@article {131285, title = {Validating saliva as a biological sample for cost-effective, rapid and routine screening for SARS-CoV-2}, journal = {INDIAN JOURNAL OF MEDICAL MICROBIOLOGY}, volume = {45}, year = {2023}, month = {09/2023}, abstract = {

Purpose: Compared to nasopharyngeal/oropharyngeal swabs (N/OPS-VTM), non-invasive saliva samples have enormous potential for scalability and routine population screening of SARS-CoV-2. In this study, we investigate the efficacy of saliva samples relative to N/OPS-VTM for use as a direct source for RT-PCR based SARS-CoV-2 detection. Methods: We collected paired nasopharyngeal/oropharyngeal swabs and saliva samples from suspected positive SARS-CoV-2 patients and tested using RT-PCR. We used generalized linear models to investigate factors that explain result agreement. Further, we used simulations to evaluate the effectiveness of saliva-based screening in restricting the spread of infection in a large campus such as an educational institution. Results: We observed a 75.4\% agreement between saliva and N/OPS-VTM, that increased drastically to 83\% in samples stored for less than three days. Such samples processed within two days of collection showed 74.5\% test sensitivity. Our simulations suggest that a test with 75\% sensitivity, but high daily capacity can be very effective in limiting the size of infection clusters in a workspace. Guided by these results, we successfully implemented a saliva-based screening in the Bangalore Life Sciences Cluster (BLiSC) campus. Conclusion: These results suggest that saliva may be a viable alternate source for SARS-CoV-2 surveillance if samples are processed immediately. Although saliva shows slightly lower sensitivity levels when compared to N/ OPS-VTM, saliva collection is logistically advantageous. We strongly recommend the implementation of salivabased screening strategies for large workplaces and in schools, as well as for population-level screening and routine surveillance as we learn to live with the SARS-CoV-2 virus.

}, doi = {10.1016/j.ijmmb.2023.100384}, author = {Ansil, B R and George, Carolin Elizabeth and Chandrasingh, Sindhulina and Viswanathan, Ashwin and Thattai, Mukund and Raghu, Padinjat and Devadiga, Santhosha and Harikumar, Arun Geetha and Harsha, Pulleri Kandi and Nair, Indu and Ramakrishnan, Uma and Mayor, Satyajit} } @article {129165, title = {Vestibular feedback for flight control in hawkmoths.}, journal = {Trends Neurosci}, year = {2023}, month = {2023 May 26}, abstract = {

Flying insects require mechanosensory feedback to rapidly generate compensatory responses to unexpected perturbations. Such feedback is critical in insects such as moths, which fly under low light levels, compromising their ability to visually compensate for aerial perturbations. Here, we describe how diverse mechanosensory organs have adapted to provide vestibular feedback in various insects, with particular focus on hawkmoths.

}, issn = {1878-108X}, doi = {10.1016/j.tins.2023.05.004}, author = {Sane, Sanjay P and Manjunath, Maitri and Mukunda, Chinmayee L} } @article {130545, title = {A view from the President of the Indian Biophysical Society.}, journal = {Biophys Rev}, volume = {15}, year = {2023}, month = {2023 Jun}, pages = {305-306}, abstract = {

This Commentary introduces the readers of Biophysical Reviews to the current president of the Indian Biophysical Society and details a few recent activities of the society in its domestic and international promotion of the biophysics as a scientific discipline.

}, issn = {1867-2450}, doi = {10.1007/s12551-023-01072-7}, author = {Rao, Madan} } @article {106150, title = {Versatile role of miR-24/24-1*/24-2*expression in cancer and other human diseases}, journal = {AMERICAN JOURNAL OF TRANSLATIONAL RESEARCH }, volume = {14}, year = {2022}, month = {01/2022}, pages = {20-54}, abstract = {

MiRNAs (miRs) have been proven to be well-validated therapeutic targets. Emerging evidence has demonstrated that intricate, intrinsic and paradoxical functions of miRs are context-dependent because of their multiple upstream regulators, broad spectrum of downstream molecular targets and distinct expression in various tissues, organs and disease states. Targeted therapy has become an emerging field of research. One key for the development of successful miR-based/targeted therapy is to acquire integrated knowledge of its regulatory network and its association with disease phenotypes to identify critical nodes of the underlying pathogenesis. Herein, we systematically summarized the comprehensive role of miR-24-3p (miR-24), along with its passenger strands miR24-1-5p* (miR-24-1) and miR-24-2-5p* (miR-24-2), emphasizing their microenvironment, intracellular targets, and associated gene networks and regulatory phenotypes in 18 different cancer types and 13 types of other disorders. MiR-24 targets and regulates numerous genes in various cancer types and enhances the expression of several oncogenes (e.g., cMyc, BCL2 and HIF1), which are challenging in terms of druggability. In contrast, several tumor suppressor proteins (p21 and p53) have been reported to be downregulated by miR-24. MiR-24 also regulates the cell cycle and is associated with numerous cancer hallmarks such as apoptosis, proliferation, metastasis, invasion, angiogenesis, autophagy, drug resistance and other diseases pathogenesis. Overall, miR-24 plays an emerging role in the diagnosis, prognosis and pathobiology of various diseases. MiR-24 is a potential target for targeted therapy in the era of precision medicine, which expands the landscape of targetable macromolecules, including undruggable proteins.

}, url = {https://e-century.us/files/ajtr/14/1/ajtr0135181.pdf}, author = {Mukherjee, Sanjukta and Shelar, Bhagyashree and Krishna, Sudhir} } @article {87007, title = {Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites}, journal = {Nucleic Acids Res}, volume = {49}, year = {2021}, month = {12/2020}, pages = {891-901}, abstract = {

An abnormally high rate of UV-light related mutations appears at transcription factor binding sites (TFBS) across melanomas. The binding of transcription factors (TFs) to the DNA impairs the repair of UV-induced lesions and certain TFs have been shown to increase the rate of generation of these lesions at their binding sites. However, the precise contribution of these two elements to the increase in mutation rate at TFBS in these malignant cells is not understood. Here, exploiting nucleotide-resolution data, we computed the rate of formation and repair of UV-lesions within the binding sites of TFs of different families. We observed, at certain dipyrimidine positions within the binding site of TFs in the Tryptophan Cluster family, an increased rate of formation of UV-induced lesions, corroborating previous studies. Nevertheless, across most families of TFs, the observed increased mutation rate within the entire DNA region covered by the protein results from the decreased repair efficiency. While the rate of mutations across all TFBS does not agree with the amount of UV-induced lesions observed immediately after UV exposure, it strongly agrees with that observed after 48 h. This corroborates the determinant role of the impaired repair in the observed increase of mutation rate.

}, doi = {10.1093/nar/gkaa1219}, author = {Frigola, J and Sabarinathan, R and Gonzalez-Perez, A and Lopez-Bigas, N} } @article {89124, title = {Varying impacts of logging frequency on tree communities and carbon storage across evergreen and deciduous tropical forests in the Andaman Islands, India}, journal = {FOREST ECOLOGY AND MANAGEMENT}, year = {2021}, month = {02/20201}, abstract = {

The majority of Earth{\textquoteright}s tropical forests have been selectively logged; some on repeated occasions. Selective logging is known to affect forest structure, composition and function in various ways, but how such effects vary with logging frequency and across forest types remains unclear. In the Andaman Archipelago in India, we examined adult and pole-sized trees in baseline (unlogged since 1990s), once-logged (logged between 2007 and 2014) and twice-logged (logged in early 1990s and between 2007 and 2014) evergreen and deciduous forests, and tested whether higher logging frequency was associated with lower canopy cover, tree density, tree diversity, aboveground carbon stocks and divergence in species composition, including increased relative abundances of deciduous species in these forests. While once-logged evergreen and deciduous forests were similar to their respective baselines for most attributes assessed, and twice-logged evergreen forests had 22-24\% lower adult tree density and diversity, twice-logged deciduous forests had 17-50\% lower canopy cover, pole density, adult species diversity and above-ground carbon stocks, and 12\% higher deciduous fractions compared to the baselines. Collectively our results reveal lasting impacts of repeated selective logging, even at relative low intensity, on tree communities and carbon storage. These impacts can potentially be mitigated by reducing logging frequency and retaining unlogged patches in logged landscapes, but management must also incorporate heterogeneity in responses and recovery across different forest types. In the Andaman Islands, all forests may require more than 15-25 years between logging events, with deciduous forests potentially requiring more stringent extraction limits compared to evergreen forests.

}, doi = {10.1016/j.foreco.2020.118791}, author = {Surendra, Akshay and Osuri, A. M and Ratnam, Jayashree} } @article {99106, title = {"Viscotaxis"- Directed Migration of Mesenchymal Stem Cells in Response to Loss Modulus Gradient.}, journal = {Acta Biomater}, year = {2021}, month = {2021 Aug 29}, abstract = {

Directed cell migration plays a crucial role in physiological and pathological conditions. One important mechanical cue, known to influence cell migration, is the gradient of substrate elastic modulus (E). However, the cellular microenvironment is viscoelastic and hence the elastic property alone is not sufficient to define its material characteristics. To bridge this gap, in this study, we investigated the influence of the gradient of viscous property of the substrate, as defined by loss modulus (G) on cell migration. We cultured human mesenchymal stem cells (hMSCs) on a collagen-coated polyacrylamide gel with constant storage modulus (G) but with a gradient in the loss modulus (G). We found hMSCs to migrate from high to low loss modulus. We have termed this form of directional cellular migration as "Viscotaxis". We hypothesize that the high loss modulus regime deforms more due to creep in the long timescale when subjected to cellular traction. Such differential deformation drives the observed Viscotaxis. To verify our hypothesis, we disrupted the actomyosin contractility with myosin inhibitor blebbistatin and ROCK inhibitor Y27632, and found the directional migration to disappear. Further, such time-dependent creep of the high loss material should lead to lower traction, shorter lifetime of the focal adhesions, and dynamic cell morphology, which was indeed found to be the case. Together, findings in this paper highlight the importance of considering the viscous modulus while preparing stiffness-based substrates for the field of tissue engineering. STATEMENT OF SIGNIFICANCE: While the effect of substrate elastic modulus has been investigated extensively in the context of cell biology, the role of substrate viscoelasticity is poorly understood. This omission is surprising as our body is not elastic, but viscoelastic. Hence, the role of viscoelasticity needs to be investigated at depth in various cellular contexts. One such important context is cell migration. Cell migration is important in morphogenesis, immune response, wound healing, and cancer, to name a few. While it is known that cells migrate when presented with a substrate with a rigidity gradient, cellular behavior in response to viscoelastic gradient has never been investigated. The findings of this paper not only reveal a completely novel cellular taxis or directed migration, it also improves our understanding of cell mechanics significantly.

}, issn = {1878-7568}, doi = {10.1016/j.actbio.2021.08.039}, author = {Shirke, Pallavi Uday and Goswami, Hiya and Kumar, Vardhman and Shah, Darshan and Beri, Sarayu and Das, Siddhartha and Bellare, Jayesh and Mayor, Satyajit and Venkatesh, K V and Seth, Jyoti R and Majumder, Abhijit} } @article {77387, title = {The Variations of Human miRNAs and Ising Like Base Pairing Models}, journal = {MATCH-COMMUNICATIONS IN MATHEMATICAL AND IN COMPUTER CHEMISTRY}, volume = {83}, year = {2020}, month = {2020}, pages = {357-372}, abstract = {

miRNAs are small about 22-base pair long, RNA molecules are of significant biological importance. Like other longer RNA molecules, messages in miRNAs are words in an alphabet consists of only four nucleotide bases. However, just like words in any language, not all combinations of these alphabets are not meaningful. In fact, we find that the distributions of nucleotides bases in human miRNAs show significant deviation from randomness. First, a miRNA sequence containing four bases are mapped into a binary string with three kinds of classifications according to their chemical properties. Our analyses based on some statistical measurement clearly demonstrate that the purines-pyrimidines class of nucleotide bases resembles all the human miRNAs. Then, we propose a simple nearest neighbor model (Ising model) to understand the statistical variations in human miRNAs. One the way, we also discuss the limitations of a mean-field model.

}, author = {Banerjee, JP and Das, JK and Choudhury, PP and Mukherjee, S and Hassan, SS and Basu, P} } @article {77434, title = {The Viral SUMO-Targeted Ubiquitin Ligase ICP0 is Phosphorylated and Activated by Host Kinase Chk2.}, journal = {J Mol Biol}, volume = {432}, year = {2020}, month = {2020 Mar 27}, pages = {1952-1977}, abstract = {

When the herpes simplex virus (HSV) genome enters the nucleus for replication and transcription, phase-segregated nuclear protein bodies called Promyelocytic leukemia protein nuclear bodies (PML NBs) colocalize with the genome and repress it. HSV encodes a small ubiquitin-like modifier (SUMO)-targeted ubiquitin ligase (STUbL) infected cell polypeptide 0 (ICP0) that degrades PML NBs to alleviate the repression. The molecular details of the mechanism used by ICP0 to target PML NBs are unclear. Here, we identify a bona fide SUMO-interacting motif in ICP0 (SIM-like sequence [SLS] 4) that is essential and sufficient to target SUMOylated proteins in PML NBs such as the PML and Sp100. We shown that phosphorylation of SLS4 creates new salt bridges between SUMO and SLS4, increases the SUMO/SLS4 affinity, and switches ICP0 into a potent STUbL. HSV activates the Ataxia-telangiectasia-mutated kinase-Checkpoint kinase 2 (ATM-Chk2) pathway to regulate the cell cycle of the host. We report that the activated Chk2 also phosphorylates ICP0 at SLS4 and enhances its STUbL activity. Our results uncover that a viral STUbL counters antiviral response by exploiting an unprecedented cross-talk of three post-translational modifications: ubiquitination, SUMOylation, and phosphorylation.

}, issn = {1089-8638}, doi = {10.1016/j.jmb.2020.01.021}, author = {Hembram, Dambarudhar Shiba Sankar and Negi, Hitendra and Biswas, Poulomi and Tripathi, Vasvi and Bhushan, Lokesh and Shet, Divya and Kumar, Vikas and Das, Ranabir} } @article {78159, title = {Visualizing mutagenic repair: novel insights into bacterial translesion synthesis.}, journal = {FEMS Microbiol Rev}, year = {2020}, month = {2020 Jun 18}, abstract = {

DNA repair is essential for cell survival. In all domains of life, error-prone and error-free repair pathways ensure maintenance of genome integrity under stress. Although mutagenic, low fidelity repair mechanisms help avoid potential lethality associated with unrepaired damage, thus making them important for genome maintenance, and in some cases, the preferred mode of repair. However, cells carefully regulate pathway choice to restrict activity of these pathways to only certain conditions. One such repair mechanism is Translesion Synthesis (TLS), where a low fidelity DNA polymerase is employed to synthesize across a lesion. In bacteria, TLS is a potent source of stress-induced mutagenesis, with potential implications in cellular adaptation as well as antibiotic resistance. Extensive genetic and biochemical studies, predominantly in Escherichia coli, have established a central role for TLS in bypassing bulky DNA lesions associated with ongoing replication, either at or behind the replication fork. More recently, imaging-based approaches have been applied to understand the molecular mechanisms of TLS and how its function is regulated. Together, these studies have highlighted replication-independent roles for TLS as well. In this review, we discuss the current status of research on bacterial TLS, with emphasis on recent insights gained mostly through microscopy at the single-cell and single-molecule level.

}, issn = {1574-6976}, doi = {10.1093/femsre/fuaa023}, author = {Joseph, Asha Mary and Badrinarayanan, Anjana} } @article {43842, title = {Vaccination and immunization strategies to design Aedes aegypti salivary protein based subunit vaccine tackling Flavivirus infection.}, journal = {Int J Biol Macromol}, volume = {122}, year = {2019}, month = {2018 Sep 13}, pages = {1203-1211}, abstract = {

Flavivirus causes arthropod-borne severe diseases that sometimes lead to the death. The Flavivirus species including Dengue virus, Zika virus and yellow fever virus are transmitted by the bite of Aedes mosquitoes. All these viral species target the people living in their respective endemic zone causing a high mortality rate. Recent studies show that immune factors present in the Ae. aegypti saliva is the hidden culprit promoting blood meal collection, suppressing host immune molecules and promoting disease establishment. This study was designed to develop a subunit vaccine using Aedes mosquito salivary proteins targeting the aforementioned Flaviviruses. Subunit vaccine was designed very precisely by combining the immunogenic B-cell epitope with CTL and HTL epitopes and also suitable adjuvant and linkers. Immunogenicity, allergenicity and physiochemical characterization were also performed for scientific validation. Molecular docking and molecular dynamics simulations studies were carried out to confirm the stable affinity between the vaccine protein (3D) and TLR3 receptor. At last, in silico cloning was executed to get the subunit vaccine restriction clone into pET28a vectro to express it in microbial expression system. Additionally, this study warrants the experimental evaluation for the validation purposes.

}, issn = {1879-0003}, doi = {10.1016/j.ijbiomac.2018.09.071}, author = {Pandey, Rajan Kumar and Dahiya, Surbhi and Mahita, Jarjapu and Sowdhamini, Ramanathan and Prajapati, Vijay Kumar} } @article {36660, title = {ViXeN: An open-source package for managing multimedia data}, journal = {METHODS IN ECOLOGY AND EVOLUTION }, volume = {9}, year = {2018}, month = {03/2018}, pages = {785-792 }, doi = {10.1111/2041-210X.12892 }, author = {Ramachandran, P and Devarajan, K} } @article {25699, title = {Variance in Female Reproductive Success Differentially Impacts Effective Population Size in the Short-Nosed Fruit Bat, Cynopterus sphinx}, journal = {Evolutionary Biology}, volume = {44}, year = {2017}, month = {09/2017}, pages = {3066-373}, abstract = {

Effective population size (Ne) quantifies the effects of micro-evolutionary processes and the rate of loss of genetic diversity in a population. Several demographic and mating parameters reduce Ne. Theoretical studies elucidate the impacts of various demographic and mating system parameters on Ne, while empirical studies illustrate realized Ne for species with differing life histories and mating systems. However, effect of intra-specific variation in mating system on effective size remains largely unexplored. In this paper we investigated the effect of promiscuous and polygynous mating on Ne in two wild populations of the short-nosed fruit bat, Cynopterus sphinx. Ne/N (ratio of effective population size to census size) was lower than unity in both populations, and much lower for the polygynous population compared to promiscuous population. Elasticity analyses reveal that Ne/N was sensitive to deviations in the sex ratio. Variance in female reproductive success had a higher impact on Ne compared to variance in male reproductive success in the promiscuous population. However, for the polygynous population, impact of variance in male reproductive success on Ne was higher than that of variance in female reproductive success. Our results suggest that depending on mating system, different populations of the same species could have alternate evolutionary trajectories. The rate of loss of genetic diversity would be lower for the promiscuous population compared to the polygynous population. Our study is the first to highlight which parameters would most significantly impact population specific Ne under different mating systems.

}, doi = {10.1007/s11692-017-9414-y}, author = {Garg, Kritika M and Ramakrishnan, Uma} } @article {1018, title = {Vesicular trafficking and salinity responses in plants.}, journal = {IUBMB Life}, volume = {67}, year = {2015}, month = {2015 Sep}, pages = {677-86}, abstract = {

Research spanning three decades has demonstrated that vesicles pinch off from the plasma membrane and traffic through the cytoplasm of plant cells, much as previously reported in animal cells. Although the well-conserved clathrin-mediated mechanism of endocytosis has been well characterized, relatively little is known about clathrin-independent pathways in plants. Modulation of endocytosis by both physical stimuli and chemical ligands has been reported in plants. Here, we review the effect of salinity-one of the most deleterious environmental assaults-on endocytosis and intracellular trafficking. {\textcopyright} 2015 IUBMB Life, 67(9):677-686, 2015.

}, issn = {1521-6551}, doi = {10.1002/iub.1425}, author = {Baral, Anirban and Shruthi, K S and Mathew, M K} }