bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studying 3D genome evolution using genomic sequence
Authors: Mourad Raphaël 
Published: May 2019

AbstractThe 3D genome is essential to numerous key processes such as the regulation of gene expression and the replication-timing program. In vertebrates, chromatin looping is often mediated by CTCF, and marked by CTCF motif pairs in convergent orientation. Comparative Hi-C recently revealed that chromatin looping evolves across species. However, Hi-C experiments are complex and costly, which currently limits their use for evolutionary studies over a large number of species. Here, we propose a novel approach to study the 3D genome evolution in vertebrates using the genomic sequence only, e.g. without the need for Hi-C data. The approach is simple and relies on comparing the distances between convergent and divergent CTCF motifs (ratio R). We show that R is a powerful statistic to detect CTCF looping encoded in the human genome sequence, thus reflecting strong evolutionary constraints encoded in DNA and associated with the 3D genome. When comparing vertebrate genomes, our results reveal that R which underlies CTCF looping and TAD organization evolves over time and suggest that ancestral character reconstruction can be used to infer R in ancestral genomes.
Structural characterization of tau in fuzzy tau:tubulin complexes
Authors: Fung Ho Yee Joyce , McKibben Kristen , Ramirez Jennifer , Gupta Kushol , Rhoades Elizabeth 
Published: May 2019

SummaryTau is a neuronal microtubule (MT) associated protein of significant interest due to its association with several neurodegenerative disorders. Tau’s intrinsic disorder and the dynamic nature of its interactions with tubulin and MTs make its structural characterization challenging. Here we use an environmentally sensitive fluorophore as a site-specific probe of tau bound to soluble tubulin. Comparison of our results with recently published tau:MT cryo-EM model reveals structural similarities between tubulin- and MT-bound tau. Analysis of residues across the repeat regions reveal a hierarchy in tubulin occupancy, which may be relevant to tau’s ability to differentiate between tubulin and MTs. As binding to soluble tubulin is a critical first step in MT polymerization, our characterization of the structural features of tau in dynamic, fuzzy tau:tubulin assemblies advances our understanding of how tau functions in the cell and how function may be disrupted in disease.
Two-color nanoscopy of organelles for extended times with HIDE probes
Authors: Chu Ling , Tyson Jonathan , Shaw Juliana E. , Rivera-Molina Felix , Koleske Anthony J. , Schepartz Alanna , Toomre Derek K. 
Published: May 2019

AbstractPerforming multi-color nanoscopy for extended times is challenging due to the rapid photobleaching rate of most fluorophores. Here we describe a new fluorophore (Yale-595) and a bio-orthogonal labeling strategy that enables both super-resolution (STED) and 3D confocal imaging of two organelles simultaneously for extended times using high-density environmentally sensitive (HIDE) probes. Because HIDE probes are small, cell-permeant molecules, they can visualize organelle pairs (ER + mitochondria, ER + plasma membrane) in hard-to-transfect cell lines at super-resolution for up to 7 minutes. The extended time domain possible using these new tools reveal novel dynamic nanoscale targeting between organelles.
Nol9 is a Spatial Regulator for the Human ITS2 pre-rRNA Processing Complex
Authors: Gordon Jacob , Pillon Monica C. , Stanley Robin E. 
Published: May 2019

AbstractThe ribosome plays a universal role in translating the cellular proteome. Defects in the ribosome assembly factor Las1L are associated with congenital lethal motor neuron disease and X-linked intellectual disability disorders, yet its role in processing precursor ribosomal RNA (pre-rRNA) is largely unclear. The Las1L endoribonuclease associates with the Nol9 polynucleotide kinase to form the internal transcribed spacer 2 (ITS2) pre-rRNA processing machinery. Together, Las1L-Nol9 catalyzes RNA cleavage and phosphorylation to mark the ITS2 for degradation. While ITS2 processing is critical for the production of functional ribosomes, the regulation of mammalian Las1L-Nol9 remains obscure. Here we characterize the human Las1L-Nol9 complex and identify critical molecular features that regulate its assembly and spatial organization. We establish that Las1L and Nol9 form a higher-order complex and identify the regions responsible for orchestrating this intricate architecture. Structural analysis by high-resolution imaging defines the intricate spatial pattern of Las1L-Nol9 within the nucleolar sub-structure linked with late pre-rRNA processing events. Furthermore, we uncover a Nol9 encoded nucleolar localization sequence that is responsible for nucleolar transport of the assembled LasL-Nol9 complex. Together, these data provide a mechanism for the assembly and nucleolar localization of the human ITS2 pre-rRNA processing complex.
Capping protein insulates Arp2/3-assembled actin patches from formins
Authors: Billault-Chaumartin Ingrid , Martin Sophie G. 
Published: May 2019

AbstractHow actin structures of distinct identities and functions co-exist within the same environment is a critical self-organization question. Fission yeast cells have a simple actin cytoskeleton made of four structures: Arp2/3 assembles actin patches around endocytic pits; the formins For3, Cdc12 and Fus1 assemble actin cables, the cytokinetic ring during division, and the fusion focus during sexual reproduction, respectively. The focus concentrates the delivery of hydrolases by myosin V to digest the cell wall for cell fusion. We discovered that cells lacking capping protein (CP), a heterodimer that blocks barbed-end dynamics and associates with actin patches, exhibit a delay in fusion. Consistent with CP-formin competition for barbed-end binding, Fus1, F-actin and the linear filament marker tropomyosin hyper-accumulate at the fusion focus in absence of CP. However, myosin V and exocytic cargoes are diverted to ectopic foci and reduced at the fusion focus, which underlies the fusion defect. Remarkably, ectopic foci coincide with actin patches, which now contain low levels of Fus1. During mitotic growth, actin patches lacking CP similarly display a dual identity, as they accumulate the formins For3 and Cdc12 and are co-decorated by tropomyosin and the patch marker fimbrin. Thus, CP serves to protect Arp2/3-nucleated structures from formin activity.
Cytogenetically-based biodosimetry after high doses of radiation
Authors: Pujol-Canadell M. , Perrier J.R. , Cunha L. , Shuryak I. , Harken A. , Garty G. , Brenner D.J. 
Published: May 2019

ABSTRACTDosimetry is an important tool for triage and treatment planning following any radiation exposure accident, and biological dosimetry, which estimates exposure dose using a biological parameter, is a practical means of determining the specific dose an individual receives. The cytokinesis-blocked micronucleus assay (CBMN) is an established biodosimetric tool to measure chromosomal damage in mitogen-stimulated human lymphocytes. The CBMN method is especially valuable for biodosimetry in triage situations thanks to simplicity in scoring and adaptability to high-throughput automated sample processing systems. While this technique produces dose-response data which fit very well to a linear-quadratic model for exposures to low linear energy transfer (LET) radiation and for doses up for 5 Gy, limitations to the accuracy of this method arise at larger doses. Resolution at higher doses is limited by the number of cells reaching mitosis. Whereas it would be expected that the yield of micronuclei increases with the dose, in many experiments it has been shown to actually decrease when normalized over the total number of cells. This variation from a monotonically increasing dose response poses a limitation for retrospective dose reconstruction. In this study we modified the standard CBMN assay to increase its resolution following exposures to higher doses of photons or a mixed neutron–photon beam. The assay is modified either through inhibitions of the G2/M and spindle checkpoints with the addition of caffeine and/or ZM447439 (an Aurora kinase inhibitor), respectively to the blood cultures at select times during the assay. Our results showed that caffeine addition improved assay performance for photon up to 10 Gy. This was achieved by extending the assay time from the typical 70 h to just 74 h. Compared to micronuclei yields without inhibitors, addition of caffeine and ZM447439 resulted in improved accuracy in the detection of micronuclei yields up to 10 Gy from photons and 4 Gy of mixed neutrons-photons. When the dose-effect curves were fitted to take into account the turnover phenomenon observed at higher doses, best fitting was achieved when the combination of both inhibitors was used. These techniques permit reliable dose reconstruction after high doses of radiation with a method that can be adapted to high-throughput automated sample processing systems.
Accelerating iterative deconvolution and multiview fusion by orders of magnitude
Authors: Guo Min , Li Yue , Su Yijun , Lambert Talley , Nogare Damian Dalle , Moyle Mark W. , Duncan Leighton H. , Ikegami Richard , Santella Anthony , Rey-Suarez Ivan , Green Daniel , Chen Jiji , Vishwasrao Harshad , Ganesan Sundar , Waters Jennifer C. , Annunziata Christina M. , Hafner Markus , Mohler William A. , Chitnis Ajay B. , Upadhyaya Arpita , Usdin Ted B. , Bao Zhirong , Colón-Ramos Daniel , Riviere Patrick La , Liu Huafeng , Wu Yicong , Shroff Hari 
Published: May 2019

AbstractWe describe theoretical and practical advances in algorithm and software design, resulting in ten to several thousand-fold faster deconvolution and multiview fusion than previous methods. First, we adapt methods from medical imaging, showing that an unmatched back projector accelerates Richardson-Lucy deconvolution by at least 10-fold, in most cases requiring only a single iteration. Second, we show that improvements in 3D image-based registration with GPU processing result in speedups of 10-100-fold over CPU processing. Third, we show that deep learning can provide further accelerations, particularly for deconvolution with a spatially varying point spread function. We illustrate the power of our methods from the subcellular to millimeter spatial scale, on diverse samples including single cells, nematode and zebrafish embryos, and cleared mouse tissue. Finally, we show that our methods facilitate the use of new microscopes that improve spatial resolution, including dual-view cleared tissue light-sheet microscopy and reflective lattice light-sheet microscopy.
Integrin-alpha-6+ Stem Cells (ISCs) are responsible for whole body regeneration in an invertebrate chordate
Authors: Kassmer Susannah H. , Langenbacher Adam , De Tomaso Anthony W. 
Published: May 2019

AbstractColonial ascidians are the only chordates able to undergo whole body regeneration (WBR), during which entire new bodies can be regenerated from small fragments of blood vessels. Here, we show that during the early stages of WBR in Botrylloides diegensis, proliferation occurs only in small, blood-borne cells that express integrin-alpha-6 (IA6), pou3 and vasa. Ablation of proliferating cells using Mitomycin C (MMC) blocks WBR in vascular fragments, but can be rescued by injection of cycling cells isolated from an untreated individual. Using prospective isolation and limit dilution analyes, we found that FACS-isolated IA6+ stem cells (ISCs) could rescue WBR in MMC treated vascular fragments, even when injecting only a single cell. Lineage tracing using EdU-labeling further revealed that donor-derived ISCs directly give rise to regenerating tissues. Inhibitors of either Notch or canonical Wnt signaling block WBR and reduce proliferation of ISCs, indicating that these two pathways regulate ISC activation.
Micro- and nanostructural characteristics of rat masseter muscle entheses -Characteristics of masseter muscle entheses-
Authors: Arakawa Keitaro , Matsunaga Satoru , Nojima Kunihiko , Nakano Takayoshi , Abe Shinichi , Yoshinari Masao , Sueishi Kenji 
Published: May 2019

AbstractThe entheses of the masticatory muscles differ slightly from those of the trunk and limb muscles. However, the bones of the skull are subject to various functional pressures, including masticatory force, resulting in a complex relationship between bone structure and muscle function that remains to be fully elucidated. The present study aimed to clarify aspects of masseter muscle-tendon-bone morphological characteristics and local load environment through quantitative analysis of biological apatite (BAp) crystallite alignment and collagen fiber orientation together with histological examination of the entheses.Result of histological observation, the present findings show that, in the entheses of the masseter muscle in the first molar region, tendon attaches to bone via unmineralized fibrocartilage, while some tendon collagen fibers insert directly into the bone, running parallel to the muscle fibers. Furthermore, BAp crystallites in the same region show uniaxial preferential alignment at an angle that matches the insertion angle of the tendon fibers. Conversely, in the entheses of the masseter muscle in the third molar region, the tendon attaches to the bone via a layer of thickened periosteum and chondrocytes. As in the first molar region, the results of bone quality analysis in the third molar region showed BAp crystallite alignment parallel to the orientation of the tendon fibers. This indicates that the local mechanical environment generates differences in enthesis morphology.The present study showed a greater degree of uniaxial BAp crystallite alignment in entheses with direct insertion rather than indirect tendon-bone attachment and the direction of alignment was parallel to the orientation of tendon fibers. These findings suggest that functional pressure from the masseter muscle greatly affects bone quality as well as the morphological characteristics of the enthesis, specifically causing micro- and nanostructural anisotropy in the direction of resistance to the applied pressure.
Toxic Effects of Crude Extracts from Chinese Herbal Toothpastes on Solenopsis invicta (Hymenoptera: Formicidae)
Authors: Xiao Qian , Hassan Babar , Luo Junzhao , Xu Yijuan 
Published: May 2019

AbstractRed imported fire ant is an invasive species with the characteristics of quick dispersion, strong ferocity and aggression. For a long time, chemical control has been used as a main means of prevention and control of this pest, but the long-term use of high toxic pesticides will lead to a serious impact on the environment and non-target organisms. The toxicity of Chinese herbal toothpaste and its crude extracts against red imported fire ant was evaluated in the laboratory bioassay. The results showed that the traditional Chinese medicine toothpaste with watermelon cream has significant toxicity to red imported fire ants. The mortality reached more than 80% after 48h treatment, and the mortality was 100% after 72h treatment. Among the fractions separated from watermelon cream after the extraction of toothpaste, the ethyl acetate fraction has higher activity, and the mortality was more than 80% when the concentration was 1% after 72h. Our results suggest that Chinese herbal toothpaste is toxic to insects and have the potential for bait application in pest control.
Molecular phylogeny of wood decay fungi of hardwood and their ability to produce laccase that correlates with triphenylmethane dye decolorization
Authors: Mahawaththage Dona Maduri Piumi Sashikala , Deraniyagala Anushi Suwanethya , Wijesinghe Priyanga , Attanayake Renuka Nilmini 
Published: May 2019

AbstractThough Sri Lanka belongs to one of the 34 biodiversity hotspots of the world, its microfolora specially fungi are not well studied and underrepresented in the global literature. Here we report the fungal species diversity of decaying hardwood of a Sri Lankan dry zone forest for the first time. Decaying hardwoods were collected from historically important Dimbulagala forest reserve, Sri Lanka and fungi associated with these woods were isolated. Out of 35 fungal species identified using morphological and molecular methods, 11 species were first records in Sri Lanka. All the tested isolates were able to utilize wood as the sole carbon source and produced varying degrees of laccase. Isolates of Perenniporia tephropora, Coriolopsis caperata, Gymnopilus dilepis, Fusarium solani and Vanderbylia fraxinea were among the top six laccase producers. Except Fusarium solani, the rest of the isolates showed more than 70% decolorization of the of triphenylmethane dye and there was a significant positive correlation between laccase production and dye decolorization. To the best of our knowledge laccase production and dye decolorization ability of Vanderbylia fraxinea and Gymnopilus dilepis have never been reported in the fungal kingdom before. Perenniporia tephropora was isolated from one of the strongest decay resistant hardwood species, Ebony (Diospyros ebenum) also known as dark wood and V. fraxinea was isolated from another medicinally important hardwood Neem (Azadirachta indica). Findings of this study confirms that decaying hardwood of Sri Lanka provide unexplode a unique niche for discovering fungal species with biotechnological applications such as high laccase producers and dye decolorizers.
A conservative approach for species delimitation based on multi-locus DNA sequences: a case study of the genusGiraffa(Mammalia, Cetartiodactyla)
Authors: Petzold Alice , Hassanin Alexandre 
Published: May 2019

AbstractMolecular data are now commonly used in taxonomy for delimiting cryptic species. In the case of giraffes, which were treated as a single species (Giraffa camelopardalis) during half of a century, several molecular studies have suggested a splitting into four to seven species, but the criteria applied for taxonomic delimitation were not fully described.In this study, we have analysed all multi-locus DNA sequences available for giraffes using multispecies coalescent (MSC: *BEAST, BPP and STACEY), population genetic (STRUCTURE, allelic networks, haplotype network and bootstrapping) and phylogenetic (MrBayes, PhyML, SuperTRI) methods to identify the number of species. Our results show that depending on the method chosen, different taxonomic hypotheses, recognizing from two to six species, can be considered for the genusGiraffa.Our results confirm that MSC methods can lead to taxonomic over-splitting, as they delimit geographic structure rather than species. The 3-species hypothesis, which recognizesG. camelopardalissensu strico,G. giraffa, andG. tippelskirchi, is highly supported by phylogenetic analyses and also corroborated by most population genetic and MSC analyses. The three species show high levels of nucleotide divergence in both nuclear (0.35-0.51 %) and mitochondrial sequences (3-4 %), and they are characterised by 7 to 12 exclusive synapomorphies (ES) detected in nine of the 21 nuclear introns analysed for this study. By contrast, other putative species, such asG. peralta,G.reticulata,G. thornicroftiorG. tippelskirchisensu stricto, do not exhibit any ES in nuclear genes.A robust mito-nuclear conflict was found for the position and monophyly ofG. giraffaandG. tippelskirchi, which is explained firstly by a mitochondrial introgression from Masai giraffe to southeastern giraffe during the Pleistocene, and secondly, by gene flow mediated by male dispersal between southern populations (subspeciesG.g. giraffaandG.g. angolensis).
Comparative Tn-Seq reveals common daptomycin resistance determinants inStaphylococcus aureusdespite strain-dependent differences in essentiality of shared cell envelope genes
Authors: Coe Kathryn A. , Lee Wonsik , Komazin-Meredith Gloria , Meredith Timothy C. , Grad Yonatan H. , Walker Suzanne 
Published: May 2019

AbstractAntibiotic-resistantStaphylococcus aureusremains a leading cause of antibiotic resistance-associated mortality in the United States. Given the reality of multi-drug resistant infections, it is imperative that we establish and maintain a pipeline of new compounds to replace or supplement our current antibiotics. A first step towards this goal is to prioritize targets by identifying the genes most consistently required for survival across theS. aureusphylogeny. Here we report the first direct comparison of gene essentiality across multiple strains ofS. aureusvia transposon sequencing. We show that mutant fitness varies by strain in key pathways, underscoring the importance of using more than one strain to differentiate between core and strain-dependent essential genes. Despite baseline differences in gene importance, several pathways, including the lipoteichoic acid pathway, become consistently essential under daptomycin exposure, suggesting core vulnerabilities that can be exploited to resensitize daptomycin-nonsusceptible isolates. We also demonstrate the merit of using transposons with outward-facing promoters capable of overexpressing nearby genes for identifying clinically-relevant gain-of-function resistance mechanisms. Together, the daptomycin vulnerabilities and resistance mechanisms support a mode of action with wide-ranging effects on the cell envelope and cell division. This work adds to a growing body of literature demonstrating the nuanced insights gained by comparing Tn-Seq results across multiple bacterial strains.Author summaryAntibiotic-resistantStaphylococcus aureuskills thousands of people every year in the United States alone. To stay ahead of the looming threat of multidrug-resistant infections, we must continue to develop new antibiotics and find ways of making our current repertoire of antibiotics more effective, including by finding pairs of compounds that perform best when administered together. In the age of next-generation sequencing, we can now use transposon sequencing to find potential targets for new antibiotics on a genome-wide scale, identified as either essential genes or genes that become essential in the presence of an antibiotic. In this work, we created a compendium of genes that are essential across a range ofS. aureusstrains, as well as those that are essential in the presence of the antibiotic daptomycin. The results will be a resource for researchers working to develop the next generation of antibiotic therapies.
Qualitative comparative analysis in corporate governance research: a systematic literature review of applications
Authors: Cucari Nicola 
Published: May 2019

Purpose
The purpose of this paper is to provide comprehensive mapping of qualitative comparative analysis (QCA) applications in business and management research and to examine the sub-fields of corporate governance research in this context.

Design/methodology/approach
Through a systematic literature review of 22 articles, the paper describes and analyses how QCA is used in the corporate governance field, what can be learned from the methodology’s implementation in corporate governance studies and why authors justify its use.

Findings
The findings highlight that QCA in corporate governance is still at an early stage of development. The paper encourages governance scholars to use this method to transform QCA from a niche into a mainstream method because it is appropriate for understanding both complex phenomena of social reality and issues of corporate governance that require an approach able to capture configurations of conditions, asymmetric patterns and equifinal explanations.

Originality/value
This is the first complete overview of the existing literature concerning QCA’s application in corporate governance research and reveals implications for its future use. In this way, it extends the previous work on QCA’s benefits to management researchers and other critical reviews of applications in QCA. This study encourages scholars to renew their understanding of corporate governance issues through a new analysis method that can help to discover conceptual and empirical relations among case-oriented and variable-oriented analyses in terms of interrelations to examine corporate governance practices holistically.