Biology subjects

Usman, M.

Publications and source records attributed to Usman, M..

5 recordsLinked to original sources

bioRxiv2026

Cross-Genera Amplification of prs/hlyA by Multiplex PCR Resulted in Misidentification of Enterococcus faecium as Listeria monocytogenes

ImportanceMolecular confirmation of Listeria monocytogenes typically employs a multiplex PCR method that targets both genus-specific prs and species-specific hlyA genes. This study assessed the specificity of this assay within Nigeria, where local microbial diversity may influence performance outcomes. MethodsOut of eight phenotypically presumptive L. monocytogenes food isolates tested, six produced the expected prs and hlyA amplicons, with five classified as serogroup 1/2b. However, all six isolates tested negative for the crucial virulence regulator prfA, necessitating further investigation. ResultsDefinitive 16S rRNA gene sequencing revealed that only two of the six PCR-positive isolates were identified as L. monocytogenes, while the remaining four were identified as Enterococcus faecium. This results in a false-positive rate of 66.7% (4/6) for the assay in this particular context. Phylogenetic analysis corroborated the taxonomic distinction, exhibiting a robust clustering of the four E. faecium isolates with reference strains. In contrast, the two confirmed L. monocytogenes isolates formed a separate sub-clade, indicating regional divergence and further underscoring the assays inability to differentiate between L. monocytogenes and Enterococcus species. ConclusionThese findings highlight a significant lack of specificity, as the prs/hlyA primers exhibited cross-reactivity with non-target E. faecium. The anomalous negative result for prfA served as a critical diagnostic indicator. Consequently, the positive outcomes from this widely utilized confirmatory assay should be regarded as presumptive and necessitate additional verification.

microbiology↗

bioRxiv2025

The human-specific RPGR isoform RPGRs14/15 and the clinically approved Rho/ROCK inhibitor Ripasudil represent therapeutic options to address RPGR-associated defects.

Pathogenic variants in the RPGR gene are the primary cause of photoreceptor degeneration in X-linked retinitis pigmentosa (RP). Previous studies have linked RPGR dysfunction to defects in ciliary structure and actin turnover. RPGR encodes three major isoforms--RPGR1-19, RPGRORF15, and the human-specific RPGRs14/15--yet the function of RPGRs14/15 remains poorly understood. There is an urgent unmet need for effective treatments targeting RPGR-associated RP. We generated RPGR mutant hTERT-RPE1 cell lines and found that the loss of all RPGR isoforms resulted in pronounced ciliary defects, including aberrant cilia length and segmentation, along with disrupted actin turnover. Strikingly, cells expressing only the human-specific isoform RPGRs14/15closely resembled wild-type controls and were largely protected from these defects, underscoring a critical role for RPGRs14/15 in maintaining ciliary integrity and actin dynamics. Furthermore, we demonstrated that pharmacological disruption of actin polymerization with cytochalasin D (CytoD) in control cells mimicked the ciliary abnormalities seen in RPGR_KO cells. Conversely, treatment with Ripasudil--a clinically approved Rho/ROCK inhibitor--rescued both ciliary and actin-related defects in RPGR_KO lines without observable side effects. In summary, our findings highlight the therapeutic relevance of the human-specific isoform RPGRs14/15 and identify Ripasudil as a promising candidate for treating RPGR-associated retinal degeneration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/653106v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1e1e6ccorg.highwire.dtl.DTLVardef@1f79a9eorg.highwire.dtl.DTLVardef@c8119forg.highwire.dtl.DTLVardef@fce447_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

In-silico heart model phantom to validate cardiac strain imaging

The quantification of cardiac strains as structural indices of cardiac function has a growing prevalence in clinical diagnosis. However, the highly heterogeneous four-dimensional (4D) cardiac motion challenges accurate "regional" strain quantification and leads to sizable differences in the estimated strains depending on the imaging modality and post-processing algorithm, limiting the translational potential of strains as incremental biomarkers of cardiac dysfunction. There remains a crucial need for a feasible benchmark that successfully replicates complex 4D cardiac kinematics to determine the reliability of strain calculation algorithms. In this study, we propose an in-silico heart phantom derived from finite element (FE) simulations to validate the quantification of 4D regional strains. First, as a proof-of-concept exercise, we created synthetic magnetic resonance (MR) images for a hollow thick-walled cylinder under pure torsion with an exact solution and demonstrated that "ground-truth" values can be recovered for the twist angle, which is also a key kinematic index in the heart. Next, we used mouse-specific FE simulations of cardiac kinematics to synthesize dynamic MR images by sampling various sectional planes of the left ventricle (LV). Strains were calculated using our recently developed non-rigid image registration (NRIR) framework in both problems. Moreover, we studied the effects of image quality on distorting regional strain calculations by conducting in-silico experiments for various LV configurations. Our studies offer a rigorous and feasible tool to standardize regional strain calculations to improve their clinical impact as incremental biomarkers.

bioengineering↗

bioRxiv2024

Trappc9 deficiency causes obesity and fatty liver disease by constraining dopamine neurotransmission

Loss-of-function mutations of the gene encoding the trafficking protein particle complex subunit 9 (trappc9) cause intellectual disability and obesity by unknown mechanisms. Genome-wide analysis links trappc9 to non-alcoholic fatty liver disease (NAFLD). The abrogation of trappc9 in mice has been shown to alter the density of neurons containing dopamine receptor D2 (DRD2) and/or DRD1 in the striatum. Here, we report that trappc9 deficiency in mice resulted in disruption of systemic glucose homeostasis and onset of obesity and NAFLD, which were relieved upon chronic treatment combining DRD2 agonist quinpirole and DRD1 antagonist SCH23390. The homeostasis of systemic glucose in trappc9-deficient mice was restored upon administrating quinpirole alone. Transcriptomic and proteomic analyses revealed signs of impairments in neurotransmitter secretion in trappc9-deficient mice. Brain examinations showed that trappc9-deficient mice synthesized dopamine normally, but their dopamine-secreting neurons had a lower abundance of structures for releasing dopamine in the striatum. Our study suggests that trappc9 loss-of-function causes obesity and NAFLD by constraining dopamine transmission.

neuroscience↗

bioRxiv2020

Transcriptomic dysregulations associated with SARS-CoV-2 infection in human nasopharyngeal and peripheral blood mononuclear cells

IntroductionOver 24 million people have been infected globally with the novel coronavirus, SARS-CoV-2, with more than 820,000 succumbing to the resulting COVID-19 disease as of the end of August 2020. The molecular mechanisms underlying the pathogenesis of the disease are not completely elucidated. Thus, we aim to understand host response to SARS-CoV-2 infection by comparing samples collected from two distinct compartments (infection site and blood), obtained from COVID-19 subjects and healthy controls. MethodsWe used two publicly available gene expression datasets generated via RNA sequencing in two different samples; nasopharyngeal swabs and peripheral blood mononuclear cells (PBMCs). We performed a differential gene expression analysis between COVID-19 subjects and healthy controls in the two datasets and then functionally profiled their differentially expressed genes (DEGs). The genes involved in innate immunity were also determined. ResultsWe found a clear difference in the host response to SARS-CoV-2 infection between the two sample groups. In COVID-19 subjects, the nasopharyngeal sample group indicated upregulation of genes involved in cytokine activity and interferon signalling pathway, as well as downregulation of genes involved in oxidative phosphorylation and viral transcription. Host response in COVID-19 subjects for the PBMC group, involved upregulation of genes involved in the complement system and immunoglobulin mediated immune response. CXCL13, GABRE, IFITM3 were upregulated and HSPA1B was downregulated in COVID-19 subjects in both sample groups. ConclusionOur results indicate the host response to SARS-CoV-2 is compartmentalized and suggests potential biomarkers of response to SARS-CoV-2 infection. HighlightsO_LITranscriptomic profiling from publicly available RNA-seq count data revealed a site-specific immune response in COVID-19. C_LIO_LIHost response was found cellular-mediated in nasopharyngeal samples and humoral-mediated in PBMCs samples. C_LIO_LICXCL13, GABRE and IFITM3 commonly upregulated and HSPA1B downregulated in both sample groups highlights the potential of these molecules as markers of response to SARS-CoV-2 infection. C_LI

immunology↗