Biology subjects

Muhammad, S.

Publications and source records attributed to Muhammad, S..

7 recordsLinked to original sources

bioRxiv2026

Genome-wide landscape of m6A regulatory genes in Marchantia polymorpha: conservation, diversification, and expression dynamics

BackgroundN6-Methyladenosine (m6A) regulates RNA fate in flowering plants, but the repertoire and expression patterns of m6A-related genes remain incompletely characterized in liverworts. Here, we characterized these gene families in the liverwort Marchantia polymorpha within a comparative framework spanning diverse plant lineages. ResultsA comparative survey of 119 plant genomes using sequence similarity and conserved-domain criteria identified 18 candidate m6A-related loci in M. polymorpha, comprising seven writer-related genes, five AlkB homolog genes, and six YTH- or CPSF30-related genes. Across the surveyed genomes, canonical writer components generally had low copy numbers, whereas AlkB homolog and reader-related families showed greater copy-number variation. Phylogenetic and domain analyses supported the family assignments of the M. polymorpha candidates. Eight of the 18 candidate loci showed detectable collinearity with Marchantia quadrata. Putative promoter analysis identified motifs annotated as hormone-, light-, and stress-responsive, with hormone-responsive motifs accounting for the largest share of predicted sites. Public transcriptome analysis revealed variation in candidate gene expression across developmental stages and tissues. Quantitative reverse-transcription PCR showed higher transcript abundance for all six YTH- or CPSF30-related genes in thalli than in gemmae or gemma cups. Cold, heat, osmotic, salt, and dark treatments elicited gene-specific expression responses. Darkness increased transcript abundance of several candidates, including MpMTA, MpALKBH1A, and MpECT2. A predicted protein-association network suggested links between subsets of the candidates and RNA-processing proteins. ConclusionsThese findings define a candidate m6A-related gene repertoire in M. polymorpha and identify tissue- and stress-responsive genes for targeted functional studies of RNA methylation in this liverwort.

bioinformatics↗

bioRxiv2026

A climate-resilient microalga, Desmodesmus ecotolerans sp. nov., for biophotovoltaic applications

Microalgae are promising biological platforms for sustainable energy production because they can convert photosynthetic activity into electricity in biophotovoltaic (BPV) systems. Identifying strains that grow well at elevated temperatures and under reduced irradiance is an important step toward BPV applications in seasonally variable environments. Microalgae were isolated from Seondong Lake (Seoul, Republic of Korea) during three sampling periods and screened for growth at different temperatures. Among 45 isolates, KHUC-11 showed the highest weighted growth index based on growth rates at 25, 30, and 35 under dark conditions and was selected for further characterization. Phylogenetic reconstruction of the 45S rRNA gene cluster, internal transcribed spacer 2 (ITS2) secondary-structure comparison, and morphological characterization supported the description of KHUC-11 as Desmodesmus ecotolerans sp. nov. D. ecotolerans produced more biomass than Chlamydomonas reinhardtii CC-125 under both moderate- and low-light conditions. Under low light, its final dry biomass concentrations were 1.81 and 1.58 times those of CC-125 under mixotrophic and photoautotrophic conditions, respectively. Despite its smaller cell size, D. ecotolerans showed higher photosynthetic performance than CC-125, and screen-printed electrode (SPE)-based electrochemical assays demonstrated enhanced anodic current generation and CV-derived estimated power output. Taken together, these findings identify D. ecotolerans as a novel climate-resilient Desmodesmus species with bioelectrochemical properties that support further evaluation for BPV applications.

microbiology↗

bioRxiv2026

The Impact of TOR-S6K-eIF5A Signaling on Translational Control is Key to Plant Root Development

Nutrient-responsive Target of Rapamycin (TOR)-S6 kinase (S6K) signaling coordinates plant growth with protein synthesis, but how it interfaces with translation elongation to produce specific developmental outputs remains unclear. Here, we identify eukaryotic translation factor 5A (eIF5A) as an S6K-associated phosphoprotein in Arabidopsis thaliana. S6K1 and S6K2 associate with all three eIF5A isoforms and phosphorylate them in vitro, with Ser2 emerging as the major S6K1-responsive site in eIF5A-2. The corresponding N-terminal serine is invariant across the analyzed Archaeplastida eIF5A proteins. Conditional depletion of TOR, S6K1/2, or eIF5A produces overlapping reductions in primary root length and root hair coverage. eIF5A depletion leaves bulk protein synthesis and polysome profiles largely unchanged while selectively decreasing output from deca-proline reporters. Reporter activity is restored by amiRNA-resistant wild-type and phosphomimetic S2D eIF5A-2, whereas S2A does not restore activity, demonstrating the functional importance of the Ser2 state. Proteomic profiling identifies a restricted set of eIF5A-responsive proteins, and five of six tested insertion mutants display altered primary root growth, root hair coverage, or both. Together, these findings uncover a regulatory connection between S6K and eIF5A and establish eIF5A-dependent selective translation as a mechanism contributing to root development in A. thaliana.

molecular biology↗

bioRxiv2023

Colchicine inhibited oxidative stress-induced endothelial cell senescence via blocking NF-κB and MAPKs: Implications in vascular diseases

Smoking, alcohol abuse, and hypertension are - among others the potential risk factors for cardiovascular diseases. These risk factors generate oxidative stress and cause oxidative stress-induced DNA damage, resulting in cellular senescence and senescence-associated secretory phenotype (SASP). The SASP factors in feed-forward response exacerbate inflammation and cause tissue remodeling, resulting in atherosclerotic plaque formation and rupture. Colchicine was used to ameliorate oxidative stress-induced senescence in human umbilical vein endothelial cells. Oxidative stress was quantified by reactive oxygen species (ROS) assay and oxidative stress-induced DNA damage was analyzed by 8-OHDG immunofluorescence staining. Endothelial cell senescence was visualized by {beta}-gal staining. The relative mRNA expression was quantified by qPCR and protein analysis was performed by Western blot. Colchicine inhibited ROS generation and mitigated oxidative stress-induced DNA damage. It dampened oxidative stress-induced endothelial cell senescence and improved the expression of DNA repair protein KU80 and aging marker Lamin B1. The drug attenuated the expression of senescence marker P21 at mRNA and protein levels. The pathway analysis showed that colchicine inhibited NF-{kappa}B and MAPKs pathways and subdued mTOR activation. Colchicine also attenuated mRNA expression of interleukin (IL)-1{beta}, IL-6, IL-8 MCP-1, ICAM-1, and E-selectin. Furthermore, colchicine reduced the mRNA and protein expression of matrix metalloproteinase (MMP-2). In summary, colchicine blocked oxidative stress-induced senescence and SASP by inhibiting the activation of NF-{kappa}B and MAPKs pathways.

molecular biology↗

bioRxiv2022

Genomic insights into metabolic flux in ruby-throated hummingbirds

Hummingbirds are very well adapted to sustain efficient and rapid metabolic shifts. They oxidize ingested nectar to directly fuel flight when foraging but have to switch to oxidizing stored lipids derived from ingested sugars during the night or long-distance migratory flights. Understanding how this organism moderates energy turnover is hampered by a lack of information regarding how relevant enzymes differ in sequence, expression, and regulation. To explore these questions, we generated a chromosome level de novo genome assembly of the ruby-throated hummingbird (A. colubris) using a combination of long and short read sequencing and scaffolding using other existing assemblies. We then used hybrid long and short-read RNA-sequencing for a comprehensive transcriptome assembly and annotation. Our genomic and transcriptomic data found positive selection of key metabolic genes in nectivorous avian species and a deletion of critical genes (GLUT4, GCK) involved in glucostasis in other vertebrates. We found expression of fructose-specific GLUT5 putatively in place of insulin-sensitive GLUT4, with predicted protein models suggesting affinity for both fructose and glucose. Alternative isoforms may even act to sequester fructose to preclude limitations from transport in metabolism. Finally, we identified differentially expressed genes from fasted and fed hummingbirds suggesting key pathways for the rapid metabolic switch hummingbirds undergo.

genomics↗

bioRxiv2021

Meta-analysis on reporting practices as a source of heterogeneity in in vitro cancer research

BackgroundHeterogeneity of results of exact same research experiments oppose a significant socio-economic burden. In vitro research presents the early step of basic science and drug development projects. Insufficient methodological reporting is likely to be one of the contributors to results heterogeneity, however, little knowledge on reporting habits of in vitro cancer research and their effects on results reproducibility is available. Glioblastoma is a form of brain cancer with largely unmet clinical need. MethodsHere we use systematic review to describe reporting practices in in vitro glioblastoma research using the U87-MG cell line and perform multilevel random-effects meta-analysis followed by meta-regression to explore sources of heterogeneity within that literature, and any associations between reporting characteristics and reported findings. ResultsIn 137 identified articles, the overall methodological reporting is disappointing, e.g., the control type, mediums glucose level and cell density are reported in only 36.5, 21.2 and 16.8 percent of the articles, respectively. After adjustments for different drug concentrations and treatment durations, a three-level meta-analysis proves meaningful results heterogeneity across the studies (I2 = 70.1%). ConclusionsOur results further support the ongoing efforts of establishing consensus reporting practices to elevate durability of results. By doing so, we hope that this work will raise awareness of how stricter reporting may help to improve the frequency of successful translation of preclinical results into human application, not only in neuro-oncology. FundingWe received no specific funding for this project.

cancer biology↗

bioRxiv2020

Glucose transporter expression and regulation following a fast in the ruby-throated hummingbird, Archilochus colubris.

Hummingbirds subsist almost exclusively on nectar sugar and face extreme challenges blood sugar regulation. Transmembrane sugar transport is mediated by facilitative glucose transporters (GLUTs) and the capacity for sugar transport is dependent on both the activity of GLUTs and their localisation to the plasma membrane (PM). In this study, we determined the relative protein abundance in whole-tissue (WT) homogenates and PM fractions via immunoblot using custom antibodies for GLUT1, GLUT2, GLUT3, and GLUT5 in flight muscle, heart, and, liver of ruby-throated hummingbirds (Archilochus colubris). GLUTs examined were detected in nearly all tissues tested. Hepatic GLUT1 was minimally present in WT homogenates and absent in PM fractions. GLUT5 was expressed in hummingbird flight muscles at levels comparable to that of their liver, consistent with the hypothesised uniquely high fructose-uptake and oxidation capacity of this tissue. To assess GLUT regulation, we fed ruby-throated hummingbirds 1M sucrose ad libitum for 24 hours followed by either 1 hour of fasting or continued ad libitum feeding until sampling. We measured relative GLUT abundance and concentrations of circulating sugars. Blood fructose concentration in fasted hummingbirds declined from [~]5mM to [~]0.18mM, while fructose-transporting PM GLUT2 and PM GLUT5 did not change in abundance. Blood glucose concentrations remained elevated in both fed and fasted hummingbirds, at [~]30mM, while glucose-transporting PM GLUT1 and PM GLUT3 in the flight muscle and liver, respectively, declined in fasted birds. Our results suggest that glucose uptake capacity is dynamically reduced in response to fasting, allowing for maintenance of elevated blood glucose levels, while fructose uptake capacity remains constitutively elevated promoting depletion of blood total fructose within the first hour of a fast. Summary statementHummingbird ingest nectar rich in glucose and fructose. When fasted, tissue capacity for circulating glucose import declines while remaining elevated for fructose. This may underlie maintenance of high blood glucose and rapid depletion of blood fructose.

zoology↗