bluuebunny/crossref_metadata_2025_split huggingface dataset:
Colloidal Suspensions
Authors: Poon Wilson C. K. 
Published: August 2017

Abstract
This article deals with the fundamentals of colloid science, with particular emphasis on the interplay of energy and entropy factors in forming colloidal suspensions. It first considers when a colloidal suspension changes from a liquid at low colloid concentration to various equilibrium, along with metastable (including kinetically arrested) structures at higher concentrations. active driven matter and the selectivity of binding in protein-based colloids. It then discusses a number of key ideas and some recent developments in colloid physics by focusing on the work of Albert Einstein and Jean Perrin. It also explores the physics of entropy, how the liquid state is formed, strategies for tuning colloidal interactions, kinetic arrest and glass transition, and mode coupling theory. Finally, it describes gelation, colloid rheology, concentration effects in colloidal fluids, the rheology of solids, and proteins as ‘a mysterious sort of colloids’.
Cell Cytoskeleton
Authors: Piel Matthieu , Voituriez Raphael 
Published: August 2017

Abstract
This article examines the ‘active’ part of the cell cytoskeleton — which mostly corresponds to actin and tubulin polymers and associated molecular motors — using theoretical tools derived from a soft matter physics coarse-grained approach. It begins with an overview of the cytoskeleton and its components, which include actin filaments and gels, microtubules and specialized microtubule-based organelles, molecular motors, intermediate filaments, the plasma membrane and glycocalix, the cell wall, and the extracellular matrix. It then describes coarse-grained models of the cytoskeleton and gives two examples of models for important cellular functions, namely cell migration and cell polarity. It also proposes a new kind of soft matter model providing a coarse-grained description of cytoskeletal polymers and associated molecular motors.
Elastomers and Rubberlike Elasticity
Authors: Mark James E. , Erman Burak 
Published: August 2017

Abstract
This article focuses on the rubberlike elasticity of elastomers, with particular emphasis on rubberlike materials that exhibit high deformability and recoverability. It begins with a discussion of the variety of practical ways to form and characterize a rubber-elastic network, including random chemical crosslinking, highly specific chemical end-linking, polymerizations with multi-functional monomers, physical aggregation, and crosslinking in solution and in the deformed state. It then considers the effects of network structure on elastomeric properties, along with the results of elasticity experiments regarding the mechanical properties of elastomeric materials. It also examines the evolution of theories of rubber elasticity describes the specific properties of swollen polymer gels where the possibility of solvent exchange leads to some dramatic transformations in the system. Finally, it evaluates new emerging classes of rubber-elastic materials, such as liquid crystalline elastomers, where the internal microstructure added to the random network leads to some unique mechanical properties.
The crowns have eyes: Multiple opsins found in the eyes of the Crown-of-Thorns StarfishAcanthaster planciincluding the first r-opsin utilized by a deuterostome eye
Authors: Lowe Elijah K. , Garm Anders , Ullrich-Lüter Esther , Ina Arnone M. 
Published: August 2017

AbstractOpsins are G protein-coupled receptors used for both visual and non-visual photoreception, and these proteins evolutionarily date back to the base of the bilaterians. In the current sequencing age, phylogenomic analysis has proven to be a powerful tool, facilitating the increase in knowledge about diversity within the opsin subclasses and, so far, nine paralogs have been identified. Within echinoderms, opsins have been studied in Echinoidea and Ophiuroidea, which do not possess proper image forming eyes, but rather widely dispersed dermal photoreceptors. However, most species of Asteroidea, the starfish, possess true eyes and studying them will shed light on the diversity of opsin usage within echinoderms and help resolve the evolutionary history of opsins. Using high-throughput RNA sequencing, we have sequenced and analyzed the transcriptomes of differentAcanthaster plancitissue samples: eyes, radial nerve, tube feet and a mixture of tissues from other organs. At least ten opsins were identified, and eight of them were found significantly differentially expressed in both eyes and radial nerve, providing new important insight into the involvement of opsins in visual and nonvisual photoreception. Of relevance, we found the first evidence of an r-opsin photopigment expressed in a well developed visual eye in a deuterostome animal.
MERS-CoV NSP16 necessary for IFN resistance and viral pathogenesis
Authors: Menachery Vineet D. , Gralinski Lisa E. , Mitchell Hugh D. , Dinnon Kenneth H. , Leist Sarah R. , Yount Boyd L. , Graham Rachel L. , McAnarney Eileen T. , Stratton Kelly G. , Cockrell Adam S. , Debbink Kari , Sims Amy C. , Waters Katrina M. , Baric Ralph S. 
Published: August 2017

AbstractCoronaviruses encode a mix of highly conserved and novel genes as well as genetic elements necessary for infection and pathogenesis, raising the possibility for common targets for attenuation and therapeutic design. In this study, we focus on the highly conserved nonstructural protein (NSP) 16, a viral 2’O methyl-transferase (MTase) that encodes critical functions in immune modulation and infection. Using reverse genetics, we disrupted a key motif in the conserved KDKE motif of MERS NSP16 (D130A) and evaluated the effect on viral infection and pathogenesis. While the absence of 2’O MTase activity had only marginal impact on propagation and replication in Vero cells, the MERS dNSP16 mutant demonstrated significant attenuation relative to control both in primary human airway cultures andin vivo.Further examination indicated the MERS dNSP16 mutant had a type I IFN based attenuation and was partially restored in the absence of IFIT molecules. Importantly, the robust attenuation permitted use of MERS dNSP16 as a live attenuated vaccine platform protecting from challenge with a mouse adapted MERS-CoV strain. These studies demonstrate the importance of the conserved 2’O MTase activity for CoV pathogenesis and highlight NSP16 as a conserved universal target for rapid live attenuated vaccine design in an expanding CoV outbreak setting.SignificanceCoronavirus emergence in both human and livestock represents a significant threat to global public health, as evidenced by the sudden emergence of SARS-CoV, MERS-CoV, PEDV and swine delta coronavirus in the 21stcentury. These studies describe an approach that effectively targets the highly conserved 2’O methyl-transferase activity of coronaviruses for attenuation. With clear understanding of the IFN/IFIT based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform as well as therapeutic development for both current and future emergent CoV strains. Importantly, other approaches targeting other conserved pan-coronavirus functions have not yet proven effective against MERS-CoV, illustrating the broad applicability of targeting viral 2’O MTase function across coronaviruses.
Effects of mutation and selection on plasticity ofTDH3promoter activity inSaccharomyces cerevisiae
Authors: Duveau Fabien , Yuan David C. , Metzger Brian P.H. , Hodgins-Davis Andrea , Wittkopp Patricia J. 
Published: August 2017

AbstractPhenotypic plasticity is an evolvable property of biological systems that can arise from environment-specific regulation of gene expression. To better understand the evolutionary and molecular mechanisms that give rise to plasticity in gene expression, we quantified the effects of 235 single nucleotide mutations in theSaccharomyces cerevisiae TDH3promoter (PTDH3) on the activity of this promoter in media containing glucose, galactose, or glycerol as a carbon source. We found that the distributions of mutational effects differed among environments because many mutations altered the plastic response exhibited by the wild type allele. Comparing the effects of these mutations to the effects of 30PTDH3polymorphisms on expression plasticity in the same environments provided evidence of natural selection acting to prevent the plastic response inPTDH3activity between glucose and galactose from becoming larger. The largest changes in expression plasticity were observed between fermentable (glucose or galactose) and nonfermentable (glycerol) carbon sources and were caused by mutations located in the RAP1 and GCR1 transcription factor binding sites. Mutations altered expression plasticity most frequently between the two fermentable environments, however, with mutations causing significant changes in plasticity between glucose and galactose distributed throughout the promoter, suggesting they might affect chromatin structure. Taken together, these results provide insight into the molecular mechanisms underlying gene-by-environment interactions affecting gene expression as well as the evolutionary dynamics affecting natural variation in plasticity of gene expression.Significance StatementFrom seasonal variation in the color of butterfly wings to trees bending toward the light, organisms often change in response to their environment. These changes, known as phenotypic plasticity, can result from differences in how genes are expressed among environments. Mutations causing environment-specific changes in gene expression provide raw material for phenotypic plasticity, but their frequency, effect size and direction of effects among environments are not well understood. This study shows that mutations in the promoter of a yeast metabolic gene often display environment-dependent effects on gene expression and that these environment-dependent effects have been shaped by selection in natural populations.
N-methyl-bacillithiol, a new metabolite discovered in theChlorobiaceae, indicates that bacillithiol and derivatives are widely phylogenetically distributed
Authors: Hiras Jennifer , Sharma Sunil V. , Raman Vidhyavathi , Tinson Ryan A. J. , Arbach Miriam , Rodrigues Dominic F. , Norambuena Javiera , Hamilton Chris J. , Hanson Thomas E. 
Published: August 2017

AbstractLow-molecular weight (LMW) thiols are metabolites that mediate redox homeostasis and the detoxification of chemical stressors in cells. LMW thiols are also thought to play a central role in sulfur oxidation pathways in phototrophic bacteria, including theChlorobiaceae. Fluorescent thiol labeling of metabolite extracts coupled with HPLC showed thatChlorobaculum tepidumcontained a novel LMW thiol with a mass of 412 ± 1 Da corresponding to a molecular formula of C14H24N2O10S. These data suggested the new thiol is closely related to bacillithiol (BSH), the major LMW thiol from low G+C% Gram-positive bacteria. By comparing the as-isolated bimane adduct with chemically synthesized candidate structures, theCba. tepidumthiol structure was identified as N-methyl-bacillithiol (N-Me-BSH), methylated on the cysteine nitrogen, a rarely observed modification in metabolism. Orthologs of bacillithiol biosynthetic genes in theCba. tepidumgenome were required for the biosynthesis of N-Me-BSH. Furthermore, the CT1040 gene product was genetically identified as the BSH N-methyltransferase. N-Me-BSH was found in allChlorobiexamined as well asPolaribactersp. strain MED152, a member of theBacteroidetes.A comparative genomic analysis indicated that BSH/N-Me-BSH is synthesized not only by members of theChlorobi,Bacteroidetes,Deinococcus-Thermus, andFirmicutes, but also byAcidobacteria,Chlamydiae,Gemmatimonadetes, andProteobacteria.Significance StatementHere, N-Me-BSH is shown to be a redox-responsive LMW thiol cofactor inCba. tepidumand the gene,nmbA, encoding the BSH N-methyltransferase responsible for its synthesis is identified. The co-occurrence of orthologs to BSH biosynthesis genes and bacillithiol N-methyltransferase was confirmed to correctly predict LMW thiol biosynthesis in phylogenetically distant genomes. The analysis indicates that BSH/N-Me-BSH are likely the most widely distributed class of LMW thiols in biology. This finding sheds light on the evolution of LMW thiol metabolism, which is central to redox homeostasis, regulation and stress resistance in all cellular life. It also sheds light on a rare chemical modification. N-Me-BSH is the fourth instance of cysteinyl nitrogen methylation in metabolism. Identification of the BSH N-methyltransferase reported here will enable detailedin vivoandin vitrodissection of the functional consequences of this modification. As a standalone N-methyltransferase, NmbA may be useful as a component of constructed biosynthetic pathways for novel product (bio)synthesis.
Structural basis of the Cope rearrangement and C–C bond-forming cascade in hapalindole/fischerindole biogenesis
Authors: Newmister Sean A. , Li Shasha , Garcia-Borràs Marc , Sanders Jacob N. , Yang Song , Lowell Andrew N. , Yu Fengan , Smith Janet L. , Williams Robert M. , Houk K. N. , Sherman David H. 
Published: August 2017

STRUCTURESThe atomic coordinates and structure factors for:HpiC1 W73M/K132M SeMet (P212121) –1.7 ÅHpiC1 native (C2) –1.5 ÅHpiC1 native (P42) –2.1 ÅHpiC1 Y101F (C2) –1.4 ÅHpiC1 Y101S (C2) –1.4 ÅHpiC1 F138S (P21) –1.7 ÅHpiC1 Y101F/F138S (P21–1.65 Å have been deposited with the Research Collaboratory for Structural Bioinformatics as Protein Data Bank entries 5WPP, 5WPR, 6AL6, 5WPR, 5WPU, 6AL7, and 6AL8 (www.rcsb.org).GRANTSThis work was supported by: The authors thank the National Science Foundation under the CCI Center for Selective C-H Functionalization (CHE-1205646), the National Institutes of Health (CA70375 to RMW and DHS), R35 GM118101, R01 GM076477 and the Hans W. Vahlteich Professorship (to DHS) for financial support. M.G-B. thanks the Ramón Areces Foundation for a postdoctoral fellowship. J.N.S. acknowledges the support of the National Institute of General Medical Sciences of the National Institutes of Health under Award Number F32GM122218. Computational resources were provided by the UCLA Institute for Digital Research and Education (IDRE) and the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by the NSF (OCI-1053575). The content does not necessarily represent the official views of the National Institutes of Health.ABSTRACTHapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These polycyclic scaffolds are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps, including a rare Cope-rearrangement, 6-exo-trigcyclization, and electrophilic aromatic substitution. Here we report the structure of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U in vitro. The 1.5 Å structure reveals a dimeric assembly with two calcium ions per monomer and the active sites located at the distal ends of the protein dimer. Mutational analysis and computational methods uncovered key residues for an acid catalyzed [3,3]-sigmatropic rearrangement and specific determinants that control the position of terminal electrophilic aromatic substitution leading to a switch from hapalindole to fischerindole alkaloids.
Development of Inflammatory Bowel Disease is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice
Authors: Sharpton Thomas , Lyalina Svetlana , Luong Julie , Pham Joey , Deal Emily M. , Armour Courtney , Gaulke Christopher , Sanjabi Shomyseh , Pollard Katherine S. 
Published: August 2017

AbstractThe gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regards to function. To investigate microbiome mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where dampened TGF-β signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis. IBD development is associated with abnormal gut microbiome temporal dynamics, including dampened acquisition of functional diversity and significant differences in abundance trajectories for KEGG modules such as glycosaminoglycan degradation, cellular chemotaxis, and type III and IV secretion systems. Most differences between sick and control mice emerge when mice begin to lose weight and heightened T cell activation is detected in peripheral blood. However, lipooligosaccharide transporter abundance diverges prior to immune activation, indicating that it could be a pre-disease indicator or microbiome-mediated disease mechanism. Taxonomic structure of the gut microbiome also significantly changes in association with IBD development, and the abundance of particular taxa, including several species ofBacteroides, correlate with immune activation. These discoveries were enabled by our use of generalized linear mixed effects models to test for differences in longitudinal profiles between healthy and diseased mice while accounting for the distributions of taxon and gene counts in metagenomic data. These findings demonstrate that longitudinal metagenomics is useful for discovering potential mechanisms through which the gut microbiome becomes altered in IBD.ImportanceIBD patients harbor distinct microbial communities with different functional capabilities compared to healthy people. But is this cause or effect? Answering this question requires data on changes in gut microbial communities leading up to disease onset. By performing weekly metagenomic sequencing and mixed effects modeling on an established mouse model of IBD, we identified several functional pathways encoded by the gut microbiome that covary with host immune status. These pathways are novel early biomarkers that may either enable microbes to live inside an inflamed gut or contribute to immune activation in IBD mice. Future work will validate the potential roles of these microbial pathways in host-microbe interactions and human disease. This study is novel in its longitudinal design and focus on microbial pathways, which provided new mechanistic insights into the role of gut microbes in IBD development.
Cerebellar Purkinje cell simple spike activity in awake mice represents phase differences between oscillations in medial prefrontal cortex and hippocampus
Authors: McAfee Samuel S. , Liu Yu , Sillitoe Roy V. , Heck Detlef H. 
Published: August 2017

AbstractThe cerebellum has long been recognized for its role in tasks involving precise timing, particularly the temporal coordination of movements. Here we asked whether cerebellar might be involved in the temporal coordination of the phases of neuronal oscillations in the medial prefrontal cortex (mPFC) and dorsal hippocampus CA1 region (CA1). These two structures and the cerebellum are jointly involved in spatial working memory. The phases of oscillations in the mPFC and CA1 have been shown to reach a stable alignment (coherence) during the decision making process in a spatial working memory task. Here we report that PC simple spike activity in the cerebellar lobulus simplex in awake, head-fixed mice represents specific phase differences between oscillations in the mPFC and CA1. Most PCs represented phase differences in more than one the conventional frequency bands (delta, theta, beta and gamma). Between the 32 PCs analyzed here, phase differences in all frequency bands were represented. PCs representing phase differences in the theta and low gamma bands showed significant population preference for mPFC phase leading CA1 phase. These findings support the possibility of a cerebellar involvement in the temporal coordination of phase relationships between oscillations in the mPFC and CA1.
Correcting palindromes in long reads after whole-genome amplification
Authors: Warris Sven , Schijlen Elio , van de Geest Henri , Vegesna Rahulsimham , Hesselink Thamara , te Lintel Hekkert Bas , Sanchez Perez Gabino , Medvedev Paul , Makova Kateryna D. , de Ridder Dick 
Published: August 2017

AbstractNext-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long reads from technologies such as PacBio and Oxford Nanopore. Here, we present Pacasus, a tool for correcting such errors in long reads. We demonstrate on two real-world datasets that it markedly improves subsequent read mapping andde novoassembly, yielding results similar to these that would be obtained with non-amplified DNA. With Pacasus long-read technologies become readily available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.
Payment mechanisms for contractors for better environmental hazard controlling in road construction projects
Authors: Walimuni Piumi Chethana , Samaraweera Aparna , De Silva Lalith 
Published: August 2017

Purpose
There is a growing concern that contractors can be motivated for environmental protection through effective fund allocation and proper payment mechanisms. However, an in-depth analysis of environmental hazard-controlling methods and related payments to the contractor in road construction in Sri Lanka is not much popular among the extant literature. Thus, the purpose of this paper is to explore different payment mechanisms that are being used with environmental hazard-controlling methods, to achieve better control in such hazards in Sri Lankan road construction projects.

Design/methodology/approach
This research was approached through a mixed research method. Initially, hazard-controlling methods and relative payment mechanisms for the contractor were identified through three exploratory case studies using interviews, observations and document survey. Next, the relative effectiveness of payment mechanisms for contractors for better environmental hazard controlling was identified through a questionnaire survey with a sample of 45 professionals involved in 15 road construction projects.

Findings
Based on the findings, a comprehensive list of environmental hazard-controlling methods was derived. Furthermore, four types of payment mechanisms were identified: (A)-payments, where a unit price was assigned; (B)-payments, where a provisional sum was established in the contract; (C)-payments, where fixed amounts (lump sums) were assigned in the contract and (D)-payments made along with some main work item in the contract. Relative effectiveness of these four mechanisms for better control of environmental hazards was varied for each hazard-controlling method being practiced in a road construction project.

Originality/value
These findings would be more beneficial for consultants, project managers, bidders and estimators in the pre-contract stage. This is by identifying cost items for environmental hazard controlling and selecting relatively more effective payment mechanisms to motivate contractors for better control of environmental hazards during project execution.