Showing papers in "Journal of Genetics in 2016"
TL;DR: It is illustrated how a unique integrative ‘Ayurgenomics’ approach can be used to integrate the trisutra concept of Ayurveda with genomics, and how EGLN1 could qualify as a molecular equivalent of tridosha that can modulate different phenotypic outcomes.
Abstract: Ayurveda, an ancient Indian system of medicine documented and practised since 1500 B.C., follows a systems approach that has interesting parallels with contemporary personalized genomic medicine approaches to the understanding and management of health and disease. It is based on the trisutra, which are the three aspects of causes, features and therapeutics that are interconnected through a common organizing principle termed 'tridosha'. Tridosha comprise three ascertainable physiological entities; vata (kinetic), pitta (metabolic) and kapha (potential) that are pervasive across systems, work in conjunction with each other, respond to the external environment and maintain homeostasis. Each individual is born with a specific proportion of tridosha that are not only genetically determined but also influenced by the environment during foetal development. Jointly they determine a person's basic constitution, which is termed their 'prakriti'. Development and progressi on of different diseases with their subtypes are thought to depend on the origin and mechanism of perturbation of the doshas, and the aim of therapeutic practice is to ensure that the doshas retain their homeostatic state. Similarly, western systems biology epitomized by translational P4 medicine envisages the integration of multiscalar genetic, cellular, physiological and environmental networks to predict phenotypic outcomes of perturbations. In this perspective article, we aim to outline the shape of a unifying scaffold that may allow the two intellectual traditions to enhance one another. Specifically, we illustrate how a unique integrative 'Ayurgenomics' approach can be used to integrate the trisutra concept of Ayurveda with genomics. We observe biochemical and molecular correlates of prakriti and show how these differ significantly in processes that are linked to intermediate patho-phenotypes, known to take different course in diseases. We also observe a significant enr ichment of the highly connected hub genes which could explain differences in prakriti, focussing on EGLN1, a key oxygen sensor that differs between prakriti types and is linked to high altitude adaptation. Integrating our observation with the current literature, we demonstrate how EGLN1 could qualify as a molecular equivalent of tridosha that can modulate different phenotypic outcomes, where hypoxia is a cause or a consequence both during health and diseased states. Our studies affirm that integration of the trisutra framework through Ayurgenomics can guide the identification of predisposed groups of individuals and enable discovery of actionable therapeutic points in an individualized manner.
50 citations
TL;DR: In silico predictions and experimental data suggested that CfCHS may be posttranscriptionally regulated by miR34, suggesting its involvement in production of flavonoids, providing protection from microbes during herbivory or mechanical wounding.
Abstract: Flavonoids are an important class of secondary metabolites that play various roles in plants such as mediating defense, floral pigmentation and plant-microbe interaction. Flavonoids are also known to possess antioxidant and antimicrobial activities. Coleus forskohlii (Willd.) Briq. (Lamiaceae) is an important medicinal herb with a diverse metabolic profile, including production of a flavonoid, genkwanin. However, components of the flavonoid pathway have not yet been studied in this plant. Chalcone synthase (CHS) catalyses the first committed step of flavonoid biosynthetic pathway. Full-length cDNA, showing homology with plant CHS gene was isolated from leaves of C. forskohlii and named CfCHS (GenBank accession no. KF643243). Theoretical translation of CfCHS nucleotide sequence shows that it encodes a protein of 391 amino acids with a molecular weight of 42.75 kDa and pI 6.57. Expression analysis of CfCHS in different tissues and elicitor treatments showed that methyl jasmonate (MeJA) strongly induced its expression. Total flavonoids content and antioxidant activity of C. forskohlii also got enhanced in response to MeJA, which correlated with increased CfCHS expression. Induction of CfCHS by MeJA suggest its involvement in production of flavonoids, providing protection from microbes during herbivory or mechanical wounding. Further, our in silico predictions and experimental data suggested that CfCHS may be posttranscriptionally regulated by miR34.
43 citations
TL;DR: It is identified that miR-195 expression was upregulated in myocardial I/R injury, and miR -195 overexpression may promote cardiomyocyte apoptosis by targeting Bcl-2 and inducing mitochondrial apoptotic pathway.
Abstract: This study aims to investigate microRNA-195 (miR-195) expression in myocardial ischaemia–reperfusion (I/R) injury and the roles of miR-195 in cardiomyocyte apoptosis though targeting Bcl-2. A mouse model of I/R injury was established. MiR-195 expression levels were detected by real-time quantitative PCR (qPCR), and the cardiomyocyte apoptosis was detected by TUNEL assay. After cardiomyocytes isolated from neonatal rats and transfected with miR-195 mimic or inhibitor, the hypoxia/reoxygenation (H/R) injury model was established. Cardiomyocyte apoptosis and mitochondrial membrane potential were evaluated using flow cytometry. Bcl-2 and Bax mRNA expressions were detected by RT-PCR. Bcl-2, Bax and cytochrome c (Cyt-c) protein levels were determined by Western blot. Caspase-3 and caspase-9 activities were assessed by luciferase assay. Compared with the sham group, miR-195 expression levels and rate of cardiomyocyte apoptosis increased significantly in I/R group (both P<0.05). Compared to H/R + negative control (NC) group, rate of cardiomyocyte apoptosis increased in H/R + miR-195 mimic group while decreased in H/R + miR-195 inhibitor group (both P<0.05). MiR-195 knockdown alleviated the loss of mitochondrial membrane potential (P<0.05). MiR-195 overexpression decreased Bcl-2 mRNA and protein expression, increased BaxmRNA and protein expression, Cyt-c protein expression and caspase-3 and caspase-9 activities (all P<0.05). While, downregulated MiR-195 increased Bcl-2 mRNA and protein expression, decreased Bax mRNA and protein expression, Cyt-c protein expression and caspase-3 and caspase-9 activities (all P<0.05). Our study identified that miR-195 expression was upregulated in myocardial I/R injury, and miR-195 overexpression may promote cardiomyocyte apoptosis by targeting Bcl-2 and inducing mitochondrial apoptotic pathway.
41 citations
TL;DR: The Ka/ Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome, and Conserved intro–exon structures and motif compositions were investigated in these genes.
Abstract: Multidrug and toxic compound extrusion (MATE) proteins are a group of secondary active transporters, which widely exist in all living organisms and play important role in the detoxication of endogenous secondary metabolites and exogenous agents. However, to date, no systematic and comprehensive study of this family is reported in maize. Here, a total of 49 MATE genes (ZmMATE) were identified and divided into seven groups by phylogenetic analysis. Conserved intro-exon structures and motif compositions were investigated in these genes. Results by gene locations indicated that these genes were unevenly distributed among all 10 chromosomes. Tandem and segmental duplications appeared to contribute to the expansion and evolution of this gene family. The Ka/Ks ratios suggested that the ZmMATE has undergone large-scale purifying selection on the maize genome. Interspecies microsynteny analysis revealed that there were independent gene duplication events of 10 ZmMATE. In addition, most maize MATE genes exhibited different expression profiles in diverse tissues and developmental stages. Sixteen MATE genes were chosen for further quantitative real-time polymerase chain reaction analysis showed differential expression patterns in response to aluminum treatment. These results provide a useful clue for future studies on the identification of MATE genes and functional analysis of MATE proteins in maize.
34 citations
TL;DR: The present results clearly suggest that the suite of phenotypes through which the evolution of greater competitive ability is achieved in fruitflies depends critically not just on larval density per unit volume of food, but also on the total amount of food available in the culture vials.
Abstract: Multiple experimental evolution studies on Drosophila melanogaster in the 1980s and 1990s indicated that enhanced competitive ability evolved primarily through increased larval tolerance to nitrogenous wastes and increased larval feeding and foraging rate, at the cost of efficiency of food conversion to biomass, and this became the widely accepted view of how adaptation to larval crowding evolves in fruitflies. We recently showed that populations of D. ananassae and D. n. nasuta subjected to extreme larval crowding evolved greater competitive ability without evolving higher feeding rates, primarily through a combination of reduced larval duration, faster attainment of minimum critical size for pupation, greater efficiency of food conversion to biomass, increased pupation height and, perhaps, greater urea/ammonia tolerance. This was a very different suite of traits than that seen to evolve under similar selection in D. melanogaster and was closer to the expectations from the theory of K-selection. At that time, we suggested two possible reasons for the differences in the phenotypic correlates of greater competitive ability seen in the studies with D. melanogaster and the other two species. First, that D. ananassae and D. n. nasuta had a very different genetic architecture of traits affecting competitive ability compared to the long-term laboratory populations of D. melanogaster used in the earlier studies, either because the populations of the former two species were relatively recently wild-caught, or by virtue of being different species. Second, that the different evolutionary trajectories in D. ananassae and D. n. nasuta versus D. melanogaster were a reflection of differences in the manner in which larval crowding was imposed in the two sets of selection experiments. The D. melanogaster studies used a higher absolute density of eggs per unit volume of food, and a substantially larger total volume of food, than the studies on D. ananassae and D. n. nasuta. Here, we show that long-term laboratory populations of D. melanogaster, descended from some of the populations used in the earlier studies, evolve essentially the same set of traits as the D. ananassae and D. n. nasuta crowding-adapted populations when subjected to a similar larval density at low absolute volumes of food. As in the case of D. ananassae and D. n. nasuta, and in stark contrast to earlier studies with D. melanogaster, these crowding-adapted populations of D. melanogaster did not evolve greater larval feeding rates as a correlate of increased competitive ability. The present results clearly suggest that the suite of phenotypes through which the evolution of greater competitive ability is achieved in fruitflies depends critically not just on larval density per unit volume of food, but also on the total amount of food available in the culture vials. We discuss these results in the context of an hypothesis about how larval density and the height of the food column in culture vials might interact to alter the fitness costs and benefits of increased larval feeding rates, thus resulting in different routes to the evolution of greater competitive ability, depending on the details of exactly how the larval crowding was implemented.
29 citations
TL;DR: Quantitative trait loci for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs) and results provide the common QTLs and for marker-assisted breeding.
Abstract: Grain yield (GY) is one of the most important and complex quantitative traits in maize (Zea mays L.) breeding practice. Quantitative trait loci (QTLs) for GY and three kernel-related traits were detected in a set of recombinant inbred lines (RILs). One hundred and seven simple sequence repeats (SSRs) and 168 insertion/deletion polymorphism markers (Indels) were used to genotype RILs. Eight QTLs were found to be associated with four yield-related traits: GY, 100-kernel weight (HKW), 10-kernel length (KL), and 10-kernel length width (KW). Each QTL explained between 5.96 (qKL2-1) and 13.05 (qKL1-1) per cent of the phenotypic variance. Notably, one common QTL, located at the marker interval between bnlg1893 and chr2- 236477 (chromosomal bin 2.09) simultaneously controlled GY and HKW; another common QTL, at bin 2.03 was simultaneously responsible for HKW and KW. Of the QTLs identified, only one pair of significant epistatic interaction involved in chromosomal region at bin 2.03 was detected for HKW; no significant QTL × environment interactions were observed. These results provide the common QTLs and for marker-assisted breeding.
27 citations
TL;DR: These transcriptome data and mungbean EST-SSRs could serve as a valuable resource for novel gene discovery and the marker-assisted selective breeding of this species.
Abstract: Mungbean (Vigna radiata L. Wilczek) is one of the most important leguminous food crops in Asia. We employed Illumina paired-end sequencing to analyse transcriptomes of three different mungbean genotypes. A total of 38.3–39.8 million paired-end reads with 73 bp lengths were generated. The pooled reads from the three libraries were assembled into 56,471 transcripts. Following a cluster analysis, 43,293 unigenes were obtained with an average length of 739 bp and N50 length of 1176 bp. Of the unigenes, 34,903 (80.6%) had significant similarity to known proteins in the NCBI nonredundant protein database (Nr), while 21,450 (58.4%) had BLAST hits in the Swiss-Prot database (E-value<10−5). Further, 1245 differential expression genes were detected among three mungbean genotypes. In addition, we identified 3788 expressed sequence tag-simple sequence repeat (EST-SSR) motifs that could be used as potential molecular markers. Among 320 tested loci, 310 (96.5%) yielded amplification products, and 151 (47.0%) exhibited polymorphisms among six mungbean accessions. These transcriptome data and mungbean EST-SSRs could serve as a valuable resource for novel gene discovery and the marker-assisted selective breeding of this species.
27 citations
TL;DR: This is the first study to analyse the LBD gene family in grape and provides valuable information for classification and functional investigation of this gene family.
Abstract: In plants, the transcription factor families have been implicated in many important biological processes. These processes include morphogenesis, signal transduction and environmental stress responses. Proteins containing the lateral organ boundaries domain (LBD), which encodes a zinc finger-like domain are only found in plants. This finding indicates that this unique gene family regulates only plant-specific biological processes. LBD genes play crucial roles in the growth and development of plants such as Arabidopsis, Oryza sativa, Zea mays, poplar, apple and tomato. However, relatively little is known about the LBD genes in grape (Vitis vinifera). In this study, we identified 40 LBD genes in the grape genome. A complete overview of the chromosomal locations, phylogenetic relationships, structures and expression profiles of this gene family during development in grape is presented here. Phylogenetic analysis showed that the LBD genes could be divided into classes I and II, together with LBDs from Arabidopsis. We mapped the 40 LBD genes on the grape chromosomes (chr1-chr19) and found that 37 of the predicted grape LBD genes were distributed in different densities across 12 chromosomes. Grape LBDs were found to share a similar intron/exon structure and gene length within the same class. The expression profiles of grape LBD genes at different developmental stages were analysed using microarray data. Results showed that 21 grape LBD genes may be involved in grape developmental processes, including preveraison, veraison and ripening. Finally, we analysed the expression patterns of six LBD genes through quantitative real-time polymerase chain reation analysis. The six LBD genes showed differential expression patterns among the three representative grape tissues, and five of these genes were found to be involved in responses to mannitol, sodium chloride, heat stress and low temperature treatments. To our knowledge, this is the first study to analyse the LBD gene family in grape and provides valuable information for classification and functional investigation of this gene family.
26 citations
TL;DR: It is suggested that the MMP-1 -1607 1G/2G polymorphism might play an important role in the risk of endometriosis and adenomyosis and more well-designed and large-scale studies regarding gene–gene and gene–environment interactions are needed in the future.
Abstract: Matrix metalloproteinase (MMP) promoter polymorphisms are considered to play roles in the aetiology of endometriosis and adenomyosis, however, the evidence available are inconsistent. We aimed to systematically review the asscociation between MMP-1 -1607 1G/2G MMP-2 -735 C/T, MMP-3 -1171 5A/6A and MMP-9 -1562 C/T polymorphisms and the risk of endometriosis and adenomyosis. A systemic search was conducted in Ovid, PubMed, Chinese National Knowledge Infrastructure and ChineseWanfang Database.We used the pooled odds ratio (OR) and their corresponding 95% confidence interval (CI) to calculate the statistical power. Besides, we evaluated the quality of individual studies based on Newcastle-Ottawa scale. A total of 13 papers with 18 studies conformed to our inclusion criteria. We observed a significant association between MMP-1 -1607 1G/2G polymorphism and the susceptibility of endometriosis and adenomyosis under recessive model (OR = 1.25, 95%CI = 1.03-1.53, P = 0.03). While no significant association was found in MMP-2 -735 C/T, MMP-3 -1171 5A/6A and MMP-9 -1562 C/T polymorphisms. This systemic review and meta-analysis suggested that theMMP-1 -1607 1G/2G polymorphism might play an important role in the risk of endometriosis and adenomyosis. Further, more well-designed and large-scale studies regarding gene-gene and gene-environment interactions are needed in the future.
26 citations
TL;DR: The results reinforce the view that the understanding of the evolution of competitive ability in fruitflies needs to be more nuanced than before, with an appreciation that there may be multiple evolutionary routes through which higher competitive ability can be attained.
Abstract: The standard view of adaptation to larval crowding in fruitflies, built on results from 25 years of multiple experimental evolution studies on Drosophila melanogaster, was that enhanced competitive ability evolves primarily through increased larval feeding and foraging rate, and increased larval tolerance to nitrogenous wastes, at the cost of efficiency of food conversion to biomass. These results were at odds from the predictions of classical K-selection theory, notably the expectation that selection at high density should result in the increase of efficiency of conversion of food to biomass, and were better interpreted through the lens of α-selection. We show here that populations of D. ananassae and D. n. nasuta subjected to extreme larval crowding evolve greater competitive ability and pre-adult survivorship at high density, primarily through a combination of reduced larval duration, faster attainment of minimum critical size for pupation, greater time efficiency of food conversion to biomass and increased pupation height, with a relatively small role of increased urea/ammonia tolerance, if at all. This is a very different suite of traits than that seen to evolve under similar selection in D. melanogaster, and seems to be closer to the expectations from the canonical theory of K-selection. We also discuss possible reasons for these differences in results across the three species. Overall, the results reinforce the view that our understanding of the evolution of competitive ability in fruitflies needs to be more nuanced than before, with an appreciation that there may be multiple evolutionary routes through which higher competitive ability can be attained.
26 citations
TL;DR: It is shown that AGT M235T polymorphism was associated with SAH risk in Caucasian-Brazilians, and no association was detected with CAD.
Abstract: The rennin-angiotensin-aldosterone system (RAAS) is a critical pathway in regulating blood pressure and salt/water homeostasis, possessing an intimate relationship with the development of systemic artery hypertension (SAH). Once hypertension is considered a risk factor for coronary artery disease (CAD), the RAAS is also related to this pathology. This investigation aimed to analyse if the frequencies of AGT M235T (rs699) and ACE I/D (rs4646994) polymorphisms are associated with CAD and SAH in African-Brazilians and Caucasian-Brazilians. In this study we analysed 714 subjects who underwent coronary angiography to detect obstructive lesions and CAD, as well as blood pressure measurement and SAH, grouped according to ethnicity: 266 African-Brazilians and 448 Caucasian-Brazilians. Among CAD and SAH cases and controls, the genotype and allele frequencies of ACE I/D polymorphism were similar in both ethnic groups. The AGT 235TT genotype and 235T allele frequencies were higher in SAH cases (32%, 54.7%) versus controls in Caucasian-Brazilians (19.8%, 46.4%; P = 0.038, P = 0.031, respectively). The AGT 235TT (OR = 1.8; P = 0.028) demonstrated to be an independent factor risk in a multivariate logistic regression increasing SAH risk in Caucasians but not in African-Brazilians. In summary, AGT M235T polymorphism was associated with SAH risk in Caucasian-Brazilians, and no association was detected with CAD. No association was also observed in ACE I/D polymorphism either in CAD or SAH in African-Brazilians and Caucasian-Brazilians.
TL;DR: Analysis of samples from a Japanese population revealed first insights into the population and colony structure of this tramp ant, including high nestmate relatedness in multi-queen colonies and a relatively high inbreeding coefficient.
Abstract: Cardiocondyla obscurior is a successful but unobtrusive tramp ant which is widely distributed throughout the tropics and subtropics. To understand its population structure and biology, we established six polymorphic microsatellite markers. We determined the general variability of the six loci by analysing individuals from four different populations. In addition, we analysed samples from a Japanese population and revealed first insights into the population and colony structure of this tramp species, including high nestmate relatedness in multi-queen colonies and a relatively high inbreeding coefficient. Numerous plants and animals have become established in areas far away from their native ranges due to human activities (Hulme 2009). Among these are several dozen tramp species of ants. Some of them, such as the red imported fire ant, the Argentine ant, and the yellow crazy ant, quickly become dominant in new ecosystems and are among the worst invasive species worldwide, on a par with tiger mosquitoes, black rats, or water hyacinths (reviewed by Holway et al. 2002; Tsutsui and Suarez 2003). The ecological impact, behavioural ecology and sociobiology of these eye-catching invaders have been intensively studied, but not much is known about tramps that less dramatically integrate in novel environments. Among the most widespread of these inconspicuous tramp ants are the ‘sneaking ants’, Cardiocondyla. At least seven of its ∼100 species are tramps and a subset of two or three of these can be found reliably on most tropical beaches, and in plantations and parks, around the tropics and subtropics (Seifert 2003; Heinze et al. 2006; Wetterer 2012a, b, 2014). Cardiocondyla exhibits a bizarre male diphenism with so-called ‘ergatoid’ wingless males in addition to the typical winged male of ants. While winged males are peaceful and
TL;DR: In silico analyses showed the possible role of p53, p27, PTEN and Elongin B in gastric cancer tumourigenesis as well as finding novel miR-222 targets based on in silico investigations.
Abstract: Despite of promising improvements in treatment of gastric cancer, the mortality rate of this malignancy remains high. Chronic infection by Helicobacter pylori, interfering with intracellular signalling pathways, is the main risk factor for gastric cancer. Some evidence suggests that microRNAs (miRNA), the small noncoding RNA molecules, can play role as oncogenes or tumour suppressors in the cells. MiR-222 is one of the remarkable miRNAs undergoing upregulation in gastric cancer. However, the association between miR-222 upregulation and H. pylori infection in gastric cancer tissues remains unclear. The aim of this study was to analyse the expression level of miR-222 in gastric cancer tissues, evaluating the relationship between miR-222 expression level and H. pylori infection and also finding novel miR-222 targets based on in silico investigations. MiR-222 expression level in 200 patients including 112 H. pylori positive and 88 H. pylori negative was relatively measured using RT-qPCR and compared with 88 healthy samples. In silico enrichment analysis of miR-222 targets was performed by DAVID database to evaluate the possible role(s) of miR-222 in gastric tumourigenesis. We observed upregulated level of miR-222 in gastric cancer tissues compared with normal samples (P<0.05). However, no significant difference between miR-222 expression in H. pylori-positive and H. pylori-negative cases was observed. Our in silico analyses showed the possible role of p53, p27, PTEN and Elongin B in gastric cancer tumourigenesis. MiR-222 functions as an onco-miRNA and its overexpression can be involved in pathogenesis of gastric cancer, independent of H. pylori infection.
TL;DR: The data suggest that FMF is remarkably common among Iranian populations, and the awareness for FMF and the implementation of augmented carrier screening programmes considering the multiethnic nature of the Iranian population should be promoted.
Abstract: Familial Mediterranean fever (FMF) is a hereditary autoinflammatory disorder caused by mutations in the MEFV gene. The disease is especially common among Armenian, Turkish, Jewish and Middle East Arab populations. To identify the frequency and the spectrum of common MEFV mutations in different Iranian populations, we investigated a cohort of 208 unselected asymptomatic individuals and 743 FMF patients. Nine hundred and fifty-one samples were analysed for the presence of 12 MEFV mutations by PCR and reverse-hybridization (FMF StripAssay, ViennaLab, Vienna, Austria). Confirmatory dideoxy sequencing of all MEFV gene exons was performed for 39 patients. Fifty-seven (27.4%) healthy individual carried mutant MEFV alleles. Three hundred and ninety-one (52.6%) FMF patients were found positive for either one (172/743; 23.1%), two or three MEFV mutations. Using dideoxy sequencing, three novel variants, A66P, R202W and H300Q, could be identified. Our analysis revealed an allele frequency and carrier rate of 15.6 and 27.4%, respectively, among healthy Iranians. Still moderate compared to neighbouring Armenia, but higher than in Turkey or Iraq, these data suggest that FMF is remarkably common among Iranian populations. E148Q was most frequent in the group of healthy individuals, whereas M694V was the most common mutation among FMF patients, thereby corroborating previous studies on MEFV mutational spectra in the Middle East. Accordingly, MEFV mutations are frequent in healthy Iranian individuals across different ethnic groups. Based on this finding, the awareness for FMF and the implementation of augmented carrier screening programmes considering the multiethnic nature of the Iranian population should be promoted.
TL;DR: The identification of SAUR genes in Urticales plants is reported and comparison of qRT-PCR data and previous RNA-Seq data suggested the reliability of this work.
Abstract: Small auxin-up RNA (SAUR) genes are important gene families in auxin signalling transduction and are commonly used as early auxin responsive markers. Till date, no SAUR gene is identified in Urticales plants despite of the published bioinformation of mulberry, hemp and ramie. In this study, we used Arabidopsis sequences as query to search against mulberry, hemp genomes and ramie transcriptome database. In total, we obtained 62, 56 and 71 SAUR genes in mulberry, hemp and ramie, respectively. Phylogenetic analysis revealed the Urticales specific expansion of SAUR genes. Expression analysis showed 15 randomly selected ramie SAUR genes that were diversely functioned in ramie tissues and revealed a series of IAA-responsive, drought-responsive and high temperature-responsive genes. Moreover, comparison of qRT-PCR data and previous RNA-Seq data suggested the reliability of our work. In this study, we first report the identification of SAUR genes in Urticales plants. These results will provide a foundation for their function validation in Urticales plant growth and development.
TL;DR: Clinicians should understand the importance of chromosomal analysis in couples with recurrent miscarriages and refer them for karyotyping after two miscarriages to rule out the possible genetic cause of recurrent miscarriage.
Abstract: Human reproduction is considered as the most inefficient event as ~15-20% of human pregnancies end in miscarriage and in the product of miscarriages, chromosomal anomalies are a common occurrence. The aim of the present retrospective study was to assess the frequency of chromosomal aberrations in couples with recurrent miscarriages in the region of Punjab and to compare with worldwide frequencies. In this study, a total of 440 cases were referred between the period 1995-2015. After lymphocyte culturing, giemsa-trypsin banding was done for each case to assess the chromosomal anomalies. The frequency of chromosomal aberrations among couples was found to be 3.41% in our study. Among these aberrations, balanced reciprocal translocations formed the largest group with 60% anomalies. We would conclude that clinicians should understand the importance of chromosomal analysis in these couples and refer them for karyotyping after two miscarriages to rule out the possible genetic cause of recurrent miscarriages.
TL;DR: Quantitative trait locus (QTL) analysis provides a powerful tool for soybean breeders to search for new sources of variation and investigate the genetic factors underlying quantitatively inherited traits.
Abstract: Soybean is one of the most important food and oil crops worldwide. It provides about 69 and 30% of dietary protein and oil, respectively. Improvement of yield potential is the most important goal of most soybean breeding programmes worldwide. Hundred-seed weight (HSW) is an important yield component in soybean and found to show a positive correlation with seed yield (Smith and Camper 1975). HSW as main component of plants is affected by seed shape. Seed shape is believed to be complex and controlled by many genes which show stability in different environments and present higher heritability (Song et al. 2004). Quantitative trait locus (QTL) analysis provides a powerful tool for soybean breeders to search for new sources of variation and investigate the genetic factors underlying quantitatively inherited traits. Previous QTL analyses for seed shape and HSW have been conducted for soybean. Salas et al. (2006) found that 19 QTLs for seed shape were mapped on 10 chromosomes. Hu et al. (2013) mapped 10 QTLs for seed shape on six chromosomes in soybean. Epistasis has a large influence on phenotype. There have been few studies on mapping QTLs bearing epistatic effects and environment interactions (QEs) for seed shape and HSW in soybean. Lü et al. (2011) identified 19 main effect QTLs (M-QTLs) and three epistatic QTLs (E-QTLs) for seed length (SL) on eight chromosomes. Xu et al. (2011) mapped a total of 121 M-QTLs, six environmental effects, eight QEs, five cytoplasmic effects and 92 cytoplasmic by QTL interactions for seed-size and seed-shape traits distributed over 14 linkage groups. Niu et al. (2013) detected 59 QTLs and 31 QEs for seed shape in 20 soybean chromosomes. To improve soybean germplasm,
TL;DR: In this article, primer pairs of 15 microsatellite markers associated with sex determination of tilapia were selected and amplified in Wami tilapsia, Oreochromis urolepis hornorum.
Abstract: In this study, primer pairs of 15 microsatellite markers associated with sex determination of tilapia were selected and amplified in Wami tilapia, Oreochromis urolepis hornorum. While one marker, UNH168, on linkage group 3 (LG3) was associated (P <0.001) with the phenotypic sex in the experimental population, nine genotypes were detected in both sexes. Only 99-bp allele was detected in the female samples, while 141, 149 and 157-bp alleles were present in both male and female samples. UNH168 was localized by fluorescence in situ hybridization (FISH) on the long arm of the largest tilapia chromosome pair (chromosome 1, equivalent to LG3). This sex-linked microsatellite marker could potentially be used for marker-assisted selection in tilapia breeding programmes to produce monosex male tilapia.
TL;DR: The findings showed that in IL10 A1082G gene polymorphism AG genotype and G allele may participate in the progression of OSCC, and that G allele was significant in OSCC cases of tobacco chewing.
Abstract: The functional polymorphism A1082G in the gene (IL10) for interleukin-10 associated with risk of oral squamous cell carcinoma (OSCC). The present case-control study was to evaluate the possible association between IL10 A1082G gene and OSCC in north Indian population. Analysis of IL10 A1082G genotype in 232 OSCC cases and 221 healthy controls of comparable age, gender, smokers, tobacco chewing and alcohol consumption. IL10 A1082G status in cases and controls were evaluated by polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP). The frequencies of IL10 A1082G polymorphism AA, AG, GG genotypes were 29.74, 68.10 and 2.15% in OSCC cases and 57.46, 42.08 and 0.45% in healthy controls. The average frequency of G mutant allele was 36.20% in OSCC cases compared with 21.50% among the controls and this allele was associated with increased risk for OSCC cases. Heterozygous AG genotype was found statistically significant in OSCC cases than in controls (OR = 1.6, 95% CI = 1.1-2.2, P = 0.003), whereas homozygous mutant GG genotype was not found significant (OR = 4.7, 95% CI = 0.55-41.1, P = 0.2). Moreover, we found that G allele was significant in OSCC cases of tobacco chewing. The frequency of IL10 A1082G polymorphism G allele and AG genotype is associated with OSCC cases as compared with controls; this may be due to smoking and tobacco chewing. Our findings showed that in IL10 A1082G gene polymorphism AG genotype and G allele may participate in the progression of OSCC.
TL;DR: This paper aims to demonstrate the efforts towards in-situ applicability of EMMARM, as to provide real-time information about the response of the immune system to EMTs.
Abstract: 1Institute for Biotechnology and Bioengineering, Centre of Genomics and Biotechnology (IBB/CGB), 3Department of Forestry Sciences and Landscape (CIFAP), and 4Centre for the Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Tras-os-Montes and Alto Douro (UTAD), P.O. Box 1013, 5001-801 Vila Real, Portugal 2Centre of Forestry Studies (CEF), ISA, UTL Tapada da Ajuda, 1349-017 Lisbon, Portugal
TL;DR: Screening of genes known to cause HRFs in patients already identified with a single MEFV mutation, can reveal quite rare but potentially causative mutational combinations at different loci, indicating further evidence for possible locus–locus interactions and phenotypes resulting from digenic inheritance.
Abstract: Familial Mediterranean fever (FMF) has traditionally been considered as a monogenic autosomal recessive disorder caused by mutations in the MEFV gene with highest incidence among Mediterranean populations. In a considerable number of patients with typical FMF, only one MEFV mutation was identified and the possibility that more than one autoinflammatory gene may be responsible for their disease was investigated. In the present study, an extensive search for possible mutations in three hereditary recurrent fever (HRF) genes was performed in 128 MEFV heterozygous Greek–Cypriots clinically diagnosed based on their phenotype with FMF-like disease from a previous study. Sequence analysis was performed for MVK, TNFRSF1A and NLRP3 genes which is also known to cause HRFs. In total, three patients were identified with heterozygous mutations and a second mutation in an autoinflammatory gene. Two patients carried a MEFV mutation and a NLRP3 mutation, and an additional third carried a MEFV mutation and a TNFRSF1A mutation. Patient 1 carried MEFV p.[Val726Ala] (NM_000243.2:c.2177T >C) and NLRP3 p.[Val198Met] (NM_001243133.1:c.592G >A) variants and patient 2 carried MEFV p.[Glu148Gln] (NM_000243.2:c.442G >C) variant which is of uncertain significance and NLRP3 p.[Arg176Trp] (NM_001243133.1:c.526C >T). Lastly, patient 3 was identified to carry MEFV p.[Met694Val] (NM_000243.2:c.2080A >G) and TNFRSF1A p.[Arg121Gln] (NM_001065.3:c.362G >A) variants. The results from this study indicate that screening of genes known to cause HRFs in patients already identified with a single MEFV mutation, can reveal quite rare but potentially causative mutational combinations at different loci. Such interaction provide further evidence for possible locus–locus interactions and phenotypes resulting from digenic inheritance.
TL;DR: A meta-analysis to establish link between maternal single-nucleotide polymorphism (SNP) and birth of Down’s syndrome (DS) child suggested that MTHFR 677 C–T is a major risk factor for DS birth.
Abstract: Methylenetetrahydrofolate reductase (MTHFR) is the most important gene that participates in folate metabolism. Presence of valine instead of alanine at position 677 and elevated levels of homocystein causes DNA hypomethylation which in turn favours nondisjunction. In this study, we conducted a meta-analysis to establish link between maternal single-nucleotide polymorphism (SNP) and birth of Down's syndrome (DS) child. A total of 37 case-control studies were selected for analysis including our own, in which we investigated 110 cases and 111 control mothers. Overall, the result of meta-analysis showed significant risk of DS affected by the presence of maternal SNP (MTHFR 677 C-T OR = 0.816, 95% CI = 0.741-0.900, P <0.0001). Heterogeneity of high magnitude was observed among the studies. The chi-square value suggested a highly significant association between homozygous mutant TT genotype and birth of DS child (χ² = 23.63, P = 0.000). Genetic models suggested that 'T' allele possesses high risk for DS whether present in dominant (OR = 1.23, 95% CI = 1.13-1.34); codominant (OR = 1.17, 95% CI = 1.10-1.25) or recessive (OR = 1.21, 95% CI = 1.05-1.38) form. The analysis from all 37 studies combined together suggested that MTHFR 677 C-T is a major risk factor for DS birth.
TL;DR: The results suggested that rs10046 could play a potential role in migraine susceptibility in Turkish population, and the rare GG genotype of rs726281 appears to influence headaches in a recessive manner in MRM subgroup of female patients.
Abstract: Migraine, a highly prevalent headache disorder, is regarded as a polygenic multifactorial disease. Single-nucleotide polymorphisms (SNPs) in the genes that involved in sex hormone metabolism may comprise risk for migraine, but the results of previous genetic association studies are conflicting. The aim of this study was to evaluate genetic variants in genes involved in oestrogen receptor and oestrogen hormone metabolism in a Turkish population. A total of 12 SNPs in the ESR1, ESR2, FSHR, CYP19A1, SHBG and NRIP1 genes were genotyped in 142 migraine cases and 141 nonmigraine controls, using a BioMark 96.96 dynamic array system. In addition, gene–gene interactions were analysed using generalized multifactor dimensionality reduction (GMDR) methods. According to GMDR analysis, our results indicated that there was a significant association between migraine and gene–gene interaction among the CYP19A1, FSHR, ESR1 and NRIP1. Single-gene variant analysis showed that a significant association was observed between the TT genotype of rs10046 and migraine susceptibility. When the analysis was performed only in women, the GG genotype of rs2229741 was different between migraineurs and controls. When the female migraine patients were divided into two groups, migraine related to menstruation (MRM) or migraine not related to menstruation (MNRM), GG genotype of rs726281 was significantly associated with MRM. These results suggested that rs10046 could play a potential role in migraine susceptibility in Turkish population. Also, the rare GG genotype of rs726281 appears to influence migraine susceptibility in a recessive manner in MRM subgroup of female patients. In addition, variant GG genotype of rs2229741 may reduce the risk of migraine in Turkish women.
TL;DR: This work evaluated five seed vigour traits in two connected recombinant inbred lines (RIL) populations under low-temperature conditions and provided an important reference for facilitating indirect selection for cold tolerance in maize breeding.
Abstract: Seed vigour, an important factor governing the seed quality, reflects potential seed germination, seedling growth, seed longevity and tolerance to adversity (Sun et al. 2007). Maize plants grown in subtropical and temperate regions are often subjected to cold stress and frequently exhibit poor earlyseason vigour that leads to delayed seedling development and poor stand establishment (Hope et al. 1992). Many studies have uncovered various quantitative trait loci (QTL) associated with the chilling tolerance of maize seedlings (Frachebound et al. 2004; Jompuk et al. 2005; Presterl et al. 2007; Rodriguez et al. 2008; Marcelo 2012). However, the physiological mechanisms and genetic basis of seed vigourrelated traits remain unknown. Here, we evaluated five seed vigour traits in two connected recombinant inbred lines (RIL) populations under low-temperature conditions. A total of 26 QTL were identified. Fourteen initial QTL were integrated into five meta-QTL (mQTL) in a meta-analysis. Our results provide an important reference for facilitating indirect selection for cold tolerance in maize breeding.
TL;DR: The results indicated that the FTO rs9939609 SNP may be linked with the risk of obesity in Taiwanese subjects and did not exhibit any significant association with obesity-related metabolic traits among the subjects.
Abstract: It is a key challenge to conduct reproducibility in genetic research, especially association studies in obesity. While susceptibility of a single-nucleotide polymorphism (SNP), rs9939609, in the fat mass and obesity-associated (FTO) gene to obesity has been reported in various populations, data from Asians is less conclusive. This replication study was carried out to test whether the FTO rs9939609 SNP is a predictive factor for obesity and obesity-related metabolic traits in a Taiwanese population. A total of 1188 Taiwanese subjects were recruited for this study. The FTO rs9939609 SNP was genotyped by the Taqman assay. Obesity-related metabolic traits such as triglyceride, waist circumference, systolic and diastolic blood pressure, total cholesterol, creatinine, alanine aminotransferase and fasting glucose were measured. Our data revealed that the FTO rs9939609 SNP exhibited a significant association with obesity (BMI ≥ 30 kg/m²) among the subjects (P = 0.026). However, the FTO rs9939609 SNP did not exhibit any significant association with obesity-related metabolic traits among the subjects. Our results indicated that the FTO rs9939609 SNP may be linked with the risk of obesity in Taiwanese subjects.
TL;DR: Kiwi fruit is a commercially valuable and nutritionally important fruit, which is well known as ‘the king of fruits’ for remarkably high vitamin C content, however, pathogen infections have lowered the yield and quality of kiwi Fruit.
Abstract: In plants, there are many layers of defense system against pathogens in the environment. The first is structural barrier and second is pathogen-associated molecular pattern (PAMP) recognition receptors. The third is resistance genes (R genes) against specific pathogens, which work in the triggering effector immunity (ETI) that produces a hypersensitive response (HR) (Jones and Dangl 2006). R genes confer resistance to a diverse range of pathogens, including bacteria, fungi, oomycetes, viruses, insects and nematodes (Martin et al. 2003). Kiwi fruit (Actinidia chinensis) is a commercially valuable and nutritionally important fruit, which is well known as ‘the king of fruits’ for remarkably high vitamin C content. However, pathogen infections have lowered the yield and quality of kiwi fruit (Ferrante and Scortichini 2010; Biondi et al. 2013; Li et al. 2013). Therefore, better understanding of resistance (R) genes in kiwi fruit could provide the strategy for improving resistance to pathogens. The class of NBS– LRR resistance genes, which encode nucleotide-binding sites (NBS) and leucine-rich repeat (LRR) domains, is one of the largest R genes families (McHale et al. 2006). NBS-encoding genes are categorized as NBS-only genes and NBS–LRR genes. Based on an N-terminal domain of toll and interleukin-1 receptors (TIR) NBS-encoding genes are divided into two subclasses, TIR type genes and nonTIR type genes. Some nonTIR NBS-encoding genes have a coil–coil motif in N-terminus (Dangl and Jones 2001), therefore, they are subdivided into CC-NBS genes (CNs), X-NBS genes (XNs), CC-NBS–LRR genes (CNLs) and X-NBS–LRR genes (XNLs). Recently, the genome of a heterozygous kiwi fruit cultivar ‘Hongyang’ (A. chinensis) was sequenced (616.1 Mb), which provides an opportunity for the study of NBS-encoding genes
TL;DR: Quantitative trait locus (QTL) mapping for GPC and FWD was conducted using a set of 131 recombinant-inbred lines derived from the cross ‘Chuan 35050 × Shannong 483’ in six environmental conditions with some important favourable QTL alleles represented.
Abstract: Grain protein content (GPC) and flour whiteness degree (FWD) are important qualitative traits in common wheat. Quantitative trait locus (QTL) mapping for GPC and FWD was conducted using a set of 131 recombinant-inbred lines derived from the cross 'Chuan 35050 × Shannong 483' in six environmental conditions. A total of 22 putative QTLs (nine GPC and 13 FWD) were identified on 12 chromosomes with individual QTL explaining 4.5-34.0% phenotypic variation. Nine QTLs (40.9%) were detected in two or more environments. The colocated QTLs were on chromosomes 1B and 4B. Among the QTLs identified for GPC, QGpc.sdau-4A from the parent Shannong 483 represented some important favourable QTL alleles. QGpc.sdau-2A.1 and QFwd.sdau-2A.1 had a significant association with both GPC and FWD. The markers detected on top of QTL regions could be potential targets for marker-assisted selection.
TL;DR: This paper presents a meta-modelling procedure called “supervised cell reprograming” that has been developed at the cellular level by a team of four scientists at the CSIR-Institute of Genomics and Integrative Biology, New Delhi.
Abstract: 1Genomics and Molecular Medicine, CSIR-Institute of Genomics and Integrative Biology, New Delhi 110 020, India 2Molecular and Human Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India 3Sachindra Nath Pradhan Centre for Neurosciences, University of Calcutta, Kolkata 700 019, India 4Dristi Pradip, Kolkata 700 068, India 5Academy of Scientific and Innovative Research (AcSIR), New Delhi 110 025, India
TL;DR: The winged helix or forkhead box (Fox) class of transcription factors constitutes a family of structurally related transcriptional activators that have been identified in species ranging from yeast to human.
Abstract: The winged helix or forkhead box (Fox) class of transcription factors constitutes a family of structurally related transcriptional activators that have been identified in species ranging from yeast to human. The first member of this transcription factor class was identified as a nuclear homeotic gene involved in embryonic development in Drosophila melanogaster (Weigel et al. 1989). The FoxO family of forkhead transcription factors represents a subfamily within the larger group of Fox transcription factors. Mammalian FoxO proteins (FoxO1, FoxO3a, FoxO4 and FoxO6), which are homologous to Caenorhabditis elegans protein DAF-16, belong to the O (‘other’) class of the Fox superfamily (Kaestner et al. 2000; Barthel et al. 2005). As transcription factors in the nucleus, the primary function of FoxO proteins is to bind to their cognate DNA target sequences as monomers. The cocrystal structure of another Fox protein, HNF-3γ , with DNA shows that there are 14 protein–DNA contacts distributed throughout the forkhead domain, but the third α-helix (H3) plays the most important role in a winged helix/forkhead protein’s DNA-binding specificity (Clark et al. 1993). In addition, both winged loops also make important interactions with DNA (Clark et al. 1993; Boura et al. 2007). Although the molecular basis of the DNA-binding specificity of FoxO transcription factors is poorly understood, high-affinity DNA-binding studies have identified a consensus FoxOrecognized element (FRE), (G/C) (T/A)AA(C/T)AA (Biggs Iii et al. 1999; Furuyama et al. 2000; Gilley et al. 2003).
TL;DR: The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp.
Abstract: The objective of this study was to quantify the molecular diversity and to determine the genetic relationships among Secale spp. and among cultivars of Secale cereale using RAPDs, ISSRs and sequence analysis of six exons of ScMATE1 gene. Thirteen ryes (cultivated and wild) were genotyped using 21 RAPD and 16 ISSR primers. A total of 435 markers (242 RAPDs and 193 ISSRs) were obtained, with 293 being polymorphic (146 RAPDs and 147 ISSRs). Two RAPD and nine ISSR primers generated more than 80% of polymorphism. The ISSR markers were more polymorphic and informative than RAPDs. Further, 69% of the ISSR primers selected achieved at least 70% of DNA polymorphism. The study of six exons of the ScMATE1 gene also demonstrated a high genetic variability that subsists in Secale genus. One difference observed in exon 1 sequences from S. vavilovii seems to be correlated with Al sensitivity in this species. The genetic relationships obtained using RAPDs, ISSRs and exons of ScMATE1 gene were similar. S. ancestrale, S. kuprijanovii and S. cereale were grouped in the same cluster and S. segetale was in another cluster. S. vavilovii showed evidences of not being clearly an isolate species and having great intraspecific differences.