Relevant bibliographies by topics / Evolution (Biology)

Contents

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

Academic literature on the topic 'Evolution (Biology)'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 July 2024

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Journal articles on the topic "Evolution (Biology)"

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Tidon, Rosana. "Gene, organismo e ambiente." Genética na Escola 1, no. 2 (April 22, 2006): 40–44. http://dx.doi.org/10.55838/1980-3540.ge.2006.20.

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Em 1973, o geneticista Theodosius Dobzhansky publicou no periódico American Biology Teacher um texto com o seguinte título – Nothing in biology makes sense except in the light of evolution – (nada faz sentido em biologia a não ser sob a luz da evolução). Este artigo de Dobzhansky, desde a sua publicação, é um texto fundamental para as discussões sobre Biologia Evolutiva e tem se mostrado cada vez mais atualizado e verdadeiro face às novas e recentes pesquisas em várias áreas, principalmente nas da Biologia Molecular e Biologia do Desenvolvimento. [...]
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Machalek, Richard, and Michael W. Martin. "Evolution, Biology, and Society." Teaching Sociology 38, no. 1 (January 2010): 35–45. http://dx.doi.org/10.1177/0092055x09354078.

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Wallace, Bruce. "Biology, Evolution, and Philosophy." Journal of Heredity 80, no. 2 (March 1989): 169–70. http://dx.doi.org/10.1093/oxfordjournals.jhered.a110826.

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Morbeck, Mary Eilen. "Biology, behavior, and evolution." Reviews in Anthropology 20, no. 2 (December 1991): 113–23. http://dx.doi.org/10.1080/00988157.1991.9977997.

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Kelley, Lawrence, and Michael Scott. "The evolution of biology." EMBO reports 9, no. 12 (November 14, 2008): 1163–67. http://dx.doi.org/10.1038/embor.2008.212.

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Clark, James M. "Crocodilian Biology and Evolution." Journal of Paleontology 77, no. 3 (May 2003): 597. http://dx.doi.org/10.1666/0022-3360(2003)077<0597:r>2.0.co;2.

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Ornelas, Marya Y., Jason E. Cournoyer, Stanley Bram, and Angad P. Mehta. "Evolution and synthetic biology." Current Opinion in Microbiology 76 (December 2023): 102394. http://dx.doi.org/10.1016/j.mib.2023.102394.

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Halaczek, Bernard. "Evolution of theological views on evolution." Anthropological Review 60 (December 30, 1997): 4–12. http://dx.doi.org/10.18778/1898-6773.60.01.

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Biology-oriented theology and philosophy-oriented biology have been a matter of controversy in the studies of human origins. This controversy terminates at the point when they both recognise their peculiarity: biology is concerned with the “how” man came into existence and theology with “what” of the existence of man.
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Westerhoff, Hans V., and Bernhard O. Palsson. "The evolution of molecular biology into systems biology." Nature Biotechnology 22, no. 10 (October 2004): 1249–52. http://dx.doi.org/10.1038/nbt1020.

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LaRue, Elizabeth A., Jason Rohr, Jonathan Knott, Walter K. Dodds, Kyla M. Dahlin, James H. Thorp, Jeremy S. Johnson, et al. "The evolution of macrosystems biology." Frontiers in Ecology and the Environment 19, no. 1 (February 2021): 11–19. http://dx.doi.org/10.1002/fee.2288.

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Dissertations / Theses on the topic "Evolution (Biology)"

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Karlberg, Olof. "Mitochondrial Evolution : Turning Bugs into Features." Doctoral thesis, Uppsala University, Molecular Evolution, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-4216.

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The bacterial origin of mitochondria from an ancient endosymbiosis is now widely accepted and the mitochondrial ancestor is generally believed to belong to the bacterial subdivision α-proteobacteria. The high fraction of mitochondrial proteins encoded in the nucleus has commonly been explained with a massive transfer of genes from the genome of the ancestral mitochondrion.

The aim of this work was to get a better understanding of the mitochondrial origin and evolution by comparative genomics and phylogenetic analyses on mitochondria and α-proteobacteria. To this end, we sequenced the genomes of the intracellular parasites Bartonella henselae and Bartonella quintana, the causative agents of cat-scratch disease and trench fever, and compared them with other α-proteobacteria as well as mitochondrial eukaryotes.

Our results suggest that the adaptation to an intracellular life-style is coupled to an increased rate of genome degradation and a reduced ability to accommodate environmental changes. Reconstruction of the α-proteobacterial ancestor and phylogenetic analyses of the mitochondrial proteome in yeast revealed that only a small fraction of the proteins used for mitochondrial functions could be traced to the α-proteobacteria. Furthermore, a substantial fraction of the mitochondrial proteins was of eukaryotic origin and while most of the genes of the α-proteobacterial ancestor have been lost, many of those that have been transferred to the nuclear genome seem to encode non-mitochondrial proteins.

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Klasson, Lisa. "Genome Evolution in Maternally Inherited Insect Endosymbionts." Doctoral thesis, Uppsala University, Department of Evolution, Genomics and Systematics, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5885.

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Symbiosis is a widely common phenomenon in nature and has undoubtedly contributed to the evolution of all organisms on earth. Symbiotic associations can be of varying character, such as parasitic or mutualistic, but all imply a close relationship. To study the evolution of genomes of insect endosymbionts, we have sequenced the genomes of the mutualist Buchnera aphidicola from the aphid Schizaphis graminum (Sg) and the reproductive manipulator Wolbachia pipientis strain wRi from Drosophila simulans that show strikingly different evolutionary patterns.

The comparison between the genome of B.aphidicola (Sg) and the genome of B.aphidicola from the aphid Acyrthosiphon pisum (Ap), that are believed to have diverged 50 million years ago, revealed a perfect gene order conservation and loss of only 14 genes in either of the lineages. In contrast, the rate of nucleotide turnover is very fast probably due to relaxed selection and loss of DNA repair genes. The genomic stasis observed in Buchnera was attributed to the loss of repeats and of the gene recA.

In striking contrast to the genomes of B.aphidicola, a vast amount of repeats were found in the genome sequence of W.pipientis strain wMel. The comparison between the genomes of W.pipientis strain wRi and W.pipientis strain wMel shows that a lot of rearrangements have occurred since their divergence. The massive amount of repeats might stem from relaxed selection pressure but possibly also from selection to create variability via recombination.

Comparisons between pairs of genomes from closely related bacteria showed that the stability of gene order and content is connected to an intracellular lifestyle and indicated that homologous recombination between repeats is an important mechanisms for causing intrachromosomal rearrangements. Our studies show that the lifestyle of a bacterium to a great extent shapes the evolution of their genetic material and future capabilities to adapt to new environments.

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Jansson, Liselotte. "Evolution of signal form." Doctoral thesis, Stockholm : Zoologiska institutionen, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-189.

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Ranjard, Louis. "Computational biology of bird song evolution." e-Thesis University of Auckland, 2010. http://hdl.handle.net/2292/5719.

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Individuals of a given population share more behavioural traits with each other than with members of other populations. For example, in humans, traditions are specific to regions or countries. These cultural relationships can tell us about the history of the populations, their origin and the amount of exchange between them. In birds, regional dialects have been described in many species. However, the mechanisms with which dialects form in populations is not fully understood because it is difficult to analyse experimentally. Translocated populations, with their known histories, offer an opportunity to study these mechanisms. From the study of bird vocalisations we can make inferences regarding population structure and relationships as well as their history, individual behavioural state, neuronal and physiological mechanisms or development of neuronal learning. Too achieve this, cross-disciplinary approaches are necessary, combining field work, bioacoustic methods, statistical tools such as machine learning, ecological knowledge and phylogenetic methods. Here, I will describe computational methods for the treatment and classification of bird vocalisations and will use them to depict the relationships between bird populations. First, I discretise the data in order to define the cultural traits. Then phylogenetic tree-building methods are used. Two approaches are possible, first to map these traits onto known phylogenies and, second, to directly build the phylogeny of these traits. I describe the application of these methods to test several hypothesis on bird songs evolution related to both their history and the mechanisms with which they evolve. Evidence for the presence of dialects in the Puget Sound white-crowned sparrow (Zonotrichia leucophrys pugetensis) is provided on the basis of the syllable content of the songs. The absence of vocal sexual dimorphism is reported in the Australasian gannet (or takapu, Morus serrator), a member of the Sulidae family for which extensive sexual dimorphism has been reported in other species. Subsequently, convergence between the begging calls of several cuckoo species and their respective hosts is suggested by various bioacoustic methods. In addition, the male calls of the hihi (or stitchbird, Notiomystis cincta) is analysed in an island population. The corresponding pattern of variation suggests a post-dispersal acquisition of calls via learning which is in agreement with the most related species in the revised phylogeny of the hihi. Finally, the mechanisms of song evolution are depicted in translocated populations of tieke (or saddleback, Philesturnus carunculatus rufusater), resulting in the development of island dialects.
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Tam, Kwok-hin, and 談國軒. "Biology students' conceptions of evolution: aphenomenography." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2000. http://hub.hku.hk/bib/B31961940.

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Sjöstrand, Joel. "Reconciling gene family evolution and species evolution." Doctoral thesis, Stockholms universitet, Numerisk analys och datalogi (NADA), 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-93346.

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Species evolution can often be adequately described with a phylogenetic tree. Interestingly, this is the case also for the evolution of homologous genes; a gene in an ancestral species may – through gene duplication, gene loss, lateral gene transfer (LGT), and speciation events – give rise to a gene family distributed across contemporaneous species. However, molecular sequence evolution and genetic recombination make the history – the gene tree – non-trivial to reconstruct from present-day sequences. This history is of biological interest, e.g., for inferring potential functional equivalences of extant gene pairs. In this thesis, we present biologically sound probabilistic models for gene family evolution guided by species evolution – effectively yielding a gene-species tree reconciliation. Using Bayesian Markov-chain Monte Carlo (MCMC) inference techniques, we show that by taking advantage of the information provided by the species tree, our methods achieve more reliable gene tree estimates than traditional species tree-uninformed approaches. Specifically, we describe a comprehensive model that accounts for gene duplication, gene loss, a relaxed molecular clock, and sequence evolution, and we show that the method performs admirably on synthetic and biological data. Further-more, we present two expansions of the inference procedure, enabling it to pro-vide (i) refined gene tree estimates with timed duplications, and (ii) probabilistic orthology estimates – i.e., that the origin of a pair of extant genes is a speciation. Finally, we present a substantial development of the model to account also for LGT. A sophisticated algorithmic framework of dynamic programming and numerical methods for differential equations is used to resolve the computational hurdles that LGT brings about. We apply the method on two bacterial datasets where LGT is believed to be prominent, in order to estimate genome-wide LGT and duplication rates. We further show that traditional methods – in which gene trees are reconstructed and reconciled with the species tree in separate stages – are prone to yield inferior gene tree estimates that will overestimate the number of LGT events.
Arters evolution kan i många fall beskrivas med ett träd, vilket redan Darwins anteckningsböcker från HMS Beagle vittnar om. Detta gäller också homologa gener; en gen i en ancestral art kan – genom genduplikationer, genförluster, lateral gentransfer (LGT) och artbildningar – ge upphov till en genfamilj spridd över samtida arter. Att från sekvenser från nu levande arter rekonstruera genfamiljens framväxt – genträdet – är icke-trivialt på grund av genetisk rekombination och sekvensevolution. Genträdet är emellertid av biologiskt intresse, i synnerhet för att det möjliggör antaganden om funktionellt släktskap mellan nutida genpar. Denna avhandling behandlar biologiskt välgrundade sannolikhetsmodeller för genfamiljsevolution. Dessa modeller tar hjälp av artevolutionens starka inverkan på genfamiljens historia, och ger väsentligen upphov till en förlikning av genträd och artträd. Genom Bayesiansk inferens baserad på Markov-chain Monte Carlo (MCMC) visar vi att våra metoder presterar bättre genträdsskattningar än traditionella ansatser som inte tar artträdet i beaktning. Mer specifikt beskriver vi en modell som omfattar genduplikationer, genförluster, en relaxerad molekylär klocka, samt sekvensevolution, och visar att metoden ger högkvalitativa skattningar på både syntetiska och biologiska data. Vidare presenterar vi två utvidgningar av detta ramverk som möjliggör (i) genträdsskattningar med tidpunkter för duplikationer, samt (ii) probabilistiska ortologiskattningar – d.v.s. att två nutida gener härstammar från en artbildning. Slutligen presenterar vi en modell som inkluderar LGT utöver ovan nämnda mekanismer. De beräkningsmässiga svårigheter som LGT ger upphov till löses med ett intrikat ramverk av dynamisk programmering och numeriska metoder för differentialekvationer. Vi tillämpar metoden för att skatta LGT- och duplikationsraten hos två bakteriella dataset där LGT förmodas ha spelat en central roll. Vi visar också att traditionella metoder – där genträd skattas och förlikas med artträdet i separata steg – tenderar att ge sämre genträdsskattningar, och därmed överskatta antalet LGT-händelser.

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.

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Tam, Kwok-hin. "Biology students' conceptions of evolution : a phenomenography /." Hong Kong : University of Hong Kong, 2000. http://sunzi.lib.hku.hk/hkuto/record.jsp?B2226677X.

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Hearn, David John. "Growth form evolution in Adenia (Passifloraceae) and a model of the evolution of succulence." Diss., The University of Arizona, 2004. http://hdl.handle.net/10150/280706.

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The architecture of a plant is intimately tied to its fitness. Knowledge of the processes and patterns of growth form evolution can therefore contribute to a richer understanding of plant evolution. The genus Adenia (Passifloraceae) of ca. 100 species is an Old World lineage in which growth form radiated. I constructed a molecular phylogeny of the group, analyzed the stem and tuber anatomy of over half the species, and investigated patterns of growth form evolution in a phylogenetic context. I also described four new species and a new combination. Predictions based on evolutionary developmental models of growth form evolution were tested in Adenia, and one of them, the homeotic switch hypothesis, was tested throughout the eudicots. The switch hypothesis claims that the storage tissue of tubers and stems results from a common developmental origin. Phylogenetic analyses revealed that growth form transitions were frequent, and anatomical studies revealed traits that are associated with each growth form; moreover, traits are shared between tubers and succulent stems as predicted by the switch hypothesis. As expected, tuberous plants and succulents are also closely related across the eudicots. The switch hypothesis is substantiated in Adenia and the eudicots as a whole.
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Chung, Hattie. "Genome evolution in structured systems." Thesis, Harvard University, 2016. http://nrs.harvard.edu/urn-3:HUL.InstRepos:33493565.

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The evolution of a genome is shaped by spatial interactions at multiple scales. At the angstrom level, structural constraints on both RNA molecules and proteins contribute to the evolution of a gene sequence. Such optimized genes are weaved together in a particular order, out of a near-infinite number of combinations, to result in a genome. The fate of a genome is intricately linked to the evolutionary fate of its host organism; in turn, the fate of an organism is governed by where it resides in space. In this dissertation, I investigate how structure shapes the evolution of a gene, genome content, and pathogen populations residing in a diseased human lung. Chapter 1 provides a brief historical overview of population genetics in structured environments. I motivate why it is important to determine the migration rate of new alleles. Chapter 2 investigates how pathogens evolve within the structure of the cystic fibrosis lung. I find that migration rate and mutation rate are on similar timescales. Selection, rather than spatial isolation, maintains diversity within a pathogen population. Chapter 3 presents a new method to probe how codon choice is optimized throughout a gene. I find that codon choice is dictated by preference for particular RNA secondary structures, rather than intrinsic properties of a codon. Chapter 4 describes an ongoing study of how rapidly P. aeruginosa populations evolve in short-term infections. Preliminary results show that gene duplication events can sweep through a population in just 11 days. Chapter 5 introduces ideas for future directions. I pose questions regarding how pathogens evolve molecular mimicry that can trigger autoimmune disease in the human host, and how cancer-inducing inflammation might be detected from mutational signatures in the microbiome.
Systems Biology
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Tuch, Brian B. "Evolution of fungal transcription circuits." Diss., Search in ProQuest Dissertations & Theses. UC Only, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3297786.

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Books on the topic "Evolution (Biology)"

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Mark, Ridley, ed. Evolution. 2nd ed. Oxford: Oxford University Press, 2004.

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1964-, Pigliucci Massimo, ed. Encyclopedia of evolution. New York, N.Y: Checkmark Books, 2007.

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Sita, Lisa. Human biology and evolution. New York: Thomson Learning, 1995.

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Minelli, Alessandro, Geoffrey Boxshall, and Giuseppe Fusco, eds. Arthropod Biology and Evolution. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-662-45798-6.

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Minelli, Alessandro, Geoffrey Boxshall, and Giuseppe Fusco, eds. Arthropod Biology and Evolution. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-36160-9.

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C, Grigg Gordon, Seebacher Frank, Franklin Craig E, University of Queensland. Dept. of Zoology and Entomology., and Crocodilian Biology and Evolution, (1998 : University of Queensland), eds. Crocodilian biology and evolution. Chipping Norton, N.S.W: Surrey Beatty & Sons, 2001.

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K, Hecht Max, Wallace Bruce 1920-, and Prance Ghillean T. 1937-, eds. Evolutionary biology. New York: Plenum Press, 1988.

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Hecht, Max K., (Ed.), Wallace B, and MacIntyre Ross J, eds. Evolutionary Biology. New York: Plenum Press, 1991.

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Ricki, Lewis. Evolution of life. Dubuque, IA: Wm. C. Brown Publishers, 1992.

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Ruthmann, August. Sexualität und Evolution. Aachen: Shaker, 2004.

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Book chapters on the topic "Evolution (Biology)"

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Kilgour, O. F. G., and P. D. Riley. "Evolution." In Mastering Biology, 327–38. London: Macmillan Education UK, 1999. http://dx.doi.org/10.1007/978-1-349-14068-8_14.

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Kilgour, O. F. G. "Evolution." In Mastering Biology, 400–413. London: Macmillan Education UK, 1987. http://dx.doi.org/10.1007/978-1-349-09692-3_17.

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Ramsden, Jeremy. "Evolution." In Computational Biology, 29–39. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-030-45607-8_4.

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Minkoff, Eli C., and Jennifer K. Hood-DeGrenier. "Evolution." In Biology Trending, 145–84. Boca Raton: CRC Press, 2023. http://dx.doi.org/10.1201/9781003391159-5.

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Barbieri, Marcello. "Semantic Biology." In Codes and Evolution, 17–38. Cham: Springer Nature Switzerland, 2024. http://dx.doi.org/10.1007/978-3-031-58484-8_3.

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O’Neil, Michael, and Conor Ryan. "Lessons From Molecular Biology." In Grammatical Evolution, 23–32. Boston, MA: Springer US, 2003. http://dx.doi.org/10.1007/978-1-4615-0447-4_3.

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Bergson, Henri. "Critical Reception in Biology." In Creative Evolution, 330–68. London: Routledge, 2022. http://dx.doi.org/10.4324/9781315537818-9.

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Hart, Neil. "Marshall’s ‘Economic Biology’." In Equilibrium and Evolution, 43–70. London: Palgrave Macmillan UK, 2012. http://dx.doi.org/10.1057/9780230361171_3.

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Nehm, Ross H. "Evolution." In Teaching Biology in Schools, 164–77. New York : Routledge, 2018. | Series: Teaching and learning in science series: Routledge, 2018. http://dx.doi.org/10.4324/9781315110158-14.

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Martin, R. D. "Primate reproductive biology." In Primate Origins and Evolution, 427–75. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-0813-0_9.

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Conference papers on the topic "Evolution (Biology)"

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Price, Colin, Earle Williams, Ilin Nikolay, Evgeny Mareev, Marina Grinberg, Vladimir Sukhov, and Vladimir Vodeneev. "Lightning, Evolution and Biology." In XXXVth URSI General Assembly and Scientific Symposium. Gent, Belgium: URSI – International Union of Radio Science, 2023. http://dx.doi.org/10.46620/ursigass.2023.0303.tmyx7166.

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Lipps, Jere H., Allen G. Collins, and M. A. Fedonkin. "Evolution of biologic complexity: evidence from geology, paleontology, and molecular biology." In SPIE's International Symposium on Optical Science, Engineering, and Instrumentation, edited by Richard B. Hoover. SPIE, 1998. http://dx.doi.org/10.1117/12.319851.

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Bersini, H. "How artificial life relates to theoretical biology." In Origins of Life: Self-Organization and/or Biological Evolution? Les Ulis, France: EDP Sciences, 2009. http://dx.doi.org/10.1051/orvie/2009006.

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Xiao, Shu-guang. "Exclusive Firm Knowledge Innovation Based on Evolution Biology." In 2008 International Conference on Information Management, Innovation Management and Industrial Engineering (ICIII). IEEE, 2008. http://dx.doi.org/10.1109/iciii.2008.26.

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Zhao, Xiao-Qiang. "SPATIAL DYNAMICS OF SOME EVOLUTION SYSTEMS IN BIOLOGY." In The International Conference on Reaction-Diffusion System and Viscosity Solutions. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789812834744_0015.

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Chen, Yi, Li He Chai, Chun Yan Li, and Yun Xia Zhang. "Dynamic principle and simulation for evolution of biology." In 2010 Sixth International Conference on Natural Computation (ICNC). IEEE, 2010. http://dx.doi.org/10.1109/icnc.2010.5584769.

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Mišianiková, Anna, Andrea Lešková, Ján Guniš, Ľubomír Šnajder, Dominika Kotlárová, and Katarína Brinziková. "STEAM Teaching Evolution by Collaborating Biology and Informatics." In 2024 47th MIPRO ICT and Electronics Convention (MIPRO). IEEE, 2024. http://dx.doi.org/10.1109/mipro60963.2024.10569291.

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Карпин, Владимир Александрович, and Ольга Ивановна Шувалова. "THEORY OF BIOLOGICAL EVOLUTION: UNSOLVED PROBLEM OF THEORETICAL BIOLOGY." In Проблемы развития современной науки и пути их решения: сборник статей всероссийской научной конференции (Томск, Апрель 2023). Crossref, 2023. http://dx.doi.org/10.58351/230408.2023.72.90.004.

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Философский принцип развития является величайшим достижением диалектического материализма, позволившим освободить науку от метафизического догматизма. Этот принцип шаг за шагом развивался, достигнув уровня универсального (глобального) эволюционизма, и здесь не последнюю роль сыграли достижения в области биологической эволюции. Ни один биологический объект или процесс, ни одно биологическое обобщение не поддается глубокому рациональному научному объяснению без использования достижений эволюционного процесса. Актуальной задачей теоретической биологии является разработка современной теории биологической эволюции, отвечающей требованиям научного знания, которая, несмотря на многолетние усилия, остается по-прежнему незавершенной проблемой. The philosophical principle of development is the greatest achievement of dialectical materialism, which made it possible to liberate science from metaphysical dogmatism. This principle has been developing step by step, reaching the level of universal (global) evolutionism, and achievements in the field of biological evolution have played an important role here. No biological object or process, no biological generalization is amenable to a deep rational scientific explanation without using the achievements of the evolutionary process. An urgent task of theoretical biology is to develop a modern theory of biological evolution that meets the requirements of scientific knowledge, which, despite many years of efforts, remains an unfinished problem.
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BERWICK, ROBERT C. "INVARIANTS AND VARIATION IN BIOLOGY AND LANGUAGE EVOLUTION: EXTENDED ABSTRACT." In Proceedings of the 8th International Conference (EVOLANG8). WORLD SCIENTIFIC, 2010. http://dx.doi.org/10.1142/9789814295222_0005.

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Bolouri, H. "Mechanisms underlying the evolution of robust nonlinear control in biology." In Proceedings of the 1999 IEEE International Symposium on Intelligent Control Intelligent Systems and Semiotics (Cat. No.99CH37014). IEEE, 1999. http://dx.doi.org/10.1109/isic.1999.796695.

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Reports on the topic "Evolution (Biology)"

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Wu, Meiye. A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics. Office of Scientific and Technical Information (OSTI), September 2014. http://dx.doi.org/10.2172/1171568.

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Ohad, Nir, and Robert Fischer. Control of Fertilization-Independent Development by the FIE1 Gene. United States Department of Agriculture, August 2000. http://dx.doi.org/10.32747/2000.7575290.bard.

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A fundamental problem in biology is to understand how fertilization initiates reproductive development. During plant reproduction, one sperm cell fuses with the egg to form an embryo, whereas a second sperm cell fuses with the adjacent central cell nucleus to form the endosperm tissue that supports embryo and/or seedling development. To understand the mechanisms that initiate reproduction, we have isolated mutants of Arabidopsis that allow for replication of the central cell and subsequent endosperm development without fertilization. In this project we have cloned the MEA gene and showed that it encode a SET- domain polycomb protein. Such proteins are known to form chromatin-protein complexes that repress homeotic gene transcription and influence cell proliferation from Drosophylla to mammals. We propose a model whereby MEA and an additional polycomb protein we have cloned, FIE , function to suppress a critical aspect of early plant reproduction and endosperm development, until fertilization occurs. Using a molecular approach we were able to determine that FIE and MEA interact physically, suggesting that these proteins have been conserved also during the evolution of flowering plants. The analysis of MEA expression pattern revealed that it is an imprinted gene that displays parent-of- origin-dependent monoallelic expression specifically in the endosperm tissue. Silencing of the paternal MEA allele in the endosperm and the phenotype of mutant mea seeds support the parental conflict theory for the evolution of imprinting in plants and mammals. These results contribute new information on the initiation of endosperm development and provide a unique entry point to study asexual reproduction and apomixis which is expected to improve crop production.
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Mawassi, Munir, and Valerian Dolja. Role of RNA Silencing Suppression in the Pathogenicity and Host Specificity of the Grapevine Virus A. United States Department of Agriculture, January 2010. http://dx.doi.org/10.32747/2010.7592114.bard.

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RNA silencing is a defense mechanism that functions against virus infection and involves sequence-specific degradation of viral RNA. Diverse RNA and DNA viruses of plants encode RNA silencing suppressors (RSSs), which, in addition to their role in viral counterdefense, were implicated in the efficient accumulation of viral RNAs, virus transport, pathogenesis, and determination of the virus host range. Despite rapidly growing understanding of the mechanisms of RNA silencing suppression, systematic analysis of the roles played by diverse RSSs in virus biology and pathology is yet to be completed. Our research was aimed at conducting such analysis for two grapevine viruses, Grapevine virus A (GVA) and Grapevine leafroll-associated virus-2 (GLRaV- 2). Our major achievements on the previous cycle of BARD funding are as follows. 1. GVA and GLRaV-2 were engineered into efficient gene expression and silencing vectors for grapevine. The efficient techniques for grapevine infection resulting in systemic expression or silencing of the recombinant genes were developed. Therefore, GVA and GLRaV-2 were rendered into powerful tools of grapevine virology and functional genomics. 2. The GVA and GLRaV-2 RSSs, p10 and p24, respectively, were identified, and their roles in viral pathogenesis were determined. In particular, we found that p10 functions in suppression and pathogenesis are genetically separable. 3. We revealed that p10 is a self-interactive protein that is targeted to the nucleus. In contrast, p24 mechanism involves binding small interfering RNAs in the cytoplasm. We have also demonstrated that p10 is relatively weak, whereas p24 is extremely strong enhancer of the viral agroinfection. 4. We found that, in addition to the dedicated RSSs, GVA and GLRaV-2 counterdefenses involve ORF1 product and leader proteases, respectively. 5. We have teamed up with Dr. Koonin and Dr. Falnes groups to study the evolution and function of the AlkB domain presents in GVA and many other plant viruses. It was demonstrated that viral AlkBs are RNA-specific demethylases thus providing critical support for the biological relevance of the novel process of AlkB-mediated RNA repair.
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Burns, Malcom, and Gavin Nixon. Literature review on analytical methods for the detection of precision bred products. Food Standards Agency, September 2023. http://dx.doi.org/10.46756/sci.fsa.ney927.

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The Genetic Technology (Precision Breeding) Act (England) aims to develop a science-based process for the regulation and authorisation of precision bred organisms (PBOs). PBOs are created by genetic technologies but exhibit changes which could have occurred through traditional processes. This current review, commissioned by the Food Standards Agency (FSA), aims to clarify existing terminologies, explore viable methods for the detection, identification, and quantification of products of precision breeding techniques, address and identify potential solutions to the analytical challenges presented, and provide recommendations for working towards an infrastructure to support detection of precision bred products in the future. The review includes a summary of the terminology in relation to analytical approaches for detection of precision bred products. A harmonised set of terminology contributes towards promoting further understanding of the common terms used in genome editing. A review of the current state of the art of potential methods for the detection, identification and quantification of precision bred products in the UK, has been provided. Parallels are drawn with the evolution of synergistic analytical approaches for the detection of Genetically Modified Organisms (GMOs), where molecular biology techniques are used to detect DNA sequence changes in an organism’s genome. The scope and limitations of targeted and untargeted methods are summarised. Current scientific opinion supports that modern molecular biology techniques (i.e., quantitative real-time Polymerase Chain Reaction (qPCR), digital PCR (dPCR) and Next Generation Sequencing (NGS)) have the technical capability to detect small alterations in an organism’s genome, given specific prerequisites of a priori information on the DNA sequence of interest and of the associated flanking regions. These techniques also provide the best infra-structure for developing potential approaches for detection of PBOs. Should sufficient information be known regarding a sequence alteration and confidence can be attributed to this being specific to a PBO line, then detection, identification and quantification can potentially be achieved. Genome editing and new mutagenesis techniques are umbrella terms, incorporating a plethora of approaches with diverse modes of action and resultant mutational changes. Generalisations regarding techniques and methods for detection for all PBO products are not appropriate, and each genome edited product may have to be assessed on a case-by-case basis. The application of modern molecular biology techniques, in isolation and by targeting just a single alteration, are unlikely to provide unequivocal evidence to the source of that variation, be that as a result of precision breeding or as a result of traditional processes. In specific instances, detection and identification may be technically possible, if enough additional information is available in order to prove that a DNA sequence or sequences are unique to a specific genome edited line (e.g., following certain types of Site-Directed Nucelase-3 (SDN-3) based approaches). The scope, gaps, and limitations associated with traceability of PBO products were examined, to identify current and future challenges. Alongside these, recommendations were made to provide the infrastructure for working towards a toolkit for the design, development and implementation of analytical methods for detection of PBO products. Recognition is given that fully effective methods for PBO detection have yet to be realised, so these recommendations have been made as a tool for progressing the current state-of-the-art for research into such methods. Recommendations for the following five main challenges were identified. Firstly, PBOs submitted for authorisation should be assessed on a case-by-case basis in terms of the extent, type and number of genetic changes, to make an informed decision on the likelihood of a molecular biology method being developed for unequivocal identification of that specific PBO. The second recommendation is that a specialist review be conducted, potentially informed by UK and EU governmental departments, to monitor those PBOs destined for the authorisation process, and actively assess the extent of the genetic variability and mutations, to make an informed decision on the type and complexity of detection methods that need to be developed. This could be further informed as part of the authorisation process and augmented via a publicly available register or database. Thirdly, further specialist research and development, allied with laboratory-based evidence, is required to evaluate the potential of using a weight of evidence approach for the design and development of detection methods for PBOs. This concept centres on using other indicators, aside from the single mutation of interest, to increase the likelihood of providing a unique signature or footprint. This includes consideration of the genetic background, flanking regions, off-target mutations, potential CRISPR/Cas activity, feasibility of heritable epigenetic and epitranscriptomic changes, as well as supplementary material from supplier, origin, pedigree and other documentation. Fourthly, additional work is recommended, evaluating the extent/type/nature of the genetic changes, and assessing the feasibility of applying threshold limits associated with these genetic changes to make any distinction on how they may have occurred. Such a probabilistic approach, supported with bioinformatics, to determine the likelihood of particular changes occurring through genome editing or traditional processes, could facilitate rapid classification and pragmatic labelling of products and organisms containing specific mutations more readily. Finally, several scientific publications on detection of genome edited products have been based on theoretical principles. It is recommended to further qualify these using evidenced based practical experimental work in the laboratory environment. Additional challenges and recommendations regarding the design, development and implementation of potential detection methods were also identified. Modern molecular biology-based techniques, inclusive of qPCR, dPCR, and NGS, in combination with appropriate bioinformatics pipelines, continue to offer the best analytical potential for developing methods for detecting PBOs. dPCR and NGS may offer the best technical potential, but qPCR remains the most practicable option as it is embedded in most analytical laboratories. Traditional screening approaches, similar to those for conventional transgenic GMOs, cannot easily be used for PBOs due to the deficit in common control elements incorporated into the host genome. However, some limited screening may be appropriate for PBOs as part of a triage system, should a priori information be known regarding the sequences of interest. The current deficit of suitable methods to detect and identify PBOs precludes accurate PBO quantification. Development of suitable reference materials to aid in the traceability of PBOs remains an issue, particularly for those PBOs which house on- and off-target mutations which can segregate. Off-target mutations may provide an additional tool to augment methods for detection, but unless these exhibit complete genetic linkage to the sequence of interest, these can also segregate out in resulting generations. Further research should be conducted regarding the likelihood of multiple mutations segregating out in a PBO, to help inform the development of appropriate PBO reference materials, as well as the potential of using off-target mutations as an additional tool for PBO traceability. Whilst recognising the technical challenges of developing and maintaining pan-genomic databases, this report recommends that the UK continues to consider development of such a resource, either as a UK centric version, or ideally through engagement in parallel EU and international activities to better achieve harmonisation and shared responsibilities. Such databases would be an invaluable resource in the design of reliable detection methods, as well as for confirming that a mutation is as a result of genome editing. PBOs and their products show great potential within the agri-food sector, necessitating a science-based analytical framework to support UK legislation, business and consumers. Differentiating between PBOs generated through genome editing compared to organisms which exhibit the same mutational change through traditional processes remains analytically challenging, but a broad set of diagnostic technologies (e.g., qPCR, NGS, dPCR) coupled with pan-genomic databases and bioinformatics approaches may help contribute to filling this analytical gap, and support the safety, transparency, proportionality, traceability and consumer confidence associated with the UK food chain.
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Microbial Evolution: This report is based on a colloquium convened by the American Academy of Microbiology on August 28-30, 2009, in San Cristobal, Ecuador. American Society for Microbiology, August 2011. http://dx.doi.org/10.1128/aamcol.28aug.2009.

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The year 2009 marked both the 200th anniversary of Darwin's birth and the 150th anniversary of the publication of his landmark book, On the Origin of Species. In August 2009, to celebrate these milestones, the American Academy of Microbiology convened a colloquium in the Galapagos Islands, where Darwin made some of his most crucial observations, to consider a new question: what would Darwin have made of the microbial world? The ability to sail to remote sites like the Galapagos, and access to specimens collected by himself and other avid naturalists, gave Darwin the information he needed to develop a conceptual framework for understanding life's visible diversity. Today, new discoveries and technical capabilities in microbiology are providing information that for the first time makes it possible to develop a conceptual framework for deepening our understanding of the diversity of the microbial world. Darwin focused his attention on visible life forms, which actually make up only a small fraction of the living world—the invisible world of microorganisms was as yet largely unexplored in his time. Yet Darwin's theory has proven remarkably robust; despite some fundamental differences between microorganisms and the rest of the living world, the two lynchpins of Darwin's theory—descent with modification and natural selection—have proven as powerful in explaining microbial evolution as they have in explaining macrobial evolution. Since Darwin, the advent of Mendelian Genetics and the Modern Synthesis have provided a wealth of new tools to evolutionists; these tools are also of fundamental importance in the modern study of microbiology. The scientists gathered at the colloquium considered two fundamental questions: ▪ Is the balance of evolutionary mechanisms, for example natural selection or drift, or individual and group selection, consistent among microbes and similar between microbes and macrobes? ▪ How are the mode and tempo of microbial evolution influenced by Earth's diversity of environments, and the changing global environment, and how are microbes themselves driving these changes? The colloquium provided an opportunity for individuals with expertise in evolutionary biology, genetic engineering, mycology, virology, microbial ecology, and other fields to discuss these issues and review the areas in which research is needed to fill gaps in our understanding.
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Microbiology in the 21st Century: Where Are We and Where Are We Going? American Society for Microbiology, 2004. http://dx.doi.org/10.1128/aamcol.5sept.2003.

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The American Academy of Microbiology convened a colloquium September 5–7, 2003, in Charleston, South Carolina to discuss the central importance of microbes to life on earth, directions microbiology research will take in the 21st century, and ways to foster public literacy in this important field. Discussions centered on: the impact of microbes on the health of the planet and its inhabitants; the fundamental significance of microbiology to the study of all life forms; research challenges faced by microbiologists and the barriers to meeting those challenges; the need to integrate microbiology into school and university curricula; and public microbial literacy. This is an exciting time for microbiology. We are becoming increasingly aware that microbes are the basis of the biosphere. They are the ancestors of all living things and the support system for all other forms of life. Paradoxically, certain microbes pose a threat to human health and to the health of plants and animals. As the foundation of the biosphere and major determinants of human health, microbes claim a primary, fundamental role in life on earth. Hence, the study of microbes is pivotal to the study of all living things, and microbiology is essential for the study and understanding of all life on this planet. Microbiology research is changing rapidly. The field has been impacted by events that shape public perceptions of microbes, such as the emergence of globally significant diseases, threats of bioterrorism, increasing failure of formerly effective antibiotics and therapies to treat microbial diseases, and events that contaminate food on a large scale. Microbial research is taking advantage of the technological advancements that have opened new fields of inquiry, particularly in genomics. Basic areas of biological complexity, such as infectious diseases and the engineering of designer microbes for the benefit of society, are especially ripe areas for significant advancement. Overall, emphasis has increased in recent years on the evolution and ecology of microorganisms. Studies are focusing on the linkages between microbes and their phylogenetic origins and between microbes and their habitats. Increasingly, researchers are striving to join together the results of their work, moving to an integration of biological phenomena at all levels. While many areas of the microbiological sciences are ripe for exploration, microbiology must overcome a number of technological hurdles before it can fully accomplish its potential. We are at a unique time when the confluence of technological advances and the explosion of knowledge of microbial diversity will enable significant advances in microbiology, and in biology in general, over the next decade. To make the best progress, microbiology must reach across traditional departmental boundaries and integrate the expertise of scientists in other disciplines. Microbiologists are becoming increasingly aware of the need to harness the vast computing power available and apply it to better advantage in research. Current methods for curating research materials and data should be rethought and revamped. Finally, new facilities should be developed to house powerful research equipment and make it available, on a regional basis, to scientists who might otherwise lack access to the expensive tools of modern biology. It is not enough to accomplish cutting-edge research. We must also educate the children and college students of today, as they will be the researchers of tomorrow. Since microbiology provides exceptional teaching tools and is of pivotal importance to understanding biology, science education in schools should be refocused to include microbiology lessons and lab exercises. At the undergraduate level, a thorough knowledge of microbiology should be made a part of the core curriculum for life science majors. Since issues that deal with microbes have a direct bearing on the human condition, it is critical that the public-at-large become better grounded in the basics of microbiology. Public literacy campaigns must identify the issues to be conveyed and the best avenues for communicating those messages. Decision-makers at federal, state, local, and community levels should be made more aware of the ways that microbiology impacts human life and the ways school curricula could be improved to include valuable lessons in microbial science.
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