Relevant bibliographies by topics / Biolog; Variation (Genetics)

Academic literature on the topic 'Biolog; Variation (Genetics)'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Biolog; Variation (Genetics)"

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Evren, Özay Hasan, Ertuǧrul Yüzbaşıoǧlu, and Mehmet Yaşar Dadandı. "Determination of intra-specific genetic variation of Phlomis kurdica and Phlomis oppositiflora and investigation for the hybridity of P. x melitenense (Lamiaceae) by means of molecular markers." Biologia 70, no. 9 (September 1, 2015): 1159–71. http://dx.doi.org/10.1515/biolog-2015-0132.

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Abstract In this study, intra-specific genetic variation and inter-specific genetic relation were investigated among Phlomis oppositiflora, P. kurdica, P. × melitenense (P. kurdica × oppositiflora), P. capitata and P. kurdica × capitata by using RAPD and ISSR markers. The hybridity of P. × melitenense and P. kurdica × capitata samples was also surveyed in terms of morphological and molecular aspects. Except for two, all bands obtained from RAPD (707 bands) and ISSR (651 bands) analyses were polymorphic. The lowest genetic distance values obtained from RAPD and ISSR analyses were 0.0156 (between P. × melitenense and P. kurdica) and 0.0142 (between P. × melitenense and P. kurdica) respectively. The highest genetic distance values obtained from RAPD and ISSR analyses were 0.0866 (between P. kotschyana and P. oppositiflora) and 0.1237 (between P. kotschyana and P. kurdica × capitata) respectively. While P. kurdica indicated the highest genetic diversity (H = 0.1572; I = 0.2646) in RAPD analysis, P. capitata displayed the highest genetic diversity (H = 0.1403; I = 0.2329) in ISSR analysis. AMOVA results showed that 86% and 75% of the total variance resided within groups based on RAPD and ISSR markers, respectively. Based on the RAPD and ISSR results, both P. × melitenense and P. kurdica × capitata samples inherited species specific bands from their parental species, which confirms their hybridity. Although both P. × melitenense and P. kurdica × capitata hybrids showed a morphological mosaic between their parental phenotypes in terms of the majority of the quantitative characters examined, P. × melitenense and P. kurdica × capitata exceeded their parental phenotypes in terms of the three and 11 quantitative characters respectively. MANOVA results from the morphological data showed significant distinction among P. kurdica, P. oppositiflora, P. × melitenense, P. capitata and P. kurdica × capitata (Wilks’ Lambda = 0.003; df = 112; P < 0.01). Average pollen fertilities of P. oppositiflora, P. × melitenense, P. capitata, P. kurdica and P. kurdica × capitata were 93.44%, 68.42%, 93.28 %, 90.12% and 92.77% respectively.
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Kehayias, George. "Spatial and temporal variation of Branchiostoma lanceolatum larvae (Cephalochordata) in a hypoxic bay." Biologia 70, no. 9 (September 1, 2015): 1234–44. http://dx.doi.org/10.1515/biolog-2015-0140.

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Abstract A 12-month zooplankton survey (September 2008 to August 2009) in the hypoxic, stratified and seasonally eutrophic Amvrakikos Gulf (western Greece) revealed the presence of larvae of the Cephalochordate Branchiostoma lanceolatum. The larvae were found at almost all sampling occasions, except September and February, and presented their peak of abundance in April (426.8 ind. m−3). The oxygen depletion in the water column affected their vertical and horizontal distribution. Thus, their abundance was greater in the subsurface layers (10-20 m) which corresponds to the well oxygenated thermocline layer. An east to west increase of their abundance in the deeper layers was associated with the severity of oxygen depletion. The lower oxygen limit for their presence seems to have been 2 mg L−1 which corresponds to hypoxia. A size-specific depth distribution was noticed, with larger larvae residing in deeper strata. A diel vertical migration of the larvae in the summer was recorded, with a night ascent in shallower depths and a day descent in deeper strata. There was an apparent coexistence in space and time between the larvae and the dinoflagellate Ceratium sp., though this could not indicate a trophic interrelation between them due to the large size of the latter. The results suggest that, during their planktonic stage, the larvae utilize the water stratification within the Amvrakikos Gulf by inhabiting the depths within or close to the thermocline, where they can satisfy their oxygen and energy demands while being protected from predation.
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Sanaei, Ehsan, Marjan Seiedy, and Farzaneh Momtazi. "A uni- and multivariate analysis approach to reveal sexual size dimorphism in Iranian populations of Hypera postica (Coleoptera: Curculionidae)." Biologia 70, no. 9 (September 1, 2015): 1228–33. http://dx.doi.org/10.1515/biolog-2015-0137.

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Abstract Body size dimorphism between genders is a commonly observed phenomenon in insects, usually manifested in larger female body size. Sexual Size Dimorphism (SSD) varies from species to species, the degree and direction influenced by certain evolutionary pressures. Intraspecific variation in SSD may also occur between populations. The Hypera postica (Gyllenhal, 1813) is a well-known alfalfa plant pest that shows a degree of morphological divergence in its populations. The female alfalfa weevils are very fecund and have a larger body size compared to males. To improve our knowledge on magnitude and direction of SSD in alfalfa weevil, we studied 200 specimens of H. postica from four Iranian populations (Karaj1, Karaj2, Tuyserkan and Jovein). 10 morphological variables from three external anatomic parts (pronotum, elytra and rostrum) and 45 ratio characters were statistically analyzed in order to determine the amount of SSD in Iranian populations. In addition we investigated for morphological divergence pattern in mentioned populations. The results of this study show that a low degree of morphological divergence occurs in Iranian populations. Measured variables indicate that the SSD pattern of H. postica is compatible with the Rensch’s rule, and is related to high fecundity of females and a lack of strong sexual selection. Also it is mentioned that the larger rostrum in females may correspond to its unique role in egg laying.
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Prince, Véronique, Anne-Marie Simao-Beaunoir, and Carole Beaulieu. "Amplified ribosomal DNA restriction analysis of free-living bacteria present in the headbox of a Canadian paper machine." Canadian Journal of Microbiology 55, no. 7 (July 2009): 810–17. http://dx.doi.org/10.1139/w09-036.

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The headbox water is the main source of bacterial contamination of paper machines. Identification of these bacterial contaminants could be an asset in developing specific control methods. An amplified ribosomal DNA restriction analysis (ARDRA) was carried out to characterize the bacterial communities associated with the headbox water of a paper machine in a Canadian mill in February and July 2006. Eight bacterial genera were identified as the main colonizers present in the headbox water. The genus Meiothermus appeared to be the dominant bacterial group in the Canadian paper machine. Some variation was observed between the February and July clone libraries. Bacterial genera such as Chelatococcus and Hydrogenophilus were only detected in February or in July, respectively. Furthermore, the proportion of Tepidimonas clones in the libraries was higher in July than in February. The metabolic profile of the February and July communities, determined using Biolog EcoPlates, also suggested that temporal variation occurred within the bacterial populations that colonized the headbox of the paper machine.
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Gadagkar, Sudhindra R. "PhyloM: A Computer Program for Phylogenetic Inference from Measurement or Binary Data, with Bootstrapping." Life 12, no. 5 (May 11, 2022): 719. http://dx.doi.org/10.3390/life12050719.

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Quantitative and binary results are ubiquitous in biology. Inasmuch as an underlying genetic basis for the observed variation in these observations can be assumed, it is pertinent to infer the evolutionary relationships among the entities being measured. I present a computer program, PhyloM, that takes measurement data or binary data as input, using which, it directly generates a pairwise distance matrix that can then be subjected to the popular neighbor-joining (NJ) algorithm to produce a phylogenetic tree. PhyloM also has the option of nonparametric bootstrapping for testing the level of support for the inferred phylogeny. Finally, PhyloM also allows the user to root the tree on any desired branch. PhyloM was tested on Biolog Gen III growth data from isolates within the genus Chromobacterium and the closely related Aquitalea sp. This allowed a comparison with the genotypic tree inferred from whole-genome sequences for the same set of isolates. From this comparison, it was possible to infer parallel evolution. PhyloM is a stand-alone and easy-to-use computer program with a user-friendly graphical user interface that computes pairwise distances from measurement or binary data, which can then be used to infer phylogeny using NJ using a utility in the same program. Alternatively, the distance matrix can be downloaded for use in another program for phylogenetic inference or other purposes. It does not require any software to be installed or computer code written and is open source. The executable and computer code are available on GitHub.
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Warren, William J., Randall M. Jeter, Robert C. Kimbrough, and John C. Zak. "Population patterns and antimicrobial resistance ofAeromonasin urban playa lakes." Canadian Journal of Microbiology 50, no. 6 (June 1, 2004): 397–404. http://dx.doi.org/10.1139/w04-029.

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Bacteria belonging to the genus Aeromonas are indigenous to aquatic environments. Once regarded as unimportant human pathogens, reports of opportunistic infections caused by these organisms have appeared increasingly in the medical literature. To estimate the potential for human infection by Aeromonas where limited water resources are being used intensively, we studied the spatial and temporal variation and incidence of antimicrobial resistance among environmental isolates of Aeromonas from two urban playa lakes in Lubbock, Texas. Aeromonas population densities varied seasonally, with the highest densities occurring from mid-April to late October. The greatest range of densities was 100-fold, from 2.50 to 255.17 colony-forming units per 0.1 mL of water sample. Densities also varied with water depth, although the variation did not display a consistent pattern. One hundred fifty-one Aeromonas isolates were divided into 10 species or subspecies groups by using the BIOLOG identification system. Nine isolates displayed resistance to co-trimoxazole, tetracycline, and cefuroxime, and none was resistant to more than one of these antimicrobial agents. In summary, the results of this study showed that the densities of Aeromonas peak in the late spring and again in late summer, times when human activity around the playa lakes is also high. Thus, we infer that human exposure to these potential pathogens varies seasonally. Compared to other published studies, the incidence of antimicrobial-resistant Aeromonas is relatively low in urban playa lakes in Lubbock, Texas. Nevertheless, resistant organisms were detected.Key words: Aeromonas, water, playa, antibiotic resistance, population dynamics.
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Charlesworth, Deborah, Nicholas H. Barton, and Brian Charlesworth. "The sources of adaptive variation." Proceedings of the Royal Society B: Biological Sciences 284, no. 1855 (May 31, 2017): 20162864. http://dx.doi.org/10.1098/rspb.2016.2864.

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The role of natural selection in the evolution of adaptive phenotypes has undergone constant probing by evolutionary biologists, employing both theoretical and empirical approaches. As Darwin noted, natural selection can act together with other processes, including random changes in the frequencies of phenotypic differences that are not under strong selection, and changes in the environment, which may reflect evolutionary changes in the organisms themselves. As understanding of genetics developed after 1900, the new genetic discoveries were incorporated into evolutionary biology. The resulting general principles were summarized by Julian Huxley in his 1942 book Evolution: the modern synthesis . Here, we examine how recent advances in genetics, developmental biology and molecular biology, including epigenetics, relate to today's understanding of the evolution of adaptations. We illustrate how careful genetic studies have repeatedly shown that apparently puzzling results in a wide diversity of organisms involve processes that are consistent with neo-Darwinism. They do not support important roles in adaptation for processes such as directed mutation or the inheritance of acquired characters, and therefore no radical revision of our understanding of the mechanism of adaptive evolution is needed.
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Wielbo, Jerzy, Monika Marek-Kozaczuk, Agnieszka Kubik-Komar, and Anna Skorupska. "Increased metabolic potential of Rhizobium spp. is associated with bacterial competitiveness." Canadian Journal of Microbiology 53, no. 8 (August 2007): 957–67. http://dx.doi.org/10.1139/w07-053.

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Of 105 rhizobial isolates obtained from nodules of commonly cultivated legumes, we selected 19 strains on the basis of a high rate of symbiotic plant growth promotion. Individual strains within the species Rhizobium leguminosarum bv. trifolii , R. leguminosarum bv. viciae , and Rhizobium etli displayed variation not only in plasmid sizes and numbers but also in the chromosomal 16S–23S internal transcribed spacer. The strains were tagged with gusA gene and their competitiveness was examined in relation to an indigenous population of rhizobia under greenhouse conditions. A group of 9 strains was thus isolated that were competitive in relation to native rhizobia in pot experiments. Nineteen selected competitive and uncompetitive strains were examined with respect to their ability to utilize various carbon and energy sources by means of commercial Biolog GN2 microplate test. The ability of the selected strains to metabolize a wide range of nutrients differed markedly and the competitive strains were able to utilize more carbon and energy sources than uncompetitive ones. A major difference concerned the utilization of amino and organic acids, which were metabolized by most of the competitive and only a few uncompetitive strains, whereas sugars and their derivatives were commonly utilized by both groups of strains. A statistically significant correlation between the ability to metabolize a broad range of substrates and nodulation competitiveness was found, indicating that metabolic properties may be an essential trait in determining the competitiveness of rhizobia.
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Taylor, John W., David M. Geiser, Austin Burt, and Vassiliki Koufopanou. "The Evolutionary Biology and Population Genetics Underlying Fungal Strain Typing." Clinical Microbiology Reviews 12, no. 1 (January 1, 1999): 126–46. http://dx.doi.org/10.1128/cmr.12.1.126.

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SUMMARY Strain typing of medically important fungi and fungal population genetics have been stimulated by new methods of tapping DNA variation. The aim of this contribution is to show how awareness of fungal population genetics can increase the utility of strain typing to better serve the interests of medical mycology. Knowing two basic features of fungal population biology, the mode of reproduction and genetic differentiation or isolation, can give medical mycologists information about the intraspecific groups that are worth identifying and the number and type of markers that would be needed to do so. The same evolutionary information can be just as valuable for the selection of fungi for development and testing of pharmaceuticals or vaccines. The many methods of analyzing DNA variation are evaluated in light of the need for polymorphic loci that are well characterized, simple, independent, and stable. Traditional population genetic and new phylogenetic methods for analyzing mode of reproduction, genetic differentiation, and isolation are reviewed. Strain typing and population genetic reports are examined for six medically important species: Coccidioides immitis, Histoplasma capsulatum, Candida albicans, Cryptococcus neoformans, Aspergillus fumigatus, and A. flavus. Research opportunities in the areas of genomics, correlation of clinical variation with genetic variation, amount of recombination, and standardization of approach are suggested.
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Karczewski, Konrad J., and Alicia R. Martin. "Analytic and Translational Genetics." Annual Review of Biomedical Data Science 3, no. 1 (July 20, 2020): 217–41. http://dx.doi.org/10.1146/annurev-biodatasci-072018-021148.

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Understanding the influence of genetics on human disease is among the primary goals for biology and medicine. To this end, the direct study of natural human genetic variation has provided valuable insights into human physiology and disease as well as into the origins and migrations of humans. In this review, we discuss the foundations of population genetics, which provide a crucial context to the study of human genes and traits. In particular, genome-wide association studies and similar methods have revealed thousands of genetic loci associated with diseases and traits, providing invaluable information into the biology of these traits. Simultaneously, as the study of rare genetic variation has expanded, so-called human knockouts have elucidated the function of human genes and the therapeutic potential of targeting them.
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Dissertations / Theses on the topic "Biolog; Variation (Genetics)"

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Larsson, Jobs Karl. "Population Fragmentation and Genetic Variation in Grouse." Doctoral thesis, Uppsala University, Department of Ecology and Evolution, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-6006.

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In this thesis the genetic variation of two grouse species, the Chinese grouse (Bonasa sewersowi) and the Black grouse (Tetrao tetrix) was examined with neutral genetic markers: microsatellites. Habitat fragmentation and isolation leads to structuring among and loss of genetic variation within populations.

The Chinese grouse in a small population in Lianhuasan nature reserve was found to have undergone a population bottleneck and as a result of isolation and possible inbreeding showed genetic impoverishment hereof.

The Black grouse populations in Europe face various different conditions from widely distributed areas of suitable habitat in the northern and eastern parts of its range to highly naturally and anthropogenically fragmented habitat landscapes in the west.

Structure among populations was found in Great Britain where Wales, Scotland and England showed characteristics of three different genetic entities, indicating very little or no geneflow between these populations.

The Dutch population showed signs of loss of genetic variation as to be expected from a population that has historically decreased in population size from several thousands to tens of individuals in a matter of decades. However the possibility to spot signs of a bottleneck was impaired due to the short time-window in which this can be observed in a population with such a low effective population size (NE).

The sampled populations in Europe clustered into five different groups of genetic identities. The different clusters were: Great Britain-, the Netherlands-, Fenno-Scandian-, Alpine- and lowland German-Austrian populations. The level of genetic variation when compared over all these different populations decreased as a sign of isolation and small NE. However it was not feasible to separate the impact of these two factors.

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Stewart, John E. B. (John Edward Bakos). "Genetic Variation in a Population of the Plains Woodrat Neotoma micropus." Thesis, University of North Texas, 1988. https://digital.library.unt.edu/ark:/67531/metadc500709/.

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Neotoma micropus from Jack County, Texas, were studied over a 9-month period. Loci from blood and saliva were used to determine genetic variation within the population. Deviations from Hardy-Weinberg equilibrium were found at one locus. The average temporal F over all seven loci was 0.040. Genetic structuring was subtle, fluctuated on a seasonal basis, and was due to differential migration or predation on genotypes. Heterozygotes tended to move more than homozygotes, and a greater proportion of heterozygotes were lost from the population during each season. Genetic variation was maintained in the population by immigrant individuals. This differential in dispersal of genotypes fits current models of reorganization within the genome of populations.
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Loh, Yong-Hwee Eddie. "Genetic variation in fast-evolving East African cichlid fishes: an evolutionary perspective." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41148.

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Cichlid fishes from the East African Rift lakes Victoria, Tanganyika and Malawi represent a preeminent example of replicated and rapid evolutionary radiation. In this single natural system, numerous morphological (eg. jaw and tooth shape, color patterns, visual sensitivity), behavioral (eg. bower-building) and physiological (eg. development, neural patterning) phenotypes have emerged, much akin to a mutagenic screen. This dissertation encompasses three studies that seek to decipher the underpinnings of such rapid evolutionary diversification, investigated via the genetic variation in East African cichlids. We generated a valuable cichlid genomic resource of five low-coverage Lake Malawi cichlid genomes, from which the general properties of the genome were characterized. Nucleotide diversity of Malawi cichlids was low at 0.26%, and a sample genotyping study found that biallelic polymorphisms segregate widely throughout the Malawi species flock, making each species a mosaic of ancestrally polymorphic genomes. A second genotyping study expanded our evolutionary analysis to cover the entire East African cichlid radiation, where we found that more than 40% of single nucleotide polymorphisms (SNPs) were ancestral polymorphisms shared across multiple lakes. Bayesian analysis of genetic structure in the data supported the hypothesis that riverine species had contributed significantly to the genomes of Malawi cichlids and that Lake Malawi cichlids are not monophyletic. Both genotyping studies also identified interesting loci involved in important sensory as well as developmental pathways that were well differentiated between species and lineages. We also investigated cichlid genetic variation in relation to the evolution of microRNA regulation, and found that divergent selection on miRNA target sites may have led to differential gene expression, which contributed to the diversification of cichlid species. Overall, the patterns of cichlid genetic variation seem to be dominated by the phenomena of extensive sharing of ancestral polymorphisms. We thus believe that standing genetic variation in the form of ancestrally inherited polymorphisms, as opposed to variations arising from new mutations, provides much of the genetic diversity on which selection acts, allowing for the rapid and repeated adaptive radiation of East African cichlids.
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Foulkes, Nicholas F. "Molecular biology of the human G 6-PD gene." Thesis, University of Oxford, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.253009.

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Fredman, David. "Computational exploration of human genome variation /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-025-7/.

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Barrera, Luis A. "Towards a Systematic Approach for Characterizing Regulatory Variation." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:26718710.

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A growing body of evidence suggests that genetic variants that alter gene expression are responsible for many phenotypic differences across individuals, particularly for the risk of developing common diseases. However, the molecular mechanisms that underlie the vast majority of associations between genetic variants and their phenotypes remain unknown. An important limiting factor is that genetic variants remain difficult to interpret, particularly in noncoding sequences. Developing truly systematic approaches for characterizing regulatory variants will require: (a) improved annotations for the genomic sequences that control gene expression, (b) a more complete understanding of the molecular mechanisms through which genetic variants, both coding and noncoding, can affect gene expression, and (c) better experimental tools for testing hypotheses about regulatory variants. In this dissertation, I present conceptual and methodological advances that directly contribute to each of these goals. A recurring theme in all of these developments is the statistical modeling of protein-DNA interactions and its integration with other data types. First, I describe enhancer-FACS-Seq, a high-throughput experimental approach for screening candidate enhancer sequences to test for in vivo, tissue-specific activity. Second, I present an integrative computational analysis of the in vivo binding of NF-kappaB, a key regulator of the immune system, yielding new insights into how genetic variants can affect NF-kappaB binding. Next, I describe the first comprehensive survey of coding variation in human transcription factors and what it reveals about additional sources of genetic variation that can affect gene expression. Finally, I present SIFTED, a statistical framework and web tool for the optimal design of TAL effectors, which have been used successfully in genome editing and can thus be used to test hypotheses about regulatory variants. Together, these developments help fulfill key needs in the quest to understand the molecular basis of human phenotypic variation.
Biophysics
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Hadzihalilovic-Numanovic, Amra. "Genetic Variation and Relatedness of Freshwater Pearl Mussel Margaritifera margaritifera L. populations." Licentiate thesis, Karlstad University, Division for Environmental Sciences, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:kau:diva-2410.

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The two papers presented in this thesis focus on population genetic study on freshwater pearl mussel populations in Sweden, using RAPD method. In paper I, I examine genetic variation within and between 5 populations in a single drainage area in south western Sweden. In paper II, I study the evolutionary relationship, and how genetic variation is related to population size, age structure and geographic isolation in 14 populations of freshwater pearl mussel in south central Sweden. In both papers I and II, I found that genetic variation was larger than found in previous studies using other techniques, and variation was larger between than within populations. I did not found any correlation between geographic and genetic distance, which indicates that mussel populations have been adapted locally to environmental factors in a relatively short time. In paper I, I found that genetic distance between populations was greater than found in other studies, despite small geographic distances. In paper II, I found that populations were highly differentiated indicating little gene flow between them. There was no significant positive relation between genetic variation and population size or age structure but there was a significant positive relation between mean age and population size indicating that many populations have gone through bottlenecks recently.

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Obaid, Jian. "What is known about genetic variation among Baltic Sea blue mussels and the promise of proteomics. A literature review." Thesis, Södertörn University College, School of Life Sciences, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:sh:diva-2701.

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The Baltic Sea is an evolutionary young sea that have developed a low salinity in its water from the fresh water that flows from the north and saltwater that flows from the south of the sea. The low salinity is too low for many marine organisms and too high for many freshwater organisms. Species like the blue mussel, which have adapted to the low salinity, may have developed different protein expression as a result. To study which protein that have been expressed in the organism proteome analysis is often used. 2-dimensional electrophoresis may be the only method that can do this kind of analysis.

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Blackman, Benjamin K. "Evolutionary genetics of flowering time regulation and variation in Helianthus." [Bloomington, Ind.] : Indiana University, 2009. 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:3373495.

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Thesis (Ph.D.)--Indiana University, Dept. of Biology 2009.
Title from home page (viewed on Jul 8, 2010). Source: Dissertation Abstracts International, Volume: 70-10, Section: B, page: 5957. Advisers: Loren H. Rieseberg; Scott D. Michaels.
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Lee, Peter Daniel. "Building a model for mapping genetic variation affecting gene expression." Thesis, McGill University, 2005. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=85931.

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The majority of genetic traits including most common diseases are believed to be multigenic and arise both from variations in coding sequences as well as from regulatory polymorphisms. Genome-wide approaches are needed to develop models for understanding this complexity. This thesis develops approaches for studying genetic variation affecting gene expression on a genome-wide scale. This included development of experimental design principles and analytical methods for microarray data. These principles were then applied to characterize differences between commonly-used A/J and C57BL/6J inbred mouse strains at the molecular level identifying over 2000 genes differentially expressed between these strains across 4 tissues. To further investigate the role of genetic variation in genome-wide expression changes, we analyzed expression profiles of lung tissue obtained from a panel of recombinant congenic strains (RCS) derived from the same inbred strains. An ANOVA was applied using a model to test the association of expression profiles with donor-strain of origin (DSO, inferred from RCS genotyping data), and with genetic background. This model identified over 1500 genes whose expression levels were associated with DSO status (P<0.05) having adjusted for the variability due to predominant strain of background, suggestive of cis-regulatory variation in these genes. We randomly selected 50 positive genes displaying association between DSO and 80 negative genes for validation using allelic imbalance (AI), a method that uses intragenic SNPs for detecting genes with cis-regulatory variation that measures allele-specific transcript levels in cDNA of heterozygous individuals. Of the genes chosen, 54% of positive versus 27% of negative genes contained at least one SNP within ≥ 1 kbp of 3' UTR sequenced (P<0.05 Fisher exact test). Al was found in 63% of positive genes versus 23% of negative genes (P<0.01 Fisher exact test) representing a greater than 10-fo
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Books on the topic "Biolog; Variation (Genetics)"

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Amaya, Julian A. Cervantes, and Miguel M. Franco Jimenez. Genetic diversity: New research. Hauppauge, N.Y: Nova Science Publisher's, Inc., 2011.

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

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Genetic variation: Methods and protocols. New York, N.Y: Humana Press, 2010.

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Çalişkan, Mahmut. Analysis of genetic variation in animals. Rijeka, Croatia: InTech, 2012.

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Mielke, James H. Human biological variation. New York, NY: Oxford University Press, 2005.

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W, Konigsberg Lyle, and Relethford John, eds. Human biological variation. New York: Oxford University Press, 2006.

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W, Konigsberg Lyle, and Relethford John, eds. Human biological variation. 2nd ed. New York: Oxford University Press, 2011.

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Life history evolution. Sunderland, Mass: Sinauer Associates, 2002.

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Masojć, Piotr. Polimorfizm genetyczny i zmienność ilościowa inhibitora endogennej alfa-amylazy w ziarnie zbóż. Szczecin: Akademia Rolnicza w Szczecinie, 1993.

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Williams, Roger John. Biochemical individuality: The basis for the genetotrophic concept. New Canaan, Ct: Keats Pub., 1998.

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Book chapters on the topic "Biolog; Variation (Genetics)"

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Twfieg, Mohammed-Elfatih, and M. Dawn Teare. "Molecular Genetics and Genetic Variation." In Methods in Molecular Biology, 3–12. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-416-6_1.

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Konigsberg, Lyle W. "Quantitative Variation and Genetics." In Human Biology, 143–73. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118108062.ch5.

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O'Rourke, Dennis, and Jake Enk. "Genetics, Geography, and Human Variation." In Human Biology, 99–142. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9781118108062.ch4.

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Marcus, Frederick B. "Genetic Variation and Diseases." In Bioinformatics and Systems Biology, 187–211. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78353-4_9.

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Antonovics, Janis, Norman C. Ellstrand, and Robert N. Brandon. "Genetic variation and environmental variation: expectations and experiments." In Plant Evolutionary Biology, 275–303. Dordrecht: Springer Netherlands, 1988. http://dx.doi.org/10.1007/978-94-009-1207-6_11.

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Yogev, David, Glenn F. Browning, and Kim S. Wise. "Genetic Mechanisms of Surface Variation." In Molecular Biology and Pathogenicity of Mycoplasmas, 417–43. Boston, MA: Springer US, 2002. http://dx.doi.org/10.1007/0-306-47606-1_19.

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Wöhrmann, K. "Genetic Variation: Prerequisite and Consequence of Evolution." In Population Biology, 7–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-74474-7_2.

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Madsen, Bo Eskerod, Palle Villesen, and Carsten Wiuf. "Short Tandem Repeats and Genetic Variation." In Methods in Molecular Biology, 297–306. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-367-1_16.

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Yegnasubramanian, Srinivasan, and William B. Isaacs. "Analysis of Inherited and Acquired Genetic Variation." In Modern Molecular Biology, 13–31. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-0-387-69745-1_2.

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Murtaugh, Michael P., Kay S. Faaberg, Judy Laber, Margaret Elam, and Vivek Kapur. "Genetic Variation in the PRRS Virus." In Advances in Experimental Medicine and Biology, 787–94. Boston, MA: Springer US, 1998. http://dx.doi.org/10.1007/978-1-4615-5331-1_102.

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Conference papers on the topic "Biolog; Variation (Genetics)"

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Hudson, Tom. "“Genetic variation and cancer”." In 2008 30th Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE, 2008. http://dx.doi.org/10.1109/iembs.2008.4649062.

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"population genetic variation of serotonin transporter gene (SLC6A4), associated with neurophysiological development." In Bioinformatics of Genome Regulation and Structure/ Systems Biology. institute of cytology and genetics siberian branch of the russian academy of science, Novosibirsk State University, 2020. http://dx.doi.org/10.18699/bgrs/sb-2020-236.

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Selamat, E. S., P. Y. Hong, and W. T. Liu. "Polyacrylamide micro-pillar based DNA microarray and its application for genetic variation analysis." In 2006 International Conference on Microtechnologies in Medicine and Biology. IEEE, 2006. http://dx.doi.org/10.1109/mmb.2006.251549.

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Hughes, James, Sheridan Houghten, Guillermo M. Mallen-Fullerton, and Daniel Ashlock. "Recentering and Restarting Genetic Algorithm variations for DNA Fragment Assembly." In 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2014. http://dx.doi.org/10.1109/cibcb.2014.6845500.

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Kurland, Sara, Nils Ryman, Ola Hössjer, and Linda Laikre. "CANCELLED: Loss of natural Baltic salmon populations can severely reduce metapopulation capacity for retaining genetic variation." In 5th European Congress of Conservation Biology. Jyväskylä: Jyvaskyla University Open Science Centre, 2018. http://dx.doi.org/10.17011/conference/eccb2018/107735.

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Printy, Blake P., Nishant Verma, Matthew C. Cowperthwaite, and Mia K. Markey. "Effects of genetic variation on the dynamics of neurodegeneration in Alzheimer's disease." In 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). IEEE, 2014. http://dx.doi.org/10.1109/embc.2014.6944121.

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Bai, Jieyun, Yijie Zhu, Andy Lo, Yaosheng Lu, and Jichao Zhao. "In Silico Assessment of Genetic Variation in PITX2 Reveals the Molecular Mechanisms of Calcium-Mediated Cellular Triggered Activity in Atrial Fibrillation*." In 2020 42nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) in conjunction with the 43rd Annual Conference of the Canadian Medical and Biological Engineering Society. IEEE, 2020. http://dx.doi.org/10.1109/embc44109.2020.9175466.

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"Molecular mechanisms of cardio- and cerebrovascular comorbidity: from experimental analysis of structural and epigenetic variations in the human genome to post-GWAS analysis of genetic correlations between diseases." In Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022) :. Institute of Cytology and Genetics, the Siberian Branch of the Russian Academy of Sciences, 2022. http://dx.doi.org/10.18699/sbb-2022-223.

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Sarkar, Kamal. "Modeling of Spin Coating Process to Control Submicron Film Thickness of Permeation Layer." In ASME 2010 First Global Congress on NanoEngineering for Medicine and Biology. ASMEDC, 2010. http://dx.doi.org/10.1115/nemb2010-13083.

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Nanochips® cartridges (Fig 1) are disposable panels with 400 micro arrays (Fig 2) that can be independently used as test sites for various assays like genetic marker. Each site (Fig 3) is a permeation layer coated electrode with 80 μ diameter and 120 μ pitch. Permeation or “perm” layer is a thin film of a proprietary hydrogel material over the proprietary chip design. Perm layers were deposited on the electrodes using spin coating process with a proprietary solution. Performance of the cartridge depended on the quality and thickness of the permeation layer over these 400 electrodes. In this process one millimeter deep tear shaped well was constructed from the ceramic base to which 20×20 array of silicon chip were attached. These wells filled with 180 μl proprietary solution and spun at fixed 1200 RPM for 20 seconds. Process was repeated three times at room temperature in a clean room. Post process treatment included 30 minutes in dry incubator, wash in Milli Q water, and finally, dry at room temperature. Quality of the 1,500 nm thick permeation layer was so demanding that more than half of the cartridges were rejected due to poor quality of the perm layer. Major causes of rejection were bubbles, high SD (Standard Deviation), and thickness (too thick or too thin) of the layer. To understand the problem focus was given to both solution making and spin coating process. Basic hypothesis was that the film thickness was based on viscosity of solution and subsequent evaporation process. Figs 4–6 showed the details of spin coating process for developing a heuristic model. Since viscosity depended strongly on the temperature and time during a chemical reaction, a viscosity profile was developed for the solution during the reaction. From the viscosity curve (Fig. 7) it was established that 75 minute at 50° C was not enough to complete the reaction as was initially thought. The time-Viscosity curve reached the plateau after 150 minutes! So, it was necessary to continue the reaction for 75 more minutes to complete the reaction. This explained a major reason (bubble forming) in the present process. Viscosity of the solution depended on a number of other factors like dispensed volume, temperature of the spinneret, time to dispense and/or in the spinneret, etc. A systematic study on these variables led to an empirical equation of the following form: Hf=Hf0+A*(τe/Vd)*ηf*(Tc−T0)n Where Hf = Predicted Average Thickness in nm. Hf0 is minimum average thickness in nm. T, V, and τ are various temperature, dispensed volume, and time parameters. A and n are curve fitting constants for experimental set-ups. The best of part of this modeling was its ability not only to predict the thickness of the film, rather its ability to control the thickness of the film in real time for a given solution. Above equation allowed appropriate dispensing volume and time to be kept in the well of the chip before spinning for a given solution with a specific viscosity. A tabular form was given to the operator who matched the information to get a specific film thickness. This model helped dropped the rejection rate to less than 10% from more than 50%. Operators were able to control the thickness of the film within 1500 nm +/− 300 nm, as demanded by the Spec. The model further allowed to target, rather control, the film thickness. We were also able to make films as thin as 800 nm or as thick as 1,500 nm with +/− 200 nm variation from the Table developed from the empirical equation. Using the assumption that viscosity plays the most important role in our spin coating process and constructing a corresponding evaporative model, we were able to identify a major shortcoming of an existing process to develop submicron thick permeation layer. Existing process was resulting in more than 50% rejection of an expensive critical component. An empirical model of spin coating process was developed to predict the film thickness within hundreds of nanometers. This dramatically improved the yield to more than 90% from less than 50%. The model allowed to correct the process in real time and allowed targeting the film thickness anywhere around one micron with few hundred nanometer accuracy.
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Reports on the topic "Biolog; Variation (Genetics)"

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Lers, Amnon, Majid R. Foolad, and Haya Friedman. genetic basis for postharvest chilling tolerance in tomato fruit. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600014.bard.

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ABSTRACT Postharvest losses of fresh produce are estimated globally to be around 30%. Reducing these losses is considered a major solution to ensure global food security. Storage at low temperatures is an efficient practice to prolong postharvest performance of crops with minimal negative impact on produce quality or human health and the environment. However, many fresh produce commodities are susceptible to chilling temperatures, and the application of cold storage is limited as it would cause physiological chilling injury (CI) leading to reduced produce quality. Further, the primary CI becomes a preferred site for pathogens leading to decay and massive produce losses. Thus, chilling sensitive crops should be stored at higher minimal temperatures, which curtails their marketing life and in some cases necessitates the use of other storage strategies. Development of new knowledge about the biological basis for chilling tolerance in fruits and vegetables should allow development of both new varieties more tolerant to cold, and more efficient postharvest storage treatments and storage conditions. In order to improve the agricultural performance of modern crop varieties, including tomato, there is great potential in introgression of marker-defined genomic regions from wild species onto the background of elite breeding lines. To exploit this potential for improving tomato fruit chilling tolerance during postharvest storage, we have used in this research a recombinant inbred line (RIL) population derived from a cross between the red-fruited tomato wild species SolanumpimpinellifoliumL. accession LA2093 and an advanced Solanum lycopersicumL. tomato breeding line NCEBR-1, developed in the laboratory of the US co-PI. The original specific objectives were: 1) Screening of RIL population resulting from the cross NCEBR1 X LA2093 for fruit chilling response during postharvest storage and estimation of its heritability; 2) Perform a transcriptopmic and bioinformatics analysis for the two parental lines following exposure to chilling storage. During the course of the project, we learned that we could measure greater differences in chilling responses among specific RILs compared to that observed between the two parental lines, and thus we decided not to perform transcriptomic analysis and instead invest our efforts more on characterization of the RILs. Performing the transcriptomic analysis for several RILs, which significantly differ in their chilling tolerance/sensitivity, at a later stage could result with more significant insights. The RIL population, (172 lines), was used in field experiment in which fruits were examined for chilling sensitivity by determining CI severity. Following the field experiments, including 4 harvest days and CI measurements, two extreme tails of the response distribution, each consisting of 11 RILs exhibiting either high sensitivity or tolerance to chilling stress, were identified and were further examined for chilling response in greenhouse experiments. Across the RILs, we found significant (P < 0.01) correlation between field and greenhouse grown plants in fruit CI. Two groups of 5 RILs, whose fruits exhibited reproducible chilling tolerant/sensitive phenotypes in both field and greenhouse experiments, were selected for further analyses. Numerous genetic, physiological, biochemical and molecular variations were investigated in response to postharvest chilling stress in the selected RILs. We confirmed the differential response of the parental lines of the RIL population to chilling stress, and examined the extent of variation in the RIL population in response to chilling treatment. We determined parameters which would be useful for further characterization of chilling response in the RIL population. These included chlorophyll fluorescence Fv/Fm, water loss, total non-enzymatic potential of antioxidant activity, ascorbate and proline content, and expression of LeCBF1 gene, known to be associated with cold acclimation. These parameters could be used in continuation studies for the identification and genetic mapping of loci contributing to chilling tolerance in this population, and identifying genetic markers associated with chilling tolerance in tomato. Once genetic markers associated with chilling tolerance are identified, the trait could be transferred to different genetic background via marker-assisted selection (MAS) and breeding. The collaborative research established in this program has resulted in new information and insights in this area of research and the collaboration will be continued to obtain further insights into the genetic, molecular biology and physiology of postharvest chilling tolerance in tomato fruit. The US Co-PI, developed the RIL population that was used for screening and measurement of the relevant chilling stress responses and conducted statistical analyses of the data. Because we were not able to grow the RIL population under field conditions in two successive generations, we could not estimate heritability of response to chilling temperatures. However, we plan to continue the research, grow the RIL progeny in the field again, and determine heritability of chilling tolerance in a near future. The IS and US investigators interacted regularly and plan to continue and expand on this study, since combing the expertise of the Co-PI in genetics and breeding with that of the PI in postharvest physiology and molecular biology will have great impact on this line of research, given the significant findings of this one-year feasibility project.
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Fridman, Eyal, Jianming Yu, and Rivka Elbaum. Combining diversity within Sorghum bicolor for genomic and fine mapping of intra-allelic interactions underlying heterosis. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597925.bard.

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Heterosis, the enigmatic phenomenon in which whole genome heterozygous hybrids demonstrate superior fitness compared to their homozygous parents, is the main cornerstone of modern crop plant breeding. One explanation for this non-additive inheritance of hybrids is interaction of alleles within the same locus. This proposal aims at screening, identifying and investigating heterosis trait loci (HTL) for different yield traits by implementing a novel integrated mapping approach in Sorghum bicolor as a model for other crop plants. Originally, the general goal of this research was to perform a genetic dissection of heterosis in a diallel built from a set of Sorghum bicolor inbred lines. This was conducted by implementing a novel computational algorithm which aims at associating between specific heterozygosity found among hybrids with heterotic variation for different agronomic traits. The initial goals of the research are: (i) Perform genotype by sequencing (GBS) of the founder lines (ii) To evaluate the heterotic variation found in the diallel by performing field trails and measurements in the field (iii) To perform QTL analysis for identifying heterotic trait loci (HTL) (iv) to validate candidate HTL by testing the quantitative mode of inheritance in F2 populations, and (v) To identify candidate HTL in NAM founder lines and fine map these loci by test-cross selected RIL derived from these founders. The genetic mapping was initially achieved with app. 100 SSR markers, and later the founder lines were genotyped by sequencing. In addition to the original proposed research we have added two additional populations that were utilized to further develop the HTL mapping approach; (1) A diallel of budding yeast (Saccharomyces cerevisiae) that was tested for heterosis of doubling time, and (2) a recombinant inbred line population of Sorghum bicolor that allowed testing in the field and in more depth the contribution of heterosis to plant height, as well as to achieve novel simulation for predicting dominant and additive effects in tightly linked loci on pseudooverdominance. There are several conclusions relevant to crop plants in general and to sorghum breeding and biology in particular: (i) heterosis for reproductive (1), vegetative (2) and metabolic phenotypes is predominantly achieved via dominance complementation. (ii) most loci that seems to be inherited as overdominant are in fact achieving superior phenotype of the heterozygous due to linkage in repulsion, namely by pseudooverdominant mechanism. Our computer simulations show that such repulsion linkage could influence QTL detection and estimation of effect in segregating populations. (iii) A new height QTL (qHT7.1) was identified near the genomic region harboring the known auxin transporter Dw3 in sorghum, and its genetic dissection in RIL population demonstrated that it affects both the upper and lower parts of the plant, whereas Dw3 affects only the part below the flag leaf. (iv) HTL mapping for grain nitrogen content in sorghum grains has identified several candidate genes that regulate this trait, including several putative nitrate transporters and a transcription factor belonging to the no-apical meristem (NAC)-like large gene family. This activity was combined with another BARD-funded project in which several de-novo mutants in this gene were identified for functional analysis.
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