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Journal articles on the topic 'American oyster Nucleotide sequence'

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Published: 4 June 2021

Last updated: 15 February 2022

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1

Reeb, C. A., and J. C. Avise. "A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American oyster, Crassostrea virginica." Genetics 124, no. 2 (1990): 397–406. http://dx.doi.org/10.1093/genetics/124.2.397.

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Abstract Restriction site variation in mitochondrial DNA (mtDNA) of the American oyster (Crassostrea virginica) was surveyed in continuously distributed populations sampled from the Gulf of St. Lawrence, Canada, to Brownsville, Texas. mtDNA clonal diversity was high, with 82 different haplotypes revealed among 212 oysters with 13 endonucleases. The mtDNA clones grouped into two distinct genetic arrays (estimated to differ by about 2.6% in nucleotide sequence) that characterized oysters collected north vs. south of a region on the Atlantic mid-coast of Florida. The population genetic "break" in

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2

Sugieda, M., K. Nakajima, and S. Nakajima. "Outbreaks of Norwalk-like virus-associated gastroenteritis traced to shellfish: coexistence of two genotypes in one specimen." Epidemiology and Infection 116, no. 3 (1996): 339–46. http://dx.doi.org/10.1017/s0950268800052663.

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SUMMARYWe determined the nucleotide sequences of Norwalk-like viruses in 10 PCR products from stool or oyster specimens obtained from four outbreaks of gastroenteritis in which shellfish was suspected as the cause in Shizuoka prefecture in Japan between 1987–94. The sequences were determined from nucleotide positions 4561–852 (292 bp) in the polymerase region. Two types of sequences were detected. One (genotype 1) had 87% sequence homology with the prototype Norwalk virus, and the other (genotype 2) had 59 % sequence homology. The sequences from isolates belonging to the same genotype were alm

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3

Robledo, Jose A. F., Anita C. Wright, Adam G. Marsh, and Gerardo R. Vasta. "Nucleotide Sequence Variability in the Nontranscribed Spacer of the rRNA Locus in the Oyster Parasite Perkinsus marinus." Journal of Parasitology 85, no. 4 (1999): 650. http://dx.doi.org/10.2307/3285738.

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4

Mwaengo, Dufton M., Richard F. Grant, James C. Demartini, and Jonathan O. Carlson. "Envelope Glycoprotein Nucleotide Sequence and Genetic Characterization of North American Ovine Lentiviruses." Virology 238, no. 1 (1997): 135–44. http://dx.doi.org/10.1006/viro.1997.8813.

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5

CHO, H. G., S. G. LEE, M. Y. LEE, et al. "An outbreak of norovirus infection associated with fermented oyster consumption in South Korea, 2013." Epidemiology and Infection 144, no. 13 (2016): 2759–64. http://dx.doi.org/10.1017/s0950268816000170.

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SUMMARYAn acute gastroenteritis (AGE) outbreak was reported in May 2013 in Gyeonggi Province, South Korea. Eight students who had eaten breakfast on 21 May 2013 at a high-school restaurant exhibited AGE symptoms. Our case-control study showed that a strong association was observed between AGE symptoms and fermented oyster consumption. Virological studies also indicated that noroviruses (NoVs) were detected from both clinical samples and fermented oyster samples, and multiple different genotypes (genogroups GII.4, GII.11 and GII.14) of NoVs were present in both samples. The nucleotide sequence

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6

Mutebi, John-Paul, René C. A. Rijnbrand, Heiman Wang, et al. "Genetic Relationships and Evolution of Genotypes of Yellow Fever Virus and Other Members of the Yellow Fever Virus Group within the Flavivirus Genus Based on the 3′ Noncoding Region." Journal of Virology 78, no. 18 (2004): 9652–65. http://dx.doi.org/10.1128/jvi.78.18.9652-9665.2004.

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ABSTRACT Genetic relationships among flaviviruses within the yellow fever (YF) virus genetic group were investigated by comparing nucleotide sequences of the 3′ noncoding region (3′NCR). Size heterogeneity was observed between members and even among strains of the same viral species. Size variation between YF strains was due to duplications and/or deletions of repeated nucleotide sequence elements (RYF). West African genotypes had three copies of the RYF (RYF1, RYF2, and RYF3); the Angola and the East and Central African genotypes had two copies (RYF1 and RYF3); and South American genotypes ha

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7

Kim, Woo-Jin, Hyungtaek Jung, Eun-Ha Shin, and Ilseon Baek. "Transferability of Cupped Oyster EST (Expressed Sequence Tag)-Derived SNP (Single Nucleotide Polymorphism) Markers to Related Crassostrea and Ostrea Species." Korean Journal of Malacology 30, no. 3 (2014): 197–210. http://dx.doi.org/10.9710/kjm.2014.30.3.197.

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8

Sudarshana, M. R., and P. H. Berger. "Nucleotide sequence of both genomic RNAs of a North American tobacco rattle virus isolate." Archives of Virology 143, no. 8 (1998): 1535–44. http://dx.doi.org/10.1007/s007050050396.

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9

Pisano, M. R., V. Mercier, V. Deubel, and H. Tolou. "Complete nucleotide sequence and phylogeny of an American strain of yellow fever virus, TRINID79A." Archives of Virology 144, no. 9 (1999): 1837–43. http://dx.doi.org/10.1007/s007050050708.

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10

Neubig, Kurt M., and J. Richard Abbott. "Interspecific hybridization in North American Polygala (Polygalaceae)." Journal of the Botanical Research Institute of Texas 14, no. 1 (2020): 47–56. http://dx.doi.org/10.17348/jbrit.v14.i1.895.

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As a part of ongoing systematic and phylogenetic studies in Polygalaceae, field collections of two pairs of North American species (Polygala balduinii and P. ramosa, and P. lutea and P. rugelii) had morphologically intermediate forms and grew sympatrically, and so were suspected to be interspecific hybrids. Although hybrids among plants are often invoked in taxonomic and floristic literature based on morphologic intermediacy, they are rarely documented and substantiated using molecular tools. We found that the morphologically intermediate individuals within intermixed populations of both speci

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11

SUZUKI, Michio, Emi MURAYAMA, Hirotaka INOUE, et al. "Characterization of Prismalin-14, a novel matrix protein from the prismatic layer of the Japanese pearl oyster (Pinctada fucata)." Biochemical Journal 382, no. 1 (2004): 205–13. http://dx.doi.org/10.1042/bj20040319.

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The mollusc shell is a hard tissue consisting of calcium carbonate and organic matrices. The organic matrices are believed to play important roles in shell formation. In the present study, we extracted and purified a novel matrix protein, named Prismalin-14, from the acid-insoluble fraction of the prismatic layer of the shell of the Japanese pearl oyster (Pinctada fucata), and determined its whole amino acid sequence by a combination of amino acid sequence analysis and MS analysis of the intact protein and its enzymic digests. Prismalin-14 consisted of 105 amino acid residues, including PIYR r

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12

Rádis-Baptista, G., N. Oguiura, M. A. F. Hayashi, et al. "Nucleotide sequence of crotamine isoform precursors from a single South American rattlesnake (Crotalus durissus terrificus)." Toxicon 37, no. 7 (1999): 973–84. http://dx.doi.org/10.1016/s0041-0101(98)00226-8.

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13

Cronin, Matthew A., Steven C. Amstrup, Gerald W. Garner, and Ernest R. Vyse. "Interspecific and intraspecific mitochondrial DNA variation in North American bears (Ursus)." Canadian Journal of Zoology 69, no. 12 (1991): 2985–92. http://dx.doi.org/10.1139/z91-421.

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We assessed mitochondrial DNA variation in North American black bears (Ursus americanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus). Divergent mitochondrial DNA haplotypes (0.05 base substitutions per nucleotide) were identified in populations of black bears from Montana and Oregon. In contrast, very similar haplotypes occur in black bears across North America. This discordance of haplotype phylogeny and geographic distribution indicates that there has been maintenance of polymorphism and considerable gene flow throughout the history of the species. Intraspecific mitochondr

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14

Matsumoto, Shogo, Kentaro Kitahara, Sadao Komori, and Junichi Soejima. "A New S-allele in Apple, `Sg', and Its Similarity to the `Sf' Allele from `Fuji'." HortScience 34, no. 4 (1999): 708–10. http://dx.doi.org/10.21273/hortsci.34.4.708.

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S-allele genotypes of nine apple (Malus ×domestica Borkh.) cultivars were identified using S-allele–specific polymerase chain reaction (PCR)–restriction fragmentlength polymorphism (RFLP) analysis. A new S-allele, Sg, was proposed to be present in `American Summer Pearmain', `Indo', `Kitanosachi', and `Meku 10'. This allele is very similar to Sf at the nucleotide sequence (92%) and deduced amino acid sequence (94%) levels.

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15

Lace, Michael J., Christina Isacson, James R. Anson, et al. "Upstream Regulatory Region Alterations Found in Human Papillomavirus Type 16 (HPV-16) Isolates from Cervical Carcinomas Increase Transcription, ori Function, and HPV Immortalization Capacity in Culture." Journal of Virology 83, no. 15 (2009): 7457–66. http://dx.doi.org/10.1128/jvi.00285-09.

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ABSTRACT Human papillomavirus (HPV) DNAs isolated from cervical and head and neck carcinomas frequently contain nucleotide sequence alterations in the viral upstream regulatory region (URR). Our study has addressed the role such sequence changes may play in the efficiency of establishing HPV persistence and altered keratinocyte growth. Genomic mapping of integrated HPV type 16 (HPV-16) genomes from 32 cervical cancers revealed that the viral E6 and E7 oncogenes, as well as the L1 region/URR, were intact in all of them. The URR sequences from integrated and unintegrated viral DNA were found to

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16

Merkuri, Jordan, Stefania Mirela Mang, Ippolito Camele, Magdalena Cara, and Gian Luigi Rana. "Molecular identification and artificial cultivation of a wild isolate of oyster mushroom in Albania." Italian Journal of Agronomy 10, no. 1s (2016): 35. http://dx.doi.org/10.4081/ija.2016.704.

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Basidiomata of a wild mushroom macroscopically recognised as <em>Pleurotus ostreatus</em> were observed on an oak trunk in a mixed wood of northern Albania. Pure cultures of the fungus were then obtained on potato-dextrose-agar medium. Molecular analyses of genomic DNA of the fungus confirmed its identification. The rDNA ITS region nucleotide sequence of the studied <em>Pleurotacea</em> matched at 99% those of two <em>P. ostreatus</em> strains already present in NCBI GenBank database. The rDNA ITS nucelotide sequences of two pure cultures of the Albanian &lt

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17

Ballinger-Crabtree, M. E., and B. R. Miller. "Partial nucleotide sequence of South American yellow fever virus strain 1899/81: structural proteins and NS1." Journal of General Virology 71, no. 9 (1990): 2115–21. http://dx.doi.org/10.1099/0022-1317-71-9-2115.

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18

Lee, Robyn S., and Marcel A. Behr. "Does Choice Matter? Reference-Based Alignment for Molecular Epidemiology of Tuberculosis." Journal of Clinical Microbiology 54, no. 7 (2016): 1891–95. http://dx.doi.org/10.1128/jcm.00364-16.

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When using genome sequencing for molecular epidemiology, short sequence reads are aligned to an arbitrary reference strain to detect single nucleotide polymorphisms. We investigated whether reference genome selection influences epidemiological inferences ofMycobacterium tuberculosistransmission by aligning sequence reads from 162 closely related lineage 4 (Euro-American) isolates to 7 different genomes. Phylogenetic trees were consistent with use of all but the most divergent genomes, suggesting that reference choice can be based on considerations other thanM. tuberculosislineage.

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19

Boutet, Isabelle, Arnaud Tanguy, and Dario Moraga. "Organization and nucleotide sequence of the European flat oyster Ostrea edulis heat shock cognate 70 (hsc70) and heat shock protein 70 (hsp70) genes." Aquatic Toxicology 65, no. 2 (2003): 221–25. http://dx.doi.org/10.1016/s0166-445x(03)00137-1.

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20

Matos de Oliveira, Gabriela Correia, Raymundo Paraná, and Luís Jesuino De Oliveira Andrade. "IN SILICO MODELING OF THE MOLECULAR STRUCTURE OF microRNAs MARKERS FOR LIVER FIBROSIS IN HEPATITIS C." Revista de Patologia Tropical / Journal of Tropical Pathology 48, no. 3 (2019): 135–47. http://dx.doi.org/10.5216/rpt.v48i3.58660.

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Molecular biology looks for evidence that microRNA (miRNAs) plays a relevant function both in the beginning and advanced stages of hepatic fibrosis (HF), and has been proposed as an additional biomarker for HF forecasting in carriers of hepatitis C virus (HCV) infection. The purpose of this study was to develop an in silico modeling of the two-dimensional (2D) molecular structure of miRNA markers for HF in carriers of HCV. A search was initially performed for the nucleotide sequence of 6 miRNAs defined as biomarkers for HF, performinga computational simulation of the molecular structure of the

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21

Schaeffer, S. W., and E. L. Miller. "Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region." Genetics 132, no. 2 (1992): 471–80. http://dx.doi.org/10.1093/genetics/132.2.471.

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Abstract The genetic structure of Drosophila pseudoobscura populations was inferred from a nucleotide sequence analysis of a 3.4-kb segment of the alcohol dehydrogenase (Adh) region. A total of 99 isochromosomal strains collected from 13 populations in North and South America were used to determine if any population departed from a neutral model and to estimate levels of gene flow between populations. This study also included the nucleotide sequences from two sibling species, D. persimilis and D. miranda. We estimated the neutral mutation parameter, 4N mu, in synonymous and noncoding sites for

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22

Kami, James A., and Paul Gepts. "Phaseolin nucleotide sequence diversity in Phaseolus. I. Intraspecific diversity in Phaseolus vulgaris." Genome 37, no. 5 (1994): 751–57. http://dx.doi.org/10.1139/g94-107.

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Most information about the molecular biology of phaseolin, the major seed storage protein in Phaseolus vulgaris, has been obtained from the T-type phaseolin, which is characteristic of the Andean gene pool of the species. In the work reported here, two cDNA clones for the S-type phaseolin representing the other major, Middle American gene pool were isolated and sequenced. Analysis of the DNA sequences revealed the presence of two subtypes of S phaseolin, α and β, depending on the presence or absence, respectively, of a 27-bp direct repeat. These are similar to the α- and β-phaseolin subtypes f

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23

Yoshinaga, Haruhiko, Masako Nakahara, Aya Shibamiya, et al. "A Single Thymine Nucleotide Deletion Responsible for Congenital Deficiency of Plasmin Inhibitor." Thrombosis and Haemostasis 88, no. 07 (2002): 144–48. http://dx.doi.org/10.1055/s-0037-1613167.

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SummaryPlasma plasmin inhibitor (PI) is a physiological inhibitor of plasminmediated fibrinolysis and constitutes a hemostatic component in blood plasma; hence its deficiency results in a severe hemorrhagic diathesis. We have carried out molecular analysis of American family members with congenital PI deficiency, and detected a single thymine deletion at nucleotide position 332 in exon 5. The deletion was found in both alleles of the homozygotes and in one allele of the heterozygotes, and the patterns of restriction fragment length polymorphism created by the mutation in the family members wer

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24

Xue, Hong, Yan Xu, Yan Boucher та Martin F. Polz. "High Frequency of a Novel Filamentous Phage, VCYϕ, within an Environmental Vibrio cholerae Population". Applied and Environmental Microbiology 78, № 1 (2011): 28–33. http://dx.doi.org/10.1128/aem.06297-11.

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ABSTRACTEnvironmentalVibrio choleraestrains isolated from a coastal brackish pond (Oyster Pond, Woods Hole, MA) carried a novel filamentous phage, VCYϕ, which can exist as a host genome integrative form (IF) and a plasmid-like replicative form (RF). Outside the cell, the phage displays a morphology typical ofInovirus, with filamentous particles ∼1.8 μm in length and 7 nm in width. Four independent RF isolates had identical genomes, except for 8 single nucleotide polymorphisms clustered in two regions. The overall genome size is 7,103 bp with 11 putative open reading frames organized into three

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25

Hao, Ruijuan, Chuchu Mo, Linda Adzigbli, Chuangye Yang, Yuewen Deng, and Qingheng Wang. "Molecular Cloning and Polymorphism Analysis of PmFGF18 from Pinctada fucata martensii." Journal of Marine Science and Engineering 8, no. 11 (2020): 896. http://dx.doi.org/10.3390/jmse8110896.

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Fibroblast growth factor 18 (FGF18) plays an important functional role in skeletal growth and development. The FGF18 gene was characterized in pearl oyster Pinctada fucata martensii (PmFGF18) with the full-length sequence containing an open reading frame of 714 bp encoding 237 amino acids. The domain analysis of PmFGF18 showed a distinctive FGF domain, with a high similarity to FGF18 protein sequences from Crassostrea gigas (43.35%) and C. virginica (37.43%). PmFGF18 expression was revealed in all analyzed tissues with a significantly higher expression level in the fast-growing group than the

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Aramaki, Kaelen, Gayle Teramura, Lakshmi Gaur та Alexander Reiner. "Analysis of Platelet Glycoprotein Ia (α2 Integrin) Allele Frequencies in Three North American Populations Reveals Genetic Association between Nucleotide 807C/T and Amino Acid 505 Glu/Lys (HPA-5) Dimorphisms". Thrombosis and Haemostasis 80, № 09 (1998): 449–56. http://dx.doi.org/10.1055/s-0037-1615228.

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SummaryGlycoprotein Ia (α2 integrin) is a subunit of the heterodimeric membrane complex (GPIa/IIa) that mediates platelet adhesion to collagen. Several nucleotide sequence variations of GPIa have been described. A nucleotide 1648 G/A dimorphism that leads to a Glu/Lys substitution at amino acid 505 is responsible for the human platelet antigen system, HPA-5. Recently, two other linked GPIa nucleotide dimorphisms involving codons Phe224 and Thr246 were identified: a C/T substitution at nucleotide 807 and a G/A substitution at nucleotide 873 (1). Using restriction enzyme digestion of amplified G

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27

Dhar, A. K., R. P. Singh, and A. Boucher. "Molecular cloning and sequencing of the capsid and the nuclear inclusion protein genes of a North American PVYN isolate." Canadian Journal of Microbiology 40, no. 9 (1994): 798–804. http://dx.doi.org/10.1139/m94-127.

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The sequence of the 3′-terminal 3258 nucleotides of a tobacco veinal necrosis strain of a potato virus Y (PVYN) isolate from North America was determined. The sequence revealed an open reading frame of 2931 nucleotides, of which the start codon was not identified. The nontranslated region contains 327 nucleotides upstream of a poly(A) tract. The open reading frame encodes a large polyprotein containing 976 amino acids. The data indicate that the coat protein (CP) and the nuclear inclusion protein (NIb) are derived from the large polypeptide by proteolytic cleavage similar to many other potyvir

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28

Dyble, Julianne, Hans W. Paerl, and Brett A. Neilan. "Genetic Characterization of Cylindrospermopsis raciborskii (Cyanobacteria) Isolates from Diverse Geographic Origins Based on nifH and cpcBA-IGS Nucleotide Sequence Analysis." Applied and Environmental Microbiology 68, no. 5 (2002): 2567–71. http://dx.doi.org/10.1128/aem.68.5.2567-2571.2002.

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ABSTRACT Isolates of the toxic, N2-fixing species Cylindrospermopsis raciborskii from various geographic locations were analyzed with respect to their genetic diversity based on the nifH and cpcBA-IGS genes. Gene sequences clustered according to their geographic origin, with the nifH sequences separating into European, Australian, and American groups and the cpcBA-IGS sequences separating into American and European or Australian groups. PCR primers for both genes were designed to exclusively amplify DNA from Cylindrospermopsis species, and an additional primer set for cpcBA-IGS was designed to

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29

Rodriguez, Luis L., Steven J. Pauszek, Thomas A. Bunch, and Kate R. Schumann. "Full-length genome analysis of natural isolates of vesicular stomatitis virus (Indiana 1 serotype) from North, Central and South America." Journal of General Virology 83, no. 10 (2002): 2475–83. http://dx.doi.org/10.1099/0022-1317-83-10-2475.

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Most studies on the molecular biology and functional analysis of vesicular stomatitis virus Indiana 1 serotype (VSV-IN1) are based on the only full-length genomic sequence currently deposited in GenBank. This sequence is a composite of several VSV-IN1 laboratory strains passaged extensively in tissue culture over the years and it is not certain that this sequence is representative of strains circulating in nature. We describe here the complete genomic sequence of three natural isolates, each representing a distinct genetic lineage and geographical origin: 98COE (North America), 94GUB (Central

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30

Jenny, Matthew J., Amy H. Ringwood, Eric R. Lacy, et al. "Potential Indicators of Stress Response Identified by Expressed Sequence Tag Analysis of Hemocytes and Embryos from the American Oyster, Crassostrea virginica." Marine Biotechnology 4, no. 1 (2002): 0081–93. http://dx.doi.org/10.1007/s10126-001-0072-8.

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31

Fontecha, Nerea, Miren Basaras, Elixabete Arrese, Silvia Hernáez, Daniel Andía, and Ramon Cisterna. "Human Papillomavirus 16 Variants May Be Identified by E6 Gene Analysis." Intervirology 58, no. 3 (2015): 143–48. http://dx.doi.org/10.1159/000381745.

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Aims: The aims of the study were (1) to characterize the genetic variability of human papillomavirus (HPV) genotype 16 in the E6 region when this genotype is present in multiple infection samples, (2) to assess the prevalence of variants in our region and (3) to analyze the relationship between variants, patients' ages and pathology. Methods: The Clinical Microbiology and Infection Control Department analyzed samples which were positive for genotype 16 and other genotypes from 2007 to 2013. Variants were assigned to European, Euro-German, Asian, Asian-American or African lineage by sequence an

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32

Ma, Yongping, Xiaobo Wen, Yasutaka Hoshino, and L. Yuan. "Cloning and nucleotide sequence analyses of 11 genome segments of two American and one British equine rotavirus strains." Veterinary Microbiology 176, no. 1-2 (2015): 172–78. http://dx.doi.org/10.1016/j.vetmic.2015.01.008.

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Ropp, Susan L., Carrie E. Mahlum Wees, Ying Fang, et al. "Characterization of Emerging European-Like Porcine Reproductive and Respiratory Syndrome Virus Isolates in the United States." Journal of Virology 78, no. 7 (2004): 3684–703. http://dx.doi.org/10.1128/jvi.78.7.3684-3703.2004.

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ABSTRACT European-like field isolates of porcine reproductive and respiratory syndrome virus (PRRSV) have recently emerged in North America. The full-length genomic sequence of an index isolate characterized in 1999, strain EuroPRRSV, served as the reference strain for further studies of the evolution and epidemiology of European-like isolates (type 1) in the United States. Strain EuroPRRSV shared 90.1 to 100% amino acid identity with the prototype European strain, Lelystad, within the structural and nonstructural open reading frames (ORFs) and 95.3% overall nucleotide identity. The 5′ untrans

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34

Mráz, I., K. Petrzik, M. Šíp, and J. Fránová-Honetšlegrová. "Variability in Coat Protein Sequence Homology Among American and European Sources of Strawberry Vein Banding Virus." Plant Disease 82, no. 5 (1998): 544–46. http://dx.doi.org/10.1094/pdis.1998.82.5.544.

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Strawberry vein banding virus (SVBV) isolates from North America, Czech Republic, Norway, and Germany were collected and their variability was determined by dot blot hybridization and confirmed by sequencing of a 431-nucleotide fragment from the middle part of the coat protein gene. Two different substitutions were found between the American and two Czech SVBV isolates, but the other isolates were identical in the compared region to the American isolate. Digoxigenin-labeled probes were prepared from these isolates and used for hybridization with polymerase chain reaction-amplified fragments of

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35

Bentzen, Paul, and Jonathan M. Wright. "Nucleotide sequence and evolutionary conservation of a minisatellite variable number tandem repeat cloned from Atlantic salmon, Salmo salar." Genome 36, no. 2 (1993): 271–77. http://dx.doi.org/10.1139/g93-038.

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We describe the nucleotide sequence, extent of polymorphism, and evolutionary conservation of a minisatellite cloned from a fish, Atlantic salmon (Salmo salar). The Ssal minisatellite contains a 16-bp repeat exhibiting partial sequence identity to bird and mammal minisatellites but most closely resembling an insect minisatellite (81% sequence identity). The Ssal locus exhibits a minimum of three to seven alleles per population in three eastern North American salmon populations. A probe based on the nonrepetitive 5′ flank of Ssal detected a polymorphic locus in a variety of salmoid species, sug

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RUIZ, A., J. M. MOLINA, A. NJUE, and R. K. PRICHARD. "Genetic variability in cysteine protease genes ofHaemonchus contortus." Parasitology 128, no. 5 (2004): 549–59. http://dx.doi.org/10.1017/s0031182004004998.

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To increase the existent genetic variability in cysteine proteases, a polymorphism study was performed inHaemonchus contortusby comparing 2 different strains of the parasite: North American (NA) and Spanish (SP) strains. For this purpose, the polymorphism of 5 previously reported genes (AC-1,AC-3,AC-4,AC-5andGCP-7) were analysed by PCR–SSCP and sequencing procedures. Based on the SSCP results, a total of 20 different alleles were identified for the 5lociassessed. Exceptlocus AC-5, all thelociwere polymorphic.Loci AC-1,AC-3,AC-4andGCP-7showed 5, 8, 2 and 4 alleles, respectively. The allelic fre

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Kalbfleisch, Theodore S., Brenda M. Murdoch, Timothy P. L. Smith, James D. Murdoch, Michael P. Heaton, and Stephanie D. McKay. "A SNP resource for studying North American moose." F1000Research 7 (January 10, 2018): 40. http://dx.doi.org/10.12688/f1000research.13501.1.

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Background: Moose (Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack

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Yin, Xiaoshen, Alberto Arias-Pérez, Tevfik Hamdi Kitapci, and Dennis Hedgecock. "High-Density Linkage Maps Based on Genotyping-by-Sequencing (GBS) Confirm a Chromosome-Level Genome Assembly and Reveal Variation in Recombination Rate for the Pacific Oyster Crassostrea gigas." G3: Genes|Genomes|Genetics 10, no. 12 (2020): 4691–705. http://dx.doi.org/10.1534/g3.120.401728.

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Studies of linkage and linkage mapping have advanced genetic and biological knowledge for over 100 years. In addition to their growing role, today, in mapping phenotypes to genotypes, dense linkage maps can help to validate genome assemblies. Previously, we showed that 40% of scaffolds in the first genome assembly for the Pacific oyster Crassostrea gigas were chimeric, containing single nucleotide polymorphisms (SNPs) mapping to different linkage groups. Here, we merge 14 linkage maps constructed of SNPs generated from genotyping-by-sequencing (GBS) methods with five, previously constructed li

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Rathinam, A. Vijay, Thomas T. Chen, and Robert M. Grossfeld. "Cloning and Sequence Analysis of a cDNA for an Inducible 70 kDa Heat Shock Protein (Hsp70) of the American Oyster (Crassostrea virginica)." DNA Sequence 11, no. 3-4 (2000): 261–64. http://dx.doi.org/10.3109/10425170009033240.

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Seo, Jung-Kil, Dong-Gyun Kim, Ji-Eun Lee, et al. "Antimicrobial Activity and Action Mechanisms of Arg-Rich Short Analog Peptides Designed from the C-Terminal Loop Region of American Oyster Defensin (AOD)." Marine Drugs 19, no. 8 (2021): 451. http://dx.doi.org/10.3390/md19080451.

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American oyster defensin (AOD) was previously purified from acidified gill extract of the American oyster, Crassostrea virginica. AOD is composed of 38 amino acids with three disulfide bonds and exhibits strong antimicrobial activity against Gram-positive bacteria as well as significant activity against Gram-negative bacteria. Here, to develop promising peptides into antibiotic candidates, we designed five arginine-rich analogs (A0, A1, A2, A3, and A4), predicted their loop and extended strand/random structures—including nine amino acids and a disulfide bond derived from the C-terminus of AOD—

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Ferreiro, C., K. Ostrówka, J. J. López-Moya, and J. R. Díaz-Ruíz. "Nucleotide sequence and symptom modulating analysis of a Peanut stunt virus-associated satellite RNA from Poland: high level of sequence identity with the American PSV satellites." European Journal of Plant Pathology 102, no. 8 (1996): 779–86. http://dx.doi.org/10.1007/bf01877153.

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Indik, Stanislav, Lubomír Valíček, Dieter Klein, and Jana Klánová. "Variations in the major envelope glycoprotein GP5 of Czech strains of porcine reproductive and respiratory syndrome virus." Journal of General Virology 81, no. 10 (2000): 2497–502. http://dx.doi.org/10.1099/0022-1317-81-10-2497.

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The major envelope glycoprotein genes (ORF5) of seven Czech isolates of porcine reproductive and respiratory syndrome virus (PRRSV) were amplified and their nucleotide sequences were determined. ORF5 displayed nucleotide and amino acid identities of 87·5–100% and 87·6–100%, respectively, among the isolates. In a phylogenetic tree, all European isolates were grouped in a genotype distinct from that of reference American strains (VR-2332, IAF-Klop). Among the European isolates, two different clades were identified. Two Czech isolates (V-501 and V-503) and Italian strain PRRSV 2156 fell into one

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Treffer, Leah K., Edward S. Rice, Anna M. Fuller, Samuel Cutler, and Jessica L. Petersen. "PSI-40 Two mitochondrial lineages revealed in North American yak." Journal of Animal Science 98, Supplement_4 (2020): 477. http://dx.doi.org/10.1093/jas/skaa278.833.

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Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compar

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Hòa, Lê Thanh, Đỗ Thị Roan, Nguyễn Thị Khuê, Đoàn Thị Thanh Hương, and Nguyễn Thị Bích Nga. "Genotypic, phylogenetic and epidemiological characteristics of porcine reproductive and respiratory syndrome virus strains (PRRSV) in Vietnam." Vietnam Journal of Biotechnology 15, no. 1 (2018): 31–38. http://dx.doi.org/10.15625/1811-4989/15/1/12317.

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Nucleotide sequence of ORF5 encoding the antigenic GP5 for 11 strains collected from different geographic localities in the country during 2008-2011 were obtained. These nucleotide sequences were analyzed for molecular properties (nucleotides and amino acids) to determine genotype, phylogenetic and molecular epidemiological characteristics compared with PRRSV circulating in Vietnam and worldwide. Analysis of nucleotides and deduced amino acids showed that there was very high level of nucleotide identity and amino acid homology (98 – 100%) between the Vietnamese and Chinese PRRSV strains. Phylo

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Ida, Cristiane M., Patrick A. Lundquist, Karen Weck, and W. Edward Highsmith. "The Power of Proficiency Testing: Unraveling Single-Nucleotide Polymorphism Interference, With Potential Impact on Clinical Testing of Spinocerebellar Ataxia Type 3." Archives of Pathology & Laboratory Medicine 143, no. 3 (2018): 349–55. http://dx.doi.org/10.5858/arpa.2017-0566-oa.

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Context.— The College of American Pathologists proficiency testing program has been instrumental in identifying problems in clinical testing. Objective.— To describe how this program was used to identify a single-nucleotide polymorphism that affects clinical testing for spinocerebellar ataxia type 3. Design.— A proficiency testing sample with discordant results for spinocerebellar ataxia type 3 analysis was further evaluated by targeted Sanger sequencing and genotype polymerase chain reaction using multiple DNA polymerases. Results.— Of 28 laboratories responding in the spinocerebellar ataxia

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Bajet, N. B., T. R. Unruh, K. L. Druffel, and K. C. Eastwell. "Occurrence of Two Little Cherry Viruses in Sweet Cherry in Washington State." Plant Disease 92, no. 2 (2008): 234–38. http://dx.doi.org/10.1094/pdis-92-2-0234.

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Little cherry disease, one of the major viral diseases of sweet cherry (Prunus avium) worldwide, is associated with either of two closteroviruses, Little cherry virus 1 (LChV-1) and Little cherry virus 2 (LChV-2). Two sets of primers corresponding to a portion of the replicase gene of LChV-1 and LChV-2 were used in one-tube reverse-transcription polymerase chain reactions to detect these viruses in total RNA extracts of field-collected sweet cherry tissues. LChV-1 and LChV-2 were detected both alone and in combination in five sweet cherry orchards in Washington State. Sequence analysis of a 24

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Charrel, Rémi N., Nicolas Lévy, Robert B. Tesh, and Laura J. Chandler. "Use of Base Excision Sequence Scanning for Detection of Genetic Variations in St. Louis Encephalitis Virus Isolates." Journal of Clinical Microbiology 37, no. 6 (1999): 1935–40. http://dx.doi.org/10.1128/jcm.37.6.1935-1940.1999.

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Twenty-two isolates of St. Louis encephalitis (SLE) virus of various geographical origins (Brazil, Argentina, Panama, Texas, Missouri, Maryland, California, and Florida) were examined for genetic variation by the base excision sequence scanning (BESS T-scan) method. A fragment was amplified in the envelope gene with the forward primer labeled in the PCR. The BESS T-scan method determined different clusters according to the profiles generated for the isolates and successfully grouped the isolates according to their geographical origins. Two major clusters, the North American cluster (cluster A)

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McClean, Phillip E., Rian K. Lee, and Phillip N. Miklas. "Sequence diversity analysis of dihydroflavonol 4-reductase intron 1 in common bean." Genome 47, no. 2 (2004): 266–80. http://dx.doi.org/10.1139/g03-103.

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Variation in common bean (Phaseolus vulgaris L.) was investigated by sequencing intron 1 of the dihydroflavonol 4-reductase (DFR) gene for 92 genotypes that represent both landraces and cultivars. We were also interested in determining if introns provide sufficient variation for genetic diversity studies and if the sequence data could be used to develop allele-specific primers that could differentiate genotypes using a standard PCR assay. Sixty-nine polymorphic sites were observed. Nucleotide variation (π/bp) was 0.0481, a value higher than that reported for introns from other plant species. T

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Balakirev, Evgeniy S., and Francisco J. Ayala. "Nucleotide Variation of theEst-6Gene Region in Natural Populations ofDrosophila melanogaster." Genetics 165, no. 4 (2003): 1901–14. http://dx.doi.org/10.1093/genetics/165.4.1901.

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AbstractWe have investigated nucleotide polymorphism in the Est-6 gene region in four samples of Drosophila melanogaster derived from natural populations of East Africa (Zimbabwe), Europe (Spain), North America (California), and South America (Venezuela). There are two divergent sequence types in the North and South American samples, which are not perfectly (North America) or not at all (South America) associated with the Est-6 allozyme variation. Less pronounced or no sequence dimorphism occurs in the European and African samples, respectively. The level of nucleotide diversity is highest in

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Hirsch, A. E., D. P. Atencio, and B. S. Rosenstein. "Screening for ATM sequence alterations in African-American women diagnosed with breast cancer." Journal of Clinical Oncology 24, no. 18_suppl (2006): 10037. http://dx.doi.org/10.1200/jco.2006.24.18_suppl.10037.

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10037 Background: Women who are heterozygous for mutations in the ATM gene, ATM carriers, are reported to have an increased risk of breast cancer compared with noncarriers of the mutation. There are few data on breast cancer susceptibility mutations in African-American women, particularly the non-BRCA mutations. We set out to determine whether there is evidence that ATM represents a breast cancer susceptibility gene in African-American women. Methods: One hundred thirty-two African-American women were screened for ATM sequence alterations. Thirty-seven (28%) were women with a histological diag

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