• Issue front cover thumbnail

      Volume 95, Issue 4

      December 2016,   pages  751-1072

    • Transgenic overexpression of BAFF regulates the expression of immune-related genes in zebrafish, Danio rerio

      LI ZHANG CHAO LIU XIN ZHOU YING XIE LIBO SU QI GENG BINGHUI LIU SHUFENG LIU

      More Details Abstract Fulltext PDF

      The B-cell activating factor (BAFF) is a member of tumour necrosis factor (TNF) superfamily that specifically regulates B lymphocyte proliferation and survival. Excess BAFF leads to overproduction of antibodies for secretion, anti-dsDNA antibodies and a lupus-like syndrome in mice. To investigate whether transgenic overexpression of the zebrafish BAFF leads to immunoglobulin changes and/or early maturing of the immune system, a Tol2-GFP-2A-BAFF/His recombinant plasmid was constructed by inserting a 2A peptide between the green fluorescent protein (GFP) and BAFF sequences. Functional GFP and BAFF proteins were expressed separately and confirmed in HeLa cells. The relative expression of immune-related genes (IgLC-1, IgLC-2, IgLC-3, IgD, IgM and IL-4), early lymphoid markers (Ikaros, Rag-1 and TCRAC), and the protooncogene Bcl-2 were evaluated by quantitative polymerase chain reaction (PCR) in F0 founder of transgenic zebrafish juveniles and adults. Ectopic expression of BAFF in adults was confirmed using Western blots and was shown to upregulate IgLC-1, IgLC- 2, IgD, IgM, IgZ/T, Ikaros, Rag-1, TCRAC, IL-4 and Bcl-2 expression in juveniles on day 21 and IgLC-1, IgLC-2, IgD, IgM, IgZ/T, Rag-1, TCRAC and Bcl-2 expression in zebrafish three months postfertilization. The relative titers of specific IgM against Edwardsiella tarda WED were assessed using modified enzyme-linked immunosorbent assay (ELISA) with the whole body homogenate of zebrafish and demonstrated a significant increase in BAFF-transgenic group. Therefore, our findings provided novel insight into further exploration of modulating adaptive immunity and studying autoimmune diseases caused by regulating BAFF.

    • Evidence of digenic inheritance in autoinflammation-associated genes

      VASSOS NEOCLEOUS STEFANIA BYROU MEROPI TOUMBA CONSTANTINA COSTI CHRISTOS SHAMMAS CHRISTINA KYRIAKOU VIOLETTA CHRISTOPHIDOU-ANASTASIADOU GEORGE A. TANTELES ADAMOS HADJIPANAYIS LEONIDAS A. PHYLACTOU

      More Details Abstract Fulltext PDF

      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 possiblemutations 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 performedfor 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 MEFVmutation 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.

    • Phylogeography, genetic diversity and demographic history of the Iranian Kurdish groups based on mtDNA sequences

      FATAH ZAREI HASSAN RAJABI-MAHAM

      More Details Abstract Fulltext PDF

      Throughout the history of modern humans, the current Kurdish-inhabited area has served as part of a tricontinental crossroad for major human migrations. Also, a significant body of archaeological evidence points to this area as the site of Neolithic transition. To investigate the phylogeography, origins and demographic history, mtDNA D-loop region of individuals representing four Kurdish groups from Iran were analysed. Our data indicated that most of the Kurds mtDNA lineages belong to branches of the haplogroups with the Western Eurasian origin; with small fractions of the Eastern Eurasian and sub-Saharan African lineages. The low level of mtDNA diversity observed in the Havrami group presented a bias towards isolation or increased drift due to small population size; while in the Kurmanji group it indicated a bias towards drift or mass migration events during the 5–18th century AD. The Mantel test showed strong isolation by distance, and AMOVA results for global and regional scales confirmed that the geography had acted as the main driving force in shaping the current pattern of mtDNA diversity, rather than linguistic similarity. The results of demographic analyses, in agreement with archaeological data, revealed a recent expansion of the Kurds (∼9,500 years before present) related to the Neolithic transition from hunting and gathering, to farmingand cattle breeding in the Near East. Further, the high frequencies of typical haplogroups for early farmers (H; 37.1%) and hunter-gatherers (U; 13.8%) in the Kurds may testify the earlier hunter-gatherers in the Kurdish-inhabited area that adopted and admixed the Kurds ancestors following the Neolithic transition.

    • Genetic variation in ecoraces of tropical tasar silkworm, Antheraea mylitta using SSR marker

      G. RENUKA G. SHAMITHA

      More Details Abstract Fulltext PDF

      The tropical tasar silkworm, Antheraea mylitta, polyphagous sericigenous insect mostly found in the tropical areas of India. It is found in these regions as ecotypes or ecoraces. It feeds primarily on plants, a variety of secondary plants like Terminalia arjuna and T. tomentosa. Tasar culture is a traditional livelihood for lakhs of tribal populace in the areas of Jharkhand, Chhatisgarh, Orissa, Maharashtra, Andhra Pradesh, West Bengal and Uttar Pradesh. In the present study, the genetic diversity of these ecoraces is identified by DNA markers, namely simple sequence repeats (SSRs), most of which produced polymorphic bands.

    • Cytological behaviour of floral organs and in silico characterization of differentially expressed transcript-derived fragments associated with ‘floral bud distortion’ in soybean

      PRASHANT B. KALE PRAVIN V. JADHAV RACHANA S. WAKEKAR M. P. MOHARIL A. G. DESHMUKH M. S. DUDHARE R. S. NANDANWAR S. S. MANE J. G. MANJAYA R. G. DANI

      More Details Abstract Fulltext PDF

      An attempt was made to understand the ‘floral bud distortion’ (FBD), an unexplored disorder prevailing in soybean. Cytological behaviour of floral reproductive organs and in silico characterization of differentially expressed transcript-derivedfragments (TDFs) in symptomatic and asymptomatic soybean plants were carried out. Pollens in asymptomatic plants do not have defects in number, size, shape and function. However, in symptomatic plant, pollens were found nonviable, abnormalin shape and with reduced germination ability. Here, we employed a computational approach, exploring invaluable resources. The tissue-specific transcript profile of symptomatic and asymptomatic sources was compared to determine differentiallyexpressed TDFs associated with FBD to improve its basic understanding. A total of 60 decamer primers produced 197 scorable amplicons, ranged 162–1130 bp, of which 171 were monomorphic and 26 were differentially regulated. Reproducible TDFs were sequenced and characterized for their homology analysis, annotation, protein–protein interaction, subcellular localization and their physical mapping. Homology-based annotation of TDFs in soybean revealed presence of two characterized and seven uncharacterized hits. Annotation of characterized sequences showed presence of genes, namely auxin response factor 9(ARF9) and forkhead-associated (FHA) domain, which are directly involved in plant development through various pathways, such as hormonal regulation, plant morphology, embryogenesis and DNA repair.

    • Application of high resolution SNP arrays in patients with congenital oral clefts in south China

      TING-YING LEI HONG-TAO WANG FAN LI YING-QIU CUI FANG FU RU LI CAN LIAO

      More Details Abstract Fulltext PDF

      Chromosome microarray analysis (CMA) has proven to be a powerful tool in postnatal patients with intellectual disabilities. However, the diagnostic capability of CMA in patients with congenital oral clefts remain mysterious. Here, we present ourclinical experience in implementing whole-genome high-resolution SNP arrays to investigate 33 patients with syndromic and nonsyndromic oral clefts in whom standard karyotyping analyses showed normal karyotypes. We aim to identify the genomic aetiology and candidate genes in patients with congenital oral clefts. CMA revealed copy number variants (CNVs) in every patient, which ranged from 2 to 9 per sample. The size of detected CNVs varied from 100 to 3.2 Mb. In 33 patients, we identified six clinically significant CNVs. The incidence of clinically significant CNVs was 18.2% (6/33). Three of these six CNVs were detected in patients with nonsyndromic clefts, including one who presented with isolated cleft lip with cleft palate (CLP) and two with cleft palate only (CPO). The remaining three CNVs were detected in patients with syndromic clefts. However, no CNV was detected in patients with cleft lip only (CLO). The six clinically significant CNVs were as follows: 8p23.1 microduplication (198 kb); 10q22.2-q22.3 microdeletion (1766 kb); 18q12.3 microduplication (638 kb); 20p12.1 microdeletion (184 kb); 6q26 microdeletion (389 kb); and 22q11.21-q11.23 microdeletion (3163 kb). In addition, two novel candidate genes for oral clefts, KAT6B and MACROD2, were putatively identified. We also found a CNV of unknown clinical significance witha detection rate of 3.0% (1/33). Our results further support the notion that CNVs significantly contributed to the genetic aetiology of oral clefts and emphasize the efficacy of whole-genome high-resolution SNP arrays to detect novel candidate genes in patients with syndromic and nonsyndromic clefts.

    • Association between smoking behaviour and genetic variants of glial cell line-derived neurotrophic factor

      ESZTER KOTYUK NORA NEMETH ZSOLT RONAI ZSOLT DEMETROVICS MARIA SASVARI-SZEKELY ANNA SZEKELY

      More Details Abstract Fulltext PDF

      Glial cell line-derived neurotrophic factor (GDNF) promotes development and differentiation of dopaminergic neurons, thus it has an important role in dopamine-related neuropsychiatric disorders. Since the role of dopamine system in smoking iswell established, we hypothesized that GDNF gene variants may affect smoking behaviour. Self-reported data on smoking behaviour (never smoked, quit, occasional, or regular smokers) and level of nicotine addiction (Hooked on Nicotine Checklist and Fagerstrom Nicotine Addiction Scale), anxiety, as well as buccal samples were obtained from 930 Hungarian young adults (18–35 years). Genetic analysis involved eight GDNF single-nucleotide polymorphisms (SNP) (rs1981844, rs3812047, rs3096140, rs2973041, rs2910702, rs1549250, rs2973050 and rs11111). Allele-wise association analyses of the eight GDNF SNPs provided a significant association between smoking behaviour and rs3096140 (P = 0.0039). The minor allele (C) was more frequent in those groups who smoked in some form (quit, occasional or regular smokers) as compared to those who neversmoked (P = 0.0046). This result remained significant after Bonferroni correction for multiple testing. In the ever smoking group, no significant differences were found in the level of nicotine addiction by the alleles of these polymorphisms. Also, nosignificant interaction of rs3096140 and smoking categories were observed on anxiety mean scores. Although previous data demonstrated an association between GDNF rs2910704 and severity of methamphetamine use to the best of our knowledge, this is the first study on the role of GDNF genetic variations in smoking behaviour. Our results suggest that GDNF rs3096140 might be involved in the genetic background of smoking, independent of anxiety characteristics.

    • Chromosomal structural changes and microsatellite variations in newly synthesized hexaploid wheat mediated by unreduced gametes

      HAO LI YAJUAN WANG XIAOXUE GUO YINPENG DU CHANGYOU WANG WANQUAN JI

      More Details Abstract Fulltext PDF

      Allohexaploid wheat was derived from interspecific hybridization, followed by spontaneous chromosome doubling. Newly synthesized hexaploid wheat by crossing Triticum turgidum and Aegilops tauschii provides a classical model to understand the mechanisms of allohexaploidization in wheat. However, immediate chromosome level variation and microsatellite level variation of newly synthesized hexaploid wheat have been rarely reported. Here, unreduced gametes were applied to develop synthesized hexaploid wheat, NA0928, population by crossing T. turgidum ssp. dicoccum MY3478 and Ae. tauschii SY41, and further S0–S3 generations of NA0928 were assayed by sequential cytological and microsatellite techniques. We demonstrated that plentiful chromosomal structural changes and microsatellite variations emerged in the early generations of newlysynthesized hexaploid wheat population NA0928, including aneuploidy with whole-chromosome loss or gain, aneuploidy with telosome formation, chromosome-specific repeated sequence elimination (indicated by fluorescence in situ hybridization) and microsatellite sequence elimination (indicated by sequencing), and many kinds of variations have not been previously reported. Additionally, we reported a new germplasm, T. turgidum accession MY3478 with excellent unreduced gametes trait, and then succeeded to transfer powdery mildew resistance from Ae. tauschii SY41 to synthesized allohexaploid wheatpopulation NA0928, which would be valuable resistance resources for wheat improvement.

    • High CpG island methylation of p16 gene and loss of p16 protein expression associate with the development and progression of tetralogy of Fallot

      SI-JU GAO GUI-FANG ZHANG RONG-PENG ZHANG

      More Details Abstract Fulltext PDF

      We examined CpG island methylation in p16 gene and its effect on p16 protein expression in tetralogy of Fallot (ToF) patients to explore its potential implications in the development and progression of ToF. The study subjects consisted of 75 healthy controls and 63 ToF patients recruited at Linyi People’s Hospital between January 2012 and June 2014. The 4 mL of peripheral venous blood of each subject was obtained and saved in ethylene diamine tetraacetic acid (EDTA) tubes. Methylation-specific polymerase chain reaction (MSP) was employed to detect CpG island methylation in p16 promoter region andWestern blotting was used to detect p16 expression of all subjects. Real-time fluorescence quantitative polymerase chain reaction (FQ-PCR) was performed to test p16 mRNA expression. The results showed that p16-methylation rates in ToF group were significantly higher than the control group (ToF group, 58.73%; control group, 13.33%; P < 0.001). Remarkably, Western blotting and FQ-PCR results derived from RVOT revealed that p16 protein expression was significantly lower in ToF group compared to the control group (0.76± 0.21 versus 2.31 ± 0.35; P < 0.001), and p16 gene expression was also markedly decreased in ToF group (1.212 ± 0.152 versus 1.346 ± 0.191, P< 0.001). Additionally, our analysis suggested that CpG island methylation in p16 promoters in ToF patients was negatively correlated with p16 protein and gene expression (both P < 0.05). Our study reports that high CpG island methylation of p16 gene and loss of p16 protein expression associate with the development and progression of ToF, which may have significant therapeutic applications for ToF.

    • Identification of a novel 15.5 kb SHOX deletion associated with marked intrafamilial phenotypic variability and analysis of its molecular origin

      ANGELOS ALEXANDROU IOANNIS PAPAEVRIPIDOU KYRIAKOS TSANGARAS IOANNA ALEXANDROU MARIOS TRYFONIDIS VIOLETTA CHRISTOPHIDOU-ANASTASIADOU ELENI ZAMBA-PAPANICOLAOU GEORGE KOUMBARIS VASSOS NEOCLEOUS LEONIDAS A. PHYLACTOU NICOS SKORDIS GEORGE A. TANTELES CAROLINA SISMANI

      More Details Abstract Fulltext PDF

      Haploinsufficiency of the short stature homeobox contaning SHOX gene has been shown to result in a spectrum of phenotypes ranging from Leri–Weill dyschondrosteosis (LWD) at the more severe end to SHOX-related short stature at the milder end of the spectrum. Most alterations are whole gene deletions, point mutations within the coding region, or microdeletions in its flanking sequences. Here, we present the clinical and molecular data as well as the potential molecular mechanism underlying a novel microdeletion, causing a variable SHOX-related haploinsufficiency disorder in a three-generation family. The phenotyperesembles that of LWD in females, in males, however, the phenotypic expression is milder. The 15523-bp SHOX intragenic deletion, encompassing exons 3–6, was initially detected by array-CGH, followed by MLPA analysis. Sequencing of thebreakpoints indicated an Alu recombination-mediated deletion (ARMD) as the potential causative mechanism.

    • An efficient method to handle the ‘large p, small n’ problem for genomewide association studies using Haseman–Elston regression

      BUJUN MEI ZHIHUA WANG

      More Details Abstract Fulltext PDF

      The ‘large p, small n’ problem in genomewide association studies (GWAS) is an important subject in genetic studies. Many approaches have been proposed for this issue, but none of them successfully combine the Haseman–Elston (H–E) regression with sliding-window scan approaches in GWAS. In this article, we extended H–E regression to GWAS, and replaced original data with different measurements of phenotype of sib pairs. Meanwhile, we also applied hidden Markov model to infer identity by state. Using subsequent simulation studies, we found that it had higher statistical power than the corresponding single-marker association studies. The advantage of the H–E regression was also sufficient to capture about 48.01% of the quantitative trait locus (QTL). Meanwhile, the results show that the power decreases with the increase in the number of QTLs,and the power of H–E regression is sensitive to heritability.

    • Complete mitochondrial genome of threatened mahseer Tor tor (Hamilton 1822) and its phylogenetic relationship within Cyprinidae family

      A. PAVAN-KUMAR SUDHANSHU RAMAN PRAKASH G. KORINGA NAMRATA PATEL TEJAS SHAH RAJEEV K. SINGH GOPAL KRISHNA C. G. JOSHI P. GIREESH-BABU APARNA CHAUDHARI

      More Details Abstract Fulltext PDF

      The mahseers (Tor, Neolissochilus and Naziritor) are an important group of fishes endemic to Asia with the conservation status of most species evaluated as threatened. Conservation plans to revive these declining wild populations are hindered by unstable taxonomy. Molecular phylogeny studies with mitochondrial genome have been successfully used to reconstruct the phylogenetic tree and to resolve taxonomic ambiguity. In the present study, complete mitochondrial genome of Tor tor has been sequenced using ion torrent next-generation sequencing platform with coverage of more than 1000×. Comparative mitogenome analysis shows higher divergence value at ND1 gene than COI gene. Further, occurrence of a distinct genetic lineage of T. tor is revealed. The phylogenetic relationship among mahseer group has been defined as Neolissochilus hexagonolepis ((T. sinensis (T. putitora, T. tor), (T. khudree, T. tambroides)).

    • In silico characterization of functional SNP within the oestrogen receptor gene

      MAHA REBAĨ AHMED REBAĨ

      More Details Abstract Fulltext PDF

      Single-nucleotide polymorphism (SNP) association studies have become crucial in uncovering the genetic correlations of genomic variants with complex diseases, quantitative traits and physiological responses to drugs. However, the identificationof SNPs responsible for specific phenotypes is a difficult problem to solve, requiring multiple testing of hundreds or thousands of SNPs in candidate genes. In this study, we performed an analysis of the genetic variations that can alter the structure and function of oestrogen receptor α using different computational tools. Among the nonsynonymous SNPs, a total of four SNPs were found to be damaging by both a sequence homology-based tool (SIFT) and a structural homology-based method (polyphen-2, SNAP), as well as by the ESEfinder program, and one nonsense nsSNP was found. For noncoding SNPs, we found that one SNP in 5'UTR may potentially change protein expression level, nine SNPs were found to affect miRNA binding site and 28 SNPs might affect transcriptional regulation of the ESR1 gene. Reviewing the literature, 89 SNPs were found to be functional among which only four were located in exons.

    • LcMKK, a MAPK kinase from Lycium chinense, confers cadmium tolerance in transgenic tobacco by transcriptional upregulation of ethylene responsive transcription factor gene

      CHUNFENG GUAN JING JI XIAOZHOU LI CHAO JIN GANG WANG

      More Details Abstract Fulltext PDF

      Cadmium (Cd) is a highly toxic element to plants. Ethylene is an important phytohormone in the regulation of plant growth, development and stress response. Mitogen-activated protein kinase (MAPK) activation has been observed in plants exposed to Cd stress and was suggested to be involved in ethylene biosynthesis. We hypothesized that there may be a link between MAPK cascades and ethylene signalling in Cd-stressed plants. To test this hypothesis, the expression of LcMKK, LchERF and LcGSH1 genes, endogenous ethylene accumulation, GSH content and Cd concentration in Lycium chinense with or without Cd stress treatment were studied. Our results showed that LcMKK gene expression can be induced by the treatment of Cd in L. chinense. The transgenic tobacco expressing 35S::LcMKK showed greater tolerance to Cd stress and enhanced expression of NtERF and NtGSH1 genes, indicating that LcMKK is associated with the enhanced expression level of ERF and GSH synthesis-related genes in tobacco. We also found that endogenous ethylene and GSH content can be induced by Cd stress inL. chinense, and inhibited by cotreatment with PD98059, an inhibitor of MAPK kinase. Evidences presented here suggest that under Cd stress, GSH accumulation occurred at least partially by enhanced LcMKK gene expression and the ethylene signal transduction pathways might be involved in this accumulation.

    • Cytogenetic analysis in couples with recurrent miscarriages: a retrospective study from Punjab, north India

      NEHA SUDHIR TAJINDER KAUR ARCHANA BERI ANUPAM KAUR

      More Details Abstract Fulltext PDF

      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 understandthe 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.

    • Marker-assisted improvement of the elite restorer line of rice, RPHR-1005 for resistance against bacterial blight and blast diseases

      V. ABHILASH KUMAR C. H. BALACHIRANJEEVI S. BHASKAR NAIK R. RAMBABU G. REKHA G. HARIKA S. K. HAJIRA K. PRANATHI S. VIJAY M. ANILA H. K. MAHADEVASWAMY M. KOUSIK A. YUGANDER J. ARUNA A. S. HARI PRASAD M. S. MADHAV G. S. LAHA S. M. BALACHANDRAN M. S. PRASAD V. RAVINDRA BABU R. M. SUNDARAM

      More Details Abstract Fulltext PDF

      This study was carried out to improve the RPHR-1005, a stable restorer line of the popular medium slender grain type rice hybrid, DRRH-3 for bacterial blight (BB) and blast resistance through marker-assisted backcross breeding (MABB). Twomajor BB resistance genes, Xa21 and Xa33 and a major blast resistance gene, Pi2 were transferred to RPHR-1005 as two individual crosses. Foreground selection for Xa21, Xa33, Pi2, Rf3 and Rf4 was done by using gene-specific functional markers, while 59 simple sequence repeat (SSR) markers polymorphic between the donors and recipient parents were used to select the best plant possessing target resistance genes at each backcross generation. Backcrossing was continued till BC₂F₂ and a promising homozygous backcross derived line possessing Xa21 + Pi2 and another possessing Xa33 were intercrossed to stack the target resistance genes into the genetic background of RPHR-1005. At ICF4, 10 promising lines possessing three resistance genes in homozygous condition along with fine-grain type, complete fertility restoration, better panicle exertion and taller plant type (compared to RPHR-1005) were identified.

    • Novel mutations in the transmembrane natriuretic peptide receptor NPR-B gene in four Indian families with acromesomelic dysplasia, type Maroteaux

      PRIYANKA SRIVASTAVA MONI TUTEJA ASHWIN DALAL KAUSIK MANDAL SHUBHA R. PHADKE

      More Details Abstract Fulltext PDF

      Acromesomelic dysplasia, type Maroteaux is a disorder characterized by disproportionate short stature predominantly affecting the middle and distal segments of the upper and lower limbs. It is an autosomal recessive disorder due to mutation in NPR2 gene which impairs skeletal growth. To screen the mutations in the gene NPR2, all of its coding exons and splice junction sites were PCR amplified from genomic DNA of affected individuals of four families and sequenced. Four homozygous mutations in four different families were identified. These include three novel mutations including a deletion frameshift mutation (p.Cys586Ter), one nonsense mutation (p.Arg479Ter), one missense mutation (p.Val187Asp) and one reported missense mutation (p.Tyr338Cys). The study describes phenotypes of Indian patients and expands the mutation spectrum of the disorder.

    • Three novel and two known androgen receptor gene mutations associated with androgen insensitivity syndrome in sex-reversed XY female patients

      BALACHANDRAN SARANYA GUNASEKARAN BHAVANI BRINDHA ARUMUGAM MEENA JAYASHANKAR SATHIYAVEDU THYAGARAJAN SANTHIYA

      More Details Abstract Fulltext PDF

      Molecular characterization of 23 cytogenetically confirmed XY females was attempted by screening coding regions of SRY and androgen receptor (AR) genes. Five of the index cases showed sequence variations in various exons of the AR gene: a deletion (n.1911delG) and substitutions n.1761G>A and n.1317C>T in exon 1; n.3510C>T transition in exon 6 and deletion mutation (n.3672delT) in exon 7. Four mutations identified here lead to the formation of truncated receptor protein, involving a substantial loss of AR functional domains which explains the phenotype in the subjects. The n.1761G>A substitution has been previously reported in cases with mild androgen insensitivity. Although the ligand-binding domain was considered as the mutational hot spot in AR gene, we report here 3/5 variations in the N-terminal domain emphasizing the significance of considering the N-terminal domain of AR as well for mutation screening. Our present observation also strengthens the role of AR gene and its direct association with AIS.

    • Adenosine monophosphate-activated protein kinase from the mud crab, Scylla paramamosain: cDNA cloning and profiles under cold stress

      CHENCUI HUANG KUN YU HUIYANG HUANG HAIHUI YE

      More Details Abstract Fulltext PDF

      Adenosine monophosphate-activated protein kinase (AMPK), an important energy sensor, is crucial for organism survival under adverse conditions. In this study, the roles of this gene under cold stress in a warm-water mud crab, Scylla paramamosain was investigated. The full-length cDNA (SpAMPK) was 1884 bp and its open reading frame of 1566 bp was isolated and characterized. The expressions of SpAMPK detected by quantitative real-time PCR (qRT-PCR) in various tissues revealed that the highest expression was in the hepatopancreas. The profiles of SpAMPK gene in the hepatopancreas, chela muscleand gill were detected when the subadult crabs were exposed to the four temperature conditions of 10, 15, 20 and 25◦C. The results showed that the expression patterns of SpAMPK mRNA in the three tissues were significantly higher when crabs were exposed to 15◦C than the other three temperature treatments, while at 10◦C treatment, the SpAMPK mRNA was lowestamong the four temperature treatments. These findings suggested that the high expression of SpAMPK mRNA might initiate ATP-producing pathways to generate energy to cope with cold stress at 15◦C treatment, which was slightly below the range of optimum temperatures; while treatment at 10◦C, far lower than optima, the low expression of SpAMPK mRNA could reduce the energy expenditure and thus induce the crabs into cold anesthesia. The results of SpAMPK in this study might contribute to the understanding of the molecular mechanism of acclimation to cold hardiness in S. paramamosain.

    • Mapping of stripe rust resistance gene in an Aegilops caudata introgression line in wheat and its genetic association with leaf rust resistance

      PUNEET INDER TOOR SATINDER KAUR MITALY BANSAL BHARAT YADAV PARVEEN CHHUNEJA

      More Details Abstract Fulltext PDF

      A pair of stripe rust and leaf rust resistance genes was introgressed from Aegilops caudata, a nonprogenitor diploid species with the CC genome, to cultivated wheat. Inheritance and genetic mapping of stripe rust resistance gene in backcrossrecombinant inbred line (BC-RIL) population derived from the cross of a wheat–Ae. caudata introgression line (IL) T291-2(pau16060) with wheat cv. PBW343 is reported here. Segregation of BC-RILs for stripe rust resistance depicted a single major gene conditioning adult plant resistance (APR) with stripe rust reaction varying from TR-20MS in resistant RILs signifying the presence of some minor genes as well. Genetic association with leaf rust resistance revealed that two genes are located at a recombination distance of 13%. IL T291-2 had earlier been reported to carry introgressions on wheat chromosomes 2D, 3D, 4D, 5D, 6D and 7D. Genetic mapping indicated the introgression of stripe rust resistance gene on wheat chromosome 5DS in the region carrying leaf rust resistance gene LrAc, but as an independent introgression. Simple sequence repeat (SSR) and sequence-tagged site (STS) markers designed from the survey sequence data of 5DS enriched the target region harbouring stripe and leaf rust resistance genes. Stripe rust resistance locus, temporarily designated as YrAc, mapped at the distal most end of 5DS linked with a group of four colocated SSRs and two resistance gene analogue (RGA)-STS markers at a distanceof 5.3 cM. LrAc mapped at a distance of 9.0 cM from the YrAc and at 2.8 cM from RGA-STS marker Ta5DS_2737450, YrAc and LrAc appear to be the candidate genes for marker-assisted enrichment of the wheat gene pool for rust resistance.

    • Association and expression analyses of the Ucp2 and Ucp3 gene polymorphisms with body measurement and meat quality traits in Qinchuan cattle

      YANING WANG WUCAI YANG LINSHENG GUI HONGBAO WANG LINSEN ZAN

      More Details Abstract Fulltext PDF

      The uncoupling proteins (UCPs) belong to the mitochondrial inner membrane anion carrier superfamily and play an important role in energy homeostasis. Genetic studies have demonstrated that Ucp2 and Ucp3 gene variants are involved in obesity and metabolic syndrome. The aim of this study was to identify associations between polymorphisms of Ucp2 and Ucp3 genes and economically-important traits in Qinchuan cattle. In the present study, one single-nucleotide polymorphism (SNP) in the 5'UTR region (SNP1: g.C-754G) of the Ucp2 gene was identified by direct sequencing of 441 Qinchuan cattle. Two SNPs in exon 3 (SNP2: g.G4877A; SNP3: g.C4902T) of the Ucp3 gene were identified by sequencing and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) among 441 Qinchuan cattle. Association analysis showed that SNP1 and SNP2 were associated with the meat quality traits (MQTs) including back fat thickness, loin muscle area and intramuscular fat content. SNP3 was found to be associated with part of the body measurement traits (BMTs) which referred to withers height and chest depth. In addition, QTL pyramiding analysis showed that individuals with diplotype P3P3 (GG–GG–CC) exhibited the best performance in terms of back fat thickness, loin muscle area, intramuscular fat content, rump length, hip width, chestdepth and chest circumference. With regard to the G4877A mutation, real time PCR analysis revealed that individuals with AA genotype of the Ucp3 gene expressed higher mRNA levels than those with GG genotype. These results suggest that thediplotype P3P3 (GG–GG–CC) could be used as a molecular marker of the combined genotypes for future selection of body measurement traits and meat quality traits in Qinchuan cattle.

    • Gene interactions and genetics for yield and its attributes in grass pea (Lathyrus sativus L.)

      A. K. PARIHAR G. P. DIXIT DEEPAK SINGH

      More Details Abstract Fulltext PDF

      Grain yield is a complex character representing a multiplicative end product of many yield attributes. However, understanding the genetics and inheritance that underlies yield and its component characters pose a prerequisite to attain the actual yieldpotential of any crop species. The knowledge pertaining to gene actions and interactions is likely to direct and strengthen the crop breeding programmes. With this objective, the present investigation was undertaken by using six generations derived from three different crosses in grass pea. The study underscores the significance of additive–dominance model, gene action involved in inheritance of quantitative characters and heritability. Of note, nonallelic interactions influencing the traits were detected by both scaling test and joint scaling test, indicating the inadequacy of the additive–dominance model alone in explaining the manifestation of complex traits such as yield. Besides, additive (d) and dominance (h) gene effects, different types of interallelic interactions (i, j, l) contributed towards the inheritance of traits in the given crosses. Nevertheless, predominanceof additive variance suggests a difference between homozygotes at a locus with positive and negative alleles being distributed between the parents. Duplicate epistasis was prevalent in most of the cases for traits like plant height, seeds/pod,100-seed weight and pod width. In view of the diverse gene actions, i.e. additive, dominant and epistasis, playing important roles in the manifestation of complex traits like yield, we advocate implementation of population improvement techniques inparticular reciprocal recurrent selection to improve productivity gains in grass pea.

    • Identification of vernalization responsive genes in the winter wheat cultivar Jing841 by transcriptome sequencing

      YALAN FENG YONGYING ZHAO KETAO WANG YONG CHUN LI XIANG WANG JUN YIN

      More Details Abstract Fulltext PDF

      This study aimed to identify vernalization responsive genes in the winter wheat cultivar Jing841 by comparing the transcriptome data with that of a spring wheat cultivar Liaochun10. For each cultivar, seedlings before and after the vernalizationtreatment were sequenced by Solexa/Illumina sequencing. Genes differentially expressed after and before vernalization were identified as differentially expressed genes (DEGs) using false discovery rate (FDR) ≤ 0.001 and |log2 (fold change)| >1 as cutoffs. The Jing841-specific DEGs were screened and subjected to functional annotation using gene ontology (GO) database.Vernalization responsive genes among the specific genes were selected for validation by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and the expression change over the time was investigated for the top 11 genes with the most significant expression differences. A total of 138,062 unigenes were obtained. Overall, 636 DEGs were identified as vernalization responsive genes including some known genes such as VRN-1 and COR14a, and some unknown contigs. The qRT-PCR validated changes in the expression of 18 DEGs that were detected by RNA-seq. Among them, 11 genes displayed four different types of expression patterns over time during the 30-day-long vernalization treatment. Genes or contigs such as VRN-A1, COR14a, IRIP, unigene1806 and Cl18953. Contig2 probably have critical roles in vernalization.

    • Dual modified antiphospho (Ser10)-acetyl (Lys14)-histone H3 predominantly mark the pericentromeric chromatin during mitosis in monokinetic plants

      SANTOSH KUMAR SHARMA MAKI YAMAMOTO YASUHIKO MUKAI

      More Details Abstract Fulltext PDF

      Epigenetic regulatory posttranslational histone modification marks not only function individually but also capable to act in combination as a unique pattern. A total of 16 plant species belonging to 11 genera of eight families (five dicots and threemonocots) including land plants, epiphytes (orchids) and the holokinetic taxa (Drosera spp.) were analysed for chromosomal distribution of dual modified antiphospho (Ser10)-acetyl (K14)-histone H3 (H3S10phK14ac) to understand the combinatorial chromatin dynamics during mitotic cell division in plants. The anti-H3S10phK14ac evidently mark the pericentromeric chromatin on mitotic chromosomes of the plants excluding the holokinetic Drosera species, which revealed the immunolabelling of whole chromosomes all along the arms. The dual modified immunosignals were absent during early stages of mitosis, appeared intensively at metaphase and remained visible until late-anaphase/telophase however, labelled the whole chromosomes during meiotic metaphase I. Colocalization of anti-H3S10phK14ac with an onion’s CENH3 antibody on mitoticchromosomes of Allium revealed the chromosomal location of anti-H3S10phK14ac in the region between signals for CENH3 detection. Overall analysis suggests that the unique localization of combinatorial histone modification mark at pericentromericchromatin might have attributed through ‘phospho-acetyl’ cross talk that ultimately facilitate the sister chromatid cohesion at pericentromeres following condensation events in mitotic chromosomes. Here, we propose that dual modified H3S10phK14ac histone may serve as an additional cytogenetic landmark to identify pericentromeric chromatin during mitosis in plants. The plausible role of histone cross talk and future perspectives of combinatorial histone modification marks in plant cytogenetics with special reference to chromatin dynamics have been discussed.

    • Different responses of soybean cyst nematode resistance between two RIL populations derived from Peking × 7605 under two ecological sites

      YONGCHUN LI NA GUO JINMING ZHAO BIN ZHOU RAN XU HUI DING WEIGUO ZHAO JUNYI GAI HAN XING

      More Details Abstract Fulltext PDF

      The soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is a plant-parasitic nematode that feeds on the roots of soybean and most economically devastating pathogen of soybean (Glycine max (L.) Merr.) worldwide. Host plant resistance is the most effective control method. To understand SCN resistance in different environments, two recombinant-inbred lines (RILs) populations NJ(RN)P7 (217 F2:8:11 lines) and JN(RN)P7 (248 F2:7:9 lines) were developed from the cross of the cultivars Peking × 7605 in Nanjing and Jinan, respectively, and examined in this study. Peking is resistant to SCN race 1 (HG types 2.5.7), while 7605 is highly susceptible. Chi-square test of frequency distribution of families’ female index (FI) showed that resistance to SCN was significantly different between NJ(RN)P7 and JN(RN)P7 populations. Three recessive genes conditioned the inheritance of resistance to SCN race 1 in both populations, but significant difference was detected for the mean of FI on two populations (DM= −16.68, P < 0.01). This indicated that natural selection may affect resistance to SCN. By analysing the variation of phenotype, the genetic structure of the two populations was determined to be different. The inheritance and variation of resistance were confirmed by simple sequence repeat (SSR) markers. For the two populations, 10 SSR markers showed polymorphism of resistant and susceptible DNA bulks. Some markers associated with the resistance of SCN races 1, 2, 3 and 5, and two markers, Satt163 and Satt309, reportedly related to rgh1 were detected both in NJ(RN)P7 and JN(RN)P7 populations. The results support the view that a disease acts as a selective force on plant resistance characteristics, which may alter the relative fitness of resistance alleles.

    • Osteoprotegerin polymorphisms are associated with alcohol-induced osteonecrosis of femoral head in Chinese Han population from Henan province

      YIZHOU LI YONGCHANG GUO QUANJIAN WANG YONGRI OUYANG YUJU CAO TIANBO JIN JIANZHONG WANG

      More Details Abstract Fulltext PDF

      Alcohol-induced osteonecrosis of femoral head (ONFH) is one of the most important pathogenesis of nontraumatic ONFH. However, its pathogenesis mechanism is still unknown. Osteoprotegerin (OPG) has been implicated in multiple functions including blocking osteoclast maturation, controlling vascular calcifications, promoting tumour growth and metastasis. This study is focussed on OPG gene polymorphisms associated with alcohol-induced ONFH. A total of 509 participants (209 patients and 300 normal individuals) were recruited, and we selected 13 single-nucleotide polymorphisms (SNPs) to evaluatethe association between genetic susceptibility variants and alcohol-induced ONFH by using the χ² test and genetic model analysis. Overall, OPG SNPs (rs1485286, rs1032128 and rs11573828) were confirmed the strongest increasing risks on alcohol-induced osteoporosis of femoral head in recessive model (rs1485286: OR, 1.71; 95% CI, 1.07–2.73; P = 0.025 for T/T); (rs1032128: OR, 1.73; 95% CI, 1.08–2.77; P = 0.022 for G/G); (rs11573828: OR, 3.89; 95% CI, 1.02–14.85; P = 0.033 for T/T). SNP rs11573856 was considered as a protective effect to the occurrence of alcohol-induced ONFH, while adjusted for age and gender in dominant and log-additive models (rs11573856: adjusted OR, 0.60; 95% CI, 0.37–0.96; P = 0.033 for G/A–A/A); (rs11573856: adjusted OR, 0.63; 95% CI, 0.41–0.96; P = 0.042). We conclude that OPG gene polymorphisms were associated with the occurrence of alcohol-induced ONFH.

    • Upregulation of miR-222 in both Helicobacter pylori-infected and noninfected gastric cancer patients

      MINA NOORMOHAMMAD SAMIRA SADEGHI HOSSEIN TABATABAEIAN KAMRAN GHAEDI ARDESHIR TALEBI MANSOUREH AZADEH MEHRI KHATAMI MOHAMMAD MEHDI HEIDARI

      More Details Abstract Fulltext PDF

      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 byDAVID 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 possiblerole 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.

    • Genomewide analysis of NBS-encoding genes in kiwi fruit (Actinidia chinensis)

      YINGJUN LI YAN ZHONG KAIHUI HUANG ZONG-MING CHENG

      More Details Abstract Fulltext PDF
    • Is the ancient permafrost bacteria able to keep DNA stable?

      ANATOLI BROUCHKOV GENNADY GRIVA OKSANA FURSOVA NADEZDA FURSOVA SERGEI IGNATOV GENNADY POGORELKO

      More Details Abstract Fulltext PDF
    • Studies on genetics, stability and possible mechanism of deltamethrin resistance in Phenacoccus solenopsis Tinsley (Homoptera: Pseudococcidae) from Pakistan

      BUSHRA SADDIQ MUHAMMAD BABAR SHAHZAD AFZAL SARFRAZ ALI SHAD

      More Details Abstract Fulltext PDF
    • Genetic dissection of seed vigour traits in maize (Zea mays L.) under low-temperature conditions

      YONG SHI GUOHUI LI ZHIQIANG TIAN ZHIYONG WANG XIAOBO WANG YUGUANG ZHU YANHUI CHEN SHULEI GUO JIANSHUANG QI XIN ZHANG LIXIA KU

      More Details Abstract Fulltext PDF
    • Genomewide analyses of pathogenic and regulatory T cells of NOD mice reveal a significant difference in DNA methylation on chromosome X

      DANG SUN QINGSHENG YU PING LI JIANYING SHEN

      More Details Abstract Fulltext PDF
    • Polymorphism in ficolin-1 (FCN1) gene is associated with an earlier onset of type 1 diabetes mellitus in children and adolescents from northeast Brazil

      ZILMA PEREIRA DOS ANJOSA MANUELLA MARIA SILVA SANTOS NATASSIA JAVORSKI RODRIGUES GLAUCIA ALYNE NUNES DE LACERDA JAQUELINE ARAUJO JAQUELINE DE AZEVÊDO SILVA NATHÁLIA DE ALENCAR CUNHA TAVARES RAFAEL LIMA GUIMARÃES SERGIO CROVELLA LUCAS ANDRÉ CAVALCANTI BRANDÃO

      More Details Abstract Fulltext PDF
    • Cytosine deletion at AP2-box region of HSP70 promoter and its influence on semen quality traits in crossbred bulls

      RAJIB DEB BASAVRAJ SAJJANAR UMESH SINGH SUSHIL KUMAR GYANENDRA SINGH SENGAR RANI ALEX A. K. DAS S. TYAGI T. V. RAJA R. R. ALYETHODI RANI SINGH V. BHANUPRAKASH B. PRAKASH

      More Details Abstract Fulltext PDF
    • Useful parasites: the evolutionary biology and biotechnology applications of transposable elements

      GEORGI N. BONCHEV

      More Details Abstract Fulltext PDF

      Transposable elements usually comprise the most abundant nongenic fraction of eukaryotic genomes. Because of their capacity to selfreplicate and to induce a wide range of mutations, transposable elements have long been considered as ‘parasitic’ or ‘selfish’. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. Numerous studies have provided evidences that mobile elements have the potential to act as agents of evolution by increasing, rearranging and diversifying the genetic repertoire of theirhosts. With large-scale sequencing becoming increasingly available, more and more scientists come across transposable element sequences in their data. I will provide examples that transposable elements, although having signatures of ‘selfish’ DNA,play a significant biological role in the maintainance of genome integrity and providing novel regulatoty networks. These features, along with the transpositional and mutagenic capacity to produce a raw genetic diversity, make the genome mobilefraction, a key player in species adaptation and microevolution. The last but not least, transposable elements stand as informative DNA markers that may complement other conventional DNA markers. Altogether, transposable elements represent a promising, but still largely unexplored research niche and deserve to be included into the agenda of molecular ecologists, evolutionary geneticists, conservation biologists and plant breeders.

    • The genus Drosophila is characterized by a large number of sibling species showing evolutionary significance

      BASHISTH N. SINGH

      More Details Abstract Fulltext PDF

      Mayr (1942) defined sibling species as sympatric forms which are morphologically very similar or indistinguishable, but which possess specific biological characteristics and are reproductively isolated. Another term, cryptic species has also been used for such species. However, this concept changed later. Sibling species are as similar as twins. This category does not necessarily include phylogenetic siblings as members of a superspecies. Since the term sibling species was defined by Mayr, a large number of cases of sibling species pairs/groups have been reported and thus they are widespread in the animal kingdom.However, they seem to be more common in some groups such as insects. In insects, they have been reported in diptera, lepidoptera, coleoptera, orthoptera, hymenoptera and others. Sibling species are widespread among the dipteran insects and as such are well studied because some species are important medically (mosquitoes), genetically (Drosophila) and cytologically(Sciara and Chironomus). The well-studied classical pairs of sibling species in Drosophila are: D. pseudoobscura and D. persimilis, and D. melanogaster and D. simulans. Subsequently, a number of sibling species have been added to these pairs and a large number of other sibling species pairs/groups in different species groups of the genus Drosophila have been reported in literature. The present review briefly summarizes the cases of sibling species pairs/groups in the genus Drosophila with their evolutionary significance.

    • Another explanation for the cause of heterosis phenomenon

      NGUYEN THIEN HUYEN

      More Details Abstract Fulltext PDF

      The explanation for heterosis phenomenon is based on ideas: (i) every trait of an organism depends on many genes. (ii) Inbreeding depression and heterosis are related to individual genetic diversity. To assess individual genetic diversity ofan organism, I suggest the term number of genetic properties. Assessing the changes of individual genetic diversity caused by self-pollination and cross-pollination reveals that self-pollinating plants of natural cross-pollinating leads to the decrease in individual genetic diversity of offspring and crossing between pure lines of genetic difference leads to the increase in individual genetic diversity of hybrids. Therefore, I propose that the decrease in individual genetic diversity is the cause the of depression and the increase in individual genetic diversity is the cause of heterosis.

  • Journal of Genetics | News

    • Change in email domain name

      Posted on 26 August 2016

      The domain part of the email address of all email addresses used by the office of Indian Academy of Sciences, including those of the staff, the journals, various programmes, and Current Science, has changed from 'ias.ernet.in' (or 'academy.ias.ernet.in') to 'ias.ac.in'. Thus, for example, the address office@ias.ernet.in (or office@academy.ias.ernet.in) has changed to office@ias.ac.in (without the string 'academy'). Please take note of this change.

© 2017 Indian Academy of Sciences, Bengaluru.