{"title":"StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.","authors":"Mousumi Banerjee, Abhishake Lahiri, Sohom Basak, Saptarshi DAS, Subhasis Mukhopadhyay, Rachana Banerjee, Kausik Basak","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>As various technological innovations are assisting medical science in a considerable way, rendering a significant leap towards 'lab-to-land' delivery, in a similar vein, algorithm development and concomitant framework-based approaches help the field to enrich its patient care. Although antimicrobial drugs revolutionized this particular area, antimicrobial resistance is a pressing global health concern as microbial strains are becoming resistant to conventional antibiotics, undermining the efficacy of these drugs and leading to increased illness and healthcare costs. To tackle this menace, apart from technological innovations such as diagnostic kits, an informatics-based framework approach is the call of the day. Despite the emergence of several computational approaches, they lack in generalization, scope, and scalability. Here, we have developed a novel framework StaLAENet (stacked LSTM-nested deep-autoencoder network) to predict antibiotic-resistant gene drug classes targeting ESKAPE pathogens. This framework comprises two modules: a feature representation module comprising a stacked LSTM-nested deep autoencoder and a classification module that leverages a dense network using latent features. StaLAENet demonstrated an efficient performance - accuracy: 0.938±0.043, specificity: 0.888±0.061, precision: 0.912±0.020, and recall: 0.881±0.021 - for <i>Enterococcus faecium</i> using 4-mer data, with similar results for other organisms using various <i>k</i>-mer data. Comparative analysis confirmed its superiority over existing pipelines. Further, independent evaluation with non-redundant sequences (sourced from another database) and with a metagenomic dataset highlighted its generalizability, robustness, and capability to analyze complex microbial communities. StaLAENet can offer a robust solution for combating AMR, enabling an efficient way of antimicrobial stewardship and patient care.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147639002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vijay Jayaraman, Shafqat Ali Khan, Kumar Perinbam, Isha Rakheja, Abhinav Koyamangalath Vadakkepat, Santosh Kumar Chaudhary, Asheesh Kumar Pandey, Joydeep Mitra
{"title":"A comparative study of low-pH tolerance and chitinase activity between toxigenic and non-toxigenic strains of <i>Vibrio cholerae</i>.","authors":"Vijay Jayaraman, Shafqat Ali Khan, Kumar Perinbam, Isha Rakheja, Abhinav Koyamangalath Vadakkepat, Santosh Kumar Chaudhary, Asheesh Kumar Pandey, Joydeep Mitra","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Survival of toxigenic and non-toxigenic strains of <i>Vibrio cholerae</i> involves adaptation to varying pH conditions, a mechanism which is poorly understood. Chitinase activity, which is essential for survival both inside and outside its human host at various pH levels, is not thoroughly profiled. We report on the growth and chitinase activity of two clinical isolates of <i>V. cholerae</i>: VC20, a <i>ctx</i><sup>+</sup> strain, and WO5, a <i>ctx</i><sup>-</sup> strain, at different pH. We compared the expression of key genes between these strains. WO5, the non-toxigenic strain, showed robust growth and higher chitinase activity across a wide pH range compared to VC20. WO5 expressed higher <i>omp</i>K and <i>tox</i>T transcripts, implicated in host cell adhesion and virulence, respectively. We propose that lower <i>hap</i>R levels in WO5, in contrast to VC20, are key to its low-pH tolerance. A sequence-based homology search revealed a widespread presence of low-pH adaptation modules - lysine-cadaverine and ornithine-putrescine - in multiple representative species of the <i>Vibrio</i> genus. Further, the loss of a nitrite reductase gene, which confers low-pH tolerance, is specific to <i>V. cholerae</i> and <i>V. mimicus</i>. We propose that <i>hap</i>R expression and other low-pH adaptation factors reported here could be molecular predictors of low-pH tolerance in toxigenic and non-toxigenic <i>V. cholerae</i>.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Response of mycorrhizal fungal communities to tree species composition and soil properties in the Miombo subtropical dry forest.","authors":"Likulunga Emmanuel Likulunga, Bethan Manley, Mashuta Kalebe, Mokwani Kaluwe, Saasa Ngonda, Kelvin Mwambu, Edwin Lungu, Mupelwa Nalupumbwe, Cyprian Katongo, Stephen Malunga Manchishi","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Miombo forests are ecologically and economically important; however, knowledge about mycorrhizal assemblages harboured by these ecosystems and the driving factors is scarce. We investigated the composition and diversity of soil arbuscular and ectomycorrhizal fungi in Miombo National Forest Reserves in Zambia across three sites with different tree species compositions, soil properties, and climatic conditions. Our DNA metabarcoding results identified distinct mycorrhizal fungal communities among the study sites, driven by soil pH, moisture, and nutrient content. Mycorrhizal diversity was highest at sites with low mean annual precipitation. Across all study sites, the variation in mycorrhizal fungal diversity could be explained by soil pH, moisture, and nutrients, while tree species composition contributed little variation. The taxonomic composition and relative abundances of mycorrhizal fungal genera varied among study sites. Our results suggest that changes in tree species composition have the potential to influence mycorrhizal communities in Miombo ecosystems, with implications for ecosystem functions and services.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838286","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dhruv Das, A S Kakatkar, A V S S Narayana Rao, Ravindranath Shashidhar
{"title":"<i>De novo</i> hybrid genome assembly and analysis of <i>Salmonella enterica</i> serovar Kentucky of Indian origins.","authors":"Dhruv Das, A S Kakatkar, A V S S Narayana Rao, Ravindranath Shashidhar","doi":"","DOIUrl":"","url":null,"abstract":"<p><p><i>Salmonella enterica</i> serovar Kentucky has emerged as a global human food-borne pathogen with a known phenotype of multidrug resistance. Whole-genome sequencing of the lab-isolated organism was performed to understand its genomic features using the Illumina platform. The assembled genome, utilizing short reads only, poses gaps that need to be resolved to completely close the genome. To improve the genome assembly, we developed a strategy that utilizes publicly available long reads produced by Nanopore sequencing of a similar strain for <i>de novo</i> hybrid assembly. This approach yielded one completely closed chromosome and three completely closed plasmids. The assembled genome showed the presence of antimicrobial-resistant genes on both chromosome as well as plasmid present in the isolate. Four prophage regions and one CRISPR cluster were also identified on the chromosome. The sequenced isolate of <i>S. enterica</i> serovar Kentucky belongs to sequence type ST198, exhibiting multidrug resistance, including to ciprofloxacin, that causes human non-typhoidal <i>Salmonella</i> infections. This study provides a simple workflow to improve the completeness of assembled genome, in the scenario where long reads of the same isolate are not available for genome assembly.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147638991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Interdependence of cytosolic and mitochondrial calcium dynamics in a hepatocyte cell due to obesity.","authors":"Vedika Mishra, Neeru Adlakha","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The intentional placement of mitochondria in close proximity to calcium ion (Ca<sup>2+</sup>) release sites enables the quick uptake of cytosolic Ca<sup>2+</sup> and the close connection of calcium signaling with energy metabolism. Ca<sup>2+</sup> dynamics have been thoroughly investigated in various cells, including hepatocytes. However, little is known about the interaction between cytosolic and mitochondrial Ca<sup>2+</sup> dynamics and how it affects adenosine triphosphate (ATP) hydrolysis and nicotinamide adenine dinucleotide (hydrogen) (NADH) production downstream, especially in pathological conditions such as obesity. In this study, we introduce a new reaction-diffusion model of hepatocyte cells that accurately depicts the linked dynamics of mitochondrial and cytosolic Ca<sup>2+</sup> in both normal and obese states. Important physiological processes, including intracellular buffering, mitochondrial calcium uniporters, Na<sup>+</sup>/Ca<sup>2+</sup> exchangers, and Ca<sup>2+</sup> input sources, are integrated into the model. For precise numerical simulations, a combination of the Crank-Nicolson scheme and a linear finite element approach is used. The results show that obese hepatocytes differ significantly from normal cells in terms of calcium signaling, ATP hydrolysis rates, and NADH production. These findings may help guide future experimental and therapeutic research aimed at metabolic liver illnesses and offer fresh insights into how obesity-induced deregulation of calcium dynamics affects cellular energy metabolism.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147639051","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Computational insights into cancer stem cell dynamics and the urokinase plasminogen activation pathway.","authors":"Kumari Neelam Verma, Debabrata Dasgupta","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This study introduces a novel computational model that integrates cancer stem cells (CSCs) and the plasminogen activation system, filling a crucial gap in cancer research. While theoretical models have separately explored CSCs and the plasminogen activation system, no prior computational framework has combined these elements. Our model focuses on the invasion dynamics of CSCs, emphasizing the critical interactions between urokinase plasminogen activator (uPA) and plasminogen activator inhibitor-1 (PAI-1). We employed reaction-diffusion equations and analyzed the determinant and eigenvalue spectra of the Jacobian matrix of the system to identify instability regions within tumors. The findings revealed that the production and binding of uPA and PAI-1 significantly enhance the invasiveness and motility of CSCs, resulting in more complex and aggressive tumor structures. Our study advances the theoretical understanding of cancer dynamics by integrating these two critical biological processes into a single computational framework. This work builds upon and extends previous models by offering a more comprehensive analysis of tumor growth, with significant implications for optimizing cancer treatment strategies. The insights of the model into the interplay between CSCs and the plasminogen activation system offer a valuable tool for both research and potential clinical applications, paving the way for more targeted and effective therapeutic approaches.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"How nettle (<i>Urtica dioica</i>) 'stings' <i>Candida albicans</i> by affecting its virulence factors.","authors":"Dua'a Riyad Husain Al-Saleh, Homa Darmani","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>With increasing incidence of drug resistance and toxicity associated with current treatments, new alternatives are needed for <i>Candida albicans</i> infections. This study evaluated the potential of <i>Urtica dioica</i> aqueous extract and essential oil as natural phytotherapeutic agents against <i>C. albicans</i>, with a focus on important virulence factors that contribute to the development of infection and survival in the host. Our findings demonstrate that <i>U. dioica</i> essential oil effectively suppressed the growth of <i>C. albicans</i> and exhibited synergistic activity with amphotericin B, suggesting that it could reduce the effective dose of amphotericin B required, and possibly limit its undesirable side effects. Significant and notable inhibition of phenotypic switching was also observed, with the most pronounced effects seen when used in combination with amphotericin B. Since hyphae are critical for host invasion, this inhibition could impede the ability of <i>C. albicans</i> to cause disseminated infections. In addition, <i>U. dioica</i> essential oil also inhibited the biofilm-forming ability of <i>C. albicans</i>, a key factor contributing to the morbidity and mortality of hospitalized patients, due to biofilm-related resistance to antimicrobial therapy. Complete inhibition of phospholipase and hemolysin activity was also observed; as key extracellular enzymes, these contribute to the virulence of <i>C. albicans</i> and its persistence in the host. In conclusion, <i>U. dioica</i> essential oil targets multiple <i>C. albicans</i> virulence factors, potentially limiting infection <i>in vivo</i>. When used in combination with amphotericin B, it may boost antifungal efficiency, offering a promising new strategy against candidiasis.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147276298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Baso Manguntungi, Iman Rusmana, Apon Zaenal Mustopa, Anja Meryandini
{"title":"Exploring <i>Psychrobacter</i> sp. EQ05 (bacterial symbiont of <i>Entaqmea quadricolor</i>): A natural anti-quorum-sensing agent against <i>Vibrio parahaemolyticus</i>.","authors":"Baso Manguntungi, Iman Rusmana, Apon Zaenal Mustopa, Anja Meryandini","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Quorum sensing (QS) is a critical communication system in bacteria that enables them to sense population density through auto-inducers, notably, N-acyl homoserine lactones (AHLs). This study focuses on the role of QS in <i>Vibrio parahaemolyticus</i>, a significant pathogen affecting vannamei shrimp, where it regulates virulence factors such as hemolysins and biofilm formation. We explored the potential of anti-QS agents derived from a <i>Psychrobacter</i> sp., which produces AHL lactonase capable of degrading AHLs and disrupting QS signaling pathways. The purification of AHL lactonase was achieved through chromatographic techniques, yielding a protein with a molecular weight of 28-30 kDa, consistent with previous findings. AHL degradation tests have demonstrated that AHL lactonase was significantly more effective than metabolites from <i>Psychrobacter</i> in breaking down AHLs. However, the metabolites exhibited superior biofilm inhibition activity, indicating distinct mechanisms in disrupting bacterial adherence and virulence. Gene expression analysis revealed that AHL lactonase effectively suppressed virulence-related genes, while the metabolites influenced gene regulation differently. This study highlights the dual mechanisms of action from a <i>Psychrobacter</i> sp. - direct AHL degradation and inhibition of AHL synthesis, offering a promising biocontrol strategy against <i>V. parahaemolyticus</i> infections in shrimp aquaculture. These findings suggest that integrating these approaches could enhance pathogen management, ultimately supporting sustainable aquaculture practices. Further research is warranted to elucidate the underlying molecular mechanisms and optimize the application of these biocontrol agents in disease management.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146029729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Human tears as social chemo-signals in taming male aggression.","authors":"Satish Suhas, Reeteka Sud, Shridhar J Utagi, Sanjeev Jain, Biju Viswanath","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The human brain is endlessly fascinating and complex. It is also highly plastic, shaped by numerous interacting factors, including sociocultural influences. Gender is one such factor, whose influence plays out on biological and cultural levels, inescapably intertwined with each other (Mei <i>et al</i>. 2022). The field of social neuroscience, which is tasked with parsing the neural, hormonal, cellular, and genetic mechanisms of social behavior is rather young, despite the possibility that chemo-signaling plays a complex role in evolution (Graziano 2022). Exposure to predator odors prompts prey animals, particularly rodents, to exhibit escape or defensive behaviors, sparking discussions on whether a single volatile compound or a combination of odors triggers these responses (Apfelbach <i>et al</i>. 2015). The effect of sex/gender on the social brain has clear clinical relevance (Pavlova 2017). Changes in odor perception are seen in many disease syndromes, including neuropsychiatric disorders. Mechanisms that interlink sex differences in the brain to disease biology, to manifest behavioral differences, thus need to be investigated (Eslinger <i>et al</i>. 2021).</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147639046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dengxing Li, Bao Liao, Huimin Wei, Fengmei Li, Jinyong Teng, Lili Wei, Yueyuan Huang, Qin Yang, Shaofa Li
{"title":"Distinct macrophage and microglia function in ischemic stroke.","authors":"Dengxing Li, Bao Liao, Huimin Wei, Fengmei Li, Jinyong Teng, Lili Wei, Yueyuan Huang, Qin Yang, Shaofa Li","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>This study aims to explore the characteristics and differentiation pathways of microglia and macrophages using single-cell transcriptome data from mouse stroke models. The clusters of microglia and macrophages in the middle cerebral artery occlusion model mouse brain were identified using the Seurat package. The signaling pathways were evaluated through Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes analyses, while transcription factor activity was analyzed using DecoupleR. Monocle2 was employed to infer the differentiation trajectory of microglia and macrophages, exploring changes in gene expression patterns during their activation process using gene dynamics analysis. Additionally, the self-differential and overlapping subclusters of macrophages and microglia following cerebral ischemia were assessed, and CellChat was used to analyze differences in cell communication. An <i>in vitro</i> oxygen-glucose deprivation model of BV2 microglia was established, and phagocytosis assays and real-time-quantitative PCR were conducted to evaluate the effects of FoxO1 knockdown on the phagocytic ability and inflammatory cytokine production of microglia. Microglia and macrophages showed significant functional changes following ischemic stroke. Microglia enhance their phagocytic capabilities, whereas macrophages exhibited a reduction in phagocytic function. The predominance of microglia in phagocytic and inflammatory pathways is primarily attributed to the differential expression of specific transcription factors, particularly FoxO1. Knockdown of FoxO1 significantly diminished the phagocytic ability of BV2 cells and increased the expression of the inflammatory cytokines CCL2, IFN-γ, and TNF. The transcription factor FoxO1 mediates the functional differences in phagocytosis and inflammatory responses between macrophages and microglia. Activation of FoxO1 can significantly enhance the phagocytic capacity of microglia while simultaneously reducing inflammatory responses, positioning it as a potential new target for the treatment of ischemic stroke.</p>","PeriodicalId":15171,"journal":{"name":"Journal of Biosciences","volume":"51 ","pages":""},"PeriodicalIF":1.9,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}