Showing papers by "Jawaharlal Nehru University published in 2021"

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

Abstract: In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

A massive rock and ice avalanche caused the 2021 disaster at Chamoli, Indian Himalaya

Abstract: On 7 Feb 2021, a catastrophic mass flow descended the Ronti Gad, Rishiganga, and Dhauliganga valleys in Chamoli, Uttarakhand, India, causing widespread devastation and severely damaging two hydropower projects. Over 200 people were killed or are missing. Our analysis of satellite imagery, seismic records, numerical model results, and eyewitness videos reveals that ~27x106 m3 of rock and glacier ice collapsed from the steep north face of Ronti Peak. The rock and ice avalanche rapidly transformed into an extraordinarily large and mobile debris flow that transported boulders >20 m in diameter, and scoured the valley walls up to 220 m above the valley floor. The intersection of the hazard cascade with downvalley infrastructure resulted in a disaster, which highlights key questions about adequate monitoring and sustainable development in the Himalaya as well as other remote, high-mountain environments.

Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review

Abstract: Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.

A systematic global stocktake of evidence on human adaptation to climate change

Abstract: Assessing global progress on human adaptation to climate change is an urgent priority. Although the literature on adaptation to climate change is rapidly expanding, little is known about the actual extent of implementation. We systematically screened >48,000 articles using machine learning methods and a global network of 126 researchers. Our synthesis of the resulting 1,682 articles presents a systematic and comprehensive global stocktake of implemented human adaptation to climate change. Documented adaptations were largely fragmented, local and incremental, with limited evidence of transformational adaptation and negligible evidence of risk reduction outcomes. We identify eight priorities for global adaptation research: assess the effectiveness of adaptation responses, enhance the understanding of limits to adaptation, enable individuals and civil society to adapt, include missing places, scholars and scholarship, understand private sector responses, improve methods for synthesizing different forms of evidence, assess the adaptation at different temperature thresholds, and improve the inclusion of timescale and the dynamics of responses. Determining progress in adaptation to climate change is challenging, yet critical as climate change impacts increase. A stocktake of the scientific literature on implemented adaptation now shows that adaptation is mostly fragmented and incremental, with evidence lacking for its impact on reducing risk.

Design and analysis of a large-scale COVID-19 tweets dataset

Abstract: As of July 17, 2020, more than thirteen million people have been diagnosed with the Novel Coronavirus (COVID-19), and half a million people have already lost their lives due to this infectious disease. The World Health Organization declared the COVID-19 outbreak as a pandemic on March 11, 2020. Since then, social media platforms have experienced an exponential rise in the content related to the pandemic. In the past, Twitter data have been observed to be indispensable in the extraction of situational awareness information relating to any crisis. This paper presents COV19Tweets Dataset (Lamsal 2020a), a large-scale Twitter dataset with more than 310 million COVID-19 specific English language tweets and their sentiment scores. The dataset’s geo version, the GeoCOV19Tweets Dataset (Lamsal 2020b), is also presented. The paper discusses the datasets’ design in detail, and the tweets in both the datasets are analyzed. The datasets are released publicly, anticipating that they would contribute to a better understanding of spatial and temporal dimensions of the public discourse related to the ongoing pandemic. As per the stats, the datasets (Lamsal 2020a, 2020b) have been accessed over 74.5k times, collectively.

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass.

Abstract: Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2-4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6-knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate-gene-biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene-trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration.

Abstract: The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE’s sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Wuhan to World: The COVID-19 Pandemic.

Abstract: COVID-19 is a Severe Acute Respiratory Syndrome (SARS), caused by SARS-CoV-2, a novel virus which belongs to the family Coronaviridae. It was first reported in December 2019 in the Wuhan city of China and soon after, the virus and hence the disease got spread to the entire world. As of February 26, 2021, SARS-CoV-2 has infected ~112.20 million people and caused ~2.49 million deaths across the globe. Although the case fatality rate among SARS-CoV-2 patient is lower (~2.15%) than its earlier relatives, SARS-CoV (~9.5%) and MERS-CoV (~34.4%), the SARS-CoV-2 has been observed to be more infectious and caused higher morbidity and mortality worldwide. As of now, only the knowledge regarding potential transmission routes and the rapidly developed diagnostics has been guiding the world for managing the disease indicating an immediate need for a detailed understanding of the pathogen and the disease-biology. Over a very short period of time, researchers have generated a lot of information in unprecedented ways in the key areas, including viral entry into the host, dominant mutation, potential transmission routes, diagnostic targets and their detection assays, potential therapeutic targets and drug molecules for inhibiting viral entry and/or its replication in the host including cross-neutralizing antibodies and vaccine candidates that could help us to combat the ongoing COVID-19 pandemic. In the current review, we have summarized the available knowledge about the pathogen and the disease, COVID-19. We believe that this readily available knowledge base would serve as a valuable resource to the scientific and clinical community and may help in faster development of the solution to combat the disease.

Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures.

Abstract: The current outbreak of a novel coronavirus, named as SARS-CoV-2 causing COVID-19 occurred in 2019, is in dire need of finding potential therapeutic agents. Recently, ongoing viral epidemic due to coronavirus (SARS-CoV-2) primarily affected mainland China that now threatened to spread to populations in most countries of the world. In spite of this, there is currently no antiviral drug/ vaccine available against coronavirus infection, COVID-19. In the present study, computer-aided drug design-based screening to find out promising inhibitors against the coronavirus (SARS-CoV-2) leads to infection, COVID-19. The lead therapeutic molecule was investigated through docking and molecular dynamics simulations. In this, binding affinity of noscapines(23B)-protease of SARS-CoV-2 complex was evaluated through MD simulations at different temperatures. Our research group has established that noscapine is a chemotherapeutic agent for the treatment of drug resistant cancers; however, noscapine was also being used as anti-malarial, anti-stroke and cough-suppressant. This study suggests for the first time that noscapine exerts its antiviral effects by inhibiting viral protein synthesis.

Rhamnolipid the Glycolipid Biosurfactant: Emerging trends and promising strategies in the field of biotechnology and biomedicine.

Abstract: Rhamnolipids (RLs) are surface-active compounds and belong to the class of glycolipid biosurfactants, mainly produced from Pseudomonas aeruginosa. Due to their non-toxicity, high biodegradability, low surface tension and minimum inhibitory concentration values, they have gained attention in various sectors like food, healthcare, pharmaceutical and petrochemicals. The ecofriendly biological properties of rhamnolipids make them potent materials to be used in therapeutic applications. RLs are also known to induce apoptosis and thus, able to inhibit proliferation of cancer cells. RLs can also act as immunomodulators to regulate the humoral and cellular immune systems. Regarding their antimicrobial property, they lower the surface hydrophobicity, destruct the cytoplasmic membrane and lower the critical micelle concentration to kill the bacterial cells either alone or in combination with nisin possibly due to their role in modulating outer membrane protein. RLs are also involved in the synthesis of nanoparticles for in vivo drug delivery. In relation to economic benefits, the post-harvest decay of food can be decreased by RLs because they prevent the mycelium growth, spore germination of fungi and inhibit the emergence of biofilm formation on food. The present review focuses on the potential uses of RLs in cosmetic, pharmaceutical, food and health-care industries as the potent therapeutic agents.

Towards Precision Agriculture: IoT-Enabled Intelligent Irrigation Systems Using Deep Learning Neural Network

Abstract: Recently, precision agriculture has gained substantial attention due to the ever-growing world population demands for food and water. Consequently, farmers will need water and arable land to meet this demand. Due to the limited availability of both resources, farmers need a solution that changes the way they operate. Precision irrigation is the solution to deliver bigger, better, and more profitable yields with fewer resources. Several machine learning-based irrigation models have been proposed to use water more efficiently. Due to the limited learning ability of these models, they are not well suited to unpredictable climates. In this context, this paper proposes a deep learning neural network-based Internet of Things (IoT)-enabled intelligent irrigation system for precision agriculture (DLiSA). This is a feedback integrated system that keeps its functionality better in the weather of any region for any period of time. DLiSA utilizes a long short-term memory network (LSTM) to predict the volumetric soil moisture content for one day ahead, irrigation period, and spatial distribution of water required to feed the arable land. It is evident from the simulation results that DLiSA uses water more wisely than state-of-the-art models in the experimental farming area.

Ant Colony Optimization Based Quality of Service Aware Energy Balancing Secure Routing Algorithm for Wireless Sensor Networks

Abstract: Existing routing protocols for wireless sensor networks (WSNs) focus primarily either on energy efficiency, quality of service (QoS), or security issues. However, a more holistic view of WSNs is needed, as many applications require both QoS and security guarantees along with the requirement of prolonging the lifetime of the network. The limited energy capacity of sensor nodes forces a tradeoff to be made between network lifetime, QoS, and security. To address these issues, an ant colony optimization based QoS aware energy balancing secure routing (QEBSR) algorithm for WSNs is proposed in this article. Improved heuristics for calculating the end-to-end delay of transmission and the trust factor of the nodes on the routing path are proposed. The proposed algorithm is compared with two existing algorithms: distributed energy balanced routing and energy efficient routing with node compromised resistance. Simulation results show that the proposed QEBSR algorithm performed comparatively better than the other two algorithms.

Molecular mechanisms of salinity tolerance in rice

Abstract: Salinity is one of the major abiotic stresses which impose constraints to plant growth and production. Rice (Oryza sativa L.) is one of the most important staple food crops and a model monocot plant. Its production is expanding into regions that are affected by soil salinity, requiring cultivars more tolerant to saline conditions. Understanding the molecular mechanisms of such tolerance could lay a foundation for varietal improvement of salt tolerance in rice. In spite of extensive studies exploring the mechanism of salt tolerance, there has been limited progress in breeding for increased salinity tolerance. In this review, we summarize the information about the major molecular mechanisms underlying salinity tolerance in rice and further discuss the limitations in breeding for salinity tolerance. We show that numerous gene families and interaction networks are involved in the regulation of rice responses to salinity, prompting a need for a comprehensive functional analysis. We also show that most studies are based on whole-plant level analyses with only a few reports focused on tissue- and/or cell-specific gene expression. More details of salt-responsive channel and transporter activities at tissue- and cell-specific level still need to be documented before these traits can be incorporated into elite rice germplasm. Thus, future studies should focus on diversity of available genetic resources and, particular, wild rice relatives, to re-incorporate salinity tolerance traits lost during domestication.

Gendering COVID-19: Impact of the Pandemic on Women's Burden of Unpaid Work in India.

Abstract: The COVID-19 pandemic has exacerbated the already existing gender inequalities with substantial implications on women. With the closure of offices and educational institutions, and the emerging norm of work from home and online education, along with the lack of services of domestic worker, the need to perform unpaid chores in the household has increased. Simultaneously, the requirements of social distancing and sanitization have created new unpaid chores. Owing to the sexual division of labour, and gendered roles and social norms of performing domestic and care work, the burden of unpaid work falls disproportionately on women. In this context, the objective of the paper is to study the impact of COVID-19 on time spent on unpaid work and the underlying gender differences in the urban centres in India. Specifically, the paper will do a comparative analysis of the gender differences in time spent on unpaid work before and during the lockdown, and analyse the reasons for the same.

Glaciohydrology of the Himalaya-Karakoram.

Abstract: Understanding the response of Himalayan-Karakoram (HK) rivers to climate change is crucial for ~1 billion people who partly depend on these water resources. Policy-makers tasked with sustainable water resources management require an assessment of the rivers' current status and potential future changes. We show that glacier and snow melt are important components of HK rivers, with greater hydrological importance for the Indus basin than for the Ganges and Brahmaputra basins. Total river runoff, glacier melt, and seasonality of flow are projected to increase until the 2050s, with some exceptions and large uncertainties. Critical knowledge gaps severely affect modeled contributions of different runoff components, future runoff volumes, and seasonality. Therefore, comprehensive field observation-based and remote sensing-based methods and models are needed.

Supernova neutrino burst detection with the Deep Underground Neutrino Experiment

Abstract: The Deep Underground Neutrino Experiment (DUNE), a 40-kton underground liquid argon time projection chamber experiment, will be sensitive to the electron-neutrino flavor component of the burst of neutrinos expected from the next Galactic core-collapse supernova. Such an observation will bring unique insight into the astrophysics of core collapse as well as into the properties of neutrinos. The general capabilities of DUNE for neutrino detection in the relevant few- to few-tens-of-MeV neutrino energy range will be described. As an example, DUNE's ability to constrain the $ u_e$ spectral parameters of the neutrino burst will be considered.

A Novel Method of Using Bifilar Spiral Resonator for Designing Thin Robust Flexible Glucose Sensors

Abstract: Nowadays, robust sensors for glucose-sensing application are almost a necessity for every diabetic individual. In this work, a (20 mm $\times10$ mm) contact-based sensor has been successfully realized on a thin and flexible polyamide substrate, with the sensing area being a bifilar spiral resonator (BSR). The proposed sensor was based on detecting resonance frequencies shifts at ultrahigh frequencies (UHFs) as a result of changes in the glucose concentration. The BSR acts as a cascaded metasurface which, at around the resonant frequency, forms a plasmon dispersion at the interface between a glucose solution and the BSR. An empirical formula has been developed to express the sensing sensitivity as a function of the loss factor, the oscillator strengths and the steady state permittivity. The model has been experimentally validated with an in vitro measurement on an aqueous glucose solution and an ex-vivo measurement on a serum blood solution. The measured results suggest that there exists a positive and linear correlation between glucose concentration and the resonant frequency shift within the clinical diabetic range. The sensor sensitivity was 250 megahertz (MHz)/(mg/mL) for the aqueous glucose solution and 130 MHz/(mg/mL) for the serum blood along with a $Q$ -factor of 20. Overall, the measured results were highly consistent with our theoretical expectation. Moreover, the proposed sensor was highly resistant to bending losses.

Silver Nanoparticles Synthesized Using Carica papaya Leaf Extract (AgNPs-PLE) Causes Cell Cycle Arrest and Apoptosis in Human Prostate (DU145) Cancer Cells

Abstract: Treatment of cancer has been limited by the poor efficacy and toxicity profiles of available drugs There is a growing demand to develop alternative approaches to combat cancer such as use of nano-formulation-based drugs Here, we report biosynthesis and characterization of silver nanoparticles (AgNPs) with papaya leaf extract (PLE) and its anti-cancer properties against different human cancer cells Purified nanoparticles were characterized by standard techniques, such as TEM, STM, SEM, EDS, XRD, and FTIR Furthermore, cytotoxic activity of AgNPs-PLE was carried out against different human cancer cells and non-tumorigenic human keratinocytes cells AgNPs-PLE when compared with AgNPs-citric acid or PLE showed better efficacy against cancer cells and was also relatively less toxic to normal cells Treatment of DU145 cells with AgNPs-PLE (05–50 μg/ml) for 24–48 h lowered total cell number by 24–36% (P < 005) Inhibition of cell growth was linked with arrest of cell cycle at G2/M phase at 24 h, while G1 and G2/M phase arrests at 48 h ROS production was observed at earlier time points in presence of AgNPs-PLE, suggesting its role behind apoptosis in DU145 cells Induction of apoptosis (57%) was revealed by AO/EB staining in DU145 cells along with induction of Bax, cleaved caspase-3, and cleaved PARP proteins G1-S phase cell cycle check point marker, cyclin D1 was down-regulated along with an increase in cip1/p21 and kip1/p27 tumor suppressor proteins by AgNPs-PLE These findings suggest the anti-cancer properties of AgNPs-PLE

Climate-resilient strategies for sustainable management of water resources and agriculture

Abstract: Warming of the earth is considered as the major adverse effect of climate change along with other abnormalities such as non-availability of water resources, decreased agriculture production, food security, rise in seawater level, glaciers melting, and loss of biodiversity. Over the years, decreased agriculture production and water quality degradation have been observed due to climatic abnormalities. Crop production is highly sensitive to climate. It gets affected by long-term trends in average rainfall and temperature, annual climate variations, shocks during different stages of growth, and extreme weather events. Globally, the areas sown for the major crops of barley, maize, rice, sorghum, soya bean, and wheat have all seen an increase in the percentage of area affected by drought as defined in terms of the Palmer Drought Severity Index since the 1960s, from approximately 5-10% to approximately 15-25%. Increase in temperature will be observed in terms of wheat yield losses - 5.5 ± 4.4% per degree Celsius for the United States, - 9.1 ± 5.4% per degree Celsius for India, and - 7.8 ± 6.3% per degree Celsius for Russia as these countries are more vulnerable to temperature increase. Water management through increasing storage capacity (or rainwater storage), fair policies for water supply and distribution, river health, and watershed management can reduce the negative effects of climate change on water resource availability. Similarly, climate change-resistant crop development, water management in irrigation, adapting climate-smart agriculture approach, and promoting indigenous knowledge can ensure the food security via increasing agricultural yield. Technical intervention can equip the farmers with the scientific analyses of the climatic parameters required for the sustainable agriculture management. These technologies may include application of software, nutrient management, water management practices, instruments for temperature measurement and soil health analysis etc. Holistic efforts of the stakeholders (farmers, local society, academia, scientists, policy makers, NGOs etc.) can provide better results to reduce the risks of climate change on agriculture and water resources as discussed in this paper. Graphical abstract.

From ‘Chinky’ to ‘Coronavirus’: racism against Northeast Indians during the Covid-19 pandemic

Abstract: The outbreak of Covid-19 has been highly racialised and stigmatised around the world based on the origin of the virus and its highly infectious nature. Profiling of Asians or mongoloid looking indi...

Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach.

Abstract: The global pandemic crisis, coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed the lives of millions of people across the world. Development and testing of anti-SARS-CoV-2 drugs or vaccines have not turned to be realistic within the timeframe needed to combat this pandemic. Here, we report a comprehensive computational approach to identify the multi-targeted drug molecules against the SARS-CoV-2 proteins, whichare crucially involved in the viral-host interaction, replication of the virus inside the host, disease progression and transmission of coronavirus infection. Virtual screening of 75 FDA-approved potential antiviral drugs against the target proteins, spike (S) glycoprotein, human angiotensin-converting enzyme 2 (hACE2), 3-chymotrypsin-like cysteine protease (3CLpro), cathepsin L (CTSL), nucleocapsid protein, RNA-dependent RNA polymerase (RdRp) and non-structural protein 6 (NSP6), resulted in the selection of seven drugs which preferentially bind to the target proteins. Further, the molecular interactions determined by molecular dynamics simulation revealed that among the 75 drug molecules, catechin can effectively bind to 3CLpro, CTSL, RBD of S protein, NSP6 and nucleocapsid protein. It is more conveniently involved in key molecular interactions, showing binding free energy (ΔGbind) in the range of -5.09 kcal/mol (CTSL) to -26.09 kcal/mol (NSP6). At the binding pocket, catechin is majorly stabilized by the hydrophobic interactions, displays ΔEvdW values: -7.59 to -37.39 kcal/mol. Thus, the structural insights of better binding affinity and favorable molecular interaction of catechin toward multiple target proteins signify that catechin can be potentially explored as a multi-targeted agent against COVID-19.