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human proteome

Mariaconcetta Varano, Marco Gaspari, Angela Quirino, Giovanni Cuda, Maria Carla Liberto, Alfredo Focà
Ochrobactrum anthropi is a gram-negative rod belonging to the Brucellaceae family, able to colonize a variety of environments, and actually reported as a human opportunistic pathogen. Despite its low virulence, the bacterium causes a growing number of hospital-acquired infections mainly, but not exclusively, in immunocompromised patients. The aim of this study was to obtain an overview of the global proteome changes occurring in O. anthropi in response to different growth temperatures, in order to achieve a major understanding of the mechanisms by which the bacterium adapts to different habitats and to identify some potential virulence factors...
October 18, 2016: Proteomics
Joana C Silva, Emmanuel Cornillot, Carrie McCracken, Sahar Usmani-Brown, Ankit Dwivedi, Olukemi O Ifeonu, Jonathan Crabtree, Hanzel T Gotia, Azan Z Virji, Christelle Reynes, Jacques Colinge, Vidya Kumar, Lauren Lawres, Joseph E Pazzi, Jozelyn V Pablo, Chris Hung, Jana Brancato, Priti Kumari, Joshua Orvis, Kyle Tretina, Marcus Chibucos, Sandy Ott, Lisa Sadzewicz, Naomi Sengamalay, Amol C Shetty, Qi Su, Luke Tallon, Claire M Fraser, Roger Frutos, Douglas M Molina, Peter J Krause, Choukri Ben Mamoun
Babesia microti, a tick-transmitted, intraerythrocytic protozoan parasite circulating mainly among small mammals, is the primary cause of human babesiosis. While most cases are transmitted by Ixodes ticks, the disease may also be transmitted through blood transfusion and perinatally. A comprehensive analysis of genome composition, genetic diversity, and gene expression profiling of seven B. microti isolates revealed that genetic variation in isolates from the Northeast United States is almost exclusively associated with genes encoding the surface proteome and secretome of the parasite...
October 18, 2016: Scientific Reports
Santiago Marfà, Josep Marti, Adalgiza Reyes, Gregori Casals, Guillermo Fernández-Varo, Silvia Carvajal, J C García-Valdecasas, Josep Fuster, Wladimiro Jiménez
Colorectal cancer (CRC) is one of the most common cancers in the developed countries, and nearly 70% of patients with CRC develop colorectal liver metastases (CRLMs). During the last decades, several scores have been proposed to predict recurrence after CRLM resection. However, these risk scoring systems do not accurately reflect the prognosis of these patients. Therefore, this investigation was designed to identify a proteomic profile in human hepatic tumor samples to classify patients with CRLM as "mild" or "severe" based on the 5-year survival...
October 2016: Translational Oncology
Dennis Wang, Nhu-An Pham, Jiefei Tong, Shingo Sakashita, Ghassan Allo, Lucia Kim, Naoki Yanagawa, Vibha Raghavan, Yuhong Wei, Christine To, Quang M Trinh, Maud H W Starmans, Michelle A Chan-Seng-Yue, Dianne Chadwick, Lei Li, Chang-Qi Zhu, Ni Liu, Ming Li, Sharon Lee, Vladimir Ignatchenko, Dan Strumpf, Paul Taylor, Nadeem Moghal, Geoffrey Liu, Paul C Boutros, Thomas Kislinger, Melania Pintilie, Igor Jurisica, Frances A Shepherd, John D McPherson, Lakshmi Muthuswamy, Michael F Moran, Ming-Sound Tsao
Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice...
October 17, 2016: International Journal of Cancer. Journal International du Cancer
Magdalena Pertynska-Marczewska, Evanthia Diamanti-Kandarakis
OBJECTIVE: The hypothalamic gonadotropin-releasing hormone pulse generator, the pituitary gonadotropes, the ovaries, and the uterus play a crucial role in female fertility. A decline in reproductive performance represents a complex interplay of actions at all levels of the hypothalamic-pituitary-ovarian axis. Recently, in the field of female reproductive aging attention is drawn to the carbonyl stress theory. Advanced glycation end products (AGEs) contribute directly to protein damage, induce a chain of oxidative stress (OS) reactions, and increase inflammatory reactions...
October 3, 2016: Menopause: the Journal of the North American Menopause Society
Xiang Sun, Hongwei Zhang, Longhua Luo, Kezhao Zhong, Yushui Ma, Linlin Fan, Da Fu, Lijuan Wan
The identification of markers for disease diagnostic, prognostic, or predictive purposes will have a great effect in improving patient management. Proteomic‑based approaches for biomarker discovery are promising strategies used in cancer research. In this study, we performed quantitative proteomic analysis on four patients including clear cell renal cell carcinoma (ccRCC) and paired adjacent non‑cancerous renal tissues using label‑free quantitative proteomics and liquid chromatography‑tandem mass spectrometry (LC‑MS/MS) to identify differentially expressed proteins...
October 11, 2016: Oncology Reports
Peizhen Li, Jun Ying, Qingli Chang, Wen Zhu, Guangjian Yang, Teng Xu, Huiguang Yi, Ruowang Pan, Enyong Zhang, Xiaofeng Zeng, Chunxia Yan, Qiyu Bao, Shengbin Li
We studied phycoerythrin (PE) in human SW480 tumor cells and the underlying molecular mechanisms of action. PE inhibited cell proliferation as evidenced by CCK-8 assay. The IC50 values of phycoerythrin were 48.2 and 27.4 µg/ml for 24 and 48 h of exposure, respectively. PE induced apoptosis and cell cycle arrest in SW480 cells as observed under electron microscopy and with flow cytometry. Apoptosis increased from 5.1 (controls) to 39.0% in 80.0 µg/ml PE-treated cells. Differences in protein expression were identified using proteomic techniques...
October 11, 2016: Oncology Reports
Igor S Bryukhovetskiy, Inessa V Dyuizen, Valeriy E Shevchenko, Andrey S Bryukhovetskiy, Polina V Mischenko, Elena V Milkina, Yuri S Khotimchenko
Glioblastoma multiforme is an aggressive malignant brain tumor with terminal consequences. A primary reason for its resistance to treatment is associated with cancer stem cells (CSCs), of which there are currently no effective ways to destroy. It remains unclear what cancer cells become a target of stem cell migration, what the role of this process is in oncogenesis and what stem cell lines should be used in developing antitumor technologies. Using modern post‑genome technologies, the present study investigated the migration of human stem cells to cancer cells in vitro, the comparative study of cell proteomes of certain stem cells (including CSCs) was conducted and stem cell migration in vivo was examined...
October 13, 2016: Molecular Medicine Reports
Huang-Joe Wang, Sung-Fang Chen, Wan-Yu Lo
The angiotensin-converting enzyme 2/angiotensin-(1-7)/Mas axis is a pathway that acts against the detrimental effects of the renin-angiotensin system. However, the effects of angiotensin-(1-7) on endothelial protein expression and the related phenotypes are unclear. We performed a duplicate of iTRAQ quantitative proteomic analysis on human aortic endothelial cells (HAECs) treated with angiotensin-(1-7) for 6 hours. Cofilin-1 was identified as a highly abundant candidate with consistent >30% coverage and >1...
October 17, 2016: Scientific Reports
Nori Sato, Takako Taniguchi, Yuichiro Goda, Hirofumi Kosaka, Kosaku Higashino, Toshinori Sakai, Shinsuke Katoh, Natsuo Yasui, Koichi Sairyo, Hisaaki Taniguchi
Connective tissues such as tendon, ligament and cartilage are mostly composed of extracellular matrix (ECM). These tissues are insoluble, mainly due to the highly cross-linked ECM proteins such as collagens. Difficulties obtaining suitable samples for mass spectrometric analysis render the application of modern proteomic technologies difficult. Complete solubilization of them would not only elucidate protein composition of normal tissues but also reveal pathophysiology of pathological tissues. Here we report complete solubilization of human Achilles tendon and yellow ligament, which is achieved by chemical digestion combined with successive protease treatment including elastase...
October 17, 2016: Journal of Proteome Research
Alexandra E Paharik, Wilmara Salgado-Pabon, David K Meyerholz, Mark J White, Patrick M Schlievert, Alexander R Horswill
The Spl proteases are a group of six serine proteases that are encoded on the νSaβ pathogenicity island and are unique to Staphylococcus aureus. Despite their interesting biochemistry, their biological substrates and functions in virulence have been difficult to elucidate. We found that an spl operon mutant of the community-associated methicillin-resistant S. aureus USA300 strain LAC induced localized lung damage in a rabbit model of pneumonia, characterized by bronchopneumonia observed histologically. Disease in the mutant-infected rabbits was restricted in distribution compared to that in wild-type USA300-infected rabbits...
September 2016: MSphere
Jeovanis Gil, Alberto Ramírez-Torres, Sergio Encarnación-Guevara
Lysine acetylation is a reversible modification controlled by two groups of enzymes: lysine acetyltransferases (KATs) and lysine deacetylases (KDACs). Acetylated lysine residues are recognized by bromodomains, a family of evolutionarily conserved domains. The use of high-resolution mass spectrometry-based proteomics, in combination with the enrichment of acetylated peptides through immunoprecipitation with anti-acetyl-lysine antibodies, has expanded the number of acetylated proteins from histones and a few nuclear proteins to more than 2000 human proteins...
October 13, 2016: Journal of Proteomics
Maurizio Cirilli, Oxana Bereshchenko, Olga Ermakova, Claus Nerlov
BACKGROUND: C/EBPa and C/EBPb are transcription factors with tissue specific expression regulating several important cellular processes. They work by recruiting protein complexes to a common DNA recognition motif and both are able to compensate each other's absence in many cell types, thus showing functional redundancy. They also play distinct roles in specific cellular pathways and their abnormal functioning gives raise to different human pathologies. METHODS: To investigate the molecular basis of C/EBPa and C/EBPb specificity and redundancy we characterized their in vivo protein-protein interaction networks by Tandem Affinity Purification and Mass Spectrometry...
October 13, 2016: Biochimica et Biophysica Acta
Roger Geiger, Jan C Rieckmann, Tobias Wolf, Camilla Basso, Yuehan Feng, Tobias Fuhrer, Maria Kogadeeva, Paola Picotti, Felix Meissner, Matthias Mann, Nicola Zamboni, Federica Sallusto, Antonio Lanzavecchia
Metabolic activity is intimately linked to T cell fate and function. Using high-resolution mass spectrometry, we generated dynamic metabolome and proteome profiles of human primary naive T cells following activation. We discovered critical changes in the arginine metabolism that led to a drop in intracellular L-arginine concentration. Elevating L-arginine levels induced global metabolic changes including a shift from glycolysis to oxidative phosphorylation in activated T cells and promoted the generation of central memory-like cells endowed with higher survival capacity and, in a mouse model, anti-tumor activity...
October 13, 2016: Cell
Maria Bruzelius, Maria Jesus Iglesias, Mun-Gwan Hong, Laura Sanchez-Rivera, Beata Gyorgy, Juan Carlos Souto, Mattias Frånberg, Claudia Fredolini, Rona J Strawbridge, Margareta Holmström, Anders Hamsten, Mathias Uhlén, Angela Silveira, Jose Manuel Soria, David M Smadja, Lynn M Butler, Jochen M Schwenk, Pierre-Emmanuel Morange, David-Alexandre Trégouët, Jacob Odeberg
There is a clear clinical need for high specificity plasma biomarkers for predicting risk of venous thromboembolism (VTE), but thus far such markers have remained elusive. Utilising affinity reagents from the human protein atlas (HPA) project and multiplexed immuoassays we extensively analysed plasma samples from two individual cohorts to identify candidate protein markers associated with VTE risk. We screened plasma samples from 88 VTE cases and 85 matched controls, collected as part of the Swedish 'Venous Thromboembolism Biomarker Study' (VEBIOS), using suspension bead arrays composed of 755 antibodies targeting 408 candidate proteins...
October 14, 2016: Blood
Meng Yang, Jinshao Ye, Huaming Qin, Yan Long, Yi Li
Perfluorooctanoic acid (PFOA) has received an increasing attention in the agricultural and food industries due to its risk to human health. To facilitate the development of novel biomarkers of Escherichia coli against PFOA through multi-omics technologies, and to reveal the resistance mechanism of E. coli against PFOA at protein levels, the interactions among pollutant stress, protein expression and cell metabolism was investigated by using iTRAQ-based quantitative proteomic analysis. The results revealed that the 63 up-regulated proteins mainly involved in tricarboxylic acid cycle, glyoxylate and dicarboxylate metabolism and fatty acid biosynthesis, whereas, the 69 down-regulated proteins related to oxidative phosphorylation, pyruvate metabolism and the cell cycle-caulobacter pathway, were also associated with the increase of membrane permeability, excessive expenditure of ATP, disruption of fatty acid biosynthesis under PFOA stress...
October 11, 2016: Environmental Pollution
Sing Ying Wong, Ching Chin Lee, Ali Ashrafzadeh, Sarni Mat Junit, Nazirahanie Abrahim, Onn Haji Hashim
Proteome analysis of the human hair remains challenging due to the poor solubility of hair proteins and the difficulty in their extraction. In the present study, we have developed a rapid extraction protocol for hair shaft protein using alkaline-based buffer. The new protocol accelerated the procedure by reducing the extraction time from at least a day to less than two hours and showed a protein recovery of 47.3 ± 3.72%. Further analyses of the extracted protein sample through sodium dodecyl sulfate polyacrylamide gel electrophoresis and Quadrupole-time-of-flight mass spectrometry analysis unveiled a total of 60 proteins, including 25 that were not previously reported...
2016: PloS One
Hideharu Domoto, Keiichi Iwaya, Fumitaka Ikomi, Hirotaka Matsuo, Yutaka Tadano, Shigenori Fujii, Kazuyoshi Tachi, Yoshiyuki Itoh, Michiya Sato, Kimitoshi Inoue, Nariyoshi Shinomiya
Saturation diving (SD) is one of the safest techniques for tolerating hyperbaric conditions for long durations. However, the changes in the human plasma protein profile that occur during SD are unknown. To identify differential protein expression during or after SD, 65 blood samples from 15 healthy Japanese men trained in SD were analyzed by two-dimensional fluorescence difference gel electrophoresis. The expression of two proteins, one 32.4 kDa with an isoelectric point (pI) of 5.8 and the other 44.8 kDa with pI 4...
2016: PloS One
Gayatri Padhy, Anamika Gangwar, Manish Sharma, Kalpana Bhargava, Niroj Kumar Sethy
Padhy Gayatri, Anamika Gangwar, Manish Sharma, Kalpana Bhargava, and Niroj Kumar Sethy. Plasma proteomics of Ladakhi natives reveal functional regulation between renin-angiotensin system and eNOS-cGMP pathway. High Alt Med Biol. 16:000-000, 2016.-Humans have been living in high altitudes for more than 25,000 years but the molecular pathways promoting survival and performance in these extreme environments are not well elucidated. In an attempt to understand human adaptation to high altitudes, we used two-dimensional gel electrophoresis combined with MALDI-TOF/TOF to identify plasma proteins and associated pathways of ethnic Ladakhi natives residing at 3520 m...
October 14, 2016: High Altitude Medicine & Biology
Amanda L Lumsden, Richard L Young, Nektaria Pezos, Damien J Keating
BACKGROUND: Huntingtin-associated Protein 1 (HAP1) is expressed in neurons and endocrine cells, and is critical for postnatal survival in mice. HAP1 shares a conserved "HAP1_N" domain with TRAfficking Kinesin proteins TRAK1 and TRAK2 (vertebrate), Milton (Drosophila) and T27A3.1 (C. elegans). HAP1, TRAK1 and TRAK2 have a degree of common function, particularly regarding intracellular receptor trafficking. However, TRAK1, TRAK2 and Milton (which have a "Milt/TRAK" domain that is absent in human and rodent HAP1) differ in function to HAP1 in that they are mitochondrial transport proteins, while HAP1 has emerging roles in starvation response...
October 13, 2016: BMC Evolutionary Biology
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