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proteomics and visualization

Brendan Joyce, Danny Lee, Alex Rubio, Aleksey Ogurtsov, Gelio Alves, Yi-Kuo Yu
OBJECTIVE: RAId is a software package that has been actively developed for the past 10 years for computationally and visually analyzing MS/MS data. Founded on rigorous statistical methods, RAId's core program computes accurate E-values for peptides and proteins identified during database searches. Making this robust tool readily accessible for the proteomics community by developing a graphical user interface (GUI) is our main goal here. RESULTS: We have constructed a graphical user interface to facilitate the use of RAId on users' local machines...
March 15, 2018: BMC Research Notes
Jun Ding, James S Hagood, Namasivayam Ambalavanan, Naftali Kaminski, Ziv Bar-Joseph
The Dynamic Regulatory Events Miner (DREM) software reconstructs dynamic regulatory networks by integrating static protein-DNA interaction data with time series gene expression data. In recent years, several additional types of high-throughput time series data have been profiled when studying biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Combining all available time series and static datasets in a unified model remains an important challenge and goal...
March 14, 2018: PLoS Computational Biology
Manjunath Siddaramaiah, BolaSadashiva Satish Rao, Manjunath B Joshi, Anirbit Datta, S Sandya, Vasudha Vishnumurthy, Subhash Chandra, Subramanya G Nayak, Kapaettu Satyamoorthy, Krishna Kishore Mahato
In the present study, we have designed a laser induced fluorescence (LIF) based instrumentation and developed a sensitive methodology for the effective separation, visualization, identification and analysis of proteins on a single platform. In this method, intrinsic fluorescence spectra of proteins were detected after separation on one or two dimensional Sodium Dodecyl Sulfate-Tris(2-carboxyethyl)phosphine (SDS-TCEP) polyacrylamide gel electrophoresis (PAGE) and the data were analyzed. The MATLAB assisted software was designed for the development of PAGE fingerprint for the visualization of protein after one and two-dimensional protein separation...
March 14, 2018: Journal of Biophotonics
Jaepyeong Cha, Roger R Nani, Michael P Luciano, Aline Broch, Kihoon Kim, Jung-Man Namgoong, Rhushikesh A Kulkarni, Jordan L Meier, Peter Kim, Martin J Schnermann
Surgical methods guided by exogenous fluorescent markers have the potential to define tissue types in real time. Small molecule dyes with efficient and selective renal clearance could enable visualization of the ureter during surgical procedures involving the abdomen and pelvis. These studies report the design and synthesis of a water soluble, net neutral C4'-O-alkyl heptamethine cyanine, Ureter-Label (UL)-766, with excellent properties for ureter visualization. This compound is accessed through a concise synthetic sequence involving an N- to O-transposition reaction that provides other inaccessible C4'-O-alkyl heptamethine cyanines...
February 24, 2018: Bioorganic & Medicinal Chemistry Letters
Bing Han, Ning Yang, Hai Pu, Tai Wang
Cell polarity is essential for generating diverse cell functions. The underlying mechanisms of how a cell establishes, maintains and changes its polarity are poorly understood. Recently, sterol-rich membrane microdomains are found to be associated with these processes. However, both its exact characteristics and importance are still unclear. Here we show microdomains change dynamically in developing and germinating rice pollen with selective enrichment in the aperture and the tip of newly-born pollen tubes by use of the sterol-specific probe filipin...
March 6, 2018: Journal of Proteome Research
Zohreh Arabshahi, Isaac Oluwaseun Afara, Hayley Ruscoe Moody, Karsten Schrobback, Jamal Kashani, Nadine Fischer, Adekunle Oloyede, Travis Jacob Klein
The conventional mechanical properties of articular cartilage, such as compressive stiffness, have been shown to have limited capacity to distinguish visually normal from degraded cartilage samples. In this study, a new mechanical indentation framework for assessing functional properties of articular cartilage during loading/unloading, i.e. deformation and recovery, was established. The capacity of a ring-shaped indenter integrated with an ultrasound transducer to distinguish mechanically intact from proteoglycan-depleted tissue was investigated...
February 23, 2018: Journal of the Mechanical Behavior of Biomedical Materials
Erica M Forsberg, Tao Huan, Duane Rinehart, H Paul Benton, Benedikt Warth, Brian Hilmers, Gary Siuzdak
Systems biology is the study of complex living organisms, and as such, analysis on a systems-wide scale involves the collection of information-dense data sets that are representative of an entire phenotype. To uncover dynamic biological mechanisms, bioinformatics tools have become essential to facilitating data interpretation in large-scale analyses. Global metabolomics is one such method for performing systems biology, as metabolites represent the downstream functional products of ongoing biological processes...
April 2018: Nature Protocols
Vagisha Sharma, Josh Eckels, Birgit Schilling, Christina Ludwig, Jacob D Jaffe, Michael J MacCoss, Brendan MacLean
To address the growing need for a centralized, community resource of published results processed with Skyline, and to provide reviewers and readers immediate visual access to the data behind published conclusions, we present Panorama Public (, a repository of Skyline documents supporting published results.  Panorama Public is built on Panorama, an open source data management system for mass spectrometry data processed with the Skyline targeted mass spectrometry environment...
February 27, 2018: Molecular & Cellular Proteomics: MCP
Arunava Ghosh, Raymond C Coakley, Teresa Mascenik, Temperance R Rowell, Eric S Davis, Keith Rogers, Megan J Webster, Hong Dang, Laura E Herring, M Flori Sassano, Alessandra Livraghi-Butrico, Scott K Van Buren, Lee M Graves, Melissa A Herman, Scott H Randell, Neil E Alexis, Robert Tarran
RATIONAL: E-cigarettes vaporize propylene glycol/vegetable glycerin (PG/VG), nicotine and flavorings. However, the long-term health effects of exposing lungs to vaped e-liquids are unknown. OBJECTIVES: To determine the effects of chronic vaping on pulmonary epithelia. METHODS: We performed research bronchoscopies on healthy non-smokers, cigarette smokers and e-cigarettes users (vapers) and obtained bronchial brush biopsies and lavage samples from these subjects for proteomic investigation...
February 26, 2018: American Journal of Respiratory and Critical Care Medicine
Yu Liu, Kun Miao, Yinghao Li, Matthew Fares, Shuyuan Chen, Xin Zhang
Protein homeostasis, or proteostasis, is essential for cellular fitness and viability. Many environmental factors compromise proteostasis, induce global proteome stress, and cause diseases. Proteome stress sensor is a powerful tool to dissect the mechanism of cellular stress and find therapeutics that ameliorate these diseases. In this work, we present a multi-color HaloTag-based sensor (named AgHalo) to visualize and quantify proteome stresses in live cells. The current AgHalo sensor is equipped with three fluorogenic probes that turn on fluorescence when the sensor forms either soluble oligomers or insoluble aggregates upon exposure to stress conditions, both in vitro and in cellulo...
February 23, 2018: Biochemistry
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
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
Steven M Adelmund, Emily R Ruskowitz, Payam E Farahani, Julie V Wolfe, Cole A DeForest
This work introduces light-activated bioorthogonal noncanonical amino acid tagging (laBONCAT) as a method to selectively label, isolate, and identify proteins newly synthesized at user-defined regions in tissue culture. By photocaging l-azidohomoalanine (Aha), metabolic incorporation into proteins is prevented. The caged compound remains stable for many hours in culture, but can be photochemically liberated rapidly and on demand with spatial control. Upon directed light exposure, the uncaged amino acid is available for local translation, enabling downstream proteomic interrogation via bioorthogonal conjugation...
February 8, 2018: ACS Chemical Biology
Han-Hsuan Liu, Daniel B Mcclatchy, Lucio Schiapparelli, Wanhua Shen, John R Yates, Hollis T Cline
Experience-dependent synaptic plasticity refines brain circuits during development. To identify novel protein synthesis-dependent mechanisms contributing to experience-dependent plasticity, we conducted a quantitative proteomic screen of the nascent proteome in response to visual experience in Xenopus optic tectum using bio-orthogonal metabolic labeling (BONCAT). We identified 83 differentially synthesized candidate plasticity proteins (CPPs). The CPPs form strongly interconnected networks and are annotated to a variety of biological functions, including RNA splicing, protein translation, and chromatin remodeling...
February 7, 2018: ELife
Michael Hecker, Ulrike Mäder, Uwe Völker
While the genome sequence is the blueprint of life, functional genomics is required to transfer the genome sequence to cell physiology. Among the Omics technologies, proteomics holds a privileged position because it deals with the main players of life, the proteins. For the model organism Staphylococcus aureus comprehensive coverage of the proteome was accomplished and used to address physiological and pathophysiological questions. This review article demonstrates that the proteomic view of physiology and pathophysiology of S...
January 5, 2018: International Journal of Medical Microbiology: IJMM
Gustav Holmgren, Peter Sartipy, Christian X Andersson, Anders Lindahl, Jane Synnergren
Anthracyclines, such as doxorubicin, are highly efficient chemotherapeutic agents against a variety of cancers. However, anthracyclines are also among the most cardiotoxic therapeutic drugs presently on the market. Chemotherapeutic-induced cardiomyopathy is one of the leading causes of disease and mortality in cancer survivors. The exact mechanisms responsible for doxorubicin-induced cardiomyopathy are not completely known, but the fact that the cardiotoxicity is dose-dependent and that there is a variation in time-to-onset of toxicity, and gender- and age differences suggests that several mechanisms may be involved...
January 27, 2018: Toxicological Sciences: An Official Journal of the Society of Toxicology
Elysian Graham, Stacia Rymarchyk, Marci Wood, Yana Cen
Sirtuins consume stoichiometric amounts of nicotinamide adenine dinucleotide (NAD+) to remove acetyl group from lysine residues. These enzymes have been implicated in regulating various cellular events and have also been suggested to mediate the beneficial effects of calorie restriction (CR). However, controversies on sirtuin biology also peaked during the last few years because of conflicting results from different research groups. This is partly because these enzymes have been discovered recently, and the intricate interaction loops between sirtuins and other proteins make the characterization of them extremely difficult...
January 31, 2018: ACS Chemical Biology
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
Angélica Torres-Arroyo, Arturo Ruiz-Lara, Adriana Castillo-Villanueva, Sara Teresa Méndez-Cruz, Sara Elvia Espinosa-Padilla, Francisco Javier Espinosa-Rosales, Flora Zarate-Mondragón, Roberto Cervantes-Bustamante, Vanessa Bosch-Canto, Iris Vizzuett-López, Juan Carlos Ordaz-Fávila, Jesús Oria-Hernández, Horacio Reyes-Vivas
Proteomics is the study of the expression of changes and post-translational modifications (PTM) of proteins along a metabolic condition either normal or pathological. In the field of health, proteomics allows obtaining valuable data for treatment, diagnosis or pathophysiological mechanisms of different illnesses. To illustrate the aforementioned, we describe two projects currently being performed at the Instituto Nacional de Pediatría: The immuno-proteomic study of cow milk allergy and the Proteomic study of childhood cataract...
May 2017: Boletín Médico del Hospital Infantil de México
Jéssica Luana Chechi, Tarsila Franckin, Lidiane Nunes Barbosa, Fernanda Cristina Bérgamo Alves, Aline de Lima Leite, Marília Afonso Rabelo Buzalaf, Lucilene Delazari Dos Santos, Sandra de Moraes Gimenes Bosco
Pythium insidiosum is the etiologic agent of pythiosis, a life-threatening disease that affects human and animals, has difficult diagnosis, and therapy. Studies on protein characterization of P. insidiosum are scarce, so we aimed to determine the protein profile of P. insidiosum by mass spectrometry and bioinformatics strategies targeting in proteins that may act as putative virulence factors. Therefore, an extraction protocol was standardized to obtain the total proteins of P. insidiosum. By the analysis of Image Master 2D Platinum software, it was found that 186 spots ranging between 12 and 89 KDa and isoelectric point from 4 to 7...
January 23, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
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