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https://www.readbyqxmd.com/read/28213128/quantitative-proteomic-analysis-of-human-testis-reveals-system-wide-molecular-and-cellular-pathways-associated-with-non-obstructive-azoospermia
#1
Mehdi Alikhani, Mehdi Mirzaei, Marjan Sabbaghian, Pouria Parsamatin, Razieh Karamzadeh, Samane Adib, Niloofar Sodeifi, Mohammad Ali Sadighi Gilani, Masoud Zabet-Moghaddam, Lindsay Parker, Yunqi Wo, Vivek Gupta, Paul A Haynes, Hamid Gourabi, Hossein Baharvand, Ghasem Hosseini Salekdeh
: Male infertility accounts for half of the infertility problems experienced by couples. Azoospermia, having no measurable level of sperm in seminal fluid, is one of the known conditions resulting in male infertility. In order to elucidate the complex molecular mechanisms causing male azoospermia, label-free quantitative shotgun proteomics was carried out on testicular tissue specimens from patients with obstructive azoospermia and non-obstructive azoospermia, including maturation arrest (MA) and Sertoli cell only syndrome (SCOS)...
February 14, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28209523/tb-iris-proteomic-analysis-of-in-vitro-pbmc-responses-to-mycobacterium-tuberculosis-and-response-modulation-by-dexamethasone
#2
Liam Bell, Janique M Peyper, Shaun Garnett, Rabecca Tadokera, Robert Wilkinson, Graeme Meintjes, Jonathan M Blackburn
Paradoxical tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) occurs in 8-54% of South African patients undergoing treatment for tuberculosis/human immunodeficiency virus co-infection. Improved TB-IRIS molecular pathogenesis understanding would enhance risk stratification, diagnosis, prognostication, and treatment. We assessed how TB-IRIS status and dexamethasone influence leukocyte proteomic responses to Mycobacterium tuberculosis (Mtb). Patient blood was obtained three weeks post-anti-retroviral therapy initiation...
February 13, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28199984/autocrine-and-paracrine-stip1-signaling-promote-osteolytic-bone-metastasis-in-renal-cell-carcinoma
#3
Jiang Wang, Hongbo You, Jun Qi, Caihong Yang, Ye Ren, Hao Cheng
Bone metastases are responsible for some of the most devastating complications of renal cell carcinoma (RCC). However, pro-metastatic factors leading to the highly osteolytic characteristics of RCC bone metastasis have barely been explored. We previously developed novel bone-seeking RCC cell lines by the in vivo selection strategy and performed a comparative proteome analysis on their total cell lysate. Here, we focused on STIP1 (stress-induced phosphoprotein 1), the high up-regulated protein in the bone-seeking cells, and explored its clinical relevance and functions in RCC bone metastasis...
February 9, 2017: Oncotarget
https://www.readbyqxmd.com/read/28199731/proteomic-profiling-analysis-reveals-a-link-between-experimental-autoimmune-uveitis-and-complement-activation-in-rats
#4
Dadong Guo, Bing Hu, Hongying Tang, Yuanyuan Sun, Bin Liu, Qingmei Tian, Hongsheng Bi
Uveitis is an autoimmune disease that usually damages the vision function, leading to poor visual quality in patients. As an autoimmune ocular inflammatory disease, the pathogenesis of uveitis is associated with abnormal expression of some proteins and aberrant regulation of multiple signaling pathways. Nevertheless, the detailed mechanism remains unclear. In this study, we induced an experimental autoimmune uveitis (EAU) model in rats. We determined the levels of C3a and membrane attack complex C5b-9 (soluble C5b-9, sC5b-9) in both plasma and aqueous humor, identified the differentially expressed proteins in plasma by liquid chromatography-tandem mass spectrometry, and employed bioinformatics algorithms to analyze differentially expressed proteins in EAU rat plasma...
February 15, 2017: Scandinavian Journal of Immunology
https://www.readbyqxmd.com/read/28198407/comparative-proteomic-analysis-of-horseweed-conyza-canadensis-biotypes-identifies-candidate-proteins-for-glyphosate-resistance
#5
Fidel González-Torralva, Adrian P Brown, Stephen Chivasa
Emergence of glyphosate-resistant horseweed (Conyza canadensis) biotypes is an example of how unrelenting use of a single mode of action herbicide in agricultural weed control drives genetic adaptation in targeted species. While in other weeds glyphosate resistance arose from target site mutation or target gene amplification, the resistance mechanism in horseweed uses neither of these, being instead linked to reduced herbicide uptake and/or translocation. The molecular components underpinning horseweed glyphosate-resistance remain unknown...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28198089/a-comprehensive-proteome-map-of-glandular-trichomes-of-hop-humulus-lupulus-l-female-cones-identification-of-biosynthetic-pathways-of-the-major-terpenoid-related-compounds-and-possible-transport-proteins
#6
Antoine Champagne, Marc Boutry
Female flowers of hop (Humulus lupulus) are an essential source of terpenoid-related compounds, which are mainly used as flavoring in the beer brewing process. The compounds involved are bitter acids, terpenophenolics, as well as mono- and sesquiterpenoids. In this work, we analyzed the proteome of purified glandular trichomes (lupulin glands) from female flowers, which produce and accumulate these compounds. An extensive 2D-LC-MS/MS analysis identified 1,015 proteins. Of these, most correspond to housekeeping and primary metabolism-related proteins, albeit predominantly including amino acid and lipid metabolism, which feeds the specialized (secondary) metabolism...
February 15, 2017: Proteomics
https://www.readbyqxmd.com/read/28196893/phosphorylation-of-%C3%AE-b-crystallin-supports-reactive-astrogliosis-in-demyelination
#7
Hedwich F Kuipers, Jane Yoon, Jack van Horssen, May H Han, Paul L Bollyky, Theo D Palmer, Lawrence Steinman
The small heat shock protein αB-crystallin (CRYAB) has been implicated in multiple sclerosis (MS) pathogenesis. Earlier studies have indicated that CRYAB inhibits inflammation and attenuates clinical disease when administered in the experimental autoimmune encephalomyelitis model of MS. In this study, we evaluated the role of CRYAB in primary demyelinating events. Using the cuprizone model of demyelination, a noninflammatory model that allows the analysis of glial responses in MS, we show that endogenous CRYAB expression is associated with increased severity of demyelination...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28195392/relative-protein-quantification-and-accessible-biology-in-lung-tumor-proteomes-from-four-lc-ms-ms-discovery-platforms
#8
Paul A Stewart, Bin Fang, Robbert J C Slebos, Guolin Zhang, Adam L Borne, Katherine Fellows, Jamie K Teer, Y Ann Chen, Eric Welsh, Steven A Eschrich, Eric B Haura, John M Koomen
Discovery proteomics experiments include many options for sample preparation and mass spectrometry data acquisition, which are capable of creating datasets for quantifying thousands of proteins. To define a strategy that would produce a dataset with sufficient content while optimizing required resources, we compared 1) single sample liquid chromatography-tandem mass spectrometry (LC-MS/MS) with data dependent acquisition (DDA) to single sample LC-MS/MS with data independent acquisition (DIA) and 2) peptide fractionation with label-free quantification (LF) to isobaric labeling followed by peptide fractionation (TMT 6-plex)...
February 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28193578/a-food-based-approach-that-targets-interleukin-6-a-key-regulator-of-chronic-intestinal-inflammation-and-colon-carcinogenesis
#9
Abigail Sido, Sridhar Radhakrishnan, Sung Woo Kim, Elisabeth Eriksson, Frank Shen, Qunhua Li, Vadiraja Bhat, Lavanya Reddivari, Jairam K P Vanamala
Studies have shown a causal link between high-calorie diet (HCD) and colon cancer. However, molecular mechanisms are not fully elucidated. To understand etiology of HCD-induced colon carcinogenesis, we screened 10 pathways linked to elevated colonic cell proliferation and chronic inflammation in an HCD-consuming human-relevant pig model. We observed elevated colonic mucosal interleukin-6 (IL-6) expression in HCD-consuming pigs compared to standard diet controls (SD, P=.04), and IL-6 strongly correlated with Ki-67 proliferative index and zone, early biomarkers of colon cancer risk (r=0...
January 28, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28192900/biphasic-affinity-chromatographic-approach-for-deep-tyrosine-phosphoproteome-analysis
#10
Zhenzhen Deng, Mingming Dong, Yan Wang, Jing Dong, Shawn S-C Li, Hanfa Zou, Mingliang Ye
Tyrosine phosphorylation (pTyr) is important for normal physiology and implicated in many human diseases, particularly cancer. Identification of pTyr sites is critical to dissecting signaling pathways and understanding disease pathologies. However, compared with serine/threonine phosphorylation (pSer/pThr), the analysis of pTyr at the proteome level is more challenging due to its low abundance. Here, we developed a biphasic affinity chromatographic approach where Src SH2 superbinder was coupled with NeutrAvidin affinity chromatography, for tyrosine phosphoproteome analysis...
February 1, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28188704/cnot1-cooperates-with-lmna-to-aggravate-osteosarcoma-tumorigenesis-through-the-hedgehog-signaling-pathway
#11
Dong-Dong Cheng, Jing Li, Shi-Jie Li, Qing-Cheng Yang, Cun-Yi Fan
While treatments for childhood osteosarcoma have improved, the overall survival for this common type of bone cancer have not changed for three decades and thus new targets for therapeutic development are needed. To identify tumor-related proteins in osteosarcoma, we used isobaric tags in a relative and absolute quantitation (iTRAQ) proteomic approach to analyze the differentially expressed proteins between osteosarcoma cells and human osteoblastic cells. Through clinical screening and functional evaluation, CCR4-NOT transcription complex subunit 1 (CNOT1) correlated to the growth of osteosarcoma cells...
February 11, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28188532/pathway-informed-discovery-and-targeted-proteomic-workflows-using-mass-spectrometry
#12
Caroline S Chu, Christine A Miller, Andy Gieschen, Steve M Fischer
Recent advancements in mass spectrometry (MS) and data analysis software have enabled new strategies for biological discovery using proteomics. Proteomics has evolved from routine discovery and identification of proteins to integrated multi-omics projects relating specific proteins to their genes and metabolites. Using additional information, such as that contained in biological pathways, has enabled the use of targeted protein quantitation for monitoring fold changes in expression as well as biomarker discovery...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28187790/retinoic-acid-and-tgf-%C3%AE-signalling-cooperate-to-overcome-mycn-induced-retinoid-resistance
#13
David J Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G Higgins, Walter Kolch
BACKGROUND: Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance...
February 10, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28186992/autophagy-is-highly-targeted-among-host-comparative-proteomes-during-infection-with-different-virulent-rabv-strains
#14
Ling Li, Hongli Jin, Hualei Wang, Zengguo Cao, Na Feng, Jianzhong Wang, Yongkun Zhao, Xuexing Zheng, Pengfei Hou, Nan Li, Hang Chi, Pei Huang, Cuicui Jiao, Qian Li, Lina Wang, Tiecheng Wang, Weiyang Sun, Yuwei Gao, Changchun Tu, Guixue Hu, Songtao Yang, Xianzhu Xia
Rabies virus (RABV) is a neurotropic virus that causes serious disease in humans and animals worldwide. It has been reported that different RABV strains can result in divergent prognoses in animal model. To identify host factors that affect different infection processes, a kinetic analysis of host proteome alterations in mouse brains infected with different virulent RABV strains was performed using isobaric tags for a relative and absolute quantification (iTRAQ)-liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach, and this analysis identified 147 differentially expressed proteins (DEPs) between the pathogenic challenge virus standard (CVS)-11 strain and the attenuated SRV9 strain...
February 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28186866/toward-postgenomics-ophthalmology-a-proteomic-map-of-the-human-choroid-retinal-pigment-epithelium-tissue
#15
Manjunath Dammalli, Krishna R Murthy, Sneha M Pinto, Kalpana Babu Murthy, Raja Sekhar Nirujogi, Anil K Madugundu, Gourav Dey, Bipin Nair, Harsha Gowda, Thottethodi Subrahmanya Keshava Prasad
Ophthalmology and visual health research have received relatively limited attention from the personalized medicine community, but this trend is rapidly changing. Postgenomics technologies such as proteomics are being utilized to establish a baseline biological variation map of the human eye and related tissues. In this context, the choroid is the vascular layer situated between the outer sclera and the inner retina. The choroidal circulation serves the photoreceptors and retinal pigment epithelium (RPE). The RPE is a layer of cuboidal epithelial cells adjacent to the neurosensory retina and maintains the outer limit of the blood-retina barrier...
February 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28186774/quantitative-map-of-%C3%AE-lactone-induced-virulence-regulation
#16
Joanna Krysiak, Matthias Stahl, Jan Vomacka, Christian Fetzer, Markus Lakemeyer, Anja Fux, Stephan A Sieber
β-Lactones have recently been introduced as the first selective ClpP inhibitors that attenuate virulence of both sensitive Staphylococcus aureus and multiresistant strains (MRSA). Although previous knockout studies showed that ClpP is essential for S. aureus alpha-toxin production, a link between β-lactone inhibition and molecular virulence mechanisms has been lacking so far. We here perform a chemical-proteomic approach to elucidate antivirulence pathways. First, we demonstrate by gel-free activity-based protein profiling that ClpP is the predominant target of β-lactones...
February 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28183283/comparative-proteomics-analysis-of-teleost-intermuscular-bones-and-ribs-provides-insight-into-their-development
#17
Chun-Hong Nie, Shi-Ming Wan, Tea Tomljanovic, Tomislav Treer, Chung-Der Hsiao, Wei-Min Wang, Ze-Xia Gao
BACKGROUND: Intermuscular bones (IBs) and ribs both are a part of skeletal system in teleosts, but with different developing process. The chemical composition of fish IBs and ribs as well as the underlying mechanism about their development have not been investigated. In the present study, histological structures showed that one bone cavity containing osteoclasts were existed in ribs, but not in IBs of Megalobrama amblycephala. We constructed the first proteomics map for fish bones including IBs and ribs, and identified the differentially expressed proteins between IBs and ribs through iTRAQ LC-MS/MS proteomic analysis...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28183064/quantitative-proteomics-analysis-reveals-perturbation-of-lipid-metabolic-pathways-in-the-liver-of-atlantic-cod-gadus-morhua-treated-with-pcb-153
#18
Fekadu Yadetie, Eystein Oveland, Anne Døskeland, Frode Berven, Anders Goksøyr, Odd André Karlsen
PCB 153 is one of the most abundant PCB congeners detected in biological samples. It is a persistent compound that is still present in the environment despite the ban on production and use of PCBs in the late 1970s. It has strong tendencies to bioaccumulate and biomagnify in biota, and studies have suggested that it is an endocrine and metabolic disruptor. In order to study mechanisms of toxicity, we exposed Atlantic cod (Gadus morhua) to various doses of PCB 153 (0, 0.5, 2 and 8mg/kg body weight) for two weeks and examined the effects on expression of liver proteins using label-free quantitative proteomics...
January 30, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28181595/comprehensive-proteomic-characterization-of-the-human-colorectal-carcinoma-reveals-signature-proteins-and-perturbed-pathways
#19
Jian-Jiang Hao, Xiaofei Zhi, Yeming Wang, Zheng Zhang, Zeyu Hao, Rong Ye, Zhijie Tang, Fei Qian, Quhui Wang, Jianwei Zhu
The global change in protein abundance in colorectal cancer (CRC) and its contribution to tumorigenesis have not been comprehensively analyzed. In this study, we conducted a comprehensive proteomic analysis of paired tumors and adjacent tissues (AT) using high-resolution Fourier-transform mass spectrometry and a novel algorithm of quantitative pathway analysis. 12380 proteins were identified and 740 proteins that presented a 4-fold change were considered a CRC proteomic signature. A significant pattern of changes in protein abundance was uncovered which consisted of an imbalance in protein abundance of inhibitory and activating regulators in key signal pathways, a significant elevation of proteins in chromatin modification, gene expression and DNA replication and damage repair, and a decreased expression of proteins responsible for core extracellular matrix architectures...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28181485/high-throughput-single-cell-analysis-for-the-proteomic-dynamics-study-of-the-yeast-osmotic-stress-response
#20
Rongfei Zhang, Haiyu Yuan, Shujing Wang, Qi Ouyang, Yong Chen, Nan Hao, Chunxiong Luo
Motorized fluorescence microscopy combined with high-throughput microfluidic chips is a powerful method to obtain information about different biological processes in cell biology studies. Generally, to observe different strains under different environments, high-throughput microfluidic chips require complex preparatory work. In this study, we designed a novel and easily operated high-throughput microfluidic system to observe 96 different GFP-tagged yeast strains in one switchable culture condition or 24 different GFP-tagged yeast strains in four parallel switchable culture conditions...
February 9, 2017: Scientific Reports
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