Biology subjects

Awad, A.

Publications and source records attributed to Awad, A..

12 recordsLinked to original sources

bioRxiv2026

The nitrification inhibitor DMPP preferentially suppresses ammonia-oxidising bacteria and reduces nitric oxide emissions in an archaeal-dominated grassland soil.

Aims Although ammonia-oxidising archaea (AOA) dominate nitrifier communities in many agricultural soils, the contribution of the less abundant ammonia-oxidising bacteria (AOB) to nitrogen oxide emissions, particularly nitric oxide, remains poorly understood. This study investigated the roles of AOA and AOB in regulating nitric oxide (NO) and nitrous oxide (N2O) emissions from a urea-fertilised grassland soil and evaluated the nitrification inhibitors dicyandiamide (DCD) and 3,4-dimethylpyrazole phosphate (DMPP). Methods A 28-day soil incubation experiment was conducted using a denitrification incubation system to continuously monitor NO and N2O emissions. In parallel, a destructive incubation experiment was performed to determine the dynamics of ammonium (NH-N) and total oxidised nitrogen (TOxN) and to assess changes in the abundance of AOA and AOB following urea application with or without DCD or DMPP. Results AOA accounted for approximately 66% of the total ammonia-oxidising community. Neither inhibitor significantly affected AOA abundance, whereas both suppressed AOB, with DMPP showing stronger and more persistent inhibition than DCD. DMPP reduced NO emissions by 16 to 75%, whereas N2O emissions decreased by only 0.2 to 27%. The greater reduction in NO, together with the preferential suppression of AOB, suggests that low-abundance AOB contributed disproportionately to NO production despite the numerical dominance of AOA. Conclusions These findings suggest that AOB can contribute disproportionately to NO emissions despite their lower abundance relative to AOA. The preferential suppression of AOB by DMPP was associated with a substantial reduction in NO emissions, highlighting AOB-associated processes as a potential target for mitigating reactive N losses from fertilised soils.

ecology↗

bioRxiv2026

Fatty Acid Oxidation Suppression Reprograms Fibroblasts in Fibrostenotic Crohns Disease

Fibrostenotic complications represent a major cause of morbidity in Crohns disease (CD), yet the cellular mechanisms that drive intestinal fibrosis independent of active inflammation remain poorly understood. Here, we identify impaired fatty acid oxidation (FAO) as a defining metabolic feature of fibroblasts in fibrostenotic CD. Untargeted lipidomics of non-inflamed colonic tissue from CD patients demonstrated enrichment of triacylglycerols and long-chain acylcarnitines, suggesting altered lipid utilization. Across three independent RNA-sequencing cohorts, including treatment-naive pediatric ileal biopsies, FAO genes (CPT1A, CPT2, SLC25A20) were selectively downregulated in patients with or destined to develop fibrostenotic disease. Single-cell RNA-sequencing localized these transcriptional alterations specifically to fibroblasts within strictured ileum. Primary fibroblasts derived from fibrostenotic CD exhibited increased neutral lipid accumulation, impaired mitochondrial fatty acid trafficking, and diminished responsiveness to PPAR{gamma}-mediated suppression of TGF{beta}-induced myofibroblast activation. Together, these findings demonstrate that FAO impairment is a conserved, fibroblast-specific metabolic program associated with intestinal fibrosis in CD and suggest that metabolic modulation of stromal cells represents a potential therapeutic strategy for fibrostenotic disease.

genomics↗

bioRxiv2025

Immune Cell Dysfunction of SARS-CoV-2: Mathematical Modeling of the Within-Host Immune Dynamics

The COVID-19 pandemic has spurred extensive research into viral transmission and control, yet the mechanisms of the human immune response to SARS-CoV-2 remain incompletely understood, particularly the role of natural killer (NK) cells and cytokine regulation in disease severity. Mathematical modeling provides a powerful approach to bridge this gap by linking viral dynamics with immune interactions. In this work, we develop a mechanistic within-host model, formulated in a system of coupled ordinary and delayed differential equations, to investigate the contributions of NK cell activity, interferon signaling, and pro-inflammatory cytokines to viral clearance and disease outcome. Model parameters are estimated from experimental data, and computational simulations are used to explore how dysregulated NK responses and cytokine feedback loops may drive divergent clinical outcomes. Local sensitivity analysis identifies the most influential parameters shaping host-pathogen dynamics, highlighting potential control points for intervention. In addition, knockdown simulations are performed to mimic potential therapeutic interventions, allowing us to evaluate their advantages and limitations in silico. These findings provide mechanistic insights into COVID-19 immune dynamics and offer a foundation for guiding the design of future treatment strategies. HighlightsO_LIWe develop a within-host mathematical model of the SARS-CoV-2 immune response. C_LIO_LIThe model incorporates key cytokines and immune cells including Natural Killer cells. C_LIO_LINumerical simulations reproduce cytokine storms and NK cell dysfunction in severe disease. C_LIO_LISensitivity analysis identifies parameter impact and potential therapeutic interventions. C_LI

immunology↗

bioRxiv2025

Reference-guided Genome Assembly of Long Non-coding RNA Transcripts reveals Target Genes Associated With Crohn's Disease

Crohns disease (CD) is highly heterogeneous in presentation and progression with no cure. Molecular phenotyping has been used to elucidate cellular and tissue-based alterations to characterize drivers and effects of disease. One currently understudied class of functional molecules is long non-coding RNAs (lncRNAs). Studying the full lncRNA landscape in IBD is challenging due in part to an incomplete lncRNA annotation and a lack of their functional characterization in tissues of interest. We used a genome-guided alignment strategy to assemble predicted lncRNA transcripts using short RNA-sequencing data from colon tissue of adult patient samples. When combining our predicted lncRNAs with previous lncRNA annotations, we determined 98 that were differentially expressed, recapitulating many from previous IBD studies while also uncovering new ones. We built gene co-expression networks to cluster lncRNAs with functionally characterized protein-coding genes. Clusters containing differential lncRNAs were correlated to disease status and associated with pathways related to the humoral immune response, metabolism, and tissue regeneration. We uncovered multiple differential lncRNAs whose expression significantly correlated with nearby differential protein-coding genes that have also been differentially expressed in other IBD datasets, such as PITX2. We focused on a predicted lncRNA that is antisense to the PITX2-adjacent lncRNA PANCR, which we called PANCR-AS1, and provide multiple lines of evidence that support PANCR-AS1 functioning as an enhancer of PITX2 expression. Overall, we determined lncRNAs that are potential contributors to CD pathogenesis. We developed a robust pipeline for identifying lncRNAs in diseased and non-diseased tissue that are absent from reference annotations. We also outlined a framework to pinpoint significant disease-associated lncRNAs with potential functional activity related to their nearby protein-coding genes.

genomics↗

bioRxiv2025

Real-time fMRI neurofeedback modulates auditory cortex activity and connectivity in schizophrenia patients with auditory hallucinations: A controlled study

Background and HypothesisWe have reported previously a reduction in superior temporal gyrus (STG) activation and in auditory verbal hallucinations (AHs) after real-time fMRI neurofeedback (NFB) in schizophrenia patients with AHs. Study DesignWith this randomized, participant-blinded, sham-controlled trial, we expanded our previous results. Specifically, we examined neurofeedback effects from the STG, an area associated with auditory hallucinations. The effects were compared to Sham-NFB from the motor cortex, a region unrelated to hallucinations. Twenty-three adults with schizophrenia or schizoaffective disorder and frequent medication-resistant hallucinations performed mindfulness meditation to ignore pre-recorded strangers voices while receiving neurofeedback either from the STG (n=10, Real-NFB) or motor cortex (n=13 Sham-NFB). Individuals randomized to Sham-NFB received Real-NFB in a subsequent visit, providing a within-subject Real-after-Sham-NFB comparison. Study ResultsBoth groups showed reduced AHs after NFB, with no group differences. Compared to the Sham-NFB group, the Real-NFB group showed more reduced activation in secondary auditory cortex (AC) and more reduced connectivity between AC and cognitive control regions including dorsolateral prefrontal cortex (DLPFC) and anterior cingulate. The connectivity reduction was also observed in the Real-after-Sham-NFB condition. Secondary AC-DLPFC connectivity reduction correlated with hallucination reduction in the Real-NFB group. Replicating prior results, both groups showed reduced primary auditory cortex activation, suggesting mindfulness meditation may regulate bottom-up processes involved in hallucinations. ConclusionsOur findings emphasize delivering NFB from brain regions involved in medication-resistant AHs. They provide insights into auditory cortex and cognitive control network interactions, highlighting complex processing dynamics and top-down modulation of sensory information.

neuroscience↗

bioRxiv2025

Real-time fMRI neurofeedback reduces default mode network and auditory cortex functional connectivity in schizophrenia

Background and HypothesisAuditory verbal hallucinations (AHs) are a cardinal symptom of schizophrenia that can cause distress but are not always responsive to antipsychotic medications. There is a critical need to develop novel interventions that target neural mechanisms underlying AHs. We developed a real-time fMRI neurofeedback (NFB) paradigm for AHs that aims at modulating default mode network (DMN) functional connectivity. Study DesignPatients with schizophrenia or schizoaffective disorders who were experiencing AHs (N = 25) attempted to decrease brain activation while listening to sentences recorded in another persons voice and increase brain activation while listening to sentences recorded in their own voice. Participants randomly assigned to the real group (n = 12) received neurofeedback based on signals from their auditory cortex in the superior temporal gyrus (STG) and those assigned to the sham group (n = 13) received neurofeedback based on motor cortex signals. Study ResultsAnalyzing resting state fMRI data collected pre- and post-NFB, we found that: (1) at baseline, stronger within-DMN connectivity between the medial prefrontal cortex (MPFC) and posterior cingulate cortex was associated with higher AHs severity; (2) after NFB, participants in the real group, compared to those in the sham group, showed greater reduction in functional connectivity between the MPFC and auditory cortices in the STG and middle temporal gyrus (MTG). Notably, the reduction in MPFC-STG/MTG connectivity was found in all participants in the real group. ConclusionsThese findings suggest that NFB can effectively and non-invasively modulate functional connectivity in regions associated with AHs in psychosis.

neuroscience↗

bioRxiv2024

Antibiotics damage the colonic mucus barrier in a microbiota-independent manner

Antibiotic use is a risk factor for development of inflammatory bowel diseases (IBDs). IBDs are characterized by a damaged mucus layer, which does not properly separate the host intestinal epithelium from the microbiota. Here, we hypothesized that antibiotics might affect the integrity of the mucus barrier. By systematically determining the effects of different antibiotics on mucus layer penetrability we found that oral antibiotic treatment led to breakdown of the mucus barrier and penetration of bacteria into the mucus layer. Using fecal microbiota transplant, RNA sequencing followed by machine learning and ex vivo mucus secretion measurements, we determined that antibiotic treatment induces ER stress in the colonic tissue which inhibits colonic mucus secretion in a microbiota-independent manner. This mucus secretion flaw led to penetration of bacteria into the colonic mucus layer, translocation of microbial antigens into circulation and exacerbation of ulcerations in a mouse model of IBD. Thus, antibiotic use might predispose to development of intestinal inflammation by impeding mucus production.

immunology↗

bioRxiv2023

Salmonella manipulates the host to drive pathogenicity via induction of interleukin 1β

Acute gastrointestinal infection with intracellular pathogens like Salmonella Typhimurium triggers the inflammasome and the release of the proinflammatory cytokine interleukin 1{beta} (IL-1{beta}). However, the role of IL-1{beta} in intestinal defense against Salmonella remains unclear. Here, we show that IL-1{beta} production is detrimental during Salmonella infection. Mice lacking IL-1{beta} (IL-1{beta} -/-) failed to recruit neutrophils to the gut during infection, which reduced tissue damage and prevented depletion of short-chain fatty acid-producing commensals. Changes in epithelial cell metabolism that typically support pathogen expansion, such as switching energy production from fatty acid oxidation to fermentation, were absent in infected IL-1{beta}-/- mice which inhibited Salmonella expansion. Additionally, we found that IL-1{beta} induces expression of complement anaphylatoxins and suppresses the complement-inactivator Carboxypeptidase N (CPN1). Disrupting this process via IL-1{beta} loss completely prevented mortality in Salmonella-infected IL-1{beta}-/- mice and led to chronic infection. Thus, Salmonella exploits IL-1{beta} signaling to outcompete commensal microbes and establish gut colonization. Moreover, our findings identify the intersection of IL-1{beta} signaling and the complement system as key host factors involved in controlling mortality during invasive Salmonellosis.

immunology↗

bioRxiv2023

Modulation of SLFN11 induces changes in DNA Damage response

BackgroundLack of Schlafen family member 11 (SLFN11) expression has been recently identified as a dominant genomic determinant of response to DNA damaging agents in numerous cancer types. Thus, strategies aimed at increasing SLFN11 could be used to restore chemosensitivity of refractory cancers. As oncogenic downregulation is often driven by methylation of the promotor region, we explore the demethylation effect of 5-aza-2-deoxycytidine (decitabine), on the SLFN11 gene methylation. Since SLFN11 has been reported as an interferon inducible gene, and interferon is secreted during an active anti-tumor immune response, we investigated the in vitro effect of IFN-{gamma} on SLFN11 expression in breast cancer cell lines. A second broader approach to show cross talk between immune cells and SLFN11 expression is indirect co-culture of breast cancer cells with activated PBMCs and evaluate if this can drive SLFN11 upregulation. Finally, as a definitive and specific way to modulate SLFN11 expression we implemented SLFN11 dCas9 (dead CRISPR associated protein 9) systems to specifically increase or decrease SLFN11 expression. ResultsWe first confirmed a correlation previously reported between methylation of SLFN11 promoter and its expression across multiple cell lines. We showed in-vitro that decitabine and IFN-{gamma} could increase moderately the expression of SLFN11 in both BT- 549 and T47D cell lines, but not in strongly methylated cell lines such as MDA-MB-231. Though, in-vitro, the co-culture of the same cell lines with CD8-CD25 activated PBMC failed to increase SLFN11 expression. On the one hand, the use of a CRISPR-dCas9 UNISAM system could increase SLFN11 expression significantly (up to 5-fold), stably and specifically in BT-549 and T47D cancer cell lines. Though, this system also failed to force a strong expression of SLFN11 in cell lines with robust SLFN11 promoter methylation such as MDA-MB-231. On the other hand, the use of CRISPR-dCas9 KRAB could significantly reduce the expression of SLFN11 in BT-549 and T47D. We then used the modified cell lines to confirm the alteration in chemo sensitivity of those cells to treatment with DNA Damaging Agents (DDAs) such as Cisplatin and Epirubicin or DNA Damage Response (DDRs) drugs like Olaparib. RNAseq was used to elucidate the mechanisms of action affected by the alteration in SLFN11 expression. ConclusionTo our knowledge this is the first report of the stable non-lethal increase of SLFN11 expression in a cancer cell line. Our results show that induction of SLFN11 expression can enhance DDA and DDR sensitivity in breast cancer cells and dCas9 systems may represent a novel approach to increase SLFN11 and achieve higher sensitivity to chemotherapeutic agents, improving outcome or decreasing required drug concentrations. SLFN11-targeting therapies might be explored pre-clinically to develop personalized approaches.

cancer biology↗

bioRxiv2022

Autophagy controls mucus secretion from intestinal goblet cells by alleviating ER stress

Colonic goblet cells are specialized epithelial cells that secrete mucus to form a barrier between the host and its microbiota, thus preventing bacterial invasion and inflammation. How goblet cells control the amount of mucus they secrete is unclear. We found that constitutive activation of autophagy in mice via Beclin 1 led to production of a thicker and less penetrable mucus layer by reducing endoplasmic reticulum (ER) stress. Accordingly, inhibiting Beclin 1-induced autophagy via Bcl-2 impaired mucus secretion. Furthermore, alleviating intestinal ER stress with a bile acid, or activating the unfolded protein response (UPR) pharmacologically via eIF2 phosphorylation, led to excessive mucus production. Over-production of mucus altered the gut microbiome, with expansion of mucus-utilizing bacteria, and protected from intestinal inflammation. Thus, ER stress is a cell-intrinsic switch that limits mucus secretion, while autophagy maintains proper mucus secretion and intestinal homeostasis by relieving ER stress.

immunology↗

bioRxiv2020

Establishment of Reference Intervals of Clinical Chemistry Analytes for the Adult Population in Egypt

BackgroundThis is the first Egyptian nationwide study for derivation of reference intervals (RIs) for 34 major chemistry analytes. It was conducted as a part of the global initiative by the IFCC Committee on Reference Intervals and Decision Limits (C-RIDL) for establishing country-specific RIs based on a harmonized protocol. Methods691 apparently healthy volunteers aged [≥]18 years were recruited from multiple regions in Egypt. Serum specimens were analyzed in two centers. The harmonization and standardization of test results were achieved by measuring value-assigned serum panel provided by C-RIDL. The RIs were calculated by parametric method. Sources of variation of reference values (RVs) were evaluated by multiple regression analysis. The need for partitioning by sex, age, and region was judged primarily by standard deviation ratio (SDR). ResultsGender-specific RIs were required for six analytes including total bilirubin (TBil), aspartate and alanine aminotransferase (AST, ALT). Seven analytes required age-partitioning including glucose and low-density lipoprotein cholesterol (LDL-C)., Regional differences were observed between northern and southern Egypt for direct bilirubin, glucose, and high-density-lipoprotein cholesterol (HDL-C) with all their RVs lower in southern Egypt. Compared with other collaborating countries, the features of Egyptian RVs were lower HDL-C and TBil and higher TG and C-reactive protein. In addition, BMI showed weak association with most of nutritional markers. These features were shared with two other Middle Eastern countries: Saudi Arabia and Turkey. ConclusionThe standardized RIs established by this study can be used as common Egyptian RI, except for a few analytes that showed regional differences. Despite high prevalence of obesity among Egyptians, their RVs of nutritional markers are less sensitive to increased BMI, compared to other collaborating countries.

cell biology↗

bioRxiv2020

Summary-data-based mendelian randomisation reveals druggable targets for multiple sclerosis

BackgroundMultiple Sclerosis (MS) is a complex autoimmune disease caused by a combination of genetic and environmental factors. Translation of Genome-Wide Association Study (GWAS) findings in MS into therapeutics and effective preventive strategies has been limited to date. MethodsWe used Summary Data-Based Mendelian Randomisation (SMR) to synthesise findings from public expression quantitative trait locus (eQTL; eQTLgen and CAGE), methylation quantitative trait locus (mQTL; Lothian Birth Cohort and Brisbane Systems Genetics Study), and MS GWAS datasets (International Multiple Sclerosis Genetics Consortium). By correlating the effects of methylation on MS (M-2-MS), methylation on expression (M-2-E), and expression on MS susceptibility (E-2-MS), we prioritise genetic loci with strong evidence of causally influencing MS susceptibility. We overlay these findings onto a list of druggable genes, i.e. genes which are currently, or could theoretically, be targeted by therapeutic compounds. We use GeNets and STRING to identify protein-protein interactions and druggable pathways enriched in our results. We extend these findings to a model of Epstein-Barr Virus-infected B cells, Lymphoblastoid Cell Lines (LCLs). We conducted a systematic review of prioritised genes using the Open Targets platform to identify completed and planned trials targeted prioritised genes in MS and related disease areas. ResultsExpression of 45 genes in peripheral was strongly associated with MS susceptibility (False discovery rate 0.05). Of these 45 genes, 20 encode a protein which is currently targeted by an existing therapeutic compound. These genes were enriched for Gene Ontology terms pertaining to immune system function and leukocyte signalling. We refined this prioritised gene list by restricting to loci where CpG site methylation was associated with MS susceptibility (M-2-MS), with gene expression (M-2-E), and where expression was associated with MS susceptibility (E-2-MS). This approach yielded a list of 15 prioritised druggable target genes for which there was evidence of a causal pathway linking methylation, expression, and MS. Five of these 15 genes are targeted by existing drugs (CD40, ERBB2, VEGFB, MERTK, and PARP1), and three were replicated in a smaller eQTL dataset (CD40, MERTK, and PARP1). In LCLs, SMR prioritised 7 druggable gene targets, of which only one was priortised by the multi-omic approach in peripheral blood (FCRL3). Systematic review of Open Targets revealed multiple early-phase trials targeting 13/20 prioritised genes in disorders related to MS. ConclusionsWe use public datasets and SMR to identify a list of prioritised druggable genetic targets in Multiple Sclerosis. We hope our findings could be translated into effective repurposing of existing drugs to provide novel therapies for MS and, potentially, provide a platform for developing preventive therapies.

genetics↗