Assessment of thermal and temporal stability of SARS-CoV-2 samples using real-time qRT-PCR.

BACKGROUND: As per the guidelines of the Indian Council of Medical Research, nasopharyngeal and oropharyngeal swabs in viral transport medium (VTM) are to be stored at 4 °C for less than 5 days and for more than 5 days at -70 °C. Samples are not transported or stored as per prescribed conditions because of the limitations, resulting in an apprehensive diagnosis. The aim of the study was to test the stability of the SARS-CoV-2 sample stored in VTM at different temperatures. METHODS: In this study, the stability of 21 positive and 9 negative samples for SARS-CoV-2 was evaluated in commercial VTM at different temperatures (-80 °C, -20 °C, 4 °C, and 25 to 30 °C). Stability was checked for up to 50 days in the above storage conditions at different intervals. PathoDetect™ and Hi-PCR® kits were used for the detection of the four genes of SARS-CoV-2. The Cycle Threshold (Ct) value for determining the positivity of samples for PathoDetect™ was < 40 and for Hi-PCR® was < 38. RESULTS: The SARS-CoV-2 confirmatory genes (RdRp and E genes) and the internal housekeeping gene remained detectable even on the 50th day of the study. The Ct of the RdRp and E genes were found to increase with storage duration, but all positive samples remained positive till the end of the study, or the Ct value remained below the cut-off level. The negative samples gave consistent results until the end of the study. When the differences in Ct values were compared between the days in a set of experiments, they were not significantly different except in a few samples. CONCLUSION: The SARS-CoV-2 genetic materials in commercial VTM were stable at room temperature to -80 °C for 50 days.

Biomedical waste plastic: bacteria, disinfection and recycling technologies-a comprehensive review.

Plastic recycling reduces the wastage of potentially useful materials as well as the consumption of virgin materials, thereby lowering the energy consumption, air pollution by incineration, soil and water pollution by landfilling. Plastics used in the biomedical sector have played a significant role. Reducing the transmission of the virus while protecting the human life in particular the frontline workers. Enormous volumes of plastics in biomedical waste have been observed during the outbreak of the pandemic COVID-19. This has resulted from the extensive use of personal protective equipment such as masks, gloves, face shields, bottles, sanitizers, gowns, and other medical plastics which has created challenges to the existing waste management system in the developing countries. The current review focuses on the biomedical waste and its classification, disinfection, and recycling technology of different types of plastics waste generated in the sector and their corresponding approaches toward end-of-life option and value addition. This review provides a broader overview of the process to reduce the volume of plastics from biomedical waste directly entering the landfill while providing a knowledge step toward the conversion of "waste" to "wealth." An average of 25% of the recyclable plastics are present in biomedical waste. All the processes discussed in this article accounts for cleaner techniques and a sustainable approach to the treatment of biomedical waste.

Burden of sickle cell disease in tribal students in Maa-Baadi institutions in southern Rajasthan - A pilot study.

Background & objectives: Sickle cell disease (SCD), an inherited disorder of erythrocytes, is highly prevalent in the tribal population of India. The tribal population of India is approximately 100 million and it is necessary to identify the magnitude of this problem. Furthermore, the prevalence of the disease is unknown among the five million tribal people of southern provinces of Rajasthan. In this study, we intended to determine the prevalence and characteristics of sickle cell disorder among the tribal inhabitants of southern Rajasthan. Methods: This cross-sectional study was conducted among the tribal students of the Maa-Baadis and hostels situated in the five tribal sub-plan districts of Rajasthan. Maa-Baadi centres are located in every village, whereas for every four to five villages, one hostel is allocated to accommodate the tribal students. The screening for SCD was done by solubility test and electrophoresis was used for confirmation. Results: A total of 36,752 tribal students were screened from 1,006 Maa-Baadi centres and 243 hostels. The prevalence of SCD among the tribal students was 5.8 per cent. The prevalence of heterozygous and homozygous conditions was 5.61 and 0.17 per cent, respectively. Among the five sub-plan districts, the highest prevalence was observed in Sirohi district (10.5%) followed by Banswara (7.42%), Udaipur (6.53%), Pratapgarh (5.51%) and Dungarpur (1.89%). Among the four major tribes belonging to these districts, the highest prevalence was recorded in Garasia tribes (13.81%). The history of leg ulcers and the mean pulse rate were significantly high in SCD individuals. Interpretation & conclusions: SCD is a significant problem among the tribes of southern Rajasthan, with the highest prevalence among the Garasia tribe. The present study recommends that a structured screening programme targeting the entire tribal population with appropriate counselling as well as providing treatment through the existing health system is the need of the hour.

Comparative analysis of contraceptive use in Punjab and Manipur: exploring beyond women's education and empowerment.

BACKGROUND: Women's education and empowerment are important predictors of contraceptive use across countries. However, two of the Indian states, namely, Punjab and Manipur, showed large variations in contraceptive use, despite the similar level of women's educational attainment and empowerment. Therefore, this paper attempts to understand variation in contraceptive use between these states, despite having similar level of educational attainment and empowerment among the married women. METHODS: This study primarily used cross-sectional data of the National Family Health Survey (NFHS) 2015-16 and to some extent the District Level Household Survey (DLHS) 2012-13 data. The analytical sample includes 13,730 currently married women in Punjab and 8,872 in Manipur. Modern contraceptive prevalence rate (mCPR) is the key outcome variable of this study. Bivariate, multivariate, and multilevel regression analysis are applied to understand the differences in mCPR between these states and its determinants. RESULTS: Mean years of schooling was about 8 years among women of both the states, and about 34% of the women in Punjab and 27% of the women in Manipur have high level of autonomy. Despite this, use of modern method was 66% in Punjab and only 13% in Manipur. Coverage of family planning program indicators were significantly lower in Manipur than Punjab - frontline workers' (FLWs) outreach for family planning was only 18% in Manipur compared to 52% in Punjab. Similarly, only 11% of the public health facilities in Manipur compared to 50% of the health facilities in Punjab were ready to provide at least one clinical method of family planning. CONCLUSION: Despite the similar level of individual level characteristics across the two states, poor coverage of family planning programs - low outreach of FLWs, low level of facility readiness, as well as sociocultural norms discouraging contraceptive use - might be responsible for lower contraceptive use in Manipur than Punjab. This implies for strengthening the health system for family planning in Manipur to meet the contraception needs of women by addressing sociocultural barriers in the state.

The transition to Xpert MTB/RIF ultra: diagnostic accuracy for pulmonary tuberculosis in Kampala, Uganda.

BACKGROUND: The World Health Organization (WHO) has endorsed the next-generation Xpert MTB/RIF Ultra (Ultra) cartridge, and Uganda is currently transitioning from the older generation Xpert MTB/RIF (Xpert) cartridge to Ultra as the initial diagnostic test for pulmonary tuberculosis (TB). We assessed the diagnostic accuracy of Ultra for pulmonary TB among adults in Kampala, Uganda. METHODS: We sampled adults referred for Xpert testing at two hospitals and a health center over a 12-month period. We enrolled adults with positive Xpert and a random 1:1 sample with negative Xpert results. Expectorated sputum was collected for Ultra, and for solid and liquid culture testing for Xpert-negative patients. We measured sensitivity and specificity of Ultra overall and by HIV status, prior history of TB, and hospitalization, in reference to Xpert and culture results. We also assessed how classification of results in the new "trace" category affects Ultra accuracy. RESULTS: Among 698 participants included, 211 (30%) were HIV-positive and 336 (48%) had TB. The sensitivity of Ultra was 90.5% (95% CI 86.8-93.4) and specificity was 98.1% (95% CI 96.1-99.2). There were no significant differences in sensitivity and specificity by HIV status, prior history of TB or hospitalization. Xpert and Ultra results were concordant in 670 (96%) participants, with Ultra having a small reduction in specificity (difference 1.9, 95% CI 0.2 to 3.6, p=0.01). When "trace" results were considered positive for all patients, sensitivity increased by 2.1% (95% CI 0.3 to 3.9, p=0.01) without a significant reduction in specificity (- 0.8, 95% CI - 0.3 to 2.0, p=0.08). CONCLUSIONS: After 1 year of implementation, Ultra had similar performance to Xpert. Considering "trace" results to be positive in all patients increased case detection without significant loss of specificity. Longitudinal studies are needed to compare the benefit of greater diagnoses to the cost of overtreatment.

Linear lesions in dermatology: a clinicoaetiopathological study.

BACKGROUND: Linear lesions are fairly common in our daily practice. However, the appearance of these lesions can vary, thus complicating the diagnosis. AIMS: To study the various clinical presentations, the demographic profile of patients and the clinicopathological correlations of dermatoses presenting with a linear distribution. METHODS: We conducted an institution-based, cross-sectional, descriptive study of 281 consecutive patients with linear lesions attending dermatology clinics. MedCalc software (V11.6) was used for statistical analysis. RESULTS: Patients were divided into eight groups: lesions along the lines of Blaschko (n = 136), lesions along blood vessels (n = 3), lesions along lymphatics (n = 3), Koebner phenomenon (n = 24), autoinoculation (n = 24), external factors (n = 45), infestations (n = 2) and 'other' (n = 44). The mean age at presentation was 24.50 ± 18.82 years and the male/female ratio was 1.32 : 1. The commonest symptom was itching/burning (56.94% of patients), while the commonest site was the arm (44.48%); followed by the leg (30.60%), trunk and abdomen (22.42%), head and neck (19.20%), and genitalia (0.35%). Apart from the common cases, there was a wide gamut of rare conditions (e.g. angiokeratoma circumscriptum naeviforme, porokeratotic eccrine ostial and dermal duct naevus, Blaschko-linear syringocystadenoma papilliferum, progressive cribriform and zosteriform hyperpigmentation, unilateral naevoid acanthosis nigricans, fixed drug eruption, discoid lupus erythematosus). CONCLUSION: Linear lesions act as diagnostic clues to many dermatological conditions, therefore, the importance of meticulous examination in clinical dermatology cannot be overemphasized.

Better late than never: Clinical outcomes of delayed fixation in thoracolumbar spinal trauma.

PURPOSE: To analyse factors influencing functional outcome and neurological recovery in patients undergoing delayed surgery for traumatic spinal cord injury (SCI) involving thoracolumbar spine. METHODS: Retrospective analysis of 33 patients with thoracolumbar SCI who underwent delayed surgery (≥ 72hrs post-trauma) with a minimum follow-up of 1 year (average:32.55 months) was done. The parameters studied included age, sex, co-morbidities, mode of trauma, associated trauma, level and number of vertebrae involved, fracture morphology, thoracolumbar injury classification and severity score (TLICS), maximal spinal cord compression (MSCC), signal changes in the cord, neurological deficit as per the American Spinal Injury Association (ASIA) scale, lower extremity motor score (LEMS), bowel bladder involvement, time interval between trauma and surgery. RESULTS: Mean time interval from injury to spine surgery was 24.45 days. At the end of 1-year follow-up, 17(51.5%), 12(36.36%), and 3(9.1%) patients had ≥ 1, ≥ 2, and ≥ 3-grade ASIA improvement, respectively. The mean LEMS rose to 33.86 from 17.09 (P < 0.001). 8 out of 20 patients with bladder involvement showed improvement. 4 patients succumbed, 22 were ambulatory, and 7 remained non-ambulatory. On comparing various parameters, pre-operative LEMS score (P-value: < 0.001), cord signal changes (P-value:0.002), and presence of cord transection (P-value:0.007) differed significantly in the above-mentioned three groups, while age (P-value:0.442), average TLICS (P-value:0.872), time from injury to surgery (P-value:0.386) did not differ significantly. CONCLUSION: This study highlights that there is still a significant scope for neurological improvement even after delayed surgery in patients with thoracolumbar SCI. The lower the LEMS score at the time of presentation, signal changes in the cord and presence of cord transection have a significant influence on unfavourable clinical outcomes at the end of 1-year post-surgery.

Linkage disequilibrium mapping for grain Fe and Zn enhancing QTLs useful for nutrient dense rice breeding.

BACKGROUND: High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain. RESULTS: A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K = 3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study. CONCLUSION: Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Biochemical, functional and molecular characterization of pigeon pea rhizobia isolated from semi-arid regions of India.

Pigeon pea (Cajanus cajan (L.) Millspaugh) is among the top ten legumes grown globally not only having high tolerance to environmental stresses along, but also has the high biomass and productivity with optimal nutritional profiles. In the present study, 55 isolates of rhizobia were identified from 22 nodule samples of pigeon pea collected from semi-arid regions of India on the basis of morphological, biochemical, plant growth promoting activities and their ability to tolerate the stress conditions viz. pH, salt, temperature and drought stress. Amongst all the 55 isolates, 37 isolates showed effective nodulation under in vitro conditions in pigeon pea. Further, five isolates having multiple PGP activities and high in vitro symbiotic efficiency were subjected to 16S rRNA sequencing and confirmed their identities as Rhizobium, Mesorhizobium, Sinorhizobium sp. Further these 37 isolates were characterized at molecular level using ARDRA and revealed significant molecular diversity. Based on UPGMA clustering analysis, these isolates showed significant molecular diversity. The high degree of molecular diversity is due to mixed cropping of legumes in the region. The assessment of genetic diversity and molecular characterization of novel strains is a very important tool for the replacement of ineffective rhizobial strains with the efficient strains for the improvement in the nodulation and pigeon pea quality. The pigeon pea isolates with multiple PGPR activities could be further used for commercial production.

Molecular Diversity Analysis of Plant Growth Promoting Rhizobium Isolated from Groundnut and Evaluation of Their Field Efficacy.

Rhizobium are nitrogen-fixing bacteria which possess the nif gene that codes for the nitrogenase enzyme involved in the reduction of atmospheric dinitrogen (N2) to ammonia. Thirty rhizobial strains were identified from ten groundnut plant root nodules collected from semi-arid regions of Rajasthan, India. The isolates were initially identified on the basis of morphological, biochemical, and molecular characteristics. These rhizobium strains were further screened for plant growth promoting activities. Twenty-eight strains were able to produce indole acetic acid, nine strains could solubilize phosphate, and twenty-nine strains exhibited positive results for siderophore and ammonia production. All the bacterial strains were able to efficiently nodulate the groundnut under pot conditions and based on multiple PGP activities six strains were selected for field evaluation. Field experiments confirmed the effectiveness of these selected rhizobium strains resulted in significantly higher nodule number, nodule dry weight, grain yield, and yield components of inoculated plants. Inoculation of the rhizobium strain GN223 followed by GN221 resulted in high yield and field efficiency. Isolation of effective microbial strains is the prerequisite to increase the yield which is evident from the field data of the present study. Hence, these strains might serve as proficient inoculants.

Vertebral, intraspinal and other organ anomalies in congenital scoliosis.

AIMS: This study was undertaken to describe the pattern of vertebral, intraspinal and other organ anomalies in patients with congenital scoliosis and to determine the correlation between them. METHODS: Complete medical and radiological records of 227 consecutive patients with congenital scoliosis were analysed. The radiographs were examined for type of vertebral anomaly, location and severity of deformity. The median curve progression index (MCPI) was calculated in 198 patients. The magnetic resonance imaging (MRI) of the whole spine was analysed to detect the presence of cord abnormalities. The presence of other organ-system anomalies was also noted. The independent sample t test was used to compare severity of deformity between those with and without cord anomalies. The Chi-square test was used to compare frequency of cord abnormalities in different vertebral and organ-system anomalies. RESULTS: Hemivertebra with contralateral bar had the highest MCPI, while block vertebrae and wedge vertebrae had the lowest MCPI. Forty-eight patients had 83 cord anomalies. There was no statistically significant difference in severity of deformity, between those with and without cord anomalies. Failure of segmentation had the highest frequency of cord anomalies (p = 0.01). There was no significant difference in the frequency of cord anomalies between those with and without other organ defects. CONCLUSION: Curve progression can be predicted by the underlying vertebral abnormalities. However, it cannot predict cord and other organ-system anomalies. Thus, all patients with congenital scoliosis must undergo MRI of the spine, electro- and echocardiography and ultrasonography of the abdomen to detect occult abnormalities and optimize the patient prior to deformity correction.

Status of pesticide residues in water, sediment, and fishes of Chilika Lake, India.

Chilika Lake is the largest coastal lagoon in Asia and the second largest in the world covering an area of 1100 km2 and spread over three districts of Odisha state of India. It is the first Indian wetland designated as a wetland of international importance under the Ramsar Convention in 1981. The lake ecosystem sustains large and diversified resources of plants and animals including fisheries. Pollution of the ecosystem caused by residues of pesticides originating from different sources was assessed through multiple sampling from 2012 to 2016 from three potential sites of contamination, viz., Palur Bridge, Daya River Estuary, and Makara River. Incidence of organochlorinated (OC) pesticide residues was noticed in about 25% water samples. HCH (α, γ&δ), DDD (op|), DDE (op|&pp.|) and heptachlor were the OCs detected in concentration varying from 0.025 to 23.4 µg/l. None of the eight targeted synthetic pyrethroid (SP) pesticides was found in water, but among the organophosphates (OP), chlorpyrifos (0.019-2.73 µg/l), and dichlorvos (0.647 µg/l) were recorded. In sediment samples, residues of OC or OP pesticides were not present, but one SP pesticide was recorded. Fish samples were contaminated to the extent of 55%, mostly with residues of OCs and OPs and less with SPs. However, their concentrations were below the permissible limit, so there was no direct threat of health hazards to humans.

Statins influence epithelial expression of the anti-microbial peptide LL-37/hCAP-18 independently of the mevalonate pathway.

Anti-microbial resistance increases among bacterial pathogens and new therapeutic avenues needs to be explored. Boosting innate immune mechanisms could be one attractive alternative in the defence against infectious diseases. The cholesterol-lowering drugs, statins, have been demonstrated to also affect the immune system. Here we investigate the effect of statins on the expression of the human cathelicidin anti-microbial peptide (CAMP) LL-37/hCAP-18 [encoded by the CAMP gene] and explore the underlying mechanisms in four epithelial cell lines of different origin. Simvastatin induced CAMP expression in bladder epithelial cells telomerase-immortalized uroepithelial cells (TERT-NHUCs), intestinal cells HT-29 and keratinocytes HEKa, but not in airway epithelial cells A549. Gene induction in HEKa cells was reversible by mevalonate, while this effect was independent of the cholesterol biosynthesis pathway in TERT-NHUCs. Instead, inhibition of histone deacetylases by simvastatin seems to be involved. For HT-29 cells, both mechanisms may contribute. In addition, simvastatin increased transcription of the vitamin D-activating enzyme CYP27B1 which, in turn, may activate LL-37/hCAP-18 production. Taken together, simvastatin is able to promote the expression of LL-37/hCAP-18, but cell line-specific differences in efficacy and the involved signalling pathways exist.

The extended posterior approach for resection of sacral tumours.

PURPOSE: The conventional posterior approach is mostly advocated for excision of sacral tumours below S2. We describe an operative technique of single-stage en bloc resection of sacral tumours, extending up to S1, through an extended posterior approach. METHOD: Nine patients, who had undergone resection of sacral tumours, by the described technique formed the basis of this study. Four patients had chordomas, whereas schwannoma, neurilemmoma, giant-cell tumour, malignant paraganglioma and recurrent Ewing's sarcoma were seen in one patient each. They were followed up at regular intervals with a mean follow-up of 45.4 months. Perioperative complications, their functional and oncological outcomes at final follow-up were analysed. RESULT: None of the patients had any perioperative complications like uncontrolled haemorrhage, injury to the rectum, deep vein thrombosis or pulmonary embolism. One patient had a superficial wound infection which subsided with regular dressing, and another patient developed a wound breakdown that required an additional flap procedure. At final follow-up, six patients were able to walk without any assistive devices, six patients had normal bladder function, and five patients had normal bowel function. Five patients did not have any recurrence at final follow-up, whereas two were alive with the disease and two had died. CONCLUSION: The reported technique allows en bloc resection of sacral tumours up to S1, through a posterior-only approach. It is less invasive with minimal morbidity. The functional and oncological outcomes are similar to those reported by other investigators. These slides can be retrieved from electronic supplementary material.

Water vapor flux in tropical lowland rice.

A field experiment was conducted at Indian Council of Agricultural Research-National Rice Research Institute, Cuttack, Odisha, India in the dry seasons of 2015 and 2016 to assess the water vapor flux (FH2O) and its relationship with other climatic variables. The FH2O and climatic variables were measured by an eddy covariance system and a micrometeorological observatory. Daily mean FH2O during the dry seasons of 2015 and 2016 were 0.009-0.092 g m-2 s-1 and 0.014-0.101 g m-2 s-1, respectively. Seasonal average FH2O was 14.6% higher in 2016 than that in 2015. Diurnal variation for FH2O showed a bell-shaped curve with its peak at 13:30-14:00 Indian Standard Time (IST) in both the years. Carbon dioxide flux was found higher with rise in FH2O. This relationship was stronger at higher vapor pressure deficit (VPD) (20 ≤ VPD ≤ 40 and VPD > 40 hPa). The FH2O showed significant positive correlation with latent heat flux, net radiation flux, photosynthatically active radiation, air, water and soil temperatures, shortwave down and upwell radiations, maximum and minimum temperatures, evaporation, and relative humidity in both the years. Principal component analysis showed that FH2O was very close to latent heat flux in both the years (Pearson correlation coefficient close to 1). The two-dimensional observation map of the principal component F1 and F2 showed the observations taken during the vegetative stage and panicle initiation stage, and flowering stage and maturity stage were closer to each other. It can be concluded that the most important climatic variables controlling the FH2O were latent heat of vaporization, net radiation, air temperature, soil temperatures, and water temperature.

Profiling of Brevibacillus borstelensis transcriptome exposed to high temperature shock.

To understand the molecular mechanisms underlying the ability of the bacteria to survive at high temperature, gene expression profile of Brevibacillusborstelensis at 55°C during 5 and 10min heat shock period was carried out by high-throughput sequencing technology. A total of 2555 non-redundant transcripts were annotated. A total of 575 genes at 5min and 400 genes at 10min exhibited significant differential expression in response to temperature upshift from 50 to 55°C. Genes up-regulated under heat shock were associated with metabolism (mtnE), membrane transport, signal transduction, transcriptional regulation (ycxD, codY) and folding and sorting (hsp90). A larger number of genes encoding hypothetical proteins were identified. RT-PCR experimental results carried out on genes expressed under heat shock were found to be consistent with transcriptome data. The results enhance our understanding of adaptation strategy of thermophilic bacteria thereby providing a strong background for in depth research in thermophiles.

Polymorphisms in host genes encoding NOSII, C-reactive protein, and adhesion molecules thrombospondin and E-selectin are risk factors for Plasmodium falciparum malaria in India.

Cytoadherence of Plasmodium falciparum-infected red blood cells (RBCs) in host microvasculature and complex regulation of the immune response are important contributors to the clinical outcome of disease. We tested the association of 23 single nucleotide polymorphisms (SNPs) and a microsatellite repeat in adhesion molecule genes THBS1 and ESEL, and immune regulatory molecule genes NOSII, CRP, and MBL2 with falciparum malaria in populations residing in a malaria-endemic and a non-endemic region of India. The THBS1 haplotype CCCCA (rs1478604, rs7170682, rs2664141, rs12912082, rs3743125) was a risk factor in the endemic region (relative risk = 3.78) and an ESEL SNP (rs5368, His468Tyr) associated with cerebral malaria (CM) [CM vs. non-cerebral malaria (NCM), odds ratio (OR) = 2.23, p = 0.03]. In the non-endemic region, an ESEL 3'UTR SNP (rs5359) associated with enhanced risk of disease (OR = 3.62, p = 1 × 10(-4)) and the CT genotype of the CRP promoter SNP (C/T/A) strongly associated with protection (severe vs. control, OR = 0.29, p = 6 × 10(-5)). Long repeat alleles of the NOSII promoter microsatellite (CCTTT)n exhibited strong association with protection and the NOSII ATG haplotype (rs3729508, rs2297520, rs9282801) was strongly protective against severe malaria in both regions (endemic, severe vs. control, OR = 0.05, p = 0.0001; non-endemic, severe vs. control, OR = 0.3, p = 1 × 10(-5)). Our results suggest differential contribution of variants of the investigated genes in determining the outcome of malaria in Indian populations.

Long-term effect of rice-based farming systems on soil health.

Integrated rice-fish culture, an age-old farming system, is a technology which could produce rice and fish sustainably at a time by optimizing scarce resource use through complementary use of land and water. An understanding of microbial processes is important for the management of farming systems as soil microbes are the living part of soil organic matter and play critical roles in soil C and N cycling and ecosystem functioning of farming system. Rice-based integrated farming system model for small and marginal farmers was established in 2001 at Central Rice Research Institute, Cuttack, Odisha. The different enterprises of farming system were rice-fish, fish-fingerlings, fruits, vegetables, rice-fish refuge, and agroforestry. This study was conducted with the objective to assess the soil physicochemical properties, microbial population, carbon and nitrogen fractions, soil enzymatic activity, and productivity of different enterprises. The effect of enterprises induced significant changes in the chemical composition and organic matter which in turn influenced the activities of enzymes (urease, acid, and alkaline phosphatase) involved in the C, N, and P cycles. The different enterprises of long-term rice-based farming system caused significant variations in nutrient content of soil, which was higher in rice-fish refuge followed by rice-fish enterprise. Highest microbial populations and enzymatic properties were recorded in rice-fish refuge system because of waterlogging and reduced condition prolonged in this system leading to less decomposition of organic matter. The maximum alkaline phosphatase, urease, and FDA were observed in rice-fish enterprise. However, highest acid phosphatase and dehydrogenase activity were obtained in vegetable enterprise and fish-fingerlings enterprise, respectively.

Upregulation of transcripts for metabolism in diverse environments is a shared response associated with survival and adaptation of Klebsiella pneumoniae in response to temperature extremes.

Klebsiella pneumoniae being ubiquitous in nature encounters wide differences in environmental condition. The organism's abundance in natural water reservoirs exposed to temperature variation forms the basis of its persistence and spread in the soil and other farm produce. In order to investigate the effect of temperature changes on the survival and adaptation of the bacteria, the transcriptional response of K. pneumoniae subjected to low (20 °C) and high (50 °C) temperature shock were executed using Applied Biosystems SOLiD platform. Approximately, 33 and 34% of protein coding genes expressed in response to 20 and 50 °C, respectively, displayed significant up- or downregulation (p < 0.01). Most of the significantly expressed transcripts mapped to metabolism, membrane transport, and cell motility were downregulated at 50 °C, except for protein folding, sorting, and degradation, suggesting that heat stress causes general downregulation of gene expression together with induction of heat shock proteins. While at 20 °C, the transcripts of carbohydrate, lipid, and amino acid metabolism were highly upregulated. Hypothetical proteins as well as canonical heat and cold shock proteins, viz. grpE, clpX, recA, and deaD were upregulated commonly in response to 20 and 50 °C. Significant upregulation of genes encoding ribosomal proteins at 20 and 50 °C possibly suggest their role in the survival of K. pneumoniae cells under low- and high-temperature stress.

Sequence polymorphism of GroEL gene in natural population of Bacillus and Brevibacillus spp. that showed variation in thermal tolerance capacity and mRNA expression.

GroEL, a class I chaperonin, plays an important role in the thermal adaptation of the cell and helps to maintain the viability of the cell under heat shock condition. Function of groEL in vivo depends on the maintenance of proper structure of the protein which in turn depends on the nucleotide and amino acid sequence of the gene. In this study, we investigated the changes in nucleotide and amino acid sequences of the partial groEL gene that may affect the thermotolerance capacity as well as mRNA expression of bacterial isolates. Sequences among the same species having differences in the amino acid level were identified as different alleles. The effect of allelic variation on the groEL gene expression was analyzed by comparison and relative quantification in each allele under thermal shock condition by RT-PCR. Evaluation of K a/K s ratio among the strains of same species showed that the groEL gene of all the species had undergone similar functional constrain during evolution. The strains showing similar thermotolerance capacity was found to carry same allele of groEL gene. The isolates carrying allele having amino acid substitution inside the highly ATP/ADP or Mg(2+)-binding region could not tolerate thermal stress and showed lower expression of the groEL gene. Our results indicate that during evolution of these bacterial species the groEL gene has undergone the process of natural selection, and the isolates have evolved with the groEL allelic sequences that help them to withstand the thermal stress during their interaction with the environment.