Evaluating Differential Gene Expression Using RNA-Sequencing: A Case Study in Diet-Induced Mouse Model Associated with Non-Alcoholic Fatty Liver Disease (NAFLD) and CXCL12-Vs- TGFβ Induced Fibroblast to Myofibroblast Phenoconversion

Unlike the genome, cell transcriptome is dynamic and specific for a given cell developmental stage. Transcriptomics study is crucial to understand the functional elements of the genome to divulge molecular constituents of cells. The recent development of high-throughput sequencing technologies has provided an unprecedented method to sequence RNA and it has been emerging as the preferred technology for both characterization and quantification of the cell transcripts. Using “Tailor_Pipeline” we have analyzed diet-induced mouse and stromal fibroblast RNA-Seq samples and deciphers the differentially expressed genes that were significantly up- and downregulated and associated with several metabolic immune responses that presumably associated with liver disease. Analyzing the diet-induced mice model allowed us to encapsulate the transcriptional differences between diet-induced mice that can aid in the understanding of NAFLD and consequent liver pathogenesis. Identification of genes downregulated in metabolic processes and upregulated in immune responses indicate that mice model exhibiting liver disease. Moreover, the finding of a premalignant signature suggests that NAFLD may begin to progress towards hepatocellular carcinoma much earlier than earlier consideration. Tissue fibrosis arises due to overgrowth, scarring of various tissues and is attributed to deposition of the extracellular matrix including collagen, influenced by the actions of several pro-fibrotic proteins that can induce myofibroblast phenoconversion. Though recent transcriptomics analysis reveals the cellular identity, its ability to provide biologically meaningful insights in fibrosis is largely unexplored. To unravel the mechanisms at the genetic level, we have considered TGFβ/TGFβR and CXCL12/CXCR4 transcriptomes in human stromal fibroblasts. Transcriptome profiling technology revealed CXCL12/CXCR4 axis is responsible for the activation of COPII vesicle formation, ubiquitination, and Golgi/ER localization/targeting. Especially, identification of CUL3 and KLHL12 are responsible for the transportation of procollagen from ER to the Golgi. Interestingly, over-expression of CUL3 and KLHL12 are highly correlated with procollagen secretion by CXCL12-treated cells, but not in TGFβ-, treated cells. Moreover, this analysis showed how activation of the CXCL12/CXCR4 axis promotes procollagen I secretion that responsible for the deposition of ECM which is a characteristic of fibrosis

Analysis of indole-and caffeine-resistant mutations of Schizophyllum commune involved in mating and fruiting

博士論文 (Doctoral dissertation)doctoral thesi

Life cycle assessment of solid waste management options: A Review

Evaluating the environmental performance of municipal solid waste management options is a complex job. LCA is an analytical tool (software) for assessing the environmental acceptability of municipal solid waste management (MSWM) options. LCA is currently being used in several countries to evaluate different strategies for integrated solid waste management and to evaluate treatment options for waste fractions. According to the characteristics of solid wastes, and availability of disposal options, LCA helps in supporting the identification of opportunities for pollution prevention and reductions in resource consumption while taking the entire solid waste life cycle. The primary elements of solid waste management are generation, collection, transportation, treatment, and disposal. Different scenarios were developed and reported as alternatives to the current waste management systems. The most prominent is material recovery facility (MRF) and other methods involve source reduction, reuse, recycling, composting, incineration, energy recovery, on-site burial, open burning and bioremediation. The goal of this review is to determine the most environmentally friendly option of MSWM system with the help of LCA

Kannan-type cyclic contraction results in 22-Menger space

summary:In this paper we establish Kannan-type cyclic contraction results in probabilistic 2-metric spaces. We use two different types of $t$-norm in our theorems. In our first theorem we use a Hadzic-type $t$-norm. We use the minimum $t$-norm in our second theorem. We prove our second theorem by different arguments than the first theorem. A control function is used in our second theorem. These results generalize some existing results in probabilistic 2-metric spaces. Our results are illustrated with an example

<em>Drosophila melanogaster</em>: A Robust Tool to Study Candidate Drug against Epidemic and Pandemic Diseases

Drosophila melanogaster is a widely used, dynamic model organism to study various pathogenic diseases observed ubiquitously in the human population. Drosophila, at present, is extensively used to conduct preclinical studies besides its counterpart rodents. The epidemic and pandemic diseases are discussed in this review to demonstrate Drosophila melanogaster as a key model. Epidemic and pandemic diseases are still claiming more than 5 million lives every year, and these diseases were well studied in flies. Currently there is no cure for the disease like HIV; the bacterial and fungal infections usually seen in HIV/AIDS patients could be demonstrated elaborately in Drosophila melanogaster. Diseases like myocardial infractions and cancer causing viral infection are long term effects of ART (anti-retroviral therapy) that could be experimented in flies. Stable Drosophila S2 cell line, Transgenic flies, transfusion of bacteria and fungi could be implemented to study several infectious diseases and for vaccine development. The latest trends in understanding pathogenic diseases and its potential biochemical markers in flies are discussed in this review to utilize the fruit flies as a functional tool and to explore further it in drug development. The advantages and disadvantages of the fly as a model of infection are discussed along with the epidemiology and the cellular pathophysiolog

PREVALENCE AND EPIDEMIOLOGY OF GASTROINTESTINAL HELMINTHS IN DAIRY COWS IN "BATHAN" AREAS OF BANGLADESH

A Thesis Submitted to the Department of Microbiology and Parasitology Sher-e-Bangla Agricultural University, Dhaka in Partial fulfillment of the requirements For the degree of MASTER OF SCIENCE (MS) IN ParasitologyA one year (2018-19) prevalence study on gastrointestinal helminth was conducted in Bathan areas (Pabna and Sirajgonj districts) of Bangladesh. The study was conducted between September,2018 to August,2019. A total of 144 samples were taken from both indigenous and crossbred cattle from 5 selected upazillas of two districts. Qualitative examination were done by a series of routine coproscopical methods including direct smear technique, sedimentation technique, centrifugal technique and floatation technique as qualitative methods and Mcmaster method of egg counting as quantitative technique. The effects of topography, season, age and gender were tested in both crossbred and local cattle. Over all prevalence was found 81.94%. Multiple infections were found in 32.2% cases. The prevalence was highest in the rainy season(85.71%) followed by summer season (81.63%) and winter season (79.24%).Total six types of helminth were listed, out of which two were trematodes and four were nematodes. Higher amount of prevalence was recorded in older cattle (85.33%) than younger catlle (78.26%).Overall prevalence of Fascilola spp. was (27.08%), which was highest in the study followed by Paramphistomum spp.(20.13%), Strongyle spp.(20.13%), Haemonchus spp.(13.88%). Average EPG found in the whole study was 211.65 which was highest in rainy 259.11 followed by summer (225.11) and winter (158.18). It can be concluded that a favorable humid condition during rainy season favors the growth of propagation of developmental stages which would be the reason of peak prevalence. Further studies can be helpful to find out the actual causes of parasitism and to develop measures against it

Is toxicity a curse or blessing, or both?—Searching answer from a disease-induced consumer-resource system

Chemical toxins exposed in environments and disease outbreaks are global threats to ecosystems in the present era of the anthropocene. Toxin favors disease progression trivially. However, it is still unclear whether the toxin impacts disease elimination too. Toxin also has a significant role in amplifying the risk of disease-induced consumer extinction. Identification of the extinction vortex and its associated precursors are the two most important pillars for understanding the effect of the toxin on the sustainability of ecosystems. On the other hand, the contribution of toxin as a potential agent for stabilizing a disease-induced consumer-resource system is still unclear. Although disease stabilizes the system in absence of toxicity. In order to address this, we consider a mathematical model of disease transmission in the consumer population where both ecological and epidemiological traits are affected by environmental toxins. The proposed model integrates two compartments (susceptible and infected) for consumers and the resource, where the toxin is incorporated in the form of species body burdens. Apart from the formal stability analysis, we extensively use codim-1 and codim-2 bifurcation through MATCONT software for understanding the different dynamical regimes of disease progression and elimination. These derived regimes will be helpful to raise the alarm and take intervention policies

Ethnozoological Perspectives on Otter Fishing in the Indian Sundarban: Evolution of Traditional Knowledge, Its Drivers and Revival Mechanisms

Otters had existed for over 23 million years, with modern forms evolving around 7 million years ago. Initially land-dwelling, they gradually adapted to aquatic environments developing webbed feet, enhanced lung capacity, and dense fur for cold-water insulation while retaining terrestrial mobility. This adaptability enabled unique human-otter interactions, such as traditional otter-assisted fishing, which had still been practiced in parts of the Sundarban World Heritage Site, India. This study investigated the evolution, drivers, and decline of otter-fishing traditions in South 24 Parganas, West Bengal, focusing on the life cycle, social behavior, foraging strategies, communication, seasonal and habitat adaptations, ecological roles, and conservation challenges of the Smooth-Coated Otter (Lutrogale perspicillata). A cross-sectional analytical approach was used, incorporating structured interviews, radar plots, and binary logistic regression among 124 otter-fishing community members (February–May 2024). Results revealed low awareness levels (39–47%) across knowledge domains, with 60.48% of respondents showing low knowledge retention and only 8.88% exhibiting high retention. Key predictors of knowledge retention included Elder Interaction (β = 1.006, p &lt; 0.01), Cooperative Membership (β = 1.390, p &lt; 0.05), and Access to Media (β = 0.856, p &lt; 0.10). Ecologically, otters had played a vital role as meso-carnivores, maintaining aquatic ecosystem balance through trophic interactions and habitat modifications. However, habitat degradation, fish stock depletion, and the erosion of intergenerational knowledge transmission had threatened this tradition. To address these challenges, this study recommended the revival of traditional knowledge through oral history documentation, the establishment of eco-museums, and media-led awareness campaigns. Strengthening community-based networks would support the coexistence of biodiversity and livelihoods in the Sundarbans, highlighting a model for integrating indigenous knowledge with conservation

SMAR1 binds to T(C/G) repeatvand inhibits tumor progression by regulating miR-371-373 cluster

Chromatin architecture and dynamics are regulated by various histone and non-histone proteins. The matrix attachment region binding proteins (MARBPs) play a central role in chromatin organization and function through numerous regulatory proteins. In the present study, we demonstrate that nuclear matrix protein SMAR1 orchestrates global gene regulation as determined by massively parallel ChIPsequencing. The study revealed that SMAR1 binds to T(C/G) repeat and targets genes involved in diverse biological pathways. We observe that SMAR1 binds and targets distinctly different genes based on the availability of p53. Our data suggest that SMAR1 binds and regulates one of the imperative microRNA clusters in cancer and metastasis, miR-371-373. It negatively regulates miR-371-373 transcription as confirmed by SMAR1 overexpression and knockdown studies. Further, deletion studies indicate that a ~200 bp region in the miR-371-373 promoter is necessary for SMAR1 binding and transcriptional repression. Recruitment of HDAC1/mSin3A complex by SMAR1, concomitant with alteration of histone marks results in downregulation of the miRNA cluster. The regulation of miR-371-373 by SMAR1 inhibits breast cancer tumorigenesis and metastasis as determined by in vivo experiments. Overall, our study highlights the binding of SMAR1 to T(C/G) repeat and its role in cancer through miR-371-37

Combined antitumor effects of bee venom and cisplatin on human cervical and laryngeal carcinoma cells and their drug resistant sublines

In the present study, we investigated the possible combined anticancer ability of bee venom (BV) and cisplatin towards two pairs of tumour cell lines: parental cervical carcinoma HeLa cells and their cisplatin-resistant HeLa CK subline, as well as laryngeal carcinoma HEp-2 cells and their cisplatin-resistant CK2 subline. Additionally, we identified several peptides of BV in the BV sample used in the course of the study and determined the exact concentration of MEL. BV applied alone in concentrations of 30 to 60 μg ml-1 displayed dose-dependent cytotoxicity against all cell lines tested. Cisplatin-resistant cervical carcinoma cells were more sensitive to BV than their parental cell lines (IC50 values were 52.50 μg ml-1 for HeLa vs. 47.64 μg ml-1 for HeLa CK cells), whereas opposite results were obtained for cisplatin-resistant laryngeal carcinoma cells (IC50 values were 51.98 μg ml-1 for HEp-2 vs. &gt; 60.00 μg ml-1 for CK2 cells). Treatment with BV alone induced a necrotic type of cell death, as shown by characteristic morphological features, fast staining with ethidium-bromide and a lack of cleavage of apoptotic marker poly (ADP-ribose) polymerase (PARP) on Western blot. Combined treatment of BV and cisplatin induced an additive and/or weak synergistic effect towards tested cell lines, suggesting that BV could enhance the killing effect of selected cells when combined with cisplatin. Therefore, a greater anticancer effect could be triggered if BV was used in the course of chemotherapy. Our results suggest that combined treatment with BV could be useful from the point of minimizing the cisplatin concentration during chemotherapy, consequently reducing and/or postponing the development of cisplatin resistance