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https://www.readbyqxmd.com/read/30097719/genome-wide-investigation-of-an-id-cohort-reveals-de-novo-3-utr-variants-affecting-gene-expression
#1
Paolo Devanna, Maartje van de Vorst, Rolph Pfundt, Christian Gilissen, Sonja C Vernes
Intellectual disability (ID) is a severe neurodevelopmental disorder with genetically heterogeneous causes. Large-scale sequencing has led to the identification of many gene-disrupting mutations; however, a substantial proportion of cases lack a molecular diagnosis. As such, there remains much to uncover for a complete understanding of the genetic underpinnings of ID. Genetic variants present in non-coding regions of the genome have been highlighted as potential contributors to neurodevelopmental disorders given their role in regulating gene expression...
August 10, 2018: Human Genetics
https://www.readbyqxmd.com/read/30007914/a-novel-differential-ion-mobility-device-expands-the-depth-of-proteome-coverage-and-the-sensitivity-of-multiplex-proteomic-measurements
#2
Sibylle Pfammatter, Eric Bonneil, Francis P McManus, Satendra Prasad, Derek J Bailey, Michael Belford, Jean-Jacques Dunyach, Pierre Thibault
The depth of proteomic analyses is often limited by the overwhelming proportion of confounding background ions that compromise the identification and quantification of low abundance peptides. To alleviate these limitations, we present a new high field asymmetric waveform ion mobility spectrometry (FAIMS) interface that can be coupled to the Orbitrap Tribrid mass spectrometers. The interface provides several advantages over previous generations of FAIMS devices including ease of operation, robustness, and high ion transmission...
July 14, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29985339/analyzing-the-photo-oxidation-of-2-propanol-at-indoor-air-level-concentrations-using-field-asymmetric-ion-mobility-spectrometry
#3
Christopher P Ireland, Michael Coto, Lauren Brown, Russell Paris, Caterina Ducati
We demonstrate a versatile protocol to be used for determining the effectiveness of photocatalysts in degrading indoor air concentration (ppb) volatile organic carbons (VOCs), illustrating this with a titanium dioxide based catalyst, and the VOC 2-propanol. The protocol takes advantage of field asymmetric ion mobility spectroscopy (FAIMS), an analysis tool that is capable of continuously identifying and monitoring the concentration of VOCs such as 2-propanol and acetone at the ppb level. The continuous nature of FAIMS allows detailed kinetic analysis, and long-term reactions, offering a significant advantage over gas chromatography, a batch process traditionally used in air purification characterization...
June 14, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29969236/rapid-and-comprehensive-single-shot-proteomics-with-lc-faims-ms-ms
#4
Alexander S Hebert, Satendra Prasad, Michael W Belford, Derek J Bailey, Graeme C McAlister, Susan E Abbatiello, Romain Huguet, Eloy R Wouters, Jean-Jacques Dunyach, Dain R Brademan, Michael S Westphall, Joshua J Coon
Liquid chromatography pre-fractionation is often implemented to increase proteomic coverage; however, while effective, this approach is laborious, requires considerable sample amount, and can be cumbersome. We describe how interfacing a recently described High Field Asymmetric Waveform Ion Mobility Spectrometry (FAIMS) device between a nanoESI-emitter and an Orbitrap hybrid mass spectrometer enables the collection of single shot proteomic data with comparable depth to conventional two-dimensional LC approaches...
July 3, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29969234/identification-of-isomers-by-multidimensional-isotopic-shifts-in-high-field-ion-mobility-spectra
#5
Pratima Pathak, Matthew A Baird, Alexandre A Shvartsburg
Nearly all molecules incorporate elements with stable isotopes. The resulting isotopologue envelopes in mass spectra tell the exact stoichiometry but nothing about the geometry. Chromatography and electrophoresis at high resolution also can distinguish isotopologues, again without revealing structural information. In high-definition differential ion mobility (FAIMS) spectra, these envelopes universally split in a structure-specific manner, providing a new general approach to isomer delineation. Here, we show that the peak shifts from instances of the same isotope are equal and can be averaged into characteristic elemental shifts, namely 13 C and 37 Cl for dichloroanilines (DCA)...
July 27, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29931245/late-onset-sepsis-in-preterm-infants-can-be-detected-preclinically-by-fecal-volatile-organic-compound-analysis-a-prospective-multicenter-cohort-study
#6
Daniel J C Berkhout, Britt J van Keulen, Hendrik J Niemarkt, Jet R Bessem, Willem P de Boode, Veerle Cossey, Neil Hoogenes, Christiaan V Hulzebos, Ellen Klaver, Peter Andriessen, Anton H van Kaam, Boris W Kramer, Richard A van Lingen, Aaron Schouten, Johannes B van Goudoever, Daniel C Vijlbrief, Mirjam M van Weissenbruch, Alfian N Wicaksono, James A Covington, Marc A Benninga, Nanne K H de Boer, Tim G J de Meij
Background: The intestinal microbiota has increasingly been considered to play a role in the etiology of late-onset sepsis (LOS). We hypothesize that early alterations in fecal volatile organic compounds (VOCs), reflecting intestinal microbiota composition and function, allow for discrimination between infants developing LOS and controls in a preclinical stage. Methods: In 9 neonatal intensive care units in the Netherlands and Belgium, fecal samples of preterm infants born at a gestational age ≤30 weeks were collected daily, up to the postnatal age of 28 days...
June 21, 2018: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29912642/investigation-of-the-potential-for-a-simplified-exposure-tool-in-medical-nutrition-setim-to-minimise-exposures-to-sweeteners-in-young-patients-aged-1-3-years-with-pku-and-cmpa
#7
Aaron J O'Sullivan, Cian O'Mahony, Leo Meunier, Nik Loveridge, Aideen I McKevitt
Children with phenylketonuria (PKU) and severe cow's milk protein allergy (CMPA) consume prescribed, specially formulated, foods for special medical purposes (FSMPs) in addition to having restricted intake of normal foods. These vulnerable patients are exposed to artificial sweeteners from the consumption of a combination of both free and prescribed foods. Young patients with PKU and CMPA aged from 1 to 3 years have a higher risk of exceeding the acceptable daily intake (ADI) for sweeteners than age-matched healthy children...
July 11, 2018: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/29860824/optimized-sampling-conditions-for-fecal-volatile-organic-compound-analysis-by-means-of-field-asymmetric-ion-mobility-spectrometry
#8
Sofie Bosch, Sofia El Manouni El Hassani, James A Covington, Alfian N Wicaksono, Marije K Bomers, Marc A Benninga, Chris J J Mulder, Nanne K H de Boer, Tim G J de Meij
Fecal volatile organic compounds (VOCs) are increasingly considered to be potential noninvasive, diagnostic biomarkers for various gastrointestinal diseases. Knowledge of the influence of sampling conditions on VOC outcomes is limited. We aimed to evaluate the effects of sampling conditions on fecal VOC profiles and to assess under which conditions an optimal diagnostic accuracy in the discrimination between pediatric inflammatory bowel disease (IBD) and controls could be obtained. Fecal samples from de novo treatment-naïve pediatric IBD patients and healthy controls (HC) were used to assess the effects of sampling conditions compared to the standard operating procedure (reference standard), defined as 500 mg of sample mass diluted with 10 mL tap water, using field asymmetric ion mobility spectrometry (FAIMS)...
July 3, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29800516/desorption-electrospray-ionization-mass-spectrometry-imaging-of-proteins-directly-from-biological-tissue-sections
#9
Kyana Y Garza, Clara L Feider, Dustin R Klein, Jake A Rosenberg, Jennifer S Brodbelt, Livia S Eberlin
Analysis of large biomolecules including proteins has proven challenging using ambient ionization mass spectrometry imaging techniques. Here, we have successfully optimized desorption electrospray ionization mass spectrometry (DESI-MS) to detect intact proteins directly from tissue sections and further integrated DESI-MS to a high field asymmetric waveform ion mobility (FAIMS) device for protein imaging. Optimized DESI-FAIMS-MS parameters were used to image mouse kidney, mouse brain, and human ovarian and breast tissue samples, allowing detection of 11, 16, 14, and 16 proteoforms, respectively...
July 3, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29707944/high-field-asymmetric-waveform-ion-mobility-spectrometry-in-nontargeted-bottom-up-proteomics-of-dried-blood-spots
#10
Cecilie Rosting, Jinglei Yu, Helen J Cooper
Despite the great potential of dried blood spots (DBS) as a source of endogenous proteins for biomarker discovery, the literature relating to nontargeted bottom-up proteomics of DBS is sparse, primarily due to the inherent complexity and very high dynamic range associated with these samples. Here, we present proof-of-concept results in which we have coupled high field asymmetric waveform ion mobility spectrometry (FAIMS) with liquid chromatography-tandem mass spectrometry (LC-MS/MS) for nontargeted bottom-up proteomics of DBS with the aim of addressing these challenges...
June 1, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29623662/gas-phase-enrichment-of-multiply-charged-peptide-ions-by-differential-ion-mobility-extend-the-comprehensiveness-of-sumo-proteome-analyses
#11
Sibylle Pfammatter, Eric Bonneil, Francis P McManus, Pierre Thibault
The small ubiquitin-like modifier (SUMO) is a member of the family of ubiquitin-like modifiers (UBLs) and is involved in important cellular processes, including DNA damage response, meiosis and cellular trafficking. The large-scale identification of SUMO peptides in a site-specific manner is challenging not only because of the low abundance and dynamic nature of this modification, but also due to the branched structure of the corresponding peptides that further complicate their identification using conventional search engines...
June 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29380926/integration-of-paper-spray-ionization-high-field-asymmetric-waveform-ion-mobility-spectrometry-for-forensic-applications
#12
Chia-Wei Tsai, Christopher A Tipple, Richard A Yost
RATIONALE: Paper spray ionization (PSI) is an attractive ambient ionization source for mass spectrometry (MS) since it allows the combination of surface sampling and ionization. The minimal sample preparation inherent in this approach greatly reduces the time needed for analysis. However, the ions generated from interfering compounds in the sample and the paper substrate may interfere with the analyte ions. Therefore, the integration of PSI with high-field asymmetric ion mobility spectrometry (FAIMS) is of significant interest since it should reduce the background ions entering the mass analyzer without complicating the analysis or increasing analysis time...
April 15, 2018: Rapid Communications in Mass Spectrometry: RCM
https://www.readbyqxmd.com/read/29359922/linear-and-differential-ion-mobility-separations-of-middle-down-proteoforms
#13
Alyssa Garabedian, Matthew A Baird, Jacob Porter, Kevin Jeanne Dit Fouque, Pavel V Shliaha, Ole N Jensen, Todd D Williams, Francisco Fernandez-Lima, Alexandre A Shvartsburg
Comprehensive characterization of proteomes comprising the same proteins with distinct post-translational modifications (PTMs) is a staggering challenge. Many such proteoforms are isomers (localization variants) that require separation followed by top-down or middle-down mass spectrometric analyses, but condensed-phase separations are ineffective in those size ranges. The variants for "middle-down" peptides were resolved by differential ion mobility spectrometry (FAIMS), relying on the mobility increment at high electric fields, but not previously by linear IMS on the basis of absolute mobility...
February 20, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29335669/portable-faims-applications-and-future-perspectives
#14
Michael T Costanzo, Jared J Boock, Robin H J Kemperman, Michael S Wei, Christopher R Beekman, Richard A Yost
Miniaturized mass spectrometry (MMS) is optimal for a wide variety of applications that benefit from field-portable instrumentation. Like MMS, field asymmetric ion mobility spectrometry (FAIMS) has proven capable of providing in situ analysis, allowing researchers to bring the lab to the sample. FAIMS compliments MMS very well, but has the added benefit of operating at atmospheric pressure, unlike MS. This distinct advantage makes FAIMS uniquely suited for portability. Since its inception, FAIMS has been envisioned as a field-portable device, as it affords less expense and greater simplicity than many similar methods...
November 2017: International Journal of Mass Spectrometry
https://www.readbyqxmd.com/read/29298074/photophysical-and-fluorescence-anisotropic-behavior-of-polyfluorene-%C3%AE-conformation-films
#15
Meng-Na Yu, Hamid Soleimaninejad, Jin-Yi Lin, Zong-Yan Zuo, Bin Liu, Yi-Fan Bo, Lu-Bing Bai, Ya-Min Han, Trevor A Smith, Man Xu, Xiang-Ping Wu, Dave E Dunstan, Rui-Dong Xia, Ling-Hai Xie, Donal D C Bradley, Wei Huang
We demonstrate a systematic visualization of the unique photophysical and fluorescence anisotropic properties of polyfluorene coplanar conformation (β-conformation) using time-resolved scanning confocal fluorescence imaging (FLIM) and fluorescence anisotropy imaging microscopy (FAIM) measurements. We observe inhomogeneous morphologies and fluorescence decay profiles at various micrometer-sized regions within all types of polyfluorene β-conformational spin-coated films. Poly(9,9-dioctylfluorene-2,7-diyl) (PFO) and poly[4-(octyloxy)-9,9-diphenylfluoren-2,7-diyl]-co-[5-(octyloxy)-9,9-diphenylfluoren-2,7-diyl] (PODPF) β-domains both have shorter lifetime than those of the glassy conformation for the longer effective conjugated length and rigid chain structures...
January 18, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29179535/differential-ion-mobility-separations-in-the-low-pressure-regime
#16
Alexandre A Shvartsburg, Anisha Haris, Roch Andrzejewski, Andrew Entwistle, Roger Giles
Ion mobility spectrometry (IMS) in conjunction with mass spectrometry (MS) has emerged as a powerful platform for biological and environmental analyses. An inherent advantage of differential or field asymmetric waveform IMS (FAIMS) based on the derivative of mobility vs electric field over linear IMS based on absolute mobility is much greater orthogonality to MS. Effective coupling of linear IMS to MS and diverse IMS/MS arrangements and modalities impossible at ambient buffer gas pressure were enabled at much reduced pressures...
January 2, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29166386/you-prime-what-you-code-the-faim-model-of-priming-of-pop-out
#17
Wouter Kruijne, Martijn Meeter
Our visual brain makes use of recent experience to interact with the visual world, and efficiently select relevant information. This is exemplified by speeded search when target- and distractor features repeat across trials versus when they switch, a phenomenon referred to as intertrial priming. Here, we present fAIM, a computational model that demonstrates how priming can be explained by a simple feature-weighting mechanism integrated into an established model of bottom-up vision. In fAIM, such modulations in feature gains are widespread and not just restricted to one or a few features...
2017: PloS One
https://www.readbyqxmd.com/read/29052245/the-longitudinal-impact-of-probiotic-and-peanut-oral-immunotherapy-on-health-related-quality-of-life
#18
A Dunn Galvin, S McMahon, A-L Ponsonby, K-C Hsiao, M L K Tang
BACKGROUND: We previously reported that probiotic and peanut oral immunotherapy (PPOIT) was effective at inducing sustained unresponsiveness compared with placebo in a double-blind, placebo-controlled randomized trial. This study evaluated the impact of PPOIT on health-related quality of life (HRQL). METHOD: Fifty-one participants (PPOIT 24; placebo 27) from the PPOIT trial completed Food Allergy Quality of Life Questionnaire (FAQLQ-PF) and Food Allergy Independent Measure (FAIM) at pre-treatment, end-of-treatment and 3 months after end-of-treatment...
March 2018: Allergy
https://www.readbyqxmd.com/read/29033200/validation-of-a-spanish-version-of-the-europrevall-food-allergy-quality-of-life-questionnaire-parental-form
#19
E Bartoll, M Nieto, B Selva, R Badillo, G Pereira, S Uixera, A Nieto, Á Mazón
BACKGROUND: Food allergy can have a major impact on quality of life of children and their parents. Questionnaires have been developed to measure the impact of this disorder. We aimed to validate the EuroPrevall questionnaire on Food Allergy-Quality of Life Questionnaire, Parent Form (FAQLQ-PF) and the Food Allergy Independent Measure (FAIM), translated into Spanish. METHODS: The internal consistency of the FAQLQ-PF and the FAIM, translated into Spanish (Spain) and completed by the parents of 74 children with IgE-mediated food allergy, were evaluated with Cronbach's alpha...
January 2018: Allergologia et Immunopathologia
https://www.readbyqxmd.com/read/28981531/identification-and-characterization-of-new-isoforms-of-human-fas-apoptotic-inhibitory-molecule-faim
#20
Elena Coccia, Isabel Calleja-Yagüe, Laura Planells-Ferrer, Blanca Sanuy, Belen Sanz, Joaquin López-Soriano, Rana S Moubarak, Francina Munell, Bruna Barneda-Zahonero, Joan X Comella, M Jose Pérez-García
Fas Apoptosis Inhibitory Molecule (FAIM) is an evolutionarily highly conserved death receptor antagonist, widely expressed and known to participate in physiological and pathological processes. Two FAIM transcript variants have been characterized to date, namely FAIM short (FAIM-S) and FAIM long (FAIM-L). FAIM-S is ubiquitously expressed and serves as an anti-apoptotic protein in the immune system. Furthermore, in neurons, this isoform promotes NGF-induced neurite outgrowth through NF-кB and ERK signaling. In contrast FAIM-L is found only in neurons, where it exerts anti-apoptotic activity against several stimuli...
2017: PloS One
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