Relevant bibliographies by topics / Organism in biology

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

Academic literature on the topic 'Organism in biology'

Author: Grafiati
Published: 24 April 2022

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Journal articles on the topic "Organism in biology"

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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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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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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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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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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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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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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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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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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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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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Dissertations / Theses on the topic "Organism in biology"

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Kendig, Catherine Elizabeth. "Biology and ontology : an organism-centred view." Thesis, University of Exeter, 2008. http://hdl.handle.net/10036/42121.

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In this dissertation I criticize and reconfigure the ontological framework within which discussions of the organization, ontogeny, and evolution of organic form have often been conducted. Explanations of organismal form are frequently given in terms of a force or essence that exists prior to the organism’s life in the world. Traits of organisms are products of the selective environment and the unbroken linear inheritance of genetically coded developmental programs. Homological traits share unbroken vertical inheritance from a single common ancestor. Species are the product of exclusive gene flow between conspecifics and vertical genetic inheritance. And likewise, race is ascribed on the basis of pre-existing essential features. In place of this underlying preformationism which locates the source of form either in the informational program of inherited genes or within a selecting environment, I suggest form is the product of an organism’s self-construction using diverse resources. This can be understood as a modification of Kant’s view of organisms as self-organizing, set out in his Critique of Judgment (1790). Recast from this perspective the meaning and reference of “trait,” “homology,” “species,” and “race” change. Firstly, a trait may be the product of the organism’s self-construction utilizing multiple ancestral resources. Given this, homologous traits may correspond in some but not all of their features or may share some but not all of their ancestral sources. Homology may be partial. Species may acquire epigenetic, cellular, behavioural, and ecological resources both vertically and horizontally. As such, they are best conceived of as recurrent successions of self-constructed and reconstructed life cycles of organisms sharing similar resources, a similar habitus, similar capacities for sustaining themselves, and repeated generative processes. Lastly, race identity is not preformed but within the control of human organisms as agents who self-construct, interpret, and ascribe their own race identities utilizing diverse sets of dynamic relationships, lived experiences, and histories.
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Naruse, Kiyoshi, Mitsuru Sakaizumi, and Akihiro Shima. "Medaka as a model organism for research in experimental biology." Laboratory of Freshwater Fish Stocks Bioscience Center Nagoya University, 1994. http://hdl.handle.net/2237/13792.

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Bándi, Gergely. "Virtual living organism : a rapid prototyping tool to emulate biology." Thesis, Cranfield University, 2011. http://dspace.lib.cranfield.ac.uk/handle/1826/7230.

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Rapid prototyping tools exist in many fields of science and engineering, but are rare in biology especially not general tools that can handle the diversity and complexity of the many spatial and temporal scales in nature. In this thesis a general use, cell-based, middle-out biology emulation programming framework (outlining a programming paradigm) is presented, that enables biologists to emulate and use virtual biological systems of previously unimaginable complexity and potentially get results accurate enough to be used in research and ultimately, in clinical practice, such as diagnosis or operations. With this technology, virtual organisms can be created that are viable, fit and can be optimised for any task that arises. The tool, realised with a programming framework created for the C++ language is detailed and demonstrated through several examples of increasing complexity, namely several example organisms and a cancer emulation, showing both viable virtual organisms and usable experimental results.
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Nicholson, Daniel James. "Organism and mechanism : a critique of mechanistic thinking in biology." Thesis, University of Exeter, 2010. http://hdl.handle.net/10036/117787.

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In this thesis I present a critical examination of the role played by mechanistic ideas in shaping our understanding of living systems. I draw on a combination of historical, philosophical, and scientific resources to uncover a number of problems which I take to result from the adoption of mechanistic thinking in biology. I provide an analysis of the historical development of the conflict between mechanistic and vitalistic conceptions of life since the seventeenth century, and I argue that the basic terms of this conflict remain central to current disputes over the nature of the organism as well as the question of how far the theories, concepts, and methods of physics, chemistry, and engineering can ultimately take us in the explanation of life. I offer a detailed critique of the machine conception of the organism, which constitutes the central unifying idea of mechanistic biology. I argue that this notion, despite its undeniable heuristic value, is fundamentally inadequate as a theory of the organism due to a number of basic differences between organisms and machines. Ultimately, I suggest that the neglected vitalistic tradition in biology actually possesses the best conceptual tools for coming to terms with the nature of living systems. I also undertake a philosophical analysis of the concept of mechanism in biology. I argue that the term ‘mechanism’ is actually an umbrella term for three distinct notions, which are unfortunately conflated in philosophical discussions. I explore the relation between mechanistic biology and the new philosophical interest in the concept of mechanism and I show that these two research programs have little to do with one another because each of them understands the concept of mechanism in a different way. Finally, I draw on the historical and philosophical foundations of cell theory to propose an epistemological perspective which enables the reductionistic explanation of the organism without having to give up the distinctive features of life in the process. In this way, I show this perspective to have significant advantages over the classic physicochemical reductionism of mechanistic biology.
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Boisvert, Catherine Anne. "The Origin of Tetrapod Limbs and Girdles: Fossil and Developmental Evidence." Doctoral thesis, Uppsala universitet, Evolutionär organismbiologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-98911.

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Around 375 million years ago, the first tetrapods appeared, marking one of the most important events in vertebrate evolutionary history. The fin to limb transition saw the appearance of fingers and a weight bearing pelvic girdle. While very little research has been done on the evolution of the tetrapod pelvic girdle, a fair amount has been done on the origins of fingers but some aspects remained controversial. A combination of palaeontology, developmental biology and comparative morphology was therefore used in this thesis to better understand the fin to limb transition. The pectoral fin of Panderichthys, a sarcopterygian fish closely related to tetrapods was CT-scanned and modeled in three dimensions and its pelvic girdle and fin were examined with traditional techniques. This information from the fossil record was integrated with comparisons of the development of the Australian lungfish, Neoceratodus forsteri, our closest living fish relative and the axolotl (Ambystoma mexicanum), a salamander representing well the condition of early tetrapods. Development of bone and cartilage was studied through clearing and staining and development of skeletal muscles through immunostaining. In situ hybridizations were performed on the lungfish to study the expression of Hoxd13, associated with the formation of digits in tetrapods. This work shows that the late expression phase of Hoxd13 is present in Neoceratodus and is associated with the formation of radials. Redescription of the pectoral fin of Panderichthys reveals that distal radials are present, which, in addition to other information, lead us to conclude that digits are not novelties in tetrapods but rather have evolved from the distal radials present in the fins of all sarcopterygian fish. The earliest tetrapods lack a full set of wrist + carpals/ankle + tarsal bones. Here, we propose that this region of the limbs evolved after fingers and toes through an expansion of the region between the proximal limb bones and the digits. As for the pelvic girdle, it is very primitive in Panderichthys but comparison of its development in Neoceratodus and Ambystoma suggest that the ischium evolved through the posterior expansion of the pubis and the ilium, through an elongation of the iliac process already present in sarcopterygian fishes. The results of this thesis help to better understand the fin to limb transition and show that it is more gradual than previously believed.
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Souza, Sergio Izidoro de. "Organismo como finalidade segundo Kant." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/8/8133/tde-08112018-092009/.

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Na teoria da experiência da terceira Crítica, Kant estabelece a articulação das três faculdades de conhecimento. A possibilidade das coisas em geral, segundo o modelo da analítica do entendimento, está ainda sendo pensada pelas categorias, contudo, em conformidade com as leis do entendimento, estas mesmas coisas dotadas de formas particulares estão sendo pensadas pela legalidade da faculdade de julgar, e ao cabo a razão pensa a possibilidade da totalidade dessas formas arranjadas em ordem em vista de um sistema, segundo a dialética da razão. A partir dessa articulação entre as faculdades mentais em função da experiência, buscou-se determinar os conceitos que possibilitam pensar o organismo mostrando que o organismo é finalidade interna produzida por epigênese e pré-formação. Para pensar a possibilidade de articulação dessas duas teorias embriológicas da história da filosofia, Kant mobilizou conceitos do entendimento, da faculdade de julgar e da razão. A terceira Crítica operou uma série de deslocamentos e articulações conceituais para pensar o organismo. A contingência que era pensada pela razão é deslocada para a faculdade de julgar em sua legalidade do contingente. A terceira Crítica ainda deslocou a produção do organismo da intenção divina para a espontaneidade natural tendo o princípio da finalidade interna como fundamento mental. Na medida do possível buscamos introduzir a lógica transcendental na representação do organismo, e por esse caminho revelamos que entre os seus conceitos estão a liberdade, a técnica, o sistema e a comunidade, sob os quais Kant articulou as opostas teorias da pré-formação e da epigênese.
In the theory of experience of the third Critique, Kant establishes the articulation of the three faculties of knowledge. The possibility of things in general, according to the model of the analytic of the understanding, is still being thought by the categories, but in conformity with the laws of the understanding these same things endowed with particular forms are being thought by the lawfulness of the faculty of judgement, and finally reason thinks the possibility of the totality of these forms arranged in the order of a system, according to the dialectic of reason. From this articulation between the mental faculties for the experience, we tried to determine the concepts that make it possible to think the organism by showing that the organism is an internal purposiveness produced by epigenesis and pre-formation. In order to think about the possibility of articulating these two embryological theories of the history of philosophy, Kant mobilized concepts of the understanding, the faculty of judgement and reason. The third Critique operated a series of dislocations and conceptual articulations to think the organism. The contingency that was thought by reason is shifted to the faculty of judgement in its lawfulness of the contingent. The third Critique still shifted the organisms production from divine intention to natural spontaneity by having the principle of internal purposiveness as a mental foundation. As far as possible we seek to introduce transcendental logic into the representation of the organism, and through this path we reveal that among its concepts are freedom, technique, system and community, under which Kant articulated the opposing theories of pre-formation and of epigenesis.
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Meglhioratti, Fernanda Aparecida [UNESP]. "O conceito de organismo: uma introdução à epistemologia do conhecimento biológico na formação de graduandos de biologia." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/101994.

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Made available in DSpace on 2014-06-11T19:31:40Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-03-27Bitstream added on 2014-06-13T19:42:08Z : No. of bitstreams: 1 meglhioratti_fa_dr_bauru.pdf: 1366175 bytes, checksum: 66b9292b49a98bb952a24879d6ea05f7 (MD5)
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Na descrição hierárquica do conhecimento biológico, o ser vivo é considerado como ponto central nas relações engendradas pelos seguintes níveis: ambiente externo (ecológico/evolutivo), organismo e ambiente interno (genético/ molecular). O organismo compreendido como nível focal da discussão biológica pode ressaltar a autonomia da Biologia em relação às outras áreas do conhecimento científico. No contexto do ensino, assume-se que as discussões epistemológicas do conhecimento biológico podem promover uma compreensão mais integrada dos fenômenos biológicos. Assim, organizou-se um grupo de pesquisa com graduandos de um curso de Ciências Biológicas para discutir conceitos centrais do conhecimento biológico, entre eles, o conceito de organismo. Esta pesquisa teve como objetivos: 1) Elaborar uma caracterização do conceito de organismo, partindo de uma abordagem hierárquica, integrando as discussões advindas da Filosofia da Biologia contemporânea referentes aos conceitos de auto-organização, autonomia agencial, propriedades emergentes e níveis hierárquicos; 2) Analisar como o conceito de organismo se impõe frente às explicações de vida presentes na literatura contemporânea da Filosofia da Biologia; 3) Utilizar a discussão teórica relativa ao conceito de organismo como fundamentação de um grupo de “Pesquisas em Epistemologia da Biologia”, verificando as contribuições desse aporte teórico para a formação de alunos de Licenciatura em Ciências Biológicas na área de Epistemologia da Biologia e Ensino de Ciências; 4) Analisar as discussões e produções escritas ocorridas no desenvolvimento do grupo de “Pesquisas em Epistemologia da Biologia” que abordaram o conceito de organismo, com a finalidade de verificar se uma abordagem hierárquica tendo o organismo como nível focal contribui para uma visão integrada do conhecimento biológico pelos...
In the hierarchical of biological knowledge, the living being could be considered as central point in the relations produced by three levels: external environment (ecological/evolution), organism and environment intern (genetic/molecular). The comprehension of the organism as a focal level in the biological debate can underline the autonomy of Biology among the other areas of the scientific knowledge. In the education context it is assumed that the epistemological discussions of the biological knowledge can promote an integrated understanding of the biological phenomena. Thus, a research group consisting of Biological Sciences undergraduates was organized to debate central concepts of the biological knowledge in which the discussions of the organism concept are included. This research aimed to: 1) develop a characterization of the concept of organism from a hierarchical approach by integrating the resulting discussions from contemporary philosophy of biology that are related to the concepts of self-organization, autonomy agents, emergent properties and hierarchical levels; 2) to analyze how the concept of organism is placed in front of the explications of life in the contemporary literature of philosophy of biology; 3) to use the theoretical discussion on the concept of organism as fundamentation for a group of Studies in Epistemology of Biology, noting the help of this theoretical contribution to the Biological Sciences students training in the Biology and Epistemology in Science Teaching; 4) to analyze discussions and written productions that occurred in the development of the ‘Research in Epistemology of Biology’s group which addressed the concept the organism in order to verify if a hierarchical approach in which the organism is the focal level contributes to an integrated view of biological knowledge for biology students. On the basis of the theoretical referential... (Complete abstract click electronic access below)
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Edmonds, Matthew. "A systematic study of palmitoylation using the model organism Caenorhabditis elegans." Thesis, University of Liverpool, 2013. http://livrepository.liverpool.ac.uk/12253/.

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Palmitoylation is a reversible post-translational modification of proteins which involves the addition of the C16 saturated fatty acid palmitic acid to sulfhydryl groups on cysteine residues, forming a thioester linkage. The addition of palmitate allows proteins to associate with different cellular membranes and membrane subdomains. Palmitoylation is catalysed by the DHHC family of palmitoyl-acyl transferases (PATs), named for their characteristic DHHC motif in a cysteine-rich domain (CRD). Reversibility is conferred by palmitoyl-protein thioesterases (PPTs), which cleave the thioester linkage. The study of palmitoylation has recently gathered pace with the development of methods which allow proteome-scale identification of candidate palmitoyl-proteins. Despite the importance of model organisms in several key studies in the field, palmitoylation has barely been studied in the simple eukaryote Caenorhabditis elegans, the nematode worm. This study commenced with the use of the C. elegans genome data to identify its PATs and PPTs, using the DHHC-CRD and homology respectively. The 15 DHHC PATs were officially named using a dhhc-x system and the two previously known PPTs were confirmed as the only ones with homology to other known PPTs. The current knowledge on palmitoylation enzymes and substrates was collated and analysed to predict possible phenotypes resulting from mutation or knockdown of the enzymes and potential substrates. All available C. elegans strains containing a mutation in an individual PAT or PPT were obtained, covering about half of the PATs and both PPTs, and assayed for various gross phenotypes. In addition a complete library of bacteria able to express double-stranded RNA against PAT or PPT genes was sourced and used to perform similar assays using feeding RNA interference (RNAi). A number of small but significant differences were seen both with mutant and RNAi-treated strains, especially in lifespan assays. To test for possible redundancy and compensation amongst the enzymes, double RNAi was performed against selected closely related PATs and both PPTs. This resulted in the largest phenotype seen: a reduction in lifespan after simultaneous knockdown of both ppt-1 and ath-1. As there are no known palmitoyl-proteins in C. elegans, the proteomic approaches acyl-biotin exchange (ABE) and acyl-resin-assisted capture (acyl-RAC) were employed to provide a list of candidates. These were first optimised using rat brain material and the results compared with previous proteomic studies to find that two-thirds of the hits had been previously found. With this validation, both methods were applied to wild-type C. elegans lysates to give 91 hits as putative palmitoyl-proteins. Mutants for the PPT ath-1 were also profiled by ABE, showing 33 hits which were not present in the wild-type profile. These are potential ATH-1 substrates whose lack of depalmitoylation in the mutant leads to their enrichment relative to wild-type. However, further repeats of these analyses are required for rigorous statistical testing. Taken together, this study shows the first characterisation of palmitoylation in C. elegans, encompassing all of the DHHC PAT and PPT enzymes, putative palmitoyl-proteins and potential substrates of the PPT enzyme ATH-1.
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Zanet, Phillip. "Characterization of two novel cysteine proteases in the free-living organism «Macrostomum ligano »." Thesis, McGill University, 2013. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=119584.

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The objective of this study was to explore Macrostomum lignano, a free-living organism, as a model organism for parasitic trematodes, such as Fasciola and Schistosoma, in order to better understand the role of their cysteine proteases (cathepsins). Using a bioinformatics approach, two novel cysteine proteases genes (mlcl1 and mlcb2) were identified and phylogenetically characterized. These genes were synthesized, cloned into the yeast secretory system Pichia pastoris (Invitrogen), and functionally-active recombinant proteins were expressed and purified. These recombinant peptidases were then characterized biochemically in terms of activity and stability in various conditions including temperature, salinity and pH. Antibodies specific for the recombinant proteins were generated through a peptide or whole-protein immunization, and tested against both the recombinant proteins and the worm extract proving that the proteins exist in the worm. These studies lay the foundation for further investigations on the biological function of the cysteine peptidases using RNAi and confocal microscopy. In conclusion, M. lignano is a tractable model organism for its parasitic counterparts.
L'objectif de cette recherche était d'explorer l'organisme, vivant en liberté dans la nature, Macrostomum lignano en tant qu'organisme modèle pour ses cousins parasites, Fasciola et Schistosoma, et de mieux comprendre le rôle de leurs protéases cystéines (cathepsins). En utilisant une approche bioinformatique, deux nouveaux gènes de protéases cystéines (mlcl1 et mlcb2) ont été découverts et caractérisés phylogénétiquement. Ces gènes ont été synthétisés, clonés dans un système de sécrétion employant la levure Pichia pastoris (Invitrogen) et exprimés en tant que protéases recombinantes et actives. Ces protéases recombinantes ont alors été caractérisées biochimiquement en termes d'activité et de stabilité dans diverses conditions telles que la température, la salinité et le pH. Des anticorps spécifiques aux protéines recombinantes ont été générés en immunisant des mammifères avec des séquences de peptides ou la protéine recombinante entière, et ont été testés avec l'extrait du vers prouvant ainsi que les protéines sont bel et bien exprimées. Ces études jettent la base pour l'investigation sur la fonction biologique des protéases cystéines par l'emploi du RNAi et de la microscopie confocale. En conclusion, M. lignano est un organisme modèle tractable pour ses cousins parasites.
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Taylor-Burt, Kari. "Shiver me titin! Elucidating titin's role in organism-level performance." Thesis, Northern Arizona University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1543984.

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The frequency of oscillatory behaviors, like shivering, depends on the animal size and the properties of the muscles driving them. Titin and other muscular proteins play an important role in determining muscle properties, such as stiffness. Because the frequency of oscillatory behaviors depends on muscle properties, we predict that changes in titin's structure would affect these behaviors. The muscular dystrophy with myositis ( mdm) mouse model is characterized by a deletion in the N2A region of titin. Homozygous mdm mutants are substantially smaller (body mass is ½ to ⅓), have a stiffer gait, and have reduced lifespans compared to their wildtype and heterozygous siblings. In addition, we observed that mutants were heterothermic while wildtypes and heterozygotes were homeothermic when exposed to ambient temperatures ranging from 20-37 °C. We measured the relationship between metabolic rate and the differential between body and ambient temperatures for all three genotypes. As the temperature differential increased, metabolic rates increased more rapidly in the mutants than in wildtype or heterozygous mice, indicating that the mutants have a much higher conductance than their age-matched siblings. We measured shivering frequency in the mdm mice. The frequency of tremor during shivering is expected to be directly proportional to (k/ m)0.5 where k is stiffness and m is body mass. Using an allometric relationship between body mass and shivering frequency, we calculated expected values for all three genotypes based on body mass alone. These predicted values allowed us to take into account the much lower body masses of the mdm mutants. The difference between expected and observed values was significantly larger for mutant mice than wildtypes or heterozygotes. Together, the heterothermy in mutants, the very high conductance, and the decreased tremor frequency demonstrate the thermoregulatory challenges faced by mice with the mdm mutation. Previous work at the whole-muscle level showed that despite the higher passive stiffness observed in mdm mutant muscles, these muscles are more compliant when activated compared to muscles from wildtype mice. The lower tremor frequencies in mutants are consistent with a reduced active muscle stiffness in vivo. These observations suggest that titin affects the tuning of shivering frequency by playing a role in setting active muscle stiffness.

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Books on the topic "Organism in biology"

1

Life and organism. Vatican City: Pontifical Council for Culture, 2006.

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1951-, Mueller Laurence D., ed. Evolution and ecology of the organism. Upper Saddle River, NJ: Pearson Prentice Hall, 2005.

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Lewontin, Richard C. The triple helix: Gene, organism, and environment. Cambridge, Mass: Harvard University Press, 2000.

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Lewontin, Richard C. The triple helix: Gene, organism, and environment. Cambridge, Mass: Harvard University Press, 2000.

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Lewontin, Richard C. The triple helix: Gene, organism, and environment. Cambridge, Mass: Harvard University Press, 2000.

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V, Belousov L. The dynamic architecture of a developing organism: An interdisciplinary approach to the development of organisms. Dordrecht: Kluwer Academic Publishers, 1998.

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Adds, John. The organism and the environment. Walton-on-Thames: Nelson, 1997.

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Hodge, Russ. Developmental biology: From a cell to an organism. New York: Facts On File, 2010.

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Perturbing the organism: The biology of stressful experience. Chicago: University of Chicago Press, 1992.

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Ramellini, Pietro. Life and organisms. Vatican City: Libreria editrice Vaticana ; Pontifical Council for Culture, 2006.

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Book chapters on the topic "Organism in biology"

1

Adami, Christoph. "Digital Organism." In Encyclopedia of Systems Biology, 573. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1556.

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Leonelli, Sabina. "Model Organism." In Encyclopedia of Systems Biology, 1398–401. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_76.

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Mendoza, Eduardo. "Model Organism Databases." In Encyclopedia of Systems Biology, 1401–3. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_1054.

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Thomas-Vaslin, Véronique, Adrien Six, Bertrand Bellier, and David Klatzmann. "Organism State, Lymphocyte." In Encyclopedia of Systems Biology, 1611–12. New York, NY: Springer New York, 2013. http://dx.doi.org/10.1007/978-1-4419-9863-7_710.

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Agee, April, and David Carter. "Whole-Organism Screening: Plants." In Methods in Molecular Biology, 77–95. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-545-3_6.

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Macieira-Coelho, Alvaro. "Aging of the Mammalian Organism." In Biology of Aging, 61–128. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-18994-4_3.

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Barbato, Robyn A. "The Soil Habitat and Considerations for Synthetic Biology." In NATO Science for Peace and Security Series C: Environmental Security, 169–75. Dordrecht: Springer Netherlands, 2021. http://dx.doi.org/10.1007/978-94-024-2086-9_11.

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AbstractMicroorganisms serve as agents for synthetic biology. It certain instances, the technology is reliant on survival of the genetically-altered microorganism in the natural environment. This chapter offers insight into the soil system to improve the performance of genetically-altered microorganisms in the natural environment. This chapter covers the soil system, the fitness of genetically altered organisms, and considerations for their survival and proliferation in nature. This chapter does not discuss the ecological consequences of survival in the natural environment or the regulatory considerations to distribute a genetically-altered organism in the environment. In addition to regulatory approval, both considerations should be critically reviewed before a genetically-altered organism is distributed in the environment.
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Pollack, Gerald S., and Sumihare Noji. "History of Cricket Biology." In The Cricket as a Model Organism, 3–16. Tokyo: Springer Japan, 2017. http://dx.doi.org/10.1007/978-4-431-56478-2_1.

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Bozzaro, Salvatore. "The Model Organism Dictyostelium discoideum." In Methods in Molecular Biology, 17–37. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-302-2_2.

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Gomes, Laidson Paes, Catarina Gouveia e Silva, Jean-Charles Gaillard, Jean Armengaud, and Ana Varela Coelho. "Characterization of Soluble Cell-Free Coelomic Fluid Proteome from the Starfish Marthasterias glacialis." In Methods in Molecular Biology, 583–97. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2172-1_31.

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AbstractProteomics combined to advanced bioinformatics tools is acquiring a pivotal role in the comprehensive understanding of living organism’s biology, in particular for non-model organisms, which includes most marine and aquatic invertebrates. Depicting of protein composition in a whole organ/organism followed by their assembling in functional protein association networks promotes the understanding of key biological processes. Here, we provide a detailed description of the extraction procedure of cell-free coelomic fluid soluble proteins and the characterization of the proteome of the starfish Marthasterias glacialis. Due to coelomic fluid richness in glycoproteins, which complicates protein identification, extracts of soluble proteins are deglycosylated prior to tandem mass spectrometry. This experimental approach is useful at improving knowledge on the coelomic fluid physiological role and deciphering its involvement in regeneration of starfish body parts when comparing different regeneration conditions.
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Conference papers on the topic "Organism in biology"

1

Ishibashi, Shojiro, Hiroshi Yoshida, Dhugal J. Lindsay, Hiroyuki Yamamoto, Tadahiro Hyakudome, Takao Sawa, Hikaru Okuno, and Takayuki Uemura. "An Underwater Vehicle for the Tracking Marine Organism “PICASSO”." In ASME 2009 28th International Conference on Ocean, Offshore and Arctic Engineering. ASMEDC, 2009. http://dx.doi.org/10.1115/omae2009-80072.

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So far, a special net is used to sample marine organism such as planktons in the marine biology. It is called as a plankton-net. However it often breaks the tissue of the marine organism. So scientists of the marine biology demand a good tool to observe the marine organism instead of the plankton-net sampling. On the other hand, an underwater vehicle has been a focus of constant attention in order to observe the marine organism. The vehicle should be equipped with devices to observe the marine organism and measure the sea characteristic. So Japan Agency for Marine-Earth Science and Technology (JAMSTEC) has developed a new underwater vehicle “PICASSO”. It is small size vehicle, but it can be equipped with various observation and measurement devices. And also it can be applied to a small ship as its own support ship owing to its size. In this paper, the outline of PICASSO and its key technologies are described, and results of sea trials carried out until now are shown.
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Reutov, Valentin Palladievich, Elena Gennad’evna Sorokina, and Oleg Ivanovich Sukmansky. "GAS TRANSMITTER CYCLES IN THE MAMMAL ORGANISM." In International conference New technologies in medicine, biology, pharmacology and ecology (NT +M&Ec ' 2020). Institute of information technology, 2020. http://dx.doi.org/10.47501/978-5-6044060-0-7.22.

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The proposed concept of the cyclic organization of gas transmitters allows us to answer the question: how do living organisms provide regulation and stabilization of these physiologically active compounds involved in intracellular and intercellular signaling.
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"How heat stress drives the expression of LTR retrotransposons in the flatworm model organism Macrostomum lignano." In SYSTEMS BIOLOGY AND BIOINFORMATICS. Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 2019. http://dx.doi.org/10.18699/sbb-2019-41.

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Odor, Peter, Bence Kovács, Gergely Boros, Ferenc Samu, Réka Aszalós, Flóra Tinya, and Zoltan Elek. "Effects of forestry treatments on forest site conditions and the biodiversity of different organism groups." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107617.

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Sharma, Rachita, Patricia Evans, and Virendra Bhavsar. "Mapping Transcription Factors from a Model to a Non-model Organism." In 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing. IEEE, 2009. http://dx.doi.org/10.1109/ijcbs.2009.124.

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Dzhimak, Stepan S., Anna Elkina, and Alexandr A. Basov. "MECHANISMS OF FRACTIONATION OF STABLE ISOTOPES IN LIVING SYSTEMS." In NEW TECHNOLOGIES IN MEDICINE, BIOLOGY, PHARMACOLOGY AND ECOLOGY. Institute of information technology, 2021. http://dx.doi.org/10.47501/978-5-6044060-1-4.17.

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Some physical laws are considered that provide stable fractionation of isotopes, leading to the accumulation of certain isotopic forms in the intracellular and intercellular space with the manifestation of these effects at various levels of the organism. It is suggested that for a more complete understanding of the above processes, it is necessary to study the mechanism of exchange interaction between particles with integer spin (bosons) and half-integer spin (fermions).
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Qiu, Weiguo, Yiding Huang, Joseph Cappello, and Xiaoyi Wu. "Electrospun Recombinant Protein Polymer Nanofibers as a Biomaterial." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13131.

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Micro/nanometer protein fibers are fundamental building blocks of extra-/intracellular matrices, providing structural support, stability and protection to cells, tissue and organism [1]. Fabricating performance protein micro/nanofibers has been extensively pursued for a variety of biomedical application. In this study, silk-elastinlike protein (SELP) polymer will be electrospun into nanofibers as a biomaterial.
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Ashlock, Daniel, and Wendy Ashlock. "Simulation of the impact of retroviruses on genome organization of an artificial organism." In 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2009. http://dx.doi.org/10.1109/cibcb.2009.4925720.

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MUTO, AI, MASAHIRO HATTORI, and MINORU KANEHISA. "ANALYSIS OF COMMON SUBSTRUCTURES OF METABOLIC COMPOUNDS WITHIN THE DIFFERENT ORGANISM GROUPS." In Proceedings of the 7th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2007). IMPERIAL COLLEGE PRESS, 2007. http://dx.doi.org/10.1142/9781860949920_0029.

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McPherson, Jeffrey D., Ian R. Grosse, Sundar Krishnamurty, Jack C. Wileden, Elizabeth R. Dumont, and Michael A. Berthaume. "Integrating Biological and Engineering Ontologies." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-13527.

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As methods for engineering data acquisition improve, methods for storing, generating knowledge from, and sharing that data for efficient reuse have become more important. Knowledge management in the engineering community can greatly benefit from advancements made in knowledge management in biology. The biological community has already made progress in knowledge management through projects such as the Gene Ontology and CellML, and it behooves the engineering community to learn from their successes. Engineering and biology overlap in the field of biosimulation, (i.e. finite-element analysis of biological systems, see www.biomesh.org) which gives an opportunity to integrate successful ontologies from the biology community into the engineering community. Previous research has led to the creation of the Biomesh project, which is a collection of biological finite element (FE) models. These FE models relate to a particular anatomical structure of an organism, and to the set of biological material properties associated with the models. Thus, knowledge management for this application requires knowledge integration from three distinct fields: engineering (materials and models), anatomy, and biological classification. The existing e-Design Framework offers the Engineering Analysis Models ontology and Materials ontology to store knowledge about materials and FE models. Similarly, the existing Minimal Anatomical Terms ontology and the NCBI Organismal Classification taxonomy were used to store information about anatomy and biological classification, respectively. In this paper these ontologies are interlinked in a single, synergistic ontology to expose and integrate knowledge in a transparent manner between previously disparate domains. A case study is presented to demonstrate the usefulness of the approach in which knowledge from a biological material and FE model are methodically stored in the new ontology, and the organismal classification and anatomical structure of the model are immediately exposed to the user.
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Reports on the topic "Organism in biology"

1

Gupta, Shweta. The Revolution of Human Organoids in Cell Biology. Natur Library, October 2020. http://dx.doi.org/10.47496/nl.blog.12.

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Organoids are a new research tool derived from human pluripotent or adult stem cells or somatic cells in vitro to form small, self-organizing 3-dimensional structures that simulate many of the functions of native organs
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Hawkins, Brian T., and Sonia Grego. A Better, Faster Road From Biological Data to Human Health: A Systems Biology Approach for Engineered Cell Cultures. RTI Press, June 2017. http://dx.doi.org/10.3768/rtipress.2017.rb.0015.1706.

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Traditionally, the interactions of drugs and toxicants with human tissue have been investigated in a reductionist way—for example, by focusing on specific molecular targets and using single-cell-type cultures before testing compounds in whole organisms. More recently, “systems biology” approaches attempt to enhance the predictive value of in vitro biological data by adopting a comprehensive description of biological systems and using computational tools that are sophisticated enough to handle the complexity of these systems. However, the utility of computational models resulting from these efforts completely relies on the quality of the data used to construct them. Here, we propose that recent advances in the development of bioengineered, three-dimensional, multicellular constructs provide in vitro data of sufficient complexity and physiological relevance to be used in predictive systems biology models of human responses. Such predictive models are essential to maximally leveraging these emerging bioengineering technologies to improve both therapeutic development and toxicity risk assessment. This brief outlines the opportunities presented by emerging technologies and approaches for the acceleration of drug development and toxicity testing, as well as the challenges lying ahead for the field.
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Dickman, Martin B., and Oded Yarden. Genetic and chemical intervention in ROS signaling pathways affecting development and pathogenicity of Sclerotinia sclerotiorum. United States Department of Agriculture, July 2015. http://dx.doi.org/10.32747/2015.7699866.bard.

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Abstract: The long-term goals of our research are to understand the regulation of sclerotial development and pathogenicity in S. sclerotior11111. The focus in this project was on the elucidation of the signaling events and environmental cues involved in the regulation of these processes, utilizing and continuously developing tools our research groups have established and/or adapted for analysis of S. sclerotiorum, Our stated objectives: To take advantage of the recent conceptual (ROS/PPs signaling) and technical (amenability of S. sclerotiorumto manipulations coupled with chemical genomics and next generation sequencing) developments to address and extend our fundamental and potentially applicable knowledge of the following questions concerning the involvement of REDOX signaling and protein dephosphorylation in the regulation of hyphal/sclerotial development and pathogenicity of S. sclerotiorum: (i) How do defects in genes involved in ROS signaling affect S. sclerotiorumdevelopment and pathogenicity? (ii) In what manner do phosphotyrosinephosphatases affect S. sclerotiorumdevelopment and pathogenicity and how are they linked with ROS and other signaling pathways? And (iii) What is the nature of activity of newly identified compounds that affect S. sclerotiori,111 growth? What are the fungal targets and do they interfere with ROS signaling? We have met a significant portion of the specific goals set in our research project. Much of our work has been published. Briefly. we can summarize that: (a) Silencing of SsNox1(NADPHoxidase) expression indicated a central role for this enzyme in both virulence and pathogenic development, while inactivation of the SsNox2 gene resulted in limited sclerotial development, but the organism remained fully pathogenic. (b) A catalase gene (Scatl), whose expression was highly induced during host infection is involved in hyphal growth, branching, sclerotia formation and infection. (c) Protein tyrosine phosphatase l (ptpl) is required for sclerotial development and is involved in fungal infection. (d) Deletion of a superoxidedismutase gene (Sssodl) significantly reduced in virulence on both tomato and tobacco plants yet pathogenicity was mostly restored following supplementation with oxalate. (e) We have participated in comparative genome sequence analysis of S. sclerotiorumand B. cinerea. (f) S. sclerotiorumexhibits a potential switch between biotrophic and necrotrophic lifestyles (g) During plant­ microbe interactions cell death can occur in both resistant and susceptible events. Non­ pathogenic fungal mutants S. sclerotior111n also cause a cell death but with opposing results. We investigated PCD in more detail and showed that, although PCD occurs in both circumstances they exhibit distinctly different features. The mutants trigger a restricted cell death phenotype in the host that unexpectedly exhibits markers associated with the plant hypersensitive (resistant) response. Using electron and fluorescence microscopy, chemical effectors and reverse genetics, we have established that this restricted cell death is autophagic. Inhibition of autophagy rescued the non-pathogenic mutant phenotype. These findings indicate that autophagy is a defense response in this interaction Thus the control of cell death, dictated by the plant (autophagy) סr the fungus (apoptosis), is decisive to the outcome of certain plant­ microbe interactions. In addition to the time and efforts invested towards reaching the specific goals mentioned, both Pls have initiated utilizing (as stated as an objective in our proposal) state of the art RNA-seq tools in order to harness this technology for the study of S. sclerotiorum. The Pls have met twice (in Israel and in the US), in order to discuss .נחd coordinate the research efforts. This included a working visit at the US Pls laboratory for performing RNA-seq experiments and data analysis as well as working on a joint publication (now published). The work we have performed expands our understanding of the fundamental biology (developmental and pathogenic) of S. sclerotioז111וז. Furthermore, based on our results we have now reached the conclusion that this fungus is not a bona fide necrotroph, but can also display a biotrophic lifestyle at the early phases of infection. The data obtained can eventually serve .נ basis of rational intervention with the disease cycle of this pathogen.
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Shenker, Moshe, Paul R. Bloom, Abraham Shaviv, Adina Paytan, Barbara J. Cade-Menun, Yona Chen, and Jorge Tarchitzky. Fate of Phosphorus Originated from Treated Wastewater and Biosolids in Soils: Speciation, Transport, and Accumulation. United States Department of Agriculture, June 2011. http://dx.doi.org/10.32747/2011.7697103.bard.

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Beneficial use of reclaimed wastewater (RW) and biosolids (BS) in soils is accompanied by large input of sewage-originated P. Prolonged application may result in P accumulation up to levelsBeneficial use of reclaimed wastewater (RW) and biosolids (BS) in soils is accompanied by large input of sewage-originated P. Prolonged application may result in P accumulation up to levels that impair plant nutrition, increase P loss, and promote eutrophication in downstream waters. This study aims to shed light on the RW- and BS-P forms in soils and to follow the processes that determine P reactivity, solubility, availability, and loss in RW and BS treated soils. The Technion group used sequential P extraction combined with measuring stable oxygen isotopic composition in phosphate (δ18OP) and with 31P-NMR studies to probe P speciation and transformations in soils irrigated with RW or fresh water (FW). The application of the δ18OP method to probe inorganic P (Pi) speciation and transformations in soils was developed through collaboration between the Technion and the UCSC groups. The method was used to trace Pi in water-, NaHCO3-, NaOH-, and HCl- P fractions in a calcareous clay soil (Acre, Israel) irrigated with RW or FW. The δ18OP signature changes during a month of incubation indicated biogeochemical processes. The water soluble Pi (WSPi) was affected by enzymatic activity yielding isotopic equilibrium with the water molecules in the soil solution. Further it interacted rapidly with the NaHCO3-Pi. The more stable Pi pools also exhibited isotopic alterations in the first two weeks after P application, likely related to microbial activity. Isotopic depletion which could result from organic P (PO) mineralization was followed by enrichment which may result from biologic discrimination in the uptake. Similar transformations were observed in both soils although transformations related to biological activity were more pronounced in the soil treated with RW. Specific P compounds were identified by the Technion group, using solution-state 31P-NMR in wastewater and in soil P extracts from Acre soils irrigated by RW and FW. Few identified PO compounds (e.g., D-glucose-6-phosphate) indicated coupled transformations of P and C in the wastewater. The RW soil retained higher P content, mainly in the labile fractions, but lower labile PO, than the FW soil; this and the fact that P species in the various soil extracts of the RW soil appear independent of P species in the RW are attributed to enhanced biological activity and P recycling in the RW soil. Consistent with that, both soils retained very similar P species in the soil pools. The HUJ group tested P stabilization to maximize the environmental safe application rates and the agronomic beneficial use of BS. Sequential P extraction indicated that the most reactive BS-P forms: WSP, membrane-P, and NaHCO3-P, were effectively stabilized by ferrous sulfate (FeSul), calcium oxide (CaO), or aluminum sulfate (alum). After applying the stabilized BS, or fresh BS (FBS), FBS compost (BSC), or P fertilizer (KH2PO4) to an alluvial soil, P availability was probed during 100 days of incubation. A plant-based bioassay indicated that P availability followed the order KH2PO4 >> alum-BS > BSC ≥ FBS > CaO-BS >> FeSul-BS. The WSPi concentration in soil increased following FBS or BSC application, and P mineralization further increased it during incubation. In contrast, the chemically stabilized BS reduced WSPi concentrations relative to the untreated soil. It was concluded that the chemically stabilized BS effectively controlled WSPi in the soil while still supplying P to support plant growth. Using the sequential extraction procedure the persistence of P availability in BS treated soils was shown to be of a long-term nature. 15 years after the last BS application to MN soils that were annually amended for 20 years by heavy rates of BS, about 25% of the added BS-P was found in the labile fractions. The UMN group further probed soil-P speciation in these soils by bulk and micro X-ray absorption near edge structure (XANES). This newly developed method was shown to be a powerful tool for P speciation in soils. In a control soil (no BS added), 54% of the total P was PO and it was mostly identified as phytic acid; 15% was identified as brushite and 26% as strengite. A corn crop BS amended soil included mostly P-Fe-peat complex, variscite and Al-P-peat complex but no Ca-P while in a BS-grass soil octacalcium phosphate was identified and o-phosphorylethanolamine or phytic acid was shown to dominate the PO fraction that impair plant nutrition, increase P loss, and promote eutrophication in downstream waters. This study aims to shed light on the RW- and BS-P forms in soils and to follow the processes that determine P reactivity, solubility, availability, and loss in RW and BS treated soils. The Technion group used sequential P extraction combined with measuring stable oxygen isotopic composition in phosphate (δ18OP) and with 31P-NMR studies to probe P speciation and transformations in soils irrigated with RW or fresh water (FW). The application of the δ18OP method to probe inorganic P (Pi) speciation and transformations in soils was developed through collaboration between the Technion and the UCSC groups. The method was used to trace Pi in water-, NaHCO3-, NaOH-, and HCl- P fractions in a calcareous clay soil (Acre, Israel) irrigated with RW or FW. The δ18OP signature changes during a month of incubation indicated biogeochemical processes. The water soluble Pi (WSPi) was affected by enzymatic activity yielding isotopic equilibrium with the water molecules in the soil solution. Further it interacted rapidly with the NaHCO3-Pi. The more stable Pi pools also exhibited isotopic alterations in the first two weeks after P application, likely related to microbial activity. Isotopic depletion which could result from organic P (PO) mineralization was followed by enrichment which may result from biologic discrimination in the uptake. Similar transformations were observed in both soils although transformations related to biological activity were more pronounced in the soil treated with RW. Specific P compounds were identified by the Technion group, using solution-state 31P-NMR in wastewater and in soil P extracts from Acre soils irrigated by RW and FW. Few identified PO compounds (e.g., D-glucose-6-phosphate) indicated coupled transformations of P and C in the wastewater. The RW soil retained higher P content, mainly in the labile fractions, but lower labile PO, than the FW soil; this and the fact that P species in the various soil extracts of the RW soil appear independent of P species in the RW are attributed to enhanced biological activity and P recycling in the RW soil. Consistent with that, both soils retained very similar P species in the soil pools. The HUJ group tested P stabilization to maximize the environmental safe application rates and the agronomic beneficial use of BS. Sequential P extraction indicated that the most reactive BS-P forms: WSP, membrane-P, and NaHCO3-P, were effectively stabilized by ferrous sulfate (FeSul), calcium oxide (CaO), or aluminum sulfate (alum). After applying the stabilized BS, or fresh BS (FBS), FBS compost (BSC), or P fertilizer (KH2PO4) to an alluvial soil, P availability was probed during 100 days of incubation. A plant-based bioassay indicated that P availability followed the order KH2PO4 >> alum-BS > BSC ≥ FBS > CaO-BS >> FeSul-BS. The WSPi concentration in soil increased following FBS or BSC application, and P mineralization further increased it during incubation. In contrast, the chemically stabilized BS reduced WSPi concentrations relative to the untreated soil. It was concluded that the chemically stabilized BS effectively controlled WSPi in the soil while still supplying P to support plant growth. Using the sequential extraction procedure the persistence of P availability in BS treated soils was shown to be of a long-term nature. 15 years after the last BS application to MN soils that were annually amended for 20 years by heavy rates of BS, about 25% of the added BS-P was found in the labile fractions. The UMN group further probed soil-P speciation in these soils by bulk and micro X-ray absorption near edge structure (XANES). This newly developed method was shown to be a powerful tool for P speciation in soils. In a control soil (no BS added), 54% of the total P was PO and it was mostly identified as phytic acid; 15% was identified as brushite and 26% as strengite. A corn crop BS amended soil included mostly P-Fe-peat complex, variscite and Al-P-peat complex but no Ca-P while in a BS-grass soil octacalcium phosphate was identified and o-phosphorylethanolamine or phytic acid was shown to dominate the PO fraction.
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