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proteomics analysis tools

Jeremy F Taylor, Robert D Schnabel, Peter Sutovsky
Whole genome sequencing has identified millions of bovine genetic variants; however, there is currently little understanding about which variants affect male fertility. It is imperative that we begin to link detrimental genetic variants to sperm phenotypes via the analysis of semen samples and measurement of fertility for bulls with alternate genotypes. Artificial insemination (AI) bulls provide a useful model system because of extensive fertility records, measured as sire conception rates (SCR). Genetic variants with moderate to large effects on fertility can be identified by sequencing the genomes of fertile and subfertile or infertile sires identified with high or low SCR as adult AI bulls or yearling bulls that failed Breeding Soundness Evaluation...
February 10, 2018: Animal Reproduction Science
Clara Fernández-Álvarez, Yolanda Torres-Corral, Ysabel Santos
In the present study, the potential of serological methods, the repetitive extragenic palindromic PCR (REP-PCR) and the enterobacterial repetitive intergenic consensus sequence PCR (ERIC-PCR) for the typing of the species Tenacibaculum maritimum, Tenacibaculum soleae and Tenacibaculum discolor was evaluated. Moreover, molecular and proteomic techniques were used to assess variability among strains belonging to different serotypes, as well as isolated from different host species and geographical areas. Slide agglutination and dot-blot assays demonstrated the lack of immunological relationships among Tenacibaculum species analyzed...
February 16, 2018: Applied Microbiology and Biotechnology
Rita Ferreira, Fábio Trindade, Rui Vitorino
Proteomics is a technology that allows to decipher the molecular networks involved in the regulation of biological processes such as spermatogenesis. Sertoli cells (SCs) are key players in the paracrine control of this process. Envisioning to increase the knowledge on the molecular networks harbored in SCs, we propose a methodology based on GeLC-MS/MS for the characterization of these cells' proteome. Proteins are separated by SDS-PAGE hyphenated to HPLC and identified by mass spectrometry. The integration of data with bioinformatics tools such as ClueGO + CluePedia from Cytoscape allows the identification of the biological pathways more prevalent in SCs, and that might be modulated by pathophysiological conditions...
2018: Methods in Molecular Biology
Ke Sherry Li, Liuqing Shi, Michael L Gross
Assessment of protein structure and interaction is crucial for understanding protein structure/function relationships. Compared to high-resolution structural tools, including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, and traditional low-resolution methods, such as circular dichroism, UV-vis, and florescence spectroscopy, mass spectrometry (MS)-based protein footprinting affords medium-to-high resolution (i.e., regional and residue-specific insights) by taking advantage of proteomics methods focused on the primary structure...
February 16, 2018: Accounts of Chemical Research
Fusako Kito, Rieko Oyama, Yoko Takai, Marimu Sakumoto, Kumiko Shiozawa, Zhiwei Qiao, Takenori Uehara, Akihiko Yoshida, Akira Kawai, Tadashi Kondo
Synovial sarcoma is an aggressive mesenchymal malignancy characterized by unique gene fusions. Tissue culture cells are essential tools for further understanding tumorigenesis and anti-cancer drug development; however, only a limited number of well-characterized synovial sarcoma cell lines exist. Thus, the objective of this study was to establish a patient-derived synovial sarcoma cell line. We established a synovial sarcoma cell line from tumor tissue isolated from a 72-year-old female patient. Prepared cells were analyzed for the presence of gene fusions by fluorescence in situ hybridization, RT-PCR, and karyotyping...
February 15, 2018: Human Cell
Xiaofei Zhang, Arne H Smits, Gabrielle Ba van Tilburg, Huib Ovaa, Wolfgang Huber, Michiel Vermeulen
Ubiquitin-binding proteins play an important role in eukaryotes by translating differently linked polyubiquitin chains into proper cellular responses. Current knowledge about ubiquitin-binding proteins and ubiquitin linkage-selective interactions is mostly based on case-by-case studies. We have recently reported a method called ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS), which enables comprehensive identification of ubiquitin interactors for all ubiquitin linkages from crude cell lysates...
March 2018: Nature Protocols
Stefan A Arnold, Shirley A Müller, Claudio Schmidli, Anastasia Syntychaki, Luca Rima, Mohamed Chami, H Stahlberg, Kenneth N Goldie, T Braun
This review compares and discusses conventional versus miniaturized specimen preparation methods for transmission electron microscopy (EM). The progress brought by direct electron detector cameras, software developments and automation have transformed transmission cryo-electron microscopy (cryo-EM) and made it an invaluable high-resolution structural analysis tool. In contrast, EM specimen preparation has seen very little progress in the last decades and is now one of the main bottlenecks in cryo-EM. Here, we discuss the challenges faced by specimen preparation for single particle EM, highlight current developments, and show the opportunities resulting from the advanced miniaturized and microfluidic sample grid preparation methods described, such as visual proteomics and time-resolved cryo-EM studies...
February 14, 2018: Proteomics
L García-Calvo, R V Ullán, M Fernández-Aguado, A M García-Lino, R Balaña-Fouce, C Barreiro
Lignocellulosic plant biomass is the most abundant carbon source in the planet, which makes it a potential substrate for biorefinery. It consists of polysaccharides and other molecules with applications in pharmaceutical, food and feed, cosmetics, paper and textile industries. The exploitation of these resources requires the hydrolysis of the plant cell wall, which is a complex process. Aiming to discover novel fungal natural isolates with lignocellulolytic capacities, a screening for feruloyl esterase activity was performed in samples taken from different metal surfaces...
February 10, 2018: Journal of Proteomics
Fangqiong Li, Dongxiao Zhao, Suwen Yang, Juan Wang, Qin Liu, Xin Jin, Wei Wang
BACKGROUND/AIMS: Triptolide (TP) is a diterpenoid triepoxide extracted from the traditional Chinese medical herb Tripterygium wilfordii that exerts prominent broad-spectrum anticancer activity to repress proliferation and induce cancer cell apoptosis through various molecular pathways. We previously observed that TP inhibits the progression of A549 cells and pancreatic cancer cells (PNCA-1) in vitro. However, the complex molecular mechanism underlying the anticancer activity of TP is not well understood...
February 2, 2018: Cellular Physiology and Biochemistry
Herlon Victor Rodrigues Silva, Paula Rodriguez-Villamil, Francisco Felipe de Magalhães, Thalles Gothardo Pereira Nunes, Luana Azevedo de Freitas, Leandro Rodrigues Ribeiro, Alexandre Rodrigues Silva, Arlindo A Moura, Lúcia Daniel Machado da Silva
Ring-tailed coati is listed as a species of least concern in the International Union for Conservation of Nature (IUCN) Red List, however, there has been a sharp decline in their population. The present study was conducted to evaluate the major proteins of both seminal plasma and sperm in ring-tailed coatis. Semen sample was collected from three adult coatis and evaluated for their morphological characteristics. Further, the sample was centrifuged to separate spermatozoa from seminal plasma, and then stored in liquid nitrogen...
January 31, 2018: Theriogenology
Biswapriya B Misra
Proteomics data processing, annotation, and analysis can often lead to major hurdles in large-scale high throughput bottom-up proteomics experiments. Given the recent rise in protein-based big datasets being generated, efforts in in silico tool development occurrences have had an unprecedented increase; so much so, that it has become increasingly difficult to keep track of all the advances in a particular academic year. However, these tools benefit the proteomics community in circumventing critical issues in data analysis and visualization, as these continually developing one-source and community-developed tools hold potential in future research efforts...
February 8, 2018: Electrophoresis
Juliane Schneider, Tilo Heydel, Linus Klasen, Michael Pees, Wieland Schrödl, Volker Schmidt
Fungal infections in captive as well as in free-living reptiles caused by emerging obligate pathogenic fungi appear with increasing frequency and give occasion to establish new and fast methods for routine diagnostics. The so-called yellow fungus disease is one of the most important and common fungal dermatomycoses in central bearded dragons (Pogona vitticeps) and green iguanas (Iguana iguana) and is caused by Nannizziopsis guarroi. The aim of this study was to prove reliability in identification of N. guarroi with Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in comparison to molecular biological analysis of ribosomal DNA genes...
October 9, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
Irina A Tarasova, Alesya V Tereshkova, Anna A Lobas, Elizaveta M Solovyeva, Alena S Sidorenko, Vladimir Gorshkov, Frank Kjeldsen, Julia A Bubis, Mark V Ivanov, Irina Y Ilina, Sergei A Moshkovskii, Peter M Chumakov, Mikhail V Gorshkov
An acquisition of increased sensitivity of cancer cells to viruses is a common outcome of malignant progression that justifies the development of oncolytic viruses as anticancer therapeutics. Studying molecular changes that underlie the sensitivity to viruses would help to identify cases where oncolytic virus therapy would be most effective. We quantified changes in protein abundances in two glioblastoma multiforme (GBM) cell lines that differ in the ability to induce resistance to vesicular stomatitis virus (VSV) infection in response to type I interferon (IFN) treatment...
January 5, 2018: Oncotarget
Ming-Hui Yang, Wan-Jou Chen, Yaw-Syan Fu, Bin Huang, Wan-Chi Tsai, Yi-Ming Arthur Chen, Po-Chiao Lin, Cheng-Hui Yuan, Yu-Chang Tyan
Glycine N-methyltransferase is a tumor suppressor gene for hepatocellular carcinoma, which can activate DNA methylation by inducing the S-adenosylmethionine to S-adenosylhomocystine. Previous studies have indicated that the expression of Glycine N-methyltransferase is inhibited in hepatocellular carcinoma. To confirm and identify missing proteins, the pathologic analysis of the tumor-bearing mice will provide critical histologic information. Such a mouse model is applied as a screening tool for hepatocellular carcinoma as well as a strategy for missing protein discovery...
January 2, 2018: Oncotarget
Yelda Asad, Sajjad Ahmad, Thanyada Rungrotmongkol, Kara E Ranaghan, Syed Sikander Azam
The bacterium Providencia stuartii, is associated with urinary tract infections and is the most common cause of purple urine bag syndrome. The increasing multi-drug resistance pattern shown by the pathogen and lack of licensed vaccines make treatment of infections caused by P. stuartii challenging. As vaccinology data against the pathogen is scarce, an in silico proteome based Reverse Vaccinology (RV) protocol, in combination with subtractive proteomics is introduced in this work to screen potential vaccine candidates against P...
January 31, 2018: Journal of Molecular Graphics & Modelling
Isabelle Poirier, Marie Pallud, Lauriane Kuhn, Philippe Hammann, Arnaud Demortière, Arash Jamali, Johana Chicher, Christelle Caplat, Régis Kevin Gallon, Martine Bertrand
In the marine environment, benthic diatoms from estuarine and coastal sediments are among the first targets of nanoparticle pollution whose potential toxicity on marine organisms is still largely unknown. It is therefore relevant to improve our knowledge of interactions between these new pollutants and microalgae, the key players in the control of marine resources. In this study, the response of P. tricornutum to CdSe nanocrystals (CdSe NPs) of 5 nm (NP5) and 12 nm (NP12) in diameter was evaluated through microscopic, physiological, biochemical and proteomic approaches...
January 25, 2018: Ecotoxicology and Environmental Safety
Michael R Hoopmann, Jason M Winget, Luis Mendoza, Robert L Moritz
Label-free quantification has grown in popularity as a means of obtaining relative abundance measures for proteomics experiments. However, easily accessible and integrated tools to perform label-free quantification have been lacking. We describe StPeter, an implementation of Normalized Spectral Index quantification for wide availability through integration into the widely-used Trans-Proteomic Pipeline. This implementation has been specifically designed for reproducibility and ease of use. We demonstrate that StPeter outperforms other state-of-the art packages using a recently reported benchmark dataset over the range of false discovery rates relevant to shotgun proteomics results...
February 5, 2018: Journal of Proteome Research
Mutsumi Watanabe, Takayuki Tohge, Salma Balazadeh, Alexander Erban, Patrick Giavalisco, Joachim Kopka, Bernd Mueller-Roeber, Alisdair R Fernie, Rainer Hoefgen
Leaf senescence is an essential developmental process that involves diverse metabolic changes associated with degradation of macromolecules allowing nutrient recycling and remobilization. In contrast to the significant progress in transcriptomic analysis of leaf senescence, metabolomics analyses have been relatively limited. A broad overview of metabolic changes during leaf senescence including the interactions between various metabolic pathways is required to gain a better understanding of the leaf senescence allowing to link transcriptomics with metabolomics and physiology...
2018: Methods in Molecular Biology
Praseeda Mol, Uday Kannegundla, Gourav Dey, Lathika Gopalakrishnan, Manjunath Dammalli, Manish Kumar, Arun H Patil, Marappa Basavaraju, Akhila Rao, Kerekoppa P Ramesha, Thottethodi Subrahmanya Keshava Prasad
Bovine milk is important for both veterinary medicine and human nutrition. Understanding the bovine milk proteome at different stages of lactation has therefore broad significance for integrative biology and clinical medicine as well. Indeed, different lactation stages have marked influence on the milk yield, milk constituents, and nourishment of the neonates. We performed a comparative proteome analysis of the bovine milk obtained at different stages of lactation from the Indian indigenous cattle Malnad Gidda (Bos indicus), a widely available breed...
February 1, 2018: Omics: a Journal of Integrative Biology
Ming Yao, Bingming Chen, Weiping Zhao, John T Mehl, Lingjun Li, Mingshe Zhu
Therapeutic biologics have become a fast-growing segment within the pharmaceutical industry during the past three decades. Although the metabolism of biologics is more predictable than small molecule drugs, biotransformation can significantly affect the activity of biologics. Unfortunately, there are only a limited number of published studies on the biotransformation of biologics, most of which are focused on one or a few types of modification. In this study, an untargeted LC-MS based differential analysis approach was developed to rapidly and precisely determine the universal biotransformation profile of biologics with the assistance of bioinformatic tools...
January 31, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
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