Harvest Time-Dependent Changes in the Composition and Function of Microglia-Derived Small Extracellular Vesicles.

Microglia are dynamic macrophage-like cells that survey the central nervous system (CNS) and mediate neuroinflammatory responses. Even under homeostatic conditions, they exhibit phenotypic plasticity in response to environmental cues. Microglia-derived small extracellular vesicles (sEVs), which are lipid bilayer vesicles encapsulating proteins, lipids, and nucleic acids, reflect the physiological state of their parent cells and influence recipient cell function.

Quantitative differences in rumen epithelium proteins and detection of lysine acetylation in lambs fed a low or high metabolizable energy diet.

Thirty-six Merino wethers (10-mo-old) were fed ad libitum for 30 d 2 diets;1) low metabolizable energy diet (LME; 30% lucerne: 70% cereal chaff) and 2) high ME diet (HME; 40% rolled barley grain: 50% lucerne: 10% cereal chaff). Effects of diet on dry matter intake (DMI), ME intake (MEI), liveweight (LWT), average daily gain (ADG), carcass lean or fat gain, liver and empty rumen weight, and plasma metabolites were analyzed. A membrane-enriched protein fraction of rumen epithelium (RE) isolated enzymatically from whole depth rumen wall was quantified for each sheep using tandem mass tag mass spectrometry (TMT-MS).

Proteomic analysis during seed development provides insight into the early establishment of seed dormancy in Xanthium strumarium.

This experiment was carried out to provide a comprehensive insight into the protein activities involved in dormancy establishment in seeds of common cocklebur (Xanthium strumarium), an annual plant with two dimorphic seeds contained in one casing known as a burr. These consist of a smaller dormant seed and a larger non-dormant seed. The proteome profile was compared between developing dormant and non-dormant seeds of Xanthium strumarium at five consecutive stages including three, 10, 20, 30, and 45 days after burr emergence (stages 1 to 5).

Proteomic analysis of the developing mammalian brain links PCDH19 to the Wnt/β-catenin signalling pathway.

Clustering Epilepsy (CE) is a neurological disorder caused by pathogenic variants of the Protocadherin 19 (PCDH19) gene. PCDH19 encodes a protein involved in cell adhesion and Estrogen Receptor α mediated-gene regulation. To gain further insights into the molecular role of PCDH19 in the brain, we investigated the PCDH19 interactome in the developing mouse hippocampus and cortex.

Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei.

Background: Trichoderma reesei is an organism extensively used in the bioethanol industry, owing to its capability to produce enzymes capable of breaking down holocellulose into simple sugars. The uptake of carbohydrates generated from cellulose breakdown is crucial to induce the signaling cascade that triggers cellulase production. However, the sugar transporters involved in this process in T.

Quantitative Differences in Rumen Epithelium Proteins in Lambs Fed Wheat, Perennial Wheat, or Perennial Wheat plus Lucerne.

The value of crops such as perennial wheat (PW) for grain and grazing compared to conventional wheat (W), or the addition of lucerne to PW (PWL) is still being determined. This research sought to determine if these diets were associated with changes in the membranebound proteins that transport nutrients in the rumen epithelium (RE). Crossbred ewes (Poll Dorset × Merino) were fed W, PW, or PWL (50:50) fresh-cut forage for 4 weeks.

Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling.

Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better target selectivity are continuously needed. On the basis of the success of monocovalent activity-based and reactivity-based probes, an approach of structurally aligned dual-modifier labeling (SADL) was investigated here on its potential in improving target precision.

Endogenous protein interactomes resolved through immunoprecipitation-coupled quantitative proteomics in cell lines.

Immunoprecipitation (IP) of endogenously expressed proteins is one of the most biologically relevant techniques to identify protein-protein interactions. We describe an adaptable IP protocol reliant on a specific antibody to the target protein. We detail a quantitative proteomics workflow for the unbiased identification of co-immunoprecipitating proteins, known collectively as an interactome.

Multiple Abiotic Stresses Applied Simultaneously Elicit Distinct Responses in Two Contrasting Rice Cultivars.

Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes-Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly.

Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat.

Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively).

The phosphoproteome of rice leaves responds to water and nitrogen supply.

The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or excess nitrogen supply, plants employ complex systems for signalling and regulation of metabolic processes. There is limited information on the involvement of one of the most important post-translational modifications (PTMs), protein phosphorylation, in plant adaptation to long-term changes in resource supply.

Identification of a Novel Ciprofloxacin Tolerance Gene, , Which Contributes to Filamentation in Acinetobacter baumannii.

Fluoroquinolones are one of the most prescribed broad-spectrum antibiotics. However, their effectiveness is being compromised by high rates of resistance in clinically important organisms, including We sought to investigate the transcriptomic and proteomic responses of the clinical strain AB5075-UW upon exposure to subinhibitory concentrations of ciprofloxacin. Our transcriptomics and proteomics analyses found that the most highly expressed genes and proteins were components of the intact prophage The next most highly expressed gene (and its protein product) under ciprofloxacin stress was a hypothetical gene, ABUW_0098, named here the profloxacin olerance () gene.

Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins.

Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies.

Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought.

Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species ( cv. Nipponbare and cv.

Amyloid-beta peptide neurotoxicity in human neuronal cells is associated with modulation of insulin-like growth factor transport, lysosomal machinery and extracellular matrix receptor interactions.

Extracellular deposits of the amyloid-beta peptide (Aβ) are known as the main pathological hallmark of Alzheimer's disease. In Alzheimer's disease, neurons are injured and die throughout the brain, a process in which Aβ neurotoxicity is considered to play an important role. However, the molecular mechanisms underlying Aβ toxicity that lead to neurodegeneration are not clearly established.

Probing the Role of the Chloroplasts in Heavy Metal Tolerance and Accumulation in .

The Zm-strain lacking chloroplasts, characterized in this study, was compared with the earlier assessed wild type Z-strain to explore the role of chloroplasts in heavy metal accumulation and tolerance. Comparison of the minimum inhibitory concentration (MIC) values indicated that both strains tolerated similar concentrations of mercury (Hg) and lead (Pb), but cadmium (Cd) tolerance of the Z-strain was twice that of the Zm-strain. The ability of the Zm-strain to accumulate Hg was higher compared to the Z-strain, indicating the existence of a Hg transportation and accumulation mechanism not depending on the presence of chloroplasts.

Proteomic Responses to Drought Vary Widely Among Eight Diverse Genotypes of Rice ().

Rice is a critically important food source but yields worldwide are vulnerable to periods of drought. We exposed eight genotypes of upland and lowland rice ( L. ssp.

Proteome profiling of Pseudomonas aeruginosa PAO1 identifies novel responders to copper stress.

Background: The opportunistic pathogen, Pseudomonas aeruginosa is well known for its environmental and metabolic versatility, yet many of the functions of its gene-products remain to be fully elucidated. This study's objective was to illuminate the potential functions of under-described gene-products during the medically relevant copper-stress condition.

Results: We used data-independent acquisition mass spectrometry to quantitate protein expression changes associated with copper stress in P.

Pseudomonas aeruginosa Proteome under Hypoxic Stress Conditions Mimicking the Cystic Fibrosis Lung.

Pseudomonas aeruginosa is a ubiquitous Gram-negative pathogen known to inhabit hypoxic mucus plugs of cystic fibrosis (CF) patient lungs. Despite the high prevalence and related patient mortality, the protein machinery enabling the bacterium to adapt to low oxygen environment remains to be fully elucidated. We investigated this by performing both SWATH mass spectrometry and data-dependent SPS-MS3 of TMT-labeled peptides to profile the proteomes of two P.

Pseudomonas aeruginosa Cell Membrane Protein Expression from Phenotypically Diverse Cystic Fibrosis Isolates Demonstrates Host-Specific Adaptations.

Pseudomonas aeruginosa is a Gram-negative, nosocomial, highly adaptable opportunistic pathogen especially prevalent in immuno-compromised cystic fibrosis (CF) patients. The bacterial cell surface proteins are important contributors to virulence, yet the membrane subproteomes of phenotypically diverse P. aeruginosa strains are poorly characterized.

Proteomics of hosts and pathogens in cystic fibrosis.

Cystic fibrosis (CF) is a congenital disease that results in great morbidity and mortality mainly in the Caucasian population. Although CF is a monogenic disease caused by mutation in the CF conductance transmembrane regulator (CFTR) gene, most of the related mortality can be attributed to infection mediated by opportunistic bacterial and fungal pathogens. Over the past decade, advancements in the field of proteomics have helped to gain insight into the repertoire of host and pathogen proteins involved in CF pathophysiology.

Serum proteome analysis of vivax malaria: An insight into the disease pathogenesis and host immune response.

Vivax malaria is the most widely distributed human malaria resulting in 80-300 million clinical cases every year. It causes severe infection and mortality but is generally regarded as a benign disease and has not been investigated in detail. The present study aimed to perform human serum proteome analysis in a malaria endemic area in India to identify potential serum biomarkers for vivax malaria and understand host response.

Proteomic databases and tools to decipher post-translational modifications.

Post-translational modifications (PTMs) are vital cellular control mechanism, which affect protein properties, including folding, conformation, activity and consequently, their functions. As a result they play a key role in various disease conditions, including cancer and diabetes. Proteomics as a rapidly growing field has witnessed tremendous advancement during the last decade, which has led to the generation of prodigious quantity of data for various organisms' proteome.