Epithelial-to-mesenchymal transition based diagnostic and prognostic signature markers in non-muscle invasive and muscle invasive bladder cancer patients.

BACKGROUND: Diagnostic and prognostic significance of epithelial-to-mesenchymal transition (EMT) associated biomarkers are evaluated in a cohort of NMIBC (non-muscle invasive bladder cancer) and MIBC (muscle invasive bladder cancer) patients. METHODS AND RESULTS: Real-time quantitative polymerase chain reaction (RT-qPCR) and immunohistochemical (IHC) staining were carried out in 100 tumor specimens (59 NMIBC and 41 MIBC). The expressions of the epithelial marker, mesenchymal markers and EMT-activating transcription factors (EMT-ATFs) were determined at transcriptome and protein level followed by their statistical associations with clinicohistopathological variables of the patients. Transcriptomic expression analysis showed statistical relevance of tumor stage with increased Twist and Zeb-1; tumor type with reduced E-cadherin and increased Snail; and smoking/tobacco chewing status (S/TC) of patients with increased N-cadherin and Snail in NMIBC patients. Tumor grade with reduced message E-cadherin, gain of N-cadherin, Snail, Twist and Zeb-1; patients' age with reduced E-cadherin and Twist gain; and tumor type with increased message N-cadherin exhibited associations in MIBC patients. Protein expression analysis identified statistical relevance of tumor grade with nuclear gain of Snail and Twist; and nuclear gain of Slug with S/TC status of NMIBC patients. Novel gain of membranous Vimentin deduced association with patients' age in MIBC patients. Survival analysis identified novel Vimentin as the positive predictor of short progression free survival (PFS) and short overall survival (OS) in MIBC patients. Study established altered EMT profile as the independent negative predictor of short recurrence free survival (RFS) in NMIBC patients and positive predictor of short PFS and OS in MIBC patients. CONCLUSIONS: EMT associated biomarkers could provide diagnostic and prognostic risk stratification and hence could be of importance in the clinical management of bladder cancer patients.

B4GAT1 Gene Associated Congenital Muscular Dystrophy Presenting with Recurrent Severe Ventriculomegaly: Case Report and Review of Literature.

BACKGROUND: Congenital muscular dystrophies (CMD) range in phenotype from an antenatal presentation with brain and eye anomalies to isolated muscular weakness. B4GAT1 gene has recently been associated with muscular dystrophy-dystroglycanopathy, type A, 13 and two families have been reported. CASE REPORT: We report the third family with B4GAT1 associated CMD presenting as recurrent severe ventriculomegaly, cerebellar and vermian hypoplasia in fetal life, which was identified after the second affected pregnancy. The mutations identified were similar to those reported in a previously reported Indian family, homozygous, p.Asn390Asp, and p. Ala406Val, suggesting founder mutation. CONCLUSION: B4GAT1 mutations are associated with CMD and may present in fetal life as severe ventriculomegaly. The homozygous B4GAT1 mutations, p.Asn390Asp, and p. Ala406Val, described in two Indian families (including this case) might represent a founder mutation.

Designing, optimization, and validation of whole blood direct T-ARMS PCR for precise and rapid genotyping of complex vertebral malformation in cattle.

BACKGROUND: DNA testing in the cattle industry undergoes multiple hurdles. Successful genotyping involves the transportation of samples from the field to the laboratory in a chilled environment followed by DNA extraction, and finally, a specific genotyping protocol is followed. Various researches are focused on overcoming these issues. Microcards offer blood transportation at ambient temperature. Direct PCR methods can save the time of DNA extraction but available only for simplex PCR. Tetra Primer-Amplification Refractory Mutation System based Polymerase Chain Reaction (T-ARMS PCR) can make DNA testing faster in a low-cost setting. The present study was aimed to design, optimize, and validate a T-ARMS PCR for faster DNA testing of SNP responsible for Complex Vertebral Malformation (CVM)-an important genetic disease of the cattle industry. Further, a direct T-ARMS PCR from whole blood was developed to avoid the DNA extraction steps. Lastly, using the optimized protocol, genotyping of blood spotted on Microcard eliminates the need for cold chain maintenance in the transportation of samples. RESULTS: The present study demonstrated a novel T-ARMS PCR-based genotyping of the SNP rs438228855, which is responsible for CVM. Here, wild genotypes were recognized by 389 bp and 199 bp bands in agarose gel, while the carrier genotype showed an additional 241 bp band. The developed protocol was validated using PCR-Primer Introduced Restriction Analysis (PCR-PIRA) and sequencing. The present study further established a direct T-ARMS PCR for this SNP from whole blood. Different conditions such as heparin and EDTA treated blood, the need for pre-treatment, and two different DNA Polymerases for the direct PCR were optimized. Finally, our optimized protocol successfully genotyped the whole blood samples dried on Insta™DNA cards. CONCLUSIONS: The present study reported the usefulness of primer modified T-ARMS PCR for detecting CVM for the first time. To the best of our knowledge, direct PCR in T-ARMS PCR has never been reported. Lastly, the use of microcards in the developed protocol can make the assay useful in the DNA testing of field samples.

Thermophilic ligno-cellulolytic fungi: The future of efficient and rapid bio-waste management.

To accelerate the process of decomposition using consortia of thermophilic ligno-cellulolytic fungi, different crop residues viz. sorghum (SG), soybean (SS), maize (MS), sugarcane (SC), cotton (CS) and pigeon pea (PS) with a varied C:N ratio and sawdust (SD) having high lignin content were collected and used for decomposition process. Compost quality assessed by evaluating different maturity and stability indices at five succeeding stages [first mesophilic (M1), thermophilic (T), second mesophilic (M2), cooling (C) and humification (H)]. A significant reduction was observed in the C:N ratio, biodegradability index, nitrification index, ratio of water-soluble carbon to organic nitrogen (WSC/Org.N) with an increase in concomitant over time while Ash (%), organic matter loss (%), CEC/TOC ratio, cellulose biodegradation ratio (BR) and lignin/cellulose ratio were significantly increased with time. By correlation study, biodegradability index (BI) and fluorescein diacetate (FDA) hydrolysis emerged as the most suitable compost maturity and stability parameters, respectively. Principal component analysis (PCA) results confirmed that BI, BR, WSC/Org. N and FDA can be regarded as key indicators for assessing compost quality. Our findings conclude that fungal consortia of Tricoderma viride, Rhizomucor pusillus, Aspergillus awamori and Aspergillus flavus can accelerate decomposition time from 8 to 12 months (which is normal farming practice) to 120 days.

Association analysis of novel polymorphisms in 2', 5'-oligoadenylate synthetase gene with reproductive traits in indigenous and cross-bred cattle of Indian Origin.

2', 5'-Oligoadenylate synthetases (OAS) are important components of an interferon-mediated antiviral pathway. No polymorphisms in exonic regions of bovine OAS1 gene have been identified and associated with reproduction traits. The objective of the study was to detect and evaluate the effects of mutations in exonic region of bovine OAS1 gene with reproduction traits in cattle. DNA samples collected from 250 individual cows of two Indian dairy breeds (Sahiwal and Frieswal) of cattle were used in the study. The genetic variants of the OAS1 gene were identified with polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and sequence analysis using seven set of primer pairs. The PCR-SSCP analysis revealed polymorphism in the fragments comprising of exon 2, exon 5 and first fragment of exon 6 while the fragments of exons 1, 3, 4 and second fragment of exon 6 were monomorphic in Sahiwal and Frieswal cattle. The mutations in the amplified region comprising of exon 2 were found to have significant association with age at first breeding and calving, service period, dry period and pregnancy rate. Significant associations were found between SNPs in the exon 5 and service and dry periods of the animal, whereas the genetic variants in the first fragment of the exon 6 showed significant association with age at first breeding and calving. To our knowledge, this study demonstrated for the first time that the polymorphisms in OAS1 gene were associated with reproductive traits and it can be chosen as a candidate gene for improvement of reproductive performance of cattle.

Functional proteomic analysis of crossbred (Holstein Friesian × Sahiwal) bull spermatozoa.

Male infertility is one of the prime concerns of dairy cattle production. The study was designed to find out differentially expressed proteins in categorized crossbred (Holstein Friesian × Sahiwal) bull semen to serve as potential biomarkers for male infertility. Frozen crossbred bull semen with satisfactory phenotypic records were defined as "good" and "poor" based on their fertility rates. A total of 1,547 proteins were detected in bull spermatozoa using liquid chromatography-mass spectrometer (LC-MS/MS) analysis. Results revealed that 558 (36.1%) and 653 (42.2%) proteins were expressed to good and poor quality bull spermatozoa, respectively. A total of 336 proteins (21.7%) were reported to be unique for both good and poor quality bull semen, and among the common proteins, 224 (66.7%) and 112 (33.3%) were up- and downregulated in good and poor quality categorized bull semen, respectively. Gene Ontology analysis of global proteomes identified different signalling pathways, and most of them were related to cellular motility, immune systems as well as cellular metabolisms. The distinctive presence of some of the proteins may provide an insight into the molecular mechanistic role played by these proteins in crossbred bull infertility.

Participatory evaluation guides the development and selection of farmers' preferred rice varieties for salt- and flood-affected coastal deltas of South and Southeast Asia.

Rice is the staple food and provides livelihood for smallholder farmers in the coastal delta regions of South and Southeast Asia. However, its productivity is often low because of several abiotic stresses including high soil salinity and waterlogging during the wet (monsoon) season and high soil and water salinity during the dry season. Development and dissemination of suitable rice varieties tolerant of these multiple stresses encountered in coastal zones are of prime importance for increasing and stabilizing rice productivity, however adoption of new varieties has been slow in this region. Here we implemented participatory varietal selection (PVS) processes to identify and understand smallholder farmers' criteria for selection and adoption of new rice varieties in coastal zones. New breeding lines together with released rice varieties were evaluated in on-station and on-farm trials (researcher-managed) during the wet and dry seasons of 2008-2014 in the Indian Sundarbans region. Significant correlations between preferences of male and female farmers in most trials indicated that both groups have similar criteria for selection of rice varieties. However, farmers' preference criteria were different from researchers' criteria. Grain yield was important, but not the sole reason for variety selection by farmers. Several other factors also governed preferences and were strikingly different when compared across wet and dry seasons. For the wet season, farmers preferred tall (140-170 cm), long duration (160-170 d), lodging resistant and high yielding rice varieties because these traits are required in lowlands where water stagnates in the field for about four months (July to October). For the dry season, farmers' preferences were for high yielding, salt tolerant, early maturing (115-130 d) varieties with long slender grains and good quality for better market value. Pest and disease resistance was important in both seasons but did not rank high. When farmers ranked the two most preferred varieties, the ranking order was sometimes variable between locations and years, but when the top four varieties that consistently ranked high were considered, the variability was low. This indicates that at least 3-4 of the best-performing entries should be considered in succeeding multi-location and multi-year trials, thereby increasing the chances that the most stable varieties are selected. These findings will help improve breeding programs by providing information on critical traits. Selected varieties through PVS are also more likely to be adopted by farmers and will ensure higher and more stable productivity in the salt- and flood-affected coastal deltas of South and Southeast Asia.

Arsenic load in rice ecosystem and its mitigation through deficit irrigation.

Rice the staple food is a notable intake source of arsenic to the rural population of eastern India through food-chain. A field survey was carried out to study the variation of arsenic load in different parts of rice genotype Shatabdi (most popular genotype of the region) exposed to varying level of arsenic present in the irrigation water and soil. As irrigation is the primary source of arsenic contamination, a study was conducted to assess arsenic load in rice ecosystem under deficit irrigation practices like intermittent ponding (IP), saturation (SAT) and aerobic (AER) imposed during stress allowable stage (16-40 days after transplanting) of the crop (genotype Shatabdi). Present survey showed that arsenic content in water and soil influenced the arsenic load of rice grain. Variation in arsenic among different water and soil samples influenced grain arsenic load to the maximum extent followed by straw. Deviation in root arsenic load due to variation in water and soil arsenic content was lowest. Arsenic concentration of grain is strongly related to the arsenic content of both irrigation water and soil. However, water has 10% higher impact on grain arsenic load over soil. Translocation of arsenic from root to shoot decreased with the increase in arsenic content of water. Imposition of saturated and aerobic environment reduced both yield and grain arsenic load. In contrast under IP a marked decrease in grain arsenic content recorded with insignificant reduction in yield. Deficit irrigation resulted in significant reduction (17.6-25%) in arsenic content of polished rice and the values were lower than that of the toxic level (<0.2 mg kg-1). In contrast the decrease in yield was to the tune of 0.9% under IP regime over CP.

Role of MCP-1 on inflammatory processes and metabolic dysfunction following high-fat feedings in the FVB/N strain.

BACKGROUND: Monocyte chemoattractant protein 1 (MCP-1) is known to be an important chemokine for macrophage recruitment. Thus, targeting MCP-1 may prevent the perturbations associated with macrophage-induced inflammation in adipose tissue. However, inconsistencies in the available animal literature have questioned the role of this chemokine in this process. The purpose of this study was to examine the role of MCP-1 on obesity-related pathologies. METHODS: Wild-type and MCP-1-deficient mice on an friend virus B NIH (FVB/N) background were assigned to either low-fat diet or high-fat diet (HFD) treatment for a period of 16 weeks. Body weight and body composition were measured weekly and monthly, respectively. Fasting blood glucose and insulin, and glucose tolerance were measured at 16 weeks. Macrophages, T-cell markers, inflammatory mediators and markers of fibrosis were examined in the adipose tissue at the time of killing the mice. RESULTS: As expected, HFD increased adiposity (body weight, fat mass, fat percent and adipocyte size), metabolic dysfunction (impaired glucose metabolism and insulin resistance) macrophage number (CD11b(+)F480(+) cells, and gene expression of EMR1 and CD11c), T-cell markers (gene expression of CD4 and CD8), inflammatory mediators (pNFκB and pJNK, and mRNA expression of MCP-1, CCL5, C-X-C motif chemokine-14, tumor necrosis factor α (TNF-α) and interleukin-6 (IL-6)) and fibrosis (expression of IL-10, IL-13, TGF-ß and matrix metalloproteinase-2 (MMP2); P<0.05). However, contrary to our hypothesis, MCP-1 deficiency exacerbated many of these responses resulting in a further increase in adiposity (body weight, fat mass, fat percent and adipocyte size), metabolic dysregulation, macrophage markers (EMR1), inflammatory cell infiltration and fibrosis (formation of type I and III collagens, mRNA expression of IL-10 and MMP2; P<0.05). CONCLUSIONS: These data suggest that MCP-1 may be a necessary component of the inflammatory response required for adipose tissue protection, remodeling and healthy expansion in the FVB/N strain in response to HFD feedings.

Immunoprotective effect of lentinan in combination with miltefosine on Leishmania-infected J-774A.1 macrophages.

Rejuvenation of deteriorated host immune functions is imperative for successful annihilation of Leishmania parasites. The use of immunomodulatory agents may have several advantages as they conquer immunosuppression and, when given in combination, improve current therapeutic regimens. We herein investigated the immunostimulatory potency of a ß-glucan, lentinan either alone or in combination with short dose of standard drug, miltefosine on Leishmania-infected J-774A.1 macrophages. Our study shows that infected macrophages when stimulated with 2.5 µg/mL and above concentrations of lentinan secreted significant amount of host-protective molecules. The in vitro interaction between lentinan and miltefosine showed some synergy (mean sum of fractional inhibitory concentration [mean ∑FIC] 0.87) at IC50 level. Lentinan (2.5 µg/mL) plus low-dose miltefosine (2 µM) displayed heightened level of pro-inflammatory cytokines, IL-12 (13.6-fold) and TNF-α (6.8-fold) along with nitric oxide (7.2-fold higher) when compared with infected control. In combination group, we also observed remarkably (P<.001) suppressed levels of anti-inflammatory cytokines, IL-10 and TGF-ß, than that of untreated macrophages. Additionally, in comparison with infected group, we observed significant induction in phagocytic activity of macrophages in combination with treated group. Collectively, these findings emphasize the immunostimulatory effect of lentinan alone and in combination with low dose of miltefosine against Leishmania donovani.

Productivity of sodic soils can be enhanced through the use of salt tolerant rice varieties and proper agronomic practices.

Regaining the agricultural potential of sodic soils in the Indo-Gangetic plains necessitates the development of suitable salt tolerant rice varieties to provide an entry for other affordable agronomic and soil manipulation measures. Thus selection of high yielding rice varieties across a range of sodic soils is central. Evaluation of breeding lines through on-station and on-farm farmers' participatory varietal selection (FPVS) resulted in the identification of a short duration (110-115 days), high yielding and disease resistant salt-tolerant rice genotype 'CSR-89IR-8', which was later released as 'CSR43' in 2011. Several agronomic traits coupled with good grain quality and market value contributed to commercialization and quick adoption of this variety in the sodic areas of the Indo-Gangetic plains of eastern India. Management practices required for rice production in salt affected soils are evidently different from those in normal soils and practices for a short duration salt tolerant variety differ from those for medium to long duration varieties. Experiments were conducted at the Indian Council of Agricultural Research-Central Soil Salinity Research Institute (ICAR-CSSRI), Regional Research Station, Lucknow, Uttar Pradesh, India during 2011 and 2013 wet seasons, to test the hypothesis that combining matching management practices (Mmp) with an improved genotype would enhance productivity and profitability of rice in sodic soils. Mmp were developed on-station by optimizing existing best management practices (Bmp) recommended for the region to match the requirements of CSR43. The results revealed that transplanting 4 seedlings hill-1 at a spacing of 15 × 20 cm produced significantly higher yield over other treatments. The highest additional net gain was US$ 3.3 at 90 kg ha-1 N, and the lowest was US$ 0.4 at 150 kg ha-1 N. Above 150 kg ha-1, the additional net gain became negative, indicating decreasing returns from additional N. Hence, 150 kg N ha-1 was considered the economic optimum N application rate for CSR43 in these sodic soils. Using 150-60-40-25 kg N-P2O5-K2O-ZnSO4·7H2O ha-1 in farmers' fields grown to CSR43 produced an average of 5.5 t ha-1 grain. The results of on-farm evaluation trials of CSR43 showed that matching management practices (Mmp) increased yield by 8% over existing best management practices (Bmp) recommended by ICAR-CSSRI for sodic soils and by 16% over framers' management practices; however, combining Mmp with CSR43 resulted in 35% higher yields over farmers' current varieties and management. This approach of combining cost effective crop and nutrient management options and a salt-tolerant variety can maximize the productivity and profitability of sodic soils in the alluvial Indo-Gangetic plains and in neighboring salt-affected areas of the Ganges mega delta in South Asia.

Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice.

KEY MESSAGE: A set of NILs carrying major blast resistance genes in a Basmati rice variety has been developed. Also, the efficacy of pyramids over monogenic NILs against rice blast pathogen Magnaporthe oryzae has been demonstrated. Productivity and quality of Basmati rice is severely affected by rice blast disease. Major genes and QTLs conferring resistance to blast have been reported only in non-Basmati rice germplasm. Here, we report incorporation of seven blast resistance genes from the donor lines DHMASQ164-2a (Pi54, Pi1, Pita), IRBLz5-CA (Pi2), IRBLb-B (Pib), IRBL5-M (Pi5) and IRBL9-W (Pi9) into the genetic background of an elite Basmati rice variety Pusa Basmati 1 (PB1). A total of 36 near-isogenic lines (NILs) comprising of 14 monogenic, 16 two-gene pyramids and six three-gene pyramids were developed through marker-assisted backcross breeding (MABB). Foreground, recombinant and background selection was used to identify the plants with target gene(s), minimize the linkage drag and increase the recurrent parent genome (RPG) recovery (93.5-98.6 %), respectively, in the NILs. Comparative analysis performed using 50,051 SNPs and 500 SSR markers revealed that the SNPs provided better insight into the RPG recovery. Most of the monogenic NILs showed comparable performance in yield and quality, concomitantly, Pusa1637-18-7-6-20 (Pi9), was significantly superior in yield and stable across four different environments as compared to recurrent parent (RP) PB1. Further, among the pyramids, Pusa1930-12-6 (Pi2+Pi5) showed significantly higher yield and Pusa1633-7-8-53-6-8 (Pi54+Pi1+Pita) was superior in cooking quality as compared to RP PB1. The NILs carrying gene Pi9 were found to be the most effective against the concoction of virulent races predominant in the hotspot locations for blast disease. Conversely, when analyzed under artificial inoculation, three-gene pyramids expressed enhanced resistance as compared to the two-gene and monogenic NILs.

Morphological and comparative genomic analyses of pathogenic and non-pathogenic Fusarium solani isolated from Dalbergia sissoo.

Sissoo or shisham (Dalbergia sissoo Roxb.) is one of the finest wood of South Asia. Fusarium solani is a causal organism of sissoo wilt, decline, or dieback. It is also a potential causal organism associated with other valuable tree species. Thirty-eight Fusarium isolates including 24 F. solani and 14 Fusarium sp., were obtained in 2005 from different geographical locations in India. All 38 (18 pathogenic and 20 non-pathogenic) isolates were characterized for genomic analysis, growth behaviour, pigmentation and sensitivity to carbendazim. Based on growth pattern, growth rate, pigmentation and sensitivity to carbendazim, all 38 isolates showed a wide range of variability, but no correlation with pathogenicity or geographical distribution. Three techniques were used for comparative genomic analysis: random amplified polymorphic DNA (RAPD); inter simple sequence repeats (ISSR); and simple sequence repeats (SSR). A total of 90 primers targeting different genome regions resulted a total of 1159 loci with an average of 12.88 loci per primer. These primers showed high genomic variability among the isolates. The maximum loci (14.64) per primer were obtained with RAPD. The total variation of the first five principal components for RAPD, ISSR, SSR and combined analysis were estimated as 47.42, 48.21, 46.30 and 46.78 %, respectively. Among the molecular markers, highest Pearson correlation value (r = 0.957) was recorded with combination of RAPD and SSR followed by RAPD and ISSR (r = 0.952), and SSR and ISSR (r = 0.942). The combination of these markers would be similarly effective as single marker system i.e. RAPD, ISSR and SSR. Based on polymorphic information content (PIC = 0.619) and highest coefficient (r = 0.995), RAPD was found to be the most efficient marker system compared to ISSR and SSR. This study will assist in understanding the population biology of wilt causing phytopathogen, F. solani, and in assisting with integrated disease management measures.

Prevalence of tuberculosis in Faridabad district, Haryana State, India.

BACKGROUND & OBJECTIVES: Epidemiological information on tuberculosis (TB) has always been vital for planning control strategies. It has now gained further importance for monitoring the impact of interventions to control the disease. The present study was done to estimate the prevalence of bacillary tuberculosis in the district of Faridabad in Haryana State of India among persons aged older than 15 years. METHODS: In this cross-sectional study, residents of Faridabad district were assessed for the prevalence of tuberculosis. Twelve rural and 24 urban clusters with estimated populations of 41,106 and 64,827 individuals were selected for the study. Two sputum samples were collected from individuals found eligible for inclusion. The samples were also cultured by modified Petroff's method and were examined for growth of Mycobacterium tuberculosis once a week for eight weeks. A person found positive by smear and/or culture was identified as sputum-positive pulmonary TB positive. RESULTS: A total of 105,202 subjects were enumerated in various clusters of the Faridabad district. There were 50,057 (47.58%) females and 55,145 (52.42%) males. Of these 98,599 (93.7%) were examined by the study group (47,976 females; 50,623 males). The overall prevalence of sputum smear or culture positive pulmonary tuberculosis in our study was found to be 101.4 per 100,000 population. INTERPRETATION & CONCLUSIONS: The present results showed that the prevalence of sputum positive pulmonary tuberculosis was higher in Faridabad district than the notification rates recorded by the World Health Organization for the contemporary period, a disparity that could be explained by a difference in case detection strategy employed for the study.

Bovine Circadian Locomotor Output Cycles Kaput (CLOCK) and Clusterin (CLU) mRNA Quantitation in Ejaculated Crossbred Bull Spermatozoa.

Mammalian circadian locomotor output cycles kaput (CLOCK) gene encodes a transcription factor that affects both the persistence and the period of circadian rhythms. Earlier reports suggested that CLOCK gene might be associated with male infertility in human. Present investigation, for the first time, reports that CLOCK gene expresses differentially between good and poor quality crossbred bull semen. The relative expression of CLOCK was significantly (p < 0.05) higher among good quality bull semen than motility-impaired ones. Clusterins (CLU) are series of genes associated with a variety of physiological activities including spermatogenesis, apoptosis and degenerative disease conditions. In the present context, we also investigated that the expression of CLU gene was significantly (p < 0.05) higher among motility-impaired crossbred bull semen compared to the good quality one.

Time-dependent Degradation Pattern of Cardiac Troponin T in Cases of Death by Burn.

OBJECTIVE: Death due to burn occurs frequently. This study investigated time-dependent alterations in cardiac troponin T (cTnT) associated with fatal burns. METHODS: Cardiac tissue samples were collected from 10 medico-legal autopsies after informed consent from the relatives and post-mortem degradation by incubation of the cardiac tissue was studied at room temperature for different time periods. The cases included in this study were the subjects of burns without any prior history of disease who died in the hospital and their exact time of death was known. An efficient extraction protocol to analyse the banding pattern of cTnT in post-mortem tissue was developed. RESULTS: The data show a distinct time-dependent profile corresponding to the degradation of cTnT by proteases found in cardiac muscle. Both post-mortem interval and cardiac tissue of burned corpses had a statistically significant effect where the greatest amount of protein breakdown was observed within the first 41.20 hours, after which intact protein slowly disappears. The average molecular weight of all fragments showed intact cTnT to be rapidly degraded into smaller fragments. CONCLUSION: In cases of burns, such knowledge will assist in knowing if there were previous scars that might have mimicked a burn and also help to properly evaluate the real cause of death.

Phosphate solubilizing and indole-3-acetic acid producing bacteria from the soil of Garhwal Himalaya aimed to improve the growth of rice.

In the present study, soil bacteria from rainfed agriculture field of Garhwal Himalaya, just prior to sowing of summer crop, were isolated and initially tested for solubilization of inorganic phosphate, production of indole acetic acid (IAA) and siderophore. Two bacterial isolates, having efficient P- solubilizing activity in solid medium, were identified using 16S rRNA sequence analysis as Pseudomonas koreensis strainYB1 Arthrobacter nitroguajacolicus strainYB3 and three bacterial isolates, producing high amount of IAA in liquid medium, were identified as Klebsiella oxytoca strainYB2 and two strain of Arthrobacter nitroguajacolicus, strainYB4 and YB5, respectively. In culture medium supplemented with L-Tryptophan, Klebsiella oxytoca produced high amount of IAA (337.44 µg l(-1)). The selected five bacterial strains were further tested for tricalcium phosphate (TCP) solubilizing abilities at three different incubation temperature viz., 4 degrees C, 10 degrees C and 28 degrees C, under in vitro conditions. At 28 degrees C, three bacterial strains Pseudomonas koreensis, Arthrobacter nitroguajacolicus strainYB4 and Klebsiella oxytoca solubilized the phosphate efficiently. At 10 degrees C only two strains, Pseudomonas koreensis and Arthrobacter nitroguajacolicus strainYB4 solubilized phosphate efficiently as compared to other strains. These five bacterial strains were tested for nitrogen, catalase activity, starch and cellulose hydrolysis as well as growth promotion activity on rice, under controlled conditions. All the five bacterial strains efficiently increased the biomass and phosphorus uptake in Swama and Swarna sub1 varieties of rice.

Transposon-based high sequence diversity in Avr-Pita alleles increases the potential for pathogenicity of Magnaporthe oryzae populations.

Magnaporthe oryzae causes rice blast that is one of the most devastating diseases of rice worldwide. Highly variable nature of this fungus has evolved itself against major resistance genes in newly released rice varieties. Understanding the population structure of this fungus is essential for proper utilization of the rice blast resistance genes in rice crop plants. In the present study, we analyzed 133 isolates of M. oryzae from ten countries to find the allelic variation of Avr-Pita gene that is triggering Pita-mediated resistance in rice plant. The diversity analysis of these alleles showed higher level of nucleotide variation in the coding regions than the noncoding regions. Evolutionary analysis of these alleles indicates that Avr-Pita gene is under purifying selection to favor its major alleles in 133 isolates analyzed in this study. We hypothesize that the selection of favorable Avr-Pita allele in these isolates may occur through a genetic mechanism known as recurrent selective sweeps. A total of 22 functional Avr-Pita protein variants were identified in this study. Insertion of Pot3 transposable element into the promoter of Avr-Pita gene was identified in virulent isolates and was suggested that mobility of repeat elements in avirulence genes of M. oryzae seems to help in emergence of new virulent types of the pathogen. Allele-specific markers developed in this study will be helpful to identify a particular type of Avr-Pita allele from M. oryzae population which can form the basis for the deployment of Pita gene in different epidemiological regions.

Activity and mechanism of action of HDVD, a novel pyrimidine nucleoside derivative with high levels of selectivity and potency against gammaherpesviruses.

A novel nucleoside analogue, 1-[(2S,4S-2-(hydroxymethyl)-1,3-dioxolan-4-yl]5-vinylpyrimidine-2,4(1H,3H)-dione, or HDVD, was evaluated against a wide variety of herpesviruses and was found to be a highly selective inhibitor of replication of the gammaherpesviruses Kaposi's sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). HDVD had also a pronounced inhibitory activity against murine herpesvirus 68 (MHV-68) and herpes simplex virus 1 (HSV-1). In contrast, replication of herpesvirus saimiri (HVS), HSV-2, and varicella-zoster virus (VZV) was weakly inhibited by the compound, and no antiviral activity was determined against human cytomegalovirus (HCMV) and rhesus rhadinovirus (RRV). The HDVD-resistant virus phenotype contained point mutations in the viral thymidine kinase (TK) of HSV-1, MHV-68, and HVS isolates. These mutations conferred cross-resistance to other TK-dependent drugs, with the exception of an MHV-68 mutant (E358D) that exhibited resistance only to HDVD. HSV-1 and HVS TK-mutants isolated under selective pressure with bromovinyldeoxyuridine (BVDU) also showed reduced sensitivity to HDVD. Oral treatment with HDVD and BVDU was assessed in an intranasal model of MHV-68 infection in BALB/c mice. In contrast to BVDU treatment, HDVD-treated animals showed a reduction in viral DNA loads and diminished viral gene expression during acute viral replication in the lungs in comparison to levels in untreated controls. The valyl ester prodrug of HDVD (USS-02-71-44) suppressed the latent infection in the spleen to a greater extent than HDVD. In the present study, HDVD emerged as a highly potent antiviral with a unique spectrum of activity against herpesviruses, in particular, gammaherpesviruses, and may be of interest in the treatment of virus-associated diseases.

Shape elongation of Zn nanoparticles in silica irradiated with swift heavy ions of different species and energies: scaling law and some insights on the elongation mechanism.

Zinc nanoparticles (NPs) embedded in silica were irradiated with swift heavy ions (SHIs) of seven different combinations of species and energies. The shape elongation induced by the irradiations was evaluated by optical linear dichroism (OLD) spectroscopy, which is a sensitive tool for determining the change in the mean aspect ratio (AR) of NPs. Although the mean AR change indicated a linear fluence dependence in the low- and medium-fluence regions, it indicated a nonlinear dependence in the high-fluence region. The data reveal that the elongation efficiency of Zn is correlated with the electronic stopping power 'Se in silica' and is not correlated with either the 'Se in Zn' or the nuclear stopping power. The elongation efficiency plotted as a function of the 'Se in silica' revealed a linear relationship, with a threshold value of ∼2 keV nm(-1), which is the same dependence exhibited by the ion-track formation in silica. The log-log plot showed that the elongation efficiency increased linearly with Se above a critical value of ∼3 keV nm(-1) and steeply decreased with Se to the power of 5 below the critical Se. The steep decrease can be ascribed to the discontinuous nature of the ion tracks, which is expected at Se ∼ 2-4 keV nm(-1) in silica. The fluence Φ dependences of AR - 1 under various irradiations are well-normalized with the electronic energy deposition of SHIs, i.e., the product of Se and Φ, with a Se greater than the same critical value of ∼3 keV nm(-1). The normalized data above the critical value fell on a linear relation, AR(Φ) - 1 ∝ SeΦ, for SeΦ < 2 keV nm(-3) and a sublinear relation, AR(Φ) - 1 ∝ (SeΦ)(1/2) for SeΦ > 2 keV nm(-3). On the basis of these experimental results, we discuss some insights into the elongation mechanism.