RNA's Dynamic Conformational Selection and Entropic Allosteric Mechanism in Controlling Cascade Protein Binding Events.

In the TAR RNA of immunodeficiency viruses, an allosteric communication exists between a distant loop and a bulge. The bulge interacts with the TAT protein vital for transactivating viral RNA, while the loop interacts with cyclin-T1, contingent on TAT binding. Through extensive atomistic and free energy simulations, we investigate TAR-TAT binding in nonpathogenic bovine immunodeficiency virus (BIV) and pathogenic human immunodeficiency virus (HIV).

Hierarchical Hydration Dynamics of RNA with Nano-Water-Pool at Its Core.

Many functional RNAs fold into a compact, roughly globular shape by minimizing the electrostatic repulsion between their negatively charged phosphodiester backbone. The fold of such close, compact RNA architecture is often so designed that its outer surface and complex core both are predominately populated by phosphate groups loosely sequestering bases in the intermediate layers. A number of helical junctions maintain the RNA core and its nano-water-pool.

Quantifying Mutational Response to Track the Evolution of SARS-CoV-2 Spike Variants: Introducing a Statistical-Mechanics-Guided Machine Learning Method.

The emergence of SARS-CoV-2 and its variants that critically affect global public health requires characterization of mutations and their evolutionary pattern from specific Variants of Interest (VOIs) to Variants of Concern (VOCs). Leveraging the concept of equilibrium statistical mechanics, we introduce a new responsive quantity defined as "Mutational Response Function (MRF)" aptly quantifying domain-wise average entropy-fluctuation in the spike glycoprotein sequence of SARS-CoV-2 based on its evolutionary database. As the evolution transits from a specific variant to VOC, we find that the evolutionary crossover is accompanied by a dramatic change in MRF, upholding the characteristic of a dynamic phase transition.

Diurnal and Seasonal Variation of Atmospheric Particulate Matter and Trace Gases in Industrial Area of Delhi: A Study.

The diurnal and seasonal variation of PM, SO, NO, NH and water-soluble compounds were studied in Naraina industrial area; Delhi from January to December, 2017. It was observed that annual average concentrations of PM SO, NO, NH SO, NO, NH,Na, K, Ca, Mg, Cl and F in the day time were 227 ± 91, 9 ± 5, 59 ± 22, 65 ± 15, 17.45 ± 5.

Regional scenario of air pollution in lockdown due to COVID-19 pandemic: Evidence from major urban agglomerations of India.

Air pollution in India during COVID-19 lockdown, which imposed on 25th March to 31st May 2020, has brought a significant improvement in air quality. The present paper mainly focuses on the scenario of air pollution level (PM, PM, SO, NO and O) across 57 urban agglomerations (UAs) of India during lockdown. For analysis, India has been divided into six regions - Northern, Western, Central, Southern, Eastern and North-Eastern.

Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions.

Canonically, protein β-hairpin motifs are stabilized by intramolecular hydrogen bonds. Here, we attempt to develop a rational design recipe for a miniature hairpin structure stabilized by hydrogen bonding as well as C-H···π interaction and try to understand how such a stabilization effect varies with different functional groups at each terminus. Database analysis shows that the α-amino acids with an aromatic side chain will not favor that kind of C-H···π stabilized hairpin structure.

Raising the Age of Purchase and Use of Tobacco Product in Bangladesh: Benefits and Challenges in Protecting Youth from the Tobacco Epidemic.

Background: Tobacco use among young and adolescents is the biggest threat to public health globally. In Bangladesh, every one in 14 youth (13-15 years) uses tobacco in some form. While this problem is growing in the country, we estimate the underage initiation of tobacco use and present evidence that policy measures like increasing the age of purchase and use from the current 18 years to 21 years in the country backed with current tobacco control efforts and adopting vendor licensing will significantly reduce future tobacco burden.

Correlation in Domain Fluctuations Navigates Target Search of a Viral Peptide along RNA.

Biological macromolecules often exhibit correlations in fluctuations involving distinct domains. This study decodes their functional implications in RNA-protein recognition and target-specific binding. The target search of a peptide along RNA in a viral TAR-Tat complex is closely monitored using atomistic simulations, steered molecular dynamics simulations, free energy calculations, and a machine-learning-based clustering technique.

Exploring short term spatio-temporal pattern of PM and PM and their relationship with meteorological parameters during COVID-19 in Delhi.

Present study aims to examine the impact of lockdown on spatio-temporal concentration of PM and PM categorized and recorded based on its levels during pre-lockdown, lockdown and unlock phases while noting the relationship of these levels with meteorological parameters (temperature, wind speed, relative humidity, rainfall, pressure, sun hour and cloud cover) in Delhi. To aid the study, a comparison was made with the last two years (2018 to 2019), covering the same periods of pre-lockdown, lockdown and unlock phases of 2020. Correlation analysis, linear regression (LR) was used to examine the impact of meteorological parameters on particulate matter (PM) concentrations in Delhi, India.

Habitat vulnerability in slum areas of India - What we learnt from COVID-19?

UN-Habitat identified the present COVID-19 pandemic as 'city-centric'. In India, more than 50% of the total cases were documented in megacities and million-plus cities. The slums of cities are the most vulnerable due to its unhygienic environment and high population density that requires an urgent implementation of public healthcare measures.

Measuring landslide vulnerability status of Chukha, Bhutan using deep learning algorithms.

Landslides are major natural hazards that have a wide impact on human life, property, and natural environment. This study is intended to provide an improved framework for the assessment of landslide vulnerability mapping (LVM) in Chukha Dzongkhags (district) of Bhutan. Both physical (22 nos.

Chelated Magnesium Logic Gate Regulates Riboswitch Pseudoknot Formation.

Magnesium plays a critical role in the structure, dynamics, and function of RNA. The precise microscopic effect of chelated magnesium on RNA structure is yet to be explored. Magnesium is known to act through its diffuse cloud around RNA, through the outer sphere (water-mediated), inner sphere, and often chelated ion-mediated interactions.

Examining the impact of lockdown (due to COVID-19) on ambient aerosols (PM): A study on Indo-Gangetic Plain (IGP) Cities, India.

The outbreak of COVID-19 pandemic has impacted all the aspects of environment. The numbers of COVID-19 cases and deaths are increasing across the globe. In many countries lockdown has been imposed at local, regional as well as national level to combat with this global pandemic that caused the improvement of air quality.

Dynamic Asymmetry Exposes 2019-nCoV Prefusion Spike.

The novel coronavirus (2019-nCoV) spike protein is a smart molecular machine that instigates the entry of coronavirus to the host cell causing the COVID-19 pandemic. In this study, a symmetry-information-loaded structure-based Hamiltonian is developed using recent Cryo-EM structural data to explore the complete conformational energy landscape of the full-length prefusion spike protein. The study finds the 2019-nCoV prefusion spike to adopt a unique strategy by undertaking a dynamic conformational asymmetry that results in two prevalent asymmetric structures of spike where one or two spike heads rotate up to provide better exposure to the host-cell receptor.