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intact cell protein profiling

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https://www.readbyqxmd.com/read/29777870/profiling-modifications-for-glioblastoma-proteome-using-ultra-tolerant-database-search-are-the-peptide-mass-shifts-biologically-relevant-or-chemically-induced
#1
Irina A Tarasova, Peter M Chumakov, Sergei A Moshkovskii, Mikhail V Gorshkov
Peptide mass shifts were profiled using ultra-tolerant database search strategy for shotgun proteomics data sets of human glioblastoma cell lines demonstrating strong response to the type I interferon (IFNα-2b) treatment. The main objective of this profiling was revealing the cell response to IFN treatment at the level of protein modifications. To achieve this objective, statistically significant changes in peptide mass shift profiles between IFN treated and untreated glioblastoma samples were analyzed. Detailed analysis of MS/MS spectra allowed further interpretation of the observed mass shifts and differentiation between post-translational and artifact modifications...
May 16, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29706543/modulation-of-protein-interaction-states-through-the-cell-cycle
#2
Lingyun Dai, Tianyun Zhao, Xavier Bisteau, Wendi Sun, Nayana Prabhu, Yan Ting Lim, Radoslaw M Sobota, Philipp Kaldis, Pär Nordlund
Global profiling of protein expression through the cell cycle has revealed subsets of periodically expressed proteins. However, expression levels alone only give a partial view of the biochemical processes determining cellular events. Using a proteome-wide implementation of the cellular thermal shift assay (CETSA) to study specific cell-cycle phases, we uncover changes of interaction states for more than 750 proteins during the cell cycle. Notably, many protein complexes are modulated in specific cell-cycle phases, reflecting their roles in processes such as DNA replication, chromatin remodeling, transcription, translation, and disintegration of the nuclear envelope...
April 21, 2018: Cell
https://www.readbyqxmd.com/read/29703133/cross-site-comparison-of-ribosomal-depletion-kits-for-illumina-rnaseq-library-construction
#3
Zachary T Herbert, Jamie P Kershner, Vincent L Butty, Jyothi Thimmapuram, Sulbha Choudhari, Yuriy O Alekseyev, Jun Fan, Jessica W Podnar, Edward Wilcox, Jenny Gipson, Allison Gillaspy, Kristen Jepsen, Sandra Splinter BonDurant, Krystalynne Morris, Maura Berkeley, Ashley LeClerc, Stephen D Simpson, Gary Sommerville, Leslie Grimmett, Marie Adams, Stuart S Levine
BACKGROUND: Ribosomal RNA (rRNA) comprises at least 90% of total RNA extracted from mammalian tissue or cell line samples. Informative transcriptional profiling using massively parallel sequencing technologies requires either enrichment of mature poly-adenylated transcripts or targeted depletion of the rRNA fraction. The latter method is of particular interest because it is compatible with degraded samples such as those extracted from FFPE and also captures transcripts that are not poly-adenylated such as some non-coding RNAs...
March 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29689242/swi-snf-protein-expression-status-in-fumarate-hydratase-deficient-renal-cell-carcinoma-immunohistochemical-analysis-of-32-tumors-from-28-patients
#4
Abbas Agaimy, Mahul B Amin, Anthony J Gill, Bernt Popp, André Reis, Daniel M Berney, Cristina Magi-Galluzzi, Mathilde Sibony, Steven C Smith, Saul Suster, Kiril Trpkov, Ondřej Hes, Arndt Hartmann
Fumarate hydratase-deficient renal cell carcinoma (FH-RCC) is a rare, aggressive RCC type, originally described in the setting of hereditary leiomyomatosis and renal cell carcinoma (HLRCC) syndrome which is defined by germline FH gene inactivation. Inactivation of components of the SWI/SNF chromatin remodelling complex is involved in renal medullary carcinoma (SMARCB1/INI1 loss), clear cell RCC (PBRM1 loss) and in subsets of dedifferentiated RCC of clear cell, chromophobe and papillary types (loss of different SWI/SNF components)...
April 21, 2018: Human Pathology
https://www.readbyqxmd.com/read/29686423/clonal-cd4-t-cells-in-the-hiv-1-latent-reservoir-display-a-distinct-gene-profile-upon-reactivation
#5
Lillian B Cohn, Israel T da Silva, Renan Valieris, Amy S Huang, Julio C C Lorenzi, Yehuda Z Cohen, Joy A Pai, Allison L Butler, Marina Caskey, Mila Jankovic, Michel C Nussenzweig
Despite suppressive combination antiretroviral therapy (ART), latent HIV-1 proviruses persist in patients. This latent reservoir is established within 48-72 h after infection, has a long half-life1,2 , enables viral rebound when ART is interrupted, and is the major barrier to a cure for HIV-1 3 . Latent cells are exceedingly rare in blood (∼1 per 1 × 106 CD4+ T cells) and are typically enumerated by indirect means, such as viral outgrowth assays4,5 . We report a new strategy to purify and characterize single reactivated latent cells from HIV-1-infected individuals on suppressive ART...
April 23, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29684406/conservation-of-cardiac-l-type-ca-2-channels-and-their-regulation-in-drosophila-a-novel-genetically-pliable-channelopathic-model
#6
Worawan B Limpitikul, Meera C Viswanathan, Brian O'Rourke, David T Yue, Anthony Cammarato
Dysregulation of L-type Ca2+ channels (LTCCs) underlies numerous cardiac pathologies. Understanding their modulation with high fidelity relies on investigating LTCCs in their native environment with intact interacting proteins. Such studies benefit from genetic manipulation of endogenous channels in cardiomyocytes, which often proves cumbersome in mammalian models. Drosophila melanogaster, however, offers a potentially efficient alternative as it possesses a relatively simple heart, is genetically pliable, and expresses well-conserved genes...
April 20, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29663868/imaging-mass-spectrometry-of-endogenous-polypeptides-and-secondary-metabolites-from-galls-induced-by-root-knot-nematodes-in-tomato-roots
#7
Eder Alves Barbosa, Mauro Ferreira Bonfim Junior, Carlos Bloch, Thales Lima Rocha, Gilbert Engler, Janice de Almeida Engler
Nematodes are devastating pests that infect most cultivated plant species and cause considerable agricultural losses worldwide. The understanding of metabolic adjustments induced during plant-nematode interaction is crucial to generate resistant plants or to select more efficient molecules to fight against this pest. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has been used herein for in situ detection and mapping endogenous polypeptides and secondary metabolites from nematode-induced gall tissue...
April 17, 2018: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/29619505/microbial-and-genomic-characterization-of-geobacillus-thermodenitrificans-os27-a-marine-thermophile-that-degrades-diverse-raw-seaweeds
#8
Kenta Fujii, Yurie Tominaga, Jyumpei Okunaka, Hisashi Yagi, Takashi Ohshiro, Hirokazu Suzuki
Seaweeds are a nonlignocellulosic biomass, but they are often abundant in unique polysaccharides that common microbes can hardly utilize; therefore, polysaccharide degradation is key for the full utilization of seaweed biomass. Here, we isolated 13 thermophiles from seaweed homogenates that had been incubated at high temperature. All of the isolates were Gram-positive and preferentially grew at 60-70 °C. Most formed endospores and were tolerant to seawater salinity. Despite different sources, all isolates were identical regarding 16S rRNA gene sequences and were categorized as Geobacillus thermodenitrificans...
April 4, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29548334/influence-of-cell-type-and-cell-culture-media-on-the-propagation-of-foot-and-mouth-disease-virus-with-regard-to-vaccine-quality
#9
Veronika Dill, Bernd Hoffmann, Aline Zimmer, Martin Beer, Michael Eschbaumer
BACKGROUND: Suspension culture of BHK cells allows large-scale virus propagation and cost-efficient vaccine production, while the shift to animal-component-free cell culture media without serum is beneficial for the quality and downstream processing of the product. Foot-and-mouth disease virus is still endemic in many parts of the world and high-quality vaccines are essential for the eradication of this highly contagious and economically devastating disease. METHODS: Changes to the viral genome sequence during passaging in an adherent and a suspension cell culture system were compared and the impact of amino acid substitutions on receptor tropism, antigenicity and particle stability was examined...
March 16, 2018: Virology Journal
https://www.readbyqxmd.com/read/29523796/glyco-engineered-long-acting-fgf21-variant-with-optimal-pharmaceutical-and-pharmacokinetic-properties-to-enable-weekly-to-twice-monthly-subcutaneous-dosing
#10
Yan Weng, Tetsuya Ishino, Annette Sievers, Saswata Talukdar, Jeffrey R Chabot, Amy Tam, Weili Duan, Kelvin Kerns, Eric Sousa, Tao He, Alison Logan, Darwin Lee, Dongmei Li, Yingjiang Zhou, Barbara Bernardo, Alison Joyce, Mania Kavosi, Denise M O'Hara, Tracey Clark, Jie Guo, Craig Giragossian, Mark Stahl, Roberto A Calle, Ron Kriz, Will Somers, Laura Lin
Pharmacological administration of FGF21 analogues has shown robust body weight reduction and lipid profile improvement in both dysmetabolic animal models and metabolic disease patients. Here we report the design, optimization, and characterization of a long acting glyco-variant of FGF21. Using a combination of N-glycan engineering for enhanced protease resistance and improved solubility, Fc fusion for further half-life extension, and a single point mutation for improving manufacturability in Chinese Hamster Ovary cells, we created a novel FGF21 analogue, Fc-FGF21[R19V][N171] or PF-06645849, with substantially improved solubility and stability profile that is compatible with subcutaneous (SC) administration...
March 9, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29510164/an-ns1abp-like-gene-promotes-white-spot-syndrome-virus-infection-by-interacting-with-the-viral-envelope-protein-vp28-in-red-claw-crayfish-cherax-quadricarinatus
#11
Xiao-Lu Xie, Xue-Jiao Chang, Yan Gao, Dong-Li Li, Ling-Ke Liu, Man-Jun Liu, Ke-Jian Wang, Hai-Peng Liu
Influenza A virus non-structural-1A binding protein (named as Ns1abp) was originally identified as a host protein from human that bound to the viral NS-1 protein. In our previous study, the expression of an Ns1abp-like gene (denoted as CqNs1abp-like gene) was found to be up-regulated in a transcriptome library from the haematopoietic tissue (Hpt) cells of red claw crayfish Cherax quadricarinatus post white spot syndrome virus (WSSV) infection. To elucidate the role of CqNs1abp-like gene involved in WSSV infection, we cloned the CqNs1abp-like gene in which the open reading frame was 2232 bp, encoding 743 amino acids with two typical domains of one BTB (Broad-Complex, Tramtrack and Bric a brac) domain at N-terminal and six Kelch domains at C-terminal...
July 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29492200/proteomic-analysis-of-chicken-embryo-fibroblast-cells-infected-with-recombinant-h5n1-avian-influenza-viruses-with-and-without-ns1-eif4gi-binding-domain
#12
Kelei Guo, Xian Lin, Yongtao Li, Wei Qian, Zhong Zou, Huanchun Chen, Hongbo Zhou, Meilin Jin
Non-structural 1 (NS1) protein is a key virulence factor that regulates replication of influenza virus. A recombinant H5N1 virus lacking the eIF4GI-binding domain of NS1 (rNS1-SD30) exhibits significantly lower pathogenicity than H5N1 virus with an intact eIF4GI-binding domain (rNS1-wt). To further investigate this phenomenon, we performed comparative proteomics analyses to profile host proteins in chicken embryo fibroblasts (CEFs) infected with rNS1-wt and rNS1-SD30 viruses. In total, 81 differentially expressed (DE) proteins were identified at 12, 24, and 36 h post-infection...
February 2, 2018: Oncotarget
https://www.readbyqxmd.com/read/29484825/-one-pot-sample-processing-method-for-proteome-wide-analysis-of-microbial-cells-and-spores
#13
Bhagyashree Nandakishor Swarge, Winfried Roseboom, Linli Zheng, Wishwas R Abhyankar, Stanley Brul, Chris G de Koster, Leo J de Koning
PURPOSE: Bacterial endospores, the transmissible forms of pathogenic bacilli and clostridia, are heterogeneous multilayered structures composed of proteins. These proteins protect the spores against a variety of stresses, thus helping spore survival, and assist in germination, by interacting with the environment to form vegetative cells. Owing to the complexity, insolubility, and dynamic nature of spore proteins, it has been difficult to obtain their comprehensive protein profiles. EXPERIMENTAL DESIGN: The intact spores of Bacillus subtilis, Bacillus cereus, and Peptoclostridium difficile and their vegetative counterparts were disrupted by bead beating in 6 m urea under reductive conditions...
February 27, 2018: Proteomics. Clinical Applications
https://www.readbyqxmd.com/read/29467434/conformational-ige-epitope-mapping-of-der-p-2-and-the-evaluations-of-two-candidate-hypoallergens-for-immunotherapy
#14
Kavita Reginald, Fook Tim Chew
Epitope mapping of Der p 2, a clinically important dust-mite allergen is the first step in designing immunotherapy hypoallergen vaccine candidates. Twenty-one single alanine mutants of Der p 2 were generated and their secondary structure was analysed using circular dichroism spectra. Only one mutant, K96A resulted in a misfolded protein. All mutants were tested for serum IgE reactivity using serum from dust mite allergic individuals by immuno dot-blots. Mutations to five residues, N10, E25, K77, K96 and E102 consistently showed reduced IgE reactions compared to wild-type Der p 2, and therefore these residues constitute the major IgE epitopes of Der p 2...
February 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29382863/visualization-of-human-karyopherin-beta-1-importin-beta-1-interactions-with-protein-partners-in-mitotic-cells-by-co-immunoprecipitation-and-proximity-ligation-assays
#15
Laura Di Francesco, Annalisa Verrico, Italia Anna Asteriti, Paola Rovella, Pietro Cirigliano, Giulia Guarguaglini, Maria Eugenia Schininà, Patrizia Lavia
Karyopherin beta-1/Importin beta-1 is a conserved nuclear transport receptor, acting in protein nuclear import in interphase and as a global regulator of mitosis. These pleiotropic functions reflect its ability to interact with, and regulate, different pathways during the cell cycle, operating as a major effector of the GTPase RAN. Importin beta-1 is overexpressed in cancers characterized by high genetic instability, an observation that highlights the importance of identifying its partners in mitosis. Here we present the first comprehensive profile of importin beta-1 interactors from human mitotic cells...
January 30, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29364904/development-of-an-activity-based-probe-for-acyl-protein-thioesterases
#16
Megan Garland, Christopher J Schulze, Ian T Foe, Wouter A van der Linden, Matthew A Child, Matthew Bogyo
Protein palmitoylation is a dynamic post-translational modification (PTM) important for cellular functions such as protein stability, trafficking, localization, and protein-protein interactions. S-palmitoylation occurs via the addition of palmitate to cysteine residues via a thioester linkage, catalyzed by palmitoyl acyl transferases (PATs), with removal of the palmitate catalyzed by acyl protein thioesterases (APTs) and palmitoyl-protein thioesterases (PPTs). Tools that target the regulators of palmitoylation-PATs, APTs and PPTs-will improve understanding of this essential PTM...
2018: PloS One
https://www.readbyqxmd.com/read/29341427/lc-ms-based-intact-igg-and-released-glycan-analysis-for-bioprocessing-applications
#17
Tianhua Wang, Kong Meng Hoi, Henning Stöckmann, Corrine Wan, Lyn Chiin Sim, Noor Hayati Bte Kamari, Shi Jie Tay, Ce Huang Poo, Susanto Woen, Yuangsheng Yang, Peiqing Zhang, Pauline M Rudd
Robust plate based antibody glycan analysis platforms are urgently needed for biopharmaceutical development and manufacturing as well as for clinical biomarker research. A 96-well plate based workflow has been developed to analyze both intact IgG antibodies and released N-glycans using an Orbitrap Fusion Mass Spectrometer and an LC/MS method on the Waters UNIFI platform. Here we describe such a workflow including protein A purification, PNGaseF digestion, 2-AB labeling and SPE clean-up. The measured IgG glycan profile is consistent with that obtained from non-plate based method and commercial kit and has the advantage of less hands-on time...
January 17, 2018: Biotechnology Journal
https://www.readbyqxmd.com/read/29321630/engineered-mesenchymal-stem-cell-sheets-patches-prevents-postoperative-pancreatic-leakage-in-a-rat-model
#18
Seong-Ryong Kim, Hye-Jin Yi, Yu Na Lee, Ji Yoon Park, Robert M Hoffman, Teruo Okano, In Kyong Shim, Song Cheol Kim
Post-operative pancreatic fistula (POPF) following pancreatic resection is a life-threatening surgical complication. Cell sheets were prepared and harvested using temperature-responsive culture dishes and transplanted as patches to seal POPF. Two different mesenchymal stem cell (MSC) sheets were compared in terms of the preventative ability for pancreatic leakage in a rat model. Both rat adipose-derived stem cell (rADSC) and bone marrow-derived stem cell (rBMSC) sheets were transplanted. Those rADSC and rBMSC sheets are created without enzymes and thus maintained their cell-cell junctions and adhesion proteins with intact fibronectin on the basal side, as well as characteristics of MSCs...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29301241/comparative-venomics-of-the-vipera-ammodytes-transcaucasiana-and-vipera-ammodytes-montandoni-from-turkey-provides-insights-into-kinship
#19
Benjamin-Florian Hempel, Maik Damm, Bayram Göçmen, Mert Karis, Mehmet Anıl Oguz, Ayse Nalbantsoy, Roderich D Süssmuth
The Nose-horned Viper ( Vipera ammodytes ) is one of the most widespread and venomous snakes in Europe, which causes high frequent snakebite accidents. The first comprehensive venom characterization of the regional endemic Transcaucasian Nose-horned Viper ( Vipera ammodytes transcaucasiana ) and the Transdanubian Sand Viper ( Vipera ammodytes montandoni ) is reported employing a combination of intact mass profiling and bottom-up proteomics. The bottom-up analysis of both subspecies identified the major snake protein families of viper venoms...
January 1, 2018: Toxins
https://www.readbyqxmd.com/read/29217487/genistein-and-daidzein-treatments-differently-affect-uterine-homeostasis-in-the-ovary-intact-middle-aged-rats
#20
Ivana Jarić, Jasmina Živanović, Marko Miler, Vladimir Ajdžanović, Duško Blagojević, Nataša Ristić, Verica Milošević, Nataša Nestorović
This study aimed to investigate the effects of soy isoflavones, genistein (GEN) and daidzein, (DAI) on the uterine function in ovary-intact middle-aged rats. GEN and DAI (35mg/kg) were subcutaneously administrated to acyclic (12-month-old) Wistar females, daily, for 4weeks. Control group received either vehicle (olive oil and ethanol, 9:1) or remained intact. We found that GEN and DAI differently affect uterine morphophysiology. GEN significantly increased the uterine wet weight which was associated with hyperplastic changes, revealed by stereological and histomorphometrical analyses...
January 15, 2018: Toxicology and Applied Pharmacology
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