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proteomics and visualization

Madhu Sudhan Ravindran, Markus R Wenk
This chapter provides a step-by-step protocol using activity-based protein profiling (ABPP) as a chemical-proteomic tool to survey the antibiotic properties of a small molecule. Here, we investigate the molecular mechanism behind the bactericidal activity of tetrahydrolipstatin (THL). ABPP relies on small molecule probes that target the active site of specific enzymes in complex proteomes. These probes in turn are equipped with a reporter tag that allows capturing, visualization, enrichment, identification, and quantification of its targets either in vitro or in situ...
2017: Methods in Molecular Biology
Monica A Schmidt, Ken Pendarvis
Oilseed crops are global commodities for their oil and protein seed content. We have engineered the oilseed Camelina sativa to exhibit increased protein content with a slight decrease in oil content. The introduction of a phytoene synthase gene with an RNAi cassette directed to suppress the storage protein 2S albumin resulted in seeds with an 11-24 % elevation in overall protein. The phytoene synthase cassette alone produced enhanced β-carotene content of an average 275 ± 6.10 μg/g dry seed and an overall altered seed composition of 11 % less protein and comparable nontransgenic amounts of both oil and carbohydrates...
October 22, 2016: Transgenic Research
Matthias Holzlechner, Katharina Strasser, Elitsa Zareva, Luise Steinhaeuser, Hanna Birnleitner, Andrea Beer, Michael Bergmann, Rudolf Oehler, Martina Marchetti-Deschmann
Tissue-resident immune cells differ from the corresponding blood cells in many functional aspects. Although the proteome of blood immune cells is well investigated there are almost no data on tissue-resident immune cells. Here we explored the potential of MALDI-TOF-MS imaging (MSI) to investigate these cells in colon tissue, which exhibits a strong immune infiltration. MSI identified several proteinaceous markers that colocalized with specific structures of the colon such as mucosa or muscularis mucosae in six patients...
October 18, 2016: Journal of Proteome Research
Liza J Burton, Mariela Rivera, Ohuod Hawsawi, Jin Zou, Tamaro Hudson, Guangdi Wang, Qiang Zhang, Luis Cubano, Nawal Boukli, Valerie Odero-Marah
Muscadine grape skin extract (MSKE) is derived from muscadine grape (Vitis rotundifolia), a common red grape used to produce red wine. Endoplasmic reticulum (ER) stress activates the unfolded protein response (UPR) that serves as a survival mechanism to relieve ER stress and restore ER homeostasis. However, when persistent, ER stress can alter the cytoprotective functions of the UPR to promote autophagy and cell death. Although MSKE has been documented to induce apoptosis, it has not been linked to ER stress/UPR/autophagy...
2016: PloS One
Mateusz Kaduk, Christian Riegler, Oliver Lemp, Erik L L Sonnhammer
HieranoiDB ( is a freely available on-line database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root. Here we present a database HieranoiDB with a web interface that makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence...
October 13, 2016: Nucleic Acids Research
Ian Streeter, Peter W Harrison, Adam Faulconbridge, Paul Flicek, Helen Parkinson, Laura Clarke
The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases...
October 12, 2016: Nucleic Acids Research
Aihua Hou, Kai Pong Law, Min Qi Tin, Yoon Pin Lim, Louis Tong
Pterygium is a triangular shaped ocular fibrous surface lesion growing from conjunctiva towards central cornea, causing ocular irritation, astigmatism, and visual disturbance. The condition is characterized by epithelial proliferation, fibrovascular growth, chronic inflammation, and prominent extracellular matrix remodeling. Studies have suggested that aberrant extracellular proteins secreted by fibroblasts lead to abnormal matrix production and tissue invasion contributing to the development of the disease...
October 7, 2016: Experimental Eye Research
Long Pei, Min Xu, Zachary Frazier, Frank Alber
BACKGROUND: Cryo-electron tomography is an important tool to study structures of macromolecular complexes in close to native states. A whole cell cryo electron tomogram contains structural information of all its macromolecular complexes. However, extracting this information remains challenging, and relies on sophisticated image processing, in particular for template-free particle extraction, classification and averaging. To develop these methods it is crucial to realistically simulate tomograms of crowded cellular environments, which can then serve as ground truth models for assessing and optimizing methods for detection of complexes in cell tomograms...
October 5, 2016: BMC Bioinformatics
Sepideh Khorasanizadeh, Fraydoon Rastinejad
Nuclear receptors (NRs) are master regulators of broad genetic programs in metazoans. These programs are regulated in part by the small-molecule ligands that bind NRs and modulate their interactions with transcriptional coregulatory factors. X-ray crystallography is now delivering more complete pictures of how the multi-domain architectures of NR homo- and heterodimers are physically arranged on their DNA elements, and how ligands and coactivator peptides act through these complexes. Complementary studies are also pointing to a variety of novel mechanisms by which NRs access their DNA response elements within chromatin...
October 5, 2016: Endocrinology
Michael S Bereman, Joshua Beri, Vagisha Sharma, Cory Nathe, Josh Eckels, Brendan MacLean, Michael J MacCoss
We report the development of a completely automated pipeline to monitor system suitability in bottom-up proteomic experiments. LC-MS/MS runs are automatically imported into Skyline and multiple identification-free metrics are extracted from targeted peptides. These data are then uploaded to the Panorama Skyline document repository where metrics can be viewed in a web-based interface using powerful process control techniques, including Levey-Jennings and Pareto plots. The interface is versatile and takes user input, which allows the user significant control over the visualization of the data...
October 4, 2016: Journal of Proteome Research
Brent M Kuenzi, Adam L Borne, Jiannong Li, Eric B Haura, Steven A Eschrich, John M Koomen, Uwe Rix, Paul A Stewart
With continuously increasing scale and depth of coverage in affinity proteomics (AP-MS) data, the analysis and visualization is becoming more challenging. A number of tools have been developed to identify high-confidence interactions; however, a cohesive and intuitive pipeline for analysis and visualization is still needed. Here we present Automated Processing of SAINT Templated Layouts (APOSTL), a freely available Galaxy-integrated software suite and analysis pipeline for reproducible, interactive analysis of AP-MS data...
October 21, 2016: Journal of Proteome Research
Jonathan A Stefely, Nicholas W Kwiecien, Elyse C Freiberger, Alicia L Richards, Adam Jochem, Matthew J P Rush, Arne Ulbrich, Kyle P Robinson, Paul D Hutchins, Mike T Veling, Xiao Guo, Zachary A Kemmerer, Kyle J Connors, Edna A Trujillo, Jacob Sokol, Harald Marx, Michael S Westphall, Alexander S Hebert, David J Pagliarini, Joshua J Coon
Mitochondrial dysfunction is associated with many human diseases, including cancer and neurodegeneration, that are often linked to proteins and pathways that are not well-characterized. To begin defining the functions of such poorly characterized proteins, we used mass spectrometry to map the proteomes, lipidomes, and metabolomes of 174 yeast strains, each lacking a single gene related to mitochondrial biology. 144 of these genes have human homologs, 60 of which are associated with disease and 39 of which are uncharacterized...
September 26, 2016: Nature Biotechnology
Xi Zhang
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples...
September 16, 2016: Proteomics
Amit Kumar Gupta, Karambir Kaur, Akanksha Rajput, Sandeep Kumar Dhanda, Manika Sehgal, Md Shoaib Khan, Isha Monga, Showkat Ahmad Dar, Sandeep Singh, Gandharva Nagpal, Salman Sadullah Usmani, Anamika Thakur, Gazaldeep Kaur, Shivangi Sharma, Aman Bhardwaj, Abid Qureshi, Gajendra Pal Singh Raghava, Manoj Kumar
Current Zika virus (ZIKV) outbreaks that spread in several areas of Africa, Southeast Asia, and in pacific islands is declared as a global health emergency by World Health Organization (WHO). It causes Zika fever and illness ranging from severe autoimmune to neurological complications in humans. To facilitate research on this virus, we have developed an integrative multi-omics platform; ZikaVR (, dedicated to the ZIKV genomic, proteomic and therapeutic knowledge. It comprises of whole genome sequences, their respective functional information regarding proteins, genes, and structural content...
2016: Scientific Reports
Krishna R Murthy, Manjunath Dammalli, Sneha M Pinto, Kalpana Babu Murthy, Raja Sekhar Nirujogi, Anil K Madugundu, Gourav Dey, Yashwanth Subbannayya, Uttam Kumar Mishra, Bipin Nair, Harsha Gowda, T S Keshava Prasad
The annual economic burden of visual disorders in the United States was estimated at $139 billion. Ophthalmology is therefore one of the salient application fields of postgenomics biotechnologies such as proteomics in the pursuit of global precision medicine. Interestingly, the protein composition of the human iris tissue still remains largely unexplored. In this context, the uveal tract constitutes the vascular middle coat of the eye and is formed by the choroid, ciliary body, and iris. The iris forms the anterior most part of the uvea...
September 2016: Omics: a Journal of Integrative Biology
José P Martínez, Rosario Blanes, Manuel Casanova, Eulogio Valentín, Amelia Murgui, Ángel Domínguez
By 2-dimensional gel electrophoresis (2-DE) and mass spectrometry we have characterized the polypeptide species present in extracts obtained by 60% ethanol treatment of whole mature (48 h) biofilms formed by a reference strain (CAI4-URA3) and four C. albicans null mutants for cell wall-related genes (ALG5, CSA1, MNN9 and PGA10) Null mutants form fragile biofilms that appeared partially split and weakly attached to the substratum contrary to those produced by the reference strain. An almost identical, electrophoretic profile consisting of about 276 spots was visualized in all extracts examined...
September 7, 2016: FEMS Yeast Research
Hye-Jung Kim, Seong Joon Ahn, Se Joon Woo, Hye Kyoung Hong, Eui Jin Suh, Jeeyun Ahn, Ji Hyun Park, Na-Kyung Ryoo, Ji Eun Lee, Ki Woong Kim, Kyu Hyung Park, Cheolju Lee
Age-related macular degeneration (AMD) is a major cause of severe, progressive visual loss among the elderly. There are currently no established serological markers for the diagnosis of AMD. In this study, we carried out a large-scale quantitative proteomics analysis to identify plasma proteins that could serve as potential AMD biomarkers. We found that the plasma levels of phospholipid transfer protein (PLTP) and mannan-binding lectin serine protease (MASP)-1 were increased in AMD patients relative to controls...
2016: Scientific Reports
Jaana Kuuskeri, Mari Häkkinen, Pia Laine, Olli-Pekka Smolander, Fitsum Tamene, Sini Miettinen, Paula Nousiainen, Marianna Kemell, Petri Auvinen, Taina Lundell
BACKGROUND: The white-rot Agaricomycetes species Phlebia radiata is an efficient wood-decaying fungus degrading all wood components, including cellulose, hemicellulose, and lignin. We cultivated P. radiata in solid state cultures on spruce wood, and extended the experiment to 6 weeks to gain more knowledge on the time-scale dynamics of protein expression upon growth and wood decay. Total proteome and transcriptome of P. radiata were analyzed by peptide LC-MS/MS and RNA sequencing at specific time points to study the enzymatic machinery on the fungus' natural growth substrate...
2016: Biotechnology for Biofuels
Idanya Serafín-Higuera, Olga Lilia Garibay-Cerdenares, Berenice Illades-Aguiar, Eugenia Flores-Alfaro, Marco Antonio Jiménez-López, Pavel Sierra-Martínez, Luz Del Carmen Alarcón-Romero
BACKGROUND: Cervical cancer (CC) is the fourth most common cancer in women worldwide with an estimated 528,000 new cases in 2012. The same year México had an incidence of 13,960 and a mortality of 4769 cases. There are several diagnosis methods of CC; among the most frequents are the conventional Pap cytology (Pap), colposcopy, and visual inspection with acetic acid (VIA), histopathological examination, tests of imaging and detection of high-risk papilloma virus (HR-HPV) with molecular tests (PCR, hybridization, sequencing)...
2016: Proteome Science
I C R M Kolder, S J van der Plas-Duivesteijn, G Tan, G F Wiegertjes, M Forlenza, A T Guler, D Y Travin, M Nakao, T Moritomo, I Irnazarow, J T den Dunnen, S Y Anvar, H J Jansen, R P Dirks, M Palmblad, B Lenhard, C V Henkel, H P Spaink
BACKGROUND: The common carp (Cyprinus carpio) is the oldest, most domesticated and one of the most cultured fish species for food consumption. Besides its economic importance, the common carp is also highly suitable for comparative physiological and disease studies in combination with the animal model zebrafish (Danio rerio). They are genetically closely related but offer complementary benefits for fundamental research, with the large body mass of common carp presenting possibilities for obtaining sufficient cell material for advanced transcriptome and proteome studies...
2016: BMC Genomics
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