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https://www.readbyqxmd.com/read/28432195/n-terminal-proteomics-assisted-profiling-of-the-unexplored-translation-initiation-landscape-in-arabidopsis-thaliana
#1
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Simon Stael, Adriaan Sticker, Lennart Martens, Frank Van Breusegem, Kris Gevaert, Petra Van Damme
Proteogenomics is an emerging research field yet lacking a uniform method of analysis. Proteogenomic studies in which N-terminal proteomics and ribosome profiling are combined, suggest that a high number of protein start sites are currently missing in genome annotations. We constructed a proteogenomic pipeline specific for the analysis of N-terminal proteomics data, with the aim of discovering novel translational start sites outside annotated protein coding regions. In summary, unidentified MS/MS spectra were matched to a specific N-terminal peptide library encompassing protein N-termini encoded in the Arabidopsis thaliana genome...
April 21, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28430394/structure-based-design-of-a-new-scaffold-for-cell-penetrating-peptidic-inhibitors-of-the-histone-demethylase-phf8
#2
Jerzy Dorosz, Lars Olsen, Signe Teuber Seger, Cornelia Steinhauer, Giorgos Bouras, Charlotte Helgstrand, Anders Wiuf, Michael Gajhede
The histone demethylase PHF8 catalyzes demethylation of mono- and di-methylated lysine 9 on histone H3 (H3K9me1/2) and is a transcriptional activator involved in development and cancer. Affinity and specificity of PHF8 towards H3K9me2 substrate is affected by interaction with both the catalytic domain and a PHD reader domain. The latter specifically recognizes tri-methylated lysine 4 on histone H3. A fragment of the histone H3 tail with tri-methylated lysine 4 was used as template for structure based design of a cyclic, cell-penetrating peptide that exhibits micromolar binding affinity to PHF8 in biochemical assays...
April 21, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28429240/clinical-setting-based-smoking-cessation-programme-and-the-quality-of-life-in-people-living-with-hiv-in-austria-and-germany
#3
Igor Grabovac, Helmut Brath, Horst Schalk, Olaf Degen, Thomas E Dorner
PURPOSE: To report on the global quality of life (QOL) in people living with HIV (PLWHIV) and how a smoking cessation intervention influences the changes in QOL. METHODS: Participants were asked to fill out a questionnaire during visits to their HIV outpatient clinic consisting of sociodemographic information, general health data and the WHOQOL HIV-Bref. Exhaled carbon monoxide measurements were used to confirm the smoking status, based on which participants classified as smokers received a short 5 min structured intervention and were offered participation in a full smoking cessation programme consisting of five sessions...
April 20, 2017: Quality of Life Research
https://www.readbyqxmd.com/read/28428068/comparative-analysis-of-gene-expression-profiles-for-several-migrating-cell-types-identifies-cell-migration-regulators
#4
Young-Kyung Bae, Frank Macabenta, Heather Leigh Curtis, Angelike Stathopoulos
Cell migration is an instrumental process that ensures cells are properly positioned to support the specification of distinct tissue types during development. To provide insight, we used fluorescence activated cell sorting (FACS) to isolate two migrating cell types from the Drosophila embryo: caudal visceral mesoderm (CVM) cells, precursors of longitudinal muscles of the gut, and hemocytes (HCs), the Drosophila equivalent of blood cells. ~350 genes were identified from each of the sorted samples using RNA-seq, and in situ hybridization was used to confirm expression within each cell type or, alternatively, within other interacting, co-sorted cell types...
April 17, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28427396/demdata-the-austrian-czech-institutional-long-term-care-project-design-and-protocol-of-a-two-centre-cross-sectional-study
#5
Stefanie Auer, Elisabeth Linsmayer, Anna Beránková, Patrick Pascher, Bernadette Firlinger, Doris Prischl, Paulina Ratajczak, Edith Span, Iva Holmerova
BACKGROUND: The organization of long-term care is one of the main challenges of public health and health policies in Europe and worldwide, especially in terms of care concepts for people with dementia. In Austria and the Czech Republic the majority of elderly institutionalized persons with dementia are cared for in nursing homes. It is however unclear, how many persons living in nursing homes in Austria and in the Czech Republic are suffering from cognitive impairment and dementia. In addition, basic information on the nutritional status, the status of mobility and the medication prescription patterns are often missing...
April 20, 2017: BMC Health Services Research
https://www.readbyqxmd.com/read/28426759/health-related-quality-of-life-in-south-african-patients-with-pulmonary-tuberculosis
#6
Tanja Kastien-Hilka, Bernd Rosenkranz, Edina Sinanovic, Bryan Bennett, Matthias Schwenkglenks
BACKGROUND: The evaluation of patient-reported health-related quality of life (HRQOL) in pulmonary tuberculosis (TB) contributes to a comprehensive understanding of the burden associated with this disease. The aim of this study was to assess the overall impact of TB on the health status and on single health domains identified in the WHO definition of health, including physical, mental and social health aspects. METHODS: Four instruments for HRQOL evaluation were applied in a longitudinal multicentre study during six-month standard TB treatment in South Africa...
2017: PloS One
https://www.readbyqxmd.com/read/28424523/cohesin-is-positioned-in-mammalian-genomes-by-transcription-ctcf-and-wapl
#7
Georg A Busslinger, Roman R Stocsits, Petra van der Lelij, Elin Axelsson, Antonio Tedeschi, Niels Galjart, Jan-Michael Peters
Mammalian genomes are spatially organized by CCCTC-binding factor (CTCF) and cohesin into chromatin loops and topologically associated domains, which have important roles in gene regulation and recombination. By binding to specific sequences, CTCF defines contact points for cohesin-mediated long-range chromosomal cis-interactions. Cohesin is also present at these sites, but has been proposed to be loaded onto DNA elsewhere and to extrude chromatin loops until it encounters CTCF bound to DNA. How cohesin is recruited to CTCF sites, according to this or other models, is unknown...
April 19, 2017: Nature
https://www.readbyqxmd.com/read/28421413/substrate-induced-conformational-changes-of-the-tyrocidine-synthetase-1-adenylation-domain-probed-by-intrinsic-trp-fluorescence
#8
Matilda Šprung, Barbara Soldo, Stjepan Orhanović, Viljemka Bučević-Popović
Nonribosomal peptide synthetases (NRPS) are multifunctional proteins that catalyze the synthesis of the peptide products with enormous biological potential. The process of biosynthesis starts with the adenylation (A) domain, which during the catalytic cycle undergoes extensive structural rearrangements. In this paper, we present the first study of the tyrocidine synthetase 1 A-domain (TycA-A) fluorescence properties. The TycA-A protein contains five potentially fluorescent Trp residues at positions 227, 301, 323, 376 and 406...
April 18, 2017: Protein Journal
https://www.readbyqxmd.com/read/28419580/liquid-liquid-interfacial-synthesis-of-click-nanosheet
#9
Amalia Rapakousiou, Ryo Shiotsuki, Ryota Sakamoto, Ryota Matsuoka, Ukyo Nakajima, Tigmansu Pal, Rintaro Shimada, Md Amran Hossain, Hiroyasu Masunaga, Satoshi Horike, Yasutaka Kitagawa, Sono Sasaki, Kenichi Kato, Takeaki Ozawa, Didier Astruc, Hiroshi Nishihara
A liquid/liquid interfacial synthesis is employed for the first time to synthesize a covalent two-dimensional polymer nanosheet. Copper-catalyzed azide-alkyne cycloaddition (CuAAC) between three-way terminal alkyne and azide at a water/dichloromethane interface generates a 1,2,3-triazole-linked nanosheet. The resultant nanosheet with a flat and smooth texture has a maximum domain size of 20 μm and minimum thickness of 5.3 nm. The starting monomers in the organic phase and the copper catalyst in the aqueous phase can meet together only at the liquid/liquid interface as a two-dimensional reaction space, which allows them to form the two-dimensional polymer...
April 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28406616/inhibition-of-huntingtin-exon-1-aggregation-by-the-molecular-tweezer-clr01
#10
Tobias Vöpel, Kenny Bravo-Rodriguez, Sumit Mittal, Shivang Vachharajani, David Gnutt, Abhishek Sharma, Anne Steinhof, Oluwaseun Fatoba, Gisa Ellrichmann, Michael Nshanian, Christian Heid, Joseph A Loo, Frank-Gerrit Klärner, Thomas Schrader, Gal Bitan, Erich E Wanker, Simon Ebbinghaus, Elsa Sanchez-Garcia
Huntington's disease is a neurodegenerative disorder associated with the expansion of the polyglutamine tract in the exon-1 domain of the huntingtin protein (htt(e1)). Above a threshold of 37 glutamine residues, htt(e1) starts to aggregate in a nucleation-dependent manner. A 17-residue N-terminal fragment of htt(e1) (N17) has been suggested to play a crucial role in modulating the aggregation propensity and toxicity of htt(e1). Here we identify N17 as a potential target for novel therapeutic intervention using the molecular tweezer CLR01...
April 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28406174/complete-fold-annotation-of-the-human-proteome-using-a-novel-structural-feature-space
#11
Sarah A Middleton, Joseph Illuminati, Junhyong Kim
Recognition of protein structural fold is the starting point for many structure prediction tools and protein function inference. Fold prediction is computationally demanding and recognizing novel folds is difficult such that the majority of proteins have not been annotated for fold classification. Here we describe a new machine learning approach using a novel feature space that can be used for accurate recognition of all 1,221 currently known folds and inference of unknown novel folds. We show that our method achieves better than 94% accuracy even when many folds have only one training example...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28400525/manipulation-of-the-host-cell-membrane-during-plasmodium-liver-stage-egress
#12
Paul-Christian Burda, Reto Caldelari, Volker T Heussler
A crucial step in the life cycle of Plasmodium parasites is the transition from the liver stage to the blood stage. Hepatocyte-derived merozoites reach the blood vessels of the liver inside host cell-derived vesicles called merosomes. The molecular basis of merosome formation is only partially understood. Here we show that Plasmodium berghei liver stage merozoites, upon rupture of the parasitophorous vacuole membrane, destabilize the host cell membrane (HCM) and induce separation of the host cell actin cytoskeleton from the HCM...
April 11, 2017: MBio
https://www.readbyqxmd.com/read/28399811/transcriptome-dynamics-in-early-zebrafish-embryogenesis-determined-by-high-resolution-time-course-analysis-of-180-successive-individual-zebrafish-embryos
#13
Han Rauwerda, Johanna F B Pagano, Wim C de Leeuw, Wim Ensink, Ulrike Nehrdich, Mark de Jong, Martijs Jonker, Herman P Spaink, Timo M Breit
BACKGROUND: Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression time series with 180 individual zebrafish embryos, obtained from nine different spawns, developmentally ordered and profiled from late blastula to mid-gastrula stage...
April 11, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28397770/prospecting-biotechnologically-relevant-monooxygenases-from-cold-sediment-metagenomes-an-in-silico-approach
#14
Matías A Musumeci, Mariana Lozada, Daniela V Rial, Walter P Mac Cormack, Janet K Jansson, Sara Sjöling, JoLynn Carroll, Hebe M Dionisi
The goal of this work was to identify sequences encoding monooxygenase biocatalysts with novel features by in silico mining an assembled metagenomic dataset of polar and subpolar marine sediments. The targeted enzyme sequences were Baeyer-Villiger and bacterial cytochrome P450 monooxygenases (CYP153). These enzymes have wide-ranging applications, from the synthesis of steroids, antibiotics, mycotoxins and pheromones to the synthesis of monomers for polymerization and anticancer precursors, due to their extraordinary enantio-, regio-, and chemo- selectivity that are valuable features for organic synthesis...
April 9, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28393467/patient-perspectives-on-the-optimal-start-of-renal-replacement-therapy
#15
Shayna L Henry, Corrine Munoz-Plaza, Jazmine Garcia Delgadillo, Nichole K Mihara, Mark P Rutkowski
BACKGROUND: Healthcare systems and providers are encouraged to prepare their patients with advanced chronic kidney disease (CKD) for a planned start to renal replacement therapies (RRT). Less well understood are the socioemotional experiences surrounding the optimal start of RRT versus suboptimal haemodialysis (HD) starts with a central catheter. OBJECTIVES: To characterise the experiences of patients beginning RRT. DESIGN: Qualitative, semi-structured phone interviews...
April 9, 2017: Journal of Renal Care
https://www.readbyqxmd.com/read/28393157/structural-modeling-of-the-ahr-arnt-complex-in-the-bhlh-pasa-pasb-region-elucidates-the-key-determinants-of-dimerization
#16
Dario Corrada, Michael S Denison, Laura Bonati
Elucidation of the dimerization process of the aryl hydrocarbon receptor (AhR) with the AhR nuclear translocator (ARNT) is crucial for understanding the mechanisms underlying the functional activity of AhR, including mediation of the toxicity of environmental contaminants. In this work, for the first time a structural model of the AhR:ARNT dimer encompassing the entire bHLH-PASA-PASB domain region is proposed. It is developed by using a template-based modeling approach, relying on the recently available crystallographic structures of two dimers of homologous systems in the bHLH-PAS family of proteins: the CLOCK:BMAL1 and the HIF2α:ARNT heterodimers...
April 10, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28389700/the-predictability-of-ocriplasmin-treatment-effects-is-there-consensus-among-retinal-experts-results-from-the-export-study
#17
Thomas Bertelmann, Joachim Wachtlin, Stefan Mennel, Michael J Koss, Mathias M Maier, Ricarda G Schumann, Sara Kazerounian, Hanna Daniel, Steffen Schmitz-Valckenberg
PURPOSE: To evaluate the agreement and predictability of ocriplasmin treatment effects among retinal experts (raters) by assessment of retinal imaging data of eyes treated for vitreomacular traction in nine different centers in Germany and Austria. METHODS: Retrospective cohort study. Combined confocal near-infrared scanning laser ophthalmoscopy and spectral-domain optical coherence tomography images (Spectralis® device, Heidelberg Engineering GmbH, Germany) from 136 eyes of 135 subjects were reviewed by 14 raters using an internet-based grading database and a standardized questionnaire...
April 7, 2017: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/28381895/emphasizing-bloom-s-affective-domain-to-reduce-pharmacy-students-stigmatizing-attitudes
#18
Andrew J Muzyk, Katie Lentz, Cynthia Green, Steve Fuller, D Byron May, Lorae Roukema
Objective. To create a learning environment using Bloom's affective domain as a framework that would reduce third-year pharmacy students' stigmatizing attitudes toward patients with mental illness. Design. Prior to the start of the module, students were asked to complete the 27-question Attribution Questionnaire Short Form (AQ-27). The teaching approach and in-class activities were designed to allow students' to experience the major categories within Bloom's affective domain. The module used patient cases, interactive-learning activities, and reflective discussions to augment pharmacological and therapeutic knowledge with a humanistic understanding of mental illness...
March 25, 2017: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/28377716/human-cytochrome-p450-3a4-as-a-biocatalyst-effects-of-the-engineered-linker-in-modulation-of-coupling-efficiency-in-3a4-bmr-chimeras
#19
Danilo Degregorio, Serena D'Avino, Silvia Castrignanò, Giovanna Di Nardo, Sheila J Sadeghi, Gianluca Catucci, Gianfranco Gilardi
Human liver cytochrome P450 3A4 is the main enzyme involved in drug metabolism. This makes it an attractive target for biocatalytic applications, such as the synthesis of pharmaceuticals and drug metabolites. However, its poor solubility, stability and low coupling have limited its application in the biotechnological context. We previously demonstrated that the solubility of P450 3A4 can be increased by creating fusion proteins between the reductase from Bacillus megaterium BM3 (BMR) and the N-terminally modified P450 3A4 (3A4-BMR)...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28375205/acute-effects-of-lsd-on-amygdala-activity-during-processing-of-fearful-stimuli-in-healthy-subjects
#20
F Mueller, C Lenz, P C Dolder, S Harder, Y Schmid, U E Lang, M E Liechti, S Borgwardt
Lysergic acid diethylamide (LSD) induces profound changes in various mental domains, including perception, self-awareness and emotions. We used functional magnetic resonance imaging (fMRI) to investigate the acute effects of LSD on the neural substrate of emotional processing in humans. Using a double-blind, randomised, cross-over study design, placebo or 100 μg LSD were orally administered to 20 healthy subjects before the fMRI scan, taking into account the subjective and pharmacological peak effects of LSD...
April 4, 2017: Translational Psychiatry
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