Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism

Background: Alu RNAs are present at elevated levels in stress conditions and, consequently, Alu repeats are increasingly being associated with the physiological stress response. Alu repeats are known to harbor transcription factor binding sites that modulate RNA pol II transcription and Alu RNAs act as transcriptional co-repressors through pol II binding in the promoter regions of heat shock responsive genes. An observation of a putative heat shock factor (HSF) binding site in Alu led us to explore whether, through HSF binding, these elements could further contribute to the heat shock response repertoire. Results: Alu density was significantly enriched in transcripts that are down-regulated following heat shock recovery in HeLa cells. ChIP analysis confirmed HSF binding to a consensus motif exhibiting positional conservation across various Alu subfamilies, and reporter constructs demonstrated a sequence-specific two-fold induction of these sites in response to heat shock. These motifs were over-represented in the genic regions of down-regulated transcripts in antisense oriented Alus. Affymetrix Exon arrays detected antisense signals in a significant fraction of the down-regulated transcripts, 50% of which harbored HSF sites within 5 kb. siRNA knockdown of the selected antisense transcripts led to the over-expression, following heat shock, of their corresponding down-regulated transcripts. The antisense transcripts were significantly enriched in processes related to RNA pol III transcription and the TFIIIC complex. Conclusions: We demonstrate a non-random presence of Alu repeats harboring HSF sites in heat shock responsive transcripts. This presence underlies an antisense-mediated mechanism that represents a novel component of Alu and HSF involvement in the heat shock response

Evaluation of Taro (Colocasia esculenta L.) Cultivars for Growth, Yield and Quality Attributes

A study on varietal evaluation in taro for growth, yield and quality attributes was carried out in a replicated experiment and morphological and chemical analysis was done. Significant differences were recorded for all the characteristics studied. 'Panchmukhi' recorded highest plant height (179.33cm), petiole length (153.11cm), petiole breadth (13.87mm) and leaf size (3095.67cm2), LAI (1.14), corm length (152.41mm) and breadth (107.77mm), average corm weight (1500.00g) and corm yield (20.00t/ha). 'C-3' recorded maximum (15.00) petiole number and cormel length (85.93mm). Cormel yield (15.29t/ha), total yield (25.92t/ha) and number of cormels per plant (30.33) was found to be maximum in cv. White Gouriya. 'ML-2' recorded maximum (7.33) number of side shoots. Highest average cormel weight (72.85g) was maximum in cv. Arcol-7, and 'Arcol-5' recorded maximum (67.43mm) cormel breadth; the least blight incidence percentage (8.00) was recorded in 'Nayabungalow'. As for biochemical constituents, 'Nainital' recorded the highest (5.85%) total sugars, 'Kandha-5' exhibited the highest (34.67%) starch content and 'Nadia Local' with showed highest levels of oxalic acid (1.05mg/100g). Highest dry matter content (27.50%) was recorded in cvs. KCA-1 and Panchmukhi, while the highest moisture percentage (82.83) was recorded in 'IG Coll-5'

Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection

Primate-specific Alus harbor different regulatory features, including miRNA targets. In this study, we provide evidence for miRNA-mediated modulation of transcript isoform levels during heat-shock response through exaptation of Alu-miRNA sites in mature mRNA. We performed genome-wide expression profiling coupled with functional validation of miRNA target sites within exonized Alus, and analyzed conservation of these targets across primates. We observed that two miRNAs (miR-15a-3p and miR-302d-3p) elevated in stress response, target RAD1, GTSE1, NR2C1, FKBP9 and UBE2I exclusively within Alu. These genes map onto the p53 regulatory network. Ectopic overexpression of miR-15a-3p downregulates GTSE1 and RAD1 at the protein level and enhances cell survival. This Alu-mediated fine-tuning seems to be unique to humans as evident from the absence of orthologous sites in other primate lineages. We further analyzed signatures of selection on Alu-miRNA targets in the genome, using 1000 Genomes Phase-I data. We found that 198 out of 3177 Alu-exonized genes exhibit signatures of selection within Alu-miRNA sites, with 60 of them containing SNPs supported by multiple evidences (global-FST > 0.3, pair-wise-FST > 0.5, Fay-Wu’s H<−20, iHS> 2.0, high ΔDAF) and implicated in p53 network. We propose that by affecting multiple genes, Alu-miRNA interactions have the potential to facilitate population-level adaptations in response to environmental challenges

Chemistry of enediynyl azides: activation through a novel pathway

The spontaneous activation of a nonaromatic enediynyl azide under ambient conditions has been demonstrated. The aromatic enediyne followed the expected cycloaddition with the alkene in the neighbouring arm to form a stable bridged bicyclic enediyne

Low Power Personalized ECG Based System Design Methodology for Remote Cardiac Health Monitoring

This paper describes a mixed-signal ECG system for personalized and remote cardiac health monitoring. The novelty of this work is four-fold. Firstly, a low power analog front end with an efficient automatic gain control mechanism, maintaining the input of the ADC to a level rendering optimum SNR and the enhanced recyclic folded cascode opamp used as an integrator for ADC. Secondly, a novel on-the-fly PQRST Boundary Detection (BD) methodology is formulated for finding the boundaries in continuous ECG signal. Thirdly, a novel low-complexity ECG feature extraction architecture is designed by reusing the same module present in the proposed BD methodology. Fourthly, the system is having the capability to reconfigure the proposed Low power ADC for low (8 bits) and high (12 bits) resolution with the use of the feedback signal obtained from the digital block when it is in processing. The proposed system has been tested and validated on patient’s data from PTBDB, CSEDB and in-house IIT Hyderabad DB (IITHDB) and we have achieved an accuracy of 99% upon testing on various normal and abnormal ECG signals. The whole system is implemented in 180 nm technology resulting in 9.47W (@ 1 MHz) power consumption and occupying 1.74mm2 silicon area

Impact of farmer producer organization on organic chilli production in Telangana, India

Input intensive modern agriculture is adversely affecting human health and environment. Farmers of Telangana state have taken up organic chilli production with the assistance of FPOs. Primary data was collected from 120 farmers comprising 60 members and 60 non-members of FPO from two districts of Telangana through semi-structured interviews. The study found that the shift to organic chilli cultivation led to decrease in input use by 9.06% and yield by 23.4%. However, the gross return from organic chilli farming was 13.85% higher over that realised by non-members due to the efforts of FPOs. DEA analysis revealed that a higher proportion of member farmers (48%) had technical efficiency of more than 60% as compared to non-members (18%). FPOs were instrumental in reduction of transaction cost and number of intermediaries leading to the realization of a higher proportion of producer’s share in consumer’s rupee (65%). Discriminant function analysis revealed that the FPO promoting institutions (44%), ease of doing business (16%) and infrastructure facilities like storage, irrigation, electricity and credit have high influence on performance of the states with respect to FPOs

Carbon Modeling of Agroforestry Systems at Farmers’ Field in Indo-Gangetic Plains of India

The Indian Green revolution region “Indo-Gangetic Plain” (IGP) comprises of four agro-climatic zones namely lower, middle, upper, and trans gangetic plains covering West Bengal, Bihar, Uttar Pradesh, Delhi, Uttarakhand, Chandigarh, Haryana, Punjab, and some part of Rajasthan state. It covers 169 districts with total geographical area of 43.70 million ha. The Indo-Gangetic plains are one of the most populous regions with its area covering nearly 13% of the total geographical area of the country. It produces about 50% of the total food grains to feed 40% of the population. The continuous cropping of rice-wheat system has degraded the soil health dramatically over the years. Hence, the incorporation of trees in agriculture would be a better option to improve the soil as well as livelihood of the farmers in IGP. Agriculture is the major enterprise of the region that is most vulnerable to climate changes particularly owing to the inadequacy of resources with the smallholder farmers. While, agroforestry has the potential to play a significant role in mitigating the atmospheric accumulation of greenhouse gases (GHG), it also helps smallholder farmers adapt to the changes. These are the reasons for recognizing agroforestry as a viable alternative to prevent and mitigate climate change (Ram Newaj et al., 2014). A considerable proportion of agroforestry area located in IGP and some of the promising tree species like Populus deltoides, Eucalyptus tereticornis, Melia azadirach, Mangifera indica, Dalbergia sissoo, and Acacia nilotica are very common in the farmer’s fields. Keeping this in view, the field survey was carried out to estimate the carbon sequestration potential at a farmer’s field in IGP

4-Hydroxyphenylpyruvate Dioxygenase (HPPD)-Inhibiting Herbicides: Past, Present, and Future

The 4-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides are primarily used for weed control in corn, barley, oat, rice, sorghum, sugarcane, and wheat production fields in the United States. The objectives of this review were to summarize (1) the history of HPPD-inhibitor and their use in the United States, (2) HPPD-inhibitor resistant weeds, their mechanism of resistance, and management, (3) interaction of HPPD-inhibitor with other herbicides, and (4) the future of HPPD-inhibitor-resistant crops. As of 2022, three broadleaf weeds (Palmer amaranth, waterhemp, and wild radish) have evolved resistance to the HPPD-inhibitor. The predominance of metabolic resistance to HPPD-inhibitor was found in aforementioned three weed species. Management of HPPD-inhibitor-resistant weeds can be accomplished using alternate herbicides such as glyphosate, glufosinate, 2,4-D, or dicamba; however, metabolic resistance poses a serious challenge, as the weeds may be cross-resistant to other herbicide sites of action, leading to limited herbicide options. The HPPD-inhibitor is commonly applied with photosystem II (PS II)-inhibitor to increase efficacy and weed control spectrum. The synergism with HPPD-inhibitor arises from depletion of plastoquinones, which allows increased binding of PS II-inhibitor to the D1 protein. New HPPD-inhibitor from azole carboxamides class is in development and expected to be available in the near future. The HPPD-inhibitor-resistant crops have been developed through overexpression of a resistant bacterial HPPD enzyme in plants and the overexpression of transgenes for HPPD and a microbial gene that enhances the production of HPPD substrate. Isoxaflutole-resistant soybean is commercially available, and it is expected that soybean resistant to other HPPD-inhibitor such as mesotrione, stacked with resistance to other herbicides, will be available in the near future

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