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https://www.readbyqxmd.com/read/29145629/the-reactome-pathway-knowledgebase
#1
Antonio Fabregat, Steven Jupe, Lisa Matthews, Konstantinos Sidiropoulos, Marc Gillespie, Phani Garapati, Robin Haw, Bijay Jassal, Florian Korninger, Bruce May, Marija Milacic, Corina Duenas Roca, Karen Rothfels, Cristoffer Sevilla, Veronica Shamovsky, Solomon Shorser, Thawfeek Varusai, Guilherme Viteri, Joel Weiser, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended version of a classic metabolic map, in a single consistent data model. Reactome functions both as an archive of biological processes and as a tool for discovering unexpected functional relationships in data such as gene expression profiles or somatic mutation catalogues from tumor cells...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29145497/rare-genetic-variants-in-the-endocannabinoid-system-genes-cnr1-and-dagla-are-associated-with-neurological-phenotypes-in-humans
#2
Douglas R Smith, Christine M Stanley, Theodore Foss, Richard G Boles, Kevin McKernan
Rare genetic variants in the core endocannabinoid system genes CNR1, CNR2, DAGLA, MGLL and FAAH were identified in molecular testing data from 6,032 patients with a broad spectrum of neurological disorders. The variants were evaluated for association with phenotypes similar to those observed in the orthologous gene knockouts in mice. Heterozygous rare coding variants in CNR1, which encodes the type 1 cannabinoid receptor (CB1), were found to be significantly associated with pain sensitivity (especially migraine), sleep and memory disorders-alone or in combination with anxiety-compared to a set of controls without such CNR1 variants...
2017: PloS One
https://www.readbyqxmd.com/read/29145401/anatomically-specific-intratubular-and-interstitial-biominerals-in-the-human-renal-medullo-papillary-complex
#3
Ling Chen, Ryan S Hsi, Feifei Yang, Benjamin A Sherer, Marshall L Stoller, Sunita P Ho
Limited information exists on the anatomically-specific early stage events leading to clinically detectable mineral aggregates in the renal papilla. In this study, quantitative multiscale correlative maps of structural, elemental and biochemical properties of whole medullo-papillary complexes from human kidneys were developed. Correlative maps of properties specific to the uriniferous and vascular tubules using high-resolution X-ray computed tomography, scanning and transmission electron microscopy, energy dispersive X-ray spectroscopy, and immunolocalization of noncollagenous proteins (NCPs) along with their association with anatomy specific biominerals were obtained...
2017: PloS One
https://www.readbyqxmd.com/read/29145027/differential-gene-expression-in-the-intestine-of-sea-cucumber-apostichopus-japonicus-under-low-and-high-salinity-conditions
#4
Libin Zhang, Qiming Feng, Lina Sun, Kui Ding, Da Huo, Yan Fang, Tao Zhang, Hongsheng Yang
Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0...
November 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29144405/genomic-analysis-of-the-asmt-gene-family-in-solanum-lycopersicum
#5
Weicheng Liu, Dake Zhao, Chunfang Zheng, Chen Chen, Xin Peng, Yuan Cheng, Hongjian Wan
Acetylserotonin methyltransferase (ASMT) is the last enzyme of melatonin biosynthesis and may play a rate-limiting role in the melatonin production of plants. In this study, systematic analysis of the ASMT gene family in tomato (Solanum lycopersicum Mill) has been presented by the integration of the structural features, phylogenetic relationships, exon/intron configuration, and expression profile during growth and development, as well as biotic stresses. The results revealed that the tomato genome encoded a minimum of 14 members, containing three probable encoded pseudogenes...
November 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29143950/-the-effect-of-a-short-term-group-stabilisation-training-in-patients-with-complex-posttraumatic-stress-disorder
#6
G Beldman, H H L M Kessels, I W de Groot
The international guideline for complex posttraumatic stress disorder (ptsd) from the International Society for Traumatic Stress Studies (istss) recommends treatment in phases, starting with stabilisation treatment. Different forms of stabilisation training have been developed the past few years, one being short-term group stabilisation training.<br/> AIM: To map out the effects of the short-term group training.<br/> METHOD: The research implemented a pre-post design. The training consisted of five group sessions...
2017: Tijdschrift Voor Psychiatrie
https://www.readbyqxmd.com/read/29143946/multi-scale-account-of-the-network-structure-of-macaque-visual-cortex
#7
Maximilian Schmidt, Rembrandt Bakker, Claus C Hilgetag, Markus Diesmann, Sacha J van Albada
Cortical network structure has been extensively characterized at the level of local circuits and in terms of long-range connectivity, but seldom in a manner that integrates both of these scales. Furthermore, while the connectivity of cortex is known to be related to its architecture, this knowledge has not been used to derive a comprehensive cortical connectivity map. In this study, we integrate data on cortical architecture and axonal tracing data into a consistent multi-scale framework of the structure of one hemisphere of macaque vision-related cortex...
November 16, 2017: Brain Structure & Function
https://www.readbyqxmd.com/read/29143921/dichloroacetate-induced-intracellular-acidification-in-glioblastoma-in-vivo-detection-using-aacid-cest-mri-at-9-4%C3%A2-tesla
#8
Mohammed Albatany, Alex Li, Susan Meakin, Robert Bartha
Intracellular pH (pHi) plays an important role in the maintenance of normal cell function, and is maintained within a narrow range by the activity of transporters located at the plasma membrane. Modulation of tumor pHi may influence proliferation, apoptosis, chemotherapy resistance, and thermosensitivity. Chemical exchange saturation transfer (CEST) is a novel MRI contrast mechanism that is dependent on cellular pH. Amine and amide concentration-independent detection (AACID) is a recently developed CEST contrast method that is intracellular pH (pHi) weighted...
November 16, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29143883/rooting-depth-varies-differentially-in-trees-and-grasses-as-a-function-of-mean-annual-rainfall-in-an-african-savanna
#9
Ricardo M Holdo, Jesse B Nippert, Michelle C Mack
A significant fraction of the terrestrial biosphere comprises biomes containing tree-grass mixtures. Forecasting vegetation dynamics in these environments requires a thorough understanding of how trees and grasses use and compete for key belowground resources. There is disagreement about the extent to which tree-grass vertical root separation occurs in these ecosystems, how this overlap varies across large-scale environmental gradients, and what these rooting differences imply for water resource availability and tree-grass competition and coexistence...
November 16, 2017: Oecologia
https://www.readbyqxmd.com/read/29143621/identification-and-characterization-of-regulatory-network-components-for-anthocyanin-synthesis-in-barley-aleurone
#10
Ksenia V Strygina, Andreas Börner, Elena K Khlestkina
BACKGROUND: Among natural populations, there are different colours of barley (Hordeum vulgare L.). The colour of barley grains is directly related to the accumulation of different pigments in the aleurone layer, pericarp and lemma. Blue grain colour is due to the accumulation of anthocyanins in the aleurone layer, which is dependent on the presence of five Blx genes that are not sequenced yet (Blx1, Blx3 and Blx4 genes clustering on chromosome 4HL and Blx2 and Blx5 on 7HL). Due to the health benefits of anthocyanins, blue-grained barley can be considered as a source of dietary food...
November 14, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29143346/a-comparative-view-on-the-potential-acting-on-an-electron-in-a-molecule-and-the-electrostatic-potential-through-the-typical-halogen-bonds
#11
Ekaterina Bartashevich, Vladimir Tsirelson
This work considers the features of the electrostatic potential (ESP), and the potential acting on an electron in a molecule (PAEM) for the series of isolated dihalide molecules and for their molecular complexes. The joint analysis of these functions enriches the vision of atomic predispositions to the halogen bond formation and reveals details for their characterization. The account for the exchange-correlation interaction in PAEM retains the specific anisotropy of the ESP, which is commonly used for the halogen bonding explanation within σ-hole concept...
November 15, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29143137/segmental-biventricular-analysis-of-myocardial-function-using-high-temporal-and-spatial-resolution-tissue-phase-mapping
#12
Marius Menza, Daniela Föll, Jürgen Hennig, Bernd Jung
OBJECTIVE: Myocardial dysfunction of the right ventricle (RV) is an important indicator of RV diseases, e.g. RV infarction or pulmonary hypertension. Tissue phase mapping (TPM) has been widely used to determine function of the left ventricle (LV) by analyzing myocardial velocities. The analysis of RV motion is more complicated due to the different geometry and smaller wall thickness. The aim of this work was to adapt and optimize TPM to the demands of the RV. MATERIALS AND METHODS: TPM measurements were acquired in 25 healthy volunteers using a velocity-encoded phase-contrast sequence and kt-accelerated parallel imaging in combination with optimized navigator strategy and blood saturation...
November 15, 2017: Magma
https://www.readbyqxmd.com/read/29142246/a-comprehensive-structural-biochemical-and-biological-profiling-of-the-human-nudix-hydrolase-family
#13
Jordi Carreras-Puigvert, Marinka Zitnik, Ann-Sofie Jemth, Megan Carter, Judith E Unterlass, Björn Hallström, Olga Loseva, Zhir Karem, José Manuel Calderón-Montaño, Cecilia Lindskog, Per-Henrik Edqvist, Damian J Matuszewski, Hammou Ait Blal, Ronnie P A Berntsson, Maria Häggblad, Ulf Martens, Matthew Studham, Bo Lundgren, Carolina Wählby, Erik L L Sonnhammer, Emma Lundberg, Pål Stenmark, Blaz Zupan, Thomas Helleday
The NUDIX enzymes are involved in cellular metabolism and homeostasis, as well as mRNA processing. Although highly conserved throughout all organisms, their biological roles and biochemical redundancies remain largely unclear. To address this, we globally resolve their individual properties and inter-relationships. We purify 18 of the human NUDIX proteins and screen 52 substrates, providing a substrate redundancy map. Using crystal structures, we generate sequence alignment analyses revealing four major structural classes...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#14
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29142224/health-and-disease-phenotyping-in-old-age-using-a-cluster-network-analysis
#15
Jesus Felix Valenzuela, Christopher Monterola, Victor Joo Chuan Tong, Tze Pin Ng, Anis Larbi
Human ageing is a complex trait that involves the synergistic action of numerous biological processes that interact to form a complex network. Here we performed a network analysis to examine the interrelationships between physiological and psychological functions, disease, disability, quality of life, lifestyle and behavioural risk factors for ageing in a cohort of 3,270 subjects aged ≥55 years. We considered associations between numerical and categorical descriptors using effect-size measures for each variable pair and identified clusters of variables from the resulting pairwise effect-size network and minimum spanning tree...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29142207/phosphorylation-dynamics-dominate-the-regulated-proteome-during-early-xenopus-development
#16
Elizabeth H Peuchen, Olivia F Cox, Liangliang Sun, Alex S Hebert, Joshua J Coon, Matthew M Champion, Norman J Dovichi, Paul W Huber
The earliest stages of animal development are largely controlled by changes in protein phosphorylation mediated by signaling pathways and cyclin-dependent kinases. In order to decipher these complex networks and to discover new aspects of regulation by this post-translational modification, we undertook an analysis of the X. laevis phosphoproteome at seven developmental stages beginning with stage VI oocytes and ending with two-cell embryos. Concurrent measurement of the proteome and phosphoproteome enabled measurement of phosphosite occupancy as a function of developmental stage...
November 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29141877/giving-invertebrates-an-eye-exam-an-ophthalmoscope-that-utilizes-the-autofluorescence-of-photoreceptors
#17
Annette Stowasser, Madeline Owens, Elke K Buschbeck
One of the most important functional features of eyes is focusing light, as both nearsightedness and farsightedness have major functional implications. Accordingly, refractive errors are frequently assessed in vertebrates, but not in the very small invertebrate eyes. We describe a micro-ophthalmoscope that takes advantage of autofluorescent properties of invertebrate photoreceptors and test the device on the relatively well-understood eyes of jumping spiders and flies. In each case, our measurements confirmed previous findings with a greater degree of accuracy...
November 15, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/29140711/probing-the-surface-charge-on-the-basal-planes-of-kaolinite-particles-with-high-resolution-atomic-force-microscopy
#18
Naveen Kumar, Martin Peter Andersson, Dirk van den Ende, Frieder Mugele, Igor Siretanu
High resolution Atomic Force Microscopy is used to map the surface charge on the basal planes of kaolinite nanoparticles in an ambient solution of variable pH and NaCl or CaCl2 concentration. Using DLVO theory with charge regulation we determine from the measured force-distance curves the surface charge distribution on both the silica-like and the gibbsite-like basal plane of the kaolinite particles. We observe that both basal planes do carry charge that varies with pH and salt concentration. The silica facet was found to be negatively charged at pH 4 and above, whereas the gibbsite facet is positively charged at pH below 7, and negatively charged at pH above 7...
November 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/29140456/minimotif-miner-4-a-million-peptide-minimotifs-and-counting
#19
Kenneth F Lyon, Xingyu Cai, Richard J Young, Abdullah-Al Mamun, Sanguthevar Rajasekaran, Martin R Schiller
Minimotif Miner (MnM) is a database and web system for analyzing short functional peptide motifs, termed minimotifs. We present an update to MnM growing the database from ∼300 000 to >1 000 000 minimotif consensus sequences and instances. This growth comes largely from updating data from existing databases and annotation of articles with high-throughput approaches analyzing different types of post-translational modifications. Another update is mapping human proteins and their minimotifs to know human variants from the dbSNP, build 150...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29139337/do-people-with-severe-traumatic-brain-injury-benefit-from-making-errors-a-randomized-controlled-trial-of-error-based-and-errorless-learning
#20
Tamara Ownsworth, Jennifer Fleming, Robyn Tate, Elizabeth Beadle, Janelle Griffin, Melissa Kendall, Julia Schmidt, Amanda Lane-Brown, Mathilde Chevignard, David H K Shum
BACKGROUND: Errorless learning (ELL) and error-based learning (EBL) are commonly used approaches to rehabilitation for people with traumatic brain injury (TBI). However, it is unknown whether making errors is beneficial in the learning process to promote skills generalization after severe TBI. OBJECTIVE: To compare the efficacy of ELL and EBL for improving skills generalization, self-awareness, behavioral competency, and psychosocial functioning after severe TBI...
November 1, 2017: Neurorehabilitation and Neural Repair
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