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Proteomes

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https://read.qxmd.com/read/30678040/sex-specific-proteomic-changes-induced-by-genetic-deletion-of-fibroblast-growth-factor-14-fgf14-a-regulator-of-neuronal-ion-channels
#1
Mark L Sowers, Jessica Di Re, Paul A Wadsworth, Alexander S Shavkunov, Cheryl Lichti, Kangling Zhang, Fernanda Laezza
Fibroblast growth factor 14 (FGF14) is a member of the intracellular FGFs, which is a group of proteins involved in neuronal ion channel regulation and synaptic transmission. We previously demonstrated that male Fgf14 -/- mice recapitulate the salient endophenotypes of synaptic dysfunction and behaviors that are associated with schizophrenia (SZ). As the underlying etiology of SZ and its sex-specific onset remain elusive, the Fgf14 -/- model may provide a valuable tool to interrogate pathways related to disease mechanisms...
January 23, 2019: Proteomes
https://read.qxmd.com/read/30634649/analysis-of-the-bacterial-and-host-proteins-along-and-across-the-porcine-gastrointestinal-tract
#2
Johanna Tröscher-Mußotter, Bruno Tilocca, Volker Stefanski, Jana Seifert
Pigs are among the most important farm animals worldwide and research to optimize their feed efficiency and improve their welfare is still in progress. The porcine intestinal microbiome is so far mainly known from sequencing-based studies. Digesta and mucosa samples from five different porcine gastrointestinal tract sections were analyzed by metaproteomics to obtain a deeper insight into the functions of bacterial groups with concomitant analyses of host proteins. Firmicutes (Prevotellaceae) dominated mucosa and digesta samples, followed by Bacteroidetes...
January 10, 2019: Proteomes
https://read.qxmd.com/read/30626002/challenges-in-clinical-metaproteomics-highlighted-by-the-analysis-of-acute-leukemia-patients-with-gut-colonization-by-multidrug-resistant-enterobacteriaceae
#3
Julia Rechenberger, Patroklos Samaras, Anna Jarzab, Juergen Behr, Martin Frejno, Ana Djukovic, Jaime Sanz, Eva M González-Barberá, Miguel Salavert, Jose Luis López-Hontangas, Karina B Xavier, Laurent Debrauwer, Jean-Marc Rolain, Miguel Sanz, Marc Garcia-Garcera, Mathias Wilhelm, Carles Ubeda, Bernhard Kuster
The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics...
January 8, 2019: Proteomes
https://read.qxmd.com/read/30577422/proteomic-profiling-of-primary-human-acute-myeloid-leukemia-cells-does-not-reflect-their-constitutive-release-of-soluble-mediators
#4
Elise Aasebø, Maria Hernandez-Valladares, Frode Selheim, Frode S Berven, Annette K Brenner, Øystein Bruserud
Acute myeloid leukemia (AML) is a heterogeneous disease, and communication between leukemic cells and their neighboring leukemia-supporting normal cells is involved in leukemogenesis. The bone marrow cytokine network is therefore important, and the mediator release profile seems more important than single mediators. It is not known whether the characterization of primary AML cell proteomes reflects the heterogeneity of the broad and dynamic constitutive mediator release profile by these cells. To address this, we compared the intracellular levels of 41 proteins in 19 AML patients with the constitutive extracellular release during in vitro culture, including chemokines, growth factors, proteases, and protease regulators...
December 20, 2018: Proteomes
https://read.qxmd.com/read/30562941/proteomic-analysis-of-the-spinophilin-interactome-in-rodent-striatum-following-psychostimulant-sensitization
#5
Darryl S Watkins, Jason D True, Amber L Mosley, Anthony J Baucum
Glutamatergic projections from the cortex and dopaminergic projections from the substantia nigra or ventral tegmental area synapse on dendritic spines of specific GABAergic medium spiny neurons (MSNs) in the striatum. Direct pathway MSNs (dMSNs) are positively coupled to protein kinase A (PKA) signaling and activation of these neurons enhance specific motor programs whereas indirect pathway MSNs (iMSNs) are negatively coupled to PKA and inhibit competing motor programs. An imbalance in the activity of these two programs is observed following increased dopamine signaling associated with exposure to psychostimulant drugs of abuse...
December 17, 2018: Proteomes
https://read.qxmd.com/read/30544882/-actinobaculum-massiliense-proteome-profiled-in-polymicrobial-urethral-catheter-biofilms
#6
Yanbao Yu, Tamara Tsitrin, Harinder Singh, Sebastian N Doerfert, Maria V Sizova, Slava S Epstein, Rembert Pieper
Actinobaculum massiliense , a Gram-positive anaerobic coccoid rod colonizing the human urinary tract, belongs to the taxonomic class of Actinobacteria. We identified A. massiliense as a cohabitant of urethral catheter biofilms (CB). The CBs also harbored more common uropathogens, such as Proteus mirabilis and Aerococcus urinae , supporting the notion that A. massiliense is adapted to a life style in polymicrobial biofilms. We isolated a clinical strain from a blood agar colony and used 16S rRNA gene sequencing and shotgun proteomics to confirm its identity as A...
December 9, 2018: Proteomes
https://read.qxmd.com/read/30544872/cell-type-specific-proteomics-a-neuroscience-perspective
#7
REVIEW
Rashaun S Wilson, Angus C Nairn
Cell-type-specific analysis has become a major focus for many investigators in the field of neuroscience, particularly because of the large number of different cell populations found in brain tissue that play roles in a variety of developmental and behavioral disorders. However, isolation of these specific cell types can be challenging due to their nonuniformity and complex projections to different brain regions. Moreover, many analytical techniques used for protein detection and quantitation remain insensitive to the low amounts of protein extracted from specific cell populations...
December 9, 2018: Proteomes
https://read.qxmd.com/read/30544849/from-synapse-to-function-a-perspective-on-the-role-of-neuroproteomics-in-elucidating-mechanisms-of-drug-addiction
#8
REVIEW
Luis A Natividad, Matthew W Buczynski, Daniel B McClatchy, John R Yates
Drug addiction is a complex disorder driven by dysregulation in molecular signaling across several different brain regions. Limited therapeutic options currently exist for treating drug addiction and related psychiatric disorders in clinical populations, largely due to our incomplete understanding of the molecular pathways that influence addiction pathology. Recent work provides strong evidence that addiction-related behaviors emerge from the convergence of many subtle changes in molecular signaling networks that include neuropeptides (neuropeptidome), protein-protein interactions (interactome) and post-translational modifications such as protein phosphorylation (phosphoproteome)...
December 9, 2018: Proteomes
https://read.qxmd.com/read/30513835/clinical-proteomics-in-colorectal-cancer-a-promising-tool-for-improving-personalised-medicine
#9
REVIEW
Anaïs Chauvin, François-Michel Boisvert
Colorectal cancer is the third most common and the fourth most lethal cancer worldwide. In most of cases, patients are diagnosed at an advanced or even metastatic stage, thus explaining the high mortality. The lack of proper clinical tests and the complicated procedures currently used for detecting this cancer, as well as for predicting the response to treatment and the outcome of a patient's resistance in guiding clinical practice, are key elements driving the search for biomarkers. In the present overview, the different biomarkers (diagnostic, prognostic, treatment resistance) discovered through proteomics studies in various colorectal cancer study models (blood, stool, biopsies), including the different proteomic techniques used for the discovery of these biomarkers, are reviewed, as well as the various tests used in clinical practice and those currently in clinical phase...
December 2, 2018: Proteomes
https://read.qxmd.com/read/30487426/mapping-the-proteome-of-the-synaptic-cleft-through-proximity-labeling-reveals-new-cleft-proteins
#10
Tony Cijsouw, Austin M Ramsey, TuKiet T Lam, Beatrice E Carbone, Thomas A Blanpied, Thomas Biederer
Synapses are specialized neuronal cell-cell contacts that underlie network communication in the mammalian brain. Across neuronal populations and circuits, a diverse set of synapses is utilized, and they differ in their molecular composition to enable heterogenous connectivity patterns and functions. In addition to pre- and post-synaptic specializations, the synaptic cleft is now understood to be an integral compartment of synapses that contributes to their structural and functional organization. Aiming to map the cleft proteome, this study applied a peroxidase-mediated proximity labeling approach and used the excitatory synaptic cell adhesion protein SynCAM 1 fused to horseradish peroxidase (HRP) as a reporter in cultured cortical neurons...
November 28, 2018: Proteomes
https://read.qxmd.com/read/30424486/paraquat-mediated-oxidative-stress-in-anopheles-gambiae-mosquitoes-is-regulated-by-an-endoplasmic-reticulum-er-stress-response
#11
Brian B Tarimo, Henry Chun Hin Law, Dingyin Tao, Rebecca Pastrana-Mena, Stefan M Kanzok, Joram J Buza, Rhoel R Dinglasan
Paraquat is a potent superoxide (O₂- )-inducing agent that is capable of inducing an oxidative imbalance in the mosquito midgut. This oxidative imbalance can super-stress the malaria parasite, leading to arrested development in the mosquito midgut and reduced transmission. While several studies have explored the effect of paraquat on malaria parasites, a fundamental understanding of the mosquito response to this compound remains unknown. Here, we quantified the mosquito midgut proteomic response to a paraquat-laced sugar meal, and found that An...
November 12, 2018: Proteomes
https://read.qxmd.com/read/30424485/deep-profiling-of-the-aggregated-proteome-in-alzheimer-s-disease-from-pathology-to-disease-mechanisms
#12
REVIEW
Brianna M Lutz, Junmin Peng
Hallmarks of Alzheimer's disease (AD), a progressive neurodegenerative disease causing dementia, include protein aggregates such as amyloid beta plaques and tau neurofibrillary tangles in a patient's brain. Understanding the complete composition and structure of protein aggregates in AD can shed light on the as-yet unidentified underlying mechanisms of AD development and progression. Biochemical isolation of aggregates coupled with mass spectrometry (MS) provides a comprehensive proteomic analysis of aggregates in AD...
November 12, 2018: Proteomes
https://read.qxmd.com/read/30404163/a-comparative-quantitative-lc-ms-ms-profiling-analysis-of-human-pancreatic-adenocarcinoma-adjacent-normal-tissue-and-patient-derived-tumour-xenografts
#13
Orla Coleman, Michael Henry, Fiona O'Neill, Sandra Roche, Niall Swan, Lorraine Boyle, Jean Murphy, Justine Meiller, Neil T Conlon, Justin Geoghegan, Kevin C Conlon, Vincent Lynch, Ninfa L Straubinger, Robert M Straubinger, Gerard McVey, Michael Moriarty, Paula Meleady, Martin Clynes
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide; it develops in a relatively symptom-free manner, leading to rapid disease progression and metastasis, leading to a 5-year survival rate of less than 5%. A lack of dependable diagnostic markers and rapid development of resistance to conventional therapies are among the problems associated with management of the disease. A better understanding of pancreatic tumour biology and discovery of new potential therapeutic targets are important goals in pancreatic cancer research...
November 6, 2018: Proteomes
https://read.qxmd.com/read/30347783/inhibiting-arginine-methylation-as-a-tool-to-investigate-cross-talk-with-methylation-and-acetylation-post-translational-modifications-in-a-glioblastoma-cell-line
#14
Sabrina Francesca Samuel, Alistair James Marsden, Srihari Deepak, Francisco Rivero, John Greenman, Pedro Beltran-Alvarez
Glioblastomas (GBM) are the most common grade 4 brain tumours; patients have very poor prognosis with an average survival of 15 months after diagnosis. Novel research lines have begun to explore aberrant protein arginine methylation (ArgMe) as a possible therapeutic target in GBM and ArgMe inhibitors are currently in clinical trials. Enzymes known as protein arginine methyltransferases (PRMT1-9) can lead to mono- or di-ArgMe, and in the latter case symmetric or asymmetric dimethylation (SDMA and ADMA, respectively)...
October 20, 2018: Proteomes
https://read.qxmd.com/read/30340394/identification-of-potential-plasma-biomarkers-for-abdominal-aortic-aneurysm-using-tandem-mass-tag-quantitative-proteomics
#15
Anders E Henriksson, Markus Lindqvist, Carina Sihlbom, Jörgen Bergström, Dan Bylund
Plasma biomarkers that identify abdominal aortic aneurysm (AAA) rupture risk would greatly assist in stratifying patients with small aneurysms. Identification of such biomarkers has hitherto been unsuccessful over a range of studies using different methods. The present study used an alternative proteomic approach to find new, potential plasma AAA biomarker candidates. Pre-fractionated plasma samples from twelve patients with AAA and eight matched controls without aneurysm were analyzed by mass spectrometry applying a tandem mass tag (TMT) technique...
October 18, 2018: Proteomes
https://read.qxmd.com/read/30326594/evaluation-of-the-phosphoproteome-of-mouse-alpha-4-beta-2-containing-nicotinic-acetylcholine-receptors-in-vitro-and-in-vivo
#16
Megan B Miller, Rashaun S Wilson, TuKiet T Lam, Angus C Nairn, Marina R Picciotto
Activation of nicotinic acetylcholine receptors containing α4 and β2 subunits (α4/β2* nAChRs) in the mammalian brain is necessary for nicotine reinforcement and addiction. We previously identified interactions between α4/β2* nAChRs and calcium/calmodulin-dependent protein kinase II (CaMKII) in mouse and human brain tissue. Following co-expression of α4/β2 nAChR subunits with CaMKII in HEK cells, mass spectrometry identified 8 phosphorylation sites in the α4 subunit. One of these sites and an additional site were identified when isolated α4/β2* nAChRs were dephosphorylated and subsequently incubated with CaMKII in vitro, while 3 phosphorylation sites were identified following incubation with protein kinase A (PKA) in vitro...
October 15, 2018: Proteomes
https://read.qxmd.com/read/30322021/phosphoproteomic-analysis-of-the-amygdala-response-to-adolescent-glucocorticoid-exposure-reveals-g-protein-coupled-receptor-kinase-2-as-a-target-for-reducing-motivation-for-alcohol
#17
Megan L Bertholomey, Kathryn Stone, TuKiet T Lam, Seojin Bang, Wei Wu, Angus C Nairn, Jane R Taylor, Mary M Torregrossa
Early life stress is associated with risk for developing alcohol use disorders (AUDs) in adulthood. Though the neurobiological mechanisms underlying this vulnerability are not well understood, evidence suggests that aberrant glucocorticoid and noradrenergic system functioning play a role. The present study investigated the long-term consequences of chronic exposure to elevated glucocorticoids during adolescence on the risk of increased alcohol-motivated behavior, and on amygdalar function in adulthood. A discovery-based analysis of the amygdalar phosphoproteome using mass spectrometry was employed, to identify changes in function...
October 12, 2018: Proteomes
https://read.qxmd.com/read/30297624/phosphorylation-of-the-ampar-tarp-complex-in-synaptic-plasticity
#18
REVIEW
Joongkyu Park
Synaptic plasticity has been considered a key mechanism underlying many brain functions including learning, memory, and drug addiction. An increase or decrease in synaptic activity of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) complex mediates the phenomena as shown in the cellular models of synaptic plasticity, long-term potentiation (LTP), and depression (LTD). In particular, protein phosphorylation shares the spotlight in expressing the synaptic plasticity. This review summarizes the studies on phosphorylation of the AMPAR pore-forming subunits and auxiliary proteins including transmembrane AMPA receptor regulatory proteins (TARPs) and discusses its role in synaptic plasticity...
October 8, 2018: Proteomes
https://read.qxmd.com/read/30301203/exploring-morphine-triggered-pkc-targets-and-their-interaction-with-signaling-pathways-leading-to-pain-via-trka
#19
REVIEW
Darlene A Pena, Mariana Lemos Duarte, Dimitrius T Pramio, Lakshmi A Devi, Deborah Schechtman
It is well accepted that treatment of chronic pain with morphine leads to μ opioid receptor (MOR) desensitization and the development of morphine tolerance. MOR activation by the selective peptide agonist, D-Ala2, N-MePhe4, Gly-ol]-enkephalin(DAMGO), leads to robust G protein receptor kinase activation, β-arrestin recruitment, and subsequent receptor endocytosis, which does not occur in an activation by morphine. However, MOR activation by morphine induces receptor desensitization, in a Protein kinase C (PKC) dependent manner...
October 6, 2018: Proteomes
https://read.qxmd.com/read/30279377/early-responses-to-severe-drought-stress-in-the-arabidopsis-thaliana-cell-suspension-culture-proteome
#20
May Alqurashi, Marco Chiapello, Chantal Bianchet, Francesco Paolocci, Kathryn S Lilley, Christoph Gehring
Abiotic stresses are considered the most deleterious factor affecting growth and development of plants worldwide. Such stresses are largely unavoidable and trigger adaptive responses affecting different cellular processes and target different compartments. Shotgun proteomic and mass spectrometry-based approaches offer an opportunity to elucidate the response of the proteome to abiotic stresses. In this study, the severe drought or water-deficit response in Arabidopsis thaliana was mimicked by treating cell suspension callus with 40% polyethylene glycol for 10 and 30 min...
October 2, 2018: Proteomes
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