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Mickley, Lyn A., Jong-Seok Lee, Zheng Weng, et al. "Genetic Polymorphism in MDR-1: A Tool for Examining Allelic Expression in Normal Cells, Unselected and Drug-Selected Cell Lines, and Human Tumors." Blood 91, no. 5 (1998): 1749–56. http://dx.doi.org/10.1182/blood.v91.5.1749.
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Abstract By using RNase protection analysis, residues 2677 and 2995 ofMDR-1 were identified as sites of genetic polymorphism. Through use of oligonucleotide hybridization, the genomic content and expression of individual MDR-1 alleles were examined in normal tissues, unselected and drug selected cell lines, and malignant lymphomas. In normal tissues, unselected cell lines, and untreated malignant lymphoma samples, expression of MDR-1 from both alleles was similar. In contrast, in drug selected cell lines, and in relapsed malignant lymphoma samples, expression of one allele was found in a large percentage of samples. To understand how expression of one allele occurs, two multidrug resistant sublines were isolated by exposing a Burkitt lymphoma cell line to increasing concentrations of vincristine. The resistant sublines expressed only one allele and had a hybrid MDR-1 gene composed of non–MDR-1 sequences proximal to MDR-1. Previous studies showing hybridMDR-1 genes after rearrangements provided a potential explanation for activation and expression of one MDR-1 allele. We conclude that oligonucleotide hybridization can be used as a sensitive tool to examine relative allelic expression of MDR-1,and can identify abnormal expression from a single allele. Acquired drug resistance in vitro and in patients is often associated with expression of a single MDR-1 allele, and this can be a marker of a hybrid MDR-1 gene.
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Mickley, Lyn A., Jong-Seok Lee, Zheng Weng, et al. "Genetic Polymorphism in MDR-1: A Tool for Examining Allelic Expression in Normal Cells, Unselected and Drug-Selected Cell Lines, and Human Tumors." Blood 91, no. 5 (1998): 1749–56. http://dx.doi.org/10.1182/blood.v91.5.1749.1749_1749_1756.
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By using RNase protection analysis, residues 2677 and 2995 ofMDR-1 were identified as sites of genetic polymorphism. Through use of oligonucleotide hybridization, the genomic content and expression of individual MDR-1 alleles were examined in normal tissues, unselected and drug selected cell lines, and malignant lymphomas. In normal tissues, unselected cell lines, and untreated malignant lymphoma samples, expression of MDR-1 from both alleles was similar. In contrast, in drug selected cell lines, and in relapsed malignant lymphoma samples, expression of one allele was found in a large percentage of samples. To understand how expression of one allele occurs, two multidrug resistant sublines were isolated by exposing a Burkitt lymphoma cell line to increasing concentrations of vincristine. The resistant sublines expressed only one allele and had a hybrid MDR-1 gene composed of non–MDR-1 sequences proximal to MDR-1. Previous studies showing hybridMDR-1 genes after rearrangements provided a potential explanation for activation and expression of one MDR-1 allele. We conclude that oligonucleotide hybridization can be used as a sensitive tool to examine relative allelic expression of MDR-1,and can identify abnormal expression from a single allele. Acquired drug resistance in vitro and in patients is often associated with expression of a single MDR-1 allele, and this can be a marker of a hybrid MDR-1 gene.
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Wang, Wubin, Bin Zhou, Jianbo He, et al. "Comprehensive Identification of Drought Tolerance QTL-Allele and Candidate Gene Systems in Chinese Cultivated Soybean Population." International Journal of Molecular Sciences 21, no. 14 (2020): 4830. http://dx.doi.org/10.3390/ijms21144830.
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Drought is one of the most important factors affecting plant growth and productivity. The previous results on drought tolerance (DT) genetic system in soybean indicated a complex of genes not only few ones were involved in the trait. This study is featured with a relatively thorough identification of QTL-allele/candidate-gene system using an efficient restricted two-stage multi-locus multi-allele genome-wide association study, on two comprehensive DT indicators, membership index values of relative plant weight (MPW) and height (MPH), instead of a single biological characteristic, in a large sample (564 accessions) of the Chinese cultivated soybean population (CCSP). Based on 24,694 multi-allele markers, 75 and 64 QTL with 261 and 207 alleles (2–12/locus) were detected for MPW and MPH, explaining 54.7% and 47.1% of phenotypic variance, respectively. The detected QTL-alleles were organized into a QTL-allele matrix for each indicator, indicating DT is a super-trait conferred by two (even more) QTL-allele systems of sub-traits. Each CCSP matrix was separated into landrace (LR) and released cultivar (RC) sub-matrices, which showed significant differentiation in QTL-allele constitutions, with 58 LR alleles excluded and 16 new ones emerged in RC. Using the matrices, optimal crosses with great DT transgressive recombinants were predicted. From the detected QTL, 177 candidate genes were annotated and validated with quantitative Real-time PCR, and grouped into nine categories, with ABA and stress responders as the major parts. The key point of the above results is the establishment of relatively full QTL-allele matrices composed of numerous gene functions jointly conferring DT, therefore, demonstrates the complexity of DT genetic system and potential of CCSP in DT breeding.
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Iwasaki, Risa L., Koji Ishiya, Hideaki Kanzawa-Kiriyama, Yosuke Kawai, Jun Gojobori, and Yoko Satta. "Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population." Genes 11, no. 7 (2020): 775. http://dx.doi.org/10.3390/genes11070775.
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A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.
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Muntau, B., T. Thye, C. Pirmez, and R. O. Horstmann. "A novel DPA1 allele (DPA1*0203) composed of known epitopes." Tissue Antigens 49, no. 6 (1997): 668–69. http://dx.doi.org/10.1111/j.1399-0039.1997.tb02821.x.
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Noizat-Pirenne, France, Ketty Lee, Pierre-Yves Le Pennec, et al. "Rare RHCE phenotypes in black individuals of Afro-Caribbean origin: identification and transfusion safety." Blood 100, no. 12 (2002): 4223–31. http://dx.doi.org/10.1182/blood-2002-01-0229.
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The molecular backgrounds of variants encountered in Afro-Caribbean black individuals and associated with the production of clinically significant antibodies against high-incidence antigens (anti-RH18, anti-RH34) and against Rhe epitopes were determined. We showed that RH:−18 phenotypes are produced by 3 distinct RHCEalleles: ceEK carrying 48G>C (exon 1), 712A>G, 787A>G, 800T>A (exon 5); ceBI carrying 48G>C (exon 1), 712A>G (exon 5), 818C>T (exon 6), 1132C>G (exon 8); and the already knownceAR allele carrying 48G>C (exon 1), 712A>G, 733C>G, 787A>G, 800T>A (exon 5), and 916A>G (exon 6). The RH:−34 phenotype is produced by the (C)ces haplotype described previously and composed of a hybrid D-CE(3-8)-D gene with 4 extra mutations next to a ces allele (733C>G; exon 5) with an extra mutation in exon 7 (1006G>T). Partial Rhe with risk of immunization against lacking epitopes can be produced by the new ces allele carrying an extra mutation in exon 3 (340C>T) and by the ceMO allele described previously. A population of sickle cell disease patients was screened to estimate the incidence of these rare alleles, with the conclusion that a procedure is required to detect the associated phenotypes in black donors to ensure transfusion safety for patients. We also described a new variant [ces(748)] and variants carrying different altered alleles in nonimmunized patients and for whom the risk of immunization is discussed.
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Medina-Rodríguez, Nathan, and Ángelo Santana. "Allele Imputation and Haplotype Determination from Databases Composed of Nuclear Families." R Journal 9, no. 2 (2017): 35. http://dx.doi.org/10.32614/rj-2017-057.
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Minegishi, Yoshiyuki, Elaine Coustan-Smith, Yui-Hsi Wang, Max D. Cooper, Dario Campana та Mary Ellen Conley. "Mutations in the Human λ5/14.1 Gene Result in B Cell Deficiency and Agammaglobulinemia". Journal of Experimental Medicine 187, № 1 (1998): 71–77. http://dx.doi.org/10.1084/jem.187.1.71.
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B cell precursors transiently express a pre–B cell receptor complex consisting of a rearranged mu heavy chain, a surrogate light chain composed of λ5/14.1 and VpreB, and the immunoglobulin (Ig)-associated signal transducing chains, Igα and Igβ. Mutations in the mu heavy chain are associated with a complete failure of B cell development in both humans and mice, whereas mutations in murine λ5 result in a leaky phenotype with detectable humoral responses. In evaluating patients with agammaglobulinemia and markedly reduced numbers of B cells, we identified a boy with mutations on both alleles of the gene for λ5/14.1. The maternal allele carried a premature stop codon in the first exon of λ5/14.1 and the paternal allele demonstrated three basepair substitutions in a 33-basepair sequence in exon 3. The three substitutions correspond to the sequence in the λ5/14.1 pseudogene 16.1 and result in an amino acid substitution at an invariant proline. When expressed in COS cells, the allele carrying the pseudogene sequence resulted in defective folding and secretion of mutant λ5/14.1. These findings indicate that expression of the functional λ5/14.1 is critical for B cell development in the human.
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Nolin, Sarah L., Xiao-hua Ding, George E. Houck, W. Ted Brown, and Carl Dobkin. "Fragile X full mutation alleles composed of few alleles: Implications for CGG repeat expansion." American Journal of Medical Genetics Part A 146A, no. 1 (2007): 60–65. http://dx.doi.org/10.1002/ajmg.a.32087.
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Suprovych, T. M., T. M. Dyman, M. P. Suprovych, T. M. Karchevska, T. V. Koval, and V. A. Kolodiy. "Population genetic structure of the Ukrainian black-pied dairy breed with the genome BoLA-DRB3." Regulatory Mechanisms in Biosystems 9, no. 4 (2018): 568–77. http://dx.doi.org/10.15421/021885.
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The second exon of the BoLA-DRB3 gene has the highest level of polymorphism among all studied loci of the major histocompatibility complex (MHC) in cattle, which allows it to be used for studying population-genetic structure and assessing the level of biodiversity of populations or comparing the biodiversity of particular herds. According to the results of typing the blood samples of 293 cows using the method of PCR-RLFP, we determined allele frequencies of the BoLA-DRB3 gene for the Ukrainian black-pied dairy breed. The study was conducted on three herds in Khmelnytskyi Oblast: LLC “Kozatska Dolyna 2006” (herd A, n = 122), agrofirm “Perlyna Podillya” (herd B, n = 82) and branch “Ridnyy kray” (herd C, n = 89). In total, 37 alleles were found: herd A 31, herd B 25 and herd C 28. In total, in the three subpopulations seven alleles were found with frequency of over 5%, the total share of which equaled 55.8%. The most widely distributed allele was BoLA-DRB3.2*24, which composed 22.2% of the allele pool of the breed. We determined a high level of observed (0.89 to 0.95) and expected (0.93 to 0.94) heterozygosity. In herds A and B, there was determined domination of homozygotes. Deviation from HWE, calculated using the value of Wright`s individual fixation index, equaled FIS(A) = 0.016 (χ2 = 0.03; P > 0.05) and FIS(B) = 0.044 (χ2 = 0.076; P > 0.05). In herd C, we found excess of heterozygotes FIS(C) = -0.017 (χ2 = 0.026; P > 0.05). Rather low values were determined for the subpopulation fixation index: FST(A) = 0.009 (χ2 = 65.9; P < 0.01), FST(B) = 0.012 (χ2 = 47.2; P < 0.05) and FST(C) = 0.003 (χ2 = 14.4; P > 0.05), which were significantly different from the mean value for cattle (FST = 0.078), indicating insignificant reduction of heterozygosity and divergence between the subpopulations by the BoLA-DRB3 gene. To assess genetic diversity, we calculated parameters of effective allele number (Ae) and Shannon’s information index (I). In spite of the different numbers of alleles found in the selections, it was suggested that for assessing their diversity, an efficiency index will be used which shows the share of effective alleles among all alleles found in a subpopulation (Ae/Nа). The calculated values of the parameters equaled: herd A Ae = 14.9, Ae/Nа = 0.48, I = 3.05; herd B Ae = 14.5, Ae/Nа = 0.58, I = 2.87; herd C Ae = 16.4, Ae/Nа = 0.59, I = 3.01. Frequencies of BoLA-DRB3 alleles were used for calculating genetic similarity and standard genetic distances according to Nei. Cows of herds B and C were found to be more genetically affinitive by the BoLA-DRB3 gene. Standard genetic distance between them was the lowest D = 0.13, which coincides with the geographic locations and historical development of these populations. The results of the study prove that the studied herds have a high level of polymorphism. Frequency characteristics, values of expected heterozygosity, effective allele number, efficiency index and Shannon’s information index compared to the similar parameters for Holstein, black-pied and some other local breeds of cattle indicate the high genetic diversity of the studied subpopulations of the Ukrainian black-pied dairy breed.
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Liu, Cheng, Xianlian Chen, Wubin Wang, et al. "Identifying Wild Versus Cultivated Gene-Alleles Conferring Seed Coat Color and Days to Flowering in Soybean." International Journal of Molecular Sciences 22, no. 4 (2021): 1559. http://dx.doi.org/10.3390/ijms22041559.
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Annual wild soybean (G. soja) is the ancestor of the cultivated soybean (G. max). To reveal the genetic changes from soja to max, an improved wild soybean chromosome segment substitution line (CSSL) population, SojaCSSLP5, composed of 177 CSSLs with 182 SSR markers (SSR-map), was developed based on SojaCSSLP1 generated from NN1138-2(max)×N24852(soja). The SojaCSSLP5 was genotyped further through whole-genome resequencing, resulting in a physical map with 1366 SNPLDBs (SNP linkage-disequilibrium blocks), which are composed of more markers/segments, shorter marker length and more recombination breakpoints than the SSR-map and caused 721 new wild substituted segments. Using the SNPLDB-map, two loci co-segregating with seed-coat color (SCC) and six loci for days to flowering (DTF) with 88.02% phenotypic contribution were identified. Integrated with parental RNA-seq and DNA-resequencing, two SCC and six DTF candidate genes, including three previously cloned (G, E2 and GmPRR3B) and five newly detected ones, were predicted and verified at nucleotide mutant level, and then demonstrated with the consistency between gene-alleles and their phenotypes in SojaCSSLP5. In total, six of the eight genes were identified with the parental allele-pairs coincided to those in 303 germplasm accessions, then were further demonstrated by the consistency between gene-alleles and germplasm phenotypes. Accordingly, the CSSL population integrated with parental DNA and RNA sequencing data was demonstrated to be an efficient platform in identifying candidate wild vs. cultivated gene-alleles.
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Satoh, Namiko, Jun-Ichi Itoh, and Yasuo Nagato. "The SHOOTLESS2 and SHOOTLESS1 Genes Are Involved in Both Initiation and Maintenance of the Shoot Apical Meristem Through Regulating the Number of Indeterminate Cells." Genetics 164, no. 1 (2003): 335–46. http://dx.doi.org/10.1093/genetics/164.1.335.
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Abstract To characterize the SHL2 and SHL1 genes in detail, we analyzed three strains carrying weak alleles of SHL2, shl2-6, shl2-7, and shl2-8, and one weak allele of SHL1, shl1-3. In contrast to strong alleles, which result in lack of shoot meristem, strains bearing these weak alleles formed shoot meristem frequently during embryogenesis. In shl2-6 and shl2-7 mutants, the meristem was lost during seed development. Only the shl2-8 mutant could survive after germination, but it showed abnormal initiation pattern and morphology of leaves. In strains bearing the weak alleles, the shoot meristem was composed of a small number of indeterminate cells and ultimately converted into leaf primordium. The shl1-3 mutant showed phenotypes similar to those of shl2-8. Thus SHL2 and SHL1 are required for both initiation and maintenance of shoot meristem. In shl2 mutants, there was a positive correlation between the size of the expression domain of OSH1 representing the number of indeterminate cells, the frequency of shoot meristem initiation, and the duration of meristem survival. Thus the shoot meristem will not initiate in an “all-or-nothing” fashion, but is formed in various degrees depending on the strength of the alleles. Double-mutant analyses indicate that SHL2 functions upstream of SHO to establish proper organization of the shoot meristem.
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Zheng, W., C. Liu, M. Lei, et al. "Evaluation of common variants in the CNR2 gene and its interaction with abdominal obesity for osteoporosis susceptibility in Chinese post-menopausal females." Bone & Joint Research 8, no. 11 (2019): 544–49. http://dx.doi.org/10.1302/2046-3758.811.bjr-2018-0284.r1.
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Objectives The objective of this study was to investigate the association of four single-nucleotide polymorphisms (SNPs) of the cannabinoid receptor 2 (CNR2) gene, gene-obesity interaction, and haplotype combination with osteoporosis (OP) susceptibility. Methods Chinese patients with OP were recruited between March 2011 and December 2015 from our hospital. In this study, a total of 1267 post-menopausal female patients (631 OP patients and 636 control patients) were selected. The mean age of all subjects was 69.2 years (sd 15.8). A generalized multifactor dimensionality reduction (GMDR) model and logistic regression model were used to examine the interaction between SNP and obesity on OP. For OP patient-control haplotype analyses, the SHEsis online haplotype analysis software ( http://analysis.bio-x.cn/ ) was employed. Results The logistic regression model revealed that the C allele of rs2501431 and the G allele of rs3003336 were associated with increased OP risk, compared with those with wild genotype. However, no significant correlations were found when analyzing the association of rs4237 and rs2229579 with OP risk. The GMDR analysis suggested that the interaction model composed of two factors, rs3003336 and abdominal obesity (AO), was the best model with statistical significance (p-value from sign test (Psign) = 0.012), indicating a potential gene-environment interaction between rs3003336 and AO. Overall, the two-locus models had a cross-validation consistency of 10/10 and had a testing accuracy of 0.641. Abdominally obese subjects with the AG or GG genotype have the highest OP risk, compared with subjects with the AA genotype and normal waist circumference (WC) (odds ratio (OR) 2.23, 95% confidence interval (CI) 1.54 to 3.51). Haplotype analysis also indicated that the haplotype containing the rs3003336-G and rs2501431-C alleles was associated with a statistically increased OP risk. Conclusion Our results suggested that the C allele of rs2501431 and the G allele of rs3003336 of the CNR2 gene, interaction between rs3003336 and AO, and the haplotype containing the rs3003336-G and rs2501431-C alleles were all associated with increased OP risk. Cite this article: Bone Joint Res 2019;8:544–549.
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Rashkova, Svetlana, Xue-Rong Zhou, Jun Chen, and Peter J. Christie. "Self-Assembly of the Agrobacterium tumefaciens VirB11 Traffic ATPase." Journal of Bacteriology 182, no. 15 (2000): 4137–45. http://dx.doi.org/10.1128/jb.182.15.4137-4145.2000.
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ABSTRACT The Agrobacterium tumefaciens VirB11 ATPase is a component of a type IV transporter dedicated to T-DNA delivery to plant cells. In this study, we tested a prediction from genetic findings that VirB11 self-associates in vivo. A chimeric protein composed of VirB11 fused to the DNA binding domain of λ cI repressor protein formed dimers, as shown by immunity of Escherichia coli to λ superinfection. An allele encoding VirB11 fused at its C terminus to the green fluorescent protein (GFP) exerted strong negative dominance when synthesized in wild-type A. tumefacienscells. Dominance was suppressed by overproduction of native VirB11, suggestive of titrating or competitive interactions between VirB11 and VirB11::GFP. In support of the titration model, a complex of native VirB11 and VirB11::GFP was recovered by precipitation with anti-GFP antibodies from detergent-solubilized A. tumefaciens cell extracts. VirB11 was shown by cI repressor fusion and immunoprecipitation assays to interact with VirB11 derivatives encoded by (i) 11 dominant negative alleles, (ii) recessive alleles bearing codon substitutions or deletions in the Walker A nucleotide binding motif, and (iii) alleles corresponding to the 5′ and 3′ halves of virB11. Further immunoprecipitation studies showed a hybrid protein composed of the N-terminal half of VirB11 fused to GFP interacted with mutant proteins exerting dominant effects and with a recessive Walker A deletion mutant (ΔGKT174-176). By contrast, a hybrid protein composed of the C-terminal half fused to GFP interacted with mutants exerting dominant effects but not the Walker A mutant protein. Together, these studies establish that VirB11 assembles as homomultimers in vivo via domains residing in each half of the protein. Furthermore, ATP binding appears to be critical for C-terminal interactions required for assembly of productive homomultimers.
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Kim, Tae Hoon, and Jin-Chul Kim. "Redox-responsive solid lipid microparticles composed of octadecyl acrylate and allyl disulfide." Journal of Biomaterials Science, Polymer Edition 29, no. 5 (2018): 476–90. http://dx.doi.org/10.1080/09205063.2017.1422854.
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M�ller, A., M. Sch�renkamp, and B. Brinkmann. "Evaluation of an ACTBP2 ladder composed of 26 sequenced alleles." International Journal of Legal Medicine 108, no. 2 (1995): 75–78. http://dx.doi.org/10.1007/bf01369908.
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Pogodaev, Vladimir, Bator Aduchiev, Lydia Kononova, Maya Aslanukova, and Irina Kardanova. "Features of polymorphism of calpastatin and somatotropin genes in young sheep, obtained from crossing ewes of Kalmyk fat-rumped sheeps and dorper rams." E3S Web of Conferences 175 (2020): 03020. http://dx.doi.org/10.1051/e3sconf/202017503020.
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The article presents the study of polymorphism of the CAST and GH genes, which determine the features of the manifestation of the productive and biological characteristics of sheep with ½ Kalmyk + ½ Dorper blood system. Calpastatin gene polymorphism represented by alleles M and N, whose frequency was 0,65 and 0,35; genotypes MM, MN – 30 and 70% accordingly. The desired NN genotype has not been identified. A relatively uniform incidence of allele N (0,35) CAST gene and B (0,40) GH was established, what contributed to an almost equal distribution of allele frequencies М (0,65) and А (0,60) genes of calpastatin and somatotropin accordingly. The frequency of heterozygous genotypes occurrence by CAST gene composed 0,7. By GH gene the following distribution of genotype frequencies is observed. Frequency of occurrence homozygous АА and heterozygous AB genotypes was equal to and is 0,4, wherein the frequency of occurrence advised homozygous ВВ genotype was 0,2. Among the animals studied, sheep with a complex genotype are most common CASTMN GHAB (40 %). The amount of percent CASTMM GHAA and CASTMN GHAA is in 22,2%. 10% is for genotypes CASTMM GHBB and CASTMN GHBB.
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Peterson, Peter A. "A Modified Autonomous En Transposon in Maize (Zea mays L.) Elicits a Differential Response of Reporter Alleles." Genetics 147, no. 3 (1997): 1329–38. http://dx.doi.org/10.1093/genetics/147.3.1329.
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Transposable elements in maize are composed of a defined molecular structure that includes coding sequences, determiners of functionality and ordered terminal motifs that provide binding sites for transposase proteins. Alterations in these components change the phenotypic expression of unstable genes with transposon inserts. The molecular basis for the altered timing and frequency of transposition as determined by the size and number of spots on kernels or stripes on leaves has generally been described for defective inserts in genes. Most differential patterns can be ascribed to alterations in the terminal motifs of the reporter allele structure that supplies a substrate (terminal inverted repeat motifs) for transposase activity. For autonomously functioning alleles, the explanations for changes in phenotype are not so clear. In this report, an En-related element identified as F-En is described that shares with En the recognition of a specific defective element c1(mr)888104 but differs from En in that this F-En element does not recognize the canonical c1(mr) elements that are recognized by En. Evidence is provided suggesting that F-En does not recognize other En/Spm-related defective elements, some of whose sequences are known. This modified En arose from a c1-m autonomously mutating En allele.
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Lubis, Bugis Mardina, Sjarif Hidajat Effendi, Ratna Akbari Ganie, and Oke Rina Ramayani. "Impact of the Neuregulin rs35753505 C/T Polymorphisms on Neuregulin 1 Levels in Preterm Infants." Open Access Macedonian Journal of Medical Sciences 7, no. 12 (2019): 1931–34. http://dx.doi.org/10.3889/oamjms.2019.554.
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BACKGROUND: Neuregulin (NRG) 1 plays an important role in the development of various organ systems in human. Single nucleotide polymorphisms rs35753505 C/Tof the gene encoding NRG1 evident as allele C and T with genotypes of CT, CC, and TT are believed to have an impact on NRG1 levels.AIM: To determine the impact of the NRGrs35753505 C/T polymorphisms on NRG1 levels in preterm infants.METHODS: A cross-sectional study was conducted from February to December 2018, whereas 48 eligible preterm infants with a gestational age of 32- < 37 weeks were enrolled. An umbilical cord blood specimen was collected for determination of NRG1 levels with enzyme-linked immunosorbent assay (ELISA) and NRG1 polymorphisms with polymerase chain reaction (PCR). Statistical analysis was performed with 95%CI and P value of < 0.05 was considered statistically significant.RESULTS: Median value of NRG1 levels (174.4 pg/ml) served as a cut off value. NRG 1 polymorphisms composed distribution of CC (31%), CT (42%), TT (27%) genotypes and distribution of C and T alleles were 52% and 48%. The median NRG1 levels in CC and CT genotypes were significantly lower compared to TT genotype (151.1 pg/ml vs 407.2 pg/ml, P = 0.005 and 159.1 pg/ml vs 407.2 pg/ml, P = 0.009). Subjects with C allele had significantly lower median NRG1 levels than T allele (151.1 pg/ml vs 407.2 pg/ml, P = 0.002). Subjects with CC and CT genotypes had higher risk to develop lower NRG1 levels compared to TT genotype (OR = 8.25, P = 0.016 and OR = 10.74, P = 0.005, respectively).CONCLUSION: Allele C is associated with lower NRG1 levels. Preterm infants with CC and CT genotypes pose a higher risk to have lower NRG1 levels.
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Kitsios, Georgios D., and Elias Zintzaras. "AnNOS3Haplotype Is Protective against Hypertension in a Caucasian Population." International Journal of Hypertension 2010 (2010): 1–7. http://dx.doi.org/10.4061/2010/865031.
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The endothelial nitric oxide synthase gene (NOS3) has been implicated in the development of hypertension, although the specific role of variants and haplotypes has not been clarified. In this study, the association of three polymorphisms (promoter T786C, intronic 4a/b, and nonsynonymous G894T) was tested in a case-control sample of 230 patients with essential hypertension and 306 healthy controls. Haplotype analysis was also performed. The mutant allele of the 4a/b polymorphism showed a protective effect against hypertension under a dominant model (odds , 95% confidence interval (0.44–0.93)), although this effect was not significant after the adjustment for covariates (). The estimated frequency of the haplotype composed of the , 4, and alleles was significantly higher in controls (5.5%) compared to cases (2%). These results indicate that although individualNOS3polymorphisms are not associated with hypertension, a rare haplotype of the gene might be protective against the development of hypertension.
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Fleury, Hervé, Sabrina Caldato, Patricia Recordon-Pinson, et al. "ART-Treated Patients Exhibit an Adaptive Immune Response against the HFVAC Peptides, a Potential HIV-1 Therapeutic Vaccine (Provir/Latitude45 Study)." Viruses 12, no. 11 (2020): 1256. http://dx.doi.org/10.3390/v12111256.
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We proposed a new HIV-1 therapeutic vaccine based on conserved cytotoxic T lymphocyte (CTL) epitopes of archived HIV-1 DNA according to their affinity to the dominant HLA-A and -B alleles of the population investigated. Our proposal (Hla Fitted VAC, HFVAC) was composed of 15 peptides originating from the RT, gag and nef parts of proviral DNA. Our aim was to investigate baseline immune reactivity to the vaccine in HIV-1 chronically infected patients at success of antiretroviral therapy (ART) who would be eligible for a therapeutic vaccine. Forty-one patients were tested. Most of them had been infected with HIV-1 subtype B and all had been receiving successful ART for 2 to 20 years. The predominant HLA-A and -B alleles were those of a Caucasian population. ELISPOT was carried out using the HFVAC peptides. In 22 patients, the PD-1 marker was investigated on CD4+ and CD8+ T cells by flow cytometry in order to evaluate global T cell exhaustion. ELISPOT positivity was 65% overall and 69% in patients exhibiting at least one HLA allele fitting with HFVAC. The percentages of CD4+ and CD8+ T cells expressing PD-1 were high (median values 23.70 and 32.60, respectively), but did not seem to be associated with an impairment of the immune response investigated in vitro. In conclusion, reactivity to HFVAC was high in this ART-treated population with dominant HLA alleles, despite potential cellular exhaustion associated with the PD-1 marker.
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Hirose, T., K. Nishimura, K. Fujita, M. Adachi, Y. Sasaki, and Y. Tanigawara. "Population pharmacokinetic analysis of S-1 including the CYP2A6 genotype in patients with advanced cancer." Journal of Clinical Oncology 27, no. 15_suppl (2009): 2507. http://dx.doi.org/10.1200/jco.2009.27.15_suppl.2507.
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2507 Background: S-1 is an oral anticancer agent composed of tegafur, CDHP, and potassium oxonate. Tegafur is a prodrug of fluorouracil (5-FU), and CDHP prevents degradation of 5-FU by inhibiting dihydropyrimidine dehydrogenase and enhances the anticancer activity of 5-FU. The biotransformation of tegafur to 5-FU is demonstrated to be catalyzed by CYP2A6. CYP2A6 polymorphisms are seen more frequently in Japanese people than Caucasian. Therefore, we performed a population pharmacokinetic (PPK) analysis of S-1 including the CYP2A6 genotype in Japanese patients with advanced cancer and developed a model describing the disposition kinetics of tegafur, CDHP, and 5-FU after oral administration of S-1. Methods: Fifty-eight patients with advanced cancer were eligible if they had a performance status of 0 to 3 and had adequate organ function. A dose of 80 mg/m2 of S-1 was given orally twice daily for 28 consecutive days, followed by 14 days of rest. The PPK analysis was performed with plasma concentration data for tegafur, CDHP, and 5-FU. The CYP2A6 genotype was analyzed with the polymerase chain reaction-restriction fragment length polymorphism method or an allele-specific polymerase chain reaction-based method. On the basis of the CYP2A6 genotype, all patients were classified into 1 of 3 groups: wild type, 1 variant allele, and 2 variant alleles. Results: Creatinine clearance correlated with the individual clearance of CDHP. Body surface area correlated with the individual clearance and volumes of CDHP and tegafur. In patients with 2 variant alleles of CYP2A6, tegafur clearance was 58% less than that in patients with wild type or 1 variant allele of CYP2A6. In addition, in patients with a history of gastrectomy, the absorption rate constant of tegafur was 66% higher than that in patients with no history of gastrectomy. The time-varying concentration of CDHP was the most appropriate model component describing the inhibitory effect on 5-FU catabolism. The individual Bayesian predictions of CDHP, tegafur, and 5-FU concentrations based on the present PPK model were in good agreement with the observed data. Conclusions: This is the first PPK model of S-1 including the CYP2A6 genotype. No significant financial relationships to disclose.
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Gigoux, Mathieu, Roberta Zappasodi, Joseph Park, et al. "444 MHC-I skewing in mutant calreticulin-positive myeloproliferative neoplasms is countered by heteroclitic peptide cancer vaccination." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A470. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0444.
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BackgroundThe majority of JAK2V617F-negative myeloproliferative neoplasms (MPN) have disease-initiating frameshift mutations in calreticulin (CALR) resulting in a common novel C-terminal mutant fragment (CALRMUT), representing an attractive source of neoantigens for cancer vaccines. However, studies have shown that CALRMUT-specific T cells are rare in CALRMUT MPN patients, but the underlying reasons for this phenomenon are unknown.MethodsIn this study, we examine class-I major histocompatibility complex (MHC-I) allele frequency in CALRMUT MPN patients from two independent cohorts and observed that MHC-I alleles that present CALRMUT neoepitopes with high affinity are under-represented in CALRMUT MPN patients. We speculate that this is due to an increased chance of immune-mediated tumor rejection by individuals expressing one of these MHC-I alleles such that the disease never clinically manifests. As a consequence of this MHC-I allele restriction, we reasoned that CALRMUT MPN patients would not efficiently respond to cancer vaccines composed of the CALRMUT fragment, but could do so when immunized with a properly modified CALRMUT heteroclitic peptide vaccine approach.ResultsWe found that heteroclitic CALRMUT peptides specifically designed for CALRMUT MPN patient MHC-I alleles efficiently elicited a cross-reactive CD8+ T cell response in human PBMC samples otherwise unable to respond to the matched weakly immunogenic CALRMUT native peptides. We also modeled this effect in mice and observed that C57BL/6J mice, which are unable to mount an immune response to the human CALRMUT fragment, can mount a cross-reactive CD8+ T cell response against a CALRMUT-derived peptide upon heteroclitic peptide immunization and this was further amplified by combining the heteroclitic peptide vaccine with blockade of the immune checkpoint molecule PD-1.ConclusionsTogether, our data underscore the therapeutic potential of heteroclitic peptide-based cancer vaccines in CALRMUT MPN patients.Ethics ApprovalApproval was obtained for the use of patient-derived specimens and access to clinical data extracted from patient charts by the Institutional Review Boards at Memorial Sloan Kettering Cancer Center, the Dana-Farber Cancer Institute and the Massachusetts General Hospital, as well as by the Danish Regional Science Ethics Committee. Mouse experiments were performed in accordance with institutional guidelines under a protocol approved by the Memorial Sloan-Kettering Cancer Center Institutional Animal Care and Use Committee.
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Moyer, Preenaa, Micholas Dean Smith, Nourredine Abdoulmoumine, et al. "Relationship between lignocellulosic biomass dissolution and physicochemical properties of ionic liquids composed of 3-methylimidazolium cations and carboxylate anions." Physical Chemistry Chemical Physics 20, no. 4 (2018): 2508–16. http://dx.doi.org/10.1039/c7cp07195g.
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Yin, Caiyong, Kaiyuan Su, Ziwei He, et al. "Genetic Reconstruction and Forensic Analysis of Chinese Shandong and Yunnan Han Populations by Co-Analyzing Y Chromosomal STRs and SNPs." Genes 11, no. 7 (2020): 743. http://dx.doi.org/10.3390/genes11070743.
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Y chromosomal short tandem repeats (Y-STRs) have been widely harnessed for forensic applications, such as pedigree source searching from public security databases and male identification from male–female mixed samples. For various populations, databases composed of Y-STR haplotypes have been built to provide investigating leads for solving difficult or cold cases. Recently, the supplementary application of Y chromosomal haplogroup-determining single-nucleotide polymorphisms (SNPs) for forensic purposes was under heated debate. This study provides Y-STR haplotypes for 27 markers typed by the Yfiler™ Plus kit and Y-SNP haplogroups defined by 24 loci within the Y-SNP Pedigree Tagging System for Shandong Han (n = 305) and Yunnan Han (n = 565) populations. The genetic backgrounds of these two populations were explicitly characterized by the analysis of molecular variance (AMOVA) and multi-dimensional scaling (MDS) plots based on 27 Y-STRs. Then, population comparisons were conducted by observing Y-SNP allelic frequencies and Y-SNP haplogroups distribution, estimating forensic parameters, and depicting distribution spectrums of Y-STR alleles in sub-haplogroups. The Y-STR variants, including null alleles, intermedia alleles, and copy number variations (CNVs), were co-listed, and a strong correlation between Y-STR allele variants (“DYS518~.2” alleles) and the Y-SNP haplogroup QR-M45 was observed. A network was reconstructed to illustrate the evolutionary pathway and to figure out the ancestral mutation event. Also, a phylogenetic tree on the individual level was constructed to observe the relevance of the Y-STR haplotypes to the Y-SNP haplogroups. This study provides the evidence that basic genetic backgrounds, which were revealed by both Y-STR and Y-SNP loci, would be useful for uncovering detailed population differences and, more importantly, demonstrates the contributing role of Y-SNPs in population differentiation and male pedigree discrimination.
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Brawley, J. V., and P. Concannon. "Modulation of promiscuous T cell receptor recognition by mutagenesis of CDR2 residues." Journal of Experimental Medicine 183, no. 5 (1996): 2043–51. http://dx.doi.org/10.1084/jem.183.5.2043.
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The T cell receptor (TCR) recognizes a ligand composed of a major histocompatibility complex (MHC) molecule and a peptide antigen. Prior studies of murine T cell clones have demonstrated that residues in the CDR3 region of TCR interact with amino acids in the peptide during MHC-restricted antigen recognition. However, the questions of whether direct TCR MHC contacts are made and where such contact sites might map in the TCR have not been resolved. In this study, we have taken advantage of the promiscuous recognition of a peptide from influenza virus (HA 307-319) by human T cell clones to map sites in the TCR that mediate differences in human leukocyte antigen-D related (HLA-DR) restriction in the presence of a common peptide antigen. Site-specific mutagenesis of cloned TCR genes and transfection into Jurkat cells were used to demonstrate that single amino acid substitutions in CDR2 of the TCR-alpha chain controlled whether a T cell was restricted by the product of a single DR allele (DR7) or would respond to the HA 307-319 peptide when presented by the products of one of several different DR alleles (DR1, DR4, DR5, or DR7). Because the relevant DR alleles are defined by polymorphism in the DR-beta chain, these results also suggest a rotational orientation for recognition in which TCR-alpha interacts with DR beta.
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Délye, Christophe, Valérie Ronchi, Frédéric Laigret, and Marie-France Corio-Costet. "Nested Allele-Specific PCR Primers Distinguish Genetic Groups of Uncinula necator." Applied and Environmental Microbiology 65, no. 9 (1999): 3950–54. http://dx.doi.org/10.1128/aem.65.9.3950-3954.1999.
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ABSTRACT Isolates of the obligately biotrophic fungus Uncinula necator cluster in three distinct genetic groups (groups I, II, and III). We designed PCR primers specific for these groups in order to monitor field populations of U. necator. We used the nucleotide sequences of the gene that encodes eburicol 14α-demethylase (CYP51) and of the ribosomal DNA internal transcribed spacer 1 (ITS1), ITS2, and 5.8S regions. We identified four point mutations (three in CYP51 and one in ITS1) that distinguished groups I and II from group III based on a sample of 132 single-spore isolates originating from Europe, Tunisia, Israel, India, and Australia. We developed a nested allele-specific PCR assay in which the CYP51 point mutations were used to detect and distinguish groups I and II from group III in crude mildewed samples from vineyards. In a preliminary study performed with samples from French vineyards in which isolates belonging to genetic groups I and III were present, we found that a shift from a population composed primarily of group I isolates to a population composed primarily of group III isolates occurred during the grapevine growing season.
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Figueiredo, Maria S., Leandro S. D’Abronzo, Melca M. Oliveira, Juliana L. Dreyfuss, and Jose Orlando Bordin. "Influence of Polymorphisms of Pro-Inflammatory (IL-12, TNFa and LTa) and Anti-Inflammatory Factors (IL-10 and CTLA4) in Autoimmune Hemolytic Anemia." Blood 110, no. 11 (2007): 3751. http://dx.doi.org/10.1182/blood.v110.11.3751.3751.
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Abstract The Autoimmune Hemolytic Anemia (AIHA) is caused by the destruction of antibody-coated red blood cells, but mechanisms that initiate the production of autoantibodies remains unclear. It had been suggest that decreased production of Th1-type cytokines and production of autoantibodies in AIHA can be secondary to the imbalance between anti- and pro-inflammatory factors. Moreover, the presence of single nucleotide polymorphisms (SNPs) showed association with different production of immunoregulatory factors which may modulate the disease expression in AIHA. OBJECTIVES: To determine the importance of SNPs of pro- and anti-inflammatory factors in the development of AIHA. PATIENTS: We studied 17 patients with AIHA who has been followed in the Hematology and Blood Transfusion Unit at the Federal University of Sao Paulo (UNIFESP/EPM), Brazil. The control group was composed by 40 healthy volunteer blood donors. METHODS: After DNA extraction from peripheral blood samples, the frequency of the SNPs was determinate by PCR-RFLP in patients and healthy individuals. The following SNPs were analyzed: Interleukin 12: IL-12 1188 (A/C), Tumor Necrosis Factor alpha: TNFa-308 (G/A), and Lymphotoxin alpha: Lta +252 (A/G); Interleukin 10: IL-10-592 (C/A), and Cytotoxic T-lymphocyte associated protein 4: CTLA4 exon 1 49 (A/G). RESULTS: The patient group was composed predominantly by female individuals (14 or 82%) and the median of age was 56 years old (18 to 76 years). The frequency observed for each allele studied in the patient group was: allele A of IL-12 = 0.82; allele G of FNTa = 0.85; allele A of Lta = 0.68; allele C of IL-10 = 0.82; allele G of CTLA4 = 0.59. No differences in allele frequency were found between patient and control groups. CONCLUSIONS: Our results suggest that these polymorphisms appear not to contribute for the development of the AIHA.
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Neff, Carrie L., and Alan B. Sachs. "Eukaryotic Translation Initiation Factors 4G and 4A from Saccharomyces cerevisiae Interact Physically and Functionally." Molecular and Cellular Biology 19, no. 8 (1999): 5557–64. http://dx.doi.org/10.1128/mcb.19.8.5557.
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ABSTRACT The initiation of translation in eukaryotes requires several multisubunit complexes, including eukaryotic translation initiation factor 4F (eIF4F). In higher eukaryotes eIF4F is composed of the cap binding protein eIF4E, the adapter protein eIF4G, and the RNA-stimulated ATPase eIF4A. The association of eIF4A withSaccharomyces cerevisiae eIF4F has not yet been demonstrated, and therefore the degree to which eIF4A’s conserved function relies upon this association has remained unclear. Here we report an interaction between yeast eIF4G and eIF4A. Specifically, we found that the growth arrest phenotype associated with three temperature-sensitive alleles of yeast eIF4G2 was suppressed by excess eIF4A and that this suppression was allele specific. In addition, in vitro translation extracts derived from an eIF4G2 mutant strain could be heat inactivated, and this inactivation could be reversed upon the addition of recombinant eIF4A. Finally, in vitro binding between yeast eIF4G and eIF4A was demonstrated, as was diminished binding between mutant eIF4G2 proteins and eIF4A. In total, these data indicate that yeast eIF4G and eIF4A physically associate and that this association performs an essential function.
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Schneider, Uwe, Yi-Yong Huang, Ananya Chakrabarti, Hai Thanh Dao, Naohide Morita, and Shū Kobayashi. "Boron-based pronucleophiles in catalytic (asymmetric) C(sp3)–allyl cross-couplings." Pure and Applied Chemistry 84, no. 11 (2012): 2417–30. http://dx.doi.org/10.1351/pac-con-12-05-01.
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Allylic and allenyl boronates or boranes were uncovered as suitable pronucleophiles in catalytic C–C bond formations with C(sp3) electrophiles such as O,O-acetals and N,O-aminals or ethers and carbohydrates. These transformations were most efficiently catalyzed by In(I) triflate. Importantly, chiral counteranion-directed, catalytic asymmetric allylation and allenylation of N,O-aminals was developed by employing a catalyst system composed of In(I) chloride and a chiral silver 2,2'-dihydroxy-1,1'-binaphthalene (BINOL)-phosphate.
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Lourenço, Natalia O., Ana Luísa H. Albuquerque, Roberta M. Basso, et al. "Canine POMC deletion (P187fs) allele frequency in Labrador Retrievers in Brazil." Pesquisa Veterinária Brasileira 39, no. 11 (2019): 909–14. http://dx.doi.org/10.1590/1678-5150-pvb-6419.
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ABSTRACT: The Labrador Retriever is among the main breeds with the greatest predisposition to obesity. Several factors, especially the interrelationships between food management, exercise and social factors; influence the likelihood of a dog becoming obese. Furthermore, genetic factors are also responsible for obesity in dogs, and in Labrador Retriever, a frameshift mutation (P187fs) in pro-opiomelanocortin (POMC) gene is strongly associated with obesity. There is no knowledge of studies that have previously evaluated the prevalence of the canine POMC deletion (P187fs) in Brazilian Labrador Retriever. Therefore, the objective of this study was to investigate this mutation in Labrador Retriever dogs in Brazil. Of the 108 Labrador Retrievers that were assessed in this study, 59 were from a previous study, composed by animals assisted in a veterinary hospital with unknown lineage, and 49 were from a prospective study, composed of 19 pet and 30 assistance/rescue Labrador Retriever dogs. The obesity risk and appetite questionnaire were applied, with some modifications, to tutors of the animals used in the prospective study. Fragments of the DNA, containing the mutation, were amplified by PCR and submitted to direct gene sequencing. The allele frequency of the mutation was 21.3% and was out of Hardy-Weinberg equilibrium (P<0.05). Using only the data of animals with known lineage, the presence of the mutated allele was higher in the Assistance/rescue Group than Pet Group (P<0.01), furthermore, the allele frequencies observed in Assistance Group (31.7%) was out of Hardy-Weinberg equilibrium (P<0.05), while that in the Pet Group (18.4%) was in equilibrium (P>0.05). Although the mutation has increased the food-motivation in the assistance/rescue dogs, other variables, especially frequent exercising, favored that these animals maintained the ideal body weight (body condition score = 5). In summary, the Hardy-Weinberg disequilibrium observed in the allele distribution of the deletion POMC_P187fs in this study, independently of the Labrador Retriever group assessed, suggesting the possibility of positive selection of the mutated allele, which may lead to the maintenance of this deleterious allele in the studied population.
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Müller, Philip, Gerhard Weinzierl, Andreas Brachmann, Michael Feldbrügge, and Regine Kahmann. "Mating and Pathogenic Development of the Smut Fungus Ustilago maydis Are Regulated by One Mitogen-Activated Protein Kinase Cascade." Eukaryotic Cell 2, no. 6 (2003): 1187–99. http://dx.doi.org/10.1128/ec.2.6.1187-1199.2003.
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ABSTRACT In the phytopathogenic fungus Ustilago maydis, pheromone-mediated cell fusion is a prerequisite for the generation of the infectious dikaryon. The pheromone signal elevates transcription of the pheromone genes and elicits formation of conjugation hyphae. Cyclic AMP and mitogen-activated protein kinase (MAPK) signaling are involved in this process. The MAPK cascade is presumed to be composed of Ubc4 (MAPK kinase kinase), Fuz7 (MAPK kinase), and Ubc3/Kpp2 (MAPK). We isolated the kpp4 gene and found it to be allelic to ubc4. Epistasis analyses with constitutively active alleles of kpp4 and fuz7 substantiate that Kpp4, Fuz7, and Kpp2/Ubc3 are components of the same module. Moreover, we demonstrate that Fuz7 activates Kpp2 and shows interactions in vitro. Signaling via this cascade regulates expression of pheromone-responsive genes, presumably through acting on the transcription factor Prf1. Interestingly, the same cascade is needed for conjugation tube formation, and this process does not involve Prf1. In addition, fuz7 as well as kpp4 deletion strains are nonpathogenic, while kpp2 deletion mutants are only attenuated in pathogenesis. Here we show that strains expressing the unphosphorylatable allele kpp2T182A/Y184F are severely affected in tumor induction and display defects in early infection-related differentiation.
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Timashev, P. S., K. N. Bardakova, S. N. Churbanov, et al. "SUPERCRITICAL FLUID TREATMENT OF THREE-DIMENSIONAL HYDROGEL MATRICES, COMPOSED OF CHITOSAN DERIVATIVES." Russian Journal of Transplantology and Artificial Organs 18, no. 3 (2016): 85–93. http://dx.doi.org/10.15825/1995-1191-2016-3-85-93.
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Aim.Controlled treatment of the physico-chemical and mechanical properties of a three-dimensional crosslinked matrix based on reactive chitosan.Materials and methods.The three-dimensional matrices were obtained using photosensitive composition based on allyl chitosan (5 wt%), poly(ethylene glycol) diacrylate (8 wt%) and the photoinitiator Irgacure 2959 (1 wt%) by laser stereolithography setting. The kinetic swelling curves were constructed for structures in the base and salt forms of chitosan using gravimetric method and the contact angles were measured using droplet spreading. The supercritical fl uid setting (40 °C, 12 MPa) was used to process matrices during 1.5 hours. Using nanohardness Piuma Nanoindenter we calculated values of Young’s modulus. The study of cytotoxicity was performed by direct contact with the culture of the NIH 3T3 mouse fi broblast cell line.Results.Architectonics of matrices fully repeats the program model. Matrices are uniform throughout and retain their shape after being transferred to the base form. Matrices compressed by 5% after treatment in supercritical carbon dioxide (scCO2 ). The elastic modulus of matrices after scCO2 treatment is 4 times higher than the original matrix. The kinetic swelling curves have similar form. In this case the maximum degree of swelling for matrices in base form is 2–2.5 times greater than that of matrices in salt form. There was a surface hydrophobization after the material was transferred to the base form: the contact angle is 94°, and for the salt form it is 66°. The basic form absorbs liquid approximately 1.6 times faster. The fi lm thickness was increased in the area of contact with the liquid droplets after absorption by 133 and 87% for the base and the salt forms, respectively. Treatment of samples in scCO2 reduces their cytotoxicity from 2 degree of reaction (initial samples) down to 1 degree of reaction.Conclusion.The use of supercritical carbon dioxide for scaffolds allows improving biocompatibility of the applied material for 1 degree and increasing the elastic modulus of the material more than 3 times. Allyl chitosan forms stable three-dimensional networks during laser photopolymerization. This enables desorbing toxic low molecular weight component without destruction of the matrix structure.
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Beigmohammadi, Fereshteh, Mahdi Mahmoudi, Jafar Karami, Nooshin Ahmadzadeh, Nasser Ebrahimi-Daryani, and Nima Rezaei. "Analysis of Killer Cell Immunoglobulin-Like Receptor Genes and Their HLA Ligands in Inflammatory Bowel Diseases." Journal of Immunology Research 2020 (September 19, 2020): 1–9. http://dx.doi.org/10.1155/2020/4873648.
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Genetic studies have illustrated that killer cell immunoglobulin-like receptor (KIR) genes could participate in various autoimmune disorders. We aimed to clarify the role of KIR genes, HLA ligands, HLA-KIR interactions, and their genotypes in inflammatory bowel disease (IBD) susceptibility. The study population was composed of 183 IBD subjects, comprising 100 ulcerative colitis (UC) patients, 83 Crohn’s disease (CD) patients, and 274 healthy subjects. Polymerase chain reaction with sequence-specific primers (PCR-SSP) was used to evaluate the absence or presence of the 15 KIR genes, 5 HLA class I ligands, and 2 pseudogenes. We did not find any significant difference in allele frequency of KIRs and pseudogenes between IBD patients and healthy controls. In the case of HLA genes, there was a significant difference in HLA-B-Bw4Thr80 frequency between UC patients and healthy controls (P=0.03, OR=0.06, 95%CI=0.008-0.4). Furthermore, we found a significant difference in HLA-C1Asn80 frequency between CD patients and healthy controls (P=0.04, OR=0.49, 95% CI=0.3-0.8). In the full-array combination of KIR genes, there was no significant frequency difference between UC patients and healthy controls, while two KIR genotypes showed a significant susceptible association with CD. Our data do not support a strong role of NK cells in IBD susceptibility, but it does not rule out a role for KIR variability in IBD patients. However, there are some protective associations such as Bw4 alleles; these associations may be due to the interaction of the alleles to TCRs rather than KIRs.
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Santoro, Gino Fellipe, Katlyn Duarte de Mello, Zair Cândido de Oliveira Netto, Gabrielle Pfutzenreuter, Julio Cesar Bassan, and Fabiano de Macedo Salgueirosa. "THE INFLUENCE OF ACE I/D GENE POLYMORPHISM IN AMATEUR AMERICAN FOOTBALL ATHLETES IN BRAZIL." Revista Brasileira de Medicina do Esporte 25, no. 6 (2019): 460–63. http://dx.doi.org/10.1590/1517-869220192506198909.
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ABSTRACT Introduction Physical performance depends on a variety of biological and mechanical properties. These different phenotypes are related through the complex interaction between the environment and the individual genetic profile. The hypothesis is that there is a hereditary component that interferes in physical fitness. ACE stands out among the genes that may influence this response. Objectives The objective of this study is to analyze the polymorphism of the ACE gene in American football athletes. Methods: At the end of the study, the sample was composed of 45 male athletes and 72 non-athletes. DNA was extracted from the jugal mucosa. ACE polymorphisms were genotyped through polymerase chain reaction and analyzed using the electrophoresis process. To compare the frequency of genotypes between athletes and the control group, we used the Chi-square test. The association between the frequencies of alleles was verified through the 2X2 contingency tables analyzed using the Chi-square test with Yates correction. The type of study was diagnostic - Investigation of a diagnostic test, level of evidence II. A p-value of ≤0.05 was considered statistically significant for all the analyses. Results The results showed a greater frequency of the D allele in American football athletes when compared with non-athletes, and a significant difference in the genotypic distribution of the athletes being composed of a higher number of the DD genotype as compared to the control group. Conclusion The study provides evidence of the allelic and genotypic influence of ACE polymorphism in amateur American football players in Brazil. Level of evidence II; Investigation of a diagnostic test.
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Di Paola, Jorge, Kayelyn Wagner, Brie Nixon, et al. "An Association Study of Candidate Modifier Genes in a Large Pedigree with Von Willebrand Disease." Blood 110, no. 11 (2007): 2135. http://dx.doi.org/10.1182/blood.v110.11.2135.2135.
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Abstract Von Willebrand Disease (VWD) is a common and highly variable bleeding disorder with incomplete penetrance and variable expressivity. Due to the complexity of VWD it is highly likely that several modifier genes influence its phenotype. We have identified and characterized an extensive Amish pedigree which is composed of 854 individuals of whom 395 have provided blood samples. 71 pedigree members are heterozygous for a missense mutation at position 4120, represented by a single base substitution (C&gt;T) that predicts an arginine to cysteine change at position 1374 (R1374C) in the A1 domain of the mature VWF molecule. Phenotypic characterization of the pedigree included several laboratory measures and a clinical bleeding phenotype determined by a validated bleeding score. The bleeding score was established by a questionnaire that consists of 10 questions that focus on seven areas related to spontaneous and trauma-related mucocutaneous bleeding. The lowest possible score is 0 and the highest is 7. A bleeding score of 3 or higher exhibited a specificity of 0.99 and sensitivity of 0.90 for VWD when given to 97 healthy controls and 63 unrelated individuals diagnosed with VWD. We performed association studies with candidate genes in the pedigree and correlated genotype and allele frequencies with severity of bleeding. The list of candidate variants studied included a total of 27 genetic polymorphisms in 20 genes that encode for the platelet receptors ITGA2, GP1BA, ITGB3 and GP6, for the coagulation factors F2, F5, F7, and F13 and for critical proteins involved in normal hemostasis, thrombosis, fibrinolysis and inflammation such as THBD, SELP, SELE, FGA, FGB, MTHFR, PLAT, PECAM1, CPB2, NOS3, SERPINE and CD14. These gene variants were selected based on their biological significance as well as their minor allele frequency. The differences in genotype distributions and allele frequencies between affected and unaffected pedigree members were evaluated using a proportional odds model for the association analysis. This model, which is a generalization of the usual logistic regression model for a binary outcome, can accommodate a multi-level ordered response variable such as the bleeding score. Five alleles were associated with increased severity of bleeding: Allele C at position 2361 of the SELP gene that encodes for P selectin and has been associated with decreased risk of thrombosis (p= 0.09 and p=0.003 and 0.001 when corrected for mutation status and sex, respectively). Allele C, at position 807 of ITGA2 that has been associated with increased bleeding (p= 0.01, and p= 0.002 and 0.01 when adjusted for mutation status and sex, respectively). Allele G, at position - 260 of CD14 that has been associated with decreased risk for myocardial infarction (p= 0.003, and p = 0.02 and 0.003 when adjusted for mutation status and sex, respectively). Allele T at position 13254 of the GP6 gene that has been associated with bleeding and thrombosis (p= 0.009, and p= 0.05 and 0.01 when adjusted for mutation status and sex, respectively). Finally, allele C at position 677 that has been described as protective for thrombosis (p= 0.02, and p= 0.01 and 0.018 when adjusted for mutation status and sex, respectively). In summary, our results demonstrate that specific genetic variants modify the bleeding phenotype of this pedigree and may contribute to the clinical variability observed in unrelated patients with VWD.
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Kirschner, Doris B., Elmar vom Baur, Christelle Thibault, et al. "Distinct Mutations in Yeast TAFII25 Differentially Affect the Composition of TFIID and SAGA Complexes as Well as Global Gene Expression Patterns." Molecular and Cellular Biology 22, no. 9 (2002): 3178–93. http://dx.doi.org/10.1128/mcb.22.9.3178-3193.2002.
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ABSTRACT The RNA polymerase II transcription factor TFIID, composed of the TATA-binding protein (TBP) and TBP-associated factors (TAFIIs), nucleates preinitiation complex formation at protein-coding gene promoters. SAGA, a second TAFII-containing multiprotein complex, is involved in transcription regulation in Saccharomyces cerevisiae. One of the essential protein components common to SAGA and TFIID is yTAFII25. We define a minimal evolutionarily conserved 91-amino-acid region of TAFII25 containing a histone fold domain that is necessary and sufficient for growth in vivo. Different temperature-sensitive mutations of yTAFII25 or chimeras with the human homologue TAFII30 arrested cell growth at either the G1 or G2/M cell cycle phase and displayed distinct phenotypic changes and gene expression patterns. Immunoprecipitation studies revealed that TAFII25 mutation-dependent gene expression and phenotypic changes correlated at least partially with the integrity of SAGA and TFIID. Genome-wide expression analysis revealed that the five TAFII25 temperature-sensitive mutant alleles individually affect the expression of between 18 and 33% of genes, whereas taken together they affect 64% of all class II genes. Thus, different yTAFII25 mutations induce distinct phenotypes and affect the regulation of different subsets of genes, demonstrating that no individual TAFII mutant allele reflects the full range of its normal functions.
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Hermand, P., P. Gane, MG Mattei, P. Sistonen, JP Cartron, and P. Bailly. "Molecular basis and expression of the LWa/LWb blood group polymorphism." Blood 86, no. 4 (1995): 1590–94. http://dx.doi.org/10.1182/blood.v86.4.1590.bloodjournal8641590.
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The Landsteiner-Wiener (LW) blood group antigens reside on a 42-kD erythrocyte membrane glycoprotein that has recently been cloned. Here, we found that the molecular basis for the LWa/LWb polymorphism is determined by a single base pair mutation (A308G) that correlates with a Pvu II restriction site and results in a Gln70Arg amino acid substitution. COS-7 cells transfected with LWa or LWb cDNAs reacted with human anti-LWa and anti-LWb sera, respectively, as well as with a murine monoclonal anti-LWab antibody, as shown by flow cytometry analysis. Moreover, a 42-kD protein was immunoprecipitated from the transfected cells with the monoclonal anti-LWab antibody. These findings indicate that LWa and LWb are alleles of the LW blood group locus as defined also by a monoclonal anti-LWab of nonhuman origin. In addition, the LW locus has been assigned to chromosome 19p13.3 by in situ hybridization. Study by Southern blot analysis indicated also that the LW locus is composed of a single gene that was not grossly rearranged in rare LW(a-b-) and Rhnull individuals deficient for LW antigens. In addition, Pvu II restriction fragment-length polymorphism analysis indicated that these variants were all homozygous for a phenotypically silent LWa allele.
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Fudal, Isabelle, Simon Ross, Hortense Brun, et al. "Repeat-Induced Point Mutation (RIP) as an Alternative Mechanism of Evolution Toward Virulence in Leptosphaeria maculans." Molecular Plant-Microbe Interactions® 22, no. 8 (2009): 932–41. http://dx.doi.org/10.1094/mpmi-22-8-0932.
Full textAbstract:
Three avirulence genes, AvrLm1, AvrLm6, and AvrLm4-7, were recently identified in Leptosphaeria maculans and found to be localized as solo genes within large noncoding, heterochromatin-like regions mainly composed of retrotransposons, truncated and degenerated by repeat-induced point mutation (RIP). The Rlm6 resistance gene has been overcome within 3 years in outdoor experiments in France and, here, we investigate the molecular basis of evolution toward virulence at the AvrLm6 locus. A region of 235 kb was sequenced in a virulent isolate and showed the deletion of AvrLm6 and three divergent mosaics of retrotransposons. AvrLm6 was found to be absent from 66% of 70 virulent isolates, with multiple events of deletion. The sequencing of virulent alleles in 24 isolates revealed a few cases of point mutations that had created stop codons in the sequence. The most frequent mutation events, however, were RIP, leading to the modification of 4 to 9% of the bases compared with the avirulent allele and generating 2 to 4 stop codons. Thus, RIP is described for the first time as an efficient mechanism leading to virulence and the multiple patterns of mutation observed suggest that multiple RIP events could occur independently in a single field population during 1 year.
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Brumfield, Robb T., and Michael J. Braun. "Phylogenetic Relationships in Bearded Manakins (Pipridae: Manacus) Indicate That Male Plumage Color is a Misleading Taxonomic Marker." Condor 103, no. 2 (2001): 248–58. http://dx.doi.org/10.1093/condor/103.2.248.
Full textAbstract:
Abstract The piprid genus Manacus is composed of four allospecies that are readily distinguishable by differences in male plumage color. Electrophoretic data for two populations of each of the four forms plus seven outgroup piprid taxa were collected from 32 isozyme loci and used to infer phylogenetic relationships. Each Manacus form was monophyletic, with the exception of M. manacus, in which the trans-Andean (west of the Andes) population was sister to M. vitellinus, rather than to its conspecific cis-Andean (east of the Andes) population. This controversial relationship, supported by the synapomorphic allele PGM-2b as well as allele frequencies at ADA, GOT-1 and LGG, is consistent with general biogeographic patterns in the region, but indicates that male plumage color is an unreliable taxonomic marker. Reconstruction of male plumage color on the tree confirms that gold plumage is a derived state in M. vitellinus, a finding consistent with the possibility that gold plumage is an evolutionary novelty in vitellinus which has spread recently under positive selection. Among piprids, there was strong support for a group composed of Antilophia, Chiroxiphia, and Corapipo, and for a group composed of Pipra mentalis, P. fasciicauda, and Dixiphia pipra. Manacus is more closely related to the P. mentalis + P. fasciicauda + D. pipra group. The isozymes supported Lepidothrix as the basal taxon of those examined.
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Whittaker, John C., Roger M. Harbord, Nicola Boxall, Ian Mackay, Gary Dawson, and Richard M. Sibly. "Likelihood-Based Estimation of Microsatellite Mutation Rates." Genetics 164, no. 2 (2003): 781–87. http://dx.doi.org/10.1093/genetics/164.2.781.
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Abstract Microsatellites are widely used in genetic analyses, many of which require reliable estimates of microsatellite mutation rates, yet the factors determining mutation rates are uncertain. The most straightforward and conclusive method by which to study mutation is direct observation of allele transmissions in parent-child pairs, and studies of this type suggest a positive, possibly exponential, relationship between mutation rate and allele size, together with a bias toward length increase. Except for microsatellites on the Y chromosome, however, previous analyses have not made full use of available data and may have introduced bias: mutations have been identified only where child genotypes could not be generated by transmission from parents' genotypes, so that the probability that a mutation is detected depends on the distribution of allele lengths and varies with allele length. We introduce a likelihood-based approach that has two key advantages over existing methods. First, we can make formal comparisons between competing models of microsatellite evolution; second, we obtain asymptotically unbiased and efficient parameter estimates. Application to data composed of 118,866 parent-offspring transmissions of AC microsatellites supports the hypothesis that mutation rate increases exponentially with microsatellite length, with a suggestion that contractions become more likely than expansions as length increases. This would lead to a stationary distribution for allele length maintained by mutational balance. There is no evidence that contractions and expansions differ in their step size distributions.
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Dutcher, Susan K., Naomi S. Morrissette, Andrea M. Preble, Craig Rackley та John Stanga. "ε-Tubulin Is an Essential Component of the Centriole". Molecular Biology of the Cell 13, № 11 (2002): 3859–69. http://dx.doi.org/10.1091/mbc.e02-04-0205.
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Centrioles and basal bodies are cylinders composed of nine triplet microtubule blades that play essential roles in the centrosome and in flagellar assembly. Chlamydomonas cells with thebld2-1 mutation fail to assemble doublet and triplet microtubules and have defects in cleavage furrow placement and meiosis. Using positional cloning, we have walked 720 kb and identified a 13.2-kb fragment that contains ε-tubulin and rescues the Bld2 defects. The bld2-1 allele has a premature stop codon and intragenic revertants replace the stop codon with glutamine, glutamate, or lysine. Polyclonal antibodies to ε-tubulin show peripheral labeling of full-length basal bodies and centrioles. Thus, ε-tubulin is encoded by the BLD2 allele and ε-tubulin plays a role in basal body/centriole morphogenesis.
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Davoudi, Pourya, Rostam Abdollahi-Arpanahi, and Ardeshir Nejati-Javaremi. "The impact of QTL allele frequency distribution on the accuracy of genomic prediction." Archives Animal Breeding 61, no. 2 (2018): 207–13. http://dx.doi.org/10.5194/aab-61-207-2018.
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Abstract. The accuracy of genomic prediction of quantitative traits based on single nucleotide polymorphism (SNP) markers depends among other factors on the allele frequency distribution of quantitative trait loci (QTL). Therefore, the aim of this study was to investigate different QTL allele frequency distributions and their effect on the accuracy of genomic estimated breeding values (GEBVs) using best linear unbiased genomic prediction (GBLUP) in simulated data. A population of 1000 individuals composed of 500 males and 500 females as well as a genome of 1000 cM consisting of 10 chromosomes and with a mutation rate of 2.5 × 10−5 per locus was simulated. QTL frequencies were derived from five distributions of allele frequency including constant, uniform, U-shaped, L-shaped and minor allele frequency (MAF) less than 0.01 (lowMAF). QTL effects were generated from a standard normal distribution. The number of QTL was assumed to be 500, and the simulation was done in 10 replications. The genomic prediction accuracy in the first-validation generation in constant, and the uniform allele frequency distribution was 0.59 and 0.57, respectively. Results showed that the highest accuracy of GEBVs was obtained with constant and uniform distributions followed by L-shaped, U-shaped and lowMAF QTL allele frequency distribution. The regression of true breeding values on predicted breeding values in the first-validation generation was 0.94, 0.92, 0.88, 0.85 and 0.75 for constant, uniform, L-shaped, U-shaped and lowMAF distributions, respectively. Depite different values of regression coefficients, in all scenarios GEBVs are biased downward. Overall, results showed that when QTL had a lower MAF relative to SNP markers, a low linkage disequilibrium (LD) was observed, which had a negative effect on the accuracy of GEBVs. Hence, the effect of the QTL allele frequency distribution on prediction accuracy can be alleviated through using a genomic relationship weighted by MAF or an LD-adjusted relationship matrix.
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Suzuki, Takuji, Takuro Sakagami, Bruce K. Rubin, et al. "Familial pulmonary alveolar proteinosis caused by mutations in CSF2RA." Journal of Experimental Medicine 205, no. 12 (2008): 2703–10. http://dx.doi.org/10.1084/jem.20080990.
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Primary pulmonary alveolar proteinosis (PAP) is a rare syndrome characterized by accumulation of surfactant in the lungs that is presumed to be mediated by disruption of granulocyte/macrophage colony-stimulating factor (GM-CSF) signaling based on studies in genetically modified mice. The effects of GM-CSF are mediated by heterologous receptors composed of GM-CSF binding (GM-CSF-Rα) and nonbinding affinity-enhancing (GM-CSF-Rβ) subunits. We describe PAP, failure to thrive, and increased GM-CSF levels in two sisters aged 6 and 8 yr with abnormalities of both GM-CSF-Rα–encoding alleles (CSF2RA). One was a 1.6-Mb deletion in the pseudoautosomal region of one maternal X chromosome encompassing CSF2RA. The other, a point mutation in the paternal X chromosome allele encoding a G174R substitution, altered an N-linked glycosylation site within the cytokine binding domain and glycosylation of GM-CSF-Rα, severely reducing GM-CSF binding, receptor signaling, and GM-CSF–dependent functions in primary myeloid cells. Transfection of cloned cDNAs faithfully reproduced the signaling defect at physiological GM-CSF concentrations. Interestingly, at high GM-CSF concentrations similar to those observed in the index patient, signaling was partially rescued, thereby providing a molecular explanation for the slow progression of disease in these children. These results establish that GM-CSF signaling is critical for surfactant homeostasis in humans and demonstrate that mutations in CSF2RA cause familial PAP.
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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 were compatible with their phenotypes. The deletion caused a frameshift leading to an alteration and shortening of the deduced amino acid sequence. The amino acid sequence consists of the first 83 amino acids of the N-terminal sequence of the normal PI and additional new amino acids, resulting in a mutant composed of 94 amino acids in contrast to 464 amino acids of the normal PI. In transient expression analysis, the mutant PI whose molecular size was compatible with the predicted amino acid sequence was detected in the lysates of the cells transfected with the mutated PI expression vector. The mutant PI was retained and underwent progressive degradation within the cells, and was minimally excreted into the media. These data indicate that this mutation is the cause of PI deficiency in this pedigree.
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Saoud, Hana, Oumaima Inoubli, Sihem Ben Fredj, et al. "Protective Effect of the MCP-1 Gene Haplotype against Schizophrenia." BioMed Research International 2019 (December 2, 2019): 1–8. http://dx.doi.org/10.1155/2019/4042615.
Full textAbstract:
While cytokines and their genetic variants have been intensively studied in schizophrenia, little attention has been focused on chemokines in the last years. The monocyte chemoattractant protein 1 (MCP-1) is known to attract peripheral monocytes to the brain during an inflammatory reaction and to affect the T helper (Th) cell development by stimulating Th2 polarization. Owing to the neuroinflammation in schizophrenia and the variable level of MCP-1 in these patients’ sera, we proposed to analyze the impact of functional genetic variants of the MCP-1 gene (MCP-1-2518A/G (rs1024611), MCP-1-362G/C (rs2857656), and MCP-1 int1del554-567 (rs3917887)) in schizophrenic patients. We conducted a case-control study on a Tunisian population composed of 200 patients and 200 controls using RFLP-PCR. Our results indicated that the minor alleles (-2518G and Del554-567) were significantly more prevalent in controls than in patients (P=0.001/adjusted OR = 0.42, P=0.04/adjusted OR = 0.64), whereas, for -362C minor allele, increased risk of schizophrenia was revealed (P=0.001, adjusted OR = 2.38). In conclusion, we have identified the haplotype combination -2581G/-362G/int1del554-567 that could mediate protection against schizophrenia (P=0.0038, OR = 0.19) and the effect could result more strongly from the MCP-1 -2582G with -362G variants, whereas the effect of int1del554-567 may in part be explained by its LD with -362.
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Seum, Carole, Daniel Pauli, Marion Delattre, Yannis Jaquet, Anne Spierer, and Pierre Spierer. "Isolation of Su(var)3-7 Mutations by Homologous Recombination in Drosophila melanogaster." Genetics 161, no. 3 (2002): 1125–36. http://dx.doi.org/10.1093/genetics/161.3.1125.
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Abstract The Su(var)3-7 gene, a haplo-suppressor and triplo-enhancer of position-effect variegation (PEV), encodes a zinc finger heterochromatin-associated protein. To understand the role of this protein in heterochromatin and genomic silencing, mutations were generated by homologous recombination. The donor fragment contained a yellow+ gene and 7.6 kb of the Su(var)3-7 gene inserted between two FRTs. The Su(var)3-7 sequence contained three stop codons flanking an I-SceI cut site located in the 5′ half of the gene. Using two different screening approaches, we obtained an allelic series composed of three mutant alleles. The three mutations are dominant suppressors of PEV. One behaves as a null mutation and results in a maternal-effect recessive lethal phenotype that can be rescued by a zygotic paternal wild-type gene. A P transposon zygotically expressing a Su(var)3-7 full-length cDNA also rescues the mutant phenotype. One hypomorphic allele is viable and the pleiotropic phenotype showed by adult flies indicates that rapidly and late dividing cells seem the most affected by reduced amounts of Su(var)3-7 protein. All three mutants were characterized at the molecular level. Each expresses a portion of the Su(var)3-7 protein that is unable to enter the nucleus and bind chromatin.
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Vojvodic, Svetlana, and Dusica Ademovic-Sazdanic. "Impact of HLA -B*27 subtypes with increased susceptibility to seronegative spondyloarthropathies in Vojvodina population." Genetika 49, no. 3 (2017): 801–8. http://dx.doi.org/10.2298/gensr1703801v.
Full textAbstract:
The aim of this study is to investigate which subtype of HLA-B*27 was associated with susceptibility of seronegative spondyloarthropathies (SpA) in Vojvodina patients. The dataset of the current study is composed of 172 SpA patients, among which there were 72 HLA-B*27+ (positive) and 100 HLA-B*27? (negative) patients. HLA-B*27 allele genotyping was carried out by Polymerase Chain Reaction-Sequence Specific Primer (PCR-SSP) method and low and high resolution tests, respectively. The association of HLA-B*27 subtypes with SpA was determined by the calculation of Relative Risk (RR) and Etiological Fraction (EF), while the allelic distribution between two group of patients was assessed by chi-square test. In HLA-B*27+ patients with SpA, the most common were patients with Reactive Arthritis (ReA) (41/72 or 56,94%) and Ankylosing Spondylitis (AS) (17/72 or 23,61%). Statistically significant difference was found in HLA-B*27+ and HLA-B*27? patients among SpA subgroups studied: Arthritis Psoriatica (PsA), Ankylosing Spondylitis (AS), Undifferentiated Spondyloarthritis (uSpA), Inflamatory Bowel Disease (IBD), Juvenilis Idiopathic Arthritis (JIA) and Reactive Arthritis (ReA). Two HLA-B*27 allele subtypes were found in SpA patients in Vojvodina: B*27:02 and B*27:05. Both HLA-B*27:02 and HLA-B*27:05 alleles have shown positive association with Ankylosing Spondylitis (RR=9.458 for B*27:02 and RR=6.585 for B*27:05), but significant Etiological Fraction (EF) or population attributive risk with value of 0.281 was found only for HLA-B*27:05 subtype. In this study we have showed, for the first time in Vojvodina population, that HLA-B*27:05 subtype have strong positive or susceptible association with Ankylosing Spondylitis. <br><br><font color="red"><b> This article has been corrected. Link to the correction <u><a href="http://dx.doi.org/10.2298/GENSR1801357V">10.2298/GENSR1801357V</a><u></b></font>
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Idenoue, Satoshi, Kazuya Yamamoto, and Jun-ichi Kadokawa. "Dissolution of Chitin in Deep Eutectic Solvents Composed of Imidazolium Ionic Liquids and Thiourea." ChemEngineering 3, no. 4 (2019): 90. http://dx.doi.org/10.3390/chemengineering3040090.
Full textAbstract:
Chitin is an abundant organic resource but shows poor solubility, leading to difficulty in utilization as materials. We have already reported that an ionic liquid (IL), 1-allyl-3-methylimidazolium bromide, dissolves chitin at concentrations up to ca. 5 wt %. However, the color of the resulting solution is blackened, mainly owing to the presence of bromide. On the other hand, some deep eutectic solvents (DESs) have been already reported to dissolve chitin. In this study, we found that DESs composed of imidazolium ILs and thiourea dissolved chitin without obvious coloring. DESs are systems formed from eutectic mixtures of hydrogen bond accepters and donors. We first prepared DESs by heating mixtures of imidazolium ILs with thiourea at 100 °C for 30 min with stirring. Predetermined amounts of chitin were then added to the DESs, and for the dissolution, the mixtures were left standing at room temperature for 24 h, followed by heating at 100 °C for 24 h with stirring. The dissolution processes were evaluated by CCD camera views, which revealed in most cases the dissolution of chitin at 2–5 wt % concentrations with the present DESs.
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Benian, G. M., T. L. Tinley, X. Tang, and M. Borodovsky. "The Caenorhabditis elegans gene unc-89, required fpr muscle M-line assembly, encodes a giant modular protein composed of Ig and signal transduction domains." Journal of Cell Biology 132, no. 5 (1996): 835–48. http://dx.doi.org/10.1083/jcb.132.5.835.
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Mutations in the Caenorhabditis elegans gene unc-89 result in nematodes having disorganized muscle structure in which thick filaments are not organized into A-bands, and there are no M-lines. Beginning with a partial cDNA from the C. elegans sequencing project, we have cloned and sequenced the unc-89 gene. An unc-89 allele, st515, was found to contain an 84-bp deletion and a 10-bp duplication, resulting in an in-frame stop codon within predicted unc-89 coding sequence. Analysis of the complete coding sequence for unc-89 predicts a novel 6,632 amino acid polypeptide consisting of sequence motifs which have been implicated in protein-protein interactions. UNC-89 begins with 67 residues of unique sequences, SH3, dbl/CDC24, and PH domains, 7 immunoglobulins (Ig) domains, a putative KSP-containing multiphosphorylation domain, and ends with 46 Ig domains. A polyclonal antiserum raised to a portion of unc-89 encoded sequence reacts to a twitchin-sized polypeptide from wild type, but truncated polypeptides from st515 and from the amber allele e2338. By immunofluorescent microscopy, this antiserum localizes to the middle of A-bands, consistent with UNC-89 being a structural component of the M-line. Previous studies indicate that myofilament lattice assembly begins with positional cues laid down in the basement membrane and muscle cell membrane. We propose that the intracellular protein UNC-89 responds to these signals, localizes, and then participates in assembling an M-line.