Relevant bibliographies by topics / DNA variation

Academic literature on the topic 'DNA variation'

Author: Grafiati
Published: 4 June 2021
Last updated: 19 February 2023

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Journal articles on the topic "DNA variation"

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Kučinskas, V. "Human mitochondrial DNA variation in Lithuania." Anthropologischer Anzeiger 52, no. 4 (December 13, 1994): 289–95. http://dx.doi.org/10.1127/anthranz/52/1994/289.

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Baughman, Joshua M., and Vamsi K. Mootha. "Buffering mitochondrial DNA variation." Nature Genetics 38, no. 11 (November 2006): 1232–33. http://dx.doi.org/10.1038/ng1106-1232.

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Lalith Perera. "CHLOROPLAST DNA VARIATION IN COCONUT IS OPPOSITE TO ITS NUCLEAR DNA VARIATION." CORD 18, no. 02 (December 1, 2002): 34. http://dx.doi.org/10.37833/cord.v18i02.359.

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The pattern of world distribution of two major fruit morphotypes of coconuts has led to development of theories on origin, domestication and dissemination of coconut. Results of recent nuclear DNA analyses are in agreement with these theories with several other new insights. Compared to the plant nuclear genome however, the plant organelle genomes, the chloroplast genome and the mitochondrial genome are highly conserved and are maternally inherited in most angiosperms. Therefore, most useful information have come from regions of DNA located in organelle genome for studying phylogeny in angiosperms and for deducing historical information and evolutionary history of populations such as past migration routes and colonization dynamics. This study was aimed to determine the feasibility of developing polymorphic cytoplasmic markers, particularly the chloroplast markers. Chloroplast DNA variation of coconut from all coconut growing regions in the world assessed by both restriction digestions and physical separation of PCR products obtained with universal primers, by chloroplast microsatellites and by sequencing showed no variation. This tends to suggest that coconut may have gone through a severe cytoplasmic bottleneck and only one chloroplast type may have participated in the colonization process.
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Collins, Francis S., Mark S. Guyer, and Aravinda Chakravarti. "Variations on a Theme: Cataloging Human DNA Sequence Variation." Science 278, no. 5343 (November 28, 1997): 1580–81. http://dx.doi.org/10.1126/science.278.5343.1580.

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Kopinski, Piotr K., Larry N. Singh, Shiping Zhang, Marie T. Lott, and Douglas C. Wallace. "Mitochondrial DNA variation and cancer." Nature Reviews Cancer 21, no. 7 (May 27, 2021): 431–45. http://dx.doi.org/10.1038/s41568-021-00358-w.

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Barbujani, Guido. "DNA Variation and Language Affinities." American Journal of Human Genetics 61, no. 5 (November 1997): 1011–14. http://dx.doi.org/10.1086/301620.

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Bernoco, D., and G. R. Byrns. "DNA fingerprint variation in horses." Animal Biotechnology 2, no. 2 (January 1991): 145–60. http://dx.doi.org/10.1080/10495399109525755.

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Srivastava, Sangeeta, and U. C. Lavania. "Evolutionary DNA variation in Papaver." Genome 34, no. 5 (October 1, 1991): 763–68. http://dx.doi.org/10.1139/g91-118.

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In 23 species of Papaver L., 2C nuclear DNA amounts range from 4.64 pg in Papaver persicum (2n = 14) to 22.43 pg in Papaver orientale (2n = 42), revealing a fivefold variation within the genus. However, such variation is limited to only twofold among the species that have the same chromosome number (2n = 14). The distribution of DNA is discontinuously spread over six groups in the genus. A strong positive correlation exists between nuclear DNA content and metaphase chromosome length. Viewed in the context of evolutionary divergence, it is revealed that DNA reduction has taken place in conjunction with speciation. This is achieved by equal reduction to each chromosome independent of chromosome size, as apparent from the estimated DNA values for individual chromosomes within the complements. The diminution in DNA amount with evolutionary specialisation appears to be a genomic strategy to dispense with the less important DNA associated with heterochromatic segments. The uniform distribution of such dispensible DNA throughout the complement is probably nucleotypically conducive to allow the genomic loss to be adaptationally operative, lest it affects the very survival of the evolving species.Key words: Papaver, evolution, DNA content, DNA systematics.
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TAYLOR, DAVID B., ALLEN L. SZALANSKI, and RICHARD D. PETERSON II. "Mitochondrial DNA variation in screwworm." Medical and Veterinary Entomology 10, no. 2 (April 1996): 161–69. http://dx.doi.org/10.1111/j.1365-2915.1996.tb00723.x.

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Ramachandran, C., and R. K. J. Narayan. "Chromosomal DNA variation in Cucumis." Theoretical and Applied Genetics 69-69, no. 5-6 (March 1985): 497–502. http://dx.doi.org/10.1007/bf00251092.

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Dissertations / Theses on the topic "DNA variation"

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Pandya, Arpita. "Human Y-chromosomal DNA variation." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298658.

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Bromham, Lindell. "Rate variation in DNA sequence evolution." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339362.

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Adur, Ashwin. "DNA copy number variation in autism." Connect to resource, 2009. http://hdl.handle.net/1811/37275.

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Hill, Catherine E. "Mitochondrial DNA variation in Island Southeast Asia." Thesis, University of Huddersfield, 2005. http://eprints.hud.ac.uk/id/eprint/22331/.

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It is known that Island Southeast Asia was colonised relatively early in the history of modem humans; however, it is still a matter of some debate as to whether the modem inhabitants of Island Southeast Asia are descended from these original inhabitants or are the result of some later migration. Currently, the prevailing theory in both archaeology and linguistics is that the modem inhabitants of Island Southeast Asia are largely descended from an agricultural people who originated in China and Taiwan around 6,000 years ago. From there they are thought to have migrated through the Philippines and into Eastern Island Southeast Asia around 2,500-1,500 B.C. assimilating or replacing the indigenous peoples. However, other researchers have suggested that a model of regional continuity is more suitable for Island Southeast Asia and that the modem inhabitants are the direct descendents of the original Pleistocene inhabitants. Still others have suggested that intermediate models would be more appropriate. This study aimed to use mitochondrial DNA to test the validity of these models. A secondary aim was to look at the mitochondrial DNA of the indigenous Orang AsH groups of the Malay Peninsula in an attempt to reconstruct a picture of the early Pleistocene variation of Southeast Asia. To this end, mitochondrial DNA was obtained and sequenced from 885 individuals from various locations in Island Southeast Asia and also 259 Orang AsHindividuals. This study has demonstrated that the populations of Island Southeast Asia contain a high level of genetic diversity, including a number of novel haplogroups. Significant differences have also been found between Eastern and Western populations suggesting that they have been established long enough to become regionally specific. Most Island Southeast Asian haplogroups date to the Pleistocene or early Holocene which suggests that they are mostly indigenous to the area. Those which could have a connection to Taiwan seem too old to have been part of an 'out of Taiwan' event as it has been traditionally visualised. Only -13% ofmtDNA types (belonging to haplogroups M7clc, D5 and Y2) could be linked to such an event suggesting that if a migration did occur it was demographically minor. xiii A number of novel haplogroups were also found in the Orang Asli which form strong support for the theory that that at least the Semang, if not all Orang Asli groups in part, are descended from the original Pleistocene inhabitants of the Malay Peninsula. These novel haplogroups diverge from the same set of founder types as the haplogroups found across the rest of Eurasia; that they diverge from close to the roots of these founder types suggests they are of considerable antiquity. This, along with expansion dates of -60,000 obtained in this study, suggests that only a single, early 'out of Africa' event took place which led to the peopling of the rest of the world by modem humans.
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Meng, Anming. "DNA fingerprinting and minisatellite variation of swans." Thesis, University of Nottingham, 1990. http://eprints.nottingham.ac.uk/13889/.

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Genetic variation in natural populations of four species of swans (Cygnus bewickii, Cygnus olor, Cygnus buccinator and Cygnus cygnus) has been investigated by examining minisatellite loci using human DNA fingerprinting probes pSPT19.6 and pSPT18.15. It has been found that swan minisatellites are highly variable. However, the degree of variation depends on the population structure and species. Bewick's Swans at Slimbridge have the highest degree of minisatellite variation, Whooper Swans at Caerlaverock come second, and then Mute Swans, and Trumpeter Swans in Montana. Comparative study of DNA fingerprints among populations and among species suggested that swan minisatellites are subject to specific as well as population differentiation, although the function of minisatellites remains an unsolved mystery. Hypervariable minisatellites of swans that are detected by DNA fingerprinting are stably inherited as codominant markers. DNA fingerprinting has been used to study mating behaviour of Mute and Whooper Swans in the wild The results showed that the Whooper swans were almost strictly monogamous and Mute Swans exhibited an adaptable reproductive system. A genomic library from Cygnus olor was constructed and dozens of minisatellites were isolated. Most of the cloned swan minisatellites were variable, some showed specific variation, and one (pcoMS6.1) detected RFLPs in PstI digests of Trumpeter Swans.
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Saunders, Nigel John. "Bacterial phase variation associated with repetitive DNA." Thesis, Open University, 1999. http://oro.open.ac.uk/57999/.

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Phase variation is mechanism of phenotypic switching used by many pathogenic bacterial species. This thesis describes work on three aspects of phase variation. Mathematical models are described which can be used to determine the rate of phase variation and subsequently the influence of variation rate and fitness differences associated with the altered phenotype on population structure. An approach to whole genome analysis has been developed which has been used to identify putative phase variable contingency genes in H. pylori, T. pallidum and N. meningitidis. This has identified many new contingency genes likely to be involved in host - bacterium and bacterium population interactions. Finally, a detailed molecular investigation of the promoter of the phase variable opc gene of N. meningitidis is presented. In this it is shown that the promoter located homopolymeric tract controls transcription by affecting the relative spacing and facing of promoter components, that this determines RNA polymerase binding to the promoter, and that this interaction involves direct contact of the a-subunit of RNA polymerase with the promoter. In addition it is shown that transcription is dependent upon an IHF consensus sequence in the opc promoter.
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Hide, Geoffrey. "Variation in repetitive DNA in African Trypanosomes." Thesis, University of Edinburgh, 1988. http://hdl.handle.net/1842/12083.

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Lundmark, Per Erik. "Genetic and Genomic Analysis of DNA Sequence Variation." Doctoral thesis, Uppsala universitet, Molekylär medicin, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-158486.

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The studies in this thesis describe the application of genotyping and allele specific expression analysis to genetic studies. The role of the gene NPC1 in Triglyceride metabolism was explored in mouse models and in humans on the population level in study I. NPC1 was found to affect hepatic triglyceride metabolism, and to be relevant for controlling serum triglyceride levels in mice and potentially in humans. In study II the utility of the HapMap CEU samples was investigated for tagSNP selection in six European populations. The HapMap CEU was found to be representative for tagSNP selection in all populations while allele frequencies differed significantly in the sample from Kuusamo, Finland. In study III the power of Allele specific expression as a tool for the mapping of cis-regulatory variation was compared to standard eQTL analysis, ASE was found to be the more powerful type of analysis for a similar sample size. Finally ASE mapping was applied to regions reported to harbour long non-coding RNAs and associated SNPs were compared to published trait-associations. This revealed strong cis-regulatory SNPs of long non-coding RNAs with reported trait or disease associations.
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Crompton, Tom. "Mobile DNA and genetic variation in Drosophila melanogaster." Thesis, University of Leicester, 1997. http://hdl.handle.net/2381/30330.

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Whilst it is commonly accepted that transposable elements can generate genetic variation, the significance of this for the maintenance and dissemination of such elements is controversial. Here long-term laboratory populations of Drosophila melanogaster, maintained at two discrete temperatures, are screened by Southern blotting for the patterns of insertion of several transposable elements (copia, mdg-2, mdg-4 and P). Consistent with a temperature-specific adaptive role for some insertions, several are apparently found at higher frequency in lines at one temperature. Further characterisation of these putatively temperature-selected insertions was attempted. Of three distinct approaches taken towards cloning these insertions, a single-stranded DNA-ligation for PCR-amplification technique, not thought to have been previously exploited for isolating transposable element insertion sites, generated the best results. One copia insertion was successfully sequenced, although single fly PCR experiments suggested that the frequency of this in caged populations was not related to temperature. A major collection of D. melanogaster from the French and Spanish Pyrenees was undertaken along four discrete altitudinal clines, with a view to screening for specific transposable element insertions. A novel strategy was developed for correlation of altitude with mean seasonal temperature of each collection site. Altitudinal variation in the frequency of Thr-Gly length polymorphism at the period locus was found to be consistent with predictions based on known latitudinal clines. This is the first known example of putatively adaptive clinal genetic variation in European populations of Drosophila collected along altitudinal transects. Finally, a fundamental re-examination of the theoretical issues surrounding the possible adaptive significance of transposable elements is developed. It is demonstrated that he extension of ideas on the 'units of selection' to transposable elements has led to confusion. A model of transposable element evolution which presents a coherent alternative to the selfish DNA approach is presented.
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Eng, Ken Khong. "Complete mitochondrial DNA genome variation in Peninsular Malaysia." Thesis, University of Leeds, 2014. http://etheses.whiterose.ac.uk/7872/.

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The peopling of Southeast Asia has been vigorously debated over the past few decades by archaeologists, linguists and anthropologists, as well as evolutionary and population geneticists. Several ethnic minorities in the region, the Orang Asli groups (the Semang, Senoi and Aboriginal Malays) from Peninsular Malaysia, are widely thought of as “relicts” of human diversity in the ancient Sunda continent. However, mitochondrial DNA (mtDNA analysis of these groups has hitherto been restricted to a small number of populations and largely based on the mtDNA control region hypervariable segment I (HVS-I), supplemented by a very small number of whole-mtDNA genomes. In this study, I have both expanded the number of populations examined and analysed 226 lineages at the level of whole-mtDNA genomes from both Orang Asli and modern Malay populations, covering most of the extant mtDNA diversity in Peninsular Malaysia, in the context of Southeast Asian variation more generally, including a total of 2206 complete mtDNA sequences in the phylogeographic analysis. This has confirmed that the Orang Asli populations indeed experienced high genetic drift, likely due to their extremely small group sizes and population subdivision. All three Orang Asli groups have local roots that trace back to ~50 ka, and all have been affected to a greater or lesser extent by subsequent migrations to Peninsular Malaysia. The Semang and Senoi show much less haplogroup diversity than the Aboriginal Malays, although the latter have some indigenous ancestry that is as deep as that of the Semang and Senoi in Peninsular Malaysia. However, this drift, and the loss of lineages that it has entailed, is compensated for by the retention of many related ancient lineages in the extant modern Malay, who therefore provide a more comprehensive view of ancient Malay Peninsula, and more generally ancient Sunda, mtDNA diversity. Indeed, contrary to the model that posits a recent ancestry for Malay in Island Southeast Asia (ISEA), a majority of their maternal lineages appear to have had a local ancestry within Mainland Southeast Asia (MSEA) and the Malay Peninsula. Combining the Orang Asli and Malay data indicates a very deep ancestry for multiple indigenous maternal lineages that date back locally (or regionally) to the late Pleistocene. Many can be traced to the original inhabitants of Southeast Asia, who colonised the Sunda region from South Asia ~50–60 ka. It appears that the spread of the so-called “Coastal Neolithic” foraging groups (who may have engaged in horticulture, but were largely pre-rice agriculture) may have provided the main contribution to the north–south lineage expansions and the spread of Austro-Asiatic languages to the Orang Asli and to the Nicobars may be connected to some of these dispersals. Apart from preserving these ancient lineages, many of which have been lost by drift in the relict populations, the modern Malay also preserve complex maternal influences from further afield at various times stretching back to the Last Glacial Maximum, from ISEA (as far east as the New Guinea region), to a lesser extent from East Asia, and to an even lesser extent South Asia. Climatic change and sea-level rises were likely the most important driving force behind the demographic history of Southeast Asia, mainland as well as insular, as shown by a sharp signal of early Holocene population crash and subsequent re-expansion in both the modern Malay and the Orang Asli. Although there is substantial lineage sharing between modern Malay and their close Sunda neighbours in Sumatra, ISEA lineages amount to little more than a quarter of the maternal variation of Malay, and even if there was a major migration to the Peninsula in the Late Holocene, the majority of their maternal ancestry seems to lie within the bounds of the Sunda continent.
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Books on the topic "DNA variation"

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Melton, Terry Weary. The influence of mitochondrial DNA variation on forensic DNA typing. [University Park, Pa.]: [s.n.], 1996.

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Probability models for DNA sequence evolution. 2nd ed. New York: Springer, 2008.

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Probability models for DNA sequence evolution. New York: Springer, 2002.

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Siemann, Liese Anne. Mitochondrial DNA sequence variation in North Atlantic long-finned pilot whales, Globicephala melas. Woods Hole, Mass: Woods Hole Oceanographic Institution, 1994.

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

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Wyandt, Herman E. Human Chromosome Variation: Heteromorphism and Polymorphism. Dordrecht: Springer Science+Business Media B.V., 2012.

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Fobes, Stephen. Genetic variation in DNA of coho salmon from the Lower Columbia River: Final report. Portland, OR: U.S. Dept. of Energy, Bonneville Power Administration, Division of Fish and Wildlife, 1993.

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Shartava, Tsisana. DNA research, genetics, and cell biology. Hauppauge, N.Y: Nova Science Publishers, 2011.

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Jadayel, Dalal Mohammed. Variation in the organization and structure of the mitochondrial DNA of species of aspergillus. Birmingham: University of Birmingham, 1986.

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Bhattacherjee, Vasker. Variation in the restriction fragment length in the DNA of species of 'Aspergillus' and 'Penicillium'. Birmingham: University of Birmingham, 1989.

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Book chapters on the topic "DNA variation"

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Coffin, John M. "Retrovirus Variation and Evolution." In The DNA Provirus, 221–44. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818302.ch16.

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Cullis, C. A. "Plant DNA Variation and Stress." In Genetics, Development, and Evolution, 143–55. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4684-5137-5_6.

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Neale, David B., and Nicholas C. Wheeler. "Noncoding and Repetitive DNA." In The Conifers: Genomes, Variation and Evolution, 61–74. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-46807-5_4.

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Kuno, Shinya, Hirofumi Zempo, and Haruka Murakami. "Mitochondrial DNA Sequence Variation and Performance." In Genetic and Molecular Aspects of Sport Performance, 215–26. Oxford, UK: Wiley-Blackwell, 2010. http://dx.doi.org/10.1002/9781444327335.ch19.

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Issa, Jean-Pierre. "Age-Related Variation in DNA Methylation." In Epigenetic Epidemiology, 185–96. Dordrecht: Springer Netherlands, 2011. http://dx.doi.org/10.1007/978-94-007-2495-2_11.

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Steck, G. J., and W. S. Sheppard. "Mitochondrial DNA Variation in Anastrepha fraterculus." In Fruit Flies, 9–14. New York, NY: Springer New York, 1993. http://dx.doi.org/10.1007/978-1-4757-2278-9_2.

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Bradshaw, John E. "DNA and the Origin of Variation." In Plant Breeding: Past, Present and Future, 75–107. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-23285-0_3.

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Keith, Kelsey, Jean-Pierre J. Issa, and Shoghag Panjarian. "Age-Related Variation in DNA Methylation." In Epigenetic Epidemiology, 235–59. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-030-94475-9_10.

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McCulloch, Richard, Liam J. Morrison, and James P. J. Hall. "DNA Recombination Strategies During Antigenic Variation in the African Trypanosome." In Mobile DNA III, 409–35. Washington, DC, USA: ASM Press, 2015. http://dx.doi.org/10.1128/9781555819217.ch19.

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Gero, John S. "Research for Cultural DNA in Design." In Computational Studies on Cultural Variation and Heredity, 1–13. Singapore: Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-10-8189-7_1.

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Conference papers on the topic "DNA variation"

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Xu, W., R. Chen, B. Hu, J. G. Zein, C. Liu, S. A. A. Comhair, M. A. Aldred, et al. "Mitochondrial DNA Variation and Severe Asthma." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a2961.

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Wildenberg, Andy, Steven Skiena, and Pavel Sumazin. "Deconvolving sequence variation in mixed DNA populations." In the sixth annual international conference. New York, New York, USA: ACM Press, 2002. http://dx.doi.org/10.1145/565196.565238.

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Kaessmann, Henrik, Ingo Ebersberger, Victor Wiebe, Rikard Erlandsson, Jim F. Wilson, Carsten Schwarz, Michaela Winkler, and Svante Pääbo. "DNA sequence variation among humans and apes (abstract only)." In the fourth annual international conference. New York, New York, USA: ACM Press, 2000. http://dx.doi.org/10.1145/332306.332365.

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Hunt, Brendan G. "Evolutionary and developmental variation in DNA methylation in Hymenoptera." In 2016 International Congress of Entomology. Entomological Society of America, 2016. http://dx.doi.org/10.1603/ice.2016.89536.

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"Interpreting non-coding genome variation with DNA sequence motifs." 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/bgrs/sb-2022-038.

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"Interpreting non-coding genome variation with DNA sequence motifs." 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-2022-038.

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Zhang, Huanan, Ze Tian, and Rui Kuang. "Transfer Learning across Cancers on DNA Copy Number Variation Analysis." In 2013 IEEE International Conference on Data Mining (ICDM). IEEE, 2013. http://dx.doi.org/10.1109/icdm.2013.58.

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Marie, Suely K., Roseli Silva, Antonio Lerario, Miyuki Uno, and Sueli Mieko Oba-Shinjo. "Abstract 3047: Mitochondrial DNA copy variation and TFAM expression in astrocytoma." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-3047.

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Rocha, M. S., and O. N. Mesquita. "Variation of entropic elasticity of DNA-Psoralen complex under UV light." In Optics & Photonics 2005, edited by Kishan Dholakia and Gabriel C. Spalding. SPIE, 2005. http://dx.doi.org/10.1117/12.619128.

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Raghavan, Sunitha, D. Roy Maahapatra, and Arnab Samanta. "Modeling and Simulation of Hydrodynamic Interaction of DNA in a Micro-Fluidic Channel." In ASME 2013 2nd Global Congress on NanoEngineering for Medicine and Biology. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/nemb2013-93127.

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The motion of DNA (in the bulk solution) and the non-Newtonian effective fluid behavior are considered separately and self-consistently with the fluid motion satisfying the no-slip boundary condition on the surface of the confining geometry in the presence of channel pressure gradients. A different approach has been developed to model DNA in the micro-channel. In this study the DNA is assumed as an elastic chain with its characteristic Young’s modulus, Poisson’s ratio and density. The force which results from the fluid dynamic pressure, viscous forces and electromotive forces is applied to the elastic chain in a coupled manner. The velocity fields in the micro-channel are influenced by the transport properties. Simulations are carried out for the DNAs attached to the micro-fluidic wall. Numerical solutions based on a coupled multiphysics finite element scheme are presented. The modeling scheme is derived based on mass conservation including biomolecular mass, momentum balance including stress due to Coulomb force field and DNA-fluid interaction, and charge transport associated to DNA and other ionic complexes in the fluid. Variation in the velocity field for the non-Newtonian flow and the deformation of the DNA strand which results from the fluid-structure interaction are first studied considering a single DNA strand. Motion of the effective center of mass is analyzed considering various straight and coil geometries. Effects of DNA statistical parameters (geometry and spatial distribution of DNAs along the channel) on the effective flow behavior are analyzed. In particular, the dynamics of different DNA physical properties such as radius of gyration, end-to-end length etc. which are obtained from various different models (Kratky-Porod, Gaussian bead-spring etc.) are correlated to the nature of interaction and physical properties under the same background fluid environment.
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Reports on the topic "DNA variation"

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Lance, Richard, and Xin Guan. Variation in inhibitor effects on qPCR assays and implications for eDNA surveys. Engineer Research and Development Center (U.S.), August 2021. http://dx.doi.org/10.21079/11681/41740.

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Aquatic environmental DNA (eDNA) surveys are sometimes impacted by polymerase chain reaction (PCR) inhibitors. We tested varying concentrations of different inhibitors (humic, phytic, and tannic acids; crude leaf extracts) for impacts on quantitative PCR (qPCR) assays designed for eDNA surveys of bighead and silver carp (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix). We also tested for inhibition by high concentrations of exogenous DNA, hypothesizing that DNA from increasingly closely related species would be increasingly inhibitory. All tested inhibitors impacted qPCR, though only at very high concentrations — likely a function, in part, of having used an inhibitor-resistant qPCR solution. Closer phylogenetic relatedness resulted in inhibition at lower exogenous DNA concentrations, but not at relatively close phylogenetic scales. Inhibition was also influenced by the qPCR reporter dye used. Importantly, different qPCR assays responded differently to the same inhibitor concentrations. Implications of these results are that the inclusion of more than one assay for the same target taxa in an eDNA survey may be an important countermeasure against false negatives and that internal positive controls may not, in the absence of efforts to maximize inhibition compatibility, provide useful information about the inhibition of an eDNA assay.
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2

Fobes, Stephen, Kathy Knudsen, and Fred Allendorf. Genetic Variation in DNA of Coho Salmon from the Lower Columbia River : Final Report 1993. Office of Scientific and Technical Information (OSTI), April 1993. http://dx.doi.org/10.2172/928002.

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Seroussi, Eyal, and George Liu. Genome-Wide Association Study of Copy Number Variation and QTL for Economic Traits in Holstein Cattle. United States Department of Agriculture, September 2010. http://dx.doi.org/10.32747/2010.7593397.bard.

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Copy number variation (CNV) has been recently identified in human and other mammalian genomes and increasing awareness that CNV might be a major source for heritable variation in complex traits has emerged. Despite this, little has been published on CNVs in Holsteins. In order to fill this knowledge-gap, we proposed a genome-wide association study between quantitative trait loci (QTL) for economic traits and CNV in the Holstein cattle. The approved feasibility study was aimed at the genome-wide characterization of CNVs in Holstein cattle and at the demonstrating of their possible association with economic traits by performing the activities of preparation of DNA samples, Comparative Genomic Hybridization (CGH), initial association study between CNVs and production traits and characterization of CNVSNP associations. For both countries, 40 genomic DNA samples of bulls representing the extreme sub-populations for economically important traits were CGH analyzed using the same reference genome on a NimbleGen tiling array. We designed this array based on the latest build of the bovine genome (UMD3) with average probe spacing of 1150 bases (total number of probes was 2,166,672). Two CNV gene clusters, PLA2G2D on BTA2 and KIAA1683 on BTA7 revealed significant association with milk percentage and cow fertility, respectively, and were chosen for further characterization and verification in a larger sample using other methodologies including sequencing, tag SNPs and real time PCR (qPCR). Comparison between these four methods indicated that there is under estimation of the number of CNV loci in Holstein cattle and their complexity. The variation in sequence between different copies seemed to affect their functionality and thus the hybridization based methods were less informative than the methods that are based on sequencing. We thus conclude that large scale sequencing effort complemented by array CGH should be considered to better detect and characterize CNVs in order to effectively employ them in marker-assisted selection.
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Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.
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Kistler, Harold Corby, Talma Katan, and Dani Zamir. Molecular Karyotypes of Pathogeic Strains of Fusarium oxysporum. United States Department of Agriculture, June 1995. http://dx.doi.org/10.32747/1995.7604927.bard.

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Genetic diversity of pathogenic strains of the fungus Fusarium oxysporum was determied by analysis of electrophoretic karyotype, as well as by DNA variation detected by Restriction Fragment Length Polymorphisms (RFLPs) and Random Amplified Polymorphic DNAs (RAPDs). The electrophoretic karyotypes for 130 isolates of the fungus pathogenic to tomato, melon, and banana were analyzed. Electrophoretic karyotype variation, reflected in differences in apparent chromosome number and genome size, was observed even among isolates from the same host and sub specific category. Sub specific categories studied were forma specialis, vegetative compatibility group (VCG) and race. Chromosome number and genome size variation was less for isolates within the same VCG than for the collection of isolates as a whole. RFLP and RAPD analysis were performed on 62 isolates of F. oxysporum from tomato and melon. Polygenetic trees were constructed from genetic diversity data. The results support the hypothesis that isolates belonging to the same VCG originate from a single ancestor compared to other isolates. The results do not support the hypothesis that all isolates belonging to the same forma specialis originate from a common ancestor. These conclusions have profound implication for breeding resistance to diseases caused by particular formae speciales of F. oxysporum.
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Belanger, Faith, Nativ Dudai, and Nurit Katzir. Genetic Linkage Mapping of Basil (Ocimum basilicum). United States Department of Agriculture, March 2010. http://dx.doi.org/10.32747/2010.7593385.bard.

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The ultimate goal of this project is to develop a genetic linkage map of basil (Ocimumbasilicum). We received 1 year of funding from BARD to conduct a feasibility study. Below is a summary of our study. During this year we evaluated the cultivars ‘Perrie’ and ‘Cardinal’ for DNA sequence polymorphisms using AFLPs and gene-based markers. We evaluated an F2 population for variation in production of volatile compounds. We also determined the nuclear DNA content of 8 species of Ocimum. All of this information will be useful in the future for genetic linkage mapping of basil.
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Cohen, Yuval, Christopher A. Cullis, and Uri Lavi. Molecular Analyses of Soma-clonal Variation in Date Palm and Banana for Early Identification and Control of Off-types Generation. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7592124.bard.

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Date palm (Phoenix dactylifera L.) is the major fruit tree grown in arid areas in the Middle East and North Africa. In the last century, dates were introduced to new regions including the USA. Date palms are traditionally propagated through offshoots. Expansion of modern date palm groves led to the development of Tissue Culture propagation methods that generate a large number of homogenous plants, have no seasonal effect on plant source and provide tools to fight the expansion of date pests and diseases. The disadvantage of this procedure is the occurrence of off-type trees which differ from the original cultivar. In the present project we focused on two of the most common date palm off-types: (1) trees with reduced fruit setting, in which most of the flowers turn into three-carpel parthenocarpic fruits. In a severe form, multi-carpel flowers and fruitlets (with up to six or eight carpels instead of the normal three-carpel flowers) are also formed. (2) dwarf trees, having fewer and shorter leaves, very short trunk and are not bearing fruits at their expected age, compared to the normal trees. Similar off-types occur in other crop species propagated by tissue culture, like banana (mainly dwarf plants) or oil palm (with a common 'Mantled' phenotype with reduced fruit setting and occurrence of supernumerary carpels). Some off-types can only be detected several years after planting in the fields. Therefore, efficient methods for prevention of the generation of off-types, as well as methods for their detection and early removal, are required for date palms, as well as for other tissue culture propagated crops. This research is aimed at the understanding of the mechanisms by which off-types are generated, and developing markers for their early identification. Several molecular and genomic approaches were applied. Using Methylation Sensitive AFLP and bisulfite sequencing, we detected changes in DNA methylation patterns occurring in off-types. We isolated and compared the sequence and expression of candidate genes, genes related to vegetative growth and dwarfism and genes related to flower development. While no sequence variation were detected, changes in gene expression, associated with the severity of the "fruit set" phenotype were detected in two genes - PdDEF (Ortholog of rice SPW1, and AP3 B type MADS box gene), and PdDIF (a defensin gene, highly homologous to the oil palm gene EGAD). We applied transcriptomic analyses, using high throughput sequencing, to identify genes differentially expressed in the "palm heart" (the apical meristem and the region of embryonic leaves) of dwarf vs. normal trees. Among the differentially expressed genes we identified genes related to hormonal biosynthesis, perception and regulation, genes related to cell expansion, and genes related to DNA methylation. Using Representation Difference Analyses, we detected changes in the genomes of off-type trees, mainly chloroplast-derived sequences that were incorporated in the nuclear genome and sequences of transposable elements. Sequences previously identified as differing between normal and off-type trees of oil palms or banana, successfully identified variation among date palm off-types, suggesting that these represent highly labile regions of monocot genomes. The data indicate that the date palm genome, similarly to genomes of other monocot crops as oil palm and banana, is quite unstable when cells pass through a cycle of tissue culture and regeneration. Changes in DNA sequences, translocation of DNA fragments and alteration of methylation patterns occur. Consequently, patterns of gene expression are changed, resulting in abnormal phenotypes. The data can be useful for future development of tools for early identification of off-type as well as for better understanding the phenomenon of somaclonal variation during propagation in vitro.
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Perl-Treves, Rafael, M. Kyle, and Esra Galun. Development and Application of a Molecular Genetic Map for Melon (Cucumis melo). United States Department of Agriculture, October 1993. http://dx.doi.org/10.32747/1993.7568094.bard.

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This project has generated a systematic survey of DNA polymorphism in Cucumis melo. An RFLP and RAPD survey of the major cultivar groups and botanical varieties of this species has been conducted, with the purpose of assessing the degree of molecular variation and phylogenetic relationships within the melon germplasm and, at the same time, develop sets of markets suitable for mapping the melon genome. Additional activities regarding variation in the melon germplasm in fruit traits and regeneration ability have been initiated as well. The necessary populations required for the development of a molecular map of the C. melo genome have been prepared. An F2 that segregated for 4 viral resistances, powdery mildew resitance and sex type has been derived from a PI 414723 x Topmark cross, and a RILs population has been prepared from it. We have confirmed the resistances in the population and have analyzed the genetic relationships between these resistances. Progress toward the construction of a molecular map of C. melo and the development of markers linked to those traits is described. We have so far screened the first few tens of markers in the F2 population, and many additional ones were screened in DNA bulks prepared from such population.
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Paran, Ilan, and Allen Van Deynze. Regulation of pepper fruit color, chloroplasts development and their importance in fruit quality. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598173.bard.

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Pepper exhibits large natural variation in chlorophyll content in the immature fruit. To dissect the genetic and molecular basis of this variation, we conducted QTL mapping for chlorophyll content in a cross between light and dark green-fruited parents, PI 152225 and 1154. Two major QTLs, pc1 and pc10, that control chlorophyll content by modulation of chloroplast compartment size in a fruit-specific manner were detected in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2- LIKE transcription factor (CaGLK2) was found as underlying pc10, similar to its effect on tomato fruit chloroplast development. A candidate gene for pc1was found as controlling chlorophyll content in pepper by the modulation of chloroplast size and number. Fine mapping of pc1 aided by bulked DNA and RNA-seq analyses enabled the identification of a zinc finger transcription factor LOL1 (LSD-One-Like 1) as a candidate gene underlying pc1. LOL1 is a positive regulator of oxidative stress- induced cell death in Arabidopsis. However, over expression of the rice ortholog resulted in an increase of chlorophyll content. Interestingly, CaAPRR2 that is linked to the QTL and was found to affect immature pepper fruit color in a previous study, did not have a significant effect on chlorophyll content in the present study. Verification of the candidate's function was done by generating CRISPR/Cas9 knockout mutants of the orthologues tomato gene, while its knockout experiment in pepper by genome editing is under progress. Phenotypic similarity as a consequence of disrupting the transcription factor in both pepper and tomato indicated its functional conservation in controlling chlorophyll content in the Solanaceae. A limited sequence diversity study indicated that null mutations in CaLOL1 and its putative interactorCaMIP1 are present in C. chinensebut not in C. annuum. Combinations of mutations in CaLOL1, CaMIP1, CaGLK2 and CaAPRR2 are required for the creation of the extreme variation in chlorophyll content in Capsicum.
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Yogev, David, Ricardo Rosenbusch, Sharon Levisohn, and Eitan Rapoport. Molecular Pathogenesis of Mycoplasma bovis and Mycoplasma agalactiae and its Application in Diagnosis and Control. United States Department of Agriculture, April 2000. http://dx.doi.org/10.32747/2000.7573073.bard.

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Mycoplasma bovis and M. agalactiae are two phylogenetically related mycoplasmas which cause economically significant diseases in their respective bovine or small ruminant hosts. These organisms cause persistent asymptomatic infections that can result in severe outbreaks upon introduction of carrier animals into susceptible herds. Little is known about the mechanisms underlying mycoplasma-host interaction, variation in virulence, or of the factors enabling avoidance of the host immune system. In recent years it has become apparent that the ability of pathogenic microorganisms to rapidly alter surface antigenic structures and to fine tune their antigenicity, a phenomena called antigenic variation, is one of the most effective strategies used to escape immune destruction and to establish chronic infections. Our discovery of a novel genetic system, mediating antigenic variation in M. bovis (vsp) as well as in M. agalactiae (avg) served as a starting point for our proposal which included the following objectives: (i) Molecular and functional characterization of the variable surface lipoproteins (Vsp) system of M. bovis and comparison with the Vsp-counterpart in M. agalactiae (ii) Determination of the role of Vsp proteins in the survival of M. bovis when confronted by host defense factors, (iii) Assessment of Vsp-based genetic and antigenic typing of M. bovis and M. agalactiae for epidemiology of infection and (iv) Improvement of diagnostic tests for M. bovis and M. agalactiae based on the vsp-and vsp-analogous systems. We have carried out an extensive molecular characterization of the vsp system and unravelled the precise molecular mechanism responsible for the generation of surface antigenic variation in M. bovis. Our data clearly demonstrated that the two pathogenic mycoplasma species possess large gene families encoding variable lipoprotein antigens that apparently play an important role in immune evasion and in pathogen-host interaction during infection. Phase variable production of these antigens was found to be mediated by a novel molecular mechanism utilizing double site-specific DNA inversions via an intermediate vsp configuration. Studies in model systems indicate that phase variation of VspA is relevant in interaction between M. bovis and macrophages or monocytes, a crucial stage in pathogenesis. Using an ELISA test with captured VspA as an antigen, phase variation was shown to occur in vivo and under field conditions. Genomic rearrangements in the avg gene family of M. agalactiae were shown to occur in vivo and may well have a role in evasion of host defences and establishment of chronic infection. An epidemiological study indicated that patterns of vsp-related antigenic variation diverge rapidly in an M. bovis infected herd. Marked divergence was also found with avg-based genomic typing of M. agalactiae in chronically infected sheep. However, avg-genomic fingerprints were found to be relatively homogeneous in different animals during acute stages of an outbreak of Contagious Agalactiae, and differ between unrelated outbreaks. These data support the concept of vsp-based genomic typing but indicate the necessity for further refinement of the methodology. The molecular knowledge on these surface antigens and their encoding genes provides the basis for generating specific recombinant tools and serological methods for serodiagnosis and epidemiological purposes. Utilization of these methods in the field may allow differentiating acutely infected herds from chronic herds and disease-free herds. In addition the highly immunogenic nature of these lipoproteins may facilitate the design of protective vaccine against mycoplasma infections.
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