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https://www.readbyqxmd.com/read/28088765/allo-allo-triploid-sphagnum-%C3%A3-falcatulum-single-individuals-contain-most-of-the-holantarctic-diversity-for-ancestrally-indicative-markers
#1
Eric F Karlin, Peter E Smouse
BACKGROUND AND AIMS: Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations...
January 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28088760/usp15-regulates-dynamic-protein-protein-interactions-of-the-spliceosome-through-deubiquitination-of-prp31
#2
Tanuza Das, Joon Kyu Park, Jinyoung Park, Eunji Kim, Michael Rape, Eunice EunKyeong Kim, Eun Joo Song
Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified with K63-linked ubiquitin chains by the PRP19 complex and deubiquitinated by USP15 and its substrate targeting factor SART3. USP15(SART3) makes a complex with USP4 and this ternary complex serves as a platform to deubiquitinate PRP31 and PRP3...
January 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28088739/the-effects-of-rurality-on-substance-use-disorder-diagnosis-a-multiple-groups-latent-class-analysis
#3
Billy Brooks, Matthew McBee, Robert Pack, Arsham Alamian
BACKGROUND: Rates of accidental overdose mortality from substance use disorder (SUD) have risen dramatically in the United States since 1990. Between 1999 and 2004 alone rates increased 62% nationwide, with rural overdose mortality increasing at a rate 3 times that seen in urban populations. Cultural differences between rural and urban populations (e.g., educational attainment, unemployment rates, social characteristics, etc.) affect the nature of SUD, leading to disparate risk of overdose across these communities...
January 6, 2017: Addictive Behaviors
https://www.readbyqxmd.com/read/28088735/long-non-coding-rna-ccat1-promotes-human-retinoblastoma-so-rb50-and-y79-cells-through-negative-regulation-of-mir-218-5p
#4
Hongxu Zhang, Jianguang Zhong, Zhenyu Bian, Xiang Fang, You Peng, Yongping Hu
OBJECTIVE: To investigate the regulatory role and potential mechanism of long non-coding RNAs (lncRNA) in human retinoblastoma (RB). METHODS: The lncRNA profile in RB tissues were analyzed by microarray and quantitative reverse transcription PCR (qRT-PCR). One of the identified lncRNAs (LncRNA CCAT1) was selected for further experiments. SO-RB50 and Y79 cells were transfected with negative control, siRNA targeting lncRNA CCAT1 (si-CCAT1) and si-CCAT1+miR218-5p inhibitor, respectively...
January 12, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28088729/new-insights-into-aox2-transcriptional-regulation-in-chlamydomonas-reinhardtii
#5
Mariya Ostroukhova, Zhanneta Zalutskaya, Elena Ermilova
A feature of the mitochondrial electron transport chain in plants, some protists and many fungi is the presence of two terminal oxidases, the energy-conserving cytochrome oxidase and another termed alternative oxidase (AOX). AOX branches from the main respiratory chain, directly coupling the oxidation of ubiquinol with reduction of oxygen to water. The AOX genes can be divided into two discrete subfamilies, AOX1 and AOX2. Although AOX has been proposed to play essential roles in stress tolerance of organisms, the role of subfamily AOX2 is largely unknown...
December 13, 2016: European Journal of Protistology
https://www.readbyqxmd.com/read/28088619/pappa-ante-portas-the-effect-of-the-husband-s-retirement-on-the-wife-s-mental-health-in-japan
#6
Marco Bertoni, Giorgio Brunello
The "Retired Husband Syndrome", that affects the mental health of wives of retired men around the world, has been anecdotally documented but never formally investigated. Using Japanese micro-data and the exogenous variation across cohorts in the maximum age of guaranteed employment induced by a 2006 Japanese reform, we estimate that the husband's earlier retirement significantly increases the probability that the wife reports symptoms related to the syndrome. We also find that retirement has a negative effect both on the household's economic situation and on the husband's own mental health, and that the higher economic distress contributes to reducing the wife's mental health...
January 9, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/28088548/soil-carbon-dioxide-emissions-from-a-rubber-plantation-on-tropical-peat
#7
Nur Wakhid, Takashi Hirano, Yosuke Okimoto, Siti Nurzakiah, Dedi Nursyamsi
Land-use change in tropical peatland potentially results in a large amount of carbon dioxide (CO2) emissions owing to drainage, which lowers groundwater level (GWL) and consequently enhances oxidative peat decomposition. However, field information on carbon balance is lacking for rubber plantations, which are expanding into Indonesia's peatlands. To assess soil CO2 emissions from an eight-year-old rubber plantation established on peat after compaction, soil CO2 efflux was measured monthly using a closed chamber system from December 2014 to December 2015, in which a strong El Niño event occurred, and consequently GWL lowered deeply...
January 12, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28088516/structural-study-of-the-effects-of-mutations-in-proteins-to-identify-the-molecular-basis-of-the-loss-of-local-structural-fluidity-leading-to-the-onset-of-autoimmune-diseases
#8
Ananya Ali, Semanti Ghosh, Angshuman Bagchi
Protein-Protein Interactions (PPIs) are crucial in most of the biological processes and PPI dysfunctions are known to be associated with the onsets of various diseases. One of such diseases is the auto-immune disease. Auto-immune diseases are one among the less studied group of diseases with very high mortality rates. Thus, we tried to correlate the appearances of mutations with their probable biochemical basis of the molecular mechanisms leading to the onset of the disease phenotypes. We compared the effects of the Single Amino Acid Variants (SAVs) in the wild type and mutated proteins to identify any structural deformities that might lead to altered PPIs leading ultimately to disease onset...
January 11, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28088499/initial-uncertainty-impacts-statistical-learning-in-sound-sequence-processing
#9
Juanita Todd, Alexander Provost, Lisa Whitson, Daniel Mullens
This paper features two studies confirming a lasting impact of first learning on how subsequent experience is weighted in early relevance-filtering processes. In both studies participants were exposed to sequences of sound that contained a regular pattern on two different timescales. Regular patterning in sound is readily detected by the auditory system and used to form "prediction models" that define the most likely properties of sound to be encountered in a given context. The presence and strength of these prediction models is inferred from changes in automatically elicited components of auditory evoked potentials...
January 11, 2017: Journal of Physiology, Paris
https://www.readbyqxmd.com/read/28088482/combined-spatiotemporal-ica-stica-for-continuous-and-dynamic-lag-structure-analysis-of-mreg-data
#10
Ville Raatikainen, Niko Huotari, Vesa Korhonen, Aleksi Rasila, Janne Kananen, Lauri Raitamaa, Tuija Keinänen, Jussi Kantola, Osmo Tervonen, Vesa Kiviniemi
This study investigated lag structure in the resting-state fMRI by applying a novel independent component (ICA) method to magnetic resonance encephalography (MREG) data. Briefly, the spatial ICA (sICA) was used for defining the frontal and back nodes of the default mode network (DMN), and the temporal ICA (tICA), which is enabled by the high temporal resolution of MREG (TR=100ms), was used to separate both neuronal and physiological components of these two spatial map regions. Subsequently, lag structure was investigated between the frontal (DMNvmpf) and posterior (DMNpcc) DMN nodes using both conventional method with all-time points and a sliding-window approach...
January 11, 2017: NeuroImage
https://www.readbyqxmd.com/read/28088446/identification-and-characterization-of-cell-bound-membrane-vesicles
#11
Qisheng Tang, Xiaojun Zhang, Wendiao Zhang, Siyuan Zhao, Yong Chen
In contrast to the released/circulating membrane vesicles (extracellular vesicles), cell-bound membrane vesicles are poorly identified and characterized. In this study, cell-bound membrane vesicles on human umbilical vein endothelial cells (HUVECs) and human hepatoma HepG-2 cells were investigated. We identified that cell-bound membrane vesicles are not co-localized with the major markers for extracellular vesicles (e.g. phosphatidylserine, CD63, CD107α, CD31, and DNA fragments for the three well-known types of extracellular vesicles) and for intracellular organelles with similar sizes (e...
January 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28088363/seasonal-variations-of-u-s-mortality-rates-roles-of-solar-ultraviolet-b-doses-vitamin-d-gene-exp-ression-and-infections
#12
REVIEW
William B Grant, Harjit Pal Bhattoa, Barbara J Boucher
Death rates in the U.S. show a pronounced seasonality. The broad seasonal variation shows about 25% higher death rates in winter than in summer with an additional few percent increase associated with the Christmas and New Year's holidays. A pronounced increase in death rates also starts in mid-September, shortly after the school year begins. The causes of death with large contributions to the observed seasonality include diseases of the circulatory system; the respiratory system; the digestive system; and endocrine, nutritional, and metabolic diseases...
January 11, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28088341/evaluation-of-an-in-house-indirect-elisa-for-detection-of-antibody-against-haemorrhagic-septicemia-in-asian-elephants
#13
Pallop Tankaew, Thawatchai Singh-La, Chatchote Titaram, Veerasak Punyapornwittaya, Preeyanat Vongchan, Takuo Sawada, Nattawooti Sthitmatee
Pasteurella multocida causes haemorrhagic septicemia in livestock and wild animals, including elephants. The disease has been reported in Asian elephants in India and Sri Lanka, but to date there have been no reported cases in Thailand. ELISA or indirect hemagglutination assays (IHA) have been demonstrated to be able to detect the antibody against the disease in cattle, but no data are available for elephants. The present study reports a novel in-house indirect ELISA for antibody detection of haemorrhagic septicemia in Asian elephants, and evaluates the sensitivity and specificity of the method using a Bayesian approach...
January 11, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28088195/automatic-liver-segmentation-based-on-appearance-and-context-information
#14
Yongchang Zheng, Danni Ai, Jinrong Mu, Weijian Cong, Xuan Wang, Haitao Zhao, Jian Yang
BACKGROUND: Automated image segmentation has benefits for reducing clinicians' workload, quicker diagnosis, and a standardization of the diagnosis. METHODS: This study proposes an automatic liver segmentation approach based on appearance and context information. The relationship between neighboring pixels in blocks is utilized to estimate appearance information, which is used for training the first classifier and obtaining the probability distribution map. The map is used for extracting context information, along with appearance features, to train the next classifier...
January 14, 2017: Biomedical Engineering Online
https://www.readbyqxmd.com/read/28088191/predicting-probable-alzheimer-s-disease-using-linguistic-deficits-and-biomarkers
#15
Sylvester O Orimaye, Jojo S-M Wong, Karen J Golden, Chee P Wong, Ireneous N Soyiri
BACKGROUND: The manual diagnosis of neurodegenerative disorders such as Alzheimer's disease (AD) and related Dementias has been a challenge. Currently, these disorders are diagnosed using specific clinical diagnostic criteria and neuropsychological examinations. The use of several Machine Learning algorithms to build automated diagnostic models using low-level linguistic features resulting from verbal utterances could aid diagnosis of patients with probable AD from a large population...
January 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28088184/anti-hepatitis-b-virus-hbv-response-of-imiquimod-based-toll-like-receptor-7-ligand-in-hbv-positive-human-hepatocelluar-carcinoma-cell-line
#16
Dipanwita Das, Isha Sengupta, Neelakshi Sarkar, Ananya Pal, Debraj Saha, Manikankana Bandopadhyay, Chandrima Das, Jimmy Narayan, Shivaram Prasad Singh, Sekhar Chakrabarti, Runu Chakravarty
BACKGROUND: Toll like receptors (TLRs) play an important role in innate immunity and various studies suggest that TLRs play a crucial role in pathogenesis of hepatitis B virus (HBV) infection. The present study aims in looking into the status of crucial host and viral gene expression on inciting TLR7. METHODS: The transcription of TLR7 pathway signaling molecules and HBV DNA viral load were quantified by Real Time-PCR after stimulation of TLR7 with its imiquimod based ligand, R837...
January 14, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#17
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28088146/photoinduced-c-i-bond-homolysis-of-5-iodouracil-a-singlet-predissociation-pathway
#18
Xiaojuan Dai, Di Song, Kunhui Liu, Hongmei Su
5-Iodouracil (5-IU) can be integrated into DNA and acts as a UV sensitive chromophore suitable for probing DNA structure and DNA-protein interactions based on the photochemical reactions of 5-IU. Here, we perform joint studies of time-resolved Fourier transform infrared (TR-FTIR) spectroscopy and ab initio calculations to examine the state-specific photochemical reaction mechanisms of the 5-IU. The fact that uracil (U) is observed in TR-FTIR spectra after 266 nm irradiation of 5-IU in acetonitrile and ascribed to the product of hydrogen abstraction by the uracil-5-yl radical (U·) provides experimental evidence for the C-I bond homolysis of 5-IU...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088140/ring-polymer-molecular-dynamics-studies-on-the-rate-coefficient-of-the-abstraction-channel-of-hydrogen-plus-ethane-propane-and-dimethyl-ether
#19
Qingyong Meng, Jun Chen
To accurately compute the rates of the abstraction channels of hydrogen plus ethane (Et), propane (Pr), and dimethyl ether (DME), ring-polymer molecular dynamics (RPMD) method is used in conjunction with the recently constructed local permutation invariant polynomial neural-networks potential energy surface of the parent H + CH4 system [Q. Meng et al., J. Chem. Phys. 144, 154312 (2016)]. For H + Et, one of the H atoms in CH4 of the parent system is replaced by a methyl group, while for the H + DME reaction, it is replaced by the methoxyl group...
January 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28088137/forces-on-nuclei-moving-on-autoionizing-molecular-potential-energy-surfaces
#20
Nimrod Moiseyev
Autoionization of molecular systems occurs in diatomic molecules and in small biochemical systems. Quantum chemistry packages enable calculation of complex potential energy surfaces (CPESs). The imaginary part of the CPES is associated with the autoionization decay rate, which is a function of the molecular structure. Molecular dynamics simulations, within the framework of the Born-Oppenheimer approximation, require the definition of a force field. The ability to calculate the forces on the nuclei in bio-systems when autoionization takes place seems to rely on an understanding of radiative damages in RNA and DNA arising from the release of slow moving electrons which have long de Broglie wavelengths...
January 14, 2017: Journal of Chemical Physics
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