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Journal of Proteomics

Lucie Hernychová, Michal Rosůlek, Alan Kádek, Václav Mareška, Josef Chmelík, Ljubina Adámková, Valéria Grobárová, Ondřej Šebesta, Zdeněk Kukačka, Kristián Skála, Vojtěch Spiwok, Jan Černý, Petr Novák
The cytotoxicity of mouse natural killer (NK) cells in response to pathological changes in target cells is regulated via the Nkrp1b receptor. Here, we characterized the Nkrp1b structure and structural features (stalk, loop, and oligomerization state) that affect its interactions. To study the Nkrp1b protein structure and the functional importance of its stalk, two Nkrp1b protein variants differing by the presence of the stalk were prepared. These variants were studied using a combination of structural mass spectrometry approaches with computational modeling to derive structural models...
November 8, 2018: Journal of Proteomics
Julien Bonnet, Camille Garcia, Thibaut Leger, Marie-Pauline Couquet, Philippe Vignoles, Vatunga Gedeao, Joseph Ndung'u, Clotilde Boudot, Sylvie Bisser, Bertrand Courtioux
Human African trypanosomiasis (HAT) is a neglected tropical disease that is endemic in sub-Saharan Africa. Control of the disease has been recently improved by better screening and treatment strategies, and the disease is on the WHO list of possible elimination. However, some physiopathological aspects of the disease transmission and progression remain unclear. We propose a new proteomic approach to identify new targets and thus possible new biomarkers of the disease. We also focused our attention on fluids classically associated with HAT (serum and cerebrospinal fluid (CSF)) and on the more easily accessible biological fluids urine and saliva...
November 7, 2018: Journal of Proteomics
Carlos Barreiro, Carlos García-Estrada
Discovery, industrial production and clinical applications of penicillin, together with scientific findings on penicillin biosynthesis and its complex regulation, are model milestones of the historical evolution of the most recognized 'magic bullet' against microbial infections available in the worldwide market. Thousands of tons of penicillin produced nowadays are the result of a huge number of technical, industrial and scientific tackled and solved challenges. This combination of, sometimes unsuspected, findings has given Proteomics the chance to support the understanding of the physiology of the high-producing fungal strains and the development of enhanced mutants by means of inverse engineering...
November 7, 2018: Journal of Proteomics
Shu-Feng Zhang, Ying Chen, Zhang-Xian Xie, Hao Zhang, Lin Lin, Da-Zhi Wang
Phosphorus (P) is a key macronutrient limiting cell growth and bloom formation of marine dinoflagellates. Physiological responses to changing ambient P have been investigated in dinoflagellates; however, the molecular mechanisms behind these responses remain limited. Here, we compared the protein expression profiles of a marine dinoflagellate Alexandrium catenella grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions using an iTRAQ-based quantitative proteomic approach...
November 7, 2018: Journal of Proteomics
France Anne Dias Ruas, Natália Rocha Barboza, William Castro-Borges, Renata Guerra-Sá
Organisms, in general, respond to environmental stress by altering their pattern of protein expression (proteome), as an alternative to growing in stressful conditions. A strain of Meyerozyma guilliermondii resistant to manganese was isolated from a sample of water collected from mine drainage in southeastern Minas Gerais (Brazil), and demonstrated manganese detoxification capacity. Protein extracts containing the soluble fractions were obtained after growth of the strain in the absence and presence of MnSO4 ...
November 7, 2018: Journal of Proteomics
María Cristina Romero-Rodríguez, Jesús V Jorrín-Novo, María Angeles Castillejo
By using two complementary proteomics, gel-based and gel-free (shotgun) approaches, the protein profiles of the non-orthodox forest tree species Quercus ilex seeds during germination and early seedling growth have been compared. Proteins were extracted from embryo axis, radicle and shoot tissues at different developmental stages. Proteins were subjected to one- and two-dimensional gel electrophoresis. A multivariate analysis (PCA) revealed that SDS-PAGE clearly separated germination (0-24 h post-imbibition), postgermination (72-216 h post-imbibition) and early seedling growth stages (2 weeks post-imbibition)...
November 5, 2018: Journal of Proteomics
Robin Korte, Daniela Oberleitner, Jens Brockmeyer
Food allergies are a growing worldwide concern and the contamination of products with food allergens represents a significant health risk to allergic consumers. With the introduction of reference doses, quantitative methods are needed for the monitoring of allergen levels, and the potential of LC-MS/MS is of hugely growing interest. In this study, we demonstrate that relevant food matrices (bakery products and chocolates) and thermal food processing substantially influence the quantification of 18 marker peptides from various nut and peanut allergens via targeted proteomics...
November 5, 2018: Journal of Proteomics
Marcello Manfredi, Eleonora Conte, Elettra Barberis, Arianna Buzzi, Elisa Robotti, Valeria Caneparo, Daniela Cecconi, Jessica Brandi, Ester Vanni, Marco Finocchiaro, Marco Astegiano, Marisa Gariglio, Emilio Marengo, Marco De Andrea
The diagnosis and management of Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is still challenging. There is no definitive gold standard diagnostic test, which is made on patient history and with endoscopic and histological findings. This study analyzed serum proteins and fatty acids using mass spectrometry-based techniques. Quantitation of serum proteins was performed by depleting 14 high-abundance proteins, followed by tryptic digestion and LC-MS analysis, while fatty acids were analyzed using GC-MS...
November 1, 2018: Journal of Proteomics
Angeline Mei Feng Oh, Choo Hock Tan, Kae Yi Tan, Naeem A Quraishi, Nget Hong Tan
The proteome of the Pakistani B. sindanus venom was investigated with reverse-phase HPLC and nano-ESI-LCMS/MS analysis. At least 36 distinct proteins belonging to 8 toxin protein families were identified. Three-finger toxin (3FTx), phospholipase A2 (including β-bungarotoxin A-chains) and Kunitz-type serine protease inhibitor (KSPI) were the most abundant, constituting ~95% of total venom proteins. The other toxin proteins of low abundance are snake venom metalloproteinase (SVMP), L-amino acid oxidase (LAAO), acetylcholinesterase (AChE), vespryn and cysteine-rich secretory protein (CRiSP)...
October 29, 2018: Journal of Proteomics
Shuangping Heng, Fengyi Chen, Chao Wei, Xianwen Li, Bin Yi, Chaozhi Ma, Jinxing Tu, Jinxiong Shen, Tingdong Fu, Jing Wen
Hau cytoplasmic male sterility (CMS) is a new type of CMS that was originally identified in Brassica juncea and subsequently transferred to B. napus and B. rapa. To further elucidate the molecular mechanism underlying hau CMS in B. napus, semithin section analysis and iTRAQ-based differential proteomic analysis were performed to compare the hau CMS and its maintainer line. Cytological analysis revealed that abnormal anther development in the hau CMS line was arrested during the differentiation of stamen archesporial cells...
October 29, 2018: Journal of Proteomics
Francisco Javier Fernández-Acero, Francisco Amil-Ruiz, María Jesús Durán-Peña, Rafael Carrasco, Carlos Fajardo, Palmira Guarnizo, Carlos Fuentes-Almagro, Roberto Andrés-Vallejo
Nannochloropsis gaditana is a non-flagellated microalgae that has been widely used for different purposes, mostly related with the industrial production of biofuels or aquiculture. However, in order to increase the economic viability of the obtained microalgae biomass from a production plant coupled to a coal power plant, a proteomic approach was initiated by using fresh and atomized microalgae samples, as the main used commercial forms. Above 51,000 high quality spectra were obtained per sample in the MS/MS analysis of whole proteome of N...
October 29, 2018: Journal of Proteomics
Claudia Fuente-Garcia, Noelia Aldai, Enrique Sentandreu, Mamen Oliván, Susana García-Torres, Daniel Franco, Carlos Zapata, Miguel Angel Sentandreu
Proteome changes derived from animals that have suffered pre-slaughter stress are a fact. In this study, Proteomic analysis was carried out on 20 bovine loin samples from Asturiana de los Valles and crossbreds cattle previously classified as normal and DFD meat at 24 h post-mortem using pH measurements. Sarcoplasmic sub-proteome of Longissimus thoracis at 24 h post-mortem was fractionated by the use of liquid isoelectric focusing (OFFGEL) in the pH range 3-10, followed by SDS-PAGE analysis of each retrieved fraction...
October 29, 2018: Journal of Proteomics
Cinzia Magagnotti, Gianpaolo Zerbini, Isabella Fermo, Rose Mary Carletti, Riccardo Bonfanti, Fabiana Vallone, Annapaola Andolfo
Despite research progresses, the chance to accurately predict the risk for diabetic nephropathy (DN) is still poor. So far, the first evidence of DN is micro-albuminuria, which is detected only 10-20 years after the onset of diabetes. Our goal is to develop new predictive tools of nephropathy starting from urine, which can be easily obtained using noninvasive procedures and it is directly related to kidney. Since it is reasonable to suppose that, in predisposed patients, the mechanisms leading to nephropathy start acting since the diabetes onset, urine from children with recent diagnosis of type 1 diabetes was subjected to proteomic analysis in comparison to age-matched controls...
October 24, 2018: Journal of Proteomics
Melissah Rowe, Sheri Skerget, Matthew A Rosenow, Timothy L Karr
Spermatozoa exhibit remarkable variability in size, shape, and performance. Our understanding of the molecular basis of this variation, however, is limited, especially in avian taxa. The zebra finch (Taeniopygia guttata) is a model organism in the study of avian sperm biology and sperm competition. Using LC-MS based proteomics, we identify and describe 494 proteins of the zebra finch sperm proteome (ZfSP). Gene ontology and associated bioinformatics analyses revealed a rich repertoire of proteins essential to sperm structure and function, including proteins linked to metabolism and energetics, as well as tubulin binding and microtubule related functions...
October 23, 2018: Journal of Proteomics
D R N Vos, I Jansen, M Lucas, M R L Paine, O J de Boer, S L Meijer, C D Savci-Heijink, H A Marquering, D M de Bruin, R M A Heeren, S R Ellis, B Balluff
Mass spectrometry imaging (MSI) has emerged as a powerful tool in biomedical research to reveal the localization of a broad scale of compounds ranging from metabolites to proteins in diseased tissues, such as malignant tumors. MSI is most commonly used for the two-dimensional imaging of tissues from multiple patients or for the three-dimensional (3D) imaging of tissue from a single patient. These applications are potentially introducing a sampling bias on a sample or patient level, respectively. The aim of this study is therefore to investigate the consequences of sampling bias on sample representativeness and on the precision of biomarker discovery for histological grading of human bladder cancers by MSI...
October 19, 2018: Journal of Proteomics
Tao Yun, Jionggang Hua, Weicheng Ye, Bin Yu, Zheng Ni, Liu Chen, Cun Zhang
Duck reovirus (DRV), a member of the genus Orthoreovirus in the family Reoviridae, was first isolated from Muscovy ducks. The disease associated with DRV causes great economic losses to the duck industry. However, the responses of duck (Cairna moschata) to the classical/novel DRV (C/NDRV) infections are largely unknown. To reveal the relationship of pathogenesis and immune response, the proteomes of duck spleen cells under the control and C/NDRV infections were compared. In total, 5986 proteins were identified, of which 5389 proteins were quantified...
October 16, 2018: Journal of Proteomics
Paulina Jackowiak, Angelika Lis, Magdalena Luczak, Ireneusz Stolarek, Marek Figlerowicz
Populations of small eukaryotic RNAs, in addition to relatively well recognized molecules such as miRNAs or siRNAs, also contain fragments derived from all classes of constitutively expressed non-coding RNAs. It has been recently demonstrated that the formation and accumulation of RNA fragments (RFs) is cell-/tissue-specific and depends on internal and external stimuli. Unfortunately, the mechanisms underlying RF biogenesis and function remain unclear. To better understand them, we employed RNA pull-down and mass spectrometry methods to characterize the interactions of seven RFs originating from tRNA, snoRNA and snRNA...
October 16, 2018: Journal of Proteomics
Solomon A Mekonnen, Laura M Palma Medina, Stephan Michalik, Marco G Loreti, Manuela Gesell Salazar, Jan Maarten van Dijl, Uwe Völker
Methicillin-resistant Staphylococcus aureus (MRSA) originally emerged in nosocomial settings and has subsequently spread into the community. In turn, community-associated (CA) MRSA lineages are nowadays introduced from the community into hospitals where they can cause hospital-associated (HA) infections. This raises the question of how the CA-MRSA lineages adapt to the hospital environment. Previous studies implicated particular virulence factors in the CA-behaviour of MRSA. However, we hypothesized that physiological changes may also impact staphylococcal epidemiology...
October 12, 2018: Journal of Proteomics
Fanwei Dai, Zhenjiang Wang, Zhiyi Li, Guoqing Luo, Yi Wang, Cuiming Tang
The aim of this work was to gain insights into the molecular mechanisms and dynamics of the mulberry (Morus atropurpurea) fruit response to Ciboria carunculoides infection. A transcriptomic and proteomic study was carried out based on RNA sequencing and isobaric tags for relative and absolute quantification analysis, respectively. These data were then validated using quantitative real-time PCR and multiple reaction monitoring assays. Comparative analyses revealed that 9.0% of the transcriptome and 20.8% of the proteome were differentially regulated after C...
October 10, 2018: Journal of Proteomics
Isma Belouah, Mélisande Blein-Nicolas, Thierry Balliau, Yves Gibon, Michel Zivy, Sophie Colombié
In bottom-up proteomics, data are acquired on peptides resulting from proteolysis. In XIC-based quantification, the quality of the estimation of protein abundance depends on how peptide data are filtered and on which quantification method is used to express peptide intensity as protein abundance. So far, these two questions have been addressed independently. Here, we studied to what extent the relative performances of the quantification methods depend on the filters applied to peptide intensity data. To this end, we performed a spike-in experiment using Universal Protein Standard to evaluate the performances of five quantification methods in five datasets obtained after application of four peptide filters...
October 10, 2018: Journal of Proteomics
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