keyword
MENU ▼
Read by QxMD icon Read
search

proteomics methods

keyword
https://www.readbyqxmd.com/read/28547889/comparison-between-chaotropic-and-detergent-based-sample-preparation-workflow-in-tendon-for-mass-spectrometry-analysis
#1
Yalda A Kharaz, Danae Zamboulis, Karen Sander, Eithne Comerford, Peter Clegg, Mandy Peffers
Exploring the tendon proteome is a challenging but important task for understanding the mechanisms of physiological/pathological processes during ageing and disease and for the development of new treatments. Several extraction methods have been utilised for tendon mass spectrometry, however different extraction methods have not been simultaneously compared. In the present study we compared protein extraction in tendon with two chaotropic agents, guanidine hydrochloride (GnHCl) and urea, a detergent, RapiGest(ۛ) , and their combinations for shotgun mass spectrometry...
May 26, 2017: Proteomics
https://www.readbyqxmd.com/read/28547526/rab21-a-novel-ps1-interactor-regulates-%C3%AE-secretase-activity-via-ps1-subcellular-distribution
#2
Zhenzhen Sun, Yujie Xie, Yintong Chen, Qinghu Yang, Zhenzhen Quan, Rongji Dai, Hong Qing
γ-Secretase has been a therapeutical target for its key role in cleaving APP to generate β-amyloid (Aβ), the primary constituents of senile plaques and a hallmark of Alzheimer's disease (AD) pathology. Recently, γ-secretase-associating proteins showed promising role in specifically modulating APP processing while sparing Notch signaling; however, the underlying mechanism is still unclear. A co-immunoprecipitation (Co-IP) coupled with mass spectrometry proteomic assay for Presenilin1 (PS1, the catalytic subunit of γ-secretase) was firstly conducted to find more γ-secretase-associating proteins...
May 25, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28546528/comparative-proteomic-profiling-of-sera-from-patients-with-refractory-multiple-myeloma-reveals-potential-biomarkers-predicting-response-to-bortezomib-based-therapy
#3
Magdalena Łuczak, Tadeusz Kubicki, Zuzanna Rzetelska, Tomasz Szczepaniak, Anna Przybyłowicz-Chalecka, Błażej Ratajczak, Joanna Czerwińska-Rybak, Adam Nowicki, Monika Joks, Andrzej Jakubowiak, Mieczysław Komarnicki, Dominik Dytfeld
INTRODUCTION    In the era of novel agent implementation in multiple myeloma (MM) regimens, drug resistance has become a key factor undermining the results of treatment. Identifying biomarkers allows the prediction of therapy outcomes with specific agents and may lead to the avoidance of resistance. OBJECTIVES    This study aimed to identify biomarkers in the pretreatment sera of patients with refractory/relapsed MM that differ from those in the sera of patients who achieved a better depth of response from bortezomib-containing therapy...
May 25, 2017: Polish Archives of Internal Medicine
https://www.readbyqxmd.com/read/28545132/proteomics-investigation-of-oscc-specific-salivary-biomarkers-in-a-hungarian-population-highlights-the-importance-of-identification-of-population-tailored-biomarkers
#4
Éva Csősz, Péter Lábiscsák, Gergő Kalló, Bernadett Márkus, Miklós Emri, Adrienn Szabó, Ildikó Tar, József Tőzsér, Csongor Kiss, Ildikó Márton
Oral squamous cell carcinoma (OSCC) accounting for about 90% of malignant oral lesions is the 6th most common malignancy worldwide. Diagnostic delay may contribute to dismal survival rate therefore, there is a need for developing specific and sensitive biomarkers to improve early detection. Hungarian population occupies the top places of statistics regarding OSCC incidence and mortality figures therefore, we aimed at finding potential salivary protein biomarkers suitable for the Hungarian population. In this study we investigated 14 proteins which were previously reported as significantly elevated in saliva of patients with OSCC...
2017: PloS One
https://www.readbyqxmd.com/read/28544616/biochemical-isolation-of-myonuclei-employed-to-define-changes-to-the-myonuclear-proteome-that-occur-with-aging
#5
Alicia A Cutler, Eric B Dammer, Duc M Doung, Nicholas T Seyfried, Anita H Corbett, Grace K Pavlath
Skeletal muscle aging is accompanied by loss of muscle mass and strength. Examining changes in myonuclear proteins with age would provide insight into molecular processes which regulate these profound changes in muscle physiology. However, muscle tissue is highly adapted for contraction and thus comprised largely of contractile proteins making the nuclear proteins difficult to identify from whole muscle samples. By developing a method to purify myonuclei from whole skeletal muscle, we were able to collect myonuclei for analysis by flow cytometry, biochemistry, and mass spectrometry...
May 23, 2017: Aging Cell
https://www.readbyqxmd.com/read/28544375/proteomic-analysis-of-hair-shafts-from-monozygotic-twins-expression-profiles-and-genetically-variant-peptides
#6
Pei-Wen Wu, Katelyn E Mason, Blythe P Durbin-Johnson, Michelle Salemi, Brett S Phinney, David M Rocke, Glendon J Parker, Robert H Rice
Forensic association of hair shaft evidence with individuals is currently assessed by comparing mitochondrial DNA haplotypes of reference and casework samples, primarily for exclusionary purposes. Present work tests and validates more recent proteomic approaches to extract quantitative transcriptional and genetic information from hair samples of monozygotic twin pairs, which would be predicted to partition away from unrelated individuals if the datasets contain identifying information. Protein expression profiles and polymorphic, genetically variant hair peptides were generated from 10 pairs of monozygotic twins...
May 22, 2017: Proteomics
https://www.readbyqxmd.com/read/28543099/evidence-of-altered-mitochondrial-protein-expression-after-chronic-ethanol-consumption-in-the-aged-estrogen-deficient-female-rat-heart
#7
Alexandra M Garvin, J L Miller-Lee, D R Sharda, G M Kanski, J C Hunter, Donna H Korzick
BACKGROUND: Estrogen loss has been implicated to increase the risk of alcoholic cardiomyopathy in post-menopausal women. The purpose of this study was to identify novel mitochondrial protein targets for the treatment of alcoholic cardiomyopathy in aged women using a state-of-the-art proteomics approach. We hypothesized that chronic ethanol (EtOH) ingestion exacerbates maladaptive mitochondrial protein expression in the aged female heart METHODS: Adult (3 mo) and aged (18 mo) F344 ovary-intact or ovariectomized (OVX) rats were randomly assigned an EtOH or control Lieber-DeCarli 'all liquid' diet for 20 wks...
May 19, 2017: Alcoholism, Clinical and Experimental Research
https://www.readbyqxmd.com/read/28542205/rots-an-r-package-for-reproducibility-optimized-statistical-testing
#8
Tomi Suomi, Fatemeh Seyednasrollah, Maria K Jaakkola, Thomas Faux, Laura L Elo
Differential expression analysis is one of the most common types of analyses performed on various biological data (e.g. RNA-seq or mass spectrometry proteomics). It is the process that detects features, such as genes or proteins, showing statistically significant differences between the sample groups under comparison. A major challenge in the analysis is the choice of an appropriate test statistic, as different statistics have been shown to perform well in different datasets. To this end, the reproducibility-optimized test statistic (ROTS) adjusts a modified t-statistic according to the inherent properties of the data and provides a ranking of the features based on their statistical evidence for differential expression between two groups...
May 25, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541380/a-fully-bayesian-latent-variable-model-for-integrative-clustering-analysis-of-multi-type-omics-data
#9
Qianxing Mo, Ronglai Shen, Cui Guo, Marina Vannucci, Keith S Chan, Susan G Hilsenbeck
Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data...
May 24, 2017: Biostatistics
https://www.readbyqxmd.com/read/28540730/surface-confined-aqueous-reversible-addition-fragmentation-chain-transfer-scaraft-polymerization-method-for-preparation-of-coated-capillary-leads-to-over-10-000-peptides-identified-from-25-ng-hela-digest-by-using-capillary-zone-electrophoresis-tandem-mass-spectrometry
#10
Zhenbin Zhang, Elizabeth H Peuchen, Norman J Dovichi
A surface-confined aqueous reversible addition-fragmentation chain transfer (SCARAFT) polymerization method was developed to coat capillaries for use in capillary zone electrophoresis (CZE). SCARAFT polymerization primarily takes place on the inner surface of the capillary instead of in solution, which greatly improves the homogeneity of the coating. Capillaries treated with this coating produced an electroosmotic mobility of 2.8 ± 0.2 × 10-6 cm2·V 1·s-1 (N=3), which is roughly an order of magnitude lower than that of commercial linear polyacrylamide (LPA) coated capillaries...
May 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28539641/revealing-the-insoluble-metasecretome-of-lignocellulose-degrading-microbial-communities
#11
Anna M Alessi, Susannah M Bird, Joseph P Bennett, Nicola C Oates, Yi Li, Adam A Dowle, Igor Polikarpov, J Peter W Young, Simon J McQueen-Mason, Neil C Bruce
Microbial communities metabolize plant biomass using secreted enzymes; however, identifying extracellular proteins tightly bound to insoluble lignocellulose in these microbiomes presents a challenge, as the rigorous extraction required to elute these proteins also lyses the microbes associated with the plant biomass releasing intracellular proteins that contaminate the metasecretome. Here we describe a technique for targeting the extracellular proteome, which was used to compare the metasecretome and meta-surface-proteome of two lignocellulose-degrading communities grown on wheat straw and rice straw...
May 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28539122/an-inference-method-from-multi-layered-structure-of-biomedical-data
#12
Myungjun Kim, Yonghyun Nam, Hyunjung Shin
BACKGROUND: Biological system is a multi-layered structure of omics with genome, epigenome, transcriptome, metabolome, proteome, etc., and can be further stretched to clinical/medical layers such as diseasome, drugs, and symptoms. One advantage of omics is that we can figure out an unknown component or its trait by inferring from known omics components. The component can be inferred by the ones in the same level of omics or the ones in different levels. METHODS: To implement the inference process, an algorithm that can be applied to the multi-layered complex system is required...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28537741/an-optimized-extraction-method-to-remove-humic-acids-interferences-from-soil-samples-prior-to-microbial-proteome-measurements
#13
Chen Qian, Robert L Hettich
The microbial composition and their activities in soil environments play a critical role in organic matter transformation and nutrient cycling. Liquid chromatography coupled to high performance mass spectrometry provides a powerful approach to characterize soil microbiomes; however, the limited microbial biomass and the presence of abundant interferences in soil samples present major challenges to proteome extraction and subsequent MS measurement. To this end, we have designed an experimental method to improve microbial proteome measurement by removing the soil-borne humic substances co-extraction from soils...
May 24, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28536642/itraq-based-proteomics-of-chronic-renal-failure-rats-after-fushengong-decoction-treatment-reveals-haptoglobin-and-alpha-1-antitrypsin-as-potential-biomarkers
#14
Yu Yang, Junmeng Wei, Xuekuan Huang, Mingjun Wu, Zhenbing Lv, Pan Tong, Rui Chang
Background. Chronic renal failure (CRF) has become a global health problem and bears a huge economic burden. FuShengong Decoction (FSGD) as traditional Chinese medicine has multiple pharmacological effects. Objectives. To understand the underlying molecular mechanism and signaling pathway involved in the FSGD treatment of CRF and screen differentially expressed proteins in rats with CRF treated with FSGD. Methods. Thirty-three male Sprague-Dawley rats were randomly divided into control group, CRF group, and FSGD group...
2017: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/28535932/charting-novel-allergens-from-date-palm-pollen-phoenix-sylvestris-using-homology-driven-proteomics
#15
Bodhisattwa Saha, Naren Pandey, Swati Gupta Bhattacharya
Pollen grains from Phoenix sylvestris (date palm), a commonly cultivated tree in India has been found to cause severe allergic diseases in an increasing percentage of hypersensitive individuals. To unearth its allergenic components, pollen protein were profiled by two-dimensional gel electrophoresis followed by immunoblotting with date palm pollen sensitive patient sera. Allergens were identified by MALDI-TOF/TOF employing a layered proteomic approach combining conventional database dependent search and manual de novo sequencing followed by homology-based search as Phoenix sylvestris is unsequenced...
May 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28534953/proteomic-analysis-of-differentially-expressed-proteins-in-kidneys-of-brain-dead-rabbits
#16
Ling Li, Ning Li, Chongxiang He, Wei Huang, Xiaoli Fan, Zibiao Zhong, Yanfeng Wang, Qifa Ye
A large number of previous clinical studies have reported a delayed graft function for brain dead donors, when compared with living relatives or cadaveric organ transplantations. However, there is no accurate method for the quality evaluation of kidneys from brain‑dead donors. In the present study, two‑dimensional gel electrophoresis and MALDI‑TOF MS‑based comparative proteomic analysis were conducted to profile the differentially‑expressed proteins between brain death and the control group renal tissues...
May 19, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28534676/applications-of-raman-spectroscopy-in-biopharmaceutical-manufacturing-a-short-review
#17
Kevin Buckley, Alan G Ryder
The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc...
June 2017: Applied Spectroscopy
https://www.readbyqxmd.com/read/28532602/inactivation-of-west-nile-virus-in-serum-with-heat-ionic-detergent-and-reducing-agent-for-proteomic-applications
#18
Louis A Altamura, Lisa H Cazares, Susan R Coyne, James G Jaissle, Alyssa M Jespersen, Sundus Ahmed, Leonard P Wasieloski, Jeff Garrison, David A Kulesh, Ernst E Brueggemann, Tara Kenny, Michael D Ward, David E Harbourt, Timothy D Minogue
Research involving biosafety level 3 pathogens such as West Nile virus (WNV) is often limited by the limited space and technical constraints of these environments. To conduct complex analytical studies outside of high containment, robust and reliable inactivation methods are needed that maintain compatibility with downstream assays. Here we report the inactivation of WNV in spiked serum samples using a commercially available SDS-PAGE sample buffer for proteomic studies. Using this method, we demonstrate its utility by identification proteins differentially expressed in the serum of mice experimentally infected with WNV...
May 19, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28532454/proteomic-profiling-of-peripheral-blood-neutrophils-identifies-two-inflammatory-phenotypes-in-stable-copd-patients
#19
Adèle Lo Tam Loi, Susan Hoonhorst, Corneli van Aalst, Jeroen Langereis, Vera Kamp, Simone Sluis-Eising, Nick Ten Hacken, Jan-Willem Lammers, Leo Koenderman
BACKGROUND: COPD is a heterogeneous chronic inflammatory disease of the airways and it is well accepted that the GOLD classification does not fully represent the complex clinical manifestations of COPD and this classification therefore is not well suited for phenotyping of individual patients with COPD. Besides the chronic inflammation in the lung compartment, there is also a systemic inflammation present in COPD patients. This systemic inflammation is associated with elevated levels of cytokines in the peripheral blood, but the precise composition is unknown...
May 22, 2017: Respiratory Research
https://www.readbyqxmd.com/read/28532181/exploring-ribosome-composition-and-newly-synthesized-proteins-through-proteomics-and-potential-biomedical-applications
#20
Miroslava Stastna, Roberta A Gottlieb, Jennifer E Van Eyk
Protein synthesis is the outcome of tightly regulated gene expression which is responsive to a variety of conditions. Efforts are ongoing to monitor individual stages of protein synthesis to ensure maximum efficiency and accuracy. Due to post-transcriptional regulation mechanisms, the correlation between translatome and proteome is higher than between transcriptome and proteome. However, the most accurate approach to assess the key modulators and final protein expression is directly by using proteomics. Areas covered: This review covers various proteomic strategies that were used to better understand post-transcriptional regulation, specifically during and early after translation...
May 26, 2017: Expert Review of Proteomics
keyword
keyword
78630
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"