keyword
MENU ▼
Read by QxMD icon Read
search

human proteome

keyword
https://www.readbyqxmd.com/read/29785746/systematic-in-depth-proteomic-analysis-of-mitochondria-associated-endoplasmic-reticulum-membranes-mam-in-mouse-and-human-testes
#1
Xiaoli Wang, Yujiao Wen, Juan Dong, Congcong Cao, Shuiqiao Yuan
Mitochondria-associated endoplasmic reticulum membranes (MAMs) regulate important cellular functions including calcium signaling, bioenergetics, and apoptosis during neurodevelopment and carcinogenesis, but its function in male reproduction and spermatogenesis remains enigmatic because the field lacks a complete understanding of the proteome within testis MAMs. To better understand the biological processes and molecular functions of MAM in testes, here, we report a global mass spectrometry-based proteomic evaluation of the MAM obtained from human testes, mouse testes and brains, respectively...
May 21, 2018: Proteomics
https://www.readbyqxmd.com/read/29785723/decreased-e-cadherin-in-mcf7-human-breast-cancer-cells-forming-multicellular-spheroids-exposed-to-simulated-microgravity
#2
Jayashree Sahana, Mohamed Zakaria Nassef, Markus Wehland, Sascha Kopp, Marcus Krüger, Thomas J Corydon, Manfred Infanger, Johann Bauer, Daniela Grimm
MCF7 human breast cancer cells were cultured under normal gravity (1g) and on a random positioning machine (RPM) preventing sedimentation. After two weeks, adherent 1g-control and adherent RPM cells (AD) as well as multicellular spheroids (MCS) were harvested. AD and MCS had been exposed to the RPM in the same culture flask. In a subsequent proteome analysis, the majority of the proteins detected showed similar label-free quantification scores (LFQ) in each of the respective subpopulations, but in both AD or MCS cultures, proteins were also found whose LFQs deviated at least twofold from their counterparts in the 1g-control cells...
May 21, 2018: Proteomics
https://www.readbyqxmd.com/read/29785401/rheumatoid-arthritis-and-mirnas-a-critical-review-through-a-functional-view
#3
REVIEW
Maria Cristina Moran-Moguel, Stefania Petarra-Del Rio, Evangelina E Mayorquin-Galvan, Maria G Zavala-Cerna
Rheumatoid arthritis (RA) is a systemic autoimmune disease with severe joint inflammation and destruction associated with an inflammatory environment. The etiology behind RA remains to be elucidated; most updated concepts include the participation of environmental, proteomic, epigenetic, and genetic factors. Epigenetic is considered the missing link to explain genetic diversification among RA patients. Within epigenetic factors participating in RA, miRNAs are defined as small noncoding molecules with a length of approximately 22 nucleotides, capable of gene expression modulation, either negatively through inhibition of translation and degradation of the mRNA or positively through increasing the translation rate...
2018: Journal of Immunology Research
https://www.readbyqxmd.com/read/29784986/a-workflow-for-the-integrative-transcriptomic-description-of-molecular-pathology-and-the-suggestion-of-normalizing-compounds-exemplified-by-parkinson-s-disease
#4
Mohamed Hamed, Yvonne Gladbach, Steffen Möller, Sarah Fischer, Mathias Ernst, Stephan Struckmann, Alexander Storch, Georg Fuellen
The volume of molecular observations on human diseases in public databases is continuously increasing at accelerating rates. A bottleneck is their computational integration into a coherent description, from which researchers may derive new well-founded hypotheses. Also, the need to integrate data from different technologies (genetics, coding and regulatory RNA, proteomics) emerged in order to identify biomarkers for early diagnosis and prognosis of complex diseases and therefore facilitating the development of novel treatment approaches...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784938/characterization-of-the-rat-cerebrospinal-fluid-proteome-following-acute-cerebral-ischemia-using-an-aptamer-based-proteomic-technology
#5
Alba Simats, Teresa García-Berrocoso, Laura Ramiro, Dolors Giralt, Natalia Gill, Anna Penalba, Alejandro Bustamante, Anna Rosell, Joan Montaner
The limited accessibility to the brain has turned the cerebrospinal fluid (CSF) into a valuable source that may contribute to the complete understanding of the stroke pathophysiology. Here we have described the CSF proteome in the hyper-acute phase of cerebral ischemia by performing an aptamer-based proteomic assay (SOMAscan) in CSF samples collected before and 30 min after male Wistar rats had undergone a 90 min Middle Cerebral Artery Occlusion (MCAO) or sham-surgery. Proteomic results indicated that cerebral ischemia acutely increased the CSF levels of 716 proteins, mostly overrepresented in leukocyte chemotaxis and neuronal death processes...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784925/acrylamide-acute-neurotoxicity-in-adult-zebrafish
#6
Melissa Faria, Tamar Ziv, Cristian Gómez-Canela, Shani Ben-Lulu, Eva Prats, Karen Adriana Novoa-Luna, Arie Admon, Benjamin Piña, Romà Tauler, Leobardo Manuel Gómez-Oliván, Demetrio Raldúa
Acute exposure to acrylamide (ACR), a type-2 alkene, may lead to a ataxia, skeletal muscles weakness and numbness of the extremities in human and laboratory animals. In the present manuscript, ACR acute neurotoxicity has been characterized in adult zebrafish, a vertebrate model increasingly used in human neuropharmacology and toxicology research. At behavioral level, ACR-treated animals exhibited "depression-like" phenotype comorbid with anxiety behavior. At transcriptional level, ACR induced down-regulation of regeneration-associated genes and up-regulation of oligodendrocytes and reactive astrocytes markers, altering also the expression of genes involved in the presynaptic vesicle cycling...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29784816/encephalitis-is-mediated-by-rop18-of-toxoplasma-gondii-a-severe-pathogen-in-aids-patients
#7
Ran An, Yuewen Tang, Lijian Chen, Haijian Cai, De-Hua Lai, Kang Liu, Lijuan Wan, Linli Gong, Li Yu, Qingli Luo, Jilong Shen, Zhao-Rong Lun, Francisco J Ayala, Jian Du
The neurotropic parasite Toxoplasma gondii is a globally distributed parasitic protozoan among mammalian hosts, including humans. During the course of infection, the CNS is the most commonly damaged organ among invaded tissues. The polymorphic rhoptry protein 18 (ROP18) is a key serine (Ser)/threonine (Thr) kinase that phosphorylates host proteins to modulate acute virulence. However, the basis of neurotropism and the specific substrates through which ROP18 exerts neuropathogenesis remain unknown. Using mass spectrometry, we performed proteomic analysis of proteins that selectively bind to active ROP18 and identified RTN1-C, an endoplasmic reticulum (ER) protein that is preferentially expressed in the CNS...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784788/mistimed-food-intake-and-sleep-alters-24-hour-time-of-day-patterns-of-the-human-plasma-proteome
#8
Christopher M Depner, Edward L Melanson, Andrew W McHill, Kenneth P Wright
Proteomics holds great promise for understanding human physiology, developing health biomarkers, and precision medicine. However, how much the plasma proteome varies with time of day and is regulated by the master circadian suprachiasmatic nucleus brain clock, assessed here by the melatonin rhythm, is largely unknown. Here, we assessed 24-h time-of-day patterns of human plasma proteins in six healthy men during daytime food intake and nighttime sleep in phase with the endogenous circadian clock (i.e., circadian alignment) versus daytime sleep and nighttime food intake out of phase with the endogenous circadian clock (i...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784049/identification-and-therapeutic-modulation-of-a-pro-inflammatory-subset-of-disease-associated-microglia-in-alzheimer-s-disease
#9
Srikant Rangaraju, Eric B Dammer, Syed Ali Raza, Priyadharshini Rathakrishnan, Hailian Xiao, Tianwen Gao, Duc M Duong, Michael W Pennington, James J Lah, Nicholas T Seyfried, Allan I Levey
BACKGROUND: Disease-associated-microglia (DAM) represent transcriptionally-distinct and neurodegeneration-specific microglial profiles with unclear significance in Alzheimer's disease (AD). An understanding of heterogeneity within DAM and their key regulators may guide pre-clinical experimentation and drug discovery. METHODS: Weighted co-expression network analysis (WGCNA) was applied to existing microglial transcriptomic datasets from neuroinflammatory and neurodegenerative disease mouse models to identify modules of highly co-expressed genes...
May 21, 2018: Molecular Neurodegeneration
https://www.readbyqxmd.com/read/29783662/spr-biosensors-in-direct-molecular-fishing-implications-for-protein-interactomics
#10
REVIEW
Anna Florinskaya, Pavel Ershov, Yuri Mezentsev, Leonid Kaluzhskiy, Evgeniy Yablokov, Alexei Medvedev, Alexis Ivanov
We have developed an original experimental approach based on the use of surface plasmon resonance (SPR) biosensors, applicable for investigation of potential partners involved in protein⁻protein interactions (PPI) as well as protein⁻peptide or protein⁻small molecule interactions. It is based on combining a SPR biosensor, size exclusion chromatography (SEC), mass spectrometric identification of proteins (LC-MS/MS) and direct molecular fishing employing principles of affinity chromatography for isolation of potential partner proteins from the total lysate of biological samples using immobilized target proteins (or small non-peptide compounds) as ligands...
May 18, 2018: Sensors
https://www.readbyqxmd.com/read/29782014/identification-of-cyclin-dependent-kinase-1-specific-phosphorylation-sites-by-an-in-vitro-kinase-assay
#11
Heying Cui, Kyle M Loftus, Crystal R Noell, Sozanne R Solmaz
Cyclin-dependent kinase 1 (Cdk1) is a master controller for the cell cycle in all eukaryotes and phosphorylates an estimated 8 - 13% of the proteome; however, the number of identified targets for Cdk1, particularly in human cells is still low. The identification of Cdk1-specific phosphorylation sites is important, as they provide mechanistic insights into how Cdk1 controls the cell cycle. Cell cycle regulation is critical for faithful chromosome segregation, and defects in this complicated process lead to chromosomal aberrations and cancer...
May 3, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781574/melanocyte-development-in-the-mouse-tail-epidermis-requires-the-adamts9-metalloproteinase
#12
Grace Tharmarajah, Ulrich Eckhard, Fagun Jain, Giada Marino, Anna Prudova, Oscar Urtatiz, Helmut Fuchs, Martin Hrabe de Angelis, Christopher M Overall, Catherine D Van Raamsdonk
The mouse tail has an important role in the study of melanogenesis, because mouse tail skin can be used to model human skin pigmentation. To better understand the development of melanocytes in the mouse tail, we cloned two dominant ENU-generated mutations of the Adamts9 gene, Und3 and Und4, which cause an unpigmented ring of epidermis in the middle of the tail, but do not alter pigmentation in the rest of the mouse. Adamts9 encodes a widely expressed zinc metalloprotease with thrombospondin type 1 repeats with few known substrates...
May 21, 2018: Pigment Cell & Melanoma Research
https://www.readbyqxmd.com/read/29780404/intrinsic-disorder-and-posttranslational-modifications-the-darker-side-of-the-biological-dark-matter
#13
REVIEW
April L Darling, Vladimir N Uversky
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins and domains that devoid stable secondary and/or tertiary structure. IDPs/IDPRs are abundantly present in various proteomes, where they are involved in regulation, signaling, and control, thereby serving as crucial regulators of various cellular processes. Various mechanisms are utilized to tightly regulate and modulate biological functions, structural properties, cellular levels, and localization of these important controllers...
2018: Frontiers in Genetics
https://www.readbyqxmd.com/read/29779948/the-eukaryotic-proteome-is-shaped-by-e3-ubiquitin-ligases-targeting-c-terminal-degrons
#14
Itay Koren, Richard T Timms, Tomasz Kula, Qikai Xu, Mamie Z Li, Stephen J Elledge
Degrons are minimal elements that mediate the interaction of proteins with degradation machineries to promote proteolysis. Despite their central role in proteostasis, the number of known degrons remains small, and a facile technology to characterize them is lacking. Using a strategy combining global protein stability (GPS) profiling with a synthetic human peptidome, we identify thousands of peptides containing degron activity. Employing CRISPR screening, we establish that the stability of many proteins is regulated through degrons located at their C terminus...
May 11, 2018: Cell
https://www.readbyqxmd.com/read/29779369/quantitative-glycomic-analysis-by-mass-defect-based-dimethyl-pyrimidinyl-ornithine-dipyro-tags-and-high-resolution-mass-spectrometry
#15
Bingming Chen, Yu Feng, Dustin C Frost, Xuefei Zhong, Amanda R Buchberger, Jillian Johnson, Meng Xu, Miriam Kim, Diane Puccetti, Carol Diamond, Chrysanthy Ikonomidou, Lingjun Li
We recently developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), for quantitative proteomic analysis at the MS1 level. In this work, we further extend the application of the DiPyrO tag, which provides amine group reactivity, optical detection capability, and improved electrospray sensitivity, to quantify N-linked glycans enzymatically released from glycoproteins in the glycosylamine form. Duplex DiPyrO tags that differ in mass by 45.3 mDa were used to label the glycosylamine moieties of freshly released N-glycosylamines from glycoprotein standards and human serum proteins...
May 20, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29778837/defining-host-responses-during-systemic-bacterial-infection-through-construction-of-a-murine-organ-proteome-atlas
#16
John D Lapek, Robert H Mills, Jacob M Wozniak, Anaamika Campeau, Ronnie H Fang, Xiaoli Wei, Kirsten van de Groep, Araceli Perez-Lopez, Nina M van Sorge, Manuela Raffatellu, Rob Knight, Liangfang Zhang, David J Gonzalez
Group A Streptococcus (GAS) remains one of the top 10 deadliest human pathogens worldwide despite its sensitivity to penicillin. Although the most common GAS infection is pharyngitis (strep throat), it also causes life-threatening systemic infections. A series of complex networks between host and pathogen drive invasive infections, which have not been comprehensively mapped. Attempting to map these interactions, we examined organ-level protein dynamics using a mouse model of systemic GAS infection. We quantified over 11,000 proteins, defining organ-specific markers for all analyzed tissues...
April 28, 2018: Cell Systems
https://www.readbyqxmd.com/read/29778605/proteomic-and-biochemical-comparison-of-the-cellular-interaction-partners-of-human-vps33a-and-vps33b
#17
Morag R Hunter, Geoffrey G Hesketh, Tomasz H Benedyk, Anne-Claude Gingras, Stephen C Graham
Multi-subunit tethering complexes control membrane fusion events in eukaryotic cells. CORVET and HOPS are two such complexes, both containing the Sec1/Munc18 protein subunit VPS33A. Metazoans additionally possess VPS33B, which has considerable sequence similarity to VPS33A but does not integrate into CORVET or HOPS complexes and instead stably interacts with VIPAR. It has been recently suggested that VPS33B and VIPAR comprise two subunits of a novel multi-subunit tethering complex (named "CHEVI"), perhaps analogous in configuration to CORVET and HOPS...
May 17, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29777872/inventory-of-proteoforms-as-a-current-challenge-of-proteomics-some-technical-aspects
#18
Stanislav Naryzhny
The main intricacy in the human proteome is that it is tremendously complex and composed from diverse and heterogeneous gene products. These products are called protein species or proteoforms and are the smallest units of the proteome. In pursuit of the comprehensive profiling of the human proteome, significant advances in the technology of so called "Top-Down" mass spectrometry based proteomics, have been made. However, the scale of performance of this approach is still far behind the "Bottom-Up", peptide-centric techniques...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29777870/profiling-modifications-for-glioblastoma-proteome-using-ultra-tolerant-database-search-are-the-peptide-mass-shifts-biologically-relevant-or-chemically-induced
#19
Irina A Tarasova, Peter M Chumakov, Sergei A Moshkovskii, Mikhail V Gorshkov
Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29777136/functional-proteomic-profiling-of-secreted-serine-proteases-in-health-and-inflammatory-bowel-disease
#20
Alexandre Denadai-Souza, Chrystelle Bonnart, Núria Solà Tapias, Marlène Marcellin, Brendan Gilmore, Laurent Alric, Delphine Bonnet, Odile Burlet-Schiltz, Morley D Hollenberg, Nathalie Vergnolle, Céline Deraison
While proteases are essential in gastrointestinal physiology, accumulating evidence indicates that dysregulated proteolysis plays a pivotal role in the pathophysiology of inflammatory bowel disease (IBD). Nonetheless, the identity of overactive proteases released by human colonic mucosa remains largely unknown. Studies of protease abundance have primarily investigated expression profiles, not taking into account their enzymatic activity. Herein we have used serine protease-targeted activity-based probes (ABPs) coupled with mass spectral analysis to identify active forms of proteases secreted by the colonic mucosa of healthy controls and IBD patients...
May 18, 2018: Scientific Reports
keyword
keyword
65152
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"