular forms. The persistent forms contain reduced levels of major outer membrane protein but high levels of chlamydial heat shock protein. Conclusion. Immunopathogenesis of chlamydial infection is one of the main focal points of current research into Chlamydia. Chlamydial infections are highly prevalent, usually asymptomatic and associated with serious sequelae. Screening programmes are the most important in the prevention of a long-term sequele.

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Idema, Timon. "Mechanics in biology." Europhysics News 51, no. 5 (September 2020): 28–30. http://dx.doi.org/10.1051/epn/2020504.

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Mechanics plays a key role in life, from simple tasks like providing protective shielding to highly complex ones such as cell division. To understand mechanical properties on the organism level, we need to zoom in to its constituent cells, then zoom back out to see how they collectively build tissues.

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Weitao, Tao. "Can an antagonist gene of unicellular organism cause chromosome instability in multicellular organisms?" DNA Repair 8, no. 2 (February 2009): 144–45. http://dx.doi.org/10.1016/j.dnarep.2008.11.003.

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Rine, Jasper. "A future of the model organism model." Molecular Biology of the Cell 25, no. 5 (March 2014): 549–53. http://dx.doi.org/10.1091/mbc.e12-10-0768.

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Changes in technology are fundamentally reframing our concept of what constitutes a model organism. Nevertheless, research advances in the more traditional model organisms have enabled fresh and exciting opportunities for young scientists to establish new careers and offer the hope of comprehensive understanding of fundamental processes in life. New advances in translational research can be expected to heighten the importance of basic research in model organisms and expand opportunities. However, researchers must take special care and implement new resources to enable the newest members of the community to engage fully with the remarkable legacy of information in these fields.

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Labunskyy, Vyacheslav. "SYSTEMS BIOLOGY OF AGING." Innovation in Aging 3, Supplement_1 (November 2019): S207. http://dx.doi.org/10.1093/geroni/igz038.752.

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Abstract The biology of aging is an immensely complex process that impacts function at the sub-cellular, cellular, tissue, organ, and whole organism levels. New technologies and systems-level approaches provide an opportunity to greatly enhance our understanding of this complexity.

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Nocek, A. J. "Transcendental Biology." Philosophy Today 63, no. 4 (2019): 1155–80. http://dx.doi.org/10.5840/philtoday2020128317.

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This essay shows how Conrad Hal Waddington is at the very center of divergent genealogies of theoretical biology: he is at once remembered for his contribution to epigenetics and complex systems biology (in its current formation) and largely forgotten for the debt that he owes to Alfred North Whitehead’s philosophy of organism. The essay traces Waddington's debt to Whitehead and demonstrates the way in which this conceptual lineage challenges the transcendental conditions of biological knowledge presupposed by the reigning paradigm of complex systems biology.

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