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Proteomics

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https://www.readbyqxmd.com/read/28330297/differential-expression-and-characterization-of-cypermethrin-degrading-potential-proteins-in-bacillus-thuringiensis-strain-sg4
#1
Pankaj, Geeta Negi, Saurabh Gangola, Priyanka Khati, Govind Kumar, Anjana Srivastava, Anita Sharma
A cypermethrin-degrading bacterium (SG4) was isolated from the pesticide-contaminated soil in the agricultural field of the crop research centre of the University, and characterized as Bacillus thuringiensis strain, SG4. The bacterium degraded 78.9 % of cypermethrin (50 ppm) in 15 days when grown in a minimal medium. To understand the functional proteins of cypermethrin degradation in Bacillus thuringiensis strain SG4, a comparative proteomic analysis was performed in the presence/absence of cypermethrin after 5 days of incubation in minimal medium...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329770/antigen-presentation-profiling-reveals-recognition-of-lymphoma-immunoglobulin-neoantigens
#2
Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M Newman, Debra K Czerwinski, Victoria E H Carlton, Martin Moorhead, Malek Faham, Holbrook E Kohrt, Jan Carette, Michael R Green, Mark M Davis, Ronald Levy, Joshua E Elias, Ash A Alizadeh
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329269/proteomics-highlights-decrease-of-matricellular-proteins-in-left-ventricular-assist-device-therapy%C3%A2
#3
Jasmin Hasmik Shahinian, Bettina Mayer, Stefan Tholen, Kerstin Brehm, Martin L Biniossek, Hannah Füllgraf, Selina Kiefer, Ulrike Heizmann, Claudia Heilmann, Florian Rüter, Martin Grapow, Oliver Thomas Reuthebuch, Friedrich Eckstein, Friedhelm Beyersdorf, Oliver Schilling, Matthias Siepe
OBJECTIVES: We investigated the impact of mechanical unloading with a left ventricular assist device (LVAD) on the myocardial proteome. METHODS: We collected 11 patient-matched samples of myocardial left ventricular tissue of patients with non-ischaemic dilate cardiomyopathy, harvested at time of LVAD implant ('pre-LVAD') and heart transplant ('post-LVAD'). Samples were studied by quantitative proteomics. Further we performed histological assessment of deposited collagens and immune infiltration in both pre- and post-LVAD samples...
February 20, 2017: European Journal of Cardio-thoracic Surgery
https://www.readbyqxmd.com/read/28329008/insulin-and-diet-induced-changes-in-the-ubiquitin-modified-proteome-of-rat-liver
#4
Shilpa R Nagarajan, Amanda E Brandon, Jessie A McKenna, Harrison C Shtein, Thinh Q Nguyen, Eurwin Suryana, Philip Poronnik, Gregory J Cooney, Darren N Saunders, Andrew J Hoy
Ubiquitin is a crucial post-translational modification regulating numerous cellular processes, but its role in metabolic disease is not well characterized. In this study, we identified the in vivo ubiquitin-modified proteome in rat liver and determined changes in this ubiquitome under acute insulin stimulation and high-fat and sucrose diet-induced insulin resistance. We identified 1267 ubiquitinated proteins in rat liver across diet and insulin-stimulated conditions, with 882 proteins common to all conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28328971/mapping-the-n-linked-glycosites-of-rice-oryza-sativa-l-germinating-embryos
#5
Jiezheng Ying, Juan Zhao, Yuxuan Hou, Yifeng Wang, Jiehua Qiu, Zhiyong Li, Xiaohong Tong, Zhaomei Shi, Jun Zhu, Jian Zhang
Germination is a key event in the angiosperm life cycle. N-glycosylation of proteins is one of the most common post-translational modifications, and has been recognized to be an important regulator of the proteome of the germinating embryo. Here, we report the first N-linked glycosites mapping of rice embryos during germination by using a hydrophilic interaction chromatography (HILIC) glycopeptides enrichment strategy associated with high accuracy mass spectrometry identification. A total of 242 glycosites from 191 unique proteins was discovered...
2017: PloS One
https://www.readbyqxmd.com/read/28328168/intrastriatal-transplantation-of-human-neural-stem-cells-restores-the-impaired-subventricular-zone-in-parkinsonian-mice
#6
Fuxing Zuo, Feng Xiong, Xia Wang, Xueyuan Li, Renzhi Wang, Wei Ge, Xinjie Bao
Cell replacement therapy using neural stem cells (NSCs) transplantation has recently emerged as a promising method of Parkinson's disease (PD) treatment; however, the underlying mechanisms are not fully understood. To gain new insights into the mechanisms of 6-hydroxydopamine (6-OHDA)-induced lesioning and therapeutic efficacy of human NSCs (hNSCs) transplantation, the striatum (ST) of intrastriatal 6-OHDA-injected parkinsonian mice were unilaterally engrafted with undifferentiated hNSCs. A high-throughput quantitative proteomic approach was used to characterize the proteome profiles of PD-related brain regions such as the SN, ST, olfactory bulb (OB), and subventricular zone (SVZ) in these mice...
March 22, 2017: Stem Cells
https://www.readbyqxmd.com/read/28327990/estimating-the-total-number-of-phosphoproteins-and-phosphorylation-sites-in-eukaryotic-proteomes
#7
Panayotis Vlastaridis, Pelagia Kyriakidou, Anargyros Chaliotis, Yves Van de Peer, Stephen G Oliver, Grigoris D Amoutzias
Background: Phosphorylation is the most frequent post-translational modification made to proteins and may regulate protein activity as either a molecular digital switch or a rheostat. Despite the cornucopia of high-throughput (HTP) phosphoproteomic data in the last decade, it remains unclear how many proteins are phosphorylated and how many phosphorylation sites (p-sites) can exist in total within a eukaryotic proteome. We present the first reliable estimates of the total number of phosphoproteins and phosphorylation sites (p-sites), for four eukaryotes (human, mouse, Arabidopsis, and yeast)...
January 7, 2017: GigaScience
https://www.readbyqxmd.com/read/28327890/draft-genome-of-the-honey-bee-ectoparasitic-mite-tropilaelaps-mercedesae-is-shaped-by-the-parasitic-life-history
#8
Xiaofeng Dong, Stuart D Armstrong, Dong Xia, Benjamin L Makepeace, Alistair C Darby, Tatsuhiko Kadowaki
Background: The number of managed honey bee colonies has considerably decreased in many developed countries in recent years and ectoparasitic mites are considered as major threats to honey bee colonies and health. However, their general biology remains poorly understood. Results: We sequenced the genome of Tropilaelaps mercedesae , the prevalent ectoparasitic mite infesting honey bees in Asia and predicted 15,190 protein-coding genes which were well supported by the mite transcriptomes and proteomic data...
February 22, 2017: GigaScience
https://www.readbyqxmd.com/read/28327659/the-immunosuppressant-mycophenolic-acid-alters-nucleotide-and-lipid-metabolism-in-an-intestinal-cell-model
#9
Svenja Heischmann, Monika Dzieciatkowska, Kirk Hansen, Dieter Leibfritz, Uwe Christians
The study objective was to elucidate the molecular mechanisms underlying the negative effects of mycophenolic acid (MPA) on human intestinal cells. Effects of MPA exposure and guanosine supplementation on nucleotide concentrations in LS180 cells were assessed using liquid chromatography-mass spectrometry. Proteomics analysis was carried out using stable isotope labeling by amino acids in cell culture combined with gel-based liquid chromatography-mass spectrometry and lipidome analysis using (1)H nuclear magnetic resonance spectroscopy...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327460/comprehensive-proteomic-characterization-of-stem-cell-derived-extracellular-matrices
#10
Héloïse Ragelle, Alexandra Naba, Benjamin L Larson, Fangheng Zhou, Miralem Prijić, Charles A Whittaker, Amanda Del Rosario, Robert Langer, Richard O Hynes, Daniel G Anderson
In the stem-cell niche, the extracellular matrix (ECM) serves as a structural support that additionally provides stem cells with signals that contribute to the regulation of stem-cell function, via reciprocal interactions between cells and components of the ECM. Recently, cell-derived ECMs have emerged as in vitro cell culture substrates to better recapitulate the native stem-cell microenvironment outside the body. Significant changes in cell number, morphology and function have been observed when mesenchymal stem cells (MSC) were cultured on ECM substrates as compared to standard tissue-culture polystyrene (TCPS)...
March 7, 2017: Biomaterials
https://www.readbyqxmd.com/read/28327085/a-shift-in-the-virulence-potential-of-corynebacterium-pseudotuberculosis-biovar-ovis-after-passage-in-a-murine-host-demonstrated-through-comparative-proteomics
#11
Wanderson M Silva, Fernanda A Dorella, Siomar C Soares, Gustavo H M F Souza, Thiago L P Castro, Núbia Seyffert, Henrique Figueiredo, Anderson Miyoshi, Yves Le Loir, Artur Silva, Vasco Azevedo
BACKGROUND: Corynebacterium pseudotuberculosis biovar ovis, a facultative intracellular pathogen, is the etiologic agent of caseous lymphadenitis in small ruminants. During the infection process, C. pseudotuberculosis changes its gene expression to resist different types of stresses and to evade the immune system of the host. However, factors contributing to the infectious process of this pathogen are still poorly documented. To better understand the C. pseudotuberculosis infection process and to identify potential factors which could be involved in its virulence, experimental infection was carried out in a murine model using the strain 1002_ovis and followed by a comparative proteomic analysis of the strain before and after passage...
March 22, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28326926/potential-protein-biomarkers-for-burning-mouth-syndrome-discovered-by-quantitative-proteomics
#12
Eoon Hye Ji, Cynthia Diep, Tong Liu, Hong Li, Robert Merrill, Diana Messadi, Shen Hu
Burning mouth syndrome (BMS) is a chronic pain disorder characterized by severe burning sensation in normal looking oral mucosa. Diagnosis of BMS remains to be a challenge to oral healthcare professionals because the method for definite diagnosis is still uncertain. In this study, a quantitative saliva proteomic analysis was performed in order to identify target proteins in BMS patients' saliva that may be used as biomarkers for simple, non-invasive detection of the disease. By using isobaric tags for relative and absolute quantitation labeling and liquid chromatography-tandem mass spectrometry to quantify 1130 saliva proteins between BMS patients and healthy control subjects, we found that 50 proteins were significantly changed in the BMS patients when compared to the healthy control subjects ( p ≤ 0...
January 2017: Molecular Pain
https://www.readbyqxmd.com/read/28326097/different-proteome-profiles-between-male-and-female-populus-cathayana-exposed-to-uv-b-radiation
#13
Yunxiang Zhang, Lihua Feng, Hao Jiang, Yuanbin Zhang, Sheng Zhang
With increasing altitude, solar UV-B radiation is enhanced. Based on the phenomenon of male-biased sex ratio of Populus cathayana Rehder in high altitude alpine area, we hypothesized that males have a faster and more sophisticated responsive mechanism to high UV-B radiation than that of females. Our previous studies have shown sexually different responses to high UV-B radiation were existed in P. cathayana at the morphological, physiological, and transcriptomic levels. However, the responses at the proteomic level remain unclear...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28326073/rhoptry-protein-5-rop5-is-a-key-virulence-factor-in-neospora-caninum
#14
Lei Ma, Jing Liu, Muzi Li, Yong Fu, Xiao Zhang, Qun Liu
Neospora caninum, of the Apicomplexa phylum, is a common cause of abortions in cattle and nervous system dysfunction in dogs. Rhoptry proteins of Apicomplexa play an important role in virulence. The objectives of this study were to study functions of NcROP5 in N. caninum by deleting the NcROP5 gene from the wild Nc-1 strain. We selected NcROP5 in ToxoDB and successfully constructed an NcROP5 gene-deleted vector, pTCR-NcROP5-CD KO. Then we screened the NcROP5 knockout strains (ΔNcROP5) at the gene, protein and transcription levels...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28325942/comparative-genomics-reveals-contraction-in-olfactory-receptor-genes-in-bats
#15
Georgia Tsagkogeorga, Steven Müller, Christophe Dessimoz, Stephen J Rossiter
Gene loss and gain during genome evolution are thought to play important roles in adaptive phenotypic diversification. Among mammals, bats possess the smallest genomes and have evolved the unique abilities of powered flight and laryngeal echolocation. To investigate whether gene family evolution has contributed to the genome downsizing and phenotypic diversification in this group, we performed comparative evolutionary analyses of complete proteome data for eight bat species, including echolocating and non-echolocating forms, together with the proteomes of 12 other laurasiatherian mammals...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28325852/extended-multiplexing-of-tmt-labeling-reveals-age-and-high-fat-diet-specific-proteome-changes-in-mouse-epididymal-adipose-tissue
#16
Deanna L Plubell, Phillip A Wilmarth, Yuqi Zhao, Alexandra M Fenton, Jessica Minnier, Ashok P Reddy, John Klimek, Xia Yang, Larry L David, Nathalie Pamir
The lack of high-throughput methods to analyze the adipose tissue protein composition limits our understanding of the protein networks responsible for age and diet related metabolic response. We have developed an approach using multiple-dimension liquid chromatography tandem mass spectrometry and extended multiplexing (24 biological samples) with TMT labeling to analyze proteomes of epididymal adipose tissues isolated from mice fed either low or high fat diet for a short or a long-term, and from mice that aged on low vs...
March 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28325629/towards-integrating-extracellular-matrix-and-immunological-pathways
#17
David F Boyd, Paul G Thomas
The extracellular matrix (ECM) is a complex and dynamic structure made up of an estimated 300 different proteins. The ECM is also a rich source of cytokines and growth factors in addition to numerous bioactive ECM degradation products that influence cell migration, proliferation, and differentiation. The ECM is constantly being remodeled during homeostasis and in a wide range of pathological contexts. Changes in the ECM modulate immune responses, which in turn regulate repair and regeneration of tissues. Here, we review the many components of the ECM, enzymes involved in ECM remodeling, and the signals that feed into immunological pathways in the context of a dynamic ECM...
March 18, 2017: Cytokine
https://www.readbyqxmd.com/read/28325592/intersexuality-in-aquatic-invertebrates-prevalence-and-causes
#18
REVIEW
Tiago F Grilo, Rui Rosa
This review is the first assembling information on intersexuality in aquatic invertebrates, from freshwater to estuarine and marine environments. Intersex is a condition whereby an individual of a gonochorist (separate sexes) species has oocytes or distinct stages of spermatogonia, at varying degrees of development, within the normal gonad of the opposite gender (i.e. spermatocytes in the ovary or oocytes in the testis), often involving alterations in the gonadal structure, reproductive tract or external genitalia...
March 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28324493/introduction-to-telomeres-and-telomerase
#19
Zhou Songyang
Telomeres are ends of chromosomes that play an important part in the biology of eukaryotic cells. Continued optimization and development of technologies have enabled researchers to probe the mechanisms of telomere maintenance in ever expanding areas. A combination of molecular, genetic, proteomic, and biochemical approaches has revealed the complex and coordinated action of telomerase and telomere-associated proteins. The length and integrity of telomeres are maintained to prevent telomere dysfunction, which has been linked to senescence, aging, disease, and cancer...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324178/complete-genome-sequence-analysis-of-a-novel-staphylococcus-phage-stap1-and-proposal-of-a-new-species-in-the-genus-silviavirus
#20
Amal Senevirathne, Kuntal Ghosh, Eunjung Roh, Kwang-Pyo Kim
Bacteriophage StAP1 was isolated from a soil sample infecting Staphylococcus aureus and S. xylosus. Its genome was found to be 135,502 base pairs (bp) long with 30.00 mol% G+C content and 192 open reading frames. While no tRNA encoding genes were identified, 7 mobile elements were found to interrupt five StAP1 open reading frames. Comparative genomic and proteomic analysis consistently supports the establishment of a new species in the genus Silviavirus.
March 21, 2017: Archives of Virology
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