Diversity and functional characterization of endophytic Methylobacterium isolated from banana cultivars of South India and its impact on early growth of tissue culture banana plantlets.

AIMS: This study aimed at determining the distribution, colonization and growth promoting nature of Methylobacterium spp. in tissue culture banana plantlets. METHODS AND RESULTS: Leaf samples from different field grown banana cultivars were used for Methylobacterium spp., isolation. Metabolic profile and functional characterization for plant growth-promoting traits of the isolates were assessed. The isolates were confirmed using 16S rRNA gene sequencing analysis, which resulted in six distinct species of Methylobacterium namely M. radiotolerans, M. salsuginis, M. thiocyanatum, M. rhodesianum, M. rhodinum and M. populi. Methylobacterium spp. inoculation experiment was conducted under hydroponic system in tissue culture banana plantlets (germ free) with eight selected isolates. A significant increase in growth parameters of Methylobacterium treated plantlets compared to uninoculated control was observed. Methylobacterium salsuginis TNMB03-gfp29 was developed and colonization micrograph was obtained using confocal laser scanning microscopy (CLSM) and scanning electron microscopy in different parts of banana plantlets (root, stem and leaves). CONCLUSION: Field grown banana plants found to harbour diverse endophytic Methylobacterium population. Our finding suggests that endophytic Methylobacterium species may provide significant plant growth promoting compounds/nutrients to the banana plants. The experimental results demonstrated the efficacy of Methylobacterium spp. as a potential bioinoculant and can be exploited as a phyllosphere and rhizosphere based bioinoculant for the initial establishment and growth of tissue culture banana plantlets. SIGNIFICANCE AND IMPACT OF THE STUDY: This study extended our knowledge on the distribution of Methylobacterium spp. in banana plants and endophytic colonization nature of this particular genus in plants. In addition, efficient isolate (M. salsuginis TNMB03) identified in this study may be promoted as bio-inoculants for banana plants after field evaluation.

HLA genetics in bipolar disorder.

OBJECTIVE: Bipolar Disorder (BD) is characterized by deregulated adaptive immune processes. Recent genome-wide association studies (GWAS) implicate the major histocompatibility complex (MHC) region in BD. The present study investigates the potential influence of variations in human leukocyte antigen (HLA) on BD risk and/or clinical presentations. This may have relevance to the dysregulated inflammatory processes commonly found in BD. METHOD: DNAs from 475 BD patients and 195 healthy controls (HC) were genotyped for classical HLA class I and II loci. RESULTS: We found that: (i) the HLA-A*02~B*44~DRB1*07 sub-haplotype is less prevalent in BD, vs. HC (pc = 2.4 × 10-2 ); (ii) the 57.1 and the 8.1-derived ancestral haplotypes i.e. HLA-A*02~B*57~Cw*06~DRB1*07~DQB1*09 and HLA-A*02~B*08~Cw*07 are associated with rapid cycling (pc = 1.9 × 10-3 and 1.05 × 10-2 , respectively); (iii) the 8.1AH-derived HLA class II-DRB*03~HLA-DQB1*02 sub-haplotype is more frequent in BD patients with a history of suicidal behaviors (pc = 2.1 × 10-2 ); and (iv) disease onset by an hypomanic episode or by psychotic symptoms are, respectively, more frequent in BD patients bearing the 7.1 AH-derived A*03~B*07~DRB1*15 sub-haplotype (pc = 8.5 × 10-3 ) and the HLA-A*02~B*07~DRB1*15 sub-haplotype (pc = 4.0 × 10-2 ). CONCLUSION: Corroborating the established link between these HLA haplotypes/sub haplotypes and common immune disorders, our findings suggest possible HLA-mediated proinflammatory processes operating in BD.

Association of NKG2D gene variants with susceptibility and severity of rheumatoid arthritis.

NKG2D (KLRK1) is a C-type lectin receptor present on natural killer (NK) cells, γδ, CD8+ and CD4+ T cells. Upon ligand binding, NKG2D mediates activatory and co-stimulatory signals to NK cells and activated CD4+ T cells, respectively. Polymorphisms in NKG2D predispose to infectious diseases, cancer, transplantation and autoimmune disorders. We studied the influence of this NK receptor polymorphism on predisposition to and modification of the disease phenotype in patients with rheumatoid arthritis (RA). Eight different single nucleotide polymorphisms (SNP) in the NKG2 gene were genotyped in 236 patients with RA and 187 controls using Taqman 5' nuclease assays. NKG2D genotype/allele frequency did not differ between patients and controls. Subgroup analysis showed that the frequency of A allele of NKG2D9 and T allele of NKG2D10 was significantly higher in patients with deformities (a marker of severe disease) [11 versus 5%, Pc = 0·03, odds ratio (OR) = 2·44, 95% confidence interval (CI) = 1·09-5·98 and 10 versus 4%, Pc = 0·04, OR = 2·45, 95% CI = 1·05-6·39, respectively], while the frequency of alleles G of NKG2D9 and A of NKG2D10 was greater in patients without deformities (Pc = 0·03, OR = 0·41, 95% CI = 0·17-0·91 and Pc = 0·04, OR = 0·41, 95% CI = 0·16-0·96). Similar trends of association were observed with deforming phenotype of RA in female patients and deforming young onset RA subgroups. Haplotype analysis revealed that the frequency of haplotype G-C-A-G-A-T-C-C was higher in patients than in controls (12 versus 8%, P = 0·04, OR = 1·61, 95% CI = 1·01-2·55), suggesting that it may predispose to RA. Our study suggests that the NKG2D gene polymorphisms may modify the risk of development and severity of RA.

Polymorphisms in the promoter region of iNOS predispose to rheumatoid arthritis in south Indian Tamils.

Nitric oxide synthase (NOS) catalyses the production of nitric oxide (NO) from L-Arginine, which participates in diverse biological processes including inflammation and apoptosis. Macrophages, chondrocytes, osteoblasts and osteoclasts express inducible NOS (iNOS) at the site of synovial inflammation. NO produced at the inflamed joint may contribute to peri-articular bone loss, mediate apoptosis and regulate Th1/Th2 balance in rheumatoid arthritis (RA). Variations in the promoter region of NOS gene regulate the nitric oxide synthase expression and iNOS (NOS2) polymorphisms have been associated with susceptibility to autoimmune disorders. Hence, this study was conducted to identify the possible contributions of NOS2 -1659G/A, -1026C/A, -277A/G promoter polymorphisms towards development of RA in South Indian Tamils. A total of 242 (219 females, 23 males) patients with RA (mean age 41.2 ± 10.9 years, disease duration 8.5 ± 4.3 years) and 279 age- and sex-matched healthy individuals of South Indian Tamil ethnicity were genotyped for NOS2 -1659C/T, -1026G/T and -277A/G promoter polymorphisms by TaqMan chemistry. Nature of disease (erosive or nonerosive), the presence of extra-articular manifestations, seropositivity for rheumatoid factor and anticyclic citrullinated peptide, serum C-reactive protein (CRP) level and response to therapy were assessed for all patients. The three single nucleotide polymorphisms (SNPs) were in Hardy-Weinberg equilibrium. The frequency of GG genotype and G allele of NOS2-277 was higher in patients (pc = 5.7 × 10-9 , OR = 6.09, 95% CI = 3.09-12.8 and pc = 4 × 10-13 , OR = 2.37, 95% CI = 2.06-3.62, respectively) compared to controls. Similarly, the frequency of NOS2-1026 (rs2779249) GT genotype and the T allele was higher in patients with RA (pc = .01, OR = 1.61, 95% CI = 1.09-2.36, and pc = .04, OR = 1.40, 95% CI = 1.02-1.91, respectively). However, no significant difference in frequency of NOS2-1659C/T polymorphism was observed between patients and controls. None of the studied SNPs were associated with erosive disease, seropositivity or extra-articular manifestations. The -277A/G and -1026 G/T promoter polymorphisms in iNOS may confer susceptibility to RA in South Indian Tamils.

Heavy metals accumulation in crab and shrimps from Pulicat lake, north Chennai coastal region, southeast coast of India.

The accumulation of heavy metals such as lead (Pb), iron (Fe), zinc (Zn), cadmium (Cd), and chromium (Cr) was examined in crab (Scylla serrata) and shrimps (Penaeus semisulcatus, Penaeus indicus, and Penaeus monodon) collected from Pulicat lake that receives effluents from industries located in north Chennai, southeast coast of India. The results showed limited difference between crab and prawns as well as significant variations between the organs. Pb is the highly accumulated metal in both crab and shrimps, except P. monodon. The highest metal concentration was mostly found in the liver followed by other organs. The concentration of metals in edible parts (muscle) was within the permissible level and safe for consumption. However, the results of the study clearly indicate the biomagnification of metals in Pulicat lake.

Human leukocyte antigen-G polymorphism influences the age of onset and autoantibody status in rheumatoid arthritis.

The study was conducted to investigate the frequency of three gene polymorphisms in the 3'-untranslated region (3'-UTR) of human leucocyte antigen-G (HLA-G) gene in south Indian patients with rheumatoid arthritis (RA) and analyze their influence on disease susceptibility, phenotype and treatment response. HLA-G 14 bp insertion (Ins)/deletion (del) (rs66554220), HLA-G +3142G>C (rs1063320) and +3187A>G (rs9380142) polymorphism was analyzed in 221 RA patients and 200 healthy controls. Frequency of HLA-G genotypes or alleles did not differ between patients and controls. Analysis based on rheumatoid factor (RF) status revealed that the frequency of allele 'A' (rs9380142) was significantly higher in RF-positive than in RF-negative patients [84% vs 74%, Yates-corrected P value (Pc) = 0.04, odds ratio (OR) = 1.8, 95% confidence interval (CI) = 1.0-3.2]. A similar difference was maintained in RF-positive female patients than their RF-negative counterparts (83% vs 71%, Pc = 0.02, OR = 1.9, 95% CI = 1.0 to 3.4) and between RF-positive and RF-negative young onset RA (YORA) patients (84% vs 73%, Pc = 0.03, OR = 1.9, 95% CI = 1.0-3.2), suggesting that rs9380142 polymorphism influenced RF status. The 14 bp Ins allele of rs66554220 was significantly more prevalent in RF-positive YORA than in RF-positive late onset RA (LORA) patients (51% vs 25%, P = 0.03, OR = 3.1, 95% CI = 1.1-9.8). Frequency of the four major haplotypes [InsGA (48%), DelGA (22%), DelCG (18%), DelCA (9.7%)] observed did not differ between cases and controls. HLA-G does not appear to be a risk factor for development of RA in south Indian Tamils but may act as a genetic modifier of clinical phenotype in terms of autoantibody production, gender preference and age at disease onset.

Clinical and molecular findings of chronic granulomatous disease in Oman: family studies.

Chronic granulomatous disease (CGD), a rare inherited disorder of the innate immune system, results from mutations in any one of the five genes encoding the subunits of the nicotinamide adenine dinucleotide phosphate-oxidase (NADPH) oxidase enzyme, and is characterized by recurrent life-threatening bacterial and fungal infections. Molecular analysis of 14 Omani CGD patients from 10 families, diagnosed to have CGD on clinical (recurrent infections) and biochemical grounds (positive for both the nitroblue tetrazolium (NBT) test and the dihydrorhodamine (DHR-1,2,3 assay), revealed that only one patient had X-linked CGD, with a large deletion involving both the gp91-phox gene (CYBB) and the McLeod gene (XK). The remaining 13 patients were all homozygotes from a previously described c.579G>A (p.Trp193X) mutation in the NCF1 gene on chromosome 7, responsible for autosomal recessive CGD (AR-CGD). Although X-linked CGD is the most common type of CGD disorder in most population groups, AR-CGD is the most prevalent type in Oman.

Violent suicidal behaviour in bipolar disorder is associated with nitric oxide synthase 3 gene polymorphism.

OBJECTIVE: Given the importance of nitric oxide system in oxidative stress, inflammation, neurotransmission and cerebrovascular tone regulation, we postulated its potential dysfunction in bipolar disorder (BD) and suicide. By simultaneously analysing variants of three isoforms of nitric oxide synthase (NOS) genes, we explored interindividual genetic liability to suicidal behaviour in BD. METHOD: A total of 536 patients with BD (DSM-IV) and 160 healthy controls were genotyped for functionally relevant NOS1, NOS2 and NOS3 polymorphisms. History of suicidal behaviour and violent suicide attempt was documented for 511 patients with BD. Chi-squared test was used to perform genetic association analyses and logistic regression to test for gene-gene interactions. RESULTS: NOS3 rs1799983 T homozygous state was associated with violent suicide attempts (26.4% vs. 10.8%, in patients and controls, P = 0.002, corrected P (Pc) = 0.004, OR: 2.96, 95% CI = 1.33-6.34), and this association was restricted to the early-onset BD subgroup (37.9% vs. 10.8%, in early-onset BD and controls, P = 0.0003, Pc = 0.0006 OR: 5.05, 95% CI: 1.95-12.45), while we found no association with BD per se and no gene-gene interactions. CONCLUSION: Our results bring further evidence for the potential involvement of endothelial NOS gene variants in susceptibility to suicidal behaviour. Future exploration of this pathway on larger cohort of suicidal behaviour is warranted.

IRF5rs2004640 single nucleotide polymorphism is associated with susceptibility to rheumatoid arthritis in South Indian Tamils.

Polymorphism of interferon regulatory factor 5 (IRF5), a latent transcription factor gene has been associated with various auto-immune diseases. Our aim was to study the IRF5rs2004640 gene polymorphism and its association with disease susceptibility, disease phenotype and treatment response in South Indian Tamil patients with rheumatoid arthritis (RA).The study was conducted on 217 RA patients fulfilling the American College of Rheumatology (ACR) 2010 criteria and 482 healthy controls (HCs) without family history of autoimmune disease. The IRF5rs2004640 genotyping was performed using a TaqMan 5' allelic discrimination assay. We found that the IRF5rs2004640T allele [P < 0.0001, odds ratio (OR) 3.25, 95% confidence interval (CI) 2.55-4.12] and TT genotype (P < 0.0001, OR 4.60, 95% CI 3.23-6.57) were significantly more frequent in RA patients as compared with HCs. No association was found between IRF5rs2004640 polymorphism, clinical manifestations, autoantibody profile and treatment response. IRF5rs2004640 T (mutant) allele may be a susceptibility factor conferring risk for RA in South Indian Tamils, whereas G allele (wild type) may be protective.

The sociopolitical in human genetics education.

Education must go beyond only countering essentialist and deterministic views of genetics.

Description of a new species, Toxorhynchites (Toxorhynchites) tyagii (Diptera: Culicidae), from Nilgiri hills, Western Ghats, southern India.

Specimens of Toxorhynchites (Toxorhynchites) tyagii, sp. n., were collected from the fringe areas of Gudaloor town, Ooty in the Nilgiri hills at an altitude of 1000 m above sea level in Western Ghats ranges in southern India during October 2011 and from Darjeeling ranges in the northern hilly region of Raymatang TG in Jalpaiguri district, West Bengal, in eastern India during February 2012. The adults, pupa and fourth-instar larva of this species are described and illustrated to distinguish it from Toxorhynchites (Tox.) splendens and Toxorhynchites (Tox.) edwardsi, which are the closest allies of Tx. (Tox.) tyagii. Besides possessing remarkable distinguishing male genital characteristics, Tx. tyagii differs from Tx. splendens also by the presence of conspicuous yellow scale-patches over the wing root that extend to the scutellum, and differs from Tx. edwardsi by having midtarsomeres 3-5 all dark whereas in Tx. edwardsi tarsomeres 3 and 4 and a larger part of 5 are white.

Distribution of CYP2C19*17 allele and genotypes in an Indian population.

WHAT IS KNOWN AND OBJECTIVE: CYP2C19*17 allele increases the metabolic activity of CYP2C19 resulting in decreased therapeutic levels of CYP2C19 substrates. There exist inter-ethnic differences in the distribution of this allele. The present study was aimed at establishing the allele and genotype frequencies of CYP2C19*17 in a South Indian Tamilian population. Furthermore, we describe the haplotype structure of the three common variant alleles of CYP2C19 in the Tamilian population. METHODS: Two hundred and six subjects of South Indian Tamilian origin were genotyped for CYP2C19*17 allele by nested polymerase chain reaction and restriction fragment length polymorphism. A subset of 87 subjects were also genotyped for CYP2C19*2 and CYP2C19*3 alleles. After ascertaining linkage disequilibrium (LD), haplotypes were constructed. Allele and genotype frequencies, LD pattern and haplotype frequency were compared with those of the HapMap populations. RESULTS AND DISCUSSION: The CYP2C19*17 allele frequency in the Tamilian population (n = 206) was found to be 19·2% (95% CI: 15·4 - 20·3). The CYP2C19*2 allele frequency (n = 87) was found to be 40·2% (95% CI: 32·9 - 47·5), whereas the CYP2C19*3 allele was not detected in the study subjects (n = 97). The high frequency of the CYP2C19*17 allele in the study population has resulted in a revision of frequencies for CYP2C19*1/*2 (31·0%) and CYP2C19*1/*1 (16·1%) genotypes in the Tamilian population. We also observed significant differences in haplotype structure and frequencies of these variant alleles in the HapMap population compared to Tamilian population. WHAT IS NEW AND CONCLUSION: CYP2C19*17 allele is present at high frequency in the Tamilian population. This study also demonstrates the need for reassessment of wild-type allele frequencies in view of CYP2C19*17 allele. The estimated high frequency of CYP2C19*17 allele will aid in genotype-phenotype association studies in the Tamilian population. Further genotype-phenotype association studies are required to evaluate the clinical utility of this allele in South Indians.

Estimation of ²¹°Po and ²¹°Pb and its dose to human beings due to consumption of marine species of Ennore Creek, South India.

A systemic study on the natural radionuclides such as (210)Po and (210)Pb in the environmental matrices and biota of Ennore Creek has been undertaken to establish a baseline data on the radiation profile of Ennore Creek environment. The environmental samples such as water, sediment, and biota (seaweeds, molluscs, crustaceans, and fishes) have been subjected to analyses. It has been observed that the concentration of (210)Po and (210)Pb in the water samples of Ennore Creek as 2.7 and 1.63 m Bq L(-1), respectively. The activity concentration of (210)Po and (210)Pb in the sediment sample was 17.9 and 28.9 Bq kg(-1), respectively. The bivalve mollusk Perna viridis have been identified to accumulate higher concentrations of (210)Po and (210)Pb suggesting that they could serve as bioindicator of radionuclides in the Ennore Creek environment. The committed effective dose for human beings was found at 81.13-216.8 and 2.1-297.2 µSv year(-1) for (210)Po and (210)Pb, respectively.

Association of IL-12p40 +1188 A/C polymorphism with nasopharyngeal cancer risk and tumor extension.

The interleukin 12 (IL-12) cytokine, encoded by polymorphic genes, plays a central role in the T helper 1 cell-mediated immunity against tumors. We investigated whether the 3' untranslated region +1188 A/C polymorphism (rs 3212227) influences the nasopharyngeal carcinoma (NPC) risk in Tunisian patients. DNA analysis of 247 patients and 284 healthy individuals showed a higher frequency of the 1188 C allele and the CC genotype in patients than in controls (P = 0.00001 and P = 0.00005) suggesting that the C variant allele is associated with the susceptibility to NPC. Additional testing showed that the homozygous CC genotype is also associated with advanced stage of the tumor extension at presentation (P = 0.022). Our data suggest that the impaired production of IL-12 behaves as a risk factor for NPC occurrence and progression.

Assessment of heavy metals (Cd, Cr and Pb) in water, sediment and seaweed (Ulva lactuca) in the Pulicat Lake, South East India.

The concentrations of three heavy metals chromium (Cr), cadmium (Cd) and lead (Pb) were examined in water, sediment and green algae (Ulva lactuca); collected from six different stations at Pulicat Lake, which receives effluents from industries located in North Chennai Coastal region. Concentrations of Cd (64.21 microg g(-1)) and Cr (28.51 microg g(-1)) were found to be high in sediment, whereas in green algae concentration of Pb (8.32 microg g(-1)) was higher than water and sediment samples. The relative abundance of these heavy metals in U. lactuca and sediment were found to be in the order Cd>Cr>Pb, whereas in water the ratio was found to be Cr>Pb>Cd. The seasonal variations in Cd and Pb followed a similar pattern in both seaweeds and sediments, but not in water samples. Spearman correlation coefficient study showed no significant correlation in the concentration of metals in U. lactuca, water and sediment samples.

Transfusion support in preterm neonates <1500 g and/or <32 weeks in a tertiary care center: A descriptive study.

BACKGROUND: Lack of recent studies focusing on indications, pattern, and benefits of transfusions in low birth weight (B.Wt) and low gestational age (GA) preterm neonates prompted us to undertake this study. AIM: To estimate the transfusion requirements and outcomes in preterm neonates <1500 g and/or <32 weeks. SETTINGS AND DESIGN: This is a cross-sectional study conducted over a period of 2 years in a tertiary care center. MATERIALS AND METHODS: This study was conducted with 101 preterm neonates <1500 g and/or <32 weeks who received blood transfusions in the Neonatal Intensive Care Unit. Restrictive pattern of transfusion was followed. Demographic details and antenatal, neonatal, laboratory, and transfusion parameters were collected. STATISTICAL ANALYSIS USED: Statistical analyses were performed using SPSS 16. RESULTS: The study participants received 311 transfusions. Transfusion requirements decreased with increasing GA and B.Wt. Majority of blood transfusions occurred during the first 2 weeks of life. Packed red blood cells (PRBCs) were the most frequent blood components transfused. Ninety-six percent of the study population had an uneventful transfusion. Mean hemoglobin improvement after PRBC transfusions was 2.3 ± 2.1 g/dl. Improvement in apnea occurred in 76% PRBC transfusions. Infants with sepsis, patent ductus arteriosus, bronchopulmonary dysplasia, disseminated intravascular coagulation, and dyselectrolytemia received more number of transfusions. CONCLUSION: This study would serve as an audit for neonatal blood transfusion therapy. Close adherence to neonatal transfusion policy and restrictive transfusion guidelines helps reduce inappropriate use of blood products and adverse transfusion reactions.

Diversity of culturable methylotrophic bacteria in different genotypes of groundnut and their potential for plant growth promotion.

This study aimed at documenting the culturable methylotrophic bacterial diversity across different groundnut genotypes and evaluating their effect on the growth of groundnut. 80 methylotrophic bacterial isolates were obtained from the phyllosphere of 15 groundnut genotypes collected from Tamil Nadu, India. The bacterial isolates were identified through sequencing of the 16S rDNA and were tested for their plant growth-promoting properties. Groundnut seeds were inoculated with methylotrophic bacteria and their effect on growth was evaluated via in vitro and pot experiments. Molecular identification revealed that the isolates belonged to 30 different species. A higher diversity of methylotrophic bacteria at genus and species level was found in groundnut genotype TMV2. Shannon diversity index was the highest in genotype TMV7, followed by VRI2 and TMV2. Similarly, geographical location also influenced the diversity of methylotrophic bacteria. In vitro seed germination assay revealed that methylotrophic isolates enhanced root growth and improved formation of root hair. The radicle length of treated seeds ranged from 2.7 to 8.4 cm. A higher shoot length was observed in the plants from seeds treated with Methylobacterium radiotolerans VRI8-A4 (27.3 cm), followed by Pseudomonas psychrotolerans TMV13-A1 (26.3 cm) and Bacillus aryabhattai K-CO3-3 (23 cm). The findings of this study strongly suggest that beneficial methylotrophic bacteria associated with the phyllosphere of groundnut play a major role in regulating plant growth.

A gene conversion located 5' to the A gamma gene in linkage disequilibrium with the Bantu haplotype in sickle cell anemia.

Cloning and sequencing of the gamma-globin gene of a sickle cell anemia patient homozygous for the Bantu haplotype has revealed a gene conversion that involves the replacement of an A gamma sequence by a G gamma sequence in the promoter area of the A gamma gene. This event is similar to another gene conversion believed to be responsible for the very high homology between gamma-globin genes, suggesting that the promoter area of these genes is prone to this type of genetic rearrangement. Further analysis demonstrated that the chromosome bearing this gene conversion has a very high frequency among Bantu chromosomes and a very low or nil frequency in other haplotypes linked to the beta s gene. No correlation was found between the G gamma/A gamma ratio and the presence of the gene conversion among Bantu haplotype patients, thus excluding a portion of the gamma gene sequence in the determination of this ratio.