Biology subjects

Karim, M. R.

Publications and source records attributed to Karim, M. R..

8 recordsLinked to original sources

bioRxiv2026

Species-level controls of foliar methane and nitrous oxide fluxes: roles of traits and microbes in temperate trees

The contribution of tree foliage to atmospheric methane (CH4) and nitrous oxide (N2O) fluxes remains a major uncertainty in global GHG budgets. We made repeated in situ measurements of foliar CH4 and N2O fluxes across 25 temperate tree species interplanted at a forest restoration site using high-resolution laser spectroscopy. Tree foliage was consistently a net CH4 sink and a net N2O source in all species. Foliar CH4 oxidation increased by [~]33% in fall relative to spring and was [~]3-fold higher in shade-tolerant than shade-intolerant angiosperm species. Species differences accounted for most of the variability in fluxes, while correlations with soil emissions were comparatively weak. Microbial DNA sequencing revealed that the highest CH4-oxidizing angiosperm species (Tilia americana) harbored abundant Type I methanotrophs, whereas the lowest-oxidizing species (Prunus virginiana) had nearly 100-fold lower methanotroph abundance, with a foliar microbial community dominated by facultative methylotrophs. Global warming potential (GWP) scaling indicates that foliar CH4 uptake overwhelmingly dominates the net climate forcing effect. Our results suggest that the large and predictable differences in foliar CH4 uptake among tree species and associated differences in foliar microbial communities are of importance in understanding and potentially enhancing the global terrestrial CH4 sink.

ecology↗

bioRxiv2025

Distribution and environmental drivers of multi-functional community traits in the Sundarbans mangrove forest

Mangrove forests are vital blue-carbon ecosystems, playing a crucial role in global carbon storage, climate regulation, and biodiversity conservation. However, escalating environmental threats, particularly salinity intrusion, necessitate a deeper understanding of their functional dynamics to inform effective conservation and restoration strategies. This study examines the distribution of multi-functional community traits (MFCT) and their environmental drivers across mangrove functional groups (pioneer, mid-successional, climax) along salinity gradients in the Sundarbans, the worlds largest mangrove forest. Using data from 62 plots, nine functional traits from 17 mangrove species were analysed to evaluate MFCT diversity and its environmental determinants. Results revealed distinct variations in MFCT diversity, with mid-successional species exhibiting the highest trait diversity (64.0 {+/-} 1.58), followed by climax (51.3 {+/-} 2.09) and pioneer groups (50.2 {+/-} 2.26). Climax species demonstrated resilience to salinity increases (R{superscript 2} = 0.29, p < 0.001), whereas mid-successional and pioneer groups were negatively affected (R{superscript 2} = 0.22, p < 0.001 and R{superscript 2} = 0.17, p < 0.001). Annual precipitation exerted contrasting effects, reducing diversity in climax species (R{superscript 2} = 0.25, p < 0.001) but enhancing it in mid-successional (R{superscript 2} = 0.22, p < 0.001) and pioneer groups (R{superscript 2} = 0.06, p = 0.05). Notably, MFCT values remained stable across salinity gradients, underscoring the ecosystems functional resilience. These findings highlight mid-successional species as keystones in sustaining mangrove multifunctionality and resilience under environmental stressors. Prioritizing these species in conservation and restoration efforts can mitigate the impacts of salinity intrusion and climate variability. By integrating the MFCT framework, resource managers can develop targeted restoration strategies to enhance ecosystem functionality and long-term stability. These insights provide a critical foundation for policymakers to align global mangrove conservation with adaptive management strategies, reinforcing coastal resilience, biodiversity conservation, and climate change mitigation.

ecology↗

bioRxiv2025

Enterococcus faecium MBBL3 Exhibits Promising Probiotic Potential and Antimicrobial Efficacy Against Bovine Mastitis-Associated Escherichia coli and Klebsiella pneumoniae

Enterococcus faecium, a promising probiotic, combats pathogens, supports gut health, strengthens immunity, and provides a natural approach to address the escalating global challenge of antimicrobial resistance. This study aimed to investigate the genome of E. faecium MBBL3, isolated from healthy cow milk, to assess its probiotic potential and antimicrobial activity against pathogens causing bovine mastitis. The strain was analyzed through whole genome sequencing, along with in-vitro and in-silico assessments were conducted to determine its antimicrobial efficacy against bovine mastitis pathogens, Klebsiella pneumoniae MBBL2 (Kp MBBL2) and Escherichia coli MBBL4 (Ec MBBL4). The genome assembly and functional annotations uncovered many important probiotic traits in MBBL3, where genome comparison revealed its high genetic similarity with other Enterococcus strains. MBBL3 demonstrated the ability to ferment a wide range of carbohydrates and possessed 76 carbohydrate-active enzyme-related genes, including five key CAZy families namely GH73, GH18, CBM50, CE4, and AA10. It also possessed importance genes for bile salt and acid tolerance, stress resistance, and surface adhesion. Additionally, MBBL3 contained metabolite regions involved in the biosynthesis of antimicrobial compounds such as 2,4-DAPG, aborycin, enterocin NKR-5-3B, and sodorifen, and bacteriocin gene clusters for sactipeptides, Enterolysin_A, and UviB. Safety assessments indicated low pathogenic potential, while in-vitro assays demonstrated antibiotic susceptibility and suppressed the growth of Kp MBBL2 and Ec MBBL4, respectively. Its bacteriocin compound Enterolysin_A exhibited strong molecular interactions with virulence proteins of these mastitis pathogens. Therefore, the promising probiotic potential and antimicrobial efficacy of E. faecium MBBL3, especially against mastitis pathogens combined with its safety, position it as a valuable candidate for therapeutic applications. Key pointsO_LIE. faecium MBBL3 genosme showed high similarity with other species of this genera. C_LIO_LIGenetic makeup of MBBL3 revealed its ability to survival and adaptation in different niches including hosts gut. C_LIO_LIIn-vitro and in-silico study results, along with several genes linked to antimicrobials demonstrated its ability to combat against mastitis pathogens. C_LI

microbiology↗

bioRxiv2024

Reference-free Analysis of scRNA-seq Data Reveals Elevated rRNA and mtRNA Transcription during Neurogenesis in Axolotl

Analysis of single-cell RNA-seq data is typically performed on a gene expression matrix estimated by aligning reads to a reference transcriptome. However, this approach is difficult to apply to organisms with no or incomplete reference transcriptomes. In addition, events deviating from the reference remain undetected. Here we present a reference-free method to analyze single-cell RNA-seq data based on k-mers. We assess the performance of our method on a metastatic renal cell carcinoma dataset and find that it is largely able to capture differentially expressed genes. We then analyze a recently generated dataset to study neurogenesis in Axolotl and observe increased levels of transcription of rRNA and mtRNA during neurogenesis as well as a miRNA with previously predicted links to neuronal development. We also detect lncRNAs and intron retention in heart disease-related genes in diseased cardiomyocytes in an analysis of a congenital heart disease dataset.

bioinformatics↗

bioRxiv2024

Internalized α-synuclein fibrils become truncated and resist degradation in neurons while glial cells rapidly degrade α-synuclein fibrils.

Parkinsons disease (PD) and other -synucleinopathies are characterized by the intracellular aggregates of -synuclein (S) believed to spread via the cell-to-cell transmission. To understand the contributions of various brain cells to the spreading of S pathology, we examined the metabolism of S aggregates in neuronal and glial cells. In neurons, while the full-length S rapidly disappeared following S PFF uptake, truncated S accumulated with a half-life of days rather than hours. Epitope mapping and fractionation studies indicate that S fibrils internalized by neurons was truncated at the C-terminal region and remained insoluble. In contrast, microglia and astrocytes rapidly metabolized S fibrils as the half-lives of S fibrils in these glial cells were <6 hours. Differential uptake and processing of S fibrils by neurons and glia was recapitulated in vivo where injection of fluorescently labeled S fibrils initially accumulated in glial cells followed by rapid clearance while neurons stably accumulated S fibrils at slower rate. Immunolocalization and subcellular fractionation studies show that internalized S PFF is initially localized to endosomes followed by lysosomes. The lysosome is largely responsible for the degradation of internalized S PFF as the inhibition of lysosomal function leads to the stabilization of S in all cell types. Significantly, S PFF causes lysosomal dysfunction in neurons. In summary, we show that neurons are inefficient in metabolizing internalized S aggregates, partially because S aggregates cause lysosomal dysfunction, potentially generating aggregation-prone truncated S. In contrast, glial cells may protect neurons from S aggregates by rapidly clearing S aggregates.

neuroscience↗

bioRxiv2023

Seroprevalence of IgG Antibody against SARS-CoV-2 Nucleocapsid protein and Associated Risk Factors

Estimation of antibody development against SARS-CoV-2 is essential means for understanding the immune response against the virus. We reported IgG antibody development status against Nucleocapsid protein of the virus and compared with lifestyle (health and food habits), co-existing diseases, vaccination and COVID-19 infection status. ELISA (Enzyme Linked Immunosorbent Assay) was performed to assess IgG antibodies targeted against the Nucleocapsid protein of SARS-CoV-2 in participants (n=500). In this seroprevalence study, serological data were estimated for a period of 10 months in the participants who were aged 10 years and above. Sociodemographic and risk factors related data were collected through a written questionnaire and chi-square test was performed to determine the association with seropositivity. The overall seroprevalence of anti-SARS-CoV-2 antibodies among the study subjects was 47.8%. Estimates were highest among the participants of 21-40 years old (55.1%), and lowest in older aged (>60 years) participants (39.5%). Among the Sinopharm vaccinated individuals 81.8% had developed anti-Nucleocapsid antibody. Physical exercise and existence of comorbidities like hypertension and diabetes were the distinguishing factors between seropositive and seronegative individuals. Seropositivity rate largely varied among symptomatic (67%) and asymptomatic (33.1%) COVID-19 infected participants. The findings suggest that residents of Dhaka city had a higher prevalence of anti-nucleocapsid antibody in the second year of the pandemic. This indicates the improvement of immunological status among the population. Finally, the study emphasizes on maintaining active and healthy lifestyle to improve immunity. However, the absence of IgG antibodies in many cases of COVID-19 infected individuals suggests that antibodies wane with time. Key messagesO_LIThe overall seroprevalence of anti-Nucleocapsid IgG among the study subjects was determined to be 47.8%. C_LIO_LIAge, regular physical exercise, existence of comorbidities were the identified parameters associated with seroprevalence. C_LIO_LIThis study observed lower prevalence of Anti-Nucleocapsid antibody among asymptomatic cases of COVID-19 infected individuals compared to symptomatic cases. C_LI

immunology↗

bioRxiv2020

Microbiological water quality of Managed Aquifer Recharge systems in the salinity-prone southwest coastal Bangladesh

Managed aquifer recharge (MAR), a hydro-geological intervention designed to dilute groundwater salinity, pumps pond water treated through a slow sand filter into the underground aquifers. We evaluated the microbiological safety of the resulting MAR water at sites from three districts in southwest coastal Bangladesh. We collected monthly paired pond-MAR water samples from July 2016-June 2017 and enumerated fecal coliforms and E. coli using the IDEXX quanti-tray technique, by the most probable number (MPN) method. We used WHO risk categories for microbiological quality; no risk (<1 MPN), low risk (1-10 MPN) and moderate to high risk (>10 MPN per 100 mL water). We estimated the difference in mean log10 MPN in pond and MAR water using linear mixed effect models with random intercepts and cluster adjusted robust standard error. Almost all pond water samples (292/299, 98%) had moderate- to high-risk level (>10 MPN) fecal coliforms and E. coli (283/299, 95%). In contrast, 81% (242/300) of MAR water samples had no or low risk level fecal coliforms (0-10 MPN), of which 60% (179/300) had no fecal coliforms. We detected no or low risk level E. coli in 94% (283/300) of MAR water samples of these 80% (240/300) had no E. coli. MAR samples had lower mean log10 MPN fecal coliforms (-2.37; 95% CI: -2.56, -2.19) and E. coli (-2.26; 95% CI: - 2.43, -2.09) than pond water; microbial reductions remained consistent during the wet (May-October) and dry seasons. MAR-systems provided water with reduced fecal indicator bacteria compared to infiltered pond water.

microbiology↗

bioRxiv2018

Blood-based molecular biomarker signatures in Alzheimer’s disease: Insights from systems biomedicine analyses

Background and objectivesAlzheimers disease (AD) is the progressive neurodegenerative disease characterized by dementia, but no peripheral biomarkers available yet that can detect the AD. This study aimed to identify systems biomarker signatures in the AD through integrative analyses.\n\nMaterials and MethodsWe used two microarray transcriptomics datasets of blood from AD patients to identify differentially expressed genes (DEGs). Geneset and protein overrepresentation analysis, protein-protein interaction (PPI), DEGs-Transcription Factor interactions, DEGs-MicroRNAs interactions, protein-drug interactions, and protein subcellular localizations analyses were done on common DEGs.\n\nResultsTotal 25 DEGs were detected between the two datasets. Integration of DEGs with biomolecular networks revealed hub proteins (TUBB, ATF3, NOL6, UQCRC1, SND1, CASP2, BTF3, INPP5K, VCAM1, and CSTF1), TFs (FOXC1, ZNF3, GEMIN7, and SMG9), miRNAs (mir-20a-5p, mir-93-5p, mir-16-5p, let-7b-5p, mir-708-5p, mir-24-3p, mir-26b-5p, mir-17-5p, mir-4270, and mir-4441). The analyses revealed candidate blood based biomarkers in the AD. We evaluated the histone modifications of the identified biomolecules. The hub genes and transcription factors (TFs) revealed that they possess several histone modification sites associated with Alzheimers disease. The protein-drug interactions revealed 10 candidate drugs consisting of antineoplastic (Vinorelbine, Vincristine, Vinblastine, Epothilone D, Epothilone B, CYT997, and ZEN-012), dermatologicals (Podofilox), and immunosuppressive agents (Colchicine) that may target the candidate systems biomarkers. The subcellular localization analysis revealed the interactions of the DEGs range from nucleus to plasma membrane through cytosol.\n\nConclusionsThis study presents blood based systems molecular biomarker signatures at RNA and protein levels which might be useful as peripheral biomarkers in the AD. The candidate drugs, histone modification sites, and subcellular localizations will be useful in future drug design in the AD.

systems biology↗