Monitoring Influenza A (H1N1, H3N2), RSV, and SARS-CoV-2 Using Wastewater-Based Epidemiology: A 2-Year Longitudinal Study in an Indian Megacity Covering Omicron and Post-Omicron Phases.

The bourgeoning field of wastewater-based epidemiology (WBE) for the surveillance of several respiratory viruses which includes Influenza A, H1N1pdm09, H3N2, respiratory syncytial viruses (RSV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of interest for public health concerns. However, there are few long-term monitoring studies globally. In this study, respiratory viruses were detected and quantified from 11 sewer sheds by utilizing reverse transcription-quantitative polymerase chain reaction analysis in Pune city, India, from Jan 2022 to Dec 2023.

Immunogenicity of SARS-CoV-2 vaccines BBV152 (COVAXIN®) and ChAdOx1 nCoV-19 (COVISHIELD™) in seronegative and seropositive individuals in India: a multicentre, nonrandomised observational study.

Background: There are limited global data on head-to-head comparisons of vaccine platforms assessing both humoral and cellular immune responses, stratified by pre-vaccination serostatus. The COVID-19 vaccination drive for the Indian population in the age group 18-45 years began in April 2021 when seropositivity rates in the general population were rising due to the delta wave of COVID-19 pandemic during April-May 2021.

Methods: Between June 30, 2021, and Jan 28, 2022, we enrolled 691 participants in the age group 18-45 years across four clinical sites in India.

Genomic surveillance reveals early detection and transition of delta to omicron lineages of SARS-CoV-2 variants in wastewater treatment plants of Pune, India.

The COVID-19 pandemic has emphasized the urgency for rapid public health surveillance methods to detect and monitor the transmission of infectious diseases. The wastewater-based epidemiology (WBE) has emerged as a promising tool for proactive analysis and quantification of infectious pathogens within a population before clinical cases emerge. In the present study, we aimed to assess the trend and dynamics of SARS-CoV-2 variants using a longitudinal approach.

Not teaching evolution is an injustice.

Since April, India has been roiled by controversy around the excision of several topics, including evolution and the periodic table, from school textbooks (up to grade 10) by the National Council for Educational Research and Training (NCERT). This was projected as an exercise in "rationalization" of content aimed at reducing the study load on students. The move was opposed by large numbers of academics and worried citizens.

A Micro-evolutionary Change in Target Binding Sites as a Key Determinant of Ultrabithorax Function in Drosophila.

Hox genes encode Homeodomain-containing transcription factors, which specify segmental identities along the anterior-posterior axis. Functional changes in Hox genes have been directly implicated in the evolution of body plans across the metazoan lineage. The Hox protein Ultrabithorax (Ubx) is expressed and required in developing third thoracic (T3) segments in holometabolous insects studied so far, particularly, of the order Coleoptera, Lepidoptera and Diptera.

A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India.

Background: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data.

Proceedings of the 3rd Indian Cancer Genome Atlas Conference 2022: Biobanking to Omics: Collecting the Global Experience.

On January 13th and 14th 2022, the Center for Translational Cancer Research organized the virtual third Indian Cancer Genome Atlas (ICGA) Conference 2022 "Biobanking to Omics - Collecting the Global Experience." This conference was planned as the steppingstone to help ICGA understand the road ahead and the probable roadblocks in its preparatory phase as ICGA begins to streamline the tumor tissue biobanking and multi-omics efforts in the Indian subcontinent. The first day of the conference was dedicated to updates on the current status of ICGA, the future prospect, and the global understanding of multi-omics efforts.

Evaluation of tumor-infiltrating lymphocytes (TILs) in molecular subtypes of an Indian cohort of breast cancer patients.

Objectives: Evaluation of tumor-infiltrating lymphocytes (TILs) distribution in an Indian cohort of breast cancer patients for its prognostic significance.

Methods: A retrospective cohort of breast cancer patients from a single onco-surgeon's breast cancer clinic with a uniform treatment strategy was evaluated for TILs. Tumor sections were H&E stained and scored for the spatial distribution and percent stromal TILs infiltration by a certified pathologist.

Burden of COVID-19 and case fatality rate in Pune, India: an analysis of the first and second wave of the pandemic.

Objective: To assess trends in case incidence and fatality rate between the first and second waves, we analyzed programmatic COVID-19 data from Pune city, an epicenter of COVID-19 cases in India.

Method: The trends of cases incidence, time-to-death and case fatality rate (CFR) were analyzed. Poisson regression models adjusted for age and gender were used to determine the independent effect of pandemic waves on mortality.

Developmental Robustness: The Haltere Case in .

Developmental processes have to be robust but also flexible enough to respond to genetic and environmental variations. Different mechanisms have been described to explain the apparent antagonistic nature of developmental robustness and plasticity. Here, we present a "self-sufficient" molecular model to explain the development of a particular flight organ that is under the control of the Hox gene () in the fruit fly .

Analyzing the influence of IL18 in regulation of YAP1 in breast oncogenesis using cBioportal.

Background: Yes-associated protein 1 (YAP1) is responsible for tumor growth, progression and metastasis. The mechanisms controlling the generation and relative ratio of the functional YAP1 and other co-factors are not well-understood. Various literature reported that co-factors like cytokines significantly influence signaling pathways to introduce epithelial immunity and regeneration, which later helps increase cancer-related phenotypes.

Breast cancer biobank from a single institutional cohort in an urban setting in india: Tumor characteristics and survival outcomes.

Background: A breast cancer biobank with retrospectively collected patient data and FFPE tissue samples was established in 2018 at Prashanti Cancer Care Mission, Pune, India. It runs a cancer care clinic with support from a single surgeon's breast cancer practice. The clinical data and tissue sample collection is undertaken with appropriate patient consent following ethical approval and guidelines.

Hox dosage contributes to flight appendage morphology in Drosophila.

Flying insects have invaded all the aerial space on Earth and this astonishing radiation could not have been possible without a remarkable morphological diversification of their flight appendages. Here, we show that characteristic spatial expression profiles and levels of the Hox genes Antennapedia (Antp) and Ultrabithorax (Ubx) underlie the formation of two different flight organs in the fruit fly Drosophila melanogaster. We further demonstrate that flight appendage morphology is dependent on specific Hox doses.

Promoter Proximal Pausing Limits Tumorous Growth Induced by the Yki Transcription Factor in .

Promoter proximal pausing (PPP) of RNA polymerase II has emerged as a crucial rate-limiting step in the regulation of gene expression. Regulation of PPP is brought about by complexes 7SK snRNP, P-TEFb (Cdk9/cycT), and the negative elongation factor (NELF), which are highly conserved from to humans. Here, we show that RNAi-mediated depletion of or of the 7SK snRNP complex or depletion of individual components of the NELF complex enhances Yki-driven growth, leading to neoplastic transformation of wing imaginal discs.

Genome-Wide Screen for Context-Dependent Tumor Suppressors Identified Using in Vivo Models for Neoplasia in .

Genetic approaches in have successfully identified many genes involved in regulation of growth control as well as genetic interactions relevant to the initiation and progression of cancer Here, we report on large-scale RNAi-based screens to identify potential tumor suppressor genes that interact with known cancer-drivers: the Epidermal Growth Factor Receptor and the Hippo pathway transcriptional cofactor Yorkie. These screens were designed to identify genes whose depletion drove tissue expressing EGFR or Yki from a state of benign overgrowth into neoplastic transformation We also report on an independent screen aimed to identify genes whose depletion suppressed formation of neoplastic tumors in an existing EGFR-dependent neoplasia model. Many of the positives identified here are known to be functional in growth control pathways.

Haltere development in D. melanogaster: implications for the evolution of appendage size, shape and function.

Differential specification of dorsal flight appendages, wing and haltere, in Drosophila provides an excellent model system to address a number of important questions in developmental biology at the levels of molecules, pathways, tissues, organs, organisms and evolution. Here we discuss the mechanism by which the Hox protein Ubx recognizes and regulates its downstream targets, implications of the same in growth control at cellular and organ level and finally the evolution of haltere from ancestral hindwings in other holometabolous insects.

Meta-Analysis of Prevalence of Triple-Negative Breast Cancer and Its Clinical Features at Incidence in Indian Patients With Breast Cancer.

Purpose: Breast cancer is the most common cancer in women in India, with higher incidence rates of aggressive subtypes, such as triple-negative breast cancer (TNBC).

Methods: A systematic review was performed to compute pooled prevalence rates of TNBC among patients with breast cancer, and clinical features at presentation were systematically compared with non-TNBC in an Indian cohort of 20,000 patients.

Results: Combined prevalence of TNBC among patients with breast cancer was found to be on the higher side (27%; 95% CI, 24% to 31%).

The Hox gene controls appendage shape by regulating extracellular matrix dynamics.

Although the specific form of an organ is frequently important for its function, the mechanisms underlying organ shape are largely unknown. In , the wings and halteres, homologous appendages of the second and third thoracic segments, respectively, bear different forms: wings are flat, whereas halteres are globular, and yet both characteristic shapes are essential for a normal flight. The Hox gene () governs the difference between wing and haltere development, but how function in the appendages prevents or allows flat or globular shapes is unknown.

Ataxin 2-binding protein 1 is a context-specific positive regulator of Notch signaling during neurogenesis in .

The role of the Notch pathway during the lateral inhibition that underlies binary cell fate choice is extensively studied, but the context specificity that generates diverse outcomes is less well understood. In the peripheral nervous system of , differential Notch signaling between cells of the proneural cluster orchestrates sensory organ specification. Here we report functional analysis of Ataxin 2-binding protein 1 (A2BP1) during this process.

A comparative genomic analysis of targets of Hox protein Ultrabithorax amongst distant insect species.

In the fruitfly Drosophila melanogaster, the differential development of wing and haltere is dependent on the function of the Hox protein Ultrabithorax (Ubx). Here we compare Ubx-mediated regulation of wing patterning genes between the honeybee, Apis mellifera, the silkmoth, Bombyx mori and Drosophila. Orthologues of Ubx are expressed in the third thoracic segment of Apis and Bombyx, although they make functional hindwings.

Gliolectin positively regulates Notch signalling during wing-vein specification in Drosophila.

Notch signalling is essential for animal development. It integrates multiple pathways controlling cell fate and specification. Here we report the genetic characterization of Gliolectin, presumably a lectin, a cytoplasmic protein, significantly enriched in Golgi bodies.

Critical role for Fat/Hippo and IIS/Akt pathways downstream of Ultrabithorax during haltere specification in Drosophila.

In Drosophila, differential development of wing and haltere, which differ in cell size, number and morphology, is dependent on the function of Hox gene Ultrabithorax (Ubx). Here we report our studies on Ubx-mediated regulation of the Fat/Hippo and IIS/dAkt pathways, which control cell number and cell size during development. Over-expression of Yki or down regulation of negative components of the Fat/Hippo pathway, such as expanded, caused considerable increase in haltere size, mainly due to increase in cell number.

ChIP for Hox proteins from Drosophila imaginal discs.

Chromatin immunoprecipitation (ChIP) is a technique that reveals in vivo location of a protein bound to DNA. ChIP coupled with DNA microarrays (ChIP-chip) or next-generation sequencing (ChIP-seq) allows for identification of binding sites of transcription factors on a global scale. Here we describe a protocol for ChIP to identify binding of the Ultrabithorax (Ubx) Hox transcription factors from imaginal discs of Drosophila larvae.