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Christoph W Turck, Christian Webhofer, Markus Nussbaumer, Larysa Teplytska, Alon Chen, Giuseppina Maccarrone, Michaela D Filiou
PURPOSE: In this work we discuss how in vivo (15) N metabolic labeling in combination with mass spectrometry simultaneously provides information on protein expression and protein turnover. EXPERIMENTAL DESIGN: We metabolically labeled mice with the stable nitrogen isotope (15) N using a (15) N-enriched diet and analyzed (15) N-labeled vs. unlabeled ((14) N) brain tissue with LC-MS/MS. We then compared the (14) N vs.(15) N peptide isotopologue clusters of (14) N and (15) N-labeled Dihydropyrimidinase-related (DPYSL) proteins...
October 20, 2016: Proteomics. Clinical Applications
Ying Zhang, Xi Wang, Dan Cui, Jun Zhu
The human whole saliva is a vital body fluid to study the physiology and pathology of oral cavity. As a powerful technique for biomarker discovery, mass spectrometry-based proteomic strategy has been introduced to saliva analysis and identified hundreds of proteins and N-glycosylation sites. However, there still lacks of quantitative analysis, which is necessary for biomarker screening and biological researches. In this study, we established an integrated workflow by the combination of stable isotope dimethyl labeling, HILIC enrichment and high resolution mass spectrometry for both quantification of global proteome and N-glycoproteome of human saliva from oral ulcer patients...
October 20, 2016: Proteomics
Melissa Francisco, Tracy Johansson, Salahuddin Kazi
The Rheumatology Informatics System for Effectiveness (RISE) Registry was developed by the American College of Rheumatology (ACR) to serve US rheumatologists for the significant challenges of a rapidly changing healthcare environment. More than 400 rheumatologists have sent data from more than 3 million encounters of more than 650,000 patients as of August 11, 2016, through their electronic medical records (EMRs), with no additional work or interference with workflow on the part of the rheumatologists. RISE includes patients with all diagnoses seen by participating rheumatologists, at no cost to the rheumatologist...
September 2016: Clinical and Experimental Rheumatology
Theodore Pincus
An MDHAQ/RAPID3 (multidimensional health assessment questionnaire/routine assessment of patient index data) was developed from the HAQ over 25 years, based on observations made from completion by every patient (with all diagnoses) at every routine rheumatology visit since 1980. Modification of the HAQ was viewed as similar to improving a laboratory test, with a primary focus on clinical value for diagnosis, prognosis, and/or management, as well as feasibility for minimal effect on clinical workflow. Rigorous attention, was also directed to validity, reliability, other methodologic and technological considerations, but after clinical value and feasibility were established...
September 2016: Clinical and Experimental Rheumatology
David Hibbett, Kessy Abarenkov, Urmas Koljalg, Maarja Opik, Benli Chai, James R Cole, Qiong Wang, Pedro W Crous, Vincent A R G Robert, Thorunn Helgason, Josh Herr, Paul Kirk, Shiloh Lueschow, Kerry O'Donnell, Henrik Nilsson, Ryoko Oono, Conrad L Schoch, Christopher Smyth, Donny Walker, Andrea Porras-Alfaro, John W Taylor, David M Geiser
Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes...
October 19, 2016: Mycologia
Deborah J Cohen, Sara R Keller, Gillian R Hayes, David A Dorr, Joan S Ash, Dean F Sittig
BACKGROUND: Patient-generated health data (PGHD) are health-related data created or recorded by patients to inform their self-care and understanding about their own health. PGHD is different from other patient-reported outcome data because the collection of data is patient-driven, not practice- or research-driven. Technical applications for assisting patients to collect PGHD supports self-management activities such as healthy eating and exercise and can be important for preventing and managing disease...
October 19, 2016: JMIR Human Factors
Ju Yeon Lee, Hyun Kyoung Lee, Gun Wook Park, Heeyoun Hwang, Hoi Keun Jeong, Ki Na Yun, Eun Sun Ji, Kwang Hoe Kim, Jun Seok Kim, Jong Won Kim, Sung Ho Yun, Chi-Won Choi, Seung Il Kim, Jong-Sun Lim, Seul-Ki Jeong, Young-Ki Paik, Soo-Youn Lee, Jisook Park, Su Yeon Kim, Young-Jin Choi, Yong-In Kim, Jawon Seo, Je-Yoel Cho, Myoung Jin Oh, Nari Seo, Hyun Joo An, Jin Young Kim, Jong Shin Yoo
Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. Herein, we sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry. Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, its tryptic N-glycopeptides were identified, and the reproducibility of the data was examined in seven laboratories running different liquid chromatography-mass tandem spectrometry (LC-MS/MS) platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow...
October 19, 2016: Journal of Proteome Research
Xin Ma, Jing Liu, Zhengxiang Zhang, Tao Bo, Yu Bai, Huwei Liu
RATIONALE: Quadrupole based tandem mass spectrometry (MS/MS) plays critical role in "omics" studies. However, when a particular m/z precursor is selected by the quadrupole, ions other than the precursor are not transmitted through, the sensitivity and dynamic range thus diminish. Therefore, separation techniques such as ion mobility (IM) is coupled with MS/MS to improve it. METHODS: In this workflow, every IM-mass spectrometry (MS) scan was followed by one high collision energy (CE) scan...
October 19, 2016: Rapid Communications in Mass Spectrometry: RCM
Diane VonBehren, Molly M Killion, Carol Burke, Betsy Finkelmeier, Brigit Zamora
Three teams of perinatal expert nurses participated in planning and designing a new maternity unit, operationalizing the move to the new space, and evaluating care processes and workflows after the move. The hospitals involved were University of California, San Francisco Benioff Children's Hospital, Prentice Women's Hospital of Northwestern Memorial Healthcare in Chicago, IL, and Florida Hospital Orlando, Florida Hospital for Women. Although each team discussed specific details and lessons learned, there is remarkable consistency among the experiences of these teams and with the discussion of the process by the team at Mercy Hospital St...
November 2016: MCN. the American Journal of Maternal Child Nursing
Qian Qi, Guoquan Yan, Chunhui Deng, Xiangmin Zhang
The process of protein digestion is a critical step for successful protein identification in proteomic analysis. Many efforts have been dedicated to enhancing the digestion efficiency for sufficient digestion. Among these approaches, protein complete denaturation with denaturants is a common process for better digestion. However, the removal of denaturants was tedious or would cause protein loss and other problems. In this work, a feasible digestion approach, immobilized protein digestion (IPD), based on covalent binding has been developed...
October 18, 2016: Analytical and Bioanalytical Chemistry
Mari-Lynn Drainoni, Elisa A Koppelman, James A Feldman, Alexander Y Walley, Patricia M Mitchell, Jacqueline Ellison, Edward Bernstein
BACKGROUND: The increase in opioid overdose deaths has become a national public health crisis. Naloxone is an important tool in opioid overdose prevention. Distribution of nasal naloxone has been found to be a feasible, and effective intervention in community settings and may have potential high applicability in the emergency department, which is often the initial point of care for persons at high risk of overdose. One safety net hospital introduced an innovative policy to offer take-home nasal naloxone via a standing order to ensure distribution to patients at risk for overdose...
October 18, 2016: BMC Research Notes
Obdulia Rabal, Fernando Pastor, Helena Villanueva, Mario M Soldevilla, Sandra Hervas-Stubbs, Julen Oyarzabal
Complementing Systematic Evolution of Ligands by EXponential Enrichment (SELEX) technologies with in silico prediction of aptamer binders has attracted a lot of interest in the recent years. We propose a workflow involving 2D structure prediction, 3D RNA modeling using Rosetta and docking to the target protein with 3dRPC for: (i) prediction of the binding mode of our two previously reported potent (Kd < 50 nmol/l) murine TIM3 aptamers, and (ii) the prioritization of TIM3 aptamers that were enriched in the SELEX workflow...
October 18, 2016: Molecular Therapy. Nucleic Acids
Maike A Seiler, Detlef Jensen, Udo Neist, Ursula K Deister, Franz Schmitz
BACKGROUND: Perchlorate salts are relatively stable, soluble in water, and migrate into groundwater sources. Groundwater is an essential source for drinking water suppliers. Perchlorate bears health risks as it is identified to impair normal thyroid function by interfering with iodine uptake by the thyroid gland. The development of a sensitive analytical method for the determination of perchlorate is therefore of the highest interest or public health. Ion chromatography is a sensitive method suitable for perchlorate determinations...
2016: Environmental Sciences Europe
Leslie Muller, Luc Fornecker, Alain Dorsselaer, Sarah Cianférani, Christine Carapito
Sample preparation, typically by in-solution or in-gel approaches, has a strong influence on the accuracy and robustness of quantitative proteomics workflows. The major benefit of in-gel procedures is their compatibility with detergents (such as SDS) for protein solubilization. However, SDS-PAGE is a time-consuming approach. Tube-gel (TG) preparation circumvents this drawback as it involves directly trapping the sample in a polyacrylamide-gel matrix without electrophoresis. We report here the first global label-free quantitative comparison between TG, stacking gel (SG), and basic liquid digestion (LD)...
October 17, 2016: Proteomics
Lucia Geis-Asteggiante, Suzanne Ostrand-Rosenberg, Catherine Fenselau, Nathan J Edwards
Spectral counting is a straightforward label-free quantitation strategy used in bottom-up proteomics workflows. The application of spectral counting in label-free top-down proteomics workflows can be similarly straightforward, but has not been applied as widely as quantitation by chromatographic peak areas or peak intensities. In this study, we evaluate spectral counting for quantitative comparisons in label-free top-down proteomics workflows by comparison with chromatographic peak areas and intensities. We tested these quantitation approaches by spiking standard proteins into a complex protein background and comparing relative quantitation by spectral counts with normalized chromatographic peak areas and peak intensities from deconvoluted extracted ion chromatograms of the spiked proteins...
October 17, 2016: Analytical Chemistry
Miguel A Gonzalez-Lozano, Patricia Klemmer, Titia Gebuis, Chopie Hassan, Pim van Nierop, Ronald E van Kesteren, August B Smit, Ka Wan Li
Development of the brain involves the formation and maturation of numerous synapses. This process requires prominent changes of the synaptic proteome and potentially involves thousands of different proteins at every synapse. To date the proteome analysis of synapse development has been studied sparsely. Here, we analyzed the cortical synaptic membrane proteome of juvenile postnatal days 9 (P9), P15, P21, P27, adolescent (P35) and different adult ages P70, P140 and P280 of C57Bl6/J mice. Using a quantitative proteomics workflow we quantified 1560 proteins of which 696 showed statistically significant differences over time...
October 17, 2016: Scientific Reports
Christopher J Benjamin, Kyle J Wright, Scott C Bolton, Seok-Hee Hyun, Kyle Krynski, Mahima Grover, Guimei Yu, Fei Guo, Tamara L Kinzer-Ursem, Wen Jiang, David H Thompson
We report the fabrication of transmission electron microscopy (TEM) grids bearing graphene oxide (GO) sheets that have been modified with N(α), N(α)-dicarboxymethyllysine (NTA) and deactivating agents to block non-selective binding between GO-NTA sheets and non-target proteins. The resulting GO-NTA-coated grids with these improved antifouling properties were then used to isolate His6-T7 bacteriophage and His6-GroEL directly from cell lysates. To demonstrate the utility and simplified workflow enabled by these grids, we performed cryo-electron microscopy (cryo-EM) of His6-GroEL obtained from clarified E...
October 17, 2016: Scientific Reports
Michael Hund, Dominic Böhm, Werner Sturm, Michael Sedlmair, Tobias Schreck, Torsten Ullrich, Daniel A Keim, Ljiljana Majnaric, Andreas Holzinger
Medical doctors and researchers in bio-medicine are increasingly confronted with complex patient data, posing new and difficult analysis challenges. These data are often comprising high-dimensional descriptions of patient conditions and measurements on the success of certain therapies. An important analysis question in such data is to compare and correlate patient conditions and therapy results along with combinations of dimensions. As the number of dimensions is often very large, one needs to map them to a smaller number of relevant dimensions to be more amenable for expert analysis...
March 21, 2016: Brain Informatics
Julian C Shillcock, Michael Hawrylycz, Sean Hill, Hanchuan Peng
Large-scale brain initiatives such as the US BRAIN initiative and the European Human Brain Project aim to marshall a vast amount of data and tools for the purpose of furthering our understanding of brains. Fundamental to this goal is that neuronal morphologies must be seamlessly reconstructed and aggregated on scales up to the whole rodent brain. The experimental labor needed to manually produce this number of digital morphologies is prohibitively large. The BigNeuron initiative is assembling community-generated, open-source, automated reconstruction algorithms into an open platform, and is beginning to generate an increasing flow of high-quality reconstructed neurons...
February 24, 2016: Brain Informatics
Koon-Pong Wong, Marvin Bergsneider, Thomas C Glenn, Vladimir Kepe, Jorge R Barrio, David A Hovda, Paul M Vespa, Sung-Cheng Huang
Traumatic brain injury (TBI) is a major cause of mortality and morbidity, placing a significant financial burden on the healthcare system worldwide. Non-invasive neuroimaging technologies have been playing a pivotal role in the study of TBI, providing important information for surgical planning and patient management. Advances in understanding the basic mechanisms and pathophysiology of the brain following TBI are hindered by a lack of reliable image analysis methods for accurate quantitative assessment of TBI-induced structural and pathophysiological changes seen on anatomical and functional images obtained from multiple imaging modalities...
March 2016: Brain Informatics
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