Biology subjects

Ullah, A.

Publications and source records attributed to Ullah, A..

8 recordsLinked to original sources

bioRxiv2025

Phage-encoded sRNA counteracts xenogenic silencing in pathogenic E. coli

Horizontal gene transfer introduces foreign DNA that can disrupt cellular processes and is therefore subject to xenogenic silencing by nucleoid-associated proteins such as H-NS and Hha. In Enterohaemorrhagic Escherichia coli (EHEC), prophages make up a large fraction of the accessory genome and encode many virulence factors, yet to be expressed they must overcome this silencing. We identify a prophage-encoded small RNA (sRNA), HnrS, that functions as an anti-silencing factor by targeting the H-NS paralogue Hha. HnrS is a short (66-nt) sRNA present in multiple copies (up to nine) in EHEC and Enteropathogenic Escherichia coli (EPEC) genomes and is enriched in E. coli strains that carry the locus of enterocyte effacement (LEE). We show that HnrS directly base-pairs with the ribosome-binding site of the hha mRNA, repressing its translation and thereby reducing Hha-enhanced H-NS silencing. This counter-silencing de-represses the LEE type III secretion system and concomitantly represses motility. Transcriptomic profiling further revealed that HnrS indirectly activates genes involved in nitrate/nitrite respiration and nitric oxide resistance, metabolic pathways that contribute to survival in the inflamed gastrointestinal tract. Deletion of hnrS reduced expression of nitrate reductase genes and impaired actin pedestal formation on host epithelial cells. Our results indicate that prophage-encoded, multicopy hnrS provides a counter-silencing mechanism that reduces Hha-H-NS repression at specific virulence loci. This likely enables expression of horizontally acquired genes without broadly disrupting the core H-NS regulon. HnrS illustrates how mobile genetic elements deploy sRNAs to counteract xenogenic silencing and promote virulence gene expression, enhancing colonisation of the host. Importance statementHorizontally acquired genes are often silenced to protect bacterial genomes, but this defence also limits the expression of new traits. We identify a prophage-encoded small RNA, HnrS, that counteracts this restriction by repressing the xenogenic silencer Hha, lifting Hha-H-NS-mediated repression of virulence and metabolic genes. HnrS activates the locus of enterocyte effacement, nitrate/nitrite respiration, and nitric oxide resistance--pathways that help E. coli survive and colonise the inflamed gut. Our findings reveal an RNA-based counter-silencing mechanism encoded by mobile genetic elements, showing how phages can reprogram bacterial regulatory networks to promote adaptation and pathogenicity.

microbiology↗

bioRxiv2023

Dual therapy with corticosteroid ablates the beneficial effect of DP2 antagonism in chronic experimental asthma.

BackgroundProstaglandin D2 (PGD2) signals via the DP1 and DP2 receptors. In Phase II trials, DP2 antagonism decreased airway inflammation and airway smooth muscle (ASM) area in patients with moderate-to-severe asthma, but in the Phase III clinical trials, DP2 antagonism failed to significantly lower the rate of exacerbations. Here, we hypothesised that DP2 antagonism resolves established ASM remodeling via endogenous PGD2/DP1 activation and that this beneficial effect is ablated by dual corticosteroid therapy. MethodsNeonatal mice were co-exposed to pneumonia virus of mice (PVM) and cockroach extract in early life to induce severe bronchiolitis, then re-infected with PVM and challenged to cockroach extract in adulthood to progress disease to chronic experimental asthma (CEA). The efficacy of DP2 antagonism monotherapy or various dual therapies was assessed in the setting of a rhinovirus (RV)-induced exacerbation. ResultsRV inoculation increased PGD2 release, mucus production, collagen deposition, transforming growth factor (TGF)-{beta}1 expression and type-2 inflammation. Treatment with a DP2 antagonist or DP1 agonist ablated the aforementioned phenotypes, increased type-1 immunity, and decreased ASM area. Dual DP1-DP2 antagonism or dual corticosteroid/DP2 antagonism, which attenuated endogenous PGD2 levels, prevented the resolution of ASM area induced by DP2 antagonism alone. The resolution of ASM remodelling following DP2 antagonism was mediated by IFN-{gamma} and associated with decreased TGF-{beta}1 expression. ConclusionDP2 antagonism resolved ASM remodelling via PGD2/DP1-mediated upregulation of interferon-{gamma} expression. Dual DP2 antagonism/corticosteroid therapy, as occurred in many of the human trials, suppressed PGD2 and IFN-{gamma} production, impairing the efficacy of DP2 antagonism.

immunology↗

bioRxiv2023

The Hsp60 C-terminus Senses Substrate and Triggers Allosteric ATP Hydrolysis

The human mitochondrial chaperonin Hsp60/Hsp10 plays an essential role in maintaining protein homeostasis through an ATP dependent protein refolding mechanism. In the absence of this chaperonin, all cells perish due to an accumulation of misfolded aggregates. Despite its importance, the detailed mechanism of ATP hydrolysis and the role of the C-terminal tail remains unresolved. Here we show that the C-terminal tail acts as a sensor for the arrival of substrate into the chaperonin internal chamber that directly leads to an allosteric trigger of ATP hydrolysis in a neighboring subunit. Our results reveal that removal of the C-terminal tail leads to normal binding of both ATP and a misfolded substrate, but the chaperonin stalls and is unable to progress along the protein folding reaction cycle because it has lost the ability to sense the presence of substrate. High resolution reconstructions reveal the detailed mechanism of ATP hydrolysis where access to the {gamma}-phosphate is blocked by the carboxylate oxygen of an aspartate residue. Binding of the C-terminal tail to substrate displaces this oxygen and allows ATP hydrolysis. These results bring a better understanding of how Hsp60 functions at an atomic level where substrate arrival activates ATP hydrolysis through an allosteric trigger.

biochemistry↗

bioRxiv2023

Long-insert sequence capture detects high copy numbers in a defence-related beta-glucosidase gene Betaglu-1 with large variations in white spruce but not Norway spruce

Conifers are long-lived and slow-evolving, thus requiring effective defences against their fast-evolving insect natural enemies. The copy number variation (CNV) of two key acetophenone biosynthesis genes Ugt5/Ugt5b and {beta}glu-1 may provide a plausible mechanism underlying the constitutively variable defence in white spruce (Picea glauca) against its primary defoliator, spruce budworm. This study develops a long-insert sequence capture probe set (Picea_hung_p1.0) for quantifying copy number of {beta}glu-1-like, Ugt5-like genes and single-copy genes on 38 Norway spruce (Picea abies) and 40 P. glauca individuals from eight and nine provenances across Europe and North America respectively. We developed local assemblies (Piabi_c1.0 and Pigla_c.1.0), full-length transcriptomes (PIAB_v1 and PIGL_v1), and gene models to characterise the diversity of {beta}glu-1 and Ugt5 genes. We observed very large copy numbers of {beta}glu-1, with up to 381 copies in a single P. glauca individual. We observed among-provenance CNV of {beta}glu-1 in P. glauca but not P. abies. Ugt5b was predominantly single-copy in both species. This study generates critical hypotheses for testing the emergence and mechanism of extreme CNV, the dosage effect on phenotype, and the varying copy number of genes with the same pathway. We demonstrate new approaches to overcome experimental challenges in genomic research in conifer defences.

evolutionary biology↗

bioRxiv2022

IL-33-induced neutrophilic inflammation and NETosis underlie rhinovirus-triggered exacerbations of asthma

Rhinovirus-induced neutrophil extracellular traps (NETs) contribute to acute asthma exacerbations, however the molecular factors that trigger NETosis in this context remain ill-defined. Here, we sought to implicate a role for IL-33, an epithelial cell-derived alarmin rapidly released in response to infection. In mice with chronic experimental asthma (CEA), but not naive controls, rhinovirus inoculation induced an early (1 day post infection; dpi) inflammatory response dominated by neutrophils, neutrophil-associated cytokines (IL-1, IL-1{beta}, CXCL1) and NETosis, followed by a later, type-2 inflammatory phase (3-7 dpi), characterized by eosinophils, elevated IL-4 levels, and goblet cell hyperplasia. Notably, both phases were ablated by HpARI (Heligmosomoides polygyrus Alarmin Release Inhibitor), which blocks IL-33 release and signalling. Instillation of exogenous IL-33 recapitulated the rhinovirus-induced early phase, including the increased presence of NETs in the airway mucosa, in a PAD4-dependent manner. Ex vivo IL-33-stimulated neutrophils from mice with CEA, but not naive mice, underwent NETosis, and produced greater amounts of IL-1/{beta}, IL-4, and IL-5. In nasal samples from rhinovirus-infected people with asthma, but not healthy controls, IL-33 levels correlated with neutrophil elastase and dsDNA. Our findings suggest that IL-33 blockade ameliorates the severity of an asthma exacerbation by attenuating neutrophil recruitment and the downstream generation of NETs.

immunology↗

bioRxiv2021

Copy number variation profile-based genomic subtyping of premenstrual dysphoric disorder in Chinese

Premenstrual dysphoric disorder (PMDD) affects nearly 5% women of reproductive age. The symptomatic heterogeneity, along with largely unknown genetics, of PMDD have greatly hindered its effective treatment. In the present study, 127 Chinese PMDD patients of the invasion and depression subtypes clinically differentiated by us earlier were analyzed together with 108 non-PMDD controls for genome-wide copy number variations (CNVs). Germline genomic DNA samples from white blood cells were subjected to AluScan sequencing-based CNV profiling, which enabled clustering of patient samples readily into the V and D groups, dominated by the "invasion" and "depression" clinical subtypes, respectively; the CNVs obtained with 100-kb windows yielded two clusters that were correlated with these subtypes with a consistency of up to 89.8%. Diagnostic correlation- and frequency-based CNV features of either CNV-gain (CNVG) or CNV-loss (CNVL) that could differentiate between V and D subtypes were selected and analyzed. CNVG features located preferentially in S2-phase replicating regions and enriched with steroid hormone biosynthesis pathway of genes were found protective against PMDD. Moreover, machine learning employing the correlation-based CNV features could predict with >80% accuracy whether a genomic sample was D-type, V-type or control. In terms of their CNV profiles, the D- and V-types differed more from one another than from the controls, thereby providing a genomic basis for the clinical D-V subtyping of PMDD. Genome-wide profiling of CNVs, as a new approach to complex disease genetics, has revealed recurrent CNVs and genomic features beyond individual genes and mutations underlying PMDD clinical diversity.

genomics↗

bioRxiv2019

Differential detection of Entamoeba species in stool samples collected from children in District Swat, Khyber Pakhtunkhwa Pakistan

BackgroundAmoebiasis is an intestinal disease caused by enteric protozoan called Entamoeba histolytica belongs to the Genus Entamoeba. The main reason of infection is the contamination of food and water due to the poor sanitation. Among Entamoeba species, Entamoeba histolytica is highly pathogenic while the other species are non-pathogenic and needs no medical treatment.\n\nMethodologyA total of 400 stool samples were collected from different areas of district Swat and were processed for screening of amoebic cells. Microscopically identified samples containing amoebic cells were stored at -20 {degrees}C till DNA extraction. Extracted DNA was used in a PCR reaction with specific reference primers to amplify the target DNA.\n\nResultsOut of all 400 stool samples 111 (27.7%) were found positive through microscopy while PCR reaction confirmed 80 out of microscope positive samples. Among 80 PCR positive samples, the infection with Entamoeba dispar was most common (57.5%) followed by E. histolytica (47.5%) and Entamoeba moshkovskii (20%). The positive cases for mono-infection of E. dispar were 33 (41.25%), followed by E.histolytica 25 (31.25%) and E. moshkovskii 7 (8.75%). The co-infection of E. histolytica with E. dispar and E. moshkovskii was 6 (7.5%) and 2 (2.5%), respectively. Similarly the co-infection of Entamoeba dispar with Entamoeba moshkovskii was also 2 (2.5%) while 5 (6.25%) samples were observed with mixed infection of E. histolytica, E. dispar and E. moshkovskii.\n\nSignificance of the studyThe aim of the study was to detect and differentiate the E. histolytica, Entamoeba dispar and Entamoeba moshkovskii using conventional microscopy and polymerase chain reaction. The results suggested that the use of PCR is necessary to differentiate E. histolytica from E. dispar and E. moshkovskii and therefore, to avoid unnecessary treatment the present study recommend the use of PCR for the routine diagnosis of amoebiasis in the study area. It is also suggested that further studies from this area may also facilitate the understanding of genetic diversity of these pathogens.

microbiology↗

bioRxiv2019

Dietary acculturation of Asian and the Middle East and North African region immigrants to Saudi Arabia: healthy or unhealthy acquired nutritional behavior?

Travel and migration influences food behavior. This study assessed the dietary acculturation of immigrants in Saudi Arabia, with regard to length of stay and health status of immigrants. This cross-sectional study included 880 university immigrant employees and their family members from Asian and Middle East and North African regions. Dietary acculturation was assessed based on knowledge and practice of methods of food preparation, type of food consumption, and nutrition label reading behavior, using a measurement tool on a 5-point Likert scale. Furthermore, a scoring system was adapted for healthy practices. Anthropometric, biochemical, and blood pressure measurements were performed as per the World Health Organization guidelines, to determine participants health and comorbid status. In addition, scores were calculated for healthy options. Factors influencing better awareness were determined by logistic regression analysis. The most adopted methods of food preparation after migration were barbeque (p=0.018), microwave cooking (p=0.002), and raw food consumption (salads) (p<0.001). Consumption of carbonated drinks (p=0.025), fried fatty and processed food (p=0.037), and sweets and candies (p=0.008) were significantly higher among recent immigrants of <5 years of residency. Label reading behavior of nutritional contents and low-fat options was higher among immigrants with [≥]5 years duration of residency (63%; p<0.001). Although female gender, longer duration of residency in Saudi Arabia and presence of comorbidity significantly improved the overall awareness and practice scores in the binary analysis, they failed to show significance in regression model except for the presence of diabetes which improved only awareness. None of the other independent factors seem to influence healthy practices. Chronic diseases like obesity, diabetes and hypertension increased with longer duration of migration(p<0.001).\n\nNew immigrants are at risk of acquiring negative dietary habits compromising health, necessitating follow-up studies to establish causation. Interventional policy measures are recommended to formulate dietary guidelines.

epidemiology↗