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Bacteria proteomics under antidepressants exposure

ABSTRACT: This project conducted proteomics on A.baylyi ADP1, E. coli K12 and P. putita KT2440 after treated with a few commonly-prescribed antidepressant (duloxetine, sertraline, fluoxetine, bupropion, escitalopram and agomelatine). The results with help to reveal how those antidepressants can promote the transfer of antibiotic resistance genes in those treated bacteria.

INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive

ORGANISM(S): Escherichia Coli Pseudomonas Putida Acinetobacter Sp. Adp1

SUBMITTER: Jianhua Guo

LAB HEAD: Jianhua Guo

PROVIDER: PXD028020 | Pride | 2024-01-26

REPOSITORIES: Pride

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			Action	DRS
	20190920_T2_002.raw	Raw
	20190920_T2_004.raw	Raw
	20190920_T2_006.raw	Raw
	20190920_T2_008.raw	Raw
	20190920_T2_010.raw	Raw

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Publications

Antidepressants promote the spread of extracellular antibiotic resistance genes via transformation.

Lu Ji J Ding Pengbo P Wang Yue Y Guo Jianhua J

ISME communications 20220728 1

The development of antibiotic resistance as an unavoidable consequence of the application of antimicrobials is a significant concern for human health. Antidepressants are being increasingly consumed globally. Human gut microbial communities are frequently exposed to antidepressants, yet little is known about the interaction between antidepressants and antibiotic resistance. This study aimed to investigate whether antidepressants can accelerate the dissemination of antibiotic resistance by increa ...[more]

PMID: 37938640

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Proteomic analysis of Acinetobacter baylyi ADP1 under exposure to artificial sweeteners

Project description:The goals of this project are to use a liquid chromatography-tandem mass spectrometer (LC-MS/MS) to detect bacterial proteomic profiles of Acinetobacter baylyi ADP1 and their quantitative protein responses under exposure to 30 mg/L of artificial sweeteners (saccharine, sucralose, aspartame, and acesulfame potassium). The control group without artificial sweeteners exposure was also set up for comparison. Each treatment was conducted in biological triplicate. By comparing the proteomic profiles of artificial sweeteners-treated groups and control group, the effects of artificial sweeteners on bacterial translational levels can be revealed.

2022-02-17 | PXD027117 | Pride

Enrichment of C3 Nitrate microorganisms

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An Abundance of Free Proteasomal Regulatory (19S) Particles Regulate Neuronal Synapses Independent of the Proteasome

Project description:The major protein-degradation machine, the proteasome, functions at brain synapses and regulates long-term information storage. Here we found that the two essential subcomplexes of the proteasome, the regulatory (19S) and catalytic (20S) particles that assemble to recognize and degrade substrates, were differentially distributed within individual rat cortical neurons. By detecting and quantifying 19 and 20S particles at single-molecule resolution, we discovered a surprising abundance of free regulatory particles (19S) near synapses. Furthermore, we found that the free neuronal 19S binds and deubiquitylates Lys63-ubiquitin, a distinct ubiquitin linkage that does not target substrates to the proteasome. Pull-down assays for Lys63 or Lys48 ubiquitin revealed a significant over-representation of synaptic molecules as Lys63 interactors, while conventional proteasome-related proteins dominated the Lys48 interactome. Inhibition of 19S deubiquitylase (DUB) activity significantly altered spontaneous excitatory synaptic transmission and reduced the synaptic availability of AMPA receptors at multiple trafficking points in a proteasome-independent manner. Together, these results reveal a moonlighting function of the regulatory proteasomal subcomplex near synapses.

2024-11-26 | PXD037893 | Pride

COVIDomics_plasma_2020_DDA-PASEF

Project description:In order to investigate variations in the endotype of COVID19 patients, we completed an integrated analysis of 112 research participants, including 74 COVID19 patients versus 37 SARS-CoV-2 negative controls. COVID19 patients tested positive for SARS-CoV-2 infection by PCR and/or antibody testing and were hospitalized due to COVID19 symptoms, but none of them had developed severe pathology requiring ICU admission at the time of blood collection. The control group was recruited from the same hospital system but tested negative for SARS-CoV-2 infection. Research blood draws were obtained from consented participants and analyzed by matched SARS-CoV-2 seroconversion assays, plasma proteomics using two alternative platforms [mass-spectrometry (MS), and SOMAscan assays], 82-plex cytokine profiling using Meso Scale Discovery (MSD) assays, and immune cell profiling via mass cytometry (MC).

2021-03-04 | PXD022817 | Pride

Surgical trauma in mice modifies the content of circulating extracellular vesicles

Project description:Surgical interventions rapidly trigger a cascade of molecular, cellular and neural signaling responses that ultimately reach remote organs, including the brain. Using a mouse model of orthopedic surgery, we have previously demonstrated hippocampal metabolic, structural, and functional changes associated with cognitive impairment. However, the nature of the underlying signals responsible for such periphery-to-brain communication remains hitherto elusive. This is the first exploratory study that tests the hypothesis of extracellular vesicles (EVs) as potential mediators carrying information from the injured tissue to the distal organs including the brain. The primary goal was to investigate whether the cargo of circulating EVs after surgery can undergo quantitative changes that could potentially trigger phenotypic modifications in the target tissues. EVs were isolated from the serum of the mice subjected to a tibia surgery after 6, 24, and 72 h, and the proteome and miRNAome were investigated using mass spectrometry and RNA-seq approaches. We found substantial differential expression of proteins and miRNAs starting at 6 h post-surgery and peaking at 24 h. Interestingly, one of the up-regulated proteins at 24 h was α-synuclein, a pathogenic hallmark of certain neurodegenerative syndromes. We conclude that surgery alters the cargo of circulating EVs in the blood, and our results suggest EVs as potential systemic signal carriers mediating remote effects of surgery on the brain.

2022-01-08 | PXD030167 | Pride

Nitrate-dependent anaerobic propane and butane oxidation coupled to anaerobic ammonium oxidation

Project description:Nitrate-dependent anaerobic propane and butane oxidation coupled to anaerobic ammonium oxidation

2024-05-24 | PXD039266 | Pride

Anaerobic ethane and butane oxidation

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2024-05-24 | PXD039267 | Pride

Serum proteomics in COVID-19 patients: Altered coagulation and complement status as a function of IL-6 level

Project description:Over 5 million people around the world have tested positive for the beta coronavirus SARS-CoV- 2 as of May 29, 2020, a third of which in the United States alone. These infections are associated with the development of a disease known as COVID-19, which is characterized by several symptoms, including persistent dry cough, shortness of breath, chills, muscle pain, headache, loss of taste or smell, and gastrointestinal distress. COVID-19 has been characterized by elevated mortality (over 100 thousand people have already died in the US alone), mostly due to thromboinflammatory complications that impair lung perfusion and systemic oxygenation in the most severe cases. While the levels of pro-inflammatory cytokines such as interleukin-6 (IL-6) have been associated with the severity of the disease, little is known about the impact of IL-6 levels on the proteome of COVID-19 patients. The present study provides the first proteomics analysis of sera from COVID-19 patients, stratified by circulating levels of IL-6, and correlated to markers of inflammation and renal function. As a function of IL-6 levels, we identified significant dysregulation in serum levels of various coagulation factors, accompanied by increased levels of anti-fibrinolytic components, including several serine protease inhibitors (SERPINs). These were accompanied by up-regulation of the complement cascade and antimicrobial enzymes, especially in subjects with the highest levels of IL- 6, which is consistent with an exacerbation of the acute phase response in these subjects. Although our results are observational, they highlight a clear increase in the levels of inhibitory components of the fibrinolytic cascade in severe COVID-19 disease, providing potential clues related to the etiology of coagulopathic complications in COVID-19 and paving the way for potential therapeutic interventions, such as the use of pro-fibrinolytic agents.

2020-07-29 | PXD020601 | Pride

RNA-seq and TRAP-seq of astrocytes and brain tissue in mouse models of Alzheimer's pathology

Project description:Alzheimer’s disease is known to alter astrocytes, but the effect of Aß and Tau pathology on these cells remains poorly understood. We investigated the transcriptomic behaviour of astrocytes (via translating ribosome affinity purification (TRAP)), and bulk brain tissue, in mouse models of APP/PS1 ß-amyloidopathy and MAPT-P301S tauopathy, in a mouse model overexpressing cytoprotective Nrf2 specifically in astrocytes (GFAP-Nrf2 model), and in crosses between the amyloidopathy and tauopathy models with the GFAP-Nrf2 mouse.

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Gene expression profiling in THP1 cells after PAPD5 or GLD2 knockdown

Project description:Next-generation sequencing experiments have shown that microRNAs are expressed in many different isoforms (isomiRs), whose biological relevance is often unclear. We found that mature miR-21, the most widely researched microRNA because of its importance in human disease, is produced in two prevalent isomiR forms that differ by one nucleotide at their 3M-bM-^@M-^Y end, and moreover that the 3M-bM-^@M-^Y end of miR-21 is post transcriptionally adenylated by the noncanonical poly(A) polymerase PAPD5. PAPD5 knockdown caused an increase in the miR-21 expression level, suggesting that PAPD5-mediated adenylation of miR-21 leads to its degradation. Exoribonuclease knockdown experiments followed by small RNA sequencing suggested that PARN degrades miR-21 in the 3M-bM-^@M-^Y-to-5M-bM-^@M-^Y direction. In accordance with this model, microarray expression profiling demonstrated that PAPD5 knockdown results in a downregulation of miR-21 target mRNAs. We found that disruption of the miR-21 adenylation and degradation pathway is a general feature in tumors across a wide range of tissues, as evidenced by data from The Cancer Genome Atlas, as well as in the non-cancerous proliferative disease psoriasis. We conclude that PAPD5 and PARN mediate degradation of oncomiR miR-21 through a tailing and trimming process, and that this pathway is disrupted in cancer and other proliferative diseases. Gene expression levels were profiled by Illumina microarrays using RNA produced previously (PMID 20719920). Briefly, total RNA was extracted from THP1 cells in four replicates 72 hours after transfection of siRNA against PAPD5 or GLD2, or of calibrator negative control siRNA. Gene expression levels were profiled in two of the PAPD5 knockdown replicates, two of the GLD2 knockdown replicates, and two of the negative control replicates.

2014-05-24 | E-GEOD-57939 | biostudies-arrayexpress

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