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A plasmid goes viral, part 2 - A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells

ABSTRACT: Analysis of protein compostition of plasmid vesicles (PVs) purified through CsCl gradients.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Halorubrum Lacusprofundi Atcc 49239

TISSUE(S): Cell Culture

SUBMITTER: Susanne Erdmann

LAB HEAD: Ricardo Cavicchioli

PROVIDER: PXD006515 | Pride | 2017-07-14

REPOSITORIES: Pride

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			Action	DRS
	F136360.mgf	Mgf
	F136360.mzid	Mzid
	F136361.mgf	Mgf
	F136361.mzid	Mzid
	F136398.mgf	Mgf

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Publications

A plasmid from an Antarctic haloarchaeon uses specialized membrane vesicles to disseminate and infect plasmid-free cells.

Erdmann Susanne S Tschitschko Bernhard B Zhong Ling L Raftery Mark J MJ Cavicchioli Ricardo R

Nature microbiology 20170821 10

The major difference between viruses and plasmids is the mechanism of transferring their genomic information between host cells. Here, we describe the archaeal plasmid pR1SE from an Antarctic species of haloarchaea that transfers via a mechanism similar to a virus. pR1SE encodes proteins that are found in regularly shaped membrane vesicles, and the vesicles enclose the plasmid DNA. The released vesicles are capable of infecting a plasmid-free strain, which then gains the ability to produce plasm ...[more]

PMID: 28827601

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A plasmid goes viral - Analysis of protein compostition of membrane vesicles (MVs), plasmid vesicles (PVs) and membrane fractions of different Halorubrum lacusprofundi strains.

Project description:Analysis of protein compostition of membrane vesicles (MVs), plasmid vesicles (PVs) and membrane fractions of different Halorubrum lacusprofundi strains.

2017-07-11 | PXD005092 | Pride

First evidence for an isoprene reductase in Acetobacterium wieringae

Project description:Isoprene-metabolizing bacteria represent a global regulator for atmospheric isoprene concentrations. Under anoxic conditions, isoprene can be used as an electron acceptor reducing it to methylbutene. This study describes the proteogenomic profiling of an isoprene reducing enrichment culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome assembled genome (MAG) of the most abundant (88 % rel. abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and RT-PCR identified a five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (HypA, HypA, HypB) and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, FAD as well as two pairs of [4Fe-4S]-clusters. Other Acetobacterium strains (A. woodii DSM 1030, A. wieringae DSM 1911, A. malicum DSM 4132 and A. dehalogenans DSM 11527) do not encode the isoprene reduction operon and could not reduce isoprene. Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes and Proteobacteria, suggesting the ability of biohydrogenation of non-functionalized conjugated doubled bonds in other unsaturated hydrocarbons.

2023-03-08 | PXD023683 | Pride

miRNA Expression Profiling in Ovarian Cell Lines compared to pooled commercial RNA samples

Project description:We investigated whether levels of serum microRNAs (miRNAs) could discriminate women with high-grade serous ovarian epithelial cancer (SEOC) from age matched healthy volunteers. miRNA expression profiling was performed on 4 SEOC cell lines and normal human ovarian surface epithelial cells (HOSE). miR-182, miR-200a, b and c were highly overexpressed in the SEOC cell lines. miR-103, miR-92a and miR-638 displayed relatively invariant expression and with RNU48, were assessed, as putative serum miRNA normalizers. The 7 miRNA and RNU48 were assessed in serum from SEOC patients (n = 30) and age-matched healthy volunteers (n = 32) by qRT-PCR following pre-amplification. No correlation between age and miRNA or RNU48 levels was observed (age range 30-79 years). miR-103 demonstrated the least variance and was chosen to normalize serum volume adjusted results. miR-200a, b and c were significantly elevated in SEOC serum (P = 0.002; 0.003; 0.0003 respectively) and a multivariate model was the best predictive classifier of SEOC (ROC-AUC = 0.806). A correlation between high miR-200b levels and residual macroscopic disease following cytoreductive surgery was identified (P = 0.006). Our results suggest that serum miR-200a, b and c may have utility as diagnostic biomarkers for SEOC. miRNA expression was arrayed in 1 human surface epithelial cells (HOSE) and 4 ovarian cancer cell lines (OV167, OV202, OVCAR-3, PE01). HOSE cells were run in triplicate (including 1 dye-swap). Ovarian cancer cell lines were run in duplicate (including 1 dye-swap).

2012-02-22 | E-GEOD-35951 | biostudies-arrayexpress

Affymetrix 6.0 study of sporadic motor neuron disease patients and controls.

Project description:This data was divided into three experiment sets: 1. A somatic study of sporadic motor neuron disease (SMND) brain samples that were compared to the blood from the same individual, normal control brains and disease control brans (Parkinson Disease patients); 2. A twin study comparing blood and other tissue samples from twins that were discordant for MND, concordant for MND and control twins and 3. A trio study of blood samples MND patients compared to their unaffected parents. Study 1: 36 sporadic motor neuron disease brain (lateral frontal cortex, Brodmann area 46), 34 matched sporadic motor neuron disease blood, 26 control brain (lateral frontal cortex, Brodmann area 46), 9 Parkinson Disease brain (disease controls, lateral frontal cortex, Brodmann area 46). Study 2 and study 3: 52 twin or trio blood, 4 twin hair, 1 twin sperm. 2 replicate twin blood and 1 replicate trio blood repeated at a different time. External control blood from Coriell GM15510 and GM10851.

2010-07-31 | E-GEOD-15826 | biostudies-arrayexpress

The acute transcriptional response of the coral Acropora millepora to immune challenge: expression of GiMAP/IAN genes links the innate immune response of corals with those of mammals and plants

Project description:This studies investigates the acute response of the coral Acropora millepora to two immunogenes: MDP (bacterial mimic) and pIC (viral mimic). Three members of the GiMAP familly were found to respond strongly to MDP treatment, showing analalogy to the immune response in vertebrates and plants. Differential gene expression following treatment with two immunogenes

2013-11-05 | E-GEOD-46389 | biostudies-arrayexpress

Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in Myelodysplastic Syndromes and Acute Myeloid Leukemia

Project description:Hypomethylating agents (HMAs) are frontline therapies effective at altering the natural course of Myelodysplastic Neoplasms (MDS). However, acquired resistance and treatment failure are hallmarks of HMA therapy. Developing effective and rational HMA-focused combinatorial therapies is challenging as the underlying mechanisms driving HMA efficacy are complex. To address this clinical need, we performed a genome-wide CRISPR-Cas9 screen in a human MDS-derived cell line, MDS-L, and characterized TOPORS as a highly ranked target that synergizes with HMAs to reduce leukemic burden and improve survival in xenograft models. We demonstrated that the depletion of TOPORS mediates sensitivity to HMAs by predisposing leukemic blasts to an impaired DNA damage response (DDR) accompanied by an accumulation of SUMOylated DNMT1 in HMA-treated TOPORS-depleted cells. Importantly, the combination of HMAs with targeting of TOPORS did not functionally impair healthy hematopoiesis. While inhibitors of TOPORS are currently unavailable, we show that inhibition of SUMOylation (upstream of TOPORS functions) with TAK-981 partially phenocopies HMA-sensitivity and DDR impairment. Overall, our data suggest that the combination of HMAs with the inhibition of SUMOylation demonstrates a favourable therapeutic index and represents a rational framework towards the treatment of High-Risk MDS (HR-MDS) or Acute Myeloid Leukemia (AML).

2024-07-25 | PXD050539 | Pride

Dehalobacterium formicoaceticum proteomics data from dichloromethane (DCM)-only medium

Project description:Dehalobacterium formicoaceticum is recognised for its unusual ability to anaerobically ferment dichloromethane (DCM), and a catabolic model has recently been proposed. D. formicoaceticum is currently the only axenic culture representative of its class, the Dehalobacteriia, however much diversity has been revealed in this lineage through recent culture-independent exploration of anoxic habitats. Here we performed a comparative analysis of 10 members of the Dehalobacteriia, representing three orders, and infer that anaerobic DCM degradation is a recently acquired trait only present in some members of the order Dehalobacteriales. Inferred traits common to the class include the use of amino acids as sole carbon sources for growth, energy generation via a remarkable range of putative electron-bifurcating protein complexes, and S-layers. The ability of D. formicoaceticum to grow on serine alone was subsequently confirmed experimentally and a high abundance of the electron-bifurcating protein complexes and S-layer proteins was noted when this organism was grown on DCM. We conclude that members of the Dehalobacteriia are low abundance fermentative scavengers in anoxic habitats.

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LILRA3-GFP and GFP only Transfected HEK293T cells LC-MSMS

Project description:The leukocyte immunoglobulin-like receptor A3 (LILRA3) is a soluble protein primarily expressed by peripheral blood monocytes and is abundant in sera of healthy donors. Extracellular LILRA3 is anti-inflammatory and displays neuro-regenerative functions in vitro. However, its intracellular expression, distribution and function(s) remain unknown. Using a combination of high-resolution confocal and super-resolution microscopy, we identified intracellular expression of native LILRA3 in the nucleus of peripheral blood monocytes and in vitro derived macrophages. This unexpected nuclear localisation of LILRA3 was confirmed in LILRA3-GFP transfected HEK293T cells. Western blot of proteins fractionated from primary macrophages and the transfected HEK293T cells confirmed nuclear localisation of the native and expressed LILRA3 proteins. Interestingly, most of the LILRA3 in the nucleus was in a monomeric form like the biologically active secreted protein, while those in the other cellular compartments were mixed monomeric, dimeric, and oligomeric forms. The predominant presence of monomeric LILRA3 in the nucleus was independently corroborated in transfected live HEK293T cells using number and molecular brightness (N&B) analysis method. Immunoprecipitation and Mass spectrometric peptide sequencing studies revealed that nuclear LILRA3 co-immunoprecipitated with several nuclear proteins involved in host protein synthesis machinery via direct interaction to a key multifunctional RNA binding protein, the Ewing sarcoma breakpoint region 1 protein (EWS).

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Human granulosa

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2014-07-14 | E-MTAB-2264 | biostudies-arrayexpress

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