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https://www.readbyqxmd.com/read/27899623/combining-transcription-factor-binding-affinities-with-open-chromatin-data-for-accurate-gene-expression-prediction
#1
Florian Schmidt, Nina Gasparoni, Gilles Gasparoni, Kathrin Gianmoena, Cristina Cadenas, Julia K Polansky, Peter Ebert, Karl Nordström, Matthias Barann, Anupam Sinha, Sebastian Fröhler, Jieyi Xiong, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Barbara Hutter, Gideon Zipprich, Bärbel Felder, Jürgen Eils, Benedikt Brors, Wei Chen, Jan G Hengstler, Alf Hamann, Thomas Lengauer, Philip Rosenstiel, Jörn Walter, Marcel H Schulz
The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27893831/retinal-pre-conditioning-by-cd59a-knockout-protects-against-light-induced-photoreceptor-degeneration
#2
Delu Song, Brooks Wilson, Liangliang Zhao, Rupak Bhuyan, Mausumi Bandyopadhyay, Arkady Lyubarsky, Chen Yu, Yafeng Li, Levi Kanu, Takashi Miwa, Wen-Chao Song, Silvia C Finnemann, Bärbel Rohrer, Joshua L Dunaief
Complement dysregulation plays a key role in the pathogenesis of age-related macular degeneration (AMD), but the specific mechanisms are incompletely understood. Complement also potentiates retinal degeneration in the murine light damage model. To test the retinal function of CD59a, a complement inhibitor, CD59a knockout (KO) mice were used for light damage (LD) experiments. Retinal degeneration and function were compared in WT versus KO mice following light damage. Gene expression changes, endoplasmic reticulum (ER) stress, and glial cell activation were also compared...
2016: PloS One
https://www.readbyqxmd.com/read/27869789/genome-guided-design-of-a-defined-mouse-microbiota-that-confers-colonization-resistance-against-salmonella-enterica-serovar-typhimurium
#3
Sandrine Brugiroux, Markus Beutler, Carina Pfann, Debora Garzetti, Hans-Joachim Ruscheweyh, Diana Ring, Manuel Diehl, Simone Herp, Yvonne Lötscher, Saib Hussain, Boyke Bunk, Rüdiger Pukall, Daniel H Huson, Philipp C Münch, Alice C McHardy, Kathy D McCoy, Andrew J Macpherson, Alexander Loy, Thomas Clavel, David Berry, Bärbel Stecher
Protection against enteric infections, also termed colonization resistance, results from mutualistic interactions of the host and its indigenous microbes. The gut microbiota of humans and mice is highly diverse and it is therefore challenging to assign specific properties to its individual members. Here, we have used a collection of murine bacterial strains and a modular design approach to create a minimal bacterial community that, once established in germ-free mice, provided colonization resistance against the human enteric pathogen Salmonella enterica serovar Typhimurium (S...
November 21, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27866566/time-trends-in-cardiometabolic-risk-factors-in-adults
#4
Jonas D Finger, Markus A Busch, Yong Du, Christin Heidemann, Hildtraud Knopf, Ronny Kuhnert, Thomas Lampert, Gert B M Mensink, Hannelore K Neuhauser, Angelika Schaffrath Rosario, Christa Scheidt-Nave, Anja Schienkiewitz, Julia Truthmann, Bärbel-Maria Kurth
BACKGROUND: Data from three representative health examination surveys in Germany were analyzed to examine secular trends in the prevalence and magnitude of cardiometabolic risk factors. METHODS: The target variables were the following cardiometabolic risk factors: lack of exercise, smoking, obesity, systolic blood pressure, total cholesterol, serum glucose, self-reported high blood pressure, hyperlipidemia, and diabetes, and the use of antihypertensive, cholesterol-lowering, and antidiabetic drugs...
October 21, 2016: Deutsches Ärzteblatt International
https://www.readbyqxmd.com/read/27861524/factors-associated-with-worse-lung-function-in-cystic-fibrosis-patients-with-persistent-staphylococcus-aureus
#5
Sibylle Junge, Dennis Görlich, Martijn den Reijer, Bärbel Wiedemann, Burkhard Tümmler, Helmut Ellemunter, Angelika Dübbers, Peter Küster, Manfred Ballmann, Cordula Koerner-Rettberg, Jörg Große-Onnebrink, Eberhardt Heuer, Wolfgang Sextro, Jochen G Mainz, Jutta Hammermann, Joachim Riethmüller, Ute Graepler-Mainka, Doris Staab, Bettina Wollschläger, Rüdiger Szczepanski, Antje Schuster, Friedrich-Karl Tegtmeyer, Sivagurunathan Sutharsan, Alexandra Wald, Jerzy-Roch Nofer, Willem van Wamel, Karsten Becker, Georg Peters, Barbara C Kahl
BACKGROUND: Staphylococcus aureus is an important pathogen in cystic fibrosis (CF). However, it is not clear which factors are associated with worse lung function in patients with persistent S. aureus airway cultures. Our main hypothesis was that patients with high S. aureus density in their respiratory specimens would more likely experience worsening of their lung disease than patients with low bacterial loads. METHODS: Therefore, we conducted an observational prospective longitudinal multi-center study and assessed the association between lung function and S...
2016: PloS One
https://www.readbyqxmd.com/read/27859042/hla-g-promotes-myeloid-derived-suppressor-cell-mdsc-accumulation-and-suppressive-activity-during-human-pregnancy-through-engagement-of-the-receptor-ilt4
#6
Natascha Köstlin, Anna-Lena Ostermeir, Bärbel Spring, Julian Schwarz, Alexander Marmé, Christina B Walter, Christian F Poets, Christian Gille
Establishing and maintaining maternal-fetal tolerance is essential for a successful pregnancy; failure of immunological adaptation to pregnancy leads to severe complications such as abortion or preterm delivery. Myeloid-derived suppressor cells (MDSCs) are innate immune cells that suppress T-cell responses, expand during pregnancy and thus may play a role in tolerance induction. Human leucocyte antigen G (HLA-G) is a major histocompatibility complex (MHC) I molecule with immune-modulatory properties, which is expressed during pregnancy...
November 10, 2016: European Journal of Immunology
https://www.readbyqxmd.com/read/27851915/epigenomic-profiling-of-human-cd4-t-cells-supports-a-linear-differentiation-model-and-highlights-molecular-regulators-of-memory-development
#7
Pawel Durek, Karl Nordström, Gilles Gasparoni, Abdulrahman Salhab, Christopher Kressler, Melanie de Almeida, Kevin Bassler, Thomas Ulas, Florian Schmidt, Jieyi Xiong, Petar Glažar, Filippos Klironomos, Anupam Sinha, Sarah Kinkley, Xinyi Yang, Laura Arrigoni, Azim Dehghani Amirabad, Fatemeh Behjati Ardakani, Lars Feuerbach, Oliver Gorka, Peter Ebert, Fabian Müller, Na Li, Stefan Frischbutter, Stephan Schlickeiser, Carla Cendon, Sebastian Fröhler, Bärbel Felder, Nina Gasparoni, Charles D Imbusch, Barbara Hutter, Gideon Zipprich, Yvonne Tauchmann, Simon Reinke, Georgi Wassilew, Ute Hoffmann, Andreas S Richter, Lina Sieverling, Hyun-Dong Chang, Uta Syrbe, Ulrich Kalus, Jürgen Eils, Benedikt Brors, Thomas Manke, Jürgen Ruland, Thomas Lengauer, Nikolaus Rajewsky, Wei Chen, Jun Dong, Birgit Sawitzki, Ho-Ryun Chung, Philip Rosenstiel, Marcel H Schulz, Joachim L Schultze, Andreas Radbruch, Jörn Walter, Alf Hamann, Julia K Polansky
The impact of epigenetics on the differentiation of memory T (Tmem) cells is poorly defined. We generated deep epigenomes comprising genome-wide profiles of DNA methylation, histone modifications, DNA accessibility, and coding and non-coding RNA expression in naive, central-, effector-, and terminally differentiated CD45RA(+) CD4(+) Tmem cells from blood and CD69(+) Tmem cells from bone marrow (BM-Tmem). We observed a progressive and proliferation-associated global loss of DNA methylation in heterochromatic parts of the genome during Tmem cell differentiation...
November 15, 2016: Immunity
https://www.readbyqxmd.com/read/27843325/the-role-of-the-multidisciplinary-health-care-team-in-the-management-of-patients-with-marfan-syndrome
#8
REVIEW
Yskert von Kodolitsch, Meike Rybczynski, Marina Vogler, Thomas S Mir, Helke Schüler, Kerstin Kutsche, Georg Rosenberger, Christian Detter, Alexander M Bernhardt, Axel Larena-Avellaneda, Tilo Kölbel, E Sebastian Debus, Malte Schroeder, Stephan J Linke, Bettina Fuisting, Barbara Napp, Anna Lena Kammal, Klaus Püschel, Peter Bannas, Boris A Hoffmann, Nele Gessler, Eva Vahle-Hinz, Bärbel Kahl-Nieke, Götz Thomalla, Christina Weiler-Normann, Gunda Ohm, Stefan Neumann, Dieter Benninghoven, Stefan Blankenberg, Reed E Pyeritz
Marfan syndrome (MFS) is a rare, severe, chronic, life-threatening disease with multiorgan involvement that requires optimal multidisciplinary care to normalize both prognosis and quality of life. In this article, each key team member of all the medical disciplines of a multidisciplinary health care team at the Hamburg Marfan center gives a personal account of his or her contribution in the management of patients with MFS. The authors show how, with the support of health care managers, key team members organize themselves in an organizational structure to create a common meaning, to maximize therapeutic success for patients with MFS...
2016: Journal of Multidisciplinary Healthcare
https://www.readbyqxmd.com/read/27826394/effect-of-exercise-order-of-resistance-training-on-strength-performance-and-indices-of-muscle-damage-in-young-active-girls
#9
Maydeye Nazari, Mohammad Ali Azarbayjani, Kamal Azizbeigi
BACKGROUND: Exercise order is one of the key variables in designing resistance training (RT) that may affect physiological and functional muscle characteristics. OBJECTIVES: The purpose of this research was to examine the effect of exercise order of RT on muscle strength, lactate dehydrogenase (LDH) and creatine kinase (CK) enzymes as indices of muscle damage in active young girls. PATIENTS AND METHODS: For this purpose, 24 active girls aged 20 - 30 years voluntarily participated in six weeks RT...
September 2016: Asian Journal of Sports Medicine
https://www.readbyqxmd.com/read/27811641/hypselobarbus-bicolor-a-new-species-of-large-barb-teleostei-cyprinidae-from-the-western-ghats-of-india
#10
J D Marcus Knight, Ashwin Rai, Ronald K P D'Souza, Siby Philip, Neelesh Dahanukar
There has been much confusion around the identity of Hypselobarbus pulchellus, an endemic large barb of the Western Ghats. Recent works highlighted the fact that it is likely that two similar-looking species have been considered as H. pulchellus. A genetic analysis helps differentiate the two forms: viz., H. pulchellus and a new species, here described as H. bicolor sp. nov. Hypselobarbus bicolor can be distinguished from all other species of Hypselobarbus based on a combination of the following characters: two pairs of barbels, lateral line complete, with 34-36+1-2 pored scales, ½6/1/3½ scales in the transverse row; 11-12 predorsal scales; last simple dorsal ray weak, dorsal fin with 9½ branched rays, gill rakers short and simple, 4-6+11-12 on first gill arch; proximal end of fifth ceratobranchial slightly curved, with 5+3+2 teeth; overall coloration dark grey with an ill-defined silver- or bronze-coloured band running along length of body, two scales high, on lateral-line scale-row and row above it; fins devoid of any markings; and small, closely-placed tubercles restricted to the tip of the snout in large males...
November 3, 2016: Zootaxa
https://www.readbyqxmd.com/read/27806254/taste-receptors-and-gustatory-associated-g-proteins-in-channel-catfish-ictalurus-punctatus
#11
Sen Gao, Shikai Liu, Jun Yao, Tao Zhou, Ning Li, Qi Li, Rex Dunham, Zhanjiang Liu
Taste sensation plays a pivotal role in nutrient identification and acquisition. This is particularly true for channel catfish (Ictalurus punctatus) that live in turbid waters with limited visibility. This biological process is mainly mediated by taste receptors expressed in taste buds that are distributed in several organs and tissues, including the barbels and skin. In the present study, we identified a complete repertoire of taste receptor and gustatory associated G protein genes in the channel catfish genome...
October 23, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/27806012/acute-effects-of-plyometric-and-resistance-training-on-running-economy-in-trained-runners
#12
Richard T Marcello, Beau Kjerulf Greer, Anna E Greer
Results regarding the acute effects of plyometric and resistance training (PRT) on running economy (RE) are conflicting. Eight male collegiate distance runners (21 ± 1 years, 62.5 ± 7.8 ml/kg/min V[Combining Dot Above]O2 peak) completed V[Combining Dot Above]O2 peak and 1 repetition maximum (1RM) testing. Seven days later, subjects completed a 12 minute RE test at 60% and 80% V[Combining Dot Above]O2 peak, followed by a PRT protocol or a rested condition of equal duration (CON). The PRT protocol consisted of 3 sets of 5 repetitions at 85% 1RM for barbell squats, Romanian deadlifts, and barbell lunges; the same volume was utilized for resisted lateral lunges, box jumps, and depth jumps...
October 28, 2016: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/27803618/effect-of-3-different-applications-of-kinesio-taping-denko%C3%A2-on-electromyographic-activity-inhibition-or-facilitation-of-the-quadriceps-of-males-during-squat-exercise
#13
Júlio C Serrão, Bruno Mezêncio, João G Claudino, Rafael Soncin, Pedro L Sampaio Miyashiro, Eric P Sousa, Eduardo Borges, Vinícius Zanetti, Igor Phillip, Luiz Mochizuki, Alberto C Amadio
: Kinesio taping consists of a technique which uses the application of an elastic adhesive tape. It has become a widely used rehabilitation modality for the prevention and treatment of musculoskeletal disorders. The objective of this study was to verify the effect of the application of Kinesio Taping Denko(®) in three conditions (facilitation, inhibition, and placebo) on the electromyographic activity of the quadriceps and hamstrings muscles on facilitating or inhibiting the muscle function and on the perceived exertion during the barbell back squat exercise in healthy male subjects...
September 2016: Journal of Sports Science & Medicine
https://www.readbyqxmd.com/read/27794119/nanometer-scale-chemistry-of-a-calcite-biomineralization-template-implications-for-skeletal-composition-and-nucleation
#14
Oscar Branson, Elisa A Bonnin, Daniel E Perea, Howard J Spero, Zihua Zhu, Maria Winters, Bärbel Hönisch, Ann D Russell, Jennifer S Fehrenbacher, Alexander C Gagnon
Plankton, corals, and other organisms produce calcium carbonate skeletons that are integral to their survival, form a key component of the global carbon cycle, and record an archive of past oceanographic conditions in their geochemistry. A key aspect of the formation of these biominerals is the interaction between organic templating structures and mineral precipitation processes. Laboratory-based studies have shown that these atomic-scale processes can profoundly influence the architecture and composition of minerals, but their importance in calcifying organisms is poorly understood because it is difficult to measure the chemistry of in vivo biomineral interfaces at spatially relevant scales...
November 15, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27787464/the-effects-of-eccentric-contraction-duration-on-muscle-strength-power-production-vertical-jump-and-soreness
#15
Jonathan Mike, Nathan Cole, Chris Herrera, Trisha McLain, Len Kravitz, Chad Kerksick
Prior research has investigated the effects of either eccentric-only training or comparing eccentric and concentric exercise on changes related to strength and power expression, but no research to date has investigated the impact of altering the duration of either the concentric or eccentric component on these parameters. Therefore, the purpose of this study was to assess the duration of eccentric (i.e. 2-second, 4-second vs. 6-second) muscle contractions and their effect on muscle strength, power production, vertical jump and soreness using a plate-loaded barbell Smith squat exercise...
October 20, 2016: Journal of Strength and Conditioning Research
https://www.readbyqxmd.com/read/27770687/the-effects-of-squatting-footwear-on-three-dimensional-lower-limb-and-spine-kinetics
#16
Daniel J Southwell, Shane A Petersen, Tyson A C Beach, Ryan B Graham
Altering footwear worn during performance of the barbell back squat has been shown to change motion patterns, but it is not completely understood how this affects biomechanical loading demands. The primary objective was to compare lower back and extremity net joint moments in 24 experienced weightlifters (12M, 12F) who performed 80% one-repetition maximum back squats under three different footwear conditions (barefoot, running shoes, weightlifting shoes). Results showed that there was a significant main effect of footwear condition on the knee extension moment (p=0...
December 2016: Journal of Electromyography and Kinesiology
https://www.readbyqxmd.com/read/27751954/gender-and-developmental-specific-n-glycomes-of-the-porcine-parasite-oesophagostomum-dentatum
#17
Carmen Jiménez-Castells, Jorick Vanbeselaere, Sonja Kohlhuber, Bärbel Ruttkowski, Anja Joachim, Katharina Paschinger
BACKGROUND: The porcine nodule worm Oesophagostomum dentatum is a strongylid class V nematode rather closely related to the model organism Caenorhabditis elegans. However, in contrast to the non-parasitic C. elegans, the parasitic O. dentatum is an obligate sexual organism, which makes both a gender and developmental glycomic comparison possible. METHODS: Different enzymatic and chemical methods were used to release N-glycans from male and female O. dentatum as well as from L3 and L4 larvae...
October 15, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27749265/occurrence-of-intersex-in-wild-freshwater-fish-in-slovenian-rivers-a-histological-evaluation
#18
Milka Vrecl, Vlasta Jenčič
The aim of this preliminary research was to establish if there are intersex occurrences in wild freshwater fish in Slovenian rivers and streams. In the first study we evaluated all fish species of both sexes obtained from the river Ljubljanica from its source to mouth. In the second study we focused on the rainbow trout (Oncorhynchus mykiss) and brown trout (Salmo trutta m. fario) males from 30 rivers and streams in different parts of Slovenia. The male gonads were histologically assessed for the presence of oocytes to determine the frequency and degree of intersex...
September 1, 2016: Arhiv za Higijenu Rada i Toksikologiju
https://www.readbyqxmd.com/read/27748770/corrigendum-the-mouse-intestinal-bacterial-collection-mibc-provides-host-specific-insight-into-cultured-diversity-and-functional-potential-of-the-gut-microbiota
#19
Ilias Lagkouvardos, Rüdiger Pukall, Birte Abt, Bärbel U Foesel, Jan P Meier-Kolthoff, Neeraj Kumar, Anne Bresciani, Inés Martínez, Sarah Just, Caroline Ziegler, Sandrine Brugiroux, Debora Garzetti, Mareike Wenning, Thi P N Bui, Jun Wang, Floor Hugenholtz, Caroline M Plugge, Daniel A Peterson, Mathias W Hornef, John F Baines, Hauke Smidt, Jens Walter, Karsten Kristiansen, Henrik B Nielsen, Dirk Haller, Jörg Overmann, Bärbel Stecher, Thomas Clavel
No abstract text is available yet for this article.
October 17, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27744584/resistance-training-intensity-and-volume-affect-changes-in-rate-of-force-development-in-resistance-trained-men
#20
Gerald T Mangine, Jay R Hoffman, Ran Wang, Adam M Gonzalez, Jeremy R Townsend, Adam J Wells, Adam R Jajtner, Kyle S Beyer, Carleigh H Boone, Amelia A Miramonti, Michael B LaMonica, David H Fukuda, Nicholas A Ratamess, Jeffrey R Stout
PURPOSE: To compare the effects of two different resistance training programs, high intensity (INT) and high volume (VOL), on changes in isometric force (FRC), rate of force development (RFD), and barbell velocity during dynamic strength testing. METHODS: Twenty-nine resistance-trained men were randomly assigned to either the INT (n = 15, 3-5 RM, 3-min rest interval) or VOL (n = 14, 10-12 RM, 1-min rest interval) training group for 8 weeks. All participants completed a 2-week preparatory phase prior to randomization...
October 15, 2016: European Journal of Applied Physiology
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