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Taslima Rahman, Zakaria Ahmed, and Anil Chandra Deb. "Non-allelic interaction of some quantitative traits in chickpea." GSC Advanced Research and Reviews 13, no. 3 (December 30, 2022): 103–8. http://dx.doi.org/10.30574/gscarr.2022.13.3.0352.
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In the present study five generations viz. P1, P2, F1, F2 and F3 of chickpea were taken for the analysis of non-allelic interaction considering five yield and yield contributing characters like as date of first flower (DFF), number of primary branches at first flower (NPBFF), plant height at first flower (PHFF), number of pods per plant (NPd/P) and number of seeds per plant (NS/P). At first Mather’s scaling test was done where scales C and D found to be significant and non-significant for all the traits, respectively. Potence was non-significant for all the characters, which revealed that there was no dominance. In the Cavalli’s joint scaling test, the χ2 values were found to be significant for all the characters, which confirm that additive-dominance model was inadequate and except additive and dominance effects there are other effects like non-allelic interaction, linkage, genotype × environment (G×E) interaction etc. are involved either individually or in combination in the inheritance of the studied traits.
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Gonzalo, Maria Jose, Luciano Carlos da Maia, Inmaculada Nájera, Carlos Baixauli, Giovanni Giuliano, Paola Ferrante, Antonio Granell, Maria Jose Asins, and Antonio Jose Monforte. "Genetic Control of Reproductive Traits under Different Temperature Regimes in Inbred Line Populations Derived from Crosses between S. pimpinellifolium and S. lycopersicum Accessions." Plants 11, no. 8 (April 14, 2022): 1069. http://dx.doi.org/10.3390/plants11081069.
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In the present work, we study the genetic control of reproductive traits under different heat stress conditions in two populations of inbred lines derived from crosses between two S. pimpinellifolium accessions and two tomato cultivars (E9×L5 and E6203×LA1589). The temperature increase affected the reproductive traits, especially at extremely high temperatures, where only a few lines were able to set fruits. Even though a relative modest number of QTLs was identified, two clusters of QTLs involved in the responses of reproductive traits to heat stress were detected in both populations on chromosomes 1 and 2. Interestingly, several epistatic interactions were detected in the E9×L5 population, which were classified into three classes based on the allelic interaction: dominant (one locus suppressed the allelic effects of a second locus), co-adaptive (the double-homozygous alleles from the same parent alleles showed a higher phenotypic value than the combination of homozygous alleles from alternative parents) and transgressive (the combination of double-homozygous alleles from different parents showed better performance than double-homozygous alleles from the same parents). These results reinforce the important role of non-additive genetic variance in the response to heat stress and the potential of the new allelic combinations that arise after wide crosses.
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Mizzen, Craig A., Andrew J. Alpert, Lyne Lévesque, Theo P. A. Kruck, and Donald R. McLachlan. "Resolution of allelic and non-allelic variants of histone H1 by cation-exchange-hydrophilic-interaction chromatography." Journal of Chromatography B: Biomedical Sciences and Applications 744, no. 1 (July 2000): 33–46. http://dx.doi.org/10.1016/s0378-4347(00)00210-3.
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Rana, M. S., M. G. Rasu, A. K. M. A. Islam, and M. M. Hossain. "Diallel Analysis of Quality and Yield Contributing Traits of Pumpkin (Cucurbita moschata Duch. ex Poir.)." Agriculturists 14, no. 1 (August 11, 2016): 15–32. http://dx.doi.org/10.3329/agric.v14i1.29097.
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A 5 X 5 diallel analysis was carried out according to Hayman on quality and yield contributing traits of pumpkin. Five (5) advanced inbreds of pumpkin viz IB 23, IB 40, IB 47, IB 50 and IB 57 were used in this study. The five parents and their F1 hybrids were arranged in a randomized complete block design with three replications for studying the quality and yield contributing traits. Analysis of variance showed significant differences among genotypes for all of the traits except dry matter and fruit yield. Parental mean suggested that all the parents contained recessive alleles with positive effect. In the 5 × 5 diallel set, Wr-Vr graph analysis revealed the presence of allelic interaction in all the characters except fruit length, dry matter, brix percentage and reducing sugar where non-allelic interaction was present.The Agriculturists 2016; 14(1) 15-32
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Jin, Jing, Heather Robeson, Pebbles Fagan, and Mohammed S. Orloff. "Association of PARP1-specific polymorphisms and haplotypes with non-small cell lung cancer subtypes." PLOS ONE 15, no. 12 (December 7, 2020): e0243509. http://dx.doi.org/10.1371/journal.pone.0243509.
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Objective The carcinogenesis role of PARP1 in lung cancer is still not clear. Analysis at allelic levels cannot fully explain the function of PARP1 on lung cancer. Our study aims to further explore the relation between PARP1 haplotypes and lung cancer. Materials and methods DNA and RNA were extracted from non-small cell lung cancer (NSCLC) tumor and adjacent normal fresh frozen tissue. Five PARP1-SNPs were genotyped and PARP1-specific SNPs were imputed using IMPUTE and SHAPEIT software. The SNPs were subjected to allelic, haplotype and SNP-SNP interaction analyses. Correlation between SNPs and mRNA/protein expressions were performed. Results SNP imputation inferred the ungenotyped SNPs and increased the power for association analysis. Tumor tissue samples are more likely to carry rs1805414 (OR = 1.85; 95% CI: 1.12–3.06; P-value: 0.017) and rs1805404 (OR = 2.74; 95%CI 1.19–6.32; P-value: 0.015) compared to normal tissues. Our study is the first study to show that haplotypes comprising of 5 SNPs on PARP1 (rs1136410, rs3219073, rs1805414, rs1805404, rs1805415) is able to differentiate the NSCLC tumor from normal tissues. Interaction between rs3219073, rs1805415, and rs1805414 were significantly associated with the NSCLC tumor with OR ranging from 3.61–6.75; 95%CI from 1.82 to 19.9; P-value<0.001. Conclusion PARP1 haplotypes may serve as a better predictor in lung cancer development and prognosis compared to single alleles.
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Virk, D. S., and Parminder S. Virk. "The assessment of genetic variation from normal, self and backcross families of a triple test cross of pure-breeding lines in wheat." Journal of Agricultural Science 106, no. 1 (February 1986): 1–6. http://dx.doi.org/10.1017/s0021859600061633.
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SUMMARYNormal, self and backcross families in a triple test cross were used to investigate the inheritance of number of days from sowing to flowering and dry plant weight for a population of pure-breeding lines of bread wheat (Triticum aestivum L.). Several tests of non-allelic interaction, additive genetic and dominance variances were made that involved triple test cross and single tester analyses. Non-allelic interaction was found to be a component of the genetic variation for both traits. The additive and dominance variances were prevalent for both traits. Alternative estimates of additive genetic and dominance variance components did not differ significantly when tested by a weighted least-squares model fitting procedure. The results are discussed in relation to genetic improvement of bread wheat.
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Karadge, Uma, Minja Gosto, and Matthew Nicotra. "Friend or foe? How an invertebrate distinguishes self from non-self in a natural histocompatibility interaction. (TRAN3P.912)." Journal of Immunology 192, no. 1_Supplement (May 1, 2014): 202.51. http://dx.doi.org/10.4049/jimmunol.192.supp.202.51.
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Abstract The existence of sophisticated self/non-self systems is not limited to vertebrates. Several colonial marine invertebrates have evolved systems that distinguish between conspecifics via cell-cell contact. This phenomenon, known as allorecognition, occurs when colonies encounter each other as they grow across their substrate. Compatible colonies fuse or co-exist, while incompatible colonies reject and often aggressively compete for space. In all taxa studied to date, allorecognition phenotypes are determined by highly polymorphic loci, which ensure that colonies are only compatible with themselves or close kin. How allorecognition molecules achieve this specificity remains unknown. Allorecognition in Hydractinia is controlled by at least two genes, alr1 and alr2, which encode highly polymorphic transmembrane proteins similar to immunoglobulin superfamily molecules. Colonies with matching alleles at alr1 and alr2 fuse, while colonies with no matching alleles reject. Using in vitro assays with recombinant proteins, we demonstrate that alr1 alleles bind to themselves but not to other alr1 alleles. We suggest that, in vivo, compatibility between colonies is also determined by allele-specific homophilic binding of alr proteins. Since fusion is rare in nature and single populations contain hundreds of unique alr alleles, the Hydractinia allorecognition system appears to be based on a biophysical mechanism with unprecedented allelic diversity and specificity.
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S, MURUGESAN, MURUGAN E, and NADARAJAN N. "BREEDING FOR IMPROVED PLANT TYPE IN PIGEONPEA." Madras Agricultural Journal 84, January (1997): 12–14. http://dx.doi.org/10.29321/maj.10.a00830.
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An attempt was made to breed for improved plant type in pigeonpen by crossing two contrasting parents viz. Vamban-I and Gulbarga-1. The F2 population clearly segregated into four distinct classes of phenotypes (plant types) in the ratio of 50 intermediate erect tall: 14 compact dwarf in the early segregants and 15 tall spreading: 1 compact bushy in the late segregants indicating that the plant type in pigeonpea was controlled by interaction of two pairs of non-allelic linkage blocks designated as DTCLSI and TALS2 and their respective allelic blocks as dtclsl and tais2.
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MATSUDA, ATSUSHI, YOSHIRO SAIMI, and MIHOKO TAKAHASHI. "An unusual complementation in non-excitable mutants in Paramecium." Genetical Research 76, no. 2 (October 2000): 125–33. http://dx.doi.org/10.1017/s0016672300004699.
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A non-excitable behavioural mutant, d4-662, was previously characterized as the fourth pawn locus mutant pwD in Paramecium tetraurelia. We now provide data demonstrating that d4-662 is in fact controlled by a pwB allele that has the unusual feature of complementing other pwB alleles in heterozygous F1 progeny. Neither the cytoplasm nor the nucleoplasm of d4-662 cured the mutational defects of pwB and in the reverse combination of d4-662 and pwB, the result was the same. On the other hand, pwA, another non-excitable mutant, was cured upon cross-injection with d4-662 and mutants carrying trichocyst non-discharge marker genes were also cured. This evidence suggests that d4-662 is a new mutant belonging to pwB, and would be better designated as pwB662. Extensive crossbreeding analyses, however, showed an unusual genetic relationship between d4-662 and pwB (pwB95 or pwB96). When d4-662 was crossed with pwB mutants, many progeny expressing wild-type phenotype or mixed clones of wild-type and pawn cells were obtained in the F1. Less than 12·5% expressed the pawn phenotype. The appearance of wild-type progeny in this F1 strongly suggests that an inter-allelic interaction between pwB662 and other pwB alleles may occur during development of the macronucleus.
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Divashuk, Mikhail, Anastasiya Chernook, Aleksandra Kroupina, Milena Vukovic, Gennady Karlov, Aleksey Ermolaev, Sergey Shirnin, et al. "TaGRF3-2A Improves Some Agronomically Valuable Traits in Semi-Dwarf Spring Triticale." Plants 10, no. 10 (September 25, 2021): 2012. http://dx.doi.org/10.3390/plants10102012.
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The breeding improvement of triticale is tightly associated with the introgression of dwarfing genes, in particular, gibberellin (GA)-insensitive Ddw1 from rye. Despite the increase in harvest index and resistance to lodging, this gene adversely affects grain weight and size. Growth regulation factor (GRF) genes are plant-specific transcription factors that play an important role in plant growth, including GA-induced stem elongation. This study presents the results of a two-year field experiment to assess the effect of alleles of the TaGRF3-2A gene in interaction with DDW1 on economically valuable traits of spring triticale plants grown in the Non-Chernozem zone. Our results show that, depending on the allelic state, the TaGRF3-2A gene in semi-dwarf spring triticale plants influences the thousand grain weight and the grain weight of the main spike in spring triticale, which makes it possible to use it to compensate for the negative effects of the dwarfing allele Ddw1. The identified allelic variants of the TaGRF3-2A gene can be included in marker-assisted breeding for triticale to improve traits.
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Hibbiny, Y. I. M. AL, A. H. Mabrouk, and Reham H. A. O. Gibely. "THE ROLE OF NON-ALLELIC INTERACTION IN INHERITANCE OF SOME ECONOMIC TRAITS IN G. BARBADENSE." Menoufia Journal of Plant Production 5, no. 11 (November 1, 2020): 399–410. http://dx.doi.org/10.21608/mjppf.2020.127541.
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AL-Hibbiny, Y. I. M., A. H. Mabrouk, and Reham H. A. O. Gibely. "THE ROLE OF NON-ALLELIC INTERACTION IN INHERITANCE OF SOME ECONOMIC TRAITS IN G. BARBADENSE." Menoufia Journal of Plant Production 5, no. 8 (November 1, 2020): 399–410. http://dx.doi.org/10.21608/mjppf.2020.172113.
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Hoes, J. A., and E. O. Kenaschuk. "Host–pathogen specificity in postseedling reaction of Linum usitatissimum to Melampsora lini." Canadian Journal of Botany 70, no. 6 (June 1, 1992): 1168–74. http://dx.doi.org/10.1139/b92-145.
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Eleven commercial flax cultivars and 10 race differentials, inoculated at the prebloom stage, showed significantly different levels of postseedling resistance to virulent races of flax rust. The effects of hosts and of races were significant or highly significant. Races differentiated hosts, hosts differentiated races, and host × race interaction was highly significant. Non-allelic, single-gene differences in host genotype were associated with higher levels of resistance and were ascribed to epistatic action by an L6-complex and by genes K1, M4, and N1. Epistatic action for susceptibility by gene L9 may have occurred in the race differentials Dakota (L9M) and Koto (L9P). The high aggressiveness of race 22 on 10 commercial race-differentiating hosts was correlated with possession of 26 virulence genes compared with 12–15 genes possessed by three other races. Indications are that allelism of host resistance genes and linked virulence of corresponding virulence genes, and also genetic background, were factors in host × pathogen interactions. The cultivar McGregor is a superior source of postseedling rust resistance because each of its genes K1 and L6 was associated with a high resistance level to race 22. Key words: adult plant, allelism, epistasis, flax.
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Wu, P., G. Zhang, N. Huang, and J. K. Ladha. "Non-allelic interaction conditioning spikelet sterility in an F2 population of indica/japonica cross in rice." Theoretical and Applied Genetics 91-91, no. 6-7 (November 1995): 825–29. http://dx.doi.org/10.1007/bf00223887.
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Geraghty, Daniel, Jodie Goodridge, Aura Burian, and Ni Lee. "HLA-F and MHC-I open conformers are ligands for natural killer cell receptor KIR3DL2. (P5004)." Journal of Immunology 190, no. 1_Supplement (May 1, 2013): 41.3. http://dx.doi.org/10.4049/jimmunol.190.supp.41.3.
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Abstract Killer Immunoglobulin-like receptors (KIR) are innate immune receptors expressed by NK and T cells classically associated with the detection of missing-self through loss of their respective MHC ligand. Some KIR specificities for allelic classical class I MHC (MHC-I) have been described, while other KIR receptor-ligand relationships, including those associated with non-classical MHC-I, have yet to be clearly defined. We report here that KIR3DL2 and the non-classical antigen HLA-F, expressed as a free form devoid of peptide, physically and functionally interact. We further extend those results to include classical MHC-I open conformers as ligands, defining new allelic relationships with KIR3DL2 and MHC-I. The data collectively suggest a broader, previously unrecognized interaction between MHC-I open conformers - with HLA-F as a prototypical example - and KIR receptors, acting in an immunoregulatory capacity centered on the inflammatory response.
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Kimbeng, C. A., and E. T. Bingham. "Population improvement in lucerne (Medicago sativa L.): components of inbreeding depression are different in original and improved populations." Australian Journal of Experimental Agriculture 38, no. 8 (1998): 831. http://dx.doi.org/10.1071/ea98112.
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Summary. Inbreeding depression, the lowered fitness of inbred individuals compared with their non-inbred counterparts, is an important concept in lucerne improvement; but is poorly understood. Two-allele autotetraploid populations are suitable for studying inbreeding depression, especially when the population improvement strategy involves inbreeding, because they are derived from chromosome-doubling of hybrid diploid plants. They have a maximum of 2 alleles and a single allelic interaction per locus. Inbreeding depression was compared in original 2-allele autotetraploid populations and populations that had undergone inbreeding and selection. The original and improved (selected) populations were produced by intercrossing 2 single-cross lines from the original and improved 2-allele autotetraploid populations respectively. Herbage yield of the S1 and intercrossed generations derived from these populations was evaluated in field trials at Arlington, Wisconsin, USA, and used to estimate inbreeding depression. Herbage yield of the S1 and intercrossed generations derived from the improved population were significantly (P<0.01) higher, by 13.3 and 24%, respectively, than those derived from the original population. Selection during inbreeding probably decreased the frequency of deleterious alleles and accumulated favourable alleles. Inbreeding depression values were higher in the improved compared with the original population. Genetic load of deleterious alleles may account for much of the inbreeding depression observed in the original population, whereas, in the improved population, loss of heterozygosity or non-additive gene interactions between favourable alleles on linked chromosome segments may account for the substantial inbreeding depression. Therefore, in a population improvement program, the causes of inbreeding depression seem to be more important than their estimated value.
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Duenk, Pascal, Piter Bijma, Mario P. L. Calus, Yvonne C. J. Wientjes, and Julius H. J. van der Werf. "The Impact of Non-additive Effects on the Genetic Correlation Between Populations." G3: Genes|Genomes|Genetics 10, no. 2 (December 19, 2019): 783–95. http://dx.doi.org/10.1534/g3.119.400663.
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Average effects of alleles can show considerable differences between populations. The magnitude of these differences can be measured by the additive genetic correlation between populations (rg). This rg can be lower than one due to the presence of non-additive genetic effects together with differences in allele frequencies between populations. However, the relationship between the nature of non-additive effects, differences in allele frequencies, and the value of rg remains unclear, and was therefore the focus of this study. We simulated genotype data of two populations that have diverged under drift only, or under drift and selection, and we simulated traits where the genetic model and magnitude of non-additive effects were varied. Results showed that larger differences in allele frequencies and larger non-additive effects resulted in lower values of rg. In addition, we found that with epistasis, rg decreases with an increase of the number of interactions per locus. For both dominance and epistasis, we found that, when non-additive effects became extremely large, rg had a lower bound that was determined by the type of inter-allelic interaction, and the difference in allele frequencies between populations. Given that dominance variance is usually small, our results show that it is unlikely that true rg values lower than 0.80 are due to dominance effects alone. With realistic levels of epistasis, rg dropped as low as 0.45. These results may contribute to the understanding of differences in genetic expression of complex traits between populations, and may help in explaining the inefficiency of genomic trait prediction across populations.
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Silva, Marlon Peres da, Antônio Teixeira do Amaral Júnior, Rosana Rodrigues, Messias Gonzaga Pereira, and Alexandre Pio Viana. "Genetic control on morphoagzronomic traits in snap bean." Brazilian Archives of Biology and Technology 47, no. 6 (November 2004): 855–62. http://dx.doi.org/10.1590/s1516-89132004000600004.
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Five divergent snap bean accessions from the vegetables germplasm bank at UENF and their ten diallel hybrids were evaluated to inheritance on five morphoagronomic traits using Hayman's methodology (1954). The results showed that additive effects were predominant for pod weight per plant, number of seeds per pod, height of the insertion of the first pod and number of days to flowering while non-additive effects were more important for number of pods per plant. The best strategy to be adopted was the use of these acessions in an intrapopulation breeding program aiming the obtaintion of superior segregants. For pod numbers the indicated strategy would be an interpopulational breeding procedure, to exploite the heterosis related to the non-additive effects. The analysis also revealed that dominant alleles increased the number of pods per plant, pod weight per plant and number of seeds per pod. Allelic interaction was overdominance to the number of pods per plant, while the partial dominance controled the expression of other traits.
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Kim, Sinil, Byeongsuk Ha, Minseek Kim, and Hyeon-Su Ro. "Investigation of Mating Pheromone–Pheromone Receptor Specificity in Lentinula edodes." Genes 11, no. 5 (May 4, 2020): 506. http://dx.doi.org/10.3390/genes11050506.
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The B mating-type locus of Lentinula edodes, a representative edible mushroom, is highly complex because of allelic variations in the mating pheromone receptors (RCBs) and the mating pheromones (PHBs) in both the Bα and Bβ subloci. The complexity of the B mating-type locus, five Bα subloci with five alleles of RCB1 and nine PHBs and three Bβ subloci with 3 alleles of RCB2 and five PHBs, has led us to investigate the specificity of the PHB–RCB interaction because the interaction plays a key role in non-self-recognition. In this study, the specificities of PHBs to RCB1-2 and RCB1-4 from the Bα sublocus and RCB2-1 from the Bb sublocus were investigated using recombinant yeast strains generated by replacing STE2, an endogenous yeast mating pheromone receptor, with the L. edodes RCBs. Fourteen synthetic PHBs with C-terminal carboxymethylation but without farnesylation were added to the recombinant yeast cells and the PHB–RCB interaction was monitored by the expression of the FUS1 gene—a downstream gene of the yeast mating signal pathway. RCB1-2 (Bα2) was activated by PHB1 (4.3-fold) and PHB2 (2.1-fold) from the Bα1 sublocus and RCB1-4 (Bα4) was activated by PHB5 (3.0-fold) and PHB6 (2.7-fold) from the Bα2 sublocus and PHB13 (3.0-fold) from the Bα5 sublocus. In particular, PHB3 from Bβ2 and PHB9 from Bβ3 showed strong activation of RCB2-1 of the Bβ1 sublocus by 59-fold. The RCB–PHB interactions were confirmed in the monokaryotic S1–10 strain of L. edodes by showing increased expression of clp1, a downstream gene of the mating signal pathway and the occurrence of clamp connections after the treatment of PHBs. These results indicate that a single PHB can interact with a non-self RCB in a sublocus-specific manner for the activation of the mating pheromone signal pathways in L. edodes.
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Stolbovaya, A. Yu, and I. V. Smirnov. "Mutation hot spots in MICA/MICB extracellular domains." Medical Immunology (Russia) 25, no. 3 (June 1, 2023): 483–88. http://dx.doi.org/10.15789/1563-0625-mhs-2680.
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MICA and MICB are non-classical MHC molecules that indicate cellular stress. They act as ligands for NKG2D receptors found on NK cells, thereby triggering a cytotoxic response against damaged, infected, or transformed cells. The production of soluble forms of MICA/MICB occurs via the cleavage of their extracellular domains (ECDs). The expression of MICA/MICB molecules in tumor sections or the levels of their soluble forms in blood have potential as diagnostic tools for cancer. They can predict important clinical outcomes for cancer patients, such as overall and recurrence-free survival. However, their extensive molecular polymorphism complicates the development of monoclonal antibodies (mAbs) for diagnostic use. Therefore, the diagnostic value of mAb-based assays may vary depending on the frequencies of allelic variants in local human populations. We examined the ECD amino acid sequences of more than 280 MICA and 50 MICB allelic variants. Additionally, we identified 172 and 58 single nucleotide polymorphisms (SNPs) located in the coding regions of the respective genes and resulting in amino acid replacements. The most frequent amino acid replacements (> 10%) in the ECD occur at 11 and 4 sites of MICA and MICB, respectively. We found that the frequencies of SNPs in the identified hot spots strongly correlate with each other in different human populations, despite the diversity of allelic variant frequencies. The functional role of only one site is known. The replacement of valine with methionine at position 152 enhances the affinity of MICA to NKG2D receptor. As the hot spots are dispersed throughout the entire ECD sequences, they may play a role other than modulating affinity with the NKG2D receptor interaction. We recommend that Ag sets used to validate anti-MICA/MICB mAbs meet two criteria. First, they should include both MICA and MICB alleles, as these genes have highly similar sequences. Second, the alleles should cover the variability observed in the identified hot spots.
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Basu, Kaustuv, Abhijit Sen, Kunal Ray, Ilora Ghosh, Kasturi Datta, and Arijit Mukhopadhyay. "Genetic Association and Gene-gene interaction ofHAS2,HABP1andHYAL3Implicate Hyaluronan Metabolic Genes in Glaucomatous Neurodegeneration." Disease Markers 33, no. 3 (2012): 145–54. http://dx.doi.org/10.1155/2012/390539.
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Hyaluronan (HA) plays a significant role in maintaining aqueous humor outflow in trabecular meshwork, the primary ocular tissue involved in glaucoma. We examined potential association of the single nucleotide polymorphisms (SNPs) of the HA synthesizing gene – hyaluronan synthase 2 (HAS2), hyaluronan binding protein 1 (HABP1) and HA catabolic gene hyaluronidase 3 (HYAL3) in the primary open angle glaucoma (POAG) patients in the Indian population. Thirteen tagged SNPs (6 forHAS2, 3 forHABP1and 4 forHYAL3) were genotyped in 116 high tension (HTG), 321 non-high tension glaucoma (NHTG) samples and 96 unrelated, age-matched, glaucoma-negative, control samples. Allelic and genotypic association were analyzed by PLINK v1.04; haplotypes were identified using PHASE v2.1 and gene-gene interaction was analyzed using multifactor dimensionality reduction (MDR) v2.0. An allelic association (rs6651224;p= 0.03; OR: 0.49; 95% CI: 0.25–0.94) was observed at the second intron (C>G) ofHAS2both for NHTG and HTG. rs1057308 revealed a genotypic association (p= 0.03) at the 5’ UTR ofHAS2with only HTG. TCT haplotype (rs1805429 – rs2472614 – rs8072363) inHABP1and TTAG and TTGA (rs2285044 – rs3774753 – rs1310073 – rs1076872) inHYAL3were found to be significantly high (p< 0.05) both for HTG and NHTG compared to controls. Gene-gene interaction revealedHABP1predominantly interacts withHAS2in HTG while it associates with bothHYAL3andHAS2in NHTG. This is the first genetic evidence, albeit from a smaller study, that the natural polymorphisms in the genes involved in hyaluronan metabolism are potentially involved in glaucomatous neurodegeneration.
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SINGH, JOGENDRA. "GENETIC ARCHITECTURE OF SOME QUANTITATIVE CHARACTERS IN COMMON WHEAT." Madras Agricultural Journal 83, september (1996): 551–54. http://dx.doi.org/10.29321/maj.10.a01050.
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rive generations involving P1, P2, F1, F2 and F3 were studied for six quantitative characters, viz., tillers/plant, ear length, grains/ear, yield/ear, yield/plant and 100-grain weight in five common wheat crosses namely, CAPAN 1962 x CC 493, CAPAN 1961 x MUW 27, CPAN 1933 x HW 517, CPAN 1959 x HUW 1 and WH 147 x CPAN 1874. Both scales (C and D) were significant in all the crosses for majority of the characters therefore, non-allelic interaction (i) and (1) type existed; (d) and (i) were more important.
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Deshmukh, Kalyani D., Vishwanath S. Khandare, and Sonam D. Jadhav. "Detection of presence of non-allelic interaction for yield and yield contributing characters in okra Abelmoschus esculentus L. Moench." International Journal of Chemical Studies 9, no. 1 (January 1, 2021): 804–7. http://dx.doi.org/10.22271/chemi.2021.v9.i1k.11325.
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Kandemis, Emine, Gulten Tuncel, Ozen Asut, Sehime G. Temel, and Mahmut C. Ergoren. "Strong Association between Serotonin Transporter 5-HTTVNTR Variant and Psychoactive Substance (Nicotine) Use in the Turkish Cypriot Population." Current Drug Metabolism 21, no. 6 (September 25, 2020): 466–70. http://dx.doi.org/10.2174/1389200221666200620201348.
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Background: The use of psychoactive substances is one of the most dangerous social problems worldwide. Nicotine dependence results from the interaction between neurobiological, environmental and genetic factors. Serotonin is a neurotransmitter that has a wide range of central nervous system activities. The serotonin transporter gene has been previously linked to psychological traits. Objective: A variable number of tandem repeats within the serotonin transporter-linked polymorphic gene region are believed to alter the transcriptional efficiency of the 5-HTT gene. Therefore, we aimed to investigate the association between this polymorphic site and smoking behavior in the Turkish Cypriot population. Methods: A total of 259 (100 smokers, 100 non-smokers and 59 ex-smokers) Turkish Cypriots were included in this population-based cross-sectional study. Genomic DNA was extracted from peripheral blood samples and the 5-HTTVNTR2 polymorphisms were determined by the PCR-RFLP. Results: The allelic frequency and genotype distribution results of this study showed a strong association (P<0.0001) between smokers and non-smokers. No statistical significance was found between non-smokers and ex-smokers. Conclusion: This is the first genetic epidemiology study to investigate the allelic frequencies of 5-HTTVNTR2 polymorphisms associated with smoking behavior in the Turkish Cypriot population. Based on the results of this study, genome-wide association studies should be designed for preventive medicine in this population.
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Riahi, Chaymaa, Juan Luis Reig-Valiente, Belén Picó, Aurora Díaz, Maria José Gonzalo, and Antonio José Monforte. "Evidence of the Role of QTL Epistatic Interactions in the Increase of Melon Fruit Flesh Content during Domestication." Agronomy 10, no. 8 (July 23, 2020): 1064. http://dx.doi.org/10.3390/agronomy10081064.
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Cultivated melon was domesticated from wild melons, which produce small fruits with non-edible fruit flesh. The increase in fruit flesh is one of the major domestication achievements in this species. In previous work, a quantitative trait locus (QTL) on chromosome 6 (paqt6.1) linked to fruit flesh content was detected in a cross between cultivated (“Piel de Sapo”, PS) and wild (Ames 24294, TRI) accessions. The QTL was introgressed into the PS background, generating the TRI_6-3 introgression line (IL) that confirmed the effects of paqt6.1. The primary objective of this work was to fine-map paqt6.1 as the first step for the map-based cloning. Two different approaches were carried out; however, the results were not consistent, precluding the fine mapping of paqt6.1. TRI_6-3 and other related ILs were genotyped by genotyping-by-sequencing, finding additional introgressions in other chromosomes. In an F2 population from TRI_6-3-x-PS, we found an epistatic interaction between paqt6.1 and another locus on chromosome 11. The interaction was verified in advanced populations, suggesting that the effects of paqt6.1 are conditioned by the allelic composition at another locus in chromosome 11. Both loci should have TRI alleles to reduce the flesh content in the PS background. The implications on the history of melon domestication are discussed.
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Kumar, Manish, Ravi Pratap Singh, Onkar Nath Singh, Prakash Singh, Pandurang Arsode, Namrata, Madhu Chaudhary, et al. "Genetic analysis for bacterial blight resistance in indica rice (Oryza sativa L.) cultivars." Oryza-An International Journal on Rice 56, no. 3 (September 30, 2019): 247–55. http://dx.doi.org/10.35709/ory.2019.56.3.1.
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Prior information on genetics of bacterial blight (BB) resistance (R) genes is imperative for its successful utilization in trait development and breeding for new resistant varietiesin rice. This experiment was aimed to assess the genetics of BB resistance in susceptible but popular rice variety HUR-917 and IRBB 66 (isogenic lines of IR 24) which harbors five R genes. Bioassay results in the parental lines and crosses were revealed resistance and susceptible disease response in R gene(s) positive and negative lines, respectively with varying range of Xoo (Xanthomonas oryzae pv oryzae) pathotype specificity. Phenomics of F2 and Back Cross (BC) generations showed existence of non-allelic interaction (13:3) between R genes with substantial variability in disease severity. The plants carrying mono hetero-allelic R gene has exsertedModerately susceptible (MS) disease reaction with 6.42 to 8.86 disease severities, however, lines carrying 2 R gene(s) could be able to disease severity Moderate susceptible MS to Moderate Resistant MR against all pathotypes existing in the region make it valid that the doses complementarity and presence of interaction in R genes are major determinant in R expression. It was recorded that presence of two or more R genes (Xa21+xa13; Xa21+ xa13+xa5) exerted broad spectrum BB resistance, hence found more suitable to combat this disease in HUR-917.
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Osmani, A. H., N. van Peij, M. Mischke, M. J. O'Connell, and S. A. Osmani. "A single p34cdc2 protein kinase (encoded by nimXcdc2) is required at G1 and G2 in Aspergillus nidulans." Journal of Cell Science 107, no. 6 (June 1, 1994): 1519–28. http://dx.doi.org/10.1242/jcs.107.6.1519.
Full textAbstract:
We have cloned and sequenced a homolog of cdc2 from Aspergillus nidulans that can complement the Schizosaccharomyces pombe cdc2-33 mutation. The gene was deleted and is required for continued nuclear DNA replication but not for mitochondrial DNA replication. Three different temperature-sensitive alleles were generated by reverse genetics. All of the mutations generate the nim phenotype of A. nidulans. The new gene was designated nimXcdc2 as it is not allelic to any of the other nim genes (nimA to nimW) of A. nidulans. Reciprocal shift experiments place an essential function for nimXcdc2 in G1 and G2. Antipeptide antibodies were generated that detect NIMXcdc2, and antisera were also generated to detect NIMEcyclinB. The two p34cdc2 protein species previously detected in A. nidulans, p34 and p37, both precipitate using NIMXcdc2 C-terminus-specific antibodies but only p34 co-precipitates with NIMEcyclinB. Dephosphorylation of denatured p34 converts it to the p37 form, showing p37 to be the non-phosphorylated form of NIMXcdc2. The phosphorylation of p34 is therefore associated with its interaction with NIMEcyclinB.
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Santoso, Juli. "TINDAK GEN KETAHANAN TERHADAP PENYAKIT KARAT (Pucinnia arachidis, Speg.) PADA KACANG TANAH." Jurnal Ilmu-Ilmu Pertanian Indonesia 9, no. 2 (December 4, 2017): 172–77. http://dx.doi.org/10.31186/jipi.9.2.172-177.
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The rust disease resistance of groundnut has inherited pattern 9 : 7, indicating that was controlled by double resessive genes. From this fact needs an explanation of gene action, so it can be used as information in the breeding system and selection. The purpose of this research is to know the gene action control, if resistant the rust disease in groundnut. The design used in this experiment was randomized block design with three replications. There were 29 genotypes as treatments (5 genotypes parents, 6 genotypes F1, 6 genotypes F2, 6 genotypes BC1.1 and 6 genotypes BC1.2). The result of the experiment showed that there was a gene non-allelic interaction, mean effect (m) and a dominant gene effect (h) in progeny of Muneng x ICGV 87358 (Six Parameters Mode). However, the gene non-ellelic interaction did not occur in other progenies. Meanwhile progenies of Gajah x ICGV 92088, Gajah x ICGV 87358, Gajah x ICGV 91227 had a mean effect (m) and a aditive gene effect (d), and Muneng x ICGV 92088, Muneng x ICGV 91227 had only a mean effect (m).
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Iraddi, Vemanna, Dayakar Reddy T, Rani Ch, Umakanth A V, and Tanmay V K. "Gene Effects for Sugar Content, Green Cane Yield and its Component Traits in Sweet Sorghum [Sorghum bicolor (L.) Moench]." Madras Agricultural Journal 101, June (2014): 109–12. http://dx.doi.org/10.29321/maj.10.001162.
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Generation mean analysis was carried out to estimate the nature and magnitude of gene effects for sugar content, green cane yield and its component traits in sweet sorghum [Sorghum bicolor (L.) Moench]. Six generations viz., P1 , P2 , F1 , F2 , BC1 and BC 2 of a cross derived from two parents viz., 27 B and NSSV 13, which are contrasting for the trait of interest i.e., grain quality and yield traits of grain sorghum and juiciness of sweet sorghum were evaluated in summer 2012. The scaling tests as well as chi square test from joint scaling test were highly significant for all the fourteen quantitative characters, indicating inadequacy of simple additive - dominance model and justifying the use of six parameter model for the detection of gene interactions. Both additive and dominance gene effects were highly significant for all the traits barring stem girth, grain yield, total biomass and fresh stalk yield where only dominance component is predominant in first two traits, while additive in later two traits. Among non allelic interactions, dominance × dominance (l) gene interaction was of greater magnitude than main gene effects for all the characters under study indicating the importance of heterosis breeding to utilize non additive gene effects.
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Vyas, N. S., L. Burke, A. Vourdas, E. Vassos, S. Frangou, and D. A. Collier. "Kibra Allelic Variation is Associated with Memory Processes in Early Onset Schizophrenia." European Psychiatry 24, S1 (January 2009): 1. http://dx.doi.org/10.1016/s0924-9338(09)71449-x.
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Background:A single nucleotide polymorphism, rs17070145, in the KIBRA protein, is thought to influence memory function in humans (Papassotiropoulos et al, 2006). We sought to investigate its effect on memory performance in people with Early Onset Schizophrenia (EOS; onset before age of 18) and their first-degree relatives.Methods:53 EOS probands and 117 non-psychotic first-degree relatives were examined on IQ (Wechsler Adult Intelligence Scale-Revised), learning and memory (California Verbal Learning Test; CVLT). the Structured Clinical Interview for DSM-IV yielded four diagnostic groups: EOS probands; relatives with Mood Disorders; other Axis I diagnoses; and no diagnosis (healthy relatives). Analysis of co-variance was performed, with diagnosis and genotype as fixed factors and age as covariate.Results:Carriers of the rs17070145 T allele achieved higher performance IQ, and recalled more words in short-delayed and long-delayed recall in the CVLT compared to C allele carriers [p< 0.003 and p< 0.009, respectively]. However TT homozygotes made more perseverative errors than C allele carriers [p=0.04]. after applying the Bonferroni for multiple comparisons, a genotype by diagnosis interaction revealed that relatives who were TT homozygotes and had mood disorders performed better on long-delayed recall [p< 0.04] but made more intrusion errors in the CVLT than the CC/CT genotype group.Conclusions:KIBRA may be involved in:1.processes that enhance overall competence in non-verbal tasks;2.phenotypic expression of cognition in mentally unwell relatives of schizophrenia patients.
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K, Bhargav, Venkata Subbareddy B, Venkata Sivakrishna K, Himaja G, Samuel Gideon Georgep, and Bhaskar Reddy K. "PHARMACOKINETIC DRUG INTERACTION BETWEEN CLOPIDOGREL AND ESOMEPRAZOLE IN ADULT HEALTHY MALE VOLUNTEERS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 7 (July 1, 2017): 336. http://dx.doi.org/10.22159/ajpcr.2017.v10i7.18855.
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Objective: Proton pump inhibitors (PPIs) are known to impair cytochrome P2C19 mediated activation of clopidogrel, the antiplatelet agent used for cardiovascular risk prevention. Esomeprazole is an optical isomer of omeprazole with better efficacy and tolerability than conventional PPIs. Esomeprazole is often co-administered with clopidogrel considering the risk of associated gastrointestinal bleeding. This study was designed to determine the effect of esomeprazole on the mean pharmacokinetic profile clopidogrel.Methods: A total of 14 adult healthy male participants who volunteered participation were enrolled, randomized equally into two cross-over sequences, dosed with clopidogrel and clopidogrel + esomeprazole in respective periods. Blood samples were collected through antecubital or forearm vein indwelling catheter. Concentration of clopidogrel parent prodrug in isolated plasma was determined using validated sensitive liquid chromatography – mass spectrometry. Pharmacokinetic modeling was carried out using PKSOLVER add-in for Microsoft Excel.Results: The pharmacokinetic profile of clopidogrel was non-significantly altered by esomeprazole. Statistically significant difference in peak plasma concentration, apparent volume of distribution, and clearance of clopidogrel was observed only during period II in participants co-dosed with esomeprazole (p=0.0483, 0.0011, and 0.0015, respectively). All other primary and secondary pharmacokinetic parameters displayed minor alterations during either period (p>0.05).Conclusion: The non-significant alteration of clopidogrel pharmacokinetics by esomeprazole can be potentiated by underlying predisposing factors such as the presence of CYP2C19 allelic variants and increasing the risk of cardiovascular events. Hence, co-administration of clopidogrel and esomeprazole should be under clinical monitoring and is not recommended in poor responders of antiplatelet therapy with clopidogrel.
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Bente, Heinrich, Andrea M. Foerster, Nicole Lettner, and Ortrun Mittelsten Scheid. "Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure." PLOS Genetics 17, no. 3 (March 9, 2021): e1009444. http://dx.doi.org/10.1371/journal.pgen.1009444.
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Paramutation is a form of non-Mendelian inheritance in which the expression of a paramutable allele changes when it encounters a paramutagenic allele. This change in expression of the paramutable alleles is stably inherited even after segregation of both alleles. While the discovery of paramutation and studies of its underlying mechanism were made with alleles that change plant pigmentation, paramutation-like phenomena are known to modulate the expression of other traits and in other eukaryotes, and many cases have probably gone undetected. It is likely that epigenetic mechanisms are responsible for the phenomenon, as paramutation forms epialleles, genes with identical sequences but different expression states. This could account for the intergenerational inheritance of the paramutated allele, providing profound evidence that triggered epigenetic changes can be maintained over generations. Here, we use a case of paramutation that affects a transgenic selection reporter gene in tetraploidArabidopsis thaliana. Our data suggest that different types of small RNA are derived from paramutable and paramutagenic epialleles. In addition, deletion of a repeat within the epiallele changes its paramutability. Further, the temperature during the growth of the epiallelic hybrids determines the degree and timing of the allelic interaction. The data further make it plausible why paramutation in this system becomes evident only in the segregating F2 population of tetraploid plants containing both epialleles. In summary, the results support a model for polyploidy-associated paramutation, with similarities as well as distinctions from other cases of paramutation.
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Maurya, Krishna, Sudhir Shukla, and Geeta Asthana. "Pattern of quantitative inheritance of yield and component traits in opium poppy (Papaver somniferum L.)." Genetika 46, no. 2 (2014): 569–78. http://dx.doi.org/10.2298/gensr1402569m.
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Generation mean analysis of cross NB-5x58/1 and its reciprocal cross was carried out to understand the nature of gene action in opium poppy. The significance of A, B, C and D scaling tests indicated presence of non-allelic interaction in the inheritance of traits except capsule size and husk yield/plant for reciprocal cross. Additive as well as dominance components of gene action were found in both the crosses. Most of the traits had greater non fixable dominance ?h? and dominance x dominance effects ?l? than fixable additive (d) and additive x additive effects (i) except leaves/plant, branches/plant, capsules/plant, stem diameter, capsule weight/plant, husk yield/plant, opium yield/plant, codeine and narcotine content which showed greater importance of additive (d) and additive x additive effects (i) effects. Inter-mating of the best parents, diallel selective mating or biparental mating in early segregating generations followed by recurrent selections were suggested for genetic improvement of opium poppy.
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Vissinga, C. S., P. Charmley, and P. Concannon. "Influence of coding region polymorphism on the peripheral expression of a human TCR V beta gene." Journal of Immunology 152, no. 3 (February 1, 1994): 1222–27. http://dx.doi.org/10.4049/jimmunol.152.3.1222.
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Abstract A number of human TCR V beta gene segments are reported to be polymorphic, with alleles differing by one or a small number of amino acid substitutions. In the absence of detailed structural information regarding the interaction of specific positions in the TCR with Ag or MHC, the significance of such variation is difficult to assess. In this report the relative use of the two common alleles of the human V beta 6.7 gene, 6.7a and 6.7b, which differ by two non-conservative amino acid substitutions, and the use of two common alleles of the V beta 12.2 gene, which differ by only silent substitutions, were measured in PBL derived from individuals heterozygous for these alleles. Equal use of V beta 12.2 alleles was observed, consistent with the inability of selection mechanisms to discriminate between the products of these alleles that are indistinguishable at the amino acid level. However, statistically significant skewing in the use of V beta 6.7 alleles was observed in 15 of 16 individuals studied. Expression levels for each allele ranged from 16 to 84% of the total V beta 6.7 signal in heterozygous individuals, with either the 6.7a or the 6.7b allele predominant in different individuals. Based on segregation studies in families, it seems unlikely that other unidentified polymorphism in the TCR beta locus, such as in the V beta 6.7 promoter, was responsible for the differential allele expression. Family studies provided no evidence for an association between specific HLA haplotypes and V beta 6.7 allele use. These results indicate that even modest allelic variation in human TCR V beta coding regions can have a significant impact on the expression of human V beta genes in the peripheral repertoire.
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Laing, Kerry J., Victoria L. Campbell, Lichun Dong, and David M. Koelle. "HLA-B*57:01 Complexed to a CD8 T-Cell Epitope from the HSV-2 ICP22 Protein Binds NK and T Cells through KIR3DL1." Viruses 14, no. 5 (May 11, 2022): 1019. http://dx.doi.org/10.3390/v14051019.
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HLA-B*57:01 is an HLA allelic variant associated with positive outcomes during viral infections through interactions with T cells and NK cells, but severe disease in persons treated with the anti-HIV-1 drug abacavir. The role of HLA-B*57:01 in the context of HSV infection is unknown. We identified an HLA-B*57:01-restricted CD8 T-cell epitope in the ICP22 (US1) protein of HSV-2. CD8 T cells reactive to the HSV-2 ICP22 epitope recognized the orthologous HSV-1 peptide, but not closely related peptides in human IFNL2 or IFNL3. Abacavir did not alter the CD8 T-cell recognition of the HSV or self-derived peptides. Unexpectedly, a tetramer of HSV-2 ICP22 epitope (228–236) and HLA-B*57:01 bound both CD8 T cells and NK cells. Tetramer specificity for KIR3DL1 was confirmed using KIR3DL1 overexpression on non-human primate cells lacking human KIR and studies with blocking anti-KIR3DL1 antibody. Interaction with KIR3DL1 was generalizable to donors lacking the HLA-B*57:01 genotype or HSV seropositivity. These findings suggest a mechanism for the recognition of HSV infection by NK cells or KIR-expressing T cells via KIR3DL1.
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Hudzenko, V. M., T. P. Polishchuk, A. A. Lysenko, I. V. Fedorenko, M. V. Fedorenko, L. V. Khudolii, V. A. Ishchenko, et al. "Elucidation of gene action and combining ability for productive tillering in spring barley." Regulatory Mechanisms in Biosystems 13, no. 2 (May 4, 2022): 197–206. http://dx.doi.org/10.15421/022225.
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The purpose of the present study is to identify breeding and genetic peculiarities for productive tillering in spring barley genotypes of different origin, purposes of usage and botanical affiliation, as well as to identify effective genetic sources to further improving of the trait. There were created two complete (6 × 6) diallel crossing schemes. Into the Scheme I elite Ukrainian (MIP Tytul and Avhur) and Western European (Datcha, Quench, Gladys, and Beatrix) malting spring barley varieties were involved. Scheme II included awnless covered barley varieties Kozyr and Vitrazh bred at the Plant Production Institute named after V. Y. Yuriev of NAAS of Ukraine, naked barley varieties Condor and CDC Rattan from Canada, as well as awned feed barley variety MIP Myroslav created at MIW and malting barley variety Sebastian from Denmark. For more reliable and informative characterization of barley varieties and their progeny for productive tillering in terms of inheritance, parameters of genetic variation and general combining ability (GCA) statistical analyses of experimental data from different (2019 and 2020) growing seasons were conducted. Accordingly to the indicator of phenotypic dominance all possible modes of inheritance were detected, except for negative dominance in the Scheme I in 2020. The degree of phenotypic dominance significantly varied depending on both varieties involved in crossing schemes and conditions of the years of trials. There was overdominance in loci in both schemes in both years. The other parameters of genetic variation showed significant differences in gene action for productive tillering between crossing Schemes. In Scheme I in both years the dominance was mainly unidirectional and due to dominant effects. In the Scheme II in both years there was multidirectional dominance. In Scheme I compliance with the additive-dominant system was revealed in 2019, but in 2020 there was a strong epistasis. In Scheme II in both years non-allelic interaction was identified. In general, the mode of gene action showed a very complex gene action for productive tillering in barley and a significant role of non-genetic factors in phenotypic manifestation of the trait. Despite this, the level of heritability in the narrow sense in both Schemes pointed to the possibility of the successful selection of individuals with genetically determined increased productive tillering in the splitting generations. In Scheme I the final selection for productive tillering will be more effective in later generations, when dominant alleles become homozygous. In Scheme II it is theoretically possible to select plants with high productive tillering on both recessive and dominant basis. In both schemes the non-allelic interaction should be taken into consideration. Spring barley varieties Beatrix, Datcha, MIP Myroslav and Kozyr can be used as effective genetic sources for involvement in crossings aimed at improving the productive tillering. The results of present study contribute to further development of studies devoted to evaluation of gene action for yield-related traits in spring barley, as well as identification of new genetic sources for plant improvement.
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Yadav, H. K., and S. P. Singh. "Inheritance of quantitative traits in opium poppy (Papaver somniferum L.)." Genetika 43, no. 1 (2011): 113–28. http://dx.doi.org/10.2298/gensr1101113y.
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Generation mean analysis was carried out using five parameter model on five cross combinations with five generations i.e. parents, F1s, F2s, and F3s randomly selected from partial diallel breeding experiment. The aim of study was to investigate the mode of gene actions involved in the inheritance of quantitative traits viz. days to 50% flowering, plant height, leaves/plant, capsules/plant, capsule size, capsule weight/plant, seed yield/plant and opium yield/plant. C and D scaling test showed the presence of non allelic interaction in the inheritance for all the traits except for plant height, seed yield/plant (ND1001xIS13) and capsule size (NBR5xND1002) which showed non interacting mode of inheritance. In general, the interaction effect together i.e. additive x additive [i] and dominance x dominance [l] found in higher magnitude than the combined main effects of additive [d] and dominance [h] effects for all the traits in all the five crosses. Dominance effect [h] was found pronounced for most of the traits except days to 50% flowering where additive effect [d] was found prevalent. Among the interaction effects dominance x dominance [l] was predominant over additive x additive [i] for all traits in all the five crosses except capsules/plant and capsule size in cross ND1001xNBRI11 and leaves/plant and opium yield/plant in cross NBRI5xND1002. As per sign of dominance (h) and dominance x dominance (l) duplicate epistasis were noticed for all the traits except plant height and leaves/plant in cross ND1001xUO1285. Potence ratio indicated presence of over dominance for almost all the traits. Substantial amount of realized heterosis, residual heterosis in F2 and F3 progenies and high heritability with moderate to high genetic advance in F2 progeny and significant correlation among important traits in desirable direction were observed. A breeding strategy of diallel selective mating or biparental mating in early segregating generation followed by recurrent selection may be used for genetic improvement.
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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 (December 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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RAHMAN, H. U. "Genetic analysis of stomatal conductance in upland cotton (Gossypium hirsutum L.) under contrasting temperature regimes." Journal of Agricultural Science 143, no. 2-3 (June 2005): 161–68. http://dx.doi.org/10.1017/s0021859605005186.
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Stomatal conductance plays an important role in the heat avoidance mechanism of crop plants. Stomatal conductance in cotton is genetically determined and has been shown to be associated with heat resistance and higher yields. Experiments were carried out with six generations (parental, F1, F2 and back crosses) of three upland cotton crosses under heat-stressed and non-stressed greenhouse and field regimes, to understand the inheritance pattern of stomatal conductance as affected by contrasting temperature regimes. The results revealed significant variation for stomatal conductance due to generations and generation×temperature regime interaction in the three crosses. In general, heat stress reduced stomatal conductance and available genetic variability. Temperature regimes exerted a significant effect on the expression of the genes responsible for stomatal conductance. High temperature or heat stress favoured the expression of genes having additive effects, while absence of heat stress favoured those having dominant effects in two of the three crosses evaluated. The third cross showed the opposite reaction. The results suggest that genes controlling stomatal conductance in the parents of the first two crosses (MNH-552, HR109-RT, CIM-448, CRIS-19) were different from those controlling stomatal conductance in FH-900 and N-Karishma, the parents of the third cross. The selection efficiency of stomatal conductance in segregating populations was likely to be affected by the complexity of its inheritance, environmental dependency, and presence of substantial non-allelic and genotype×temperature regime interactions.
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Jeleń, Agnieszka, Marta Żebrowska-Nawrocka, Aleksandra Sałagacka-Kubiak, Izabela Zawadzka, Mariusz Łochowski, and Ewa Balcerczak. "The Interaction between Four Polymorphisms and Haplotype of ABCB1, the Risk of Non-Small Cell Lung Cancer, and the Disease Phenotype." Journal of Oncology 2023 (January 24, 2023): 1–8. http://dx.doi.org/10.1155/2023/7925378.
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P-glycoprotein, product of the ABCB1 (ATP binding cassette subfamily B member 1) gene, has been reported to play an important role in multiple drug resistance during cancer therapy. However, its influence on non-small cell lung cancer (NSCLC) risk has not been clearly defined. The aim of the present study was to examine the association between clinicopathological factors and SNPs T-129C, C1236T, G2677T/A, and C3435T, as well as its haplotype, and to investigate the role of ABCB1 polymorphisms in NSCLC development. The study included 80 patients who suffered from NSCLC and underwent surgery to remove the tumour and 96 healthy controls. The tissues were genotyped by PCR-RFLP and sequencing methods, and the haplotype frequencies in both groups were estimated. The SNP C3435T was identified as a NSCLC risk factor. The presence of mutated allelic variant T ( p = 0.0103 ) or homozygote TT ( p = 0.0099 ) was observed significantly more often in cancer patients than in healthy controls. The two groups also demonstrated a highly significant difference in common haplotype frequency ( p = 0.01 ). The T−129-T1236-T2677-T3435 haplotype was found to be most closely associated with NSCLC risk. Although the investigated polymorphisms were not related to demographic features, clinicopathological lung tumour characteristics, or blood morphology indices, marginally significant correlations were found with some variables: C1236T with age of disease onset ( p = 0.0410 ); C3435T with smoking status ( p = 0.0561 ). As the findings indicate, lung cancer and control groups demonstrate significantly different patterns of −129/1236/2677/3435 haplotype distribution; T-T-T-T haplotype contributes to NSCLC susceptibility, and this effect is probably mainly dependent on C3435T. So far, similar studies were published in other populations.
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Welch, Carrie L., Sara Bretschger, Ping-Zi Wen, Margarete Mehrabian, Nashat Latib, Jamila Fruchart-Najib, Jean Charles Fruchart, Christy Myrick, and Aldons J. Lusis. "Novel QTLs for HDL levels identified in mice by controlling for Apoa2 allelic effects: confirmation of a chromosome 6 locus in a congenic strain." Physiological Genomics 17, no. 1 (March 12, 2004): 48–59. http://dx.doi.org/10.1152/physiolgenomics.00124.2003.
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Atherosclerosis is a complex disease resulting from the interaction of multiple genes, including those causing dyslipidemia. Relatively few of the causative genes have been identified. Previously, we identified Apoa2 as a major determinant of high-density lipoprotein cholesterol (HDL-C) levels in the mouse model. To identify additional HDL-C level quantitative trait loci (QTLs), while controlling for the effect of the Apoa2 locus, we performed linkage analysis in 179 standard diet-fed F2 mice derived from strains BALB/cJ and B6.C- H25c (a congenic strain carrying the BALB/c Apoa2 allele). Three significant QTLs and one suggestive locus were identified. A female-specific locus mapping to chromosome 6 (Chr 6) also exhibited effects on plasma non-HDL-C, apolipoprotein AII (apoAII), apoB, and apoE levels. A Chr 6 QTL was independently isolated in a related congenic strain (C57BL/6J vs. B6.NODc6: P = 0.003 and P = 0.0001 for HDL-C and non-HDL-C levels, respectively). These data are consistent with polygenic inheritance of HDL-C levels in the mouse model and provide candidate loci for HDL-C and non-HDL-C level determination in humans.
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Nigro, Domenica, Linda Monaci, Rosa Pilolli, and Agata Gadaleta. "Allelic variation of gliadin-encoding genes in a collection of tetraploid wheat genotypes." Cereal Research Communications 48, no. 4 (August 9, 2020): 507–15. http://dx.doi.org/10.1007/s42976-020-00061-w.
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AbstractWheat is one of the main crops bred worldwide. Durum wheat, specifically, is a key element of the Mediterranean diet, representing an élite crop grown in Italy. Durum wheat nutritional and technological values are largely due to the grain protein content (GPC), a complex genetic trait strongly affected by environmental factors and management practices. In the last decades, several breeding programs have been focused on improving GPC by both traditional and innovative approaches. Among seed storage proteins, prolamins, including both gliadins and glutenins, represent the major component. These two classes of proteins are indeed responsible of gluten formation and confer the extensibility and elasticity to the dough. Besides being of crucial importance for both technological properties and rheological characteristics, prolamins, and especially gliadins, have been found to be major triggers for human health, as involved in a number of wheat consumption-related conditions, such as the celiac disease, non-celiac gluten sensitivity, defined as the onset of a variety of manifestations related to wheat, rye and barley ingestion, and wheat allergies, both due to wheat ingestion or inhalation (of flour or pollen). The identification of loci responsible for the gliadin expression, and particularly of polymorphism in the aforementioned genes, which could result in a lower immunogenic/toxic potential, could be of great importance in breeding programs. For this purpose, we screened a collection of tetraploid wheat genotypes for allelic variants of annotated gliadin genes in the durum wheat genome, in order to identify genetic resources available to breeders to improve wheat nutritional and technological properties. Phylogenetic analysis among different species of Triticum genus and an in silico expression data analysis may also be useful in the exploitation of the complex scenario of gliadin–glutenin interaction and gluten role in the adverse reactions due to wheat consumption.
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Wang, Zhoutao, Hui Ren, Fu Xu, Guilong Lu, Wei Cheng, Youxiong Que, and Liping Xu. "Genome-Wide Characterization of Lectin Receptor Kinases in Saccharum spontaneum L. and Their Responses to Stagonospora tainanensis Infection." Plants 10, no. 2 (February 8, 2021): 322. http://dx.doi.org/10.3390/plants10020322.
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Sugarcane is an important sugar and bioenergy ethanol crop, and the hyperploidy has led to stagnant progress in sugarcane genome decipherment, which also hindered the genome-wide analyses of versatile lectin receptor kinases (LecRKs). The published genome of Saccharum spontaneum, one of the two sugarcane ancestor species, enables us to study the characterization of LecRKs and their responses to sugarcane leaf blight (SLB) triggered by Stagonospora tainanensis. A total of 429 allelic and non-allelic LecRKs, which were classified into evolved independently three types according to signal domains and phylogeny, were identified based on the genome. Regarding those closely related LecRKs in the phylogenetic tree, their motifs and exon architectures of representative L- and G-types were similar or identical. LecRKs showed an unequal distribution on chromosomes and more G-type tandem repeats may come from the gene expansion. Comparing the differentially expressed LecRKs (DELs) in response to SLB in sugarcane hybrid and ancestor species S. spontaneum, we found that the DEL number in the shared gene sets was highly variable among each sugarcane accession, which indicated that the expression dynamics of LecRKs in response to SLB were quite different between hybrids and particularly between sugarcane hybrid and S. spontaneum. In addition, C-type LecRKs may participate in metabolic processes of plant–pathogen interaction, mainly including pathogenicity and plant resistance, indicating their putative roles in sugarcane responses to SLB infection. The present study provides a basic reference and global insight into the further study and utilization of LecRKs in plants.
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Ganapathi, Mythily, Loukas Argyriou, Francisco Martínez-Azorín, Susanne Morlot, Gökhan Yigit, Teresa M. Lee, Bernd Auber, et al. "Bi-allelic missense disease-causing variants in RPL3L associate neonatal dilated cardiomyopathy with muscle-specific ribosome biogenesis." Human Genetics 139, no. 11 (June 8, 2020): 1443–54. http://dx.doi.org/10.1007/s00439-020-02188-6.
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Abstract Dilated cardiomyopathy (DCM) belongs to the most frequent forms of cardiomyopathy mainly characterized by cardiac dilatation and reduced systolic function. Although most cases of DCM are classified as sporadic, 20–30% of cases show a heritable pattern. Familial forms of DCM are genetically heterogeneous, and mutations in several genes have been identified that most commonly play a role in cytoskeleton and sarcomere-associated processes. Still, a large number of familial cases remain unsolved. Here, we report five individuals from three independent families who presented with severe dilated cardiomyopathy during the neonatal period. Using whole-exome sequencing (WES), we identified causative, compound heterozygous missense variants in RPL3L (ribosomal protein L3-like) in all the affected individuals. The identified variants co-segregated with the disease in each of the three families and were absent or very rare in the human population, in line with an autosomal recessive inheritance pattern. They are located within the conserved RPL3 domain of the protein and were classified as deleterious by several in silico prediction software applications. RPL3L is one of the four non-canonical riboprotein genes and it encodes the 60S ribosomal protein L3-like protein that is highly expressed only in cardiac and skeletal muscle. Three-dimensional homology modeling and in silico analysis of the affected residues in RPL3L indicate that the identified changes specifically alter the interaction of RPL3L with the RNA components of the 60S ribosomal subunit and thus destabilize its binding to the 60S subunit. In conclusion, we report that bi-allelic pathogenic variants in RPL3L are causative of an early-onset, severe neonatal form of dilated cardiomyopathy, and we show for the first time that cytoplasmic ribosomal proteins are involved in the pathogenesis of non-syndromic cardiomyopathies.
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Arsode, Pandurang B., Ravi P. Singh, SK Singh, Manish Kumar, Namrata, Madhu Choudhary, Debarchana Jena, et al. "Genetics of grain yield and its component traits in drought tolerance rice." JUNE 59, no. 2 (June 29, 2022): 150–56. http://dx.doi.org/10.35709/ory.2022.59.2.2.
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The facts pertaining to the inheritance of basic and value addition traits are prerequisite in designing much suited breeding strategies to harness substantial genetic gain in crop plants. The present study was aimed at comprehensive scrutiny of the quantitative traits, responding drought tolerance in rice through generation mean analysis (GMA). We have evaluated six generations ( P1, P2, F1, F2, B1 and B2) of cross, HUR-917 × DRR Dhan-42. The results revealed that all scales, A, B, C and D were significant for yield and attributing traits under irrigated and drought conditions, reflecting the presence of epistasis. Major yield contributing traits like days to 50% flowering (DFF), days to maturity (DM), plant height (PH), panicle length (PL), flag leaf length (FLL), number of grains per panicle (NGPP) and test weight (TW) showed the presence of duplicate epistasis under both conditions. Whereas, traits like the number of earbearing tillers (NEBT) and grain yield per plant (GYPP) shown duplicate epistasis under drought. The results suggest the prevalence of additive gene effect and non-allelic interactions/epistasis effect on the genetic control of majority of the yield traits. Additive (d) effect and dominant × dominant (l) gene interaction was the only significant portion of gene controlling grain yield per plant in the rice. The positive additive gene effect indicates that HUR-917 contributes more to the trait than DRR Dhan-42 and vice versa.
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Zhang, Huawen, Runfeng Wang, Bin Liu, Erying Chen, Yanbing Yang, Ling Qin, Feifei Li, et al. "Inclusive composite-interval mapping reveals quantitative trait loci for plant architectural traits in sorghum (Sorghum bicolor)." Crop and Pasture Science 70, no. 8 (2019): 659. http://dx.doi.org/10.1071/cp18408.
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Architecture-efficient sorghum (Sorghum bicolor (L.) Moench) has erect leaves forming a compact canopy that enables highly effective utilisation of solar radiation; it is suitable for high-density planting, resulting in an elevated overall production. Development of sorghum ideotypes with optimal plant architecture requires knowledge of the genetic basis of plant architectural traits. The present study investigated seven production-related architectural traits by using 181 sorghum recombinant inbred lines (RILs) with contrasting architectural phenotypes developed from the cross Shihong 137 × L-Tian. Parents along with RILs were phenotyped for plant architectural traits for two consecutive years (2012, 2013) at two locations in the field. Analysis of variance revealed significant (P ≤ 0.05) differences among RILs for architectural traits. All traits showed medium to high broad-sense heritability estimates (0.43–0.94) and significant (P ≤ 0.05) genotype × environment effects. We employed 181 simple sequence repeat markers to identify quantitative trait loci (QTLs) and the effects of QTL × environment interaction based on the inclusive composite interval mapping algorithm. In total, 53 robust QTLs (log of odds ≥4.68) were detected for these seven traits and explained 2.11–12.11% of phenotypic variation. These QTLs had small effects of QTL × environment interaction and yet significant epistatic effects, indicating that they could stably express across environments but influence phenotypes through strong interaction with non-allelic loci. The QTLs and linked markers need to be verified through function and candidate-gene analyses. The new knowledge of the genetic regulation of architectural traits in the present study will provide a theoretical basis for the genetic improvement of architectural traits in sorghum.
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STEFFENS, D. C., M. C. NORTON, A. D. HART, I. SKOOG, C. CORCORAN, and J. C. S. BREITNER. "Apolipoprotein E genotype and major depression in a community of older adults. The Cache County Study." Psychological Medicine 33, no. 3 (April 2003): 541–47. http://dx.doi.org/10.1017/s0033291702007201.
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Background. The role of allelic variation in APOE, the genetic locus for apolipoprotein E, in geriatric depression is poorly understood. There are conflicting reports as to an association between the ε4 allele and depression in late life.Method. Using a community based study of non-demented elders in Cache County, Utah, that included many very old individuals, we examined the relationship between APOE and late-onset (age >60) depression, with particular attention to possible age effects.Results. There was no overall association between APOE and depression. However, there was a significant interaction effect of APOE and age such that the relationship of late-onset depression with respect to presence of the ε4 allele was larger among those 80 and older compared with those below age 80. Consistent with previous studies, women were more likely to experience late-onset depression than men.Conclusions. Because we excluded prevalent cases of dementia, this pattern of relative risk with age may reflect the appearance of depressive symptoms as a prodrome of Alzheimer's disease or vascular dementia. Longitudinal studies should help to confirm or refute this explanation of the data.
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Tsao, Ming-Sound, Sarit Aviel-Ronen, Keyue Ding, Davina Lau, Ni Liu, Akira Sakurada, Marlo Whitehead, et al. "Prognostic and Predictive Importance of p53 and RAS for Adjuvant Chemotherapy in Non–Small-Cell Lung Cancer." Journal of Clinical Oncology 25, no. 33 (November 20, 2007): 5240–47. http://dx.doi.org/10.1200/jco.2007.12.6953.
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Purpose p53 and RAS are multifunctional proteins that are critical to cell cycle regulation, apoptosis, cell survival, gene transcription, response to stress, and DNA repair. We have evaluated the prognostic and predictive value of p53 gene/protein aberrations using tumor samples from JBR.10, a North American phase III intergroup trial that randomly assigned 482 patients with completely resected stage IB and II non–small-cell lung cancer (NSCLC) to receive four cycles of adjuvant cisplatin plus vinorelbine or observation alone. Methods p53 protein expression was evaluated by immunohistochemistry. Mutations in exons 5 to 9 of the p53 gene were determined by denaturing high-performance liquid chromatography and confirmed by sequencing. RAS mutations were identified by allelic specific oligonucleotide hybridization. Results Of 253 patients, 132 (52%) were positive for p53 protein overexpression. Untreated p53-positive patients had significantly shorter overall survival than did patients with p53-negative tumors (hazard ratio [HR] = 1.89; 95% CI, 1.07 to 3.34; P = .03). However, these p53-positive patients also had a significantly greater survival benefit from adjuvant chemotherapy (HR = 0.54; P = .02) compared with patients with p53-negative tumors (HR = 1.40; P = .26; interaction P = .02). Mutations of p53 and RAS genes were found in 124 (31%) of 397 and 117 (26%) of 450 patients, respectively. Mutations in these genes were neither prognostic for survival nor predictive of a differential benefit from adjuvant chemotherapy. Conclusion p53 protein overexpression is a significant prognostic marker of shortened survival, and also a significant predictive marker for a differentially greater benefit from adjuvant chemotherapy in completely resected NSCLC patients.
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Pirlog, Radu, Rares Drula, Andreea Nutu, George Adrian Calin, and Ioana Berindan-Neagoe. "The Roles of the Colon Cancer Associated Transcript 2 (CCAT2) Long Non-Coding RNA in Cancer: A Comprehensive Characterization of the Tumorigenic and Molecular Functions." International Journal of Molecular Sciences 22, no. 22 (November 19, 2021): 12491. http://dx.doi.org/10.3390/ijms222212491.
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Colon cancer-associated transcript 2 (CCAT2) is an intensively studied lncRNA with important regulatory roles in cancer. As such, cumulative studies indicate that CCAT2 displays a high functional versatility due to its direct interaction with multiple RNA binding proteins, transcription factors, and other species of non-coding RNA, especially microRNA. The definitory mechanisms of CCAT2 are its role as a regulator of the TCF7L2 transcription factor, enhancer of MYC expression, and activator of the WNT/β-catenin pathway, as well as a role in promoting and maintaining chromosome instability through the BOP1–AURKB pathway. Additionally, we highlight how the encompassing rs6983267 SNP has been shown to confer CCAT2 with allele-specific functional and structural particularities, such as the allelic-specific reprogramming of glutamine metabolism. Additionally, we emphasize CCAT2’s role as a competitive endogenous RNA (ceRNA) for multiple tumor suppressor miRNAs, such as miR-4496, miR-493, miR-424, miR-216b, miR-23b, miR-34a, miR-145, miR-200b, and miR-143 and the pro-tumorigenic role of the altered regulatory axis. Additionally, due to its upregulation in tumor tissues, wide distribution across cancer types, and presence in serum samples, we outline CCAT2’s potential as a biomarker and disease indicator and its implications for the development of resistance against current cancer therapy regiments and metastasis.
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Eaves, Deborah J., Carlos Flores-Ortiz, Tamanna Haque, Zongcheng Lin, Nianjun Teng, and Vernonica E. Franklin-Tong. "Self-incompatibility in Papaver: advances in integrating the signalling network." Biochemical Society Transactions 42, no. 2 (March 20, 2014): 370–76. http://dx.doi.org/10.1042/bst20130248.
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Self-fertilization, which results in reduced fitness of offspring, is a common problem in hermaphrodite angiosperms. To prevent this, many plants utilize SI (self-incompatibility), which is determined by the multi-allelic S-locus, that allows discrimination between self (incompatible) and non-self (compatible) pollen by the pistil. In poppy (Papaver rhoeas), the pistil S-determinant (PrsS) is a small secreted protein which interacts with the pollen S-determinant PrpS, a ~20 kDa novel transmembrane protein. Interaction of matching pollen and pistil S-determinants results in self-recognition, initiating a Ca2+-dependent signalling network in incompatible pollen. This triggers several downstream events, including alterations to the cytoskeleton, phosphorylation of sPPases (soluble inorganic pyrophosphatases) and an MAPK (mitogen-activated protein kinase), increases in ROS (reactive oxygen species) and nitric oxide (NO), and activation of several caspase-like activities. This results in the inhibition of pollen tube growth, prevention of self-fertilization and ultimately PCD (programmed cell death) in incompatible pollen. The present review focuses on our current understanding of the integration of these signals with their targets in the SI/PCD network. We also discuss our recent functional expression of PrpS in Arabidopsis thaliana pollen.