<p>Shiv Nadar University is a comprehensive, multidisciplinary, research-focused, and student-centric University offering a full range of academic programs at the undergraduate, postgraduate and doctoral level. With state-of-the-art infrastructure, the University comprises of academic wings, sophisticated labs, international standard sports facilities, amphitheaters, auditorium, conference rooms and smart classrooms. The University&rsquo;s goal is to become internationally recognized for the quality of its research and creative endeavors and their applicability to improving quality of life, generating new insights and expanding the boundaries of human knowledge creativity. Committed to excellence in teaching, research and service, the University aims to serve the higher education needs of India and the world beyond.</p>

Shiv Nadar University

(SoNS) School of Natural Sciences

Pulp and paper industry generates large wastewater volumes containing recalcitrant and toxic compounds in various forms. These compounds are highly toxic and standard primary/secondary treatments are unable to filter heavy metal contaminants besides organic species. An emerging demand of advance level treatment is the motivation of current work that explores possibility of using thick sand of deep aquifers as an adsorbent to remove inorganic and organic contaminants simultaneously from wastewater besides desalination. Popular ultrasonic cavitation is used to accelerate degradation of toxic organic effluent into less toxic open ring structures besides curing heavy metals to form new bonds during adsorption. Because of extreme local environment due to cavitation, heavy metals coagulate in silicon-aluminum atomic meshes and carbon nano tubes for less toxic new crystalline structure. Significant changes in physico-chemical investigations like pH, chemical oxygen demand and colour towards drinkable water standards indicate effective adsorption resulting into wastewater purification. © 2019

Chemical Engineering

(SoE) School of Engineering

Physics

Colloids and Surfaces A: Physicochemical and Engineering Aspects

Ultrasonic cavitation tailored wastewater purification and desalination using thick sand of highly permeable deep aquifer

World University root node

Mathematics

International Game Theory Review

Preface to the Special Issue on-Operations Research and Game Theory: Modeling and Computation

MicroRNAs (miRNAs) and transcription factors (TFs) are the largest families of trans-acting gene regulatory species, which are pivotal players in a complex regulatory network. Recently, extensive research on miRNAs and TFs in agriculture has identified these trans-acting regulatory species, as an effective tool for engineering new crop cultivars to increase yield and quality as well tolerance to environmental stresses but our knowledge of regulatory network is still not sufficient to decipher the exact mechanism. In the current work, stress-specific TF-miRNA-gene network was built for Arabidopsis under drought, cold, salt and waterlogging stress using data from reliable publically available databases; and transcriptome and degradome sequence data analysis by meta-analysis approach. Further network analysis elucidated significantly dense, scale-free, small world and hierarchical backbone of interactions. The various centrality measures highlighted several genes/TF/miRNAs as potential targets for tolerant variety cultivation. This comprehensive regulatory information will accelerate the advancement of current understanding on stress specific transcriptional and post-transcriptional regulatory mechanism and has promising utilizations for experimental biologist who are intended to improve plant crop performance under multiple Abiotic stress environments. © 2019

Life Sciences

Fulltext

Genomics

Abiotic stress induced miRNA-TF-gene regulatory network: A structural perspective

A recent surge in finding new candidate vaccines and potential antivirals to tackle atypical pneumonia triggered by the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) needs new and unexplored approaches in solving this global pandemic. The homotrimeric transmembrane spike (S) glycoprotein of coronaviruses which facilitates virus entry into the host cells is covered with N-linked glycans having oligomannose and complex sugars. These glycans provide a unique opportunity for their targeting via carbohydrate-binding agents (CBAs) which have shown their antiviral potential against coronaviruses and enveloped viruses. However, CBA–ligand interaction is not fully explored in developing novel carbohydrate-binding-based antivirals due to associated unfavorable responses with CBAs. CBAs possess unique carbohydrate-binding specificity, therefore, CBAs like mannose-specific plant lectins/lectin-like mimic Pradimicin-A (PRM-A) can be used for targeting N-linked glycans of S glycoproteins. Here, we report studies on the binding and stability of lectins (NPA, UDA, GRFT, CV-N and wild-type and mutant BanLec) and PRM-A with the S glycoprotein glycans via docking and MD simulation. MM/GBSA calculations were also performed for docked complexes. Interestingly, stable BanLec mutant (H84T) also showed similar docking affinity and interactions as compared to wild-type BanLec, thus, confirming that uncoupling the mitogenic activity did not alter the lectin binding activity of BanLec. The stability of the docked complexes, i.e. PRM-A and lectins with SARS-CoV-2 S glycoprotein showed favorable intermolecular hydrogen-bond formation during the 100 ns MD simulation. Taking these together, our predicted in silico results will be helpful in the design and development of novel CBA-based antivirals for the SARS-CoV-2 neutralization. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.

Journal of Biomolecular Structure and Dynamics

Sensing the interactions between carbohydrate-binding agents and N-linked glycans of SARS-CoV-2 spike glycoprotein using molecular docking and simulation studies

Background/Objective: There is a paucity of data on the management of gastrointestinal (GI) bleeding in patients with Coronavirus disease -2019 (COVID-19) amid concerns about the risk of transmission during endoscopic procedures. We aimed to study the outcomes of conservative treatment for GI bleeding in patients with COVID-19. Methods: In this retrospective analysis, 24 of 1342 (1.8%) patients with COVID-19, presenting with GI bleeding from 22nd April to 22nd July 2020, were included. Results: The mean age of patients was 45.8 ± 12.7 years; 17 (70.8%) were males; upper GI (UGI) bleeding: lower GI (LGI) 23:1. Twenty-two (91.6%) patients had evidence of cirrhosis- 21 presented with UGI bleeding while one had bleeding from hemorrhoids. Two patients without cirrhosis were presumed to have non-variceal bleeding. The medical therapy for UGI bleeding included vasoconstrictors-somatostatin in 17 (73.9%) and terlipressin in 4 (17.4%) patients. All patients with UGI bleeding received proton pump inhibitors and antibiotics. Packed red blood cells (PRBCs), fresh frozen plasma (FFPs) and platelets were transfused in 14 (60.9%), 3 (13.0%) and 3 (13.0%), respectively. The median PRBCs transfused was 1 (0–3) unit(s). The initial control of UGI bleeding was achieved in all 23 patients and none required an emergency endoscopy. At 5-day follow-up, none rebled or died. Two patients later rebled, one had intermittent bleed due to gastric antral vascular ectasia, while another had rebleed 19 days after discharge. Three (12.5%) cirrhosis patients succumbed to acute hypoxemic respiratory failure during hospital stay. Conclusion: Conservative management strategies including pharmacotherapy, restrictive transfusion strategy, and close hemodynamic monitoring can successfully manage GI bleeding in COVID-19 patients and reduce need for urgent endoscopy. The decision for proceeding with endoscopy should be taken by a multidisciplinary team after consideration of the patient's condition, response to treatment, resources and the risks involved, on a case to case basis. © 2020 Indian National Association for Study of the Liver

Journal of Clinical and Experimental Hepatology

Outcome of Conservative Therapy in Coronavirus disease-2019 Patients Presenting With Gastrointestinal Bleeding

The aluminum industrial waste red mud was successfully utilized as a novel adsorbent for the removal of arsenic (As) ions from water. The arsenate (As (V)) adsorption efficacy of red mud nanoparticles was also investigated. Red mud nanoparticles were prepared by ball milling raw red mud for 10 h, yielding particles’ size of 20 nm on average. The As (V) adsorption on these nanoparticles strongly depended on the size of the nanoparticles. As (V) removal increased from 58 to 83\% by reducing the size of red mud particles from 200 to 20 nm. Detail kinetics and transport study confirmed the pseudo-second-order kinetic process which was governed by external mass transport. The Freundlich (and Langmuir) isotherms confirm that the arsenate adsorption capacity changes from 2.28 mg/g (1.84 mg/g) to 2.54 mg/g (1.96 mg/g) for reduction of particles from size 200 nm to 20 nm. Water filter columns made with red mud nanoparticles prepared by ball milling for 10 h showed better filtration performance than the filter packed with raw red mud. Both the hydraulic conductivity and the As (V) removal (8 mm/h and 61\% respectively) of influent 1 mg/L As (V) by red mud nanoparticles were greater than the raw red mud (3.2 mm/h and 54\%). The modified red mud column filters also exhibited a higher efficiency than the raw red mud filters to remove Escherichia coli and Staphylococcus aureus from the water. Overall, this research shows that nanomaterials derived from aluminum processing waste can be a promising material for water filtration. © 2020, Springer Nature Switzerland AG.

SN Applied Sciences

Potential use of smartly engineered red mud nanoparticles for removal of arsenate and pathogens from drinking water

Chemistry

Stereochemical Control of the Triflate Mediated Intramolecular Schmidt Reaction

Primary cardiac neoplasms are extremely rare and are far outnumbered by metastases. These are difficult to diagnose and differentiate clinically due to lack of specific clinical manifestations. Technological advances have revolutionised cardiac imaging, with the cardiac magnetic resonance imaging (CMRI) showing promising results in the non-invasive evaluation of cardiac masses. Further, CMRI may envisage the malignant potential of a lesion based on its location, morphology, and signal characteristics, in addition to determining its impact on cardiac function. With the ever-increasing application of CMRI in the evaluation of neoplasms, comprehensive knowledge of their imaging characteristics becomes crucial. © 2019 The Royal College of Radiologists

Clinical Radiology

Cardiac MRI for the evaluation of cardiac neoplasms

Scaffold proteins play pivotal role as modulators of cellular processes by operating as multipurpose conformation clamps. 14-3-3 proteins are gold-standard scaffold modules that recognize phosphoSer/Thr (pS/pT) containing conserved motifs, and confer conformational changes leading to modulation of functional parameters of their target proteins. Modulation in functional activity of kinases has been attributed to their interaction with 14-3-3 proteins. Herein, we have annotated and characterized PF3D7_0818200 as 14-3-3 isoform I in Plasmodium falciparum 3D7, and its interaction with one of the key kinases of the parasite, Calcium-Dependent Protein Kinase 1 (CDPK1) by performing various analytical biochemistry and biophysical assays. Molecular dynamics simulation studies indicated that CDPK1 polypeptide sequence (61KLGpS64) behaves as canonical Mode I-type (RXXpS/pT) consensus 14-3-3 binding motif, mediating the interaction. The 14-3-3I/CDPK1 interaction was validated in vitro with ELISA and SPR, which confirmed that the interaction is phosphorylation dependent, with binding affinity constant of 670 ± 3.6 nM. The interaction of 14-3-3I with CDPK1 was validated with well characterized optimal 14-3-3 recognition motifs: Mode I-type ARSHpSYPA and Mode II-type RLYHpSLPA, by simulation studies and ITC. This interaction was found to marginally enhance CDPK1 functional activity. Furthermore, interaction antagonizing peptidomimetics showed growth inhibitory impact on the parasite indicating crucial physiological role of 14-3-3/CDPK1 interaction. Overall, this study characterizes 14-3-3I as a scaffold protein in the malaria parasite and unveils CDPK1 as its previously unidentified target. This sets a precedent for the rational design of 14-3-3 based PPI inhibitors by utilizing 14-3-3 recognition motif peptides, as a potential antimalarial strategy. © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society

Biochemical Journal

Molecular dynamics simulations and biochemical characterization of Pf14-3-3 and PfCDPK1 interaction towards its role in growth of human malaria parasite

Upon Plasmodium falciparum merozoites exposure to low [K+] environment in blood plasma, there is escalation of cytosolic [Ca2+] which activates Ca2+-Dependent Protein Kinase 1 (CDPK1), a signaling hub of intra-erythrocytic proliferative stages of parasite. Given its high abundance and multidimensional attributes in parasite life-cycle, this is a lucrative target for designing antimalarials. Towards this, we have virtually screened MyriaScreenII diversity collection of 10,000 drug-like molecules, which resulted in 18 compounds complementing ATP-binding pocket of CDPK1. In vitro screening for toxicity in mammalian cells revealed that these compounds are non-toxic in nature. Furthermore, SPR analysis demonstrated differential binding affinity of these compounds towards recombinantly purified CDPK1 protein. Selection of lead compound 1 was performed by evaluating their inhibitory effects on phosphorylation and ATP binding activities of CDPK1. Furthermore, in vitro biophysical evaluations by ITC and FS revealed that binding of compound 1 is driven by formation of energetically favorable non-covalent interactions, with different binding constants in presence and absence of Ca2+, and TSA authenticated stability of compound 1 bound CDPK1 complex. Finally, compound 1 strongly inhibited intra-erythrocytic growth of P. falciparum in vitro. Conceivably, we propose a novel CDPK1-selective inhibitor, step towards developing pan-CDPK kinase inhibitors, prerequisite for cross-stage anti-malarial protection. © 2020 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society

Development of novel anti-malarial from structurally diverse library of molecules, targeting plant-like CDPK1, a multistage growth regulator of P. falciparum