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Journal of Proteomics & Bioinformatics

Denong Wang
No abstract text is available yet for this article.
January 2017: Journal of Proteomics & Bioinformatics
Haiou Li, Qiang Lyu, Jianlin Cheng
Protein structure prediction is an important problem in computational biology, and is widely applied to various biomedical problems such as protein function study, protein design, and drug design. In this work, we developed a novel deep learning approach based on a deeply stacked denoising autoencoder for protein structure reconstruction. We applied our approach to a template-based protein structure prediction using only the 3D structural coordinates of homologous template proteins as input. The templates were identified for a target protein by a PSI-BLAST search...
December 2016: Journal of Proteomics & Bioinformatics
Rui Yang, Xinhua Liu, Smathorn Thakolwiboon, Jianhui Zhu, Xiucong Pei, Mingrui An, Zhijing Tan, David M Lubman
ALDH has been shown to be a marker that denotes a sub-population of cancer stem cells in colorectal and other cancers. This sub-population of cells shows an increased risk for tumor initiation, metastasis, and resistance to chemotherapy and radiation resulting in recurrence and death. It is thus essential to identify the important signaling pathways related to ALDH1+ CSCs in colon cancer. The essential issue becomes to isolate pure sub-populations of cells from heterogeneous tissues for further analysis. To achieve this goal, tissues from colorectal cancer Stage III patients were immuno-stained with ALDH1 antibody...
October 2016: Journal of Proteomics & Bioinformatics
Ragnhild Reehorst Lereim, Eystein Oveland, Yichuan Xiao, Øivind Torkildsen, Stig Wergeland, Kjell-Morten Myhr, Shao-Cong Sun, Frode S Berven
The ubiquitin ligase Peli1 has previously been suggested as a potential treatment target in multiple sclerosis. In the multiple sclerosis disease model, experimental autoimmune encephalomyelitis, Peli1 knock-out led to less activated microglia and less inflammation in the central nervous system. Despite being important in microglia, Peli1 expression has also been detected in glial and neuronal cells. In the present study the overall brain proteomes of Peli1 knock-out mice and wild-type mice were compared prior to experimental autoimmune encephalomyelitis induction, at onset of the disease and at disease peak...
September 2016: Journal of Proteomics & Bioinformatics
James C Wright, Jyoti S Choudhary
Accurate statistical evaluation of sequence database peptide identifications from tandem mass spectra is essential in mass spectrometry based proteomics experiments. These statistics are dependent on accurately modelling random identifications. The target-decoy approach has risen to become the de facto approach to calculating FDR in proteomic datasets. The main principle of this approach is to search a set of decoy protein sequences that emulate the size and composition of the target protein sequences searched whilst not matching real proteins in the sample...
June 27, 2016: Journal of Proteomics & Bioinformatics
Alex Dussaq, Joshua C Anderson, Christopher D Willey, Jonas S Almeida
Kinases play a role in every cellular process involved in tumorigenesis ranging from proliferation, migration, and protein synthesis to DNA repair. While genetic sequencing has identified most kinases in the human genome, it does not describe the 'kinome' at the level of activity of kinases against their substrate targets. An attempt to address that limitation and give researchers a more direct view of cellular kinase activity is found in the PamGene PamChip® system, which records and compares the phosphorylation of 144 tyrosine or serine/threonine peptides as they are phosphorylated by cellular kinases...
May 2016: Journal of Proteomics & Bioinformatics
Deepanwita Sengupta, Alan J Tackett
Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients...
April 2016: Journal of Proteomics & Bioinformatics
Morgan L Wright, Ken Pendarvis, Bindu Nanduri, Mariola J Edelmann, Haley N Jenkins, Joseph S Reddy, Jessica G Wilson, Xuan Ding, Paul R Broadway, Mais G Ammari, Oindrila Paul, Brandy Roberts, Janet R Donaldson
Listeria monocytogenes is a Gram-positive facultative anaerobe that is the causative agent of the disease listeriosis. The infectious ability of this bacterium is dependent upon resistance to stressors encountered within the gastrointestinal tract, including bile. Previous studies have indicated bile salt hydrolase activity increases under anaerobic conditions, suggesting anaerobic conditions influence stress responses. Therefore, the goal of this study was to determine if reduced oxygen availability increased bile resistance of L...
April 2016: Journal of Proteomics & Bioinformatics
Victor P Andreev, Brenda W Gillespie, Brian T Helfand, Robert M Merion
Unsupervised classification methods are gaining acceptance in omics studies of complex common diseases, which are often vaguely defined and are likely the collections of disease subtypes. Unsupervised classification based on the molecular signatures identified in omics studies have the potential to reflect molecular mechanisms of the subtypes of the disease and to lead to more targeted and successful interventions for the identified subtypes. Multiple classification algorithms exist but none is ideal for all types of data...
2016: Journal of Proteomics & Bioinformatics
Garni Barkhoudarian, Julian P Whitelegge, Daniel F Kelly, Margaret Simonian
The aim of this pilot study was to evaluate the use of advanced proteomics techniques to identify novel protein markers that contribute to the transformation of benign meningiomas to more aggressive and malignant subtypes. Multiplex peptide stable isotope dimethyl labelling and nano-LCMS was used to identify and quantify the differentially expressed proteins in WHO Grade I, II and III meningioma tissues. The proteins identified will help elucidate the process of transformation to malignancy and may contribute to improved diagnosis and treatment of these aggressive tumors...
2016: Journal of Proteomics & Bioinformatics
Stephanie D Byrum, Marie S Burdine, Lisa Orr, Linley Moreland, Samuel G Mackintosh, Simon Authier, Mylene Pouliot, Martin Hauer-Jensen, Alan J Tackett
The molecular effects of total body gamma-irradiation exposure are of critical importance as large populations of people could be exposed either by terrorists, nuclear blast, or medical therapy. In this study, we aimed to identify changes in the urine proteome using a non-human primate model system, Rhesus macaque, in order to characterize effects of acute radiation syndrome following whole body irradiation (Co-60) at 6.7 Gy and 7.4 Gy with a twelve day observation period. The urine proteome is potentially a valuable and non-invasive diagnostic for radiation exposure...
2016: Journal of Proteomics & Bioinformatics
Melissa E Ellis, James A Mobley, Ross P Holmes, John Knight
Oxalobacter formigenes is a unique intestinal organism that relies on oxalate degradation to meet most of its energy and carbon needs. A lack of colonization is a risk factor for calcium oxalate kidney stone disease. The release of the genome sequence of O. formigenes has provided an opportunity to increase our understanding of the biology of O. formigenes. This study used mass spectrometry based shotgun proteomics to examine changes in protein levels associated with the transition of growth from log to stationary phase...
2016: Journal of Proteomics & Bioinformatics
Yu Zhou, Zhen Meng, Maria Edman-Woolcott, Sarah F Hamm-Alvarez, Ebrahim Zandi
Liquid chromatography-mass spectrometry (LC-MS) based proteomics is one of the most widely used analytical platforms for global protein discovery and quantification. One of the challenges is the difficulty of identifying low abundance biomarker proteins from limited biological samples. Extensive fractionation could expand proteomics dynamic range, however, at the cost of high sample and time consumption. Extensive fractionation would increase the sample need and the labeling cost. Also quantitative proteomics depending on high resolution MS have the limitation of spectral acquisition speed...
November 2015: Journal of Proteomics & Bioinformatics
Boris Zybailov, Kuppan Gokulan, Jadon Wiese, Ramanagouda Ramanagoudr-Bhojappa, Alicia K Byrd, Galina Glazko, Mihir Jaiswal, Samuel Mackintosh, Kottayil I Varughese, Kevin D Raney
Defining protein-protein contacts is a challenging problem and cross-linking is a promising solution. Here, we present a case of mitochondrial single strand binding protein Rim1 and helicase Pif1, an interaction first observed in immuno-affinity pull-down from yeast cells using Pif1 bait. We found that only the short succinimidyl-diazirine cross-linker or formaldehyde captured the interaction between recombinant Rim1 and Pif1. In addition, Pif1 needed to be stripped of its N-terminal and C-terminal domains, and Rim1's C-terminus needed to be modified for the cross-linked product to become visible...
November 2015: Journal of Proteomics & Bioinformatics
Anna V Mathew, Lixia Zeng, Jaeman Byun, Subramaniam Pennathur
Atherosclerotic cardiovascular disease is the leading cause of death in patients with chronic kidney disease (CKD), but the mechanisms underlying vascular disease has not been fully understood. As the nitrogen donor in nitric oxide (NO(·)) synthesis, arginine and its metabolic products are integrally linked to vascular health and information. We hypothesized that derangements in this pathway could explain, in part, increased atherosclerotic risk in CKD. We developed a targeted metabolomic platform to profile quantitatively arginine metabolites in plasma by liquid chromatography tandem mass spectrometry (LC/MS)...
October 2015: Journal of Proteomics & Bioinformatics
Kelli M Sas, Viji Nair, Jaeman Byun, Pradeep Kayampilly, Hongyu Zhang, Jharna Saha, Frank C Brosius, Matthias Kretzler, Subramaniam Pennathur
Both type 1 and type 2 diabetes are associated with altered lipid metabolism, which might in part contribute to debilitating complications such as diabetic kidney disease (DKD). Ceramides are bioactive sphingolipids that have been implicated in a variety of diseases as they can regulate cellular responses to stress and invoke a myriad of downstream signaling responses. To investigate a potential role of altered ceramide metabolism in DKD, we utilized a highly sensitive and specific mass spectrometry (MS) method to quantitatively measure species in plasma and kidney cortex from the C57BLKS db/db mouse model of DKD and littermate controls...
October 2015: Journal of Proteomics & Bioinformatics
Ralph L Kodell, Randy S Haun, Eric R Siegel, Chuanlei Zhang, Angela B Trammel, Martin Hauer-Jensen, Alexander F Burnett
BACKGROUND: Whole-pelvis radiation therapy is common practice in the post-surgical treatment of cervical and endometrial cancer. Gastrointestinal mucositis is an adverse side effect of radiation therapy, and is a primary concern in patient management. We investigate whether proteomic information obtained from blood samples drawn from patients scheduled to receive radiation therapy for gynecological cancers could be used to predict which patients are most susceptible to radiation-induced gastrointestinal mucositis, in order to improve the individualization of radiation therapy...
July 2015: Journal of Proteomics & Bioinformatics
Lingling Fang, Kyoko Kojima, Lihua Zhou, David K Crossman, James A Mobley, Jayleen Grams
No longer regarded as simply a storage depot, fat is a dynamic organ acting locally and systemically to modulate energy homeostasis, glucose sensitivity, insulin resistance, and inflammatory pathways. Here, mass spectrometry was used to survey the proteome of patient matched subcutaneous fat and visceral fat in 20 diabetic vs 22 nondiabetic patients with morbid obesity. A similar number of proteins (~600) were identified in each tissue type. When stratified by diabetic status, 19 and 41 proteins were found to be differentially abundant in subcutaneous fat and omentum, respectively...
June 2015: Journal of Proteomics & Bioinformatics
Candice Z Ulmer, Richard A Yost, Jing Chen, Clayton E Mathews, Timothy J Garrett
Metabolomics is the comprehensive study of metabolism as it pertains to an organism or biological system. Lipidomics, a subset discipline of metabolomics, encompasses the study of cellular lipid functions: including pathways, networks, and interactions. The abundance of metabolites and lipids, along with their contribution to health and disease, makes metabolomics a valuable tool for biomarker research. Disease biomarker identification requires a reproducible, sensitive, and accurate analytical platform. Although transcriptomic and proteomic areas have well-established protocols for sample preparation and data processing, the metabolomics field is still developing comparable standardized conventions...
June 2015: Journal of Proteomics & Bioinformatics
Il Kyu Cho, Mihye Jeong, Are-Sun You, Kyung Hun Park, Qing X Li
Paraquat (PQ) has been one of the most widely used herbicides in the world. PQ, when ingested, is toxic to humans and may cause acute respiratory distress syndrome. To investigate molecular perturbation in lung tissues caused by PQ, Sprague Dawley male rats were fed with PQ at a dose of 25 mg/kg body weight for 20 times in four weeks. The effects of PQ on cellular processes and biological pathways were investigated by analyzing proteome in the lung tissues in comparison with the control. Among the detected proteins, 321 and 254 proteins were over-represented and under-represented, respectively, in the PQ-exposed rat lung tissues in comparison with the no PQ control...
May 2015: Journal of Proteomics & Bioinformatics
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