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https://www.readbyqxmd.com/read/29237467/estimating-drivers-of-cell-state-transitions-using-gene-regulatory-network-models
#1
Daniel Schlauch, Kimberly Glass, Craig P Hersh, Edwin K Silverman, John Quackenbush
BACKGROUND: Specific cellular states are often associated with distinct gene expression patterns. These states are plastic, changing during development, or in the transition from health to disease. One relatively simple extension of this concept is to recognize that we can classify different cell-types by their active gene regulatory networks and that, consequently, transitions between cellular states can be modeled by changes in these underlying regulatory networks. RESULTS: Here we describe MONSTER, MOdeling Network State Transitions from Expression and Regulatory data, a regression-based method for inferring transcription factor drivers of cell state conditions at the gene regulatory network level...
December 13, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29234348/diurnal-transcriptome-and-gene-network-represented-through-sparse-modeling-in-brachypodium-distachyon
#2
Satoru Koda, Yoshihiko Onda, Hidetoshi Matsui, Kotaro Takahagi, Yukiko Yamaguchi-Uehara, Minami Shimizu, Komaki Inoue, Takuhiro Yoshida, Tetsuya Sakurai, Hiroshi Honda, Shinto Eguchi, Ryuei Nishii, Keiichi Mochida
We report the comprehensive identification of periodic genes and their network inference, based on a gene co-expression analysis and an Auto-Regressive eXogenous (ARX) model with a group smoothly clipped absolute deviation (SCAD) method using a time-series transcriptome dataset in a model grass, Brachypodium distachyon. To reveal the diurnal changes in the transcriptome in B. distachyon, we performed RNA-seq analysis of its leaves sampled through a diurnal cycle of over 48 h at 4 h intervals using three biological replications, and identified 3,621 periodic genes through our wavelet analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29229523/inference-in-population-genetics-using-forward-and-backward-discrete-and-continuous-time-processes
#3
Juraj Bergman, Dominik Schrempf, Carolin Kosiol, Claus Vogl
A central aim of population genetics is the inference of the evolutionary history of a population. To this end, the underlying process can be represented by a model of the evolution of allele frequencies parametrized by e.g., the population size, mutation rates and selection coefficients. A large class of models use forward-in-time models, such as the discrete Wright-Fisher and Moran models and the continuous forward diffusion, to obtain distributions of population allele frequencies, conditional on an ancestral initial allele frequency distribution...
December 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29228063/what-matters-in-chronic-burkholderia-cenocepacia-infection-in-cystic-fibrosis-insights-from-comparative-genomics
#4
Jaroslav Nunvar, Vaclav Capek, Karel Fiser, Libor Fila, Pavel Drevinek
Burkholderia cenocepacia causes severe pulmonary infections in cystic fibrosis (CF) patients. Since the bacterium is virtually untreatable by antibiotics, chronic infections persist for years and might develop into fatal septic pneumonia (cepacia syndrome, CS). To devise new strategies to combat chronic B. cenocepacia infections, it is essential to obtain comprehensive knowledge about their pathogenesis. We conducted a comparative genomic analysis of 32 Czech isolates of epidemic clone B. cenocepacia ST32 isolated from various stages of chronic infection in 8 CF patients...
December 11, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/29222478/viscosity-jump-in-the-lower-mantle-inferred-from-melting-curves-of-ferropericlase
#5
Jie Deng, Kanani K M Lee
Convection provides the mechanism behind plate tectonics, which allows oceanic lithosphere to be subducted into the mantle as "slabs" and new rock to be generated by volcanism. Stagnation of subducting slabs and deflection of rising plumes in Earth's shallow lower mantle have been suggested to result from a viscosity increase at those depths. However, the mechanism for this increase remains elusive. Here, we examine the melting behavior in the MgO-FeO binary system at high pressures using the laser-heated diamond-anvil cell and show that the liquidus and solidus of (Mg x Fe1-x )O ferropericlase (x = ~0...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222064/evolution-in-the-amphi-atlantic-tropical-genus-guibourtia-fabaceae-detarioideae-combining-ngs-phylogeny-and-morphology
#6
Félicien Tosso, Olivier J Hardy, Jean-Louis Doucet, Kasso Daïnou, Esra Kaymak, Jérémy Migliore
Tropical rain forests support a remarkable diversity of tree species, questioning how and when this diversity arose. The genus Guibourtia (Fabaceae, Detarioideae), characterized by two South American and 13 African tree species growing in various tropical biomes, is an interesting model to address the role of biogeographic processes and adaptation to contrasted environments on species diversification. Combining whole plastid genome sequencing and morphological characters analysis, we studied the timing of speciation and diversification processes in Guibourtia through molecular dating and ancestral habitats reconstruction...
December 5, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29216360/comprehensive-genome-wide-classification-reveals-that-many-plant-specific-transcription-factors-evolved-in-streptophyte-algae
#7
Per K I Wilhelmsson, Cornelia Mühlich, K Ullrich Kristian, Stefan A Rensing
Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availability of plant genomes. We have updated and expanded previous rule sets for domain-based classification of transcription associated proteins (TAPs), comprising transcription factors and transcriptional regulators...
December 5, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29212722/first-satellite-tracks-of-south-atlantic-sea-turtle-lost-years-seasonal-variation-in-trans-equatorial-movement
#8
Katherine L Mansfield, Milagros L Mendilaharsu, Nathan F Putman, Maria A G Dei Marcovaldi, Alexander E Sacco, Gustave Lopez, Thais Pires, Yonat Swimmer
In the South Atlantic Ocean, few data exist regarding the dispersal of young oceanic sea turtles. We characterized the movements of laboratory-reared yearling loggerhead turtles from Brazilian rookeries using novel telemetry techniques, testing for differences in dispersal during different periods of the sea turtle hatching season that correspond to seasonal changes in ocean currents. Oceanographic drifters deployed alongside satellite-tagged turtles allowed us to explore the mechanisms of dispersal (passive drift or active swimming)...
December 6, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29211022/tracking-functional-tumor-cell-subpopulations-of-malignant-glioma-by-phasor-fluorescence-lifetime-imaging-microscopy-of-nadh
#9
Andrew L Trinh, Hongtao Chen, Yumay Chen, Yuanjie Hu, Zhenzhi Li, Eric R Siegel, Mark E Linskey, Ping H Wang, Michelle A Digman, Yi-Hong Zhou
Intra-tumoral heterogeneity is associated with therapeutic resistance of cancer and there exists a need to non-invasively identify functional tumor subpopulations responsible for tumor recurrence. Reduced nicotinamide adenine dinucleotide (NADH) is a metabolic coenzyme essential in cellular respiration. Fluorescence lifetime imaging microscopy (FLIM) of NADH has been demonstrated to be a powerful label-free indicator for inferring metabolic states of living cells. Using FLIM, we identified a significant shift towards longer NADH fluorescence lifetimes, suggesting an increase in the fraction of protein-bound NADH, in the invasive stem-like tumor-initiating cell (STIC) subpopulation relative to the tumor mass-forming cell (TMC) subpopulation of malignant gliomas...
December 6, 2017: Cancers
https://www.readbyqxmd.com/read/29207942/a-reconstruction-of-sexual-modes-throughout-animal-evolution
#10
Daniel A Sasson, Joseph F Ryan
BACKGROUND: Although most extant animals have separate sexes, simultaneous hermaphrodites can be found in lineages throughout the animal kingdom. However, the sexual modes of key ancestral nodes including the last common ancestor (LCA) of all animals remain unclear. Without these data, it is difficult to infer the reproductive-state transitions that occurred early in animal evolution, and thus a broad understanding of the evolution of animal reproduction remains elusive. In this study, we use a composite phylogeny from four previously published studies, two alternative topologies (ctenophores or sponges as sister to the rest of animals), and multiple phylogenetic approaches to conduct the most extensive analysis to date of the evolution of animal sexual modes...
December 6, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/29206842/from-menarche-to-menopause-a-population-based-assessment-of-water-sanitation-and-hygiene-risk-factors-for-reproductive-tract-infection-symptoms-over-life-stages-in-rural-girls-and-women-in-india
#11
Kelly K Baker, Bijaya Padhi, Belen Torondel, Padmalaya Das, Ambarish Dutta, Krushna Chandra Sahoo, Bhabani Das, Robert Dreibelbis, Bethany Caruso, Matthew C Freeman, Lauren Sager, Pinaki Panigrahi
Women face greater challenges than men in accessing water, sanitation, and hygiene (WASH) resources to address their daily needs, and may respond to these challenges by adopting unsafe practices that increase the risk of reproductive tract infections (RTIs). WASH practices may change as women transition through socially-defined life stage experiences, like marriage and pregnancy. Thus, the relationship between WASH practices and RTIs might vary across female reproductive life stages. This cross-sectional study assessed the relationship between WASH exposures and self-reported RTI symptoms in 3,952 girls and women from two rural districts in India, and tested whether social exposures represented by reproductive life stage was an effect modifier of associations...
2017: PloS One
https://www.readbyqxmd.com/read/29203767/crystal-plasticity-as-an-indicator-of-the-viscous-brittle-transition-in-magmas
#12
J E Kendrick, Y Lavallée, E Mariani, D B Dingwell, J Wheeler, N R Varley
Understanding the flow of multi-phase (melt, crystals and bubbles) magmas is of great importance for interpreting eruption dynamics. Here we report the first observation of crystal plasticity, identified using electron backscatter diffraction, in plagioclase in andesite dome lavas from Volcán de Colima, Mexico. The same lavas, deformed experimentally at volcanic conduit temperature and load conditions, exhibit a further, systematic plastic response in the crystalline fraction, observable as a lattice misorientation...
December 4, 2017: Nature Communications
https://www.readbyqxmd.com/read/29196741/bayesian-inference-of-epidemiological-parameters-from-transmission-experiments
#13
Ben Hu, Jose L Gonzales, Simon Gubbins
Epidemiological parameters for livestock diseases are often inferred from transmission experiments. However, there are several limitations inherent to the design of such experiments that limits the precision of parameter estimates. In particular, infection times and latent periods cannot be directly observed and infectious periods may also be censored. We present a Bayesian framework accounting for these features directly and employ Markov chain Monte Carlo techniques to provide robust inferences and quantify the uncertainty in our estimates...
December 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29188837/synthesis-spectroscopic-characterisation-and-transmetalation-of-lithium-and-potassium-diaminophosphanide-boranes
#14
M Blum, J Kappler, S H Schlindwein, M Nieger, D Gudat
A secondary diaminophosphane-borane (Et2N)2PH(BH3) was prepared from a chlorophosphane precursor and LiBH4 and metalated by reaction with anion bases (n-BuLi, KN(SiMe3)2) to yield the corresponding metal diaminophosphanide-boranes [(Et2N)2P(BH3)]M (M = Li, K). Multinuclear NMR studies permitted the first spectroscopic characterisation of the metalation products and revealed the presence of monomeric (for M = Li) contact ion pairs in solution. NMR spectroscopic evidence that the ions in each pair interact via LiP- rather than LiH3B-interactions as had been inferred for a Ph-substituted analogue was confirmed by DFT studies, which revealed also that the borane coordination plays a decisive role in boosting the PH-acidity of the original secondary diaminophosphane precursor...
November 30, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29183981/robust-zero-resistance-in-a-superconducting-high-entropy-alloy-at-pressures-up-to-190-gpa
#15
Jing Guo, Honghong Wang, Fabian von Rohr, Zhe Wang, Shu Cai, Yazhou Zhou, Ke Yang, Aiguo Li, Sheng Jiang, Qi Wu, Robert J Cava, Liling Sun
We report the observation of extraordinarily robust zero-resistance superconductivity in the pressurized (TaNb)0.67(HfZrTi)0.33 high-entropy alloy--a material with a body-centered-cubic crystal structure made from five randomly distributed transition-metal elements. The transition to superconductivity (TC ) increases from an initial temperature of 7.7 K at ambient pressure to 10 K at ∼60 GPa, and then slowly decreases to 9 K by 190.6 GPa, a pressure that falls within that of the outer core of the earth. We infer that the continuous existence of the zero-resistance superconductivity from 1 atm up to such a high pressure requires a special combination of electronic and mechanical characteristics...
November 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29180424/causes-of-ice-age-intensification-across-the-mid-pleistocene-transition
#16
Thomas B Chalk, Mathis P Hain, Gavin L Foster, Eelco J Rohling, Philip F Sexton, Marcus P S Badger, Soraya G Cherry, Adam P Hasenfratz, Gerald H Haug, Samuel L Jaccard, Alfredo Martínez-García, Heiko Pälike, Richard D Pancost, Paul A Wilson
During the Mid-Pleistocene Transition (MPT; 1,200-800 kya), Earth's orbitally paced ice age cycles intensified, lengthened from ∼40,000 (∼40 ky) to ∼100 ky, and became distinctly asymmetrical. Testing hypotheses that implicate changing atmospheric CO2 levels as a driver of the MPT has proven difficult with available observations. Here, we use orbitally resolved, boron isotope CO2 data to show that the glacial to interglacial CO2 difference increased from ∼43 to ∼75 μatm across the MPT, mainly because of lower glacial CO2 levels...
November 27, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29179670/detecting-transitions-in-protein-dynamics-using-a-recurrence-quantification-analysis-based-bootstrap-method
#17
Wael I Karain
BACKGROUND: Proteins undergo conformational transitions over different time scales. These transitions are closely intertwined with the protein's function. Numerous standard techniques such as principal component analysis are used to detect these transitions in molecular dynamics simulations. In this work, we add a new method that has the ability to detect transitions in dynamics based on the recurrences in the dynamical system. It combines bootstrapping and recurrence quantification analysis...
November 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29175095/phylogeny-and-biogeography-of-east-asian-evergreen-oaks-quercus-section-cyclobalanopsis-fagaceae-insights-into-the-cenozoic-history-of-evergreen-broad-leaved-forests-in-subtropical-asia
#18
Min Deng, Xiao-Long Jiang, Andrew L Hipp, Paul S Manos, Marlene Hahn
The evolutionary history of Quercus section Cyclobalanopsis, a dominant lineage in East Asian evergreen broadleaved forests (EBLFs), has not been comprehensively studied using molecular tools. In this study, we reconstruct the first comprehensive phylogeny of this lineage using a genomic approach (restriction-site associated DNA sequencing, RAD-seq), sampling 35 of the ca. 90 species currently recognized, representing all main morphological groups of section Cyclobalanopsis. In addition, 10 other species of Quercus and two outgroups were also sampled...
November 21, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29171963/indium-selenide-monolayer-strain-enhanced-optoelectronic-response-and-dielectric-environment-tunable-2d-exciton-features
#19
Imen Ben Amara, Aida Hichri, Sihem Jaziri
Electronic and optical performances of the β-InSe monolayer (ML) are considerably boosted by tuning the corresponding band energies through lattice in-plane compressive strain engineering. First principles calculations show an indirect-direct gap transition with a large bandgap size. The crossover is due to different responses of the near-gap state energies with respect to strain. This is explained by the variation of In-Se bond length, the bond nature of near-band-edge electronic orbital and of the momentum angular contribution versus in-plane compressive strain...
November 24, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29168077/progress-and-challenges-of-sequencing-and-analyzing-circulating-tumor-cells
#20
REVIEW
Zhongyi Zhu, Si Qiu, Kang Shao, Yong Hou
Circulating tumor cells (CTCs) slough off primary tumor tissues and are swept away by the circulatory system. These CTCs can remain in circulation or colonize new sites, forming metastatic clones in distant organs. Recently, CTC analyses have been successfully used as effective clinical tools to monitor tumor progression and prognosis. With advances in next-generation sequencing (NGS) and single-cell sequencing (SCS) technologies, scientists can obtain the complete genome of a CTC and compare it with corresponding primary and metastatic tumors...
November 22, 2017: Cell Biology and Toxicology
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