SARS-CoV-2 variants and spike mutations involved in second wave of COVID-19 pandemic in India.

Against the backdrop of the second wave of COVID-19 pandemic in India that started in March 2021, we have monitored the spike (S) protein mutations in all the reported (GISAID portal) whole-genome sequences of SARS-CoV-2 circulating in India from 1 January 2021 to 31 August 2021. In the 43,102 SARS-CoV-2 genomic sequences analysed, we have identified 24,260 amino acid mutations in the S protein, based on which 265 Pango lineages could be categorized. The dominant lineage in most of the 28 states of India and its 8 union territories was B.1.617.2 (the delta variant). However, the states Madhya Pradesh, Jammu & Kashmir, and Punjab had B.1.1.7 (alpha variant) as the major lineage, while the Himachal Pradesh state reported B.1.36 as the dominating lineage. A detailed analysis of various domains of S protein was carried out for detecting mutations having a prevalence of >1%; 70, 18, 7, 3, 9, 4, and 1 (N = 112) such mutations were observed in the N-terminal domain, receptor binding domain, C -terminal domain, fusion peptide region, heptapeptide repeat (HR)-1 domains, signal peptide domain, and transmembrane region, respectively. However, no mutations were recorded in the HR-2 and cytoplasmic domains of the S protein. Interestingly, 13.39% (N = 15) of these mutations were reported to increase the infectivity and pathogenicity of the virus; 2% (N = 3) were known to be vaccine breakthrough mutations, and 0.89% (N = 1) were known to escape neutralizing antibodies. The biological significance of 82% (N = 92) of the reported mutations is yet unknown. As SARS-CoV-2 variants are emerging rapidly, it is critical to continuously monitor local viral mutations to understand national trends of virus circulation. This can tremendously help in designing better preventive regimens in the country, and avoid vaccine breakthrough infections.

Microfluidic Protein Imaging Platform: Study of Tau Protein Aggregation and Alzheimer's Drug Response.

Tau protein aggregation is identified as one of the key phenomena associated with the onset and progression of Alzheimer's disease. In the present study, we performed on-chip confocal imaging of tau protein aggregation and tau-drug interactions using a spiral-shaped passive micromixing platform. Numerical simulations and experiments were performed in order to validate the performance of the micromixer design. We performed molecular modeling of adenosine triphosphate (ATP)-induced tau aggregation in order to successfully validate the concept of helical tau filament formation. Tau aggregation and native tau restoration were realized using an immunofluorescence antibody assay. The dose-response behavior of an Alzheimer's drug, methylthioninium chloride (MTC), was monitored on-chip for defining the optimum concentration of the drug. The proposed device was tested for reliability and repeatability of on-chip tau imaging. The amount of the tau protein sample used in our experiments was significantly less than the usage for conventional techniques, and the whole protein-drug assay was realized in less than two hours. We identified that intensity-based tau imaging could be used to study Alzheimer's drug response. In addition, it was demonstrated that cell-free, microfluidic tau protein assays could be used as potential on-chip drug evaluation tools for Alzheimer's disease.

Evaluation of the reproductive toxicity of antiretroviral drug loaded lactoferrin nanoparticles.

Multiple prevention therapy has gained importance for the prevention and treatment of sexually transmitted diseases, especially HIV/AIDS. Antiretroviral drugs encapsulated in nanoparticles have been developed for efficient delivery of the drugs to the vaginal surface. Lactoferrin nanoparticles (LFNPs) encapsulating anticancer or antiretroviral drugs are found to be promising agents to specifically deliver drugs at the target sites. Recent studies indicate that the bioavailability is higher for antiretroviral drugs delivered by LFNPs than when the drugs are administered alone. Although LFNP-mediated drug delivery via the oral or vaginal route for the treatment of HIV/AIDS is promising, the effect of such administrations is not well studied. Drug-loaded LFNPs when administered to rats by the vaginal route did not show any effect on the reproductive performance, fertility, and postnatal development. Oral administration of drug-loaded LFNPs caused a significant decrease in litter size, whereas the reproductive performance and postnatal development remained normal. In our model system, the results indicate that vaginal administration of drug-loaded LFNPs appears safer and can be projected for the delivery of antiretroviral agents via the vaginal route. Abbreviations: LFNPs: lactoferrin nanoparticles; STIs: sexually transmitted diseases infections; NPs: nanoparticles; LF: lactoferrin; DL-LFNPs: drug loaded lactoferrin nanoparticles; MPT: multiple prevention techniques.

Status of topoisomerase-2ß protein in all-trans retinoic acid-treated human neuroblastoma (SK-N-SH) cells.

Of the mammalian topoisomerase (Topo)-2 isozymes (α and ß), Topo-2ß protein has been reported to regulate neuronal development and differentiation. However, the status of Topo-2ß in all-trans retinoic acid (ATRA)-treated human neuroblastoma (SK-N-SH) cells is not understood. More information about the effects of ATRA on SK-N-SH cells is needed to reveal the role of ATRA in the regulation of Topo-2ß levels and spontaneous regression of SK-N-SH cells to predict the clinical activity. This study was proposed to investigate the status and role of Topo-2ß protein in ATRA-induced survival and neuronal differentiation of SK-N-SH cells. Microscopic, sodium dodecyl sulfate polyacrylamide gel electrophoresis after immunoprecipitations and Western blot analysis were used to study and compare Topo-2ß protein among 10 µM ATRA-treated SK-N-SH cells and controls at different time points. The level of Topo-2ß protein increased in the initial days of treatment but markedly decreased upon induction of differentiation by ATRA in later stages. Upon ATRA treatment, SK-N-SH cells stretched, exhibited neurite extensions, and acquired a neuronal phenotype. Both treated and untreated SK-N-SH cells were able to migrate, occupy the scratched area, and completely recolonized 24 hours later. These results suggest an indirect role of Topo-2ß protein in regulation of genes involved in cell migration and differentiation of ATRA-treated SK-N-SH cells. This study suggests that Topo-2ß may be part of activation/repression of protein complexes activated by epigenetic modifying agents, differentiating signals, and inducible locus. However, detailed studies are needed to explore the ATRA-downstream genes leading to Topo-2ß regulation and regulatory proteins of neuronal differentiation.

Rv0474 is a copper-responsive transcriptional regulator that negatively regulates expression of RNA polymerase ß subunit in Mycobacterium tuberculosis.

We characterize Rv0474, a putative transcriptional regulatory protein of Mycobacterium tuberculosis, which is found to function as a copper-responsive transcriptional regulator at toxic levels of copper. It is an autorepressor, but at elevated levels (10-250 µm) of copper ions the repression is relieved resulting in an increase in Rv0474 expression. Copper-bound Rv0474 is recruited to the rpoB promoter leading to its repression resulting in the growth arrest of the bacterium. Mutational analysis showed that the helix-turn-helix and leucine zipper domains of Rv0474 are essential for its binding to Rv0474 and rpoB promoters, respectively. The mechanism of Rv0474-mediated rpoB regulation seems to be operational only in pathogenic mycobacteria that can persist inside the host.

Evaluation of Antiproliferative Activity, Safety and Biodistribution of Oxaliplatin and 5-Fluorouracil Loaded Lactoferrin Nanoparticles for the Management of Colon Adenocarcinoma: an In Vitro and an In Vivo Study.

PURPOSE: Colon adenocarcinoma is the most common form of gastro intestinal tract cancer, predominantly in ageing population. Chemotherapy with 5-Fluorouracil and oxaliplatin is an indispensable treatment regimen, nevertheless having limitation of systemic toxicity and lower therapeutic index. The present study is based on evaluation of anti-proliferative potential, pharmacokinetics parameters, safety profile, biodistribution and efficacy of 5-FU/oxaliplatin loaded lactoferrin nanoparticles in cell lines and wistar rats in order to overcome the above limitation. METHODS: Nanoparticles were prepared by Water-in-oil process. The anti-proliferative efficacy and mode of cellular entry was evaluated in COLO-205 cells. The pharmacokinetics and biodistribution analysis were performed in healthy rats while efficacy and safety assay were performed in ACF induced rats. RESULTS: 5-FU and oxaliplatin loaded nanoparticles shows enhanced antiproliferative activity as compare to free drugs in COLO-205 cells. Lactoferrin nanoparticles also improve the pharmacokinetics profile, safety parameters and efficacy of 5-FU and Oxaliplatin. CONCLUSION: Lactoferrin nanoparticles demonstrated an attractive drug delivery module to manage the colon adenocarcinoma as it has improved the antiproliferative activity of 5-FU and Oxaliplatin against colon adenocarcinoma cells. Moreover, it also improves the pharmacokinetic profile and safety parameters of the same drug in wistar rat.

Receptor-mediated targeted delivery of DNA using Lactoferrin nanoparticles.

Efficient gene delivery facilitated by non-viral vectors, is comparatively safer alternative than viral carriers. Current approaches to gene delivery largely depends on methods that overcome cellular and tissue barriers impeding efficient DNA delivery. While the conventional delivery systems have the drawback of low cellular uptake and off target effects, the receptor-mediated gene delivery system has shown remarkable breakthrough. In that context exploiting the specific receptor targeting properties of lactoferrin protein, we have developed pDNA loaded lactoferrin protein nanoparticles (pDNA-LfNPs). pDNA-LfNPs were spherical in shape within the size range of 140±20nm. They were found to be resistant against nuclease digestion and stable under long storage. Additionally, LfNPs were biocompatible and have targeting ability to facilitate gene uptake by receptor mediated internalization in lactoferrin receptor expressing cell lines. It is also evident from our studies that Lf nanoparticles did not exhibit any cytotoxicity even at the highest concentration. Here we first time report the use of lactoferrin nanoparticles as a gene delivery carrier with targeting abilities.

Factors associated with conversion of long-term non-progressors to progressors: a prospective study of HIV perinatally infected paediatric survivors.

BACKGROUND & OBJECTIVES: Survival pattern among children infected with the human immune deficiency virus (HIV) follows a bimodel distribution. Some children survive beyond 9 years age and are known as long term survivors (LTS) while others had a more rapid course to death during the first few years of life. In the LTS group of children, two sub-populations have emerged, the long term non-progressors (LTNP) who have remained asymptomatic over a period of years and those who have survived despite clinical and laboratory evidence of disease progression, the long term progressors (LTP). The aim of the present study was to determine the factors influencing the conversion of LTNPs to LTPs in a group of perinatally HIV infected children who were followed up for five years. METHODS: A total of 26 HIV seropositive paediatric patients were monitored from 2006 to 2011 with CD4 cell counts, onset of clinical manifestations, body weight, biochemical, haematological and immunological parameters. Statistical analyses, both qualitative and quantitative, were used to determine the degree of conversion of non-progressors to progressors. RESULTS: All 26 (13 female and 13 male) perinatally HIV infected children, born during 1991-1996 were healthy until 2006. But by 2011, 18 were placed in progressors group with antiretroviral therapy (ART), while six remained in non progressors group and two died. As per the Kaplan-Meier survival analysis, AIDS free median survival period (years) in LTP group (CD4 count) of the cohort was 10 ± 0.66 (<200; P=<0.05); 11 ± 0.61 (200-350, P=<0.05), 12 ± 0.18 (>350, P=<0.05). Intercurrent and opportunistic infections (OIs) were observed in LTPs only. The incidence of OI in LTPs was higher when compared to general paediatric population. INTERPRETATION & CONCLUSIONS: Our findings show that CD4 counts and OIs play an important role in influencing the survival chances of perinatally HIV infected children.

Cultured cerebellar granule neurons as an in vitro aging model: topoisomerase IIß as an additional biomarker in DNA repair and aging.

Aging in the brain is a multicellular process manifesting as neurodegeneration and associated functional impairment. In the present study, we report that cerebellar granule neurons (CGNs) in culture show senescence-mediated molecular changes indicating establishment of aging processes in vitro. CGNs were viable for 5 weeks followed by cellular degeneration. Molecular changes correlated with cellular senescence and aging include the elevation of senescence-mediated beta galactosidase (SA-ß-gal) activity and intracellular Ca(2+) levels. Decreased base excision repair (BER) as well as non-homologous end joining (NHEJ) activities in CGNs were also observed upon aging in vitro. The decrease in NHEJ activity was shown correlated with corresponding decrease in the levels of topoisomerase IIß (topo IIß), Ku 70 and Ku 80 suggesting a crucial role for topo IIß in repair capacity of CGNs. These studies, besides establishing that CGNs would serve as a good in vitro model for analysis of aging phenomena, also brought out that topo IIß, by virtue of its significant role in controlling NHEJ activity, would serve as an additional biomarker for studying aging process.

An efficient targeted drug delivery through apotransferrin loaded nanoparticles.

BACKGROUND: Cancerous state is a highly stimulated environment of metabolically active cells. The cells under these conditions over express selective receptors for assimilation of factors essential for growth and transformation. Such receptors would serve as potential targets for the specific ligand mediated transport of pharmaceutically active molecules. The present study demonstrates the specificity and efficacy of protein nanoparticle of apotransferrin for targeted delivery of doxorubicin. METHODOLOGY/PRINCIPAL FINDINGS: Apotransferrin nanoparticles were developed by sol-oil chemistry. A comparative analysis of efficiency of drug delivery in conjugated and non-conjugated forms of doxorubicin to apotransferrin nanoparticle is presented. The spherical shaped apotransferrin nanoparticles (nano) have diameters of 25-50 etam, which increase to 60-80 etam upon direct loading of drug (direct-nano), and showed further increase in dimension (75-95 etam) in conjugated nanoparticles (conj-nano). The competitive experiments with the transferrin receptor specific antibody showed the entry of both conj-nano and direct-nano into the cells through transferrin receptor mediated endocytosis. Results of various studies conducted clearly establish the superiority of the direct-nano over conj-nano viz. (a) localization studies showed complete release of drug very early, even as early as 30 min after treatment, with the drug localizing in the target organelle (nucleus) (b) pharmacokinetic studies showed enhanced drug concentrations, in circulation with sustainable half-life (c) the studies also demonstrated efficient drug delivery, and an enhanced inhibition of proliferation in cancer cells. Tissue distribution analysis showed intravenous administration of direct nano lead to higher drug localization in liver, and blood as compared to relatively lesser localization in heart, kidney and spleen. Experiments using rat cancer model confirmed the efficacy of the formulation in regression of hepatocellular carcinoma with negligible toxicity to kidney and liver. CONCLUSIONS: The present study thus demonstrates that the direct-nano is highly efficacious in delivery of drug in a target specific manner with lower toxicity to heart, liver and kidney.