Relevant bibliographies by topics / Molecular evolution

Academic literature on the topic 'Molecular evolution'

Author: Grafiati
Published: 4 June 2021
Last updated: 31 August 2024

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Journal articles on the topic "Molecular evolution"

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Del Cortona, Andrea, and Frederik Leliaert. "Molecular evolution and morphological diversification of ulvophytes (Chlorophyta)." Perspectives in Phycology 5, no. 1 (June 1, 2018): 27–43. http://dx.doi.org/10.1127/pip/2017/0075.

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Flook, Paul. "Molecular evolution." Journal of Evolutionary Biology 12, no. 3 (May 1999): 628–29. http://dx.doi.org/10.1046/j.1420-9101.1999.0072b.x.

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MacIntyre, Ross J. "Molecular Evolution." BioEssays 21, no. 3 (March 29, 1999): 265–66. http://dx.doi.org/10.1002/(sici)1521-1878(199903)21:3<265::aid-bies14>3.0.co;2-j.

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CLEGG, M. T. "Molecular Evolution: Molecular Evolutionary Genetics." Science 235, no. 4788 (January 30, 1987): 599. http://dx.doi.org/10.1126/science.235.4788.599.

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Trifonov, Edward N. "Early Molecular Evolution." Israel Journal of Ecology and Evolution 52, no. 3-4 (April 12, 2006): 375–87. http://dx.doi.org/10.1560/ijee_52_3-4_375.

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Four fundamentally novel, recent developments make a basis for the Theory of Early Molecular Evolution. The theory outlines the molecular events from the onset of the triplet code to the formation of the earliest sequence/structure/function modules of proteins. These developments are: (1) Reconstruction of the evolutionary chart of codons; (2) Discovery of omnipresent protein sequence motifs, apparently conserved since the last common ancestor; (3) Discovery of closed loops—standard structural modules of modern proteins; (4) Construction of protein sequence space of module size fragments, with far-reaching evolutionary implications. The theory generates numerous predictions, confirmed by massive nucleotide and protein sequence analyses, such as existence of two distinct classes of amino acids, and their periodical distribution along the sequences. The emerging picture of the earliest molecular evolutionary events is outlined: consecutive engagement of codons, formation of the earliest short peptides, and growth of the polypeptide chains to the size of loop closure, 25-30 residues.
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Joyce, Gerald F. "Directed Molecular Evolution." Scientific American 267, no. 6 (December 1992): 90–97. http://dx.doi.org/10.1038/scientificamerican1292-90.

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Kauffman, Stuart A. "Applied molecular evolution." Journal of Theoretical Biology 157, no. 1 (July 1992): 1–7. http://dx.doi.org/10.1016/s0022-5193(05)80753-2.

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Posada, David. "Cancer Molecular Evolution." Journal of Molecular Evolution 81, no. 3-4 (August 20, 2015): 81–83. http://dx.doi.org/10.1007/s00239-015-9695-7.

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Lin, Shu-Kun. "Molecular diversity evolution." Molecular Diversity 10, no. 1 (February 2006): 1. http://dx.doi.org/10.1007/s11030-006-5684-5.

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Easteal, Simon. "Disciplining molecular evolution." Trends in Ecology & Evolution 13, no. 8 (August 1998): 336. http://dx.doi.org/10.1016/s0169-5347(98)01404-9.

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Dissertations / Theses on the topic "Molecular evolution"

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Strain, Errol Alan. "Plant Molecular Evolution." NCSU, 2006. http://www.lib.ncsu.edu/theses/available/etd-04252006-234357/.

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The current dissertation looks at the molecular evolution of protein-coding genes in the flowering plant Arabidopsis thaliana and within two RNA viruses, humanimmunodeficiency virus (HIV) and Astroviridae. We analyzed members of the receptor-like kinase (RLK) gene family in Arabidopsis thaliana for positive selection. Likelihood analysis found evidence for positive selection in 12 of the 52 RLK family sequences groups. These 12 groups represent 97 of the 403 sequences analyzed. The majority of genes in groups subject to positive selection have not been functionally characterized, but sites under selection are predominantly located in the extracellular region. In HIV we use Akaike Information Criteria (AIC) based model averaging for models of nucleotide evolution to examine estimates of genetic distance and the ratio of transition/transversion (ts/tv). AIC weighted estimates of distance and ts/tv were shown to be robust relative to model assumptions. AIC weighted estimates of the ts/tv ratio in simulated HIV sequences generally had less variance than similar estimates made by selecting the single best scoring AIC model. Astroviruses are a leading cause of viral gastroenteritis in infants worldwide and little is known about the mechanisms of astrovirus-induced diarrhea or the virally encoded components responsible for disease. We report the genomic sequence of nine novel TAstV-2 isolates. Nucleotide and amino acid identities for the isolates were generally > 90% conserved. Phylogenies constructed using genomic RNA and the individual open reading frames (ORF) provide evidence for recombination and indicate differences in substitution rates between non-structural and structural genes. Analysis of the viral capsid genes using codon models of evolution indicate site-specific positive selection in both turkey and human astroviruses.
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Davidson, Colin John. "Molecular evolution of haemostasis." Thesis, Imperial College London, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368908.

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Venditti, Christopher D. "Speciation and molecular evolution." Thesis, University of Reading, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.493810.

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Speciation is fundamental to genetical evolution in being the process that separates reproductively isolated populations of genes into two or more independently replicating communities of genes. The theory of Punctuated Equilibrium and the Red Queen hypothesis are two enduring and controversial macro-evolutionary ideas proposed by palaeontologists from examination of the fossil record through time. One has implications for the nature of genetical evolution at speciation, the other for its timing.
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Mika, Katelyn Marie. "Molecular Evolution of Pregnancy." Thesis, The University of Chicago, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10817198.

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Unraveling the molecular etiology of a novel phenotype is still a major challenge. Mammalian pregnancy, a novel phenotype, preserves its stepwise evolution in extant species, which gives us additional tools to use to begin to unravel its evolution. Within this thesis, the evolution of three components of pregnancy are explored- the regulation of TAP2 expression, the regulation of HLA-F expression, and the possible role of transposable elements in rewiring the regulatory networks underlying major gene expression shifts at the maternal-fetal interface.

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Fontanillas, Eric. "Molecular evolution in Metazoa : causes and consequences of variation in rate of molecular evolution." Thesis, University of Sussex, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.506953.

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Vázquez, García Ignacio. "Molecular evolution of biological sequences." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284174.

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Evolution is an ubiquitous feature of living systems. The genetic composition of a population changes in response to the primary evolutionary forces: mutation, selection and genetic drift. Organisms undergoing rapid adaptation acquire multiple mutations that are physically linked in the genome, so their fates are mutually dependent and selection only acts on these loci in their entirety. This aspect has been largely overlooked in the study of asexual or somatic evolution and plays a major role in the evolution of bacterial and viral infections and cancer. In this thesis, we put forward a theoretical description for a minimal model of evolutionary dynamics to identify driver mutations, which carry a large positive fitness effect, among passenger mutations that hitchhike on successful genomes. We examine the effect this mode of selection has on genomic patterns of variation to infer the location of driver mutations and estimate their selection coefficient from time series of mutation frequencies. We then present a probabilistic model to reconstruct genotypically distinct lineages in mixed cell populations from DNA sequencing. This method uses Hidden Markov Models for the deconvolution of genetically diverse populations and can be applied to clonal admixtures of genomes in any asexual population, from evolving pathogens to the somatic evolution of cancer. To understand the effects of selection on rapidly adapting populations, we constructed sequence ensembles in a recombinant library of budding yeast (S. cerevisiae). Using DNA sequencing, we characterised the directed evolution of these populations under selective inhibition of rate-limiting steps of the cell cycle. We observed recurrent patterns of adaptive mutations and characterised common mutational processes, but the spectrum of mutations at the molecular level remained stochastic. Finally, we investigated the effect of genetic variation on the fate of new mutations, which gives rise to complex evolutionary dynamics. We demonstrate that the fitness variance of the population can set a selective threshold on new mutations, setting a limit to the efficiency of selection. In summary, we combined statistical analyses of genomic sequences, mathematical models of evolutionary dynamics and experiments in molecular evolution to advance our understanding of rapid adaptation. Our results open new avenues in our understanding of population dynamics that can be translated to a range of biological systems.
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Pedersen, Jakob Skou. "Structured models of molecular evolution." Connect to this title online (PDF format) Connect to this title online (PostScript format), 2004. http://birc.dk/Publications/Theses/jsp_phd_feb04.ps.

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Thesis (Ph. D.)--University of Aarhus, 2004.
Title from PDF title page (viewed on Jan 3, 2007). Includes articles and manuscripts co-authored with others. Includes bibliographical references. Also available in PostScript format.
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Klaere, Steffen. "Stochastic Models of Molecular Evolution." Diss., lmu, 2005. http://nbn-resolving.de/urn:nbn:de:bvb:19-39922.

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Barnett, Ross. "Molecular evolution of extinct fields." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.437376.

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Ho, Simon Yue-Wah. "Estimating rates of molecular evolution." Thesis, University of Oxford, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432279.

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Books on the topic "Molecular evolution"

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Ratner, Vadim A., Andrey A. Zharkikh, Nikolay Kolchanov, Sergey N. Rodin, Viktor V. Solovyov, and Andrey S. Antonov. Molecular Evolution. Berlin, Heidelberg: Springer Berlin Heidelberg, 1996. http://dx.doi.org/10.1007/978-3-662-12530-4.

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Li, Wen-Hsiung. Molecular evolution. Sunderland, Mass: Sinauer Associates, 1997.

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Aleksandrovich, Ratner Vadim, ed. Molecular evolution. Berlin: Springer, 1996.

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1953-, Graur Dan, ed. Fundamentals of molecular evolution. Sunderland, Mass: Sinauer Associates, 1991.

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Lewin, Roger. Patterns in evolution: The new molecular view. New York: Scientific American Library, 1996.

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Doyle, Jeff J., and Brandon S. Gaut, eds. Plant Molecular Evolution. Dordrecht: Springer Netherlands, 2000. http://dx.doi.org/10.1007/978-94-011-4221-2.

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J, Doyle Jeff, and Gaut Brandon S, eds. Plant molecular evolution. Dordrecht: Kluwer, 2000.

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Higgs, Paul G., and Teresa K. Attwood. Bioinformatics and Molecular Evolution. Malden, MA USA: Blackwell Publishing Ltd., 2004. http://dx.doi.org/10.1002/9781118697078.

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Wen-Hsiung, Li, ed. Fundamentals of molecular evolution. 2nd ed. Sunderland, Mass: Sinauer Associates, 2000.

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Dr, Cooper David N., and Kehrer-Sawatzki Hildegard, eds. Handbook of molecular evolution. Chichester, West Sussex: John Wiley & Sons, 2008.

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Book chapters on the topic "Molecular evolution"

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Dietrich, Michael R. "Molecular Evolution." In The Philosophy of Biology, 239–48. Dordrecht: Springer Netherlands, 2013. http://dx.doi.org/10.1007/978-94-007-6537-5_12.

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Urich, Klaus. "Molecular Evolution." In Comparative Animal Biochemistry, 111–83. Berlin, Heidelberg: Springer Berlin Heidelberg, 1994. http://dx.doi.org/10.1007/978-3-662-06303-3_4.

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Schuster, Peter. "Evolution, Molecular." In Encyclopedia of Astrobiology, 783–88. Berlin, Heidelberg: Springer Berlin Heidelberg, 2015. http://dx.doi.org/10.1007/978-3-662-44185-5_544.

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Schuster, Peter. "Evolution, Molecular." In Encyclopedia of Astrobiology, 526–30. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-11274-4_544.

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Padua, David, Amol Ghoting, John A. Gunnels, Mark S. Squillante, José Meseguer, James H. Cownie, Duncan Roweth, et al. "Molecular Evolution." In Encyclopedia of Parallel Computing, 1173. Boston, MA: Springer US, 2011. http://dx.doi.org/10.1007/978-0-387-09766-4_2421.

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Evans, Steven N. "Molecular Evolution." In Selected Works of Terry Speed, 441–70. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-1347-9_11.

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Tiwary, Basant K. "Molecular Evolution." In Bioinformatics and Computational Biology, 87–116. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-16-4241-8_6.

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Schuster, Peter. "Evolution, Molecular." In Encyclopedia of Astrobiology, 1–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-27833-4_544-3.

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Schuster, Peter. "Evolution, Molecular." In Encyclopedia of Astrobiology, 966–71. Berlin, Heidelberg: Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-65093-6_544.

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Modrow, Susanne, Dietrich Falke, Uwe Truyen, and Hermann Schätzl. "Viral Evolution." In Molecular Virology, 155–61. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-20718-1_12.

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Conference papers on the topic "Molecular evolution"

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Omer, Markovitch, and Lancet Doron. "Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology." In European Conference on Artificial Life 2013. MIT Press, 2013. http://dx.doi.org/10.7551/978-0-262-31709-2-ch020.

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Omer, Markovitch, and Lancet Doron. "Prebiotic Evolution of Molecular Assemblies: From Molecules to Ecology." In European Conference on Artificial Life 2013. MIT Press, 2013. http://dx.doi.org/10.1162/978-0-262-31709-2-ch020.

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VANYUSHIN, B. F. "EPIGENETICS AND EVOLUTION." In 5TH MOSCOW INTERNATIONAL CONFERENCE "MOLECULAR PHYLOGENETICSAND BIODIVERSITY BIOBANKING". TORUS PRESS, 2018. http://dx.doi.org/10.30826/molphy2018-11.

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YOUNG, JUDITH S. "MOLECULAR GAS IN GALAXIES IN THE LOCAL UNIVERSE." In Implications for Galaxy Formation and Evolution. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812811738_0005.

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"Computer-assisted analysis of caspases molecular evolution." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-095.

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"Computer-assisted analysis of caspases molecular evolution." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-370.

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Horibata, Yasuhiro, Keishi Sakaguchi, Nozomu Okino, and Makoto Ito. "MOLECULAR EVOLUTION AND POSSIBLE FUNCTION OF ENDOGLYCOCERAMIDASE." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.738.

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Bosak, Tanja, Kelsey R. Moore, Gregory P. Fournier, Lily Momper, and Cara Magnabosco. "CALIBRATING THE MOLECULAR RECORD OF CYANOBACTERIAL EVOLUTION." In GSA Annual Meeting in Seattle, Washington, USA - 2017. Geological Society of America, 2017. http://dx.doi.org/10.1130/abs/2017am-301789.

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Koohi-Moghadam, Mohamad, and Adel Torkaman Rahmani. "Molecular docking with opposition-based differential evolution." In the 27th Annual ACM Symposium. New York, New York, USA: ACM Press, 2012. http://dx.doi.org/10.1145/2245276.2231996.

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Sakai, Nami. "TOWARD UNDERSTANDING CHEMICAL EVOLUTION ALONG PROTOPLANETARY DISK FORMATION." In 74th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2019. http://dx.doi.org/10.15278/isms.2019.rg01.

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Reports on the topic "Molecular evolution"

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Jana, Arijit, Amoghavarsha Ramachandra Kini, and Thalappil Pradeep. Atomically Precise Clusters: Chemical Evolution of Molecular Matter at the Nanoscale. The Israel Chemical Society, March 2023. http://dx.doi.org/10.51167/acm00040.

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Foster, Michael S. Support for a Symposium on Molecular Approaches to Phylogeny, Evolution and Biogeography. Fort Belvoir, VA: Defense Technical Information Center, December 1992. http://dx.doi.org/10.21236/ada262112.

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Hill, Christian. International Atomic and Molecular Code Centres Network: Database Services for Radiation Damage in Nuclear Materials. IAEA Nuclear Data Section, January 2020. http://dx.doi.org/10.61092/iaea.agtk-r4gy.

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The International Code Centres Network (CCN) is a group of experts developing codes and models for atomic, molecular and plasma-surface interaction data relevant to fusion applications. Variable subsets of the group are brought together by the IAEA Atomic and Molecular Data (AMD) Unit in order to discuss computational and scientific issues associated with code developments. At the 6th Technical Meeting described in this report, 11 experts in the field of Molecular Dynamics (MD) simulations of radiation damage reviewed CascadesDB, a database of atomic configurations generated by MD simulations of collision cascades. This database is developed and hosted by the AMD Unit and provides a central repository for the results of MD simulations of the evolution of a material’s structure following an impact by a high energy particle. Further plans to extend and enhance CascadesDB, and to establish a new database resource, DefectDB, containing density functional theory calculations of defect structures were also discussed.
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Ullman, Diane, James Moyer, Benjamin Raccah, Abed Gera, Meir Klein, and Jacob Cohen. Tospoviruses Infecting Bulb Crops: Evolution, Diversity, Vector Specificity and Control. United States Department of Agriculture, September 2002. http://dx.doi.org/10.32747/2002.7695847.bard.

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Objectives. The overall goal of the proposed research was to develop a mechanistic understanding of tospovirus evolution, diversity and vector specificity that could be applied to development of novel methods for limiting virus establishment and spread. Our specific objectives were: 1) To characterize newly intercepted tospoviruses in onion, Hippeastrum and other bulb crops and compare them with the known tomato spotted wilt virus (TSWV) and its isolates; 2) To characterize intra- and interspecific variation in the virus transmission by thrips of the new and distinct tospoviruses. and, 3) To determine the basis of vector specificity using biological, cellular and molecular approaches. Background. New tospoviruses infecting bulb crops were detected in Israel and the US in the mid-90s. Their plant host ranges and relationships with thrips vectors showed they differed from the type member of the Tospovirus genus, tomato spotted wilt virus (TSWV). Outbreaks of these new viruses caused serious crop losses in both countries, and in agricultural and ornamental crops elsewhere. In the realm of plant infecting viruses, the tospoviruses (genus: Tospovirus , family: Bunyaviridae ) are among the most aggressive emerging viruses. Tospoviruses are transmitted by several species of thrips in a persistent, propagative fashion and the relationships between the viruses and their thrips vectors are often specific. With the emergence of new tospoviruses, new thrips vector/tospovirus relationships have also arisen and vector specificities have changed. There is known specificity between thrips vector species and particular tospoviruses, although the cellular and molecular bases for this specificity have been elusive. Major conclusions, solutions and achievements. We demonstrated that a new tospovirus, iris yellow spot virus (IYSV) caused "straw bleaching" in onion (Allium cepa) and lisianthus necrosis in lisianthus (Eustoma russellianum). Characterization of virus isolates revealed genetic diversity among US, Brazilian, Dutch and Israeli isolates. IYSV was not seed transmitted, and in Israel, was not located in bulbs of infected plants. In the US, infected plants were generated from infected bulbs. The relationship between IYSV and Thrips tabaci was shown to be specific. Frankliniella occidentalis, the primary vector of many other tospoviruses, did not transmit IYSV isolates in Israel or the US. Furthermore, 1': tabaci populations varied in their transmission ability. Transmission was correlated to IYSV presence in thrips salivary glands. In Israel, surveys in onion fields revealed that the onion thrips, Thrips tabaci Lindeman was the predominant species and that its incidence was strongly related to that of IYSV infection. In contrast, in the U.S., T. tabaci and F. occidentalis were present in high numbers during the times sampled. In Israel, insecticides reduced onion thrips population and caused a significant yield increase. In the US, a genetic marker system that differentiates non-thrips transmissible isolates from thrips transmissible isolate demonstrated the importance of the M RNA to thrips transmission of tospoviruses. In addition, a symbiotic Erwinia was discovered in thrips and was shown to cause significant artifacts in certain types of virus binding experiments. Implications, scientific and agricultural. Rapid emergence of distinct tospoviruses and new vector relationships is profoundly important to global agriculture. We advanced the understanding of IYSV in bulb crops and its relationships with thrips vector species. The knowledge gained provided growers with new strategies for control and new tools for studying the importance of particular viral proteins in thrips specificity and transmission efficiency.
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Hill, C. Summary Report of the 7th Biennial Technical Meeting of the Code Centres Network of the International Atomic and Molecular Code Centres Network: Database Services for Radiation Damage in Nuclear Materials. IAEA Nuclear Data Section, October 2021. http://dx.doi.org/10.61092/iaea.25ex-cn8n.

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The International Code Centres Network (CCN) is a group of experts developing codes and models for atomic, molecular and plasma-surface interaction data relevant to fusion applications. Variable subsets of the group are brought together by the IAEA Atomic and Molecular Data (AMD) Unit in order to discuss computational and scientific issues associated with code developments. At the 7th Technical Meeting described in this report, which was held virtually from 18 – 20 October 2021, 18 experts in the field of Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations of radiation damage reviewed the status of and proposed developments to the DefectDB and CascadesDB databases. These services, which are hosted by the AMD Unit, provide a central repository for the results of computational simulations of the evolution of a material’s structure following an impact by a high energy particle.
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Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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Izhar, Shamay, Maureen Hanson, and Nurit Firon. Expression of the Mitochondrial Locus Associated with Cytoplasmic Male Sterility in Petunia. United States Department of Agriculture, February 1996. http://dx.doi.org/10.32747/1996.7604933.bard.

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The main goal of the proposed research was to continue the mutual investigations into the molecular basis of CMS and male fertility restoration [MRF], with the ultimate goal of understanding these phenomena in higher plants. The experiments focused on: (1) dissecting apart the complex CMS - specific mitochondrial S-Pcf locus, in order to distinguish its essential parts which cause sterility from other parts and study its molecular evolution. (2) Studying the expression of the various regions of the S-Pcf locus in fertile and sterile lines and comparing the structure and ultrastructure of sterile and fertile tissues. (3) Determine whether alteration in respiration is genetically associated with CMS. Our mutual investigations further substantiated the association between the S-Pcf locus and CMS by the findings that the fertile phenotype of a population of unstable petunia somatic hybrids which contain the S-Pcf locus, is due to the presence of multiple muclear fertility restoration genes in this group of progenies. The information obtained by our studies indicate that homologous recombination played a major role in the molecular evolution of the S-Pcf locus and the CMS trait and in the generation of mitochondrial mutations in general. Our data suggest that the CMS cytoplasm evolved by introduction of a urs-s containing sublimon into the main mitochondrial genome via homologous recombination. We have also found that the first mutation detected so far in S-Pcf is a consequence of a homologous recombination mechanism involving part of the cox2 coding sequence. In all the cases studied by us, at the molecular level, we found that fusion of two different cells caused mitochondrial DNA recombination followed by sorting out of a specific mtDNA population or sequences. This sequence of events suggested as a mechanism for the generation of novel mitochondrial genomes and the creation of new traits. The present research also provides data concerning the expression of the recombined and complex CMS-specific S-Pcf locus as compared with the expression of additional mitochondrial proteins as well as comparative histological and ultrastructural studies of CMS and fertile Petunia. Evidence is provided for differential localization of mitochondrially encoded proteins in situ at the tissue level. The similar localization patterns of Pcf and atpA may indicate that Pcf product could interfere with the functioning of the mitochondrial ATPase in a tissue undergoing meiosis and microsporogenesis. Studies of respiration in CMS and fertile Petunia lines indicate that they differe in the partitioning of electron transport through the cytochrome oxidase and alternative oxidase pathways. The data indicate that the electron flux through the two oxidase pathways differs between mitochondria from fertile and sterile Petunia lines at certain redox states of the ubiquinone pool. In summary, extensive data concerning the CMS-specific S-Pcf locus of Petunia at the DNA and protein levels as well as information concerning different biochemical activity in CMS as compared to male fertile lines have been accumulated during the three years of this project. In addition, the involvement of the homologous recombination mechanism in the evolution of mt encoded traits is emphasized.
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8

Hulata, Gideon, Thomas D. Kocher, and Micha Ron. Elucidating the molecular pathway of sex determination in cultured Tilapias and use of genetic markers for creating monosex populations. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695855.bard.

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The objectives of this project were to: 1) Identify genetic markers linked to sex-determining genes in various experimental and commercial stocks of O. niloticusand O. aureus, as well as red tilapias; 2) Develop additional markers tightly linked to these sex determiners, and develop practical, non-destructive genetic tests for identifying genotypic sex in young tilapia; A third aim, to map sex modifier loci, was removed during budget negotiations at the start of the project. Background to the topic. A major obstacle to profitable farming of tilapia is the tendency of females to reproduce at a small size during the production cycle, diverting feed and other resources to a large population of small, unmarketable fish. Several approaches for producing all-male fingerlings have been tried, including interspecific hybridization, hormonal masculinization, and the use of YY-supermale broodstock. Each method has disadvantages that could be overcome with a better understanding of the genetic basis of sex determination in tilapia. The lack of sex-linked markers has been a major impediment in research and development of efficient monosex populations for tilapia culture. Major conclusions, solutions, achievements. We identified DNA markers linked to sex determining genes in six closely related species of tilapiine fishes. The mode of sex determination differed among species. In Oreochromis karongaeand Tilapia mariaethe sex-determining locus is on linkage group (LG) 3 and the female is heterogametic (WZ-ZZ system). In O. niloticusand T. zilliithe sex-determining locus is on LG1 and the male is heterogametic (XX-XY system). We have nearly identified the series of BAC clones that completely span the region. A more complex pattern was observed in O. aureus and O. mossambicus, in which markers on both LG1 and LG3 were associated with sex. We found evidence for sex-linked lethal effects on LG1, as well as interactions between loci in the two linkage groups. Comparison of genetic and physical maps demonstrated a broad region of recombination suppression harboring the sex-determining locus on LG3. We also mapped 29 genes that are considered putative regulators of sex determination. Amhand Dmrta2 mapped to separate QTL for sex determination on LG23. The other 27 genes mapped to various linkage groups, but none of them mapped to QTL for sex determination, so they were excluded as candidates for sex determination in these tilapia species. Implications, both scientific and agricultural. Phylogenetic analysis suggests that at least two transitions in the mode of sex determination have occurred in the evolution of tilapia species. This variation makes tilapias an excellent model system for studying the evolution of sex chromosomes in vertebrates. The genetic markers we have identified on LG1 in O. niloticusaccurately diagnose the phenotypic sex and are being used to develop monosex populations of tilapia, and eliminate the tedious steps of progeny testing to verify the genetic sex of broodstock animals.
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9

Eyal, Yoram, and Sheila McCormick. Molecular Mechanisms of Pollen-Pistil Interactions in Interspecific Crossing Barriers in the Tomato Family. United States Department of Agriculture, May 2000. http://dx.doi.org/10.32747/2000.7573076.bard.

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During the evolutionary process of speciation in plants, naturally occurring barriers to reproduction have developed that affect the transfer of genes within and between related species. These barriers can occur at several different levels beginning with pollination-barriers and ending with hybrid-breakdown. The interaction between pollen and pistils presents one of the major barriers to intra- and inter-specific crosses and is the focus of this research project. Our long-term goal in this research proposal was defined to resolve questions on recognition and communication during pollen-pistil interactions in the extended tomato family. In this context, this work was initiated and planned to study the potential involvement of tomato pollen-specific receptor-like kinases (RLK's) in the interaction between pollen and pistils. By special permission from BARD the objectives of this research were extended to include studies on pollen-pistil interactions and pollination barriers in horticultural crops with an emphasis on citrus. Functional characterization of 2 pollen-specific RLK's from tomato was carried out. The data shows that both encode functional kinases that were active as recombinant proteins. One of the kinases was shown to accumulate mainly after pollen germination and to be phosphorylated in-vitro in pollen membranes as well as in-vivo. The presence of style extract resulted in dephosphorylation of the RLK, although no species specificity was observed. This data implies a role for at least one RLK in pollination events following pollen germination. However, a transgenic plant analysis of the RLK's comprising overexpression, dominant-negative and anti-sense constructs failed to provide answers on their role in pollination. While genetic effects on some of the plants were observed in both the Israeli and American labs, no clear functional answers were obtained. An alternative approach to addressing function was pursued by screening for an artificial ligand for the receptor domain using a peptide phage display library. An enriched peptide sequence was obtained and will be used to design a peptide-ligand to be tested for its effect o pollen germination and tube growth. Self-incompatibility (SI) in citrus was studied on 3 varieties of pummelo. SI was observed using fluorescence microscopy in each of the 3 varieties and compatibility relations between varieties was determined. An initial screen for an S-RNase SI mechanism yielded only a cDNA homologous to the group of S-like RNases, suggesting that SI results from an as yet unknown mechanism. 2D gel electrophoresis was applied to compare pollen and style profiles of different compatibility groups. A "polymorphic" protein band from style extracts was observed, isolated and micro-sequenced. Degenerate primers designed based on the peptide sequence date will be used to isolate the relevant genes i order to study their potential involvement in SI. A study on SI in the apple cultivar Top red was initiated. SI was found, as previously shown, to be complete thus requiring a compatible pollinator variety. A new S-RNase allele was discovered fro Top red styles and was found to be highly homologous to pear S-RNases, suggesting that evolution of these genes pre-dated speciation into apples and pears but not to other Rosaceae species. The new allele provides molecular-genetic tools to determine potential pollinators for the variety Top red as well as a tool to break-down SI in this important variety.
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10

Iudicone, Daniele, and Marina Montresor. Omics community protocols. EuroSea, 2023. http://dx.doi.org/10.3289/eurosea_d3.19.

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The aim of the WP3 “Network Integration and Improvements” is to coordinate and enhance key aspects of integration of European observing technology (and related data flows) for its use in the context of international ocean monitoring activities. One of the dimensions of the integrations is the constitution of thematic networks, that is, networks whose aim is to address specific observational challenges and thus to favor innovation, innovation that will ultimately support the Blue economy. In this context, the specific aim of Task 3.8 is to accelerate the adoption of molecular methods such as genomic, transcriptomic (and related “omics”) approaches, currently used as monitoring tools in human health, to the assessment of the state and change of marine ecosystems. It was designed to favor the increase the capacity to evaluate biological diversity and the organismal metabolic states in different environmental conditions by the development of “augmented observatories”, utilizing state-of-art methodologies in genomic-enabled research at multidisciplinary observatories at well-established marine LTERs, with main focus on a mature oceanographic observatory in Naples, NEREA. In addition, an effort is dedicated to connecting existing observatories that intend to augment their observations with molecular tools. Molecular approaches come with many different options for the protocols (size fractioning, sample collection and storage, sequencing etc). One main challenge in systematically implementing those approaches is thus their standardization across observatories. Based on a survey of existing methods and on a 3-year experience in collecting, sequencing and analyzing molecular data, this deliverable is thus dedicated to present the SOPs implemented and tested at NEREA. The SOPs consider a size fractioning of the biological material to avoid biases toward more abundant, smaller organisms such as bacteria. They cover both the highly stable DNA and the less stable RNA and they are essentially an evolution of the ones developed for the highly successful Tara Oceans Expedition and recently updated for the Expedition Mission Microbiomes, an All-Atlantic expedition organised and executed by the EU AtlantECO project. Importantly, they have only slight variations with respect the ones adopted by the network of genomic observatories EMOBON. Discussions are ongoing with EMOBON to perfectly align the protocols. The SOPs are being disseminated via the main national and international networks. (EuroSea Deliverable, D3.19)
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