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https://www.readbyqxmd.com/read/28453684/mappi-dat-data-management-and-analysis-for-protein-protein-interaction-data-from-the-high-throughput-mappit-cell-microarray-platform
#1
Surya Gupta, Veronic De Puysseleyr, José Van der Heyden, Davy Maddelein, Irma Lemmens, Sam Lievens, Sven Degroeve, Jan Tavernier, Lennart Martens
Summary: Protein-protein interaction (PPI) studies have dramatically expanded our knowledge about cellular behaviour and development in different conditions. A multitude of high-throughput PPI techniques have been developed to achieve proteome-scale coverage for PPI studies, including the microarray based Mammalian Protein-Protein Interaction Trap (MAPPIT) system. Because such high-throughput techniques typically report thousands of interactions, managing and analysing the large amounts of acquired data is a challenge...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28446534/proteomics-analysis-of-tissue-samples-reveals-changes-in-mitochondrial-protein-levels-in-parathyroid-hyperplasia-over-adenoma
#2
Gurler Akpinar, Murat Kasap, Nuh Zafer Canturk, Mehin Zulfigarova, Eylül Ece Islek, Sertac Ata Guler, Turgay Simsek, Zeynep Canturk
BACKGROUND/AIM: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. MATERIALS AND METHODS: Protein extracts were prepared from tissue samples (n=8 per group)...
May 2017: Cancer Genomics & Proteomics
https://www.readbyqxmd.com/read/28444347/fluxomics-links-cellular-functional-analyses-to-whole-plant-phenotyping
#3
Christophe Salon, Jean-Christophe Avice, Sophie Colombié, Martine Dieuaide-Noubhani, Karine Gallardo, Christian Jeudy, Alain Ourry, Marion Prudent, Anne-Sophie Voisin, Dominique Rolin
Fluxes through metabolic pathways reflect the integration of genetic and metabolic regulations. While it is attractive to measure all the mRNAs (transcriptome), all the proteins (proteome), and a large number of the metabolites (metabolome) in a given cellular system, linking and integrating this information remains difficult. Measurement of metabolome-wide fluxes (termed the fluxome) provides an integrated functional output of the cell machinery and a better tool to link functional analyses to plant phenotyping...
April 22, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28444311/expression-of-als-ftd-linked-mutant-ccnf-in-zebrafish-leads-to-increased-cell-death-in-the-spinal-cord-and-an-aberrant-motor-phenotype
#4
Alison L Hogan, Emily K Don, Stephanie L Rayner, Albert Lee, Angela S Laird, Maxinne Watchon, Claire Winnick, Ingrid S Tarr, Marco Morsch, Jennifer A Fifita, Serene Gwee, Isabel Formella, Elinor Hortle, Kristy Yuan, Mark P Molloy, Kelly L Williams, Garth A Nicholson, Roger S Chung, Ian P Blair, Nicholas J Cole
Amyotrophic lateral sclerosis (ALS) is a rapidly progressive, fatal neurodegenerative disease characterised by the death of upper and lower motor neurons. Approximately 10% of cases have a known family history of ALS and disease-linked mutations in multiple genes have been identified. ALS-linked mutations in CCNF were recently reported, however the pathogenic mechanisms associated with these mutations are yet to be established. To investigate possible disease mechanisms, we developed in vitro and in vivo models based on an ALS-linked missense mutation in CCNF...
April 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28438609/novel-replicons-and-trans-encapsidation-systems-for-hepatitis-c-virus-proteins-live-imaging-and-virus-host-interaction-proteomics
#5
Ovidiu Vlaicu, Tudor Selescu, Florin Pastrama, Cristian Munteanu, Laura Riva, Jean Dubuisson, Yves Rouille, Costin-Ioan Popescu
Proteomics and imaging techniques are used more and more in tandem to investigate the virus-host interaction. Herein we present novel replicons, methods and trans-encapsidation systems suitable for determination of Hepatitis C Virus (HCV) proteins interactomes and live imaging of viral proteins dynamics in HCV cell culture (HCVcc) system. To identify endogenous factors involved in the HCV life cycle, we constructed full-length functional replicons with affinity purification (AP) tags fused to NS2 and NS5A proteins...
April 21, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28437088/hilaq-a-novel-strategy-for-newly-synthesized-protein-quantification
#6
Yuanhui Ma, Daniel B McClatchy, Salim Barkallah, William W Wood, John R Yates Iii
Here we describe a new strategy, HILAQ (Heavy Isotope Labeled Azidohomoalanine Quantification), to rapidly quantify the molecular vulnerability profile to oxytosis, which is an oxidative stress-induced programed cell death pathway that has been reported to be involved in aging and neurodegenerative diseases. HILAQ was able to quantify 1,962 Newly Synthesized Proteins (NSPs) after 1h pulse labeling in HEK293T cell line, while 353 proteins were quantified using the previously published QuaNCAT protocol. HILAQ was successfully applied to the HT22 oxytosis model...
April 24, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28435456/physiological-effects-of-ac4mannaz-and-optimization-of-metabolic-labeling-for-cell-tracking
#7
Sang-Soo Han, Dong-Eun Lee, Hye-Eun Shim, Sangmin Lee, Taekhee Jung, Jung-Hwa Oh, Hyang-Ae Lee, Sung-Hwan Moon, Jongho Jeon, Seokjoo Yoon, Kwangmeyung Kim, Sun-Woong Kang
Metabolic labeling techniques are powerful tools for cell labeling, tracking and proteomic analysis. However, at present, the effects of the metabolic labeling agents on cell metabolism and physiology are not known. To address this question, in this study, we analyzed the effects of cells treated with Ac4ManNAz through microarray analysis and analyses of membrane channel activity, individual bio-physiological properties, and glycolytic flux. According to the results, treatment with 50 μM Ac4ManNAz led to the reduction of major cellular functions, including energy generation capacity, cellular infiltration ability and channel activity...
2017: Theranostics
https://www.readbyqxmd.com/read/28435053/in-depth-analysis-of-the-synaptic-plasma-membrane-proteome-of-small-hippocampal-slices-using-an-integrated-approach
#8
Rui Qiao, Shuiming Li, Mi Zhou, Penghui Chen, Zhao Liu, Min Tang, Jian Zhou
Comprehensive knowledge of the synaptic plasma membrane (SPM) proteome of a distinct brain region in a defined pathological state would greatly advance the understanding of the underlying biology of synaptic plasticity. The development of innovative approaches for studying the SPM proteome of small brain tissues is highly desired. This study presents a suitable protocol that integrates biotinylation-based affinity capture of cell surface-exposed proteins, isolation of synaptosomes, and biochemical extraction of SPM proteins from biotinylated hippocampal slices...
April 20, 2017: Neuroscience
https://www.readbyqxmd.com/read/28433920/proteomic-analysis-of-sockeye-salmon-serum-as-a-tool-for-biomarker-discovery-and-new-insight-into-the-sublethal-toxicity-of-diluted-bitumen
#9
Sarah L Alderman, Laura A Dindia, Christopher J Kennedy, Anthony P Farrell, Todd E Gillis
Pipelines carrying diluted bitumen (dilbit) from Canada's oil sands traverse North America, including the freshwater habitat of Pacific salmon, posing a risk of environmental release and aquatic exposure. Swimming performance is impacted in juvenile sockeye (Oncorhynchus nerka) exposed to dilbit; therefore biomarkers of dilbit exposure will be valuable for monitoring at-risk salmon stocks. This study characterized changes in the serum proteome of sockeye exposed to a sub-lethal and environmentally relevant concentration of dilbit using isobaric tags for relative and absolute quantitation (iTRAQ), and included a range of experimental conditions to permit identification of biomarkers that are robust across time (1 and 4wk) and exercise level (at rest and following a swim test)...
April 12, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28430122/a-comprehensive-diverse-omics-approach-to-better-understanding-the-molecular-pathomechanisms-of-down-syndrome
#10
REVIEW
Keiichi Ishihara, Satoshi Akiba
Diverse '-omics' technologies permit the comprehensive quantitative profiling of a variety of biological molecules. Comparative '-omics' analyses, such as transcriptomics and proteomics, are powerful and useful tools for unraveling the molecular pathomechanisms of various diseases. As enhanced oxidative stress has been demonstrated in humans and mice with Down syndrome (DS), a redox proteomic analysis is useful for understanding how enhanced oxidative stress aggravates the state of individuals with oxidative stress-related disorders...
April 21, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28425052/dmso-assisted-electrospray-ionization-for-the-detection-of-small-peptide-hormones-in-urine-by-dilute-and-shoot-liquid-chromatography-high-resolution-mass-spectrometry
#11
Péter Judák, Janelle Grainger, Catrin Goebel, Peter Van Eenoo, Koen Deventer
The mobile phase additive (DMSO) has been described as a useful tool to enhance electrospray ionization (ESI) of peptides and proteins. So far, this technique has mainly been used in proteomic/peptide research, and its applicability in a routine clinical laboratory setting (i.e., doping control analysis) has not been described yet. This work provides a simple, easy to implement screening method for the detection of doping relevant small peptides (GHRPs, GnRHs, GHS, and vasopressin-analogues) with molecular weight less than 2 kDa applying DMSO in the mobile phase...
April 19, 2017: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/28421530/time-of-day-dependent-neuronal-injury-after-ischemic-stroke-implication-of-circadian-clock-transcriptional-factor-bmal1-and-survival-kinase-akt
#12
Mustafa Caglar Beker, Berrak Caglayan, Esra Yalcin, Ahmet Burak Caglayan, Seyma Turkseven, Busra Gurel, Taha Kelestemur, Elif Sertel, Zafer Sahin, Selim Kutlu, Ulkan Kilic, Ahmet Tarik Baykal, Ertugrul Kilic
Occurrence of stroke cases displays a time-of-day variation in human. However, the mechanism linking circadian rhythm to the internal response mechanisms against pathophysiological events after ischemic stroke remained largely unknown. To this end, temporal changes in the susceptibility to ischemia/reperfusion (I/R) injury were investigated in mice in which the ischemic stroke induced at four different Zeitgeber time points with 6-h intervals (ZT0, ZT6, ZT12, and ZT18). Besides infarct volume and brain swelling, neuronal survival, apoptosis, ischemia, and circadian rhythm related proteins were examined using immunohistochemistry, Western blot, planar surface immune assay, and liquid chromatography-mass spectrometry tools...
April 18, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28420318/advancing-clinicopathologic-diagnosis-of-high-risk-neuroblastoma-using-computerized-image-analysis-and-proteomic-profiling
#13
M Khalid Khan Niazi, Jonathan H Chung, Katherine J Heaton-Johnson, Daniel Martinez, Raquel Castellanos, Meredith S Irwin, Stephen R Master, Bruce R Pawel, Metin N Gurcan, Daniel A Weiser
A subset of patients with neuroblastoma are at extremely high risk for treatment failure, though they are not identifiable at diagnosis and therefore have the highest mortality with conventional treatment approaches. Despite tremendous understanding of clinical and biological features that correlate with prognosis, neuroblastoma at ultra-high risk for treatment failure remains a diagnostic challenge. As a first step towards improving prognostic risk stratification within the high-risk group of patients, we determined the feasibility of using computerized image analysis and proteomic profiling on single slides from diagnostic tissue specimens...
January 1, 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28418607/current-trends-in-quantitative-proteomics-an-update
#14
Huiyan Li, Jun Han, Jingxi Pan, Teng Liu, Carol E Parker, Christoph H Borchers
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics...
April 18, 2017: Journal of Mass Spectrometry: JMS
https://www.readbyqxmd.com/read/28418253/species-level-discrimination-of-psychrotrophic-pathogenic-and-spoilage-gram-negative-raw-milk-isolates-using-a-combined-maldi-tof-ms-proteomics-bioinformatics-based-approach
#15
Nuwan R Vithanage, Thomas Richard Yeager, Jeevana Bhongir, Snehal R Jadhav, Chaminda Senaka Ranadheera, Enzo A Palombo, Nivedita Datta
Identification of psychrotrophic pathogenic and spoilage Gram-negative bacteria using rapid and reliable techniques is important in commercial milk processing, as these bacteria can produce heat-resistant proteases and act as post-processing contaminants in pasteurised milk. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is a proven technology for identification of bacteria in food, however may require optimisation for identification of pathogenic and spoilage bacteria in milk and dairy products...
April 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28417377/isolation-and-preparation-of-extracellular-proteins-from-lignocellulose-degrading-fungi-for-comparative-proteomic-studies-using-mass-spectrometry
#16
Robert J Gruninger, Adrian Tsang, Tim A McAllister
Fungi utilize a unique mechanism of nutrient acquisition involving extracellular digestion. To understand the biology of these microbes, it is important to identify and characterize the function of proteins that are secreted and involved in this process. Mass spectrometry-based proteomics is a powerful tool to study complex mixtures of proteins and understand how the proteins produced by an organism change in response to different conditions. Many fungi are efficient decomposers of plant cell wall, and anaerobic fungi are well recognized for their ability to digest lignocellulose...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28394336/msfragger-ultrafast-and-comprehensive-peptide-identification-in-mass-spectrometry-based-proteomics
#17
Andy T Kong, Felipe V Leprevost, Dmitry M Avtonomov, Dattatreya Mellacheruvu, Alexey I Nesvizhskii
There is a need to better understand and handle the 'dark matter' of proteomics-the vast diversity of post-translational and chemical modifications that are unaccounted in a typical mass spectrometry-based analysis and thus remain unidentified. We present a fragment-ion indexing method, and its implementation in peptide identification tool MSFragger, that enables a more than 100-fold improvement in speed over most existing proteome database search tools. Using several large proteomic data sets, we demonstrate how MSFragger empowers the open database search concept for comprehensive identification of peptides and all their modified forms, uncovering dramatic differences in modification rates across experimental samples and conditions...
May 2017: Nature Methods
https://www.readbyqxmd.com/read/28393831/determining-the-bacterial-cell-biology-of-planctomycetes
#18
Christian Boedeker, Margarete Schüler, Greta Reintjes, Olga Jeske, Muriel C F van Teeseling, Mareike Jogler, Patrick Rast, Daniela Borchert, Damien P Devos, Martin Kucklick, Miroslava Schaffer, Roberto Kolter, Laura van Niftrik, Susanne Engelmann, Rudolf Amann, Manfred Rohde, Harald Engelhardt, Christian Jogler
Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail...
April 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28393582/insights-into-the-human-brain-proteome-disclosing-the-biological-meaning-of-protein-networks-in-cerebrospinal-fluid
#19
Paulo Bastos, Rita Ferreira, Bruno Manadas, Paula I Moreira, Rui Vitorino
Cerebrospinal fluid (CSF) is an excellent source of biological information regarding the nervous system, once it is in close contact and accurately reflects alterations in this system. Several studies have analyzed differential protein profiles of CSF samples between healthy and diseased human subjects. However, the pathophysiological mechanisms and how CSF proteins relate to diseases are still poorly known. By applying bioinformatics tools, we attempted to provide new insights on the biological and functional meaning of proteomics data envisioning the identification of putative disease biomarkers...
April 10, 2017: Critical Reviews in Clinical Laboratory Sciences
https://www.readbyqxmd.com/read/28391377/pro-angiogenic-capacities-of-microvesicles-produced-by-skin-wound-myofibroblasts
#20
Mays Merjaneh, Amélie Langlois, Sébastien Larochelle, Chanel Beaudoin Cloutier, Sylvie Ricard-Blum, Véronique J Moulin
Wound healing is a very highly organized process where numerous cell types are tightly regulated to restore injured tissue. Myofibroblasts are cells that produce new extracellular matrix and contract wound edges. We previously reported that the human myofibroblasts isolated from normal wound (WMyos) produced microvesicles (MVs) in the presence of the serum. In this study, MVs were further characterized using a proteomic strategy and potential functions of the MVs were determined. MV proteins isolated from six WMyo populations were separated using two-dimensional differential gel electrophoresis...
April 8, 2017: Angiogenesis
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