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Project description:Incomplete antibiotic removal in pharmaceutical wastewater treatment plants (PWWTPs) could lead to the development and spread of antibiotic-resistant bacteria (ARBs) and genes (ARGs) in the environment, posing a growing public health threat. In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. The N1 strain was highly resistant to ampicillin, cefazolin, chloramphenicol, tetracycline, and norfloxacin, while the N2 strain exhibited high resistance to ampicillin, chloramphenicol, and cefazolin. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity. Overall, this research provides insights into the potential risks posed by ARBs in pharmaceutical wastewater and emphasizes the need for further studies on their impact and mitigation strategies.
2024-10-20 | E-MTAB-14497 | biostudies-arrayexpress
Project description:In this study, two multiantibiotic-resistant bacteria, Ochrobactrum intermedium (N1) and Stenotrophomonas acidaminiphila (N2), were isolated from the sludge of a PWWTP in Guangzhou, China. Whole-genome sequencing revealed that N1 and N2 had genome sizes of 0.52 Mb and 0.37 Mb, respectively, and harbored 33 and 24 ARGs, respectively. The main resistance mechanism in the identified ARGs included efflux pumps, enzymatic degradation, and target bypass, with the N1 strain possessing more multidrug-resistant efflux pumps than the N2 strain (22 vs 12). This also accounts for the broader resistance spectrum of N1 than of N2 in antimicrobial susceptibility tests. Additionally, both genomes contain numerous mobile genetic elements (89 and 21 genes, respectively) and virulence factors (276 and 250 factors, respectively), suggesting their potential for horizontal transfer and pathogenicity.
2024-10-20 | E-MTAB-14496 | biostudies-arrayexpress
Project description:With increasingly concerning strains of antimicrobial resistant strains of the commensal, gram-negative bacteria Klebsiella pneumoniae emerging, there is a pressing need to better understand the pathogen and mechanisms behind its pathogenicity. This study investigated the regulatory mechanisms in strain MGH 78578 of two major sigma factors, the house-keeping sigma factor RpoD, and the general stress response sigma factor RpoS, in mid-exponential and early stationary phase using chromatin immunoprecipitation with exonuclease treatment (ChIP-exo) followed by deep sequencing. Combining ChIP-exo and transcriptome analysis allowed for the determination of sigma factor binding sites, binding motifs, and genes included in the phase-specific sigmulons. The number of genes included in the RpoS sigmulon was greater than in the RpoD sigmulon, with 1,833 and 1,690 genes included, respectively; however, a majority of sigmulon genes were found in all phase-specific sigmulons. Focussing on pathogenicity genes, 20 antimicrobial resistance genes (ARGs) and 155 virulence genes, only two ARGs were found exclusively in one phase-specific sigmulon, an oxacillin-hydrolysing class D beta-lactamase and chloramphenicol efflux MFS transporter CmlA5, which were found in the RpoD sigmulon in early stationary phase. Notably, six unnamed proteins that are or pertain to fimbrial proteins were found uniquely in the RpoS sigmulon in early stationary phase. From this, it can be hypothesised that early stationary phase might be an important phase for pathogenicity gene regulation. While there is little conservation in RpoS sigmulons from strain to strain, RpoS appears to have a consistent overarching role across strains, including a role as a regulator of pathogenicity genes.
2025-02-24 | GSE226119 | GEO
Project description:We identified ARGs in a genome-wide manner, in fly brains as well as in sorted neurons; they included dopaminergic neurons (DA) and a subset of circadian-related neurons (PDF+ neurons).
2016-12-12 | GSE83975 | GEO
Project description:The cerebral cortex is a highly organized structure whose development depends on different progenitor cell types. These give rise to post-mitotic neurons that migrate across the developing cortical wall to their final positions in the cortical plate. Apical radial glia cells (aRGs) are the main progenitor type in early corticogenesis, responsible for the production of other progenitors, and regulating the final neuronal output. Abnormal behavior of aRG can severely impact corticogenesis resulting in cortical malformations. Mutations in the microtubule associated protein Eml1 lead to severe subcortical heterotopia, characterized by the presence of aberrantly located neurons beneath the normotopic cortex. Mutations in EML1/Eml1 have been reported in three families presenting severe atypical heterotopia, as well as in the Heterotopic cortex ‘HeCo’ spontaneous mouse mutant. In the latter, ectopically cycling aRGs were found cycling outside their normal proliferative ventricular zone (VZ) from early stages of corticogenesis (Croquelois et al., 2009, Kielar et al., 2014, Shaheen et al., 2017). Ectopic aRGs are likely to be responsible for the formation of the heterotopia. It is thus crucial to understand the role of Eml1 in aRGs to elucidate the physiological and pathological mechanisms causing aRGs to leave the VZ. The role of Eml1 in aRGs remains vastly unexplored. We have thus performed mass spectrometry with embryonic cortex lysates (E13.5) to shed light on the intracellular pathways and molecular mechanisms in which Eml1 could be involved. This data combined with other cell biology and biochemistry approaches will contribute to understand the role of this heterotopia protein at early stages of development.
2019-06-20 | PXD012714 | Pride
Project description:Introduction: Anoikis is a form of programmed cell death. Anoikis resistance in hepatocellular carcinoma (HCC) promotes cancer cells shedding from the primary tumor site, thus contributing to survival and distant metastasis. However, the prognostic significance of anoikis-related genes (ARGs) and the biological functions of crucial genes in HCC have not been reported. Objectives: This study aimed to construct a model for predicting the outcome of patients with HCC based on ARGs and to investigate the clinicopathological significance and function of Rac family small GTPase 3 (RAC3) in HCC.
2025-03-26 | GSE273947 | GEO
Project description:Autophagy is essential for plant response to a variety of developmental and environmental factors. However, unlike yeast and animals, only a few autophagy genes in plants are functionally conserved in the biological world. An important question is, how plants form autophagy related functions in evolution? Here, we developed and verified a workflow that identified 997 high-confidence autophagy related genes (ARG) in A.thaliana using multi-group data from nearly 10,000 samples and established a co-network of autophagy containing 3,419 new presumptive connections. Of note, through the genomic analysis of 76 representative plants from lower to higher levels, we found that ARGs were preferentially retained after polyploidization followed by terrestrialization, forming plant-specific autophagy-related functions. In addition, we provide the evolutionary gains and losses of ARGs function in monocotyledons and dicotyledons, and verified two novel genes ml2 and ml5 presumed to be involved in autophagy and leaf senescence. This work provides valuable resources for the study of plant autophagy and highlights that ARGs may selectively promote the success of plant autophagy through polyploidy in the process of evolution.
2022-08-26 | GSE211896 | GEO
Project description:We identified ARGs in a genome-wide manner, in fly brains as well as in sorted neurons; they included dopaminergic neurons (DA) and a subset of circadian-related neurons (PDF+ neurons).
2016-12-12 | GSE83974 | GEO