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Journal of Proteomics

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https://www.readbyqxmd.com/read/28535932/charting-novel-allergens-from-date-palm-pollen-phoenix-sylvestris-using-homology-driven-proteomics
#1
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/28533178/mucin-and-carbohydrate-stimulated-adhesion-and-subproteome-changes-of-the-probiotic-bacterium-lactobacillus-acidophilus-ncfm
#2
Hasan Ufuk Celebioglu, Sita Vaag Olesen, Kennie Prehn, Sampo J Lahtinen, Susanne Brix, Maher Abou Hachem, Birte Svensson
Adhesion to intestinal mucosa is a crucial property for probiotic bacteria. Adhesion is thought to increase host-bacterial interactions, thus potentially enabling health benefits to the host. Molecular events connected with adhesion and surface proteome changes were investigated for the probiotic Lactobacillus acidophilus NCFM cultured with established or emerging prebiotic carbohydrates as carbon source and in the presence of mucin, the glycoprotein of the epithelial mucus layer. Variation in adhesion to HT29-cells and mucin was associated with carbon source and mucin-induced subproteome abundancy differences...
May 19, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28528990/proteomics-survey-of-solanaceae-family-current-status-and-challenges-ahead
#3
Arindam Ghatak, Palak Chaturvedi, Puneet Paul, Ganesh Kumar Agrawal, Randeep Rakwal, Sun Tae Kim, Wolfram Weckwerth, Ravi Gupta
Solanaceae is one of the major economically important families of higher plants and has played a central role in human nutrition since the dawn of human civilization. Therefore, researchers have always been interested in understanding the complex behavior of Solanaceae members to identify key transcripts, proteins or metabolites, which are potentially associated with major traits. Proteomics studies have contributed significantly to understanding the physiology of Solanaceae members. A compilation of all the published reports showed that both gel-based (75%) and gel-free (25%) proteomic technologies have been utilized to establish the proteomes of different tissues, organs, and organelles under normal and adverse environmental conditions...
May 18, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28528009/identification-of-novel-haemophilus-parasuis-serovar-5-vaccine-candidates-using-an-immunoproteomic-approach
#4
Gang Li, Fang Xie, Jianjun Li, Jiao Liu, Dapeng Li, Yanhe Zhang, Paul R Langford, Yanwen Li, Siguo Liu, Chunlai Wang
Haemophilus parasuis is the aetiological agent of Glässer's disease, which is responsible for cases of fibrinous polyserositis, polyarthritis and meningitis. No vaccine is known that provides cross-protection against all serovars. The identification of novel immunoprotective antigens would undoubtedly contribute to the development of efficient subunit vaccines. In the present study, an immunoproteomic approach was used to analyze secreted proteins of H. parasuis and six proteins with high immunogenicity were identified...
May 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526530/insights-into-the-early-stage-of-pinus-nigra-arn-somatic-embryogenesis-using-discovery-proteomics
#5
Katarína Klubicová, Lubica Uvácková, Maksym Danchenko, Peter Nemecek, Ludovít Skultéty, Ján Salaj, Terézia Salaj
The somatic embryogenesis in conifers represents a suitable model of plant regeneration system facilitating studies of fundamental aspects of an early development as well as in vitro micropropagation. The aim of our study was to deeper understand the somatic embryogenesis in the conifer tree Pinus nigra Arn. Comparative proteomic analysis based on 2D-PAGE in 1) proliferating embryogenic tissues (E) initiated from immature zygotic embryos, 2) non-embryogenic calli (NEC) initiated from cotyledons of somatic seedlings of the same genotypes, 3) embryogenic tissues that lost the maturation capacity (E-L) of two cell lines (E362, E366)...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#6
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28522339/proteomics-analysis-of-fusarium-proliferatum-under-various-initial-ph-during-fumonisin-production
#7
Taotao Li, Liang Gong, Yong Wang, Feng Chen, Vijai Kumar Gupta, Qijie Jian, Xuewu Duan, Yueming Jiang
Fusarium proliferatum as a fungal pathogen can produce fumonisin which causes a great threat to animal and human health. Proteomic approach was a useful tool for investigation into mycotoxin biosynthesis in fungal pathogens. In this study, we analyzed the fumonisin content and mycelium proteins of Fusarium proliferatum cultivated under the initial pH5 and 10. Fumonisin production after 10days was significantly induced in culture condition at pH10 than pH5. Ninety nine significantly differently accumulated protein spots under the two pH conditions were detected using two dimensional polyacrylamide gel electrophoresis and 89 of these proteins were successfully identified by MALDI-TOF/TOF and LC-ESI-MS/MS analysis...
May 15, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28511789/salicylic-acid-mediated-growth-physiological-and-proteomic-responses-in-two-wheat-varieties-under-drought-stress
#8
Marisha Sharma, Sunil K Gupta, Baisakhi Majumder, Vivek K Maurya, Farah Deeba, Afroz Alam, Vivek Pandey
Salicylic acid (SA) induced drought tolerance can be a key trait for increasing and stabilizing wheat production. These SA induced traits were studied in two Triticum aestivum L. varieties; drought tolerant, Kundan and drought sensitive, Lok1 under two different water deficit regimes: and rehydration at vegetative and flowering stages. SA alleviated the negative effects of water stress on photosynthesis more in Kundan. SA induced defense responses against drought by increasing antioxidative enzymes and osmolytes (proline and total soluble sugars)...
May 13, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28506863/the-null-test-for-peptide-identification-algorithm-in-shotgun-proteomics
#9
Shu-Rong Zhang, Yi-Chu Shan, Hao Jiang, Jian-Hui Liu, Yuan Zhou, Li-Hua Zhang, Yu-Kui Zhang
The present research proposed general evaluation strategy named Null-Test for peptide identification algorithm in Shotgun proteomics. The Null-Test method based on random matching can be utilized to check whether the algorithm has a tendency to make a mistake or has potential bugs, faultiness, errors etc., and to validate the reliability of the identification algorithm. Unfortunately, none of the five famous identification software could pass the most stringent Null-Test. PatternLab had good performance in both Null-Test and routine search by making a good control on the overfitting with sound design...
May 12, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28502737/gel-free-label-free-proteomic-photosynthetic-and-biochemical-analysis-of-cowpea-vigna-unguiculata-l-walp-resistance-against-cowpea-severe-mosaic-virus-cpsmv
#10
Anna Lidia N Varela, Setsuko Komatsu, Xin Wang, Rodolpho G G Silva, Pedro Filho N Souza, Ana Karla M Lobo, Ilka M Vasconcelos, Joaquim A G Silveira, Jose T A Oliveira
Cowpea severe mosaic virus (CPSMV) causes significant losses in cowpea (Vigna unguiculata) production. In this present study biochemical, physiological, and proteomic analysis were done to identify pathways and defense proteins that are altered during the incompatible interaction between the cowpea genotype BRS-Marataoã and CPSMV. The leaf protein extracts from mock- (MI) and CPSMV-inoculated plantlets (V) were evaluated at 2 and 6days post-inoculation (DPI). Data support the assumptions that increases in biochemical (high hydrogen peroxide, antioxidant enzymes, and secondary compounds) and physiological responses (high photosynthesis index and chlorophyll content), confirmed by label-free comparative proteomic approach, in which quantitative changes in proteasome proteins, proteins related to photosynthesis, redox homeostasis, regulation factors/RNA processing proteins were observed may be implicated in the resistance of BRS-Marataoã to CPSMV...
May 11, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28499913/integration-of-gel-based-and-gel-free-proteomic-data-for-functional-analysis-of-proteins-through-soybean-proteome-database
#11
Setsuko Komatsu, Xin Wang, Xiaojian Yin, Yohei Nanjo, Hajime Ohyanagi, Katsumi Sakata
The Soybean Proteome Database (SPD) stores data on soybean proteins obtained with gel-based and gel-free proteomic techniques. The database was constructed to provide information on proteins for functional analyses. The majority of the data is focused on soybean (Glycine max 'Enrei'). The growth and yield of soybean are strongly affected by environmental stresses such as flooding. The database was originally constructed using data on soybean proteins separated by two-dimensional polyacrylamide gel electrophoresis, which is a gel-based proteomic technique...
May 9, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28495502/multipronged-quantitative-proteomics-reveals-serum-proteome-alterations-in-breast-cancer-intrinsic-subtypes
#12
Akshada Gajbhiye, Raju Dabhi, Khushman Taunk, Mashanipalya G Jagadeeshaprasad, Sourav RoyChoudhury, Anupama Mane, Santhakumari Bayatigeri, Koel Chaudhury, Manas K Santra, Srikanth Rapole
Being molecularly heterogeneous, breast cancer tends to be a complicated oncological disease with high incidence rates throughout the world. The primary aim of this study was to identify the set of serum proteins with discriminatory capabilities towards the four major subtypes of breast cancer. We employed multipronged quantitative proteomic approaches like 2D-DIGE, iTRAQ and SWATH-MS and identified 307 differentially regulated proteins. Luminal A subtype consisted of 24, Luminal B subtype 38, HER2 Enriched subtype 17 and Triple negative breast cancer subtype 10 differentially regulated subtype specific proteins...
May 8, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28495501/semen-modulated-secretory-activity-of-oviductal-epithelial-cells-is-linked-to-cellular-proteostasis-network-remodeling-proteomic-insights-into-the-early-phase-of-interaction-in-the-oviduct-in-vivo
#13
Birgit Steinberger, Hans Yu, Theodor Brodmann, Daniela Milovanovic, Ursula Reichart, Urban Besenfelder, Konstantin Artemenko, Ebrahim Razzazi-Fazeli, Gottfried Brem, Corina Mayrhofer
The oviductal epithelium is crucial for the integrity of the female organ. Previously we got evidence that the surface proteome of oviductal epithelial cells (Oecs) is promptly altered in response to insemination and thus suggested that this early phase plays a notable regulatory role in maintaining cellular function. This study further aimed to assess the effect of semen on the cellular and molecular mechanisms in rabbit Oecs. A quantitative gel-based proteomic approach was applied to analyze changes at three time points (0h, 1h, 2h) after intrauterine insemination (IUI) compared to time matched controls...
May 8, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28483534/comparative-secretomic-analysis-of-lignocellulose-degradation-by-lentinula-edodes-grown-on-microcrystalline-cellulose-lignosulfonate-and-glucose
#14
Yingli Cai, Yuhua Gong, Wei Liu, Yue Hu, Lianfu Chen, Lianlian Yan, Yan Zhou, Yinbing Bian
Lentinula edodes has the potential to degrade woody and nonwoody lignocellulosic biomass. However, the mechanism of lignocellulose degradation by L. edodes is unclear. The aim of this work is to explore the profiling of soluble secreted proteins involved in lignocellulose degradation in L. edodes. For that, we compared the secretomes of L. edodes grown on microcrystalline cellulose, cellulose with lignosulfonate and glucose. Based on nanoliquid chromatography coupled with tandem mass spectrometry of whole-protein hydrolysate, 230 proteins were identified...
May 5, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28479398/isolation-and-characterization-of-conohyal-p1-a-hyaluronidase-from-the-injected-venom-of-conus-purpurascens
#15
Carolina Mӧller, Evan Clark, Helena Safavi-Hemani, Anthony DeCaprio, Frank Marí
Hyaluronidases are ubiquitous enzymes commonly found in venom and their main function is to degrade hyaluran, which is the major glycosaminoglycan of the extracellular matrix in animal tissues. Here we describe the purification and characterization of a 60kDa hyaluronidase found in the injected venom from Conus purpurascens, Conohyal-P1. Using a combined strategy based on transcriptomic and proteomic analysis, we determined the Conohyal-P1 sequence. Conohyal-P1 has conserved consensus catalytic and positioning domain residues characteristic of hyaluronidases and a C-terminus EGF-like domain...
May 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28478308/deep-coverage-of-the-beer-proteome
#16
Martina Grochalová, Hana Konečná, Karel Stejskal, David Potěšil, Danuše Fridrichová, Eva Srbová, Kateřina Ornerová, Zbyněk Zdráhal
We adopted an approach based on peptide immobilized pH gradient-isoelectric focusing (IPG-IEF) separation, coupled with LC-MS/MS, in order to maximize coverage of the beer proteome. A lager beer brewed using traditional Czech technology was degassed, desalted and digested. Tryptic peptides were separated by isoelectric focusing on an immobilized pH gradient strip and, after separation, the gel strip was divided into seven equally sized parts. Peptides extracted from gel fractions were analyzed by LC-MS/MS. This approach resulted in a three-fold increase in the number of proteins identified (over 1700) when compared to analysis of unfractionated beer processed by a filter-aided sample preparation (FASP)...
May 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28478307/differential-representation-of-albumins-and-globulins-during-grain-development-in-durum-wheat-and-its-possible-functional-consequences
#17
Simona Arena, Chiara D'Ambrosio, Monica Vitale, Fiorella Mazzeo, Gianfranco Mamone, Luigia Di Stasio, Marco Maccaferri, Pasquale Luca Curci, Gabriella Sonnante, Nicola Zambrano, Andrea Scaloni
Durum wheat (Triticum turgidum ssp. durum (Desf.) Husn.) is an economically important crop used for the production of semolina, which is the basis of pasta and other food products. Its grains provide proteins and starch for human consumption. Grain development is a key process in wheat physiology; it is highly affected by a number of enzymes that control the metabolic processes governing accumulation of starch and storage proteins and ultimately grain weight. Most of these enzymes are present in the albumin/globulin grain fraction, which represents about a quarter of total seed proteins...
May 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28478306/proteomic-profiling-reveals-dna-damage-nucleolar-and-ribosomal-stress-are-the-main-responses-to-oxaliplatin-treatment-in-cancer-cells
#18
Tomas Ozdian, Dusan Holub, Zuzana Maceckova, Lakshman Varanasi, Gabriela Rylova, Jiri Rehulka, Jana Vaclavkova, Hanus Slavik, Pavel Moudry, Pawel Znojek, Jarmila Stankova, Juan Bautista de Sanctis, Marian Hajduch, Petr Dzubak
Oxaliplatin is widely used to treat colorectal cancer in both palliative and adjuvant settings. It is also being tested for use in treating hematological, esophageal, biliary tract, pancreatic, gastric, and hepatocellular cancers. Despite its routine clinical use, little is known about the responses it induces in cancer cells. Therefore the whole-cell proteomics study was conducted to characterize the cellular response induced by oxaliplatin. Chemosensitive CCRF-CEM cells were treated with oxaliplatin at 29...
May 3, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28476572/venomics-of-bungarus-caeruleus-indian-krait-comparable-venom-profiles-variable-immunoreactivities-among-specimens-from-sri-lanka-india-and-pakistan
#19
Angeline Mei Feng Oh, Choo Hock Tan, Gnanathasan Christeine Ariaranee, Naeem Quraishi, Nget Hong Tan
The Indian krait (Bungarus caeruleus) is one of the "Big Four" venomous snakes widely distributed in South Asia. The present venomic study reveals that its venom (Sri Lankan origin) is predominated by phospholipases A2 (68.2% of total proteins), in which at least 8.3% are presynaptically-acting β-bungarotoxins. Three-finger toxins (19.0%) are the second most abundant, comprising 15.6% κ-neurotoxins, the potent postsynaptically-acting long neurotoxins. Comparative chromatography showed that venom samples from Sri Lanka, India and Pakistan did not exhibit significant variation...
May 2, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28461040/structural-characterisation-of-medically-relevant-protein-assemblies-by-integrating-mass-spectrometry-with-computational-modelling
#20
REVIEW
Argyris Politis, Carla Schmidt
Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and assemblies which makes it universal among the conventional structural techniques. In this review we summarise recent advances and challenges in structural mass spectrometric techniques. We describe how the combination of the different mass spectrometry-based methods with computational strategies enable structural models at molecular levels of resolution...
April 28, 2017: Journal of Proteomics
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