Biology subjects

Mohamed, M. A.

Publications and source records attributed to Mohamed, M. A..

5 recordsLinked to original sources

bioRxiv2026

Serial intravascular labeling resolves dynamic decidual NK residency and gestational remodeling toward T-bet-Low states

Decidual natural killer (dNK) cells are the predominant immune population at the maternal-fetal interface during early pregnancy. However, how vascular trafficking, tissue residency, proliferation, and apoptosis-associated activity are coordinated to establish and maintain the dNK population throughout pregnancy remains unclear. We hypothesized that gestational remodeling of the dNK compartment reflects coordinated changes in these cellular processes in association with progressive T-bet downregulation. We combined serial intravascular labeling (SIVL), flow cytometry, BrdU incorporation, active caspase-3 detection, spatial imaging, and Tbx21 fate mapping to examine NK cells in virgin mice and across gestation. Pregnancy altered CD49a/CD49b-defined dNK-cell composition and redistributed dNK cells among SIVL-defined vascular-accessibility states, supporting a model of dynamic dNK-cell tissue residency. Trafficking-associated marker scores displayed continuous gradients of tissue retention, circulatory/egress potential, and chemokine responsiveness rather than defining a single resident state. Spatial imaging demonstrated greater dNK-cell density in the mesometrial decidua and preferential CD31 vessel contact by recently intravascular dNK cells during early and mid-gestation. BrdU incorporation and active caspase-3 positivity peaked during early pregnancy and varied across SIVL-defined states. Tbx21 fate mapping identified a progressive and selective shift from current T-bet expression toward ex-T-bet and non-fate-mapped Eomes dNK states. T-bet-low states preferentially maintained proliferation at mid-gestation, whereas current T-bet expression was associated with greater circulatory/egress potential. However, active caspase-3 was not selectively increased in current T-bet-expressing cells. Collectively, these findings identify pregnancy-induced dNK-cell remodeling as a coordinated process integrating dynamic tissue residency, vascular accessibility, local proliferation, and apoptosis-associated activity, alongside a progressive shift toward T-bet-low dNK states.

immunology↗

bioRxiv2024

Contingencies in biofilm adaptation of Mycobacterium tuberculosis

Biofilms are structured microbial communities that offer protection from a range of environmental stressors. Studies of experimental evolution within biofilms have yielded important insights into mechanisms of biofilm formation, as well as fundamental principles governing bacterial adaptation within these structured communities. Building on research using tractable species, our lab created a model for studying biofilm adaptation in Mycobacterium tuberculosis (M. tb), a fastidious, slow growing and lethal pathogen of humans. Here, we evolved eighteen M. tb populations arising from six parental genetic backgrounds under biofilm selection to investigate diversity in mechanisms of M. tb biofilm adaptation. We found that fine-scale differences among strains at the initiation of the experiment influenced the degree of replicability in their evolution. Adaptive paths were highly parallel for some strains, whereas others evolved distinct mutations across iterations of the experiment. Our data suggest that differences in replicability arise from mutational biases and variable fitness impacts of mutations across genetic backgrounds. Comparison of our results with genomic data from M. tb populations within hosts with tuberculosis (TB) revealed that several mutations associated with biofilm selection are also among the most common to emerge during natural infection. These biofilm-associated variants are not maintained in natural M. tb populations, suggesting that biofilm selection in our model mimics selection pressures that are transiently encountered by M. tb during specific phases of infection. Overall, these results support development of biofilm directed therapies for TB and demonstrate the importance of subtle genetic variation in shaping M. tb responses to changing selection pressures. SignificanceMycobacterium tuberculosis (M. tb), the causative agent of tuberculosis (TB), a difficult-to-treat, persistent infection with high mortality. One cause of this persistence is the ability of M. tb to form biofilms, aggregated structures capable of resisting antibiotics and host defenses. Here, we used an evolutionary model to investigate mechanisms of M. tb biofilm formation. We found adaptation to biofilm growth to be affected by mutational biases and interactions among mutations. Our simple in vitro model appears to mimic aspects of natural infection, as identical mutations emerge in the laboratory under biofilm selection and within hosts with TB. These results expand our knowledge of M. tb biofilm development and inform our understanding of how this bacterium responds to novel selection pressures.

evolutionary biology↗

bioRxiv2023

Portrait of a generalist bacterium: pathoadaptation, metabolic specialization and extreme environments shape diversity of Staphylococcus saprophyticus

Staphylococcus saprophyticus is a Gram-positive, coagulase-negative staphylococcus found in diverse environments including soil and freshwater, meat, and dairy foods. S. saprophyticus is also an important cause of urinary tract infections (UTIs) in humans, and mastitis in cattle. However, the genetic determinants of virulence have not yet been identified, and it remains unclear whether there are distinct sub-populations adapted to human and animal hosts. Using a diverse sample of S. saprophyticus isolates from food, animals, environmental sources, and human infections, we characterized the population structure and diversity of global populations of S. saprophyticus. We found that divergence of the two major clades of S. saprophyticus is likely facilitated by barriers to horizontal gene transfer (HGT) and differences in metabolism. Using genome-wide association study (GWAS) tools we identified the first Type VII secretion system (T7SS) described in S. saprophyticus and its association with bovine mastitis. Finally, we found that in general, strains of S. saprophyticus from different niches are genetically similar with the exception of built environments, which function as a sink for S. saprophyticus populations. This work increases our understanding of the ecology of S. saprophyticus and of the genomics of bacterial generalists. Data summaryRaw sequencing data for newly sequenced S. saprophyticus isolates have been deposited to the NCBI SRA under the project accession PRJNA928770. A list of all genomes used in this work and their associated metadata are available in the supplementary material. Custom scripts used in the comparative genomics and GWAS analyses are available here: https://github.com/myoungblom/sapro_genomics. Impact statementIt is not known whether human and cattle diseases caused by S. saprophyticus represent spillover events from a generalist adapted to survive in a range of environments, or whether the capacity to cause disease represents a specific adaptation. Seasonal cycles of S. saprophyticus UTIs and molecular epidemiological evidence suggest that these infections may be environmentally-acquired rather than via transmission from person to person. Using comparative genomics and genome wide association study tools, we found that S. saprophyticus appears adapted to inhabit a wide range of environments (generalist), with isolates from animals, food, natural environments and human infections being closely related. Bacteria that routinely switch environments, particularly between humans and animals, are of particular concern when it comes to the spread of antibiotic resistance from farm environments into human populations. This work provides a framework for comparative genomic analyses of bacterial generalists and furthers our understanding of how bacterial populations move between humans, animals, and the environment.

microbiology↗

bioRxiv2021

Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.

microbiology↗

bioRxiv2019

Prevalence and risk factors profile of seropositive Toxoplasmosis gondii infection among apparently immunocompetent Sudanese women

ObjectivesToxoplasma gondii is an opportunistic parasite that cause a clinical manifestation known as toxoplasmosis. We investigated the prevalence and potential risk factors of T. gondii infection among women in Khartoum, Sudan. A sero-parasitological cross-sectional study included 100 women aging between 15-50 years old was conducted in Khartoum, Sudan between January - November 2018. Serum samples were collected and investigated for presence of anti-T. gondii immunoglobulins.\n\nResultsMean age of the women population included was 26.75{+/-}8.25 with a range between 15 and 50 years. Sero-prevalence of T. gondii antibodies was 27% (27/100) with a 95% confidence interval (CI) of 18.6 - 36.8%. Among seropositive population 81% (22/27), 15% (4/27) and 4% (1/27) were seropositive for IgG antibodies, IgM antibodies and both antibodies respectively. Age group 21-30 years old had the highest frequency of detected IgG (10/45) and IgM (3/45). Married women had the highest frequency of detected IgG or IgM, 18/79 and 3/79, respectively. Risk factors analysis showed a total of 37/100 participants were having direct contact with cats and 66/100 have a frequent raw meat consumption, neither direct cats contact nor raw meat consumption had statistically significant association with seropositivity to T. gondii (P. value =0.052 and 0.565, respectively).

microbiology↗