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https://www.readbyqxmd.com/read/28934478/tuning-rna-folding-and-function-through-rational-design-of-junction-topology
#1
May Daher, Anthony M Mustoe, Alex Morriss-Andrews, Charles L Brooks Iii, Nils G Walter
Structured RNAs such as ribozymes must fold into specific 3D structures to carry out their biological functions. While it is well-known that architectural features such as flexible junctions between helices help guide RNA tertiary folding, the mechanisms through which junctions influence folding remain poorly understood. We combine computational modeling with single molecule Förster resonance energy transfer (smFRET) and catalytic activity measurements to investigate the influence of junction design on the folding and function of the hairpin ribozyme...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934431/genetic-profiling-and-comorbidities-of-zika-infection
#2
Mohammad Ali Moni, Pietro Lio'
Background: The difficulty in distinguishing infection by Zika virus (ZIKV) from other flaviviruses is a global health concern, particularly given the high risk of neurologic complications (including Guillain-Barré syndrome [GBS]) with ZIKV infection. Methods: We developed quantitative frameworks to compare and explore infectome, diseasome, and comorbidity of ZIKV infections. We analyzed gene expression microarray and RNA-Seq data from ZIKV, West Nile fever (WNF), chikungunya, dengue, yellow fever, Japanese encephalitis virus, GBS, and control datasets...
September 15, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28934378/investigating-difficult-nodes-in-the-placental-mammal-tree-with-expanded-taxon-sampling-and-thousands-of-ultraconserved-elements
#3
Jacob A Esselstyn, Carl H Oliveros, Mark T Swanson, Brant C Faircloth
The phylogeny of eutherian mammals contains some of the most recalcitrant nodes in the tetrapod tree of life. We combined comprehensive taxon and character sampling to explore three of the most debated interordinal relationships among placental mammals. We performed in silico extraction of ultraconserved element loci from 72 published genomes and invitro enrichment and sequencing of ultraconserved elements from 28 additional mammals, resulting in alignments of 3,787 loci. We analyzed these data using concatenated and multispecies coalescent phylogenetic approaches, topological tests, and exploration of support among individual loci to identify the root of Eutheria and the sister groups of tree shrews (Scandentia) and horses (Perissodactyla)...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28934236/automated-computer-assisted-quantitative-analysis-of-intact-murine-lungs-at-the-alveolar-scale
#4
Goran Lovric, Ioannis Vogiatzis Oikonomidis, Rajmund Mokso, Marco Stampanoni, Matthias Roth-Kleiner, Johannes C Schittny
Using state-of-the-art X-ray tomographic microscopy we can image lung tissue in three dimensions in intact animals down to a micrometer precision. The structural complexity and hierarchical branching scheme of the lung at this level of details, however, renders the extraction of biologically relevant quantities particularly challenging. We have developed a methodology for a detailed description of lung inflation patterns by measuring the size and the local curvature of the parenchymal airspaces. These quantitative tools for morphological and topological analyses were applied to high-resolution murine 3D lung image data, inflated at different pressure levels under immediate post mortem conditions...
2017: PloS One
https://www.readbyqxmd.com/read/28934171/design-and-analysis-of-an-efficient-energy-algorithm-in-wireless-social-sensor-networks
#5
Naixue Xiong, Longzhen Zhang, Wei Zhang, Athanasios V Vasilakos, Muhammad Imran
Because mobile ad hoc networks have characteristics such as lack of center nodes, multi-hop routing and changeable topology, the existing checkpoint technologies for normal mobile networks cannot be applied well to mobile ad hoc networks. Considering the multi-frequency hierarchy structure of ad hoc networks, this paper proposes a hybrid checkpointing strategy which combines the techniques of synchronous checkpointing with asynchronous checkpointing, namely the checkpoints of mobile terminals in the same cluster remain synchronous, and the checkpoints in different clusters remain asynchronous...
September 21, 2017: Sensors
https://www.readbyqxmd.com/read/28933827/three-cadmium-coordination-polymers-with-carboxylate-and-pyridine-mixed-ligands-luminescent-sensors-for-fe-iii-and-cr-vi-ions-in-an-aqueous-medium
#6
Yanna Lin, Xiaoping Zhang, Wenjie Chen, Wei Shi, Peng Cheng
Three new water-stable luminescent Cd(II) coordination polymers (CPs), {[Cd2(bptc)(2,2'-bipy)2(H2O)2]}n (1), {[Cd2(bptc)(phen)2]·4H2O}n (2), and {[Cd2(bptc)(4,4'-bipy)(H2O)2]·4H2O}n (3), were solvothermally synthesized with mixed ligands of 3,3',5,5'-biphenyltetracarboxylic acid (H4bptc) and N-donor ligands (2,2'-bipy = 2,2'-bipyridine; phen = 1,10-phenanthroline; 4,4'-bipy = 4,4'-bipyridine). The CPs 1-3 show structural diversity from a 1D ladder chain to a 2D layer to a 3D porous framework, tuned by different ancillary ligands...
September 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28933539/a-3d-coordination-network-built-from-cu-ii-4cl3-h2o-2-linear-clusters-and-tetrapyridyl-tetrahedral-silane-ligands-reversible-iodine-uptake-and-friedel-crafts-alkylation-reactions
#7
Mahesh S Deshmukh, Atul Chaudhary, Pavel N Zolotarev, Ramamoorthy Boomishankar
A novel three-dimensional coordination network 1 in a new 4,5,6-connected topology (4,5,6T115) built from linear Cu(II)4Cl3(H2O)2 clusters and tetrahedral tetrakis(3-pyridyl)vinylsilane ligands is reported. Utilizing a similar tetrahedral ligand, tetrakis(3-pyridyl)ethylsilane, a different framework 2 having Cu(II)2Cl(H2O)2 clusters is obtained in tcs topology. The activated sample of 1 shows an excellent and reversible uptake of I2 in solid as well as in solution phases owing to the presence of uncoordinated chloride ions and electron rich vinylic groups in it...
September 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28933427/tunable-interacting-composite-fermion-phases-in-a-half-filled-bilayer-graphene-landau-level
#8
A A Zibrov, C Kometter, H Zhou, E M Spanton, T Taniguchi, K Watanabe, M P Zaletel, A F Young
Non-Abelian anyons are a type of quasiparticle with the potential to encode quantum information in topological qubits protected from decoherence. Experimental systems that are predicted to harbour non-Abelian anyons include p-wave superfluids, superconducting systems with strong spin-orbit coupling, and paired states of interacting composite fermions that emerge at even denominators in the fractional quantum Hall (FQH) regime. Although even-denominator FQH states have been observed in several two-dimensional systems, small energy gaps and limited tunability have stymied definitive experimental probes of their non-Abelian nature...
September 20, 2017: Nature
https://www.readbyqxmd.com/read/28933027/learning-directed-acyclic-graphs-from-large-scale-genomics-data
#9
Fabio Nikolay, Marius Pesavento, George Kritikos, Nassos Typas
In this paper, we consider the problem of learning the genetic interaction map, i.e., the topology of a directed acyclic graph (DAG) of genetic interactions from noisy double-knockout (DK) data. Based on a set of well-established biological interaction models, we detect and classify the interactions between genes. We propose a novel linear integer optimization program called the Genetic-Interactions-Detector (GENIE) to identify the complex biological dependencies among genes and to compute the DAG topology that matches the DK measurements best...
September 20, 2017: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28932994/investigation-of-shape-with-patients-suffering-from-unilateral-lymphoedema
#10
Kevork Karakashian, Lawrence Shaban, Cheryl Pike, Raoul van Loon
This study investigates the use of a 3D depth sensing camera for analysing the shape of lymphoedematous arms, and seeks to identify suitable metrics for monitoring lymphoedema clinically. A fast, simple protocol was developed for scanning upper limb lymphoedema, after which a robust data pre- and post-processing framework was built that consistently and quickly identifies arm shape and volume. The framework was then tested on 24 patients with mild unilateral lymphoedema, who were also assessed using tape measurements...
September 20, 2017: Annals of Biomedical Engineering
https://www.readbyqxmd.com/read/28932836/recent-advances-in-structural-studies-of-heterometallic-uranyl-containing-coordination-polymers-and-polynuclear-closed-species
#11
Pierre Thuéry, Jack Harrowfield
An overview is given of recent structural studies on heterometallic uranyl-containing species, with particular emphasis on those formed with carboxylate ligands, showing the effect of the additional metal cations and ancillary ligands on the dimensionality, geometry and topology of the assemblies generated. These examples illustrate the level of elaboration which is now possible in the design and synthesis of both uranyl clusters and coordination polymers, properties and potential applications of which are also briefly discussed...
September 21, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28932458/kinas2o7-a-new-diarsenate-with-the-tlinas2o7-structure-type
#12
Karolina Schwendtner, Uwe Kolitsch
Potassium indium diarsenate(V) was grown under mild hydro-thermal conditions (T = 493 K, 7 d) at a pH value of about 1. It adopts the TlInAs2O7 structure type (P-1, Z = 4) and is closely related to the KAlP2O7 (P21/c) and RbAlAs2O7 (P-1) structure types. The framework topology of KInAs2O7 is built of two symmetrically non-equivalent As2O7 groups which share corners with InO6 octa-hedra. The K atoms are located in channels extending along [010].
September 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/28932428/a-one-dimensional-coordination-polymer-catena-poly-n-ethyl-n-pyridin-4-ylmeth-yl-di-thio-carbamato-%C3%AE%C2%BA-2-s-s-zinc-ii-%C3%AE-2-n-ethyl-n-pyridin-4-ylmeth-yl-di-thio-carbamato-%C3%AE%C2%BA-3-s-s-n-4-methyl-pyridine-hemisolvate
#13
Pavel Poplaukhin, Hadi D Arman, Edward R T Tiekink
The title compound, {[Zn(C9H11N2S2)2]·0.5C6H7N} n , comprises two independent, but chemically similar, Zn[S2CN(Et)CH2py]2 residues and a 4-methyl-pyridine solvent mol-ecule in the asymmetric unit. The Zn-containing units are connected into a one-dimensional coordination polymer (zigzag topology) propagating in the [010] direction, with one di-thio-carbamate ligand bridging in a μ2-κ(3) mode, employing one pyridyl N and both di-thio-carbamate S atoms, while the other is κ(2)-chelating. In each case, the resultant ZnNS4 coordination geometry approximates a square pyramid, with the pyridyl N atom in the apical position...
July 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/28931836/matching-dmft-calculations-with-photoemission-spectra-of-heavy-fermion-insulators-universal-properties-of-the-near-gap-spectra-of-smb6
#14
Chul-Hee Min, F Goth, P Lutz, H Bentmann, B Y Kang, B K Cho, J Werner, K-S Chen, F Assaad, F Reinert
Paramagnetic heavy fermion insulators consist of fully occupied quasiparticle bands inherent to Fermi liquid theory. The gap emergence below a characteristic temperature is the ultimate sign of coherence for a many-body system, which in addition can induce a non-trivial band topology. Here, we demonstrate a simple and efficient method to compare a model study and an experimental result for heavy fermion insulators. The temperature dependence of the gap formation in both local moment and mixed valence regimes is captured within the dynamical mean field (DMFT) approximation to the periodic Anderson model (PAM)...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931825/disrupted-topological-organization-of-structural-brain-networks-in-childhood-absence-epilepsy
#15
Wenchao Qiu, Chuanyong Yu, Yuan Gao, Ailiang Miao, Lu Tang, Shuyang Huang, Wenwen Jiang, Jintao Sun, Jing Xiang, Xiaoshan Wang
Childhood absence epilepsy (CAE) is the most common paediatric epilepsy syndrome and is characterized by frequent and transient impairment of consciousness. In this study, we explored structural brain network alterations in CAE and their association with clinical characteristics. A whole-brain structural network was constructed for each participant based on diffusion-weighted MRI and probabilistic tractography. The topological metrics were then evaluated. For the first time, we uncovered modular topology in CAE patients that was similar to healthy controls...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931690/conformational-changes-in-the-5-end-of-the-hiv-1-genome-dependent-on-the-debranching-enzyme-dbr1-during-early-stages-of-infection
#16
Alvaro E Galvis, Hugh E Fisher, Hung Fan, David Camerini
Previous studies in our laboratory showed that the RNA debranching enzyme (DBR1) is not required for early steps in HIV cDNA formation, but is necessary for synthesis of intermediate and late cDNA products. To further characterize this effect, we evaluated the topology of the 5' end of the HIV-1 RNA genome during early infection with and without inhibition of DBR1 synthesis. Cells were transfected with DBR1 shRNA followed 48 hours later by infection with an HIV-1 derived vector containing an RNase H deficient reverse transcriptase...
September 20, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28931613/interacting-networks-of-brain-regions-underlie-human-spatial-navigation-a-review-and-novel-synthesis-of-the-literature
#17
Arne D Ekstrom, Derek J Huffman, Michael Starrett
Navigation is an inherently dynamic and multimodal process, making isolation of the unique cognitive components underlying it challenging. The assumptions of much of the literature on human spatial navigation are that: 1) spatial navigation involves modality independent, discrete metric representations (i.e., egocentric vs. allocentric) 2) such representations can be further distilled to elemental cognitive processes 3) these cognitive processes can be ascribed to unique brain regions. Here, we argue that modality independent spatial representations, instead of providing exact metrics about our surrounding environment, more often involve heuristics for estimating spatial topology useful to the current task at hand...
September 20, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28931578/lipid-topology-and-electrostatic-interactions-underpin-lytic-activity-of-linear-cationic-antimicrobial-peptides-in-membranes
#18
David J Paterson, Manlio Tassieri, Julien Reboud, Rab Wilson, Jonathan M Cooper
Linear cationic antimicrobial peptides are a diverse class of molecules that interact with a wide range of cell membranes. Many of these peptides disrupt cell integrity by forming membrane-spanning pores that ultimately lead to their death. Despite these peptides high potency and ability to evade acquired bacterial drug resistance, there is a lack of knowledge on their selectivity and activity mechanisms. Such an understanding would provide an informative framework for rational design and could lead to potential antimicrobial therapeutic targets...
September 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28931522/three-dimensional-morphometric-analysis-of-the-renal-vasculature
#19
Zohaib Khan, Jennifer P Ngo, Bianca Le, Roger G Evans, James Todd Pearson, Bruce S Gardiner, David W Smith
Vascular topology and morphology is critical in the regulation of blood flow and the transport of small solutes including oxygen, carbon dioxide, nitric oxide and hydrogen sulfide. Renal vascular morphology is particularly challenging as many arterial walls are partially wrapped by the walls of veins. In the absence of a precise characterization of three-dimensional branching vascular geometry, accurate computational modeling of the intrarenal transport of small diffusible molecules is impossible. An enormous manual effort was required to achieve a relatively precise characterization of rat renal vascular geometry, highlighting the need for an automated method for analysis of branched vasculature morphology to allow characterization of the renal vascular geometry of other species, including humans...
September 20, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28931413/topological-organization-and-dynamic-regulation-of-human-trna-genes-during-macrophage-differentiation
#20
Kevin Van Bortle, Douglas H Phanstiel, Michael P Snyder
BACKGROUND: The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout the genome and, in many cases, linearly organized into genomic clusters with other tDNAs. Whether the location and three-dimensional organization of tDNAs contribute to the activity of these genes has remained difficult to address, due in part to unique challenges related to tRNA sequencing...
September 20, 2017: Genome Biology
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