Linkage analysis for drought tolerance in kharif rice of Assam using microsatellite markers

371-375Drought stress in rainfed ecosystem significantly limits the production of Ranjit, the most predominant high yielding rice variety of Assam. A mapping population comprising 85 F4 individuals between Ranjit and a drought tolerant cultivar, ARC10372 was developed and genotyped with 80 microsatellite markers in order to understand the genetic basis of drought tolerance. The linkage map constructed based on a framework linkage map using these markers showed that the marker loci were distributed across 12 chromosomes spanning a distance of 273.4 cM with an average interval of 3.41 cM between marker loci. Most of the marker loci were found to be in good fit with the expected Mendelian segregation ratio; however, thirteen marker loci in total showed segregation distortion on six chromosomes. The linkage map generated in the study will facilitate mapping of quantitative trait loci imparting drought tolerance in rice of Assam and their map-based cloning

Paternal and maternal influences on differences in birth weight between Europeans and Indians born in the UK.

BACKGROUND: Ethnic groups differ significantly in adult physique and birth weight. We aimed to improve understanding of maternal versus paternal contributions to ethnic differences in birth weight, by comparing the offspring of same-ethnic versus mixed-ethnic unions amongst Europeans and South Asian Indians in the UK. METHODOLOGY AND PRINCIPAL FINDINGS: We used data from the UK Office for National Statistics Longitudinal Study (LS) and the Chelsea and Westminster Hospital (CWH), London. In the combined sample at all gestational ages, average birth weight of offspring with two European parents was significantly greater than that of offspring with two Indian parents [Δ = 344 (95% CI 329, 360) g]. Compared to offspring of European mothers, the offspring of Indian mothers had lower birth weight, whether the father was European [Δ = -152 (95% CI -92, -212) g] or Indian [Δ = -254 (95% -315, -192) g]. After adjustment for various confounding factors, average birth weight of offspring with European father and Indian mother was greater than that of offspring with two Indian parents [LS: Δ = 249 (95% CI 143, 354) g; CWH: Δ = 236 (95% CI 62, 411) g]. Average birth weight of offspring with Indian father and European mother was significantly less than that of offspring with two European parents [LS: Δ = -117 (95% CI -207, -26) g; CWH: Δ = -83 (-206, 40) g]. CONCLUSIONS/SIGNIFICANCE: Birth weight of offspring with mixed-ethnic parentage was intermediate between that of offspring with two European or two Indian parents, demonstrating a paternal as well as a maternal contribution to ethnic differences in fetal growth. This can be interpreted as demonstrating paternal modulation of maternal investment in offspring. We suggest long-term nutritional experience over generations may drive such ethnic differences through parental co-adaptation

Extracts from Acacia catechu suppress HIV-1 replication by inhibiting the activities of the viral protease and Tat

Background: Acacia catechu (Mimosa family) stem bark extracts have been used traditionally as a dietary supplement as well as a folk medicine given its reported anti-inflammatory, immunomodulatory, hepatoprotective, antioxidant, anti-microbial and anti-tumor activities. The present study was undertaken to evaluate the anti-HIV-1 activity of the extracts from stem bark of A. catechu. Methods. The aqueous and 50% ethanolic extracts of A. catechu stem bark were prepared and 50% ethanolic extract was further fractioned by successively partitioning with petroleum ether, chloroform and n-butanol. All the extracts and fractions were evaluated for cytotoxicity and anti-HIV-1 activity using different in vitro assays. The active n-butanol fraction was evaluated for its inhibition against HIV-1 reverse transcriptase, integrase, protease, pro-viral genome integration and viral Tat protein mediated transactivation. The effect of n-butanol fraction on the induction of pro-inflammatory cytokines secretion in Vk2/E6E7 cells and transepithelial resistance in Caco-2 and HEC-1A cells was investigated. Results: The aqueous and 50% ethanolic extracts of A. catechu showed IC§ssub§50§esub§ values of 1.8 ± 0.18 μg/ml and 3.6 ± 0.31 μg/ml, respectively in cell-free virus based assay using TZM-bl cells and HIV-1§ssub§NL4.3§esub§ (X-4 tropic). In the above assay, n-butanol fraction exhibited anti-HIV-1 activity with an IC§ssub§50§esub§ of 1.7 ± 0.12 μg/ml. The n-butanol fraction showed a dose-dependent inhibition against HIV-1§ssub§NL4.3§esub§ infection of the peripheral blood lymphocytes and against HIV-1§ssub§BaL§esub§(R-5-tropic) as well as two different primary viral isolates of HIV-1 infection of TZM-bl cells. The n-butanol fraction demonstrates a potent inhibitory activity against the viral protease (IC§ssub§50§esub§ = 12.9 μg/ml), but not reverse transcriptase or integrase. Further, in Alu-PCR no effect on viral integration was observed. The n-butanol fraction interfered with the Tat-mediated Long Terminal Repeat transactivation in TZM-bl cells, mRNA quantitation (qRT-PCR) and electrophoretic mobility shift assay (EMSA). The n-butanol fraction did not cause an enhanced secretion of pro-inflammatory cytokines in Vk2/E6E7 cells. Additionally, no adverse effects were observed to the monolayer formed by the Caco-2 and HEC-1A epithelial cells. Conclusions: The results presented here show a potential anti-HIV-1 activity of A. catechu mediated by the inhibition of the functions of the viral protein and Tat. © 2013 Nutan et al.; licensee BioMed Central Ltd

SSR marker-based DNA fingerprinting of Sub1 introgressed lines in the background of traditional rice varieties of Assam India

350-356Rice varieties are usually characterized by agro-morphological descriptors used for seed certification and seed characterization by following distinctiveness, uniformity, and stability (DUS) test. But in fact, these primary distinguishing morphological descriptors among rice varieties are very limited and hence face problems to distinguish germplasm accessions. Germplasm certification in NBPGR requires a DNA fingerprinting profile to explain germplasm uniqueness compared to existing varieties. Varietal identification has gained a key role worldwide, particularly in plant variety protection. Sixty-two morphological descriptors studies have shown the Sub1 introgressed advanced lines E-6, C-210, C-196, 1189-1 and 1160-1 are distinct from the other varieties for more than 15morphological traits, based on these variations the lines were selected for DNA fingerprinting. About68 SSRs markers were used for DNA fingerprinting in seven genotypes, two of which were parents (Ranjit, Bahadur) and three Sub1 introgressed advanced lines (E6, C210, C196) in Ranjit background, and two Sub1 introgressed advanced lines (1189-1, 1160-1) in Bahadur background. DNA fingerprinting was done on these genotypes of rice using SSR markers. Among the 68 SSR markers, total 65 markers were amplified and three were found not amplified. Out of 65 markersfour of them viz. RM 152, RM 172, RM 251, and RM 346 showed better polymorphism with amplicon size ranges from 155-163 bp, 150-159 bp, 137-147 bp, and 166-175 bp, respectively, and remaining 61 showed monomorphic amplification. Therefore, SSR (Simple-sequence repeats) based DNA fingerprinting helped to differentiate Ranjit, Bahadur, E-6, C-210, C-196, 1189-1, and 1160-1. Hence, the research reveals that newly developed high-yielding Sub1 introgressed advanced lines in the background of traditional Assam rice varieties (Ranjit and Bahadur) are unique in their identity

What do we know about chronic kidney disease in India: first report of the Indian CKD registry

<p>Abstract</p> <p>Background</p> <p>There are no national data on the magnitude and pattern of chronic kidney disease (CKD) in India. The Indian CKD Registry documents the demographics, etiological spectrum, practice patterns, variations and special characteristics.</p> <p>Methods</p> <p>Data was collected for this cross-sectional study in a standardized format according to predetermined criteria. Of the 52,273 adult patients, 35.5%, 27.9%, 25.6% and 11% patients came from South, North, West and East zones respectively.</p> <p>Results</p> <p>The mean age was 50.1 ± 14.6 years, with M:F ratio of 70:30. Patients from North Zone were younger and those from the East Zone older. Diabetic nephropathy was the commonest cause (31%), followed by CKD of undetermined etiology (16%), chronic glomerulonephritis (14%) and hypertensive nephrosclerosis (13%). About 48% cases presented in Stage V; they were younger than those in Stages III-IV. Diabetic nephropathy patients were older, more likely to present in earlier stages of CKD and had a higher frequency of males; whereas those with CKD of unexplained etiology were younger, had more females and more frequently presented in Stage V. Patients in lower income groups had more advanced CKD at presentation. Patients presenting to public sector hospitals were poorer, younger, and more frequently had CKD of unknown etiology.</p> <p>Conclusions</p> <p>This report confirms the emergence of diabetic nephropathy as the pre-eminent cause in India. Patients with CKD of unknown etiology are younger, poorer and more likely to present with advanced CKD. There were some geographic variations.</p

Factors influencing agreement between child self-report and parent proxy-reports on the Pediatric Quality of Life Inventory™ 4.0 (PedsQL™) generic core scales

BACKGROUND: In situations where children are unable or unwilling to respond for themselves, measurement of quality of life (QOL) is often obtained by parent proxy-report. However the relationship between child self and parent proxy-reports has been shown to be poor in some circumstances. Additionally the most appropriate statistical method for comparing ratings between child and parent proxy-reports has not been clearly established. The objectives of this study were to assess the: 1) agreement between child and parent proxy-reports on an established child QOL measure (the PedsQL™) using two different statistical methods; 2) effect of chronological age and domain type on agreement between children's and parents' reports on the PedsQL™; 3) relationship between parents' own well-being and their ratings of their child's QOL. METHODS: One hundred and forty-nine healthy children (5.5 – 6.5, 6.5 – 7.5, and 7.5 – 8.5 years) completed the PedsQL™. One hundred and three of their parents completed these measures in relation to their child, and a measure of their own QOL (SF-36). RESULTS: Consistency between child and parent proxy-reports on the PedsQL™ was low, with Intra-Class correlation coefficients ranging from 0.02 to 0.23. Correlations were higher for the oldest age group for Total Score and Psychosocial Health domains, and for the Physical Health domain in the youngest age group. Statistically significant median differences were found between child and parent-reports on all subscales of the PedsQL™. The largest median differences were found for the two older age groups. Statistically significant correlations were found between parents' own QOL and their proxy-reports of child QOL across the total sample and within the middle age group. CONCLUSION: Intra-Class correlation coefficients and median difference testing can provide different information on the relationship between parent proxy-reports and child self-reports. Our findings suggest that differences in the levels of parent-child agreement previously reported may be an artefact of the statistical method used. In addition, levels of agreement can be affected by child age, domains investigated, and parents' own QOL. Further studies are needed to establish the optimal predictors of levels of parent-child agreement

TNF-α promoter polymorphism: a factor contributing to the different immunological and clinical phenotypes in Japanese encephalitis

<p>Abstract</p> <p>Background</p> <p>More than three billion populations are living under the threat of Japanese encephalitis in South East Asian (SEA) countries including India. The pathogenesis of this disease is not clearly understood and is probably attributed to genomic variations in viral strains as well as the host genetic makeup. The present study is to determine the role of polymorphism of TNF-alpha promoter regions at positions -238G/A, -308G/A, -857C/T and -863C/A in the severity of Japanese encephalitis patients.</p> <p>Methods</p> <p>Total of 142 patients including 66 encephalitis case (IgM/RT-PCR positive), 16 fever cases (IgM positive) without encephalitis and 60 apparently healthy individuals (IgG positive) were included in the study. Polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) using site specific restriction enzymes were implemented for polymorphism study of TNF alpha promoter.</p> <p>Results</p> <p>Following the analysis of the digestion patterns of four polymorphic sites of the TNF- alpha promoter region, a significant association was observed between the allele -308A and -863C with the patients of Japanese encephalitis.</p> <p>Conclusions</p> <p>TNF- alpha 308 G/A has been shown to be associated with elevated TNF- alpha transcriptional activity. On the other hand, polymorphism at position -863C/A in the promoter region has been reported to be associated with reduced TNF- alpha promoter activity and lower plasma TNF levels. As per the literature search, this is the first study to identify the role of TNF- alpha promoter in JE infection. Our results show that subjects with - 308A and -863C alleles are more vulnerable to the severe form of JE infection.</p

Using Recombinant Proteins from Lutzomyia longipalpis Saliva to Estimate Human Vector Exposure in Visceral Leishmaniasis Endemic Areas

During the blood meal, female sand flies (insects that transmit the parasite Leishmania) inject saliva containing a large variety of molecules with different pharmacological activities that facilitate the acquisition of blood. These molecules can induce the production of anti-saliva antibodies, which can then be used as markers for insect (vector) biting or exposure. Epidemiological studies using sand fly salivary gland sonicate as antigens are hampered by the difficulty of obtaining large amounts of salivary glands. In the present study, we have investigated the use of two salivary recombinant proteins from the sand fly Lutzomyia longipalpis, considered the main vector of visceral leishmaniasis, as an alternative method for screening of exposure to the sand fly. We primarily tested the suitability of using the recombinant proteins to estimate positive anti-saliva ELISA test in small sets of serum samples. Further, we validated the assay in a large sample of 1,077 individuals from an epidemiological survey in a second area endemic for visceral leishmaniasis. Our findings indicate that these proteins represent a promising epidemiological tool that can aid in implementing control measures against leishmaniasis

Tuberculous meningitis: new tools and new approaches required [version 1; peer review: not peer reviewed]

Tuberculous meningitis is the most severe form of tuberculosis and causes widespread mortality and morbidity. Understanding of the epidemiology and pathogenesis is incomplete, and the optimal diagnosis and treatment are poorly defined. To generate research collaboration and coordination, as well as to promote sharing of ideas and advocacy efforts, the International Tuberculous Meningitis Research Consortium was formed in 2009. During the most recent meeting of this group in Lucknow, India, in March 2019, the Consortium decided to bring together key articles on tuberculous meningitis in one supplement. The supplement covers recent scientific updates, expert perspectives on specific clinical challenges, consensus statements on how to conduct research, and a set of priorities for future investigation

Targeting HSP90 for cancer therapy

Heat-shock proteins (HSPs) are molecular chaperones that regulate protein folding to ensure correct conformation and translocation and to avoid protein aggregation. Heat-shock proteins are increased in many solid tumours and haematological malignancies. Many oncogenic proteins responsible for the transformation of cells to cancerous forms are client proteins of HSP90. Targeting HSP90 with chemical inhibitors would degrade these oncogenic proteins, and thus serve as useful anticancer agents. This review provides an overview of the HSP chaperone machinery and the structure and function of HSP90. We also highlight the key oncogenic proteins that are regulated by HSP90 and describe how inhibition of HSP90 could alter the activity of multiple signalling proteins, receptors and transcriptional factors implicated in carcinogenesis