Journal of Biosciences最新文献

Tumors have drawn increasing attention recently because of their heterogeneous interior structures. Particularly, single-cell RNA (scRNA) mechanics have made important contributions to the field of tumor research. To investigate the cell types and identify similar types of gene markers present inside a tumor, machine learning classifier, optimization, and neural network models were applied to scRNA sequencing data. Indeed, even though single-cell analysis is a more powerful tool, several issues have been identified, such as transcriptional noise that alters gene expression and degrades mRNA. Recently, optimization models for single-cell analysis have been developed to address these kinds of issues, and encouraging results have been reported. scRNA sequencing is popular because it produces biological information in the form of patterns that are displayed within the transcriptome profile. The neural network approach plays an important role in understanding and identifying these distinct patterns. A single layer perceptron was introduced to better analyze the data pattern within gene expression profiles. Finally, recently developed optimization models with machine learning classifiers are compared with the proposed single layer perceptron. The single layer perceptron performs better compared with other models such as extra tree classifier with genetic algorithm, k-nearest neighbors with bat optimization, decision tree with gray wolf optimization, random forest with firefly optimization, and Gaussian naïve Bayes with artificial bee colony optimization. This study also focused on classifying these unique cell types and gene markers using scRNA sequence datasets. The proposed single layer perceptron was assessed using two datasets: normal mucosa and colorectal tumors. Our findings showed that the proposed single layer perceptron performed exceptionally well with accuracy, precision, recall, and F1 value.

Abstract

Cell type-specific expression of genes plays a pivotal role in the development and evolution of multicellular organisms over millions of years. The majority of regulatory control resides within the non-coding regions of the genome, referred to as ‘dark matter’, which contains cis-regulatory modules. These cis-regulatory modules function collectively and can impact gene expression even when located far from the target gene, exhibiting context-specific behaviour. Consequently, the cis-regulatory code governing gene expression patterns is intricate, in contrast to the universally understood genetic code. This overview centres on the current knowledge regarding cis-regulatory elements, primarily enhancers and their role in governing the spatiotemporal gene expression patterns, and how they have evolved and adapted across different species.

Phototrophic organisms harbor two main bioenergetic hubs, photosynthesis and respiration, and these processes dynamically exchange and share metabolites to balance the energy of the cell. In microalgae and cyanobacteria, the crosstalk between the light-triggered reactions of photosynthesis and respiration is particularly prominent with respiratory O₂ uptake which can be stimulated upon illumination. Since its discovery, this light-enhanced respiration has been proposed to be critical in dissipating the excess reducing power generated by photosynthesis. Importantly, the physiological role and putative molecular mechanism involved have just recently started to be understood. Here, we revisit the physiological functions and discuss possible molecular mechanisms of interactions between the photosynthetic and respiratory electron flows in microalgae and cyanobacteria.

Stomatal guard cells are unique in that they have more mitochondria than chloroplasts. Several reports emphasized the importance of mitochondria as the major energy source during stomatal opening. We re-examined their role during stomatal closure. The marked sensitivity of stomata to both menadione (MD) and methyl viologen (MV) demonstrated that both mitochondria and chloroplasts helped to promote stomatal closure in Arabidopsis. As in the case of abscisic acid (ABA), a plant stress hormone, MD and MV induced stomatal closure at micromolar concentration. All three compounds generated superoxide and H₂O₂, as indicated by fluorescence probes, BES-So-AM and CM-H₂DCFDA, respectively. Results from tiron (a superoxide scavenger) and catalase (an H₂O₂ scavenger) confirmed that both the superoxide and H₂O₂ were requisites for stomatal closure. Co-localization of the superoxide and H₂O₂ in mitochondria and chloroplasts using fluorescent probes revealed that exposure to MV initially triggered higher superoxide and H₂O₂ generation in mitochondria. In contrast, MD elevated superoxide/H₂O₂ levels in chloroplasts. However, with prolonged exposure, MD and MV induced ROS production in other organelles. We conclude that ROS production in mitochondria and chloroplasts leads to stomatal closure. We propose that stomatal guard cells can be good models for examining inter-organellar interactions.

Snake venom L-amino acid oxidases (LAAOs) are flavoenzymes with diverse physiological and pharmacological effects. These enzymes are found to showcase anticoagulant, antiplatelet, cytotoxicity and other biological effects in bite victims. However, the exact mechanism through which they exhibit several biological properties is not yet fully understood. The current study focussed on the purification of cobra venom LAAO and the functional characterization of purified LAAO. A novel L-amino acid oxidase NNLAAO70 with a molecular weight ~70 kDa was purified from the venom of an Indian spectacled cobra (Naja naja). NNLAAO70 showed high substrate specificity for L-His, L-Leu, and L-Arg during its LAAO activity. It inhibited adenosine di-phosphate (ADP) and collagen-induced platelet aggregation process in a dose-dependent manner. About 60% inhibition of collagen-induced and 40% inhibition of ADP-induced platelet aggregation was observed with a 40 μg/ml dose of NNLAAO70. NNLAAO70 exhibited bactericidal activity on Bacillus subtilis, Escherichia coli, Bacillus megaterium, and Pseudomonas fluorescens. NNLAAO70 also showed cytotoxicity on A549 cells in vitro. It showed severe bactericidal activity on P. fluorescens and lysed 55% of cells. NNLAAO70 also exhibited drastic cytotoxicity on A549 cells. At 1 μg/ml dosage, it demonstrated a 60% reduction in A549 viability and induced apoptosis upon 24-h incubation. H₂O₂ released during oxidative deamination reactions played a major role in NNLAAO70-induced cytotoxicity. NNLAAO70 significantly increased intracellular reactive oxygen species (ROS) levels in A549 cells by six fold when compared to untreated cells. Oxidative stress-mediated cell injury is the primary cause of NNLAAO70-induced apoptosis in A549 cells and prolonged oxidative stress caused DNA fragmentation and activated cellular secondary necrosis.

In recent years, several experimental evidences suggest that amino acid repeats are closely linked to many disease conditions, as they have a significant role in evolution of disordered regions of the polypeptide segments. Even though many algorithms and databases were developed for such analysis, each algorithm has some caveats, like limitation on the number of amino acids within the repeat patterns and number of query protein sequences. To this end, in the present work, a new method called the internal sequence repeats across multiple protein sequences (ISRMPS) is proposed for the first time to identify identical repeats across multiple protein sequences. It also identifies distantly located repeat patterns in various protein sequences. Our method can be applied to study evolutionary relationships, epitope mapping, CRISPR-Cas sequencing methods, and other comparative analytical assessments of protein sequences.

Multiple endocytic processes operate in cells in tandem to uptake multiple cargoes involved in diverse cellular functions, including cell adhesion and migration. The best-studied clathrin-mediated endocytosis (CME) involves the formation of a well-defined cytoplasmic clathrin coat to facilitate cargo uptake. According to the glycolipid–lectin (GL–Lect) hypothesis, galectin-3 (Gal3) binds to glycosylated membrane receptors and glycosphingolipids (GSLs) to drive membrane bending and tubular membrane invaginations that undergo scission to form a morphologically distinct class of uptake structures, termed clathrin-independent carriers (CLICs). Which components from cytoskeletal machinery are involved in the scission of CLICs remains to be explored. In this study, we propose that dynein is recruited onto Gal3-induced tubular endocytic pits and provides the pulling force for friction-driven scission. The uptake of Gal3 and its cargoes (CD98/CD147) is significantly dependent on dynein activity, whereas only transferrin (CME marker) is slightly affected upon dynein inhibition. Our study reveals that Gal3 and Gal3-dependent (CD98 and CD147) clathrin-independent cargoes require dynein for the clathrin-independent endocytosis.

Inherited genetic disorders are progressive in nature and lead to organ dysfunction or death in severe cases. At present, there are no permanent treatment options for >95% of inherited disorders. Different modes of inheritance, type of gene(s) involved, and population-based variations add further complexity to finding suitable cures for approximately 400 million patients worldwide. Gene therapy is a very promising molecular technique for the treatment of rare genetic disorders. Gene therapy functions on the basis of restoration, replacement, inhibition, and, most recently, editing of gene(s) to rescue the disease phenotype. Recent reports show that increasing numbers of gene therapy clinical trials are using viral vectors (64.2%) when compared with non-viral vectors. Rapid development of efficient viral vector systems like the adeno-associated virus (AAV) and lentivirus has significantly contributed to this progress. Notably, AAV-mediated gene therapy has shown high potential for genetic disease treatment as evident from recent clinical trials for the eye (NCT00999609), blood (NCT00979238), and neuro-muscular systems (NCT02122952). Safety and efficacy are the two most critical features required for vector(s) to qualify for pre-clinical and clinical trial approval. The process of clinical-grade vector production, evaluation, and approvals for gene therapy products requires significant technological development, knowledge enhancement, and large financial investments. Additionally, trained manpower is required to meet the demands for constant technical innovation. These factors together contribute towards exorbitant prices for every dose of a gene therapy product and thus pose a challenge for the gene therapy field. The Indian subcontinent has traditionally lagged behind North America, Europe, Japan, and others in gene therapy clinical trials due to factors like inadequate industrial-scientific infrastructure, lack of accessible and organized patient databases, low financial investments, etc. However, over the last decade, increasing awareness of rare diseases, and international approvals of gene therapies such as Luxturna, Zolgensma, Hemgenix, etc., have spurred gene therapy development in India as well. In view of these advances, this article outlines gene therapy research, regulatory processes, and the launch of gene therapy clinical trials in India in the context of major developments worldwide. We briefly describe ongoing gene therapy research across Indian organizations and the nascent gene therapy product manufacturing. Further, we highlight the various initiatives from the medical and patient community to avail rehabilitation and gene therapy options. We briefly discuss the roles of regulatory agencies and guidelines for gene therapy clinical trials in India. We anticipate that this concise review will highlight the promise of gene therapy for the large population of rare disease patients in India.

Gaucher disease (GD) is a prevalent lysosomal storage disorder (LSD) that significantly impacts individuals’ lives. However, the exorbitant prices of GD medications pose a major hurdle in ensuring widespread availability and affordability of treatment in India. The country heavily relies on imported medications, leading to high costs and limited access for many patients. This article aims to address this issue by advocating for the establishment of indigenous manufacturing capabilities for GD medicines in India. Through an examination of the current landscape of GD treatment, including the availability, affordability, and challenges associated with imported medications, this article highlights the urgent need for localized production. By focusing on the potential benefits of indigenous manufacturing, such as reduced costs, increased accessibility, and enhanced availability, this research aims to provide insights and recommendations to policymakers, healthcare professionals, and relevant stakeholders. The findings underscore the importance of developing domestic manufacturing capabilities to address the affordability and accessibility challenges faced by GD patients in India. The research also emphasizes the potential positive impact on the healthcare system, the pharmaceutical industry, and the overall well-being of individuals with GD. Ultimately, this article seeks to stimulate discussions and actions towards creating a sustainable framework for indigenous manufacturing of GD medicines, thereby improving the lives of those affected by this rare and debilitating condition.

Spinal muscular atrophy (SMA) is a neuromuscular, rare genetic disorder caused due to loss-of-function mutations in the survival motor neuron-1 (SMN1) gene, leading to deficiency of the SMN protein. The severity of the disease phenotype is inversely proportional to the copy number of another gene, SMN2, that differs from SMN1 by a few nucleotides. The current diagnostic methods for SMA include symptom-based diagnosis, biochemical methods like detection of serum creatine kinase, and molecular detection of disease-causing mutations using polymerase chain reaction (PCR), multiplex ligation-dependent probe amplification (MLPA), and exome or next-generation sequencing (NGS). Along with detection of the disease-causing mutation in the SMN1 gene, it is crucial to identify the copy number of the SMN2 gene, which is a disease modifier. Therapeutic options like gene therapy, antisense therapy, and small molecules are available for SMA, but, the costs are prohibitively high. This review discusses the prevalence, diagnosis, available therapeutic options for SMA, and their clinical trials in the Indian context, and highlights the need for measures to make indigenous diagnostic and therapeutic interventions.