Vellore Institute of Technology (VIT) is a private university located in&nbsp;Tamil Nadu, India. Founded in 1984, as Vellore Engineering College, the institution offers 20 undergraduate, 34 postgraduate, four integrated and four research programs. It has campuses in Vellore, Amravati, Bhopal and Chennai.

VIT is one of the top ranked private universities in India according to NIRF, THE and QS Rankings.&nbsp;Govt. of India has recognized&nbsp;VIT, Vellore as an&nbsp;Institution of Eminence. This has allowed VIT to take independent quality initiatives and move up in world ranking.

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VIT University

Department of Biotechnology

Krabbe disease (KD), also known as globoid cell leukodystrophy disease, is an autosomal recessive lysosomal storage genetic disorder, which is caused by the deficiency of galactocerebrosidase (GALC) coding gene (GALC). This study aimed to use extensive computational pipelines in understanding the missense mutations in GALC. We retrieved 176 mutations from the public databases and subjected them to pathogenicity, stability, and conservation analyses. The PredictSNP, iStable, and ConSurf prediction tools predicted 45, 95, and 47 mutations to be deleterious, destabilizing, and highly conserved, respectively. The R396L and R396W were the most deleterious and destabilizing to GALC, and were therefore prioritized for further analysis. Systematic validation on the impact of the R396L and R396W mutations to the chaperone alpha lobeline was performed using the molecular docking approach. The docking analysis revealed that the mutant R396W interacted with minimal binding affinity compared with both the R396L mutant and native GALC. Furthermore, the repetitive molecular dynamics simulation analysis showed that the mutant R396W demonstrated less compactness and reduced number of intramolecular hydrogen bonds compared with the mutant R396L and the native GALC. Overall, we observed higher structural and functional modifications in R396W positioned in the substrate-binding site. This was highly supported by the MMPBSA and DSSP analysis of the GROMACS. DSSP showed the transformation of turns to bends, indicating a loss of stability due to the R396W mutation. This study is expected to serve as a platform for prioritizing mutant proteins that could be a platform for both drug and target therapeutics Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor &amp; Francis Group.

World University root node

School of Bio Sciences and Technology

Vellore Campus

Department of Integrative Biology

Journal of Biomolecular Structure and Dynamics

Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe’s disease

Globally, waste electrical and electronic equipment is one of the fastest-growing waste sectors. Mobile phones constitute the major portion of the telecommunication e-waste category. Over the years, waste mobile phones were considered as a potential source of secondary metals. This study aims to determine the physical and chemical composition of the discarded mobile phones and to evaluate its recovery potential. The printed circuit boards from the discarded (waste) mobile phones (MPCB) were collected and samples of different sizes 3 × 3 cm, 2 mm, 1 mm, 500 µm, and 150 µm were obtained after milling and sieving. Elemental composition revealed the presence of base metals, Cu, Zn, Fe, Ni, and Pb, in higher quantities with a significant amount of precious metals Au and Ag. Amount of base metals present in different MPCB size fractions was found in the order 3 × 3 cm > 2 mm > 1 mm > 500 µm >150 µm. The amount of precious metals like Ag and Au was found to be higher in large-sized MPCB fractions. FTIR studies declared the presence of polymers like ABS, PC, and HIPs in MPCB samples. TCLP tests for toxic metals revealed that MPCBs contained high concentrations of cadmium, lead, and mercury highlighting their hazardous potential. The ultimate analysis revealed that NMF has a GCV of 12.34 MJ/kg and a volatile content of 42.25%, which can be a potential source of energy that can be recovered through the gasification or pyrolysis process. Overall, the comprehensive characterization of waste MPCBs will systematically provide a better understanding of e-waste recycling processes for beneficiation purpose and sustainable resource utilization. Implications: A comprehensive characterization of waste mobile phone printed circuit boards for its elemental composition was performed. Mechanical treatment steps before MPCBs processing increased the exposure of metals resulting in a higher concentration of metals in acid-digested samples. The elemental analysis of MPCBs revealed that MPCBs possessed significant quantities of base and precious metals. The amount of precious metals like Ag and Au was also found in higher ranges in large-sized MPCB fractions, which elucidated fact to be considered in the pre-treatment process for metal recoveries. The high content of base and precious metals in waste mobile phones displayed their economic potential in the market. This new source may compensate for the escalating global demand for gold and silver. Results from the study indicated that MPCBs can serve as an excellent secondary source for various metals and as an efficient alternative fuel. © 2021 A&WMA.

Journal of the Air and Waste Management Association

Characterization of end-of-life mobile phone printed circuit boards for its elemental composition and beneficiation analysis

Initial phase of COVID-19 infection is associated with the binding of viral spike protein S1 receptor binding domain (RBD) with the host cell surface receptor, ACE2. Peptide inhibitors typically interact with spike proteins in order to block its interaction with ACE2, and this knowledge would promote the use of such peptides as therapeutic scaffolds. The present study examined the competitive inhibitor activity of a broad spectrum antimicrobial peptide, Dermaseptin-S4 (S4) and its analogues. Three structural S4 analogues viz., S4 (K4), S4 (K20) and S4 (K4K20) were modelled by substituting charged lysine for non-polar residues in S4 and subsequently, docked with S1. Further, the comparative analysis of inter-residue contacts and non-covalent intermolecular interactions among S1–S4 (K4), S1–S4 (K4K20) and S1–ACE2 complexes were carried out to explore their mode of binding with S1. Interestingly, S1–S4 (K4) established more inter-molecular interactions compared to S4 (K4K20) and S1–ACE2. In order to substantiate this study, the normal mode analysis (NMA) was conducted to show how the structural stability of the flexible loop region in S1 is affected by atomic displacements in unbound S1 and docked complexes. Markedly, the strong interactions consistently maintained by S1–S4 (K4) complex revealed their conformational transition over the harmonic motion period. Moreover, S1–S4 (K4) peptide complex showed a higher energy deformation profile compared to S1–S4 (K4K20), where the higher energy deformation suggests the rigidity of the docked complex and thus it’s harder deformability, which is also substantiated by molecular dynamics simulation. In conclusion, S1–S4 (K4) complex has definitely exhibited a functionally significant dynamics compared to S1–ACE2 complex; this peptide inhibitor, S4 (K4) will need to be considered as the best therapeutic scaffold to block SARS-CoV-2 infection. © 2021, The Author(s), under exclusive licence to Springer Nature B.V. part of Springer Nature.

Fulltext

International Journal of Peptide Research and Therapeutics

Could Dermaseptin Analogue be a Competitive Inhibitor for ACE2 Towards Binding with Viral Spike Protein Causing COVID19?: Computational Investigation

Ocellatin AMPs (antimicrobial peptides) are considered to be promising alternative therapeutics to conventional antibiotics. Three-dimensional (3D) structures of ocellatin-F1 with 25 residues have been reported to be potent in terms of bacterial membrane permeability. To investigate the influence of similar ocellatin peptides with 25 residues pertaining to antimicrobial effect, ocellatin-1, K1 and S1 peptides were modelled with ocellatin-F1 as template. Comparative analyses between these peptides were carried out, using computational approaches. From the results of in silico toxicity profile, all peptides were found to be non-toxic with no haemolytic activity. Further sequence analysis, net charge, hydrophobicity and hydrophobic moment revealed the membrane permeable efficacy of ocellatin-1 peptide. Besides, the investigation of peptide electronic structures through density functional theory and quantum chemical (HOMO and LUMO) calculations predicted ocellatin-1 to be a suitable peptide, which can be used as a scaffold for therapeutics. Furthermore, the determination of structural contours such as RMSD, RMSF and Rg through trajectory analysis revealed that ocellatin-1 exhibited strong structural stability. In addition, the trajectory analysis of elements of secondary structure illustrated the alpha helical conformations to be retained in all peptides, except ocellatin-1. On the aforementioned grounds, ocellatin-1 was found to possess the important role of peptide penetration of the bacterial membrane. This study becomes significant, since it is the first time where the structural importance of ocellatin peptides were explored in detail and the therapeutic potential of ocellatin-1 as a peptide-based antimicrobial drug have been theoretically revealed. © 2021, The Author(s), under exclusive licence to Springer-Verlag GmbH, DE part of Springer Nature.

Journal of Molecular Modeling

Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics—quantum and molecular mechanical approaches

There is a colossal demand for natural pigments and its applications in recent times. In the study, a novel lactone pigment was isolated from a predominant endophytic fungus residing in Bixa orellana L. (Bixaceae) leaves. The endophyte was identified as Fusarium verticillioides through morphological and molecular investigations. The optimum growth parameters of the endophyte for pigment production were at 33 ºC with pH 6.5 in dark. Through comprehensive spectroscopic studies, the structure of the isolated lactone was resolved and identified as (E)-3, 3-dimethyl-4-(pent-1-en-1-yl)-4-propyldihydrofuran-2(3H)-one. The acute oral toxicity study of the pigment investigated upon female Wistar rats indicated the median lethal dose (LD50) value above 1000 mg/kg body weight affirming safety. Thus, the red pigment from the isolated endophyte may be employed as a sustainable source for natural colorant in industries owing to its non-toxicity. © 2021, King Abdulaziz City for Science and Technology.

Department of Chemistry

School of Advanced Sciences

3 Biotech

Mycosynthesis of novel lactone in foliar endophytic fungus isolated from Bixa orellana L.

To feed the increasing population of the world farmers and the crop growers rely on the use of synthetic chemicals as pesticide and fertilizer for the enhancement of soil nutrition, pest and disease management of the crops to increase the yield. However, these synthetic chemicals further aggregate the existing problem of environmental contamination, food safety, and are more harmful to the entire ecosystem. Owing to the ability to promote the growth and development of the plant and protection against various stresses and diseases the only technology to meet all the challenges is the use of beneficial microorganisms. Recently the development of fungi as the biocontrol agents and biofertilizers is increasing rapidly among the scientific community. Fungi such as Arbuscular mycorrhiza, Piriformospora indica, Penicillium, and various others have proved to play a beneficial role in nutrition enhancement, phosphate solubilization, and protection against various stresses by establishing a symbiotic relationship with the host plants. Several fungi are mass produced and commercially available in the market to promote the growth and development of plant as well as to increase the plant defense mechanism. This chapter focuses on various fungal communities that play a significant role in the overall growth and yield of the crop.

Fungal Biology

Agriculturally Important Fungi for Crop Protection

Shoot tips from two different cultivars of banana known as Grand Naine (AAA) and Elakki (AB), were evaluated for their&nbsp;in vitro&nbsp;response in different concentrations of cytokinin and auxin which included 6-benzylaminopurine (6-BAP; 2, 3, and 4&nbsp;mg&nbsp;L−1) and α-naphthalene acetic acid (NAA; 1&nbsp;mg&nbsp;L−1) which was added to Murashige and Skoog (MS) basal media. The mean survival rates for cultured Grand Naine and Elakki explants in the varied growth regulator treatments were 66.25% and 52.5%, respectively. Rooting was initiated in the seventh passage using half-strength MS medium supplemented with 200&nbsp;mg&nbsp;L−1&nbsp;activated charcoal and 20&nbsp;mg&nbsp;L−1&nbsp;adenine sulfate (AS). The highest mean number of shoots generated per explant at the end of the seventh subculture from Grand Naine was 20.10 ± 0.73, and in Elakki, it was 11.20 ± 0.53. MS media supplemented with 2&nbsp;mg&nbsp;L−1&nbsp;6-BAP, and 1&nbsp;mg&nbsp;L−1&nbsp;NAA was found to be the best combination for shoot proliferation in both the cultivars. The&nbsp;in vitro-regenerated plants were hardened primarily under shade net conditions using cocopeat substrate and were later transferred to a 1:1:1 ratio of cocopeat, red soil, and sand mix before exposure to field conditions. The survival rate for Grand Naine and Elakki cultivars was 98.5% and 96.5%, respectively, during the acclimatization period of the micropropagules under shade net conditions. Polymorphism was not observed between the mother plant and the&nbsp;in vitro-regenerated micropropagules when analyzed for specific randomly amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR).

VIT Unitversity

In Vitro Cellular & Developmental Biology - Plant

Maximization of micropropagule production in banana cultivars Grand naine (AAA) and Elakki (AB)

Improving bioavailability of vitamin A in food by encapsulation: An update. In:  Nanoscience in Medicine Volume 1. Eds: Hemant Kumar Daima, Navya PN, Shivendu Ranjan, Nandita Dasgupta and Eric Lichtfouse, Environmental Chemistry for a Sustainable World, Springer, pp. 117-145. https://doi.org/10.1007/978-3-030-29207-2_4 ISBN: 978-3-030-29206-5

Integration of semi-active devices in Automotive Seating System (ASS) with intelligent control policies help attenuation of the vibration transmitted to the occupant. The current work investigates the effectiveness of a semi-active magnetorheological (MR) damper with ASS for a quarter car model with the application of suitable control algorithms. The system controller calculates the desired damping force using proportional integral derivative (PID), skyhook on/off, PID tuned using genetic algorithm (GA), skyhook continuous and modified skyhook controllers. The signum function damper controller estimates the command voltage required for tracking the desired damping force. The displacement and acceleration of the passive seat system was compared with the semi-active seat suspension system in time and frequency domains. The results from the frequency domain shows that the lowest resonance peaks for the seat system can be achieved using the modified skyhook control policy. The effectiveness of the modified skyhook controller is evaluated in terms of peak to peak (PTP) acceleration, root mean square (RMS) acceleration, frequency weighted RMS acceleration, seat effective amplitude transmissibility (SEAT), vibration dose value (VDV) and crest factor (CF) for enhancing the ride quality. The modified skyhook controller can dissipate the energy better than the passive system. The modified skyhook controller increased the occupant ride quality of SEAT, VDV and CF by 30.41%, 52.84% and 11.62% on account of small bump excitation and 31.76%, 53.27% and 11.02% on account of large bump excitation compared with passive system. The modified skyhook control policy attenuates the vibration better than other control policies addressed in this paper. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

Mechanical

School of Mechanical Engineering

Chennai Campus

International Journal of Dynamics and Control

Response characteristics of car seat suspension using intelligent control policies under small and large bump excitations

Phytochemicals, especially botanical insecticides are currently of interest because of their successful application in plant protection as biocontrol agents. Biological activity of leaf aqueous extract of ten selected medicinal plants were evaluated against the fourth-instar larvae of gram pod borer Helicoverpa armigera (H¨ubner), (Lepidoptera: Noctuidae). Antifeedant activity of leaf aqueous extracts of Abutilon indicum L., Achyranthus aspera L., Aerva lanata L., Albiziz amara (Roxb), Andrographis paniculata Ness., Cardiospermum halicacabum L., Cassia tora L., Catharanthus roseus L (G) Don., Datura metal L. and Tribulus terrestris L. were evaluated in this study. Preliminary screening after 24 h of exposure with leaf aqueous extracts of the selected plants at a concentration of 1,000 ppm exhibited significant larval mortality rate. The percentage mortality rate ranged considerably from 10.8 to 72.8. The mortality rate was observed in the decreasing order of A. paniculata > C. roseus > D. metal > A. amara > C. halicacabum > A. indicum > C. tora > T. terrestris > A. aspera >A. lanata against the larvae of H. armigera. The results imply that leaf aqueous extract of A. paniculata, C. roseus and D. metal can potentially be used as eco-friendly pest control agents against the larva of H. armigera.