Relevant bibliographies by topics / Genetic adaptations

Academic literature on the topic 'Genetic adaptations'

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Published: 10 December 2022
Last updated: 28 January 2023

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Journal articles on the topic "Genetic adaptations"

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Provorov, Nikolay A., and Sergey V. Mylnikov. "Genetic mechanisms of individual and cooperative adaptations." Ecological genetics 5, no. 1 (March 15, 2007): 25–30. http://dx.doi.org/10.17816/ecogen5125-30.

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The purpose of the course "Genetic mechanisms of individual and cooperative adaptation" (12 semester 18 hours) - is to provide students with a broad view in population mechanisms of the different types of adaptation. The problem of the course consists in benchmark analysis of the ways and mechanisms of the origin of these adaptations, as well as in their possible macroevolution consequence. The individual adaptation is considered on model of stressful influence on populations. Cooperative adaptation is considered basically on model of symbiosis, whose formation associates with origin of new traits, which greatly increase evolution potential of biological species. The course develops the knowledge obtained from prerequisite courses, such as "General genetics" "Symbiogenetics", "General ecology" and "Theory of evolution".
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Scher, Steven J. "Are adaptations necessarily genetic?" American Psychologist 54, no. 6 (1999): 436–37. http://dx.doi.org/10.1037/0003-066x.54.6.436.

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Coombes, David, James W. B. Moir, Anthony M. Poole, Tim F. Cooper, and Renwick C. J. Dobson. "The fitness challenge of studying molecular adaptation." Biochemical Society Transactions 47, no. 5 (October 23, 2019): 1533–42. http://dx.doi.org/10.1042/bst20180626.

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Abstract Advances in bioinformatics and high-throughput genetic analysis increasingly allow us to predict the genetic basis of adaptive traits. These predictions can be tested and confirmed, but the molecular-level changes — i.e. the molecular adaptation — that link genetic differences to organism fitness remain generally unknown. In recent years, a series of studies have started to unpick the mechanisms of adaptation at the molecular level. In particular, this work has examined how changes in protein function, activity, and regulation cause improved organismal fitness. Key to addressing molecular adaptations is identifying systems and designing experiments that integrate changes in the genome, protein chemistry (molecular phenotype), and fitness. Knowledge of the molecular changes underpinning adaptations allow new insight into the constraints on, and repeatability of adaptations, and of the basis of non-additive interactions between adaptive mutations. Here we critically discuss a series of studies that examine the molecular-level adaptations that connect genetic changes and fitness.
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De Conti, Giulia, Matheus Henrique Dias, and René Bernards. "Fighting Drug Resistance through the Targeting of Drug-Tolerant Persister Cells." Cancers 13, no. 5 (March 5, 2021): 1118. http://dx.doi.org/10.3390/cancers13051118.

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Designing specific therapies for drug-resistant cancers is arguably the ultimate challenge in cancer therapy. While much emphasis has been put on the study of genetic alterations that give rise to drug resistance, much less is known about the non-genetic adaptation mechanisms that operate during the early stages of drug resistance development. Drug-tolerant persister cells have been suggested to be key players in this process. These cells are thought to have undergone non-genetic adaptations that enable survival in the presence of a drug, from which full-blown resistant cells may emerge. Such initial adaptations often involve engagement of stress response programs to maintain cancer cell viability. In this review, we discuss the nature of drug-tolerant cancer phenotypes, as well as the non-genetic adaptations involved. We also discuss how malignant cells employ homeostatic stress response pathways to mitigate the intrinsic costs of such adaptations. Lastly, we discuss which vulnerabilities are introduced by these adaptations and how these might be exploited therapeutically.
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Zahn, L. M. "Mapping genetic adaptations to pollution." Science 354, no. 6317 (December 8, 2016): 1245–46. http://dx.doi.org/10.1126/science.354.6317.1245-e.

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Shi, Hong, and Bing Su. "Molecular Adaptation of Modern Human Populations." International Journal of Evolutionary Biology 2011 (December 30, 2011): 1–8. http://dx.doi.org/10.4061/2011/484769.

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Modern humans have gone through varied processes of genetic adaptations when their ancestors left Africa about 100,000 years ago. The environmental stresses and the social transitions (e.g., emergence of the Neolithic culture) have been acting as the major selective forces reshaping the genetic make-up of human populations. Genetic adaptations have occurred in many aspects of human life, including the adaptation to cold climate and high-altitude hypoxia, the improved ability of defending infectious diseases, and the polished strategy of utilizing new diet with the advent of agriculture. At the same time, the adaptations once developed during evolution may sometimes generate deleterious effects (e.g., susceptibility to diseases) when facing new environmental and social changes. The molecular (especially the genome-wide screening of genetic variations) studies in recent years have detected many genetic variants that show signals of Darwinian positive selection in modern human populations, which will not only provide a better understanding of human evolutionary history, but also help dissecting the genetic basis of human complex diseases.
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Bahl, P. N., J. Kumar, and D. B. Raju. "Genetic Variations and Adaptations in Chickpea." Plant Breeding 106, no. 2 (February 1991): 164–67. http://dx.doi.org/10.1111/j.1439-0523.1991.tb00495.x.

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Birkeland, Siri, A. Lovisa S. Gustafsson, Anne K. Brysting, Christian Brochmann, and Michael D. Nowak. "Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae." Molecular Biology and Evolution 37, no. 7 (March 13, 2020): 2052–68. http://dx.doi.org/10.1093/molbev/msaa068.

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Abstract Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.
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DeLorenzo, Leah, Victoria DeBrock, Aldo Carmona Baez, Patrick Ciccotto, Erin Peterson, Clare Stull, Natalie Roberts, Reade Roberts, and Kara Powder. "Morphometric and Genetic Description of Trophic Adaptations in Cichlid Fishes." Biology 11, no. 8 (August 3, 2022): 1165. http://dx.doi.org/10.3390/biology11081165.

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Since Darwin, biologists have sought to understand the evolution and origins of phenotypic adaptations. The skull is particularly diverse due to intense natural selection on feeding biomechanics. We investigated the genetic and molecular origins of trophic adaptation using Lake Malawi cichlids, which have undergone an exemplary evolutionary radiation. We analyzed morphological differences in the lateral and ventral head shape among an insectivore that eats by suction feeding, an obligate biting herbivore, and their F2 hybrids. We identified variation in a series of morphological traits—including mandible width, mandible length, and buccal length—that directly affect feeding kinematics and function. Using quantitative trait loci (QTL) mapping, we found that many genes of small effects influence these craniofacial adaptations. Intervals for some traits were enriched in genes related to potassium transport and sensory systems, the latter suggesting co-evolution of feeding structures and sensory adaptations for foraging. Despite these indications of co-evolution of structures, morphological traits did not show covariation. Furthermore, phenotypes largely mapped to distinct genetic intervals, suggesting that a common genetic basis does not generate coordinated changes in shape. Together, these suggest that craniofacial traits are mostly inherited as separate modules, which confers a high potential for the evolution of morphological diversity. Though these traits are not restricted by genetic pleiotropy, functional demands of feeding and sensory structures likely introduce constraints on variation. In all, we provide insights into the quantitative genetic basis of trophic adaptation, identify mechanisms that influence the direction of morphological evolution, and provide molecular inroads to craniofacial variation.
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Neff, Bryan D., Shawn R. Garner, and Trevor E. Pitcher. "Conservation and enhancement of wild fish populations: preserving genetic quality versus genetic diversity 1This paper is derived from the J.C. Stevenson Memorial Lecture delivered by Bryan Neff at the Canadian Conference for Fisheries Research in Winnipeg, Manitoba, January 2010." Canadian Journal of Fisheries and Aquatic Sciences 68, no. 6 (June 2011): 1139–54. http://dx.doi.org/10.1139/f2011-029.

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Nearly 40% of commercial fisheries have now collapsed or are in serious decline. In response, governments have invested millions of dollars into artificial breeding programs, but many programs have failed to rehabilitate dwindling wild stocks. This failure may in part lie in the lack of knowledge about the genetic architecture of fitness: the genes and genotypes that are associated with individual performance. In this paper we discuss (i) artificial breeding programs, (ii) the genetic architecture of fitness, (iii) additive and nonadditive genetic effects on fitness, (iv) genetic diversity and evolvability, and (v) natural breeding and adaptation. We argue that most breeding programs do not maintain genetic adaptations and may consequently be ineffective at rehabilitating or enhancing wild populations. Moreover, there is no evidence that preserving genetic diversity as measured from neutral genetic markers increases fish performance or population viability outside of populations that experience strong inbreeding depression, and limited data that genetic diversity increases the potential for populations to adapt to changing environments. We suggest that artificial breeding programs should be used only as a last resort when populations face imminent extirpation and that such programs must shift the focus from solely preserving genetic diversity to preserving genetic adaptations.
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Dissertations / Theses on the topic "Genetic adaptations"

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Haram, Per Magnus. "Genetic vs. Aquired fitness: Metabolic, Vascular and Cardiomyocyte Adaptations." Doctoral thesis, Norwegian University of Science and Technology, Department of Circulation and Medical Imaging, 2006. http://urn.kb.se/resolve?urn=urn:nbn:no:ntnu:diva-1921.

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Al, Naqi Asmaa. "Dynamic and fault tolerant three-dimensional cellular genetic algorithms." Thesis, University of Edinburgh, 2012. http://hdl.handle.net/1842/7715.

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In the area of artificial intelligence, the development of Evolutionary Algorithms (EAs) has been very active, especially in the last decade. These algorithms started to evolve when scientists from various regions of the world applied the principles of evolution to algorithmic search and problem solving. EAs have been utilised successfully in diverse complex application areas. Their success in tackling hard problems has been the engine of the field of Evolutionary Computation (EC). Nowadays, EAs are considered to be the best solution to use when facing a hard search or optimisation problem. Various improvements are continually being made with the design of new operators, hybrid models, among others. A very important example of such improvements is the use of parallel models of GAs (PGAs). PGAs have received widespread attention from various researchers as they have proved to be more effective than panmictic GAs, especially in terms of efficacy and speedup. This thesis focuses on, and investigates, cellular Genetic Algorithms (cGAs)-a competitive variant of parallel GAs. In a cGA, the tentative solutions evolve in overlapped neighbourhoods, allowing smooth diffusion of the solutions. The benefits derived from using cGAs come not only from flexibility gains and their fitness to the objective target in combination with a robust behaviour but also from their high performance and amenability to implementation using advanced custom silicon chip technologies. Nowadays, cGAs are considered as adaptable concepts for solving problems, especially complex optimisation problems. Due to their structural characteristics, cGAs are able to promote an adequate exploration/exploitation trade-off and thus maintain genetic diversity. Moreover, cGAs are characterised as being massively parallel and easy to implement. The structural characteristics inherited in a cGA provide an active area for investigation. Because of the vital role grid structure plays in determining the effectiveness of the algorithm, cellular dimensionality is the main issue to be investigated here. The implementation of cGAs is commonly carried out on a one- or two-dimensional structure. Studies that investigate higher cellular dimensions are lacking. Accordingly, this research focuses on cGAs that are implemented on a three-dimensional structure. Having a structure with three dimensions, specifically a cubic structure, facilitates faster spreading of solutions due to the shorter radius and denser neighbourhood that result from the vertical expansion of cells. In this thesis, a comparative study of cellular dimensionality is conducted. Simulation results demonstrate higher performance achieved by 3D-cGAs over their 2D-cGAs counterparts. The direct implementation of 3D-cGAs on the new advanced 3D-IC technology will provide added benefits such as higher performance combined with a reduction in interconnection delays, routing length, and power consumption. The maintenance of system reliability and availability is a major concern that must be addressed. A system is likely to fail due to either hard or soft errors. Therefore, detecting a fault before it deteriorates system performance is a crucial issue. Single Event Upsets (SEUs), or soft errors, do not cause permanent damage to system functionality, and can be handled using fault-tolerant techniques. Existing fault-tolerant techniques include hardware or software fault tolerance, or a combination of both. In this thesis, fault-tolerant techniques that mitigate SEUs at the algorithmic level are explored and the inherent abilities of cGAs to deal with these errors are investigated. A fault-tolerant technique and several mitigation techniques are also proposed, and faulty critical data are evaluated critical fault scenarios (stuck at ‘1’ and stuck at ‘0’ faults) are taken into consideration. Chief among several test and real world problems is the problem of determining the attitude of a vehicle using a Global Positioning System (GPS), which is an example of hard real-time application. Results illustrate the ability of cGAs to maintain their functionality and give an adequate performance even with the existence of up to 40% errors in fitness score cells. The final aspect investigated in this thesis is the dynamic characteristic of cGAs. cGAs, and EAs in general, are known to be stochastic search techniques. Hence, adaptive systems are required to continue to perform effectively in a changing environment, particularly when tackling real-world problems. The adaptation in cellular engines is mainly achieved through dynamic balancing between exploration and exploitation. This area has received considerable attention from researchers who focus on improving the algorithmic performance without incurring additional computational effort. The structural properties and the genetic operations provide ways to control selection pressure and, as a result, the exploration/exploitation trade-off. In this thesis, the genetic operations of cGAs, particularly the selection aspect and their influence on the search process, are investigated in order to dynamically control the exploration/exploitation trade-off. Two adaptive-dynamic techniques that use genetic diversity and convergence speeds to guide the search are proposed. Results obtained by evaluating the proposed approaches on a test bench of diverse-characteristic real-world and test problems showed improvement in dynamic cGAs performance over their static counterparts and other dynamic cGAs. For example, the proposed Diversity-Guided 3D-cGA outperformed all the other dynamic cGAs evaluated by obtaining a higher search success rate that reached to 55%.
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Rittershaus, Emily S. C. "Identification of Essential Metabolic and Genetic Adaptations to the Quiescent State in Mycobacterium Tuberculosis: A Dissertation." eScholarship@UMMS, 2012. http://escholarship.umassmed.edu/gsbs_diss/876.

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Mycobacterium tuberculosis stably adapts to respiratory limited environments by entering into a nongrowing but metabolically active state termed quiescence. This state is inherently tolerant to antibiotics due to a reduction in growth and activity of associated biosynthetic pathways. Understanding the physiology of the quiescent state, therefore, may be useful in developing new strategies to improve drug efficiency. Here, we used an established in vitro model of respiratory stress, hypoxia, to induce quiescence. We utilized metabolomic and genetic approaches to identify essential and active pathways associated with nongrowth. Our metabolomic profile of hypoxic M. tuberculosis revealed an increase in several free fatty acids, metabolite intermediates in the oxidative pathway of the tricarboxylic acid (TCA) cycle, as well as, the important chemical messenger, cAMP. In tandem, a high-throughput transposon mutant library screen (TnSeq) revealed that a cAMP-regulated protein acetyltransferase, MtPat, was conditionally essential for survival in the hypoxic state. Via 13C-carbon flux tracing we show an MtPat mutant is deficient in re-routing hypoxic metabolism away from the oxidative TCA cycle and that MtPat is involved in inhibiting fatty-acid catabolism in hypoxia. Additionally, we show that reductive TCA metabolism is required for survival of hypoxia by depletion of an essential TCA enzyme, malate dehydrogenase (Mdh) both in in vitro hypoxia and in vivo mouse infection. Inhibition of Mdh with a novel compound resulted in a significantly greater killing efficiency than the first-line anti-M. tuberculosis drug isoniazid (INH). In conclusion, we show that understanding the physiology of the quiescent state can lead to new drug targets for M. tuberculosis.
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Rittershaus, Emily S. C. "Identification of Essential Metabolic and Genetic Adaptations to the Quiescent State in Mycobacterium Tuberculosis: A Dissertation." eScholarship@UMMS, 2016. https://escholarship.umassmed.edu/gsbs_diss/876.

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Mycobacterium tuberculosis stably adapts to respiratory limited environments by entering into a nongrowing but metabolically active state termed quiescence. This state is inherently tolerant to antibiotics due to a reduction in growth and activity of associated biosynthetic pathways. Understanding the physiology of the quiescent state, therefore, may be useful in developing new strategies to improve drug efficiency. Here, we used an established in vitro model of respiratory stress, hypoxia, to induce quiescence. We utilized metabolomic and genetic approaches to identify essential and active pathways associated with nongrowth. Our metabolomic profile of hypoxic M. tuberculosis revealed an increase in several free fatty acids, metabolite intermediates in the oxidative pathway of the tricarboxylic acid (TCA) cycle, as well as, the important chemical messenger, cAMP. In tandem, a high-throughput transposon mutant library screen (TnSeq) revealed that a cAMP-regulated protein acetyltransferase, MtPat, was conditionally essential for survival in the hypoxic state. Via 13C-carbon flux tracing we show an MtPat mutant is deficient in re-routing hypoxic metabolism away from the oxidative TCA cycle and that MtPat is involved in inhibiting fatty-acid catabolism in hypoxia. Additionally, we show that reductive TCA metabolism is required for survival of hypoxia by depletion of an essential TCA enzyme, malate dehydrogenase (Mdh) both in in vitro hypoxia and in vivo mouse infection. Inhibition of Mdh with a novel compound resulted in a significantly greater killing efficiency than the first-line anti-M. tuberculosis drug isoniazid (INH). In conclusion, we show that understanding the physiology of the quiescent state can lead to new drug targets for M. tuberculosis.
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Griffin, Jennifer E. "A Global Analysis of the Adaptations Required for Sterol Catabolism in Mycobacterium Tuberculosis: A Dissertation." eScholarship@UMMS, 2011. https://escholarship.umassmed.edu/gsbs_diss/571.

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Systems biology approaches have allowed for comprehensive understanding of complicated biological processes. Here, we’ve developed a global phenotypic profiling method by improving upon transposon mutagenesis methods for identifying genes required for bacterial growth in various conditions. By using the massively parallel power of Illumina sequencing, we precisely redefined the genes required for the growth of Mycobacterium Tuberculosis (Mtb) in vitro. This adapted technique provided more informative data with both increased dynamic range and resolution. As a result, we quantitatively assessed the fitness of individual mutants, as well as identified sub-genic essentiality. Mtb is well adapted to its nutrient-limiting intracellular niche. One important and novel adaptation is its ability to consume cholesterol for both energy and carbon. A combination of this genome-wide phenotypic analysis and global metabolite profiling was used to define the dedicated cholesterol catabolic pathway, as well as important transcriptional and metabolic adaptations required for the consumption of this carbon source. We identified the methylcitrate cycle (MCC) and an unexpected gluconeogenic route as essential pathways. Furthermore, we found that the cholesterol-dependent transcriptional induction of these metabolic enzymes was also essential for growth on this substrate, a function mediated by the Rv1129c regulatory protein. Using a combination of genetic and chemical methods to inhibit these pathways, we show that cholesterol represents a significant source of carbon during intracellular growth in macrophages. Finally, we have begun to define the mechanism by which lipids, such as cholesterol, are imported into the cell by investigating the assembly of the ABC-like lipid transporter, Mce1. The subunits of this system are localized to the cell wall and data is provided to support a novel mechanism for Mce-dependent import of lipids, such as cholesterol. In sum, this global analysis of host cholesterol utilization during infection provides insight into each step of this complicated process; import into the bacterial cell, the degradation of the molecule into primary metabolites, and the transformation of these metabolites into carbon and energy.
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Salser, Mark Alexander. "Genetic differentiation, local life history adaptations, and geographic distribution in subspecies of the grasshopper Melanoplus sanguinipes in California /." For electronic version search Digital dissertations database. Restricted to UC campuses. Access is free to UC campus dissertations, 2003. http://uclibs.org/PID/11984.

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Gardon, Olivier. "Role of the Mu opioid receptor in addiction : searching for transcriptional adaptations in the extended amygdala and designing new genetic models." Strasbourg, 2010. http://www.theses.fr/2010STRA6283.

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L’addiction est une pathologie mentale chronique caractérisée par une recherche et une prise compulsive de drogue malgré la perception de conséquences physiques et psychologiques négatives. L’amygdale étendue (EA) est une entité neuroanatomique impliquée dans les réponses comportementales au stress et à l’anxiété et est placée à l’interface des circuits du stress et de la récompense. Les neuroadaptations se produisant dans l’EA durant la consommation chronique de drogue sont impliquées dans l’émergence d’un état émotionnel négatif apparaissant et se développant avec le sevrage. Les modifications se déroulant dans l’AE sont susceptibles d’être impliquées dans les phénomènes de recherche compulsive de drogue et dans la rechute. Les récepteurs aux opioïdes mu font partie du système opioïde endogène et leur activation est cruciale pour la médiation des effets récompensants des drogues. Dans la première partie de cette thèse, nous avons étudié les variations du niveau d’expression des gènes mu-dépendants au niveau de l’EA après un traitement chronique à l’alcool. Nous avons vérifié si l’expression des gènes régulés par l’activation chronique du récepteur mu était également régulée par l’exposition chronique à des drogues non opiacées. Les régulations observées suggèrent que le développement de l’addiction à l’alcool est accompagné d’un remodelage des épines dendritiques et d’une modification de l’activité neuronale dans l’EA. Dans la seconde partie de cette thèse, nous avons créé et caractérisé de nouveaux modèles génétiques qui seront utiles pour améliorer notre compréhension concernant le rôle joué par le récepteur aux opioïdes mu dans l’expression des conduites addictives
Addiction is a chronic relapsing disorder characterized by compulsive drug-seeking and drug-taking despite negative consequences. The extended amygdala (EA) is a neuroanatomical entity that interfaces brain reward and stress systems and that is involved in behavioral responses related to stress and anxiety. Neuroadaptations within this neural circuit during chronic drug of abuse consumption are involved in the emergence of the negative emotional state that appears with drug withdrawal and that increases with the development of addiction. Therefore modifications occurring within this structure are likely involved in molecular mechanisms underlying drug craving and relapse. Mu opioid receptors are part of the endogenous opioid system and its activation was shown to be crucial for the reinforcing and addictive properties of opiate as well as other drugs of abuse. The first aim of this thesis project was to study variations occurring in the expression of mu opioid receptor-dependent genes in the EA following alcohol exposure. We investigated whether the expression of genes whose transcription is modulated by the chronic activation of mu opioid receptor in the EA is also regulated by chronic treatments using non opiate drugs of abuse. The observed transcriptional regulations suggest that the development of alcohol addiction is accompanied with dendritic spine remodeling and modifications in neuronal activity in the EA. The second aim of this thesis work consisted in the generation and characterization of novel murine genetic models that would be useful to expand our understanding on mu opioid receptor implication in addictive behaviors
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Rogell, Björn. "Genetic variation and local adaptation in peripheral populations of toads." Uppsala : Acta Universitatis Upsaliensis, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-107395.

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Key, Felix-Michael. "Human Adaptation in the Light of Ancient and Modern Genomes." Doctoral thesis, Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-204412.

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Modern humans originated in Africa around 200,000 years ago and today have settled in nearly every corner of earth. During migrations humans became exposed to new pathogens, food sources and have encountered vastly different environments. Natural selection likely contributed to the survival under such diverse conditions by promoting the raise in frequency of advantageous alleles. Thereby natural selection leaves genetic footprints that we can identify. The thesis at hand is about understanding how natural selection has shaped different human populations by analyzing these genetic footprints. In the first study, I infer the evolutionary history of an insertion-substitution variant using present-day human genomic data. This variant is interesting because the ancestral allele encodes a previously unannotated open-reading frame for a gene with antiviral ac- tivity (IFNL4 ), while the derived allele truncates this open-reading frame and is strongly associated with improved clearance of Hepatitis C, a major health care problem. Using an approximate bayesian computation approach I infer a complex evolutionary history, where the derived, truncating allele evolved under weak positive selection in Africa, with selection strength increasing in non-African populations, especially in East Asian popu- lations where the truncating allele is nearly fixed today. Hence, the changes in selection and resulting population differences in allele frequency contribute to the variation in Hep- atitis C clearance observed across human populations today. In the second study, I use ancient human genomes to estimate genome-wide allele frequencies in the past to understand present-day population differentiation. I develop a new statistic and incorporate the genome of Ust’-Ishim, a modern human that lived 45,000 year ago in Siberia, to study to what extent natural selection and drift have contributed to human population differentiation. The results suggest that European populations carry high frequency alleles in protein-coding (genic) regions that evolved under strong, recent positive selection. Further, the genic alleles that rose in frequency recently in Europeans were already present in ancient hunter-gatherers more often than in ancient farmers. This suggests that during the colonization of Europe local, positive selection changed the frequency of advantageous alleles in hunter-gatherer populations prior to the influx of farming individuals and those alleles remained beneficial also in the later admixed populations.
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Delava, Émilie. "Impacts du réchauffement climatique sur la distribution géographique des insectes et mise en place des adaptations locales : cas d'un parasitoïde de drosophiles dans le sud-est de la France." Thesis, Lyon 1, 2013. http://www.theses.fr/2013LYO10315.

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Prédire les réponses de la biodiversité aux changements climatiques anthropiques est devenu un champ de recherche avec des enjeux scientifiques et sociétaux majeurs. Mon travail de thèse a consisté à évaluer les impacts du réchauffement climatique sur un parasitoïde de drosophiles, Leptopilina boulardi, à une petite échelle géographique, le sud-est de la France. L'objectif était non seulement d'examiner l'évolution de la distribution du parasitoïde en réponse à une hausse des températures qu'il fallait préciser à cette échelle géographique, mais aussi d'appréhender les adaptations mises en place dans la zone de progression de l'espèce. Dans un premier temps, l'analyse de données d'échantillonnages et de données météorologiques m'ont permis de mettre en évidence une rapide expansion de l'aire de répartition du parasitoïde vers le nord, à un taux moyen de 90km/décennie, simultanément à une augmentation moyenne de la température de 1,57°C ces 30 dernières années, dans l'aire d'étude. Après avoir identifié les principaux facteurs environnementaux, structurant la répartition spatiale de L. boulardi, j'ai modélisé sa distribution potentielle dans le sud-est de la France, sous conditions climatiques actuelles et pour 2050, pour deux scénarios d'émission de CO2. En 2050, la distribution géographique de L. boulardi devrait considérablement s'étendre vers le nord sous l'effet des changements climatiques. Ensuite, en mesurant plusieurs traits d'histoire de vie selon 4 régimes thermiques fluctuants, j'ai montré que les populations de L. boulardi situées en limite d'aire de répartition sont génétiquement différenciées de celles situées dans l'aire centrale de répartition. Le fait que les populations marginales aient une valeur sélective plus importante à faible température suggère une adaptation locale des parasitoïdes dans la zone de progression de l'aire de répartition. La dernière partie de ce travail de thèse a pour objectif de mieux comprendre le processus de colonisation de L. boulardi. Pour cela, j'ai entrepris le développement de marqueurs RAD-sequencing sur 15 populations de cette espèce, distribuées le long d'un cline de latitude dans le sud-est de la France. Les nombreuses données issues du séquençage Illumina me permettront de connaître la structuration génétique de ces populations. L'ensemble de ces résultats obtenus au cours de ma thèse révèlent la force avec laquelle les changements climatiques peuvent impacter les espèces, principalement celles de haut niveau trophique, en provoquant des changements très rapide de distribution et des modifications génotypiques et phénotypiques permettant une meilleure adaptation locale
Predicting biodiversity responses to anthropogenic climate change has become a field of research with major scientific and societal issues. The main goal of my thesis was to evaluate the impacts of global warming on a Drosophila parasitoid, Leptopilina boulardi, at a small geographical scale, the South-East of France. The aim was not only to examine the change in the distribution of the parasitoid in response to rising temperatures, but also to understand the adaptations associated with this change. First, the analysis of insect sampling and meteorological data allowed me to demonstrate a rapid expansion of the parasitoid range to the north with an average rate of 90km/decade as well as a simultaneous temperature increase of 1.57°C on average over the past 30 years in the studied area. Following the identification of the main environmental factors structuring the spatial distribution of L. boulardi, I fitted a model predicting its potential distribution in the south-east of France, under the current climate and in 2050, for two CO2 emission scenarios. In 2050, the geographical distribution of L. boulardi should significantly extend northward as a result of climate change. Then, by measuring several life history traits under four fluctuating temperature regimes, I have shown that populations of L. boulardi located on the border of the range are genetically differentiated from those in the central range. The fact that marginal populations have a greater fitness at low temperature suggests local adaptation of parasitoids in the area of progression of range. The last part of this thesis aimed to better understand the process of colonization of L. boulardi. For this, I undertook the development of RAD-sequencing markers to genotype 15 populations of this species distributed along a cline of latitude in the southeast of France. Numerous data from Illumina sequencing will allow me to characterize the genetic structure of the populations. All the results obtained in my thesis highlight the force with which climate change may impact species, in particular those of high trophic level, causing rapid changes in distribution along with genotypic and phenotypic changes underlying local adaptation
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Books on the topic "Genetic adaptations"

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Foundation, Ciba, ed. Characterizing human psycholocial adaptations. Chichester: Wiley, 1997.

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Johanknecht, Susan. The transgenic tale of Lily Goat Gruff. London: Gefn Press, 2000.

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Mauricio, Rodney, ed. Genetics of Adaptation. Dordrecht: Springer Netherlands, 2005. http://dx.doi.org/10.1007/1-4020-3836-4.

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Rodney, Mauricio, ed. Genetics of adaptation. Dordrecht: Springer, 2005.

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L, Mahoney Conner, and Springer Douglas A, eds. Genetic diversity. Hauppauge, NY: Nova Science Publishers, 2009.

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McKnight, Jim. Straight science?: Homosexuality, evolution and adaptation. London: Routledge, 1997.

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Mopper, Susan, and Sharon Y. Strauss, eds. Genetic Structure and Local Adaptation in Natural Insect Populations. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4757-0902-5.

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Sivasankar, Shoba, Noel Ellis, Ljupcho Jankuloski, and Ivan Ingelbrecht, eds. Mutation breeding, genetic diversity and crop adaptation to climate change. Wallingford: CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0000.

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Abstract This book presents reviews on the application of the technology for crop improvement towards food and nutrition security, and research status on mutation breeding and associated biotechnologies in both seed crops and vegetatively propagated crops. It also presents perspectives on the significance of next-generation sequencing and bioinformatics in determining the molecular variants underlying mutations and on emerging biotechnologies such as gene editing. Reviews and articles are organized into five sections in the publication: (1) Contribution of Crop Mutant Varieties to Food Security; (2) Mutation Breeding in Crop Improvement and Climate-Change Adaptation; (3) Mutation Induction Techniques for Enhanced Genetic Variation; (4) Mutation Breeding in Vegetatively Propagated and Ornamental Crops; and (5) Induced Genetic Variation for Crop Improvement in the Genomic Era. The contents of this volume present excellent reference material for researchers, students and policy makers involved in the application of induced genetic variation in plants for the maintenance of biodiversity and the acceleration of crop adaptation to climate change to feed a growing global population in the coming years and decades.
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1955-, Rose Michael R., and Lauder George V, eds. Adaptation. San Diego: Academic Press, 1996.

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Adaptation. New York: Little, Brown Books for Young Readers, 2012.

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Book chapters on the topic "Genetic adaptations"

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Sharma, Hitaishi, Shampa Ghosh, and Jitendra Kumar Sinha. "Physiological Adaptation: Genetic and Environmental Adaptations." In Encyclopedia of Sexual Psychology and Behavior, 1–6. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-08956-5_173-1.

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Gibson, John P. "Livestock Genetic Resources: Preserving Genetic Adaptations for Future Use." In Adaptation and Fitness in Animal Populations, 229–32. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-1-4020-9005-9_15.

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Wisløff, Ulrik, Per Magnus Haram, and Ole Johan Kemi. "Genetic Vs. Acquired Fitness: Cardiomyocyte Adaptations." In Role of Physical Exercise in Preventing Disease and Improving the Quality of Life, 61–81. Milano: Springer Milan, 2007. http://dx.doi.org/10.1007/978-88-470-0376-7_4.

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Shepard, Roger N. "The Genetic Basis of Human Scientific Knowledge." In Ciba Foundation Symposium 208 - Characterizing Human Psychological Adaptations, 23–38. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470515372.ch3.

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Chapin, F. Stuart. "Adaptations and physiological responses of wild plants to nutrient stress." In Genetic Aspects of Plant Mineral Nutrition, 15–25. Dordrecht: Springer Netherlands, 1987. http://dx.doi.org/10.1007/978-94-009-3581-5_2.

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Levings, C. D. "Requirements for Genetic Data on Adaptations to Environment and Habitats of Salmonids." In Genetic Conservation of Salmonid Fishes, 49–66. Boston, MA: Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2866-1_4.

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Kumar, Pankaj, Ajay Kumar Thakur, and Dinesh Kumar Srivastava. "Genetic Engineering Approaches for Abiotic Stress Tolerance in Broccoli: Recent Progress." In Metabolic Adaptations in Plants During Abiotic Stress, 361–68. Boca Raton, FL : CRC Press, Taylor & Francis Group, 2018.: CRC Press, 2018. http://dx.doi.org/10.1201/b22206-30.

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Maranville, Jerry W., and S. Madhavan. "Physiological adaptations for nitrogen use efficiency in sorghum." In Food Security in Nutrient-Stressed Environments: Exploiting Plants’ Genetic Capabilities, 81–90. Dordrecht: Springer Netherlands, 2002. http://dx.doi.org/10.1007/978-94-017-1570-6_10.

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Gangestad, Steven W. "Evolutionary Psychology and Genetic Variation: Non-Adaptive, Fitness-Related and Adaptive." In Ciba Foundation Symposium 208 - Characterizing Human Psychological Adaptations, 212–30. Chichester, UK: John Wiley & Sons, Ltd., 2007. http://dx.doi.org/10.1002/9780470515372.ch12.

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Satya, Pratik, Suman Roy, Laxmi Sharma, Soham Ray, Amit Bera, and Srinjoy Ghosh. "Mining Genetic Resources for Plant Traits Suited to Changing Climatic Conditions." In Conservation Agriculture and Climate Change Impacts and Adaptations, 385–404. London: CRC Press, 2022. http://dx.doi.org/10.1201/9781003364665-30.

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Conference papers on the topic "Genetic adaptations"

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Ozcivici, Engin, and Stefan Judex. "Genetic Determinants of Musculoskeletal Adaptations to Unloading and Reloading." In 2019 9th International Conference on Recent Advances in Space Technologies (RAST). IEEE, 2019. http://dx.doi.org/10.1109/rast.2019.8767426.

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Sultana, Sharmin, Md Sad Salabi Sawrav, Md Bokhtiar Rahma, Md Shohorab Hossain, and Md Azizul Haque. "Isolation and Biochemical Characterization of Xylanase Enzyme Producing Bacteria from Goat Rumen." In International Conference on Emerging Trends in Engineering and Advanced Science. AIJR Publisher, 2022. http://dx.doi.org/10.21467/proceedings.123.1.

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The rumen microbial communities of ruminants are thought to be the most promising biochemical source of inordinately diversified and multi-functional cellulolytic enzymes with unique functional adaptations to improve biotechnological processes. The exploitation of rumen microbial genetic variety has been limited due to a lack of effective screening culture techniques and a lack of understanding of the rumen microbial genetic diversity. This study is conducted to isolate and characterize rumen bacteria from goat rumen that have capability to produce xylanase enzyme. Serial dilutions technique is applied to isolate bacteria from goat rumen and repeated tubing of the selectively enriched microbial cultures by using the specific media for rumen bacteria. Following that, all of the isolates were underwent Methyl Red (MR) test & Voges-Proskauer (VP) test to identify organisms metabolic pathway, Triple Sugar Iron Agar (TSI) Test to determine bacterial ability to utilize sugar, Motility Indole and Urease activity test (MIU) to determine motility, Urease utilization and can produce Indole or not, Citrate utilization test to utilize citrate as carbon and energy source, Oxidase test, Catalase test to check the presence of catalytic enzyme where all isolates found promising which indicates that all five isolates are superior and capable to produce xylanase.
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Jiao, Yibo, and Dragan Djurdjanovic. "Allocation of Flexible Tooling for Optimal Stochastic Multistation Manufacturing Process Quality Control." In ASME 2008 International Manufacturing Science and Engineering Conference collocated with the 3rd JSME/ASME International Conference on Materials and Processing. ASMEDC, 2008. http://dx.doi.org/10.1115/msec_icmp2008-72443.

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Stream of Variance (SoV) modeling of multi-station manufacturing process has been studied for the past 15 years and was used for identification of root causes of manufacturing errors, characterization and optimal allocation of measurements in multi-station manufacturing processes, process-oriented tolerance allocation, and most recently, for optimal in-process adaptations of programmable, flexible tooling (flexible fixtures, CNC machines) for autonomous minimization of errors in dimensional product quality. However, due to the high cost of flexible tooling, it is plausible to strategically position such devices across a manufacturing system in a way that one’s ability to mitigate quality problems is maximized. In this paper, a distributed stochastic feed-forward control method is devised which gives the optimal (in least square sense) reduction of the variance-covariance matrix of errors in dimensional workpiece quality in a multi-station manufacturing process with a limited number of flexible tooling components. Genetic Algorithm is proposed to enable optimal allocation of flexible tooling devices. Theoretical results have been evaluated and demonstrated using the SoV model of a real industrial process.
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Tsoutsanis, E., Y. G. Li, P. Pilidis, and M. Newby. "Part-Load Performance of Gas Turbines: Part II — Multi-Point Adaptation With Compressor Map Generation and GA Optimization." In ASME 2012 Gas Turbine India Conference. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/gtindia2012-9581.

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Accurate gas turbine performance simulation is a vital aid to the operational and maintenance strategy of thermal plants having gas turbines as their prime mover. Prediction of the part load performance of a gas turbine depends on the quality of the engine’s component maps. Taking into consideration that compressor maps are proprietary information of the manufacturers, several methods have been developed to encounter the above limitation by scaling and adapting component maps. This part of the paper presents a new off-design performance adaptation approach with the use of a novel compressor map generation method and Genetic Algorithms (GA) optimization. A set of coefficients controlling a generic compressor performance map analytically is used in the optimization process for the adaptation of the gas turbine performance model to match available engine test data. The developed method has been tested with off-design performance simulations and applied to a GE LM2500+ aeroderivative gas turbine operating in Manx Electricity Authority’s combined cycle power plant in the Isle of Man. It has been also compared with an earlier off-design performance adaptation approach, and shown some advantages in the performance adaptation.
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Lehre, Per Kristian, and Xiaoyu Qin. "Self-adaptation via multi-objectivisation." In GECCO '22: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2022. http://dx.doi.org/10.1145/3512290.3528836.

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Akimoto, Youhei, and Nikolaus Hansen. "CMA-ES and advanced adaptation mechanisms." In GECCO '19: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2019. http://dx.doi.org/10.1145/3319619.3323390.

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Akimoto, Youhei, and Nikolaus Hansen. "CMA-ES and advanced adaptation mechanisms." In GECCO '17: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2017. http://dx.doi.org/10.1145/3067695.3067698.

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Akimoto, Youhei, and Nikolaus Hansen. "CMA-ES and advanced adaptation mechanisms." In GECCO '18: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3205651.3207854.

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Akimoto, Youhei, Anne Auger, and Nikolaus Hansen. "CMA-ES and Advanced Adaptation Mechanisms." In GECCO '16: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2016. http://dx.doi.org/10.1145/2908961.2926980.

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Akimoto, Youhei, and Nikolaus Hansen. "CMA-ES and advanced adaptation mechanisms." In GECCO '21: Genetic and Evolutionary Computation Conference. New York, NY, USA: ACM, 2021. http://dx.doi.org/10.1145/3449726.3462748.

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Reports on the topic "Genetic adaptations"

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Rajarajan, Kunasekaran, Alka Bharati, Hirdayesh Anuragi, Arun Kumar Handa, Kishor Gaikwad, Nagendra Kumar Singh, Kamal Prasad Mohapatra, et al. Status of perennial tree germplasm resources in India and their utilization in the context of global genome sequencing efforts. World Agroforestry, 2020. http://dx.doi.org/10.5716/wp20050.pdf.

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Tree species are characterized by their perennial growth habit, woody morphology, long juvenile period phase, mostly outcrossing behaviour, highly heterozygosity genetic makeup, and relatively high genetic diversity. The economically important trees have been an integral part of the human life system due to their provision of timber, fruit, fodder, and medicinal and/or health benefits. Despite its widespread application in agriculture, industrial and medicinal values, the molecular aspects of key economic traits of many tree species remain largely unexplored. Over the past two decades, research on forest tree genomics has generally lagged behind that of other agronomic crops. Genomic research on trees is motivated by the need to support genetic improvement programmes mostly for food trees and timber, and develop diagnostic tools to assist in recommendation for optimum conservation, restoration and management of natural populations. Research on long-lived woody perennials is extending our molecular knowledge and understanding of complex life histories and adaptations to the environment, enriching a field that has traditionally drawn its biological inference from a few short-lived herbaceous species. These concerns have fostered research aimed at deciphering the genomic basis of complex traits that are related to the adaptive value of trees. This review summarizes the highlights of tree genomics and offers some priorities for accelerating progress in the next decade.
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Christopher, David A., and Avihai Danon. Plant Adaptation to Light Stress: Genetic Regulatory Mechanisms. United States Department of Agriculture, May 2004. http://dx.doi.org/10.32747/2004.7586534.bard.

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Original Objectives: 1. Purify and biochemically characterize RB60 orthologs in higher plant chloroplasts; 2. Clone the gene(s) encoding plant RB60 orthologs and determine their structure and expression; 3. Manipulate the expression of RB60; 4. Assay the effects of altered RB60 expression on thylakoid biogenesis and photosynthetic function in plants exposed to different light conditions. In addition, we also examined the gene structure and expression of RB60 orthologs in the non-vascular plant, Physcomitrella patens and cloned the poly(A)-binding protein orthologue (43 kDa RB47-like protein). This protein is believed to a partner that interacts with RB60 to bind to the psbA5' UTR. Thus, to obtain a comprehensive view of RB60 function requires analysis of its biochemical partners such as RB43. Background & Achievements: High levels of sunlight reduce photosynthesis in plants by damaging the photo system II reaction center (PSII) subunits, such as D1 (encoded by the chloroplast tpsbAgene). When the rate of D1 synthesis is less than the rate of photo damage, photo inhibition occurs and plant growth is decreased. Plants use light-activated translation and enhanced psbAmRNA stability to maintain D1 synthesis and replace the photo damaged 01. Despite the importance to photosynthetic capacity, these mechanisms are poorly understood in plants. One intriguing model derived from the algal chloroplast system, Chlamydomonas, implicates the role of three proteins (RB60, RB47, RB38) that bind to the psbAmRNA 5' untranslated leader (5' UTR) in the light to activate translation or enhance mRNA stability. RB60 is the key enzyme, protein D1sulfide isomerase (Pill), that regulates the psbA-RN :Binding proteins (RB's) by way of light-mediated redox potentials generated by the photosystems. However, proteins with these functions have not been described from higher plants. We provided compelling evidence for the existence of RB60, RB47 and RB38 orthologs in the vascular plant, Arabidopsis. Using gel mobility shift, Rnase protection and UV-crosslinking assays, we have shown that a dithiol redox mechanism which resembles a Pill (RB60) activity regulates the interaction of 43- and 30-kDa proteins with a thermolabile stem-loop in the 5' UTR of the psbAmRNA from Arabidopsis. We discovered, in Arabidopsis, the PD1 gene family consists of II members that differ in polypeptide length from 361 to 566 amino acids, presence of signal peptides, KDEL motifs, and the number and positions of thioredoxin domains. PD1's catalyze the reversible formation an disomerization of disulfide bonds necessary for the proper folding, assembly, activity, and secretion of numerous enzymes and structural proteins. PD1's have also evolved novel cellular redox functions, as single enzymes and as subunits of protein complexes in organelles. We provide evidence that at least one Pill is localized to the chloroplast. We have used PDI-specific polyclonal and monoclonal antisera to characterize the PD1 (55 kDa) in the chloroplast that is unevenly distributed between the stroma and pellet (containing membranes, DNA, polysomes, starch), being three-fold more abundant in the pellet phase. PD1-55 levels increase with light intensity and it assembles into a high molecular weight complex of ~230 kDa as determined on native blue gels. In vitro translation of all 11 different Pill's followed by microsomal membrane processing reactions were used to differentiate among PD1's localized in the endoplasmic reticulum or other organelles. These results will provide.1e insights into redox regulatory mechanisms involved in adaptation of the photosynthetic apparatus to light stress. Elucidating the genetic mechanisms and factors regulating chloroplast photosynthetic genes is important for developing strategies to improve photosynthetic efficiency, crop productivity and adaptation to high light environments.
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Zimmerman, Albert H. Adaptation and Speciation in Genetic Modeling of Physical Systems. Fort Belvoir, VA: Defense Technical Information Center, September 2009. http://dx.doi.org/10.21236/ada514694.

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Zhou, Aifen, Kristina Hillesland, Zhili He, Marcin Joachimiak, Grant Zane, Paramvir Dehal, Adam Arkin, et al. Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough. Office of Scientific and Technical Information (OSTI), May 2010. http://dx.doi.org/10.2172/985929.

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Sorensen, Soren J. Importance of Mobile Genetic Elements and Conjugal Gene Transfer for Subsurface Microbial Community Adaptation to Biotransformation of Metals. Office of Scientific and Technical Information (OSTI), June 2005. http://dx.doi.org/10.2172/893590.

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Sorensen, Soren J. Importance of Mobile Genetic Elements and Conjugal Gene Transfer for Subsurface Microbial Community Adaptation to Biotransformation of Metals. Office of Scientific and Technical Information (OSTI), June 2004. http://dx.doi.org/10.2172/893687.

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Di Giulio, Richard T. Adaptation of a Population of Fundulus heteroclitus to a Creosote-Contaminated Environment: Mechanisms, Genetic Consequences and Fitness Trade-Offs. Fort Belvoir, VA: Defense Technical Information Center, September 2005. http://dx.doi.org/10.21236/ada437526.

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Paterson, Andrew H., Yehoshua Saranga, and Dan Yakir. Improving Productivity of Cotton (Gossypsum spp.) in Arid Region Agriculture: An Integrated Physiological/Genetic Approach. United States Department of Agriculture, December 1999. http://dx.doi.org/10.32747/1999.7573066.bard.

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Objectives: We seek to establish the basis for improving cotton productivity under arid conditions, by studying the water use efficiency - evaporative cooling interrelationship. Specifically, we will test the hypothesis that cotton productivity under arid conditions can be improved by combining high seasonal WUE with efficient evaporative cooling, evaluate whether high WUE and/or evaporative cooling are based on specific physiological factors such as diurnal flexibility in stomatal conductance, stomatal density, photosynthetic capacity, chlorophyll fluorescence, and plant water status. Genes influencing both WUE and evaporative cooling, as well as other parameters such as economic products (lint yield, quality, harvest index) of cotton will also be mapped, in order to evaluate influences of water relations on these parameters. Approach: Carbon isotope ratio will be used to evaluate WUE, accompanied by additional parameters to elucidate the relationship between WUE, evaporative cooling, and cotton productivity. A detailed RFLP map will be used to determine the number, location, and phenotypic effects of genes underlying genetic variation in WUE between cultivated cottons, as well as test associations of these genes with traits of economic importance such as harvest index, lint yield, and lint quality. Major Conclusions: Productivity and quality of cotton grown under well-watered versus water-limited conditions was shown to be partly accounted for by different quantitative trait loci (QTLs). Among a suite of physiological traits often found to differ between genotypes adapted to arid versus well-watered conditions, genetic mapping implicated only reduced plant osmotic potential in improved cotton productivity under arid conditions. Our findings clearly implicate OP as a major component of cotton adaptation to arid conditions. However, testing of further physiological hypotheses is clearly needed to account for additional QTL alleles conferring higher seed-cotton yield under arid conditions, such as three of the five we found. Near-isogenic lines being made for QTLs discovered herein will offer a powerful new tool useful toward identification of the underlying gene(s) by using fine-scale mapping approaches (Paterson et al 1990). Implications: Adaptation to both arid and favorable conditions can be combined into the same genotype. We have identified diagnostic DNA markers that are being applied to creation of such desirable genotypes. Simultaneous improvement of productivity (and/or quality) for both arid and irrigated conditions will require more extensive field testing and the manipulation of larger numbers of genes, reducing the expected rate of genetic gain These difficulties may be at least partly ameliorated by efficiencies gained through identification and use of diagnostic DNA markers. Genomic tools and approaches may expedite adaptation of crops to arid cultivation, help to test roles of additional physiological factors, and guide the isolation of the underlying genes that protect crop performance under arid conditions.
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Abbo, Shahal, Hongbin Zhang, Clarice Coyne, Amir Sherman, Dan Shtienberg, and George J. Vandemark. Winter chickpea; towards a new winter pulse for the semiarid Pacific Northwest and wider adaptation in the Mediterranean basin. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7597909.bard.

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Original objectives: [a] Screen an array of chickpea and wild annual Cicer germplasm for winter survival. [b] Genetic analysis of winter hardiness in domesticated x wild chickpea crosses. [c] Genetic analysis of vernalization response in domesticated x wild chickpea crosses. [d] Digital expression analysis of a core selection of breeding and germplasm lines of chickpea that differ in winter hardiness and vernalization. [e] Identification of the genes involved in the chickpea winter hardiness and vernalization and construction of gene network controlling these traits. [f] Assessing the phenotypic and genetic correlations between winter hardiness, vernalization response and Ascochyta blight response in chickpea. The complexity of the vernalization response and the inefficiency of our selection experiments (below) required quitting the work on ascochyta response in the framework of this project. Background to the subject: Since its introduction to the Palouse region of WA and Idaho, and the northern Great Plains, chickpea has been a spring rotation legume due to lack of winter hardiness. The short growing season of spring chickpea limits its grain yield and leaves relatively little stubble residue for combating soil erosion. In Israel, chilling temperatures limit pod setting in early springs and narrow the effective reproductive time window of the crop. Winter hardiness and vernalization response of chickpea alleles were lost due to a series of evolutionary bottlenecks; however, such alleles are prevalent in its wild progenitor’s genepool. Major conclusions, solutions, achievements: It appears that both vernalization response and winter hardiness are polygenic traits in the wild-domesticated chickpea genepool. The main conclusion from the fieldwork in Israel is that selection of domesticated winter hardy and vernalization responsive types should be conducted in late flowering and late maturity backgrounds to minimize interference by daylength and temperature response alleles (see our Plant Breeding paper on the subject). The main conclusion from the US winter-hardiness studies is that excellent lines have been identified for germplasm release and continued genetic study. Several of the lines have good seed size and growth habit that will be useful for introgressing winter-hardiness into current chickpea cultivars to develop releases for autumn sowing. We sequenced the transcriptomes and profiled the expression of genes in 87 samples. Differential expression analysis identified a total of 2,452 differentially expressed genes (DEGs) between vernalized plants and control plants, of which 287 were shared between two or more Cicer species studied. We cloned 498 genes controlling vernalization, named CVRN genes. Each of the CVRN genes contributes to flowering date advance (FDA) by 3.85% - 10.71%, but 413 (83%) other genes had negative effects on FDA, while only 83 (17%) had positive effects on FDA, when the plant is exposed to cold temperature. The cloned CVRN genes provide new toolkits and knowledge to develop chickpea cultivars that are suitable for autumn-sowing. Scientific & agricultural implications: Unlike the winter cereals (barley, wheat) or pea, in which a single allelic change may induce a switch from winter to spring habit, we were unable to find any evidence for such major gene action in chickpea. In agricultural terms this means that an alternative strategy must be employed in order to isolate late flowering – ascochyta resistant (winter types) domesticated forms to enable autumn sowing of chickpea in the US Great Plains. An environment was identified in U.S. (eastern Washington) where autumn-sown chickpea production is possible using the levels of winter-hardiness discovered once backcrossed into advanced cultivated material with acceptable agronomic traits. The cloned CVRN genes and identified gene networks significantly advance our understanding of molecular mechanisms underlying plant vernalization in general, and chickpea in particular, and provide a new toolkit for switching chickpea from a spring-sowing to autumn-sowing crop.
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10

Abbott, Albert G., Doron Holland, Douglas Bielenberg, and Gregory Reighard. Structural and Functional Genomic Approaches for Marking and Identifying Genes that Control Chilling Requirement in Apricot and Peach Trees. United States Department of Agriculture, September 2009. http://dx.doi.org/10.32747/2009.7591742.bard.

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Structural and functional genomic approaches for marking and identifying genes that control chilling requirement in apricot and peach trees. Specific aims: 1) Identify and characterize the genetic nature of chilling requirement for flowering and dormancy break of vegetative shoots in Prunusgermplasm through the utilization of existing apricot (NeweYa'ar Research Center, ARO) and peach (Clemson University) genetic mapping populations; 2) Use molecular genetic mapping techniques to identify markers flanking genomic regions controlling chilling; 3) Comparatively map the regions controlling chilling requirement in apricot and peach and locate important genomic regions influencing chilling requirement on the Prunus functional genomic database as an initial step for identification of candidate genes; 4) Develop from the functional genomics database a set of markers facilitating the development of cultivars with optimized chilling requirements for improved and sustained fruit production in warm-winter environments. Dormant apricot (prunus armeniaca L.) and peach [Prunus persica (L.) Batsch] trees require sustained exposure to low, near freezing, temperatures before vigorous floral and vegetative bud break is possible after the resumption of warm temperatures in the spring. The duration of chilling required (the chilling requirement, CR) is determined by the climatic adaptation of the particular cultivar, thus limiting its geographic distribution. This limitation is particularly evident when attempting to introduce superior cultivars to regions with very warm winter temperatures, such as Israel and the coastal southern United States. The physiological mechanism of CR is not understood and although breeding programs deliberately manipulate CR in apricot and peach crosses, robust closely associated markers to the trait are currently not available. We used segregating populations of apricot (100 Fl individuals, NeweYa'ar Research Center, ARO) and peach (378 F2 individuals, Clemson University) to discover several discreet genomic loci that regulate CR and blooming date. We used the extensive genomic/genetic resources available for Prunus to successfully combine our apricot and peach genetic data and identify five QTL with strong effects that are conserved between species as well as several QTL that are unique to each species. We have identified markers in the key major QTL regions for testing in breeding programs which we are carrying out currently; we have identified an initial set of candidate genes using the peach physical/transcriptome map and whole peach genome sequences and we are testing these currently to identify key target genes for manipulation in breeding programs. Our collaborative work to date has demonstrated the following: 1) CR in peach and apricot is predominantly controlled by a limited number ofQTL loci, seven detected in a peach F2 derived map comprising 65% of the character and 12 in an apricot Fl map comprising 71.6% and 55.6% of the trait in the Perfection and A. 1740 parental maps, respectively and that peach and apricot appear in our initial maps to share five genomic intervals containing potentially common QTL. 2) Application of common anchor markers of the Prunus/peach, physical/genetic map resources has allowed us not only to identify the shared intervals but also to have immediately available some putative candidate gene information from these intervals, the EVG region on LG1 in peach the TALY 1 region in apricot on LG2 in peach; and several others involved in vernalization pathways (LGI and LG7). 3) Mapped BACcontigs are easily defined from the complete physical map resources in peach through the common SSR markers that anchor our CR maps in the two species, 4) Sequences of BACs in these regions can be easily mined for additional polymorphic markers to use in MAS applications.
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